From 8110306a787e7c4abf2882c3e334232ee332b696 Mon Sep 17 00:00:00 2001 From: Eric Messick <ericm@nanorex.com> Date: Fri, 19 Sep 2008 23:11:18 +0000 Subject: test structures for AMBER AtomType patterns --- cad/tests/AMBER_test_structures/README.txt | 40 + .../dot_in/all/ACE_ACE_BEGINNING_GROUP.in_frag | 9 + .../dot_in/all/ALA_ALANINE.in_frag | 13 + .../dot_in/all/ARG_ARGININE.in_frag | 27 + .../dot_in/all/ASH_ASP_neutral.in_frag | 16 + .../dot_in/all/ASN_ASPARAGINE.in_frag | 17 + .../dot_in/all/ASP_ASPARTIC_ACID.in_frag | 15 + .../dot_in/all/CYS_CYSTEINE.in_frag | 16 + .../all/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 15 + .../dot_in/all/D2AP_2-AMINO_PURINE.in_frag | 32 + .../dot_in/all/DADE_D-ADENOSINE.in_frag | 32 + .../dot_in/all/DCYT_D-CYTOSINE.in_frag | 30 + .../dot_in/all/DGUA_D-GUANOSINE.in_frag | 33 + .../dot_in/all/DOHE_D-OH_END.in_frag | 5 + .../dot_in/all/DPOM_PHOSMI_D.in_frag | 6 + .../dot_in/all/DTHY_D-THY.in_frag | 32 + .../dot_in/all/GLH_GLU_neutral.in_frag | 19 + .../dot_in/all/GLN_GLUTAMINE.in_frag | 20 + .../dot_in/all/GLU_GLUTAMIC_ACID.in_frag | 18 + .../dot_in/all/GLY_GLYCINE.in_frag | 10 + .../dot_in/all/HB_H_BEGINNING.in_frag | 4 + .../dot_in/all/HE_H_END.in_frag | 4 + .../dot_in/all/HID_HISTIDINE_DELTAH.in_frag | 20 + .../dot_in/all/HIE_HISTIDINE_EPSILONH.in_frag | 20 + .../dot_in/all/HIP_HISTIDINE_PLUS.in_frag | 21 + .../dot_in/all/ILE_ISOLEUCINE.in_frag | 22 + .../dot_in/all/LEU_LEUCINE.in_frag | 22 + .../dot_in/all/LYH_LYSINE.in_frag | 24 + .../dot_in/all/LYS_LYSINE.in_frag | 25 + .../dot_in/all/MET_METHIONINE.in_frag | 22 + .../dot_in/all/NHE_NH2_ENDING_GROUP.in_frag | 6 + .../dot_in/all/NME_N-methyl_all_atom.in_frag | 9 + .../dot_in/all/OHB_OH_BEGINNING.in_frag | 5 + .../dot_in/all/PHE_PHENYLALANINE.in_frag | 23 + .../dot_in/all/POHE_PROTEIN-OH_END.in_frag | 5 + .../dot_in/all/PRO_PROLINE.in_frag | 17 + .../dot_in/all/RADE_R-ADENOSINE.in_frag | 33 + .../dot_in/all/RCYT_R-CYTOSINE.in_frag | 31 + .../dot_in/all/RGUA_R-GUANOSINE.in_frag | 34 + .../dot_in/all/ROHE_R-OH_END.in_frag | 5 + .../dot_in/all/RPOM_PHOSMI_R.in_frag | 6 + .../dot_in/all/RURA_R-URACIL.in_frag | 30 + .../dot_in/all/SER_SERINE.in_frag | 14 + .../dot_in/all/THR_THREONINE.in_frag | 17 + .../dot_in/all/TRP_TRYPTOPHAN.in_frag | 27 + .../dot_in/all/TYR_TYROSINE.in_frag | 24 + .../dot_in/all/VAL_VALINE.in_frag | 19 + .../dot_in/all/WT3_WATER,_TIP3P_MODEL.in_frag | 6 + cad/tests/AMBER_test_structures/dot_in/all/all.in | 1431 +++++++ .../all_amino02.r1/ACE_ACE_BEGINNING_GROUP.in_frag | 9 + .../dot_in/all_amino02.r1/ALA_ALANINE.in_frag | 13 + .../dot_in/all_amino02.r1/ARG_ARGININE.in_frag | 27 + .../dot_in/all_amino02.r1/ASH_ASP_neutral.in_frag | 16 + .../dot_in/all_amino02.r1/ASN_ASPARAGINE.in_frag | 17 + .../all_amino02.r1/ASP_ASPARTIC_ACID.in_frag | 15 + .../dot_in/all_amino02.r1/CIM_Chloride_Ion.in_frag | 4 + .../dot_in/all_amino02.r1/CIP_Sodium_Ion.in_frag | 4 + .../CYM_CYSTEINE_with_negative_charge.in_frag | 13 + .../dot_in/all_amino02.r1/CYS_CYSTEINE.in_frag | 14 + .../CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 13 + .../dot_in/all_amino02.r1/GL0_GLYCIN0.in_frag | 10 + .../dot_in/all_amino02.r1/GLH_GLU_neutral.in_frag | 19 + .../dot_in/all_amino02.r1/GLN_GLUTAMINE.in_frag | 20 + .../all_amino02.r1/GLU_GLUTAMIC_ACID.in_frag | 18 + .../dot_in/all_amino02.r1/GLY_GLYCINE.in_frag | 10 + .../all_amino02.r1/HID_HISTIDINE_DELTAH.in_frag | 20 + .../all_amino02.r1/HIE_HISTIDINE_EPSILONH.in_frag | 20 + .../all_amino02.r1/HIP_HISTIDINE_PLUS.in_frag | 21 + .../dot_in/all_amino02.r1/ILE_ISOLEUCINE.in_frag | 22 + .../dot_in/all_amino02.r1/LEU_LEUCINE.in_frag | 22 + .../all_amino02.r1/LYN_LYSINE_neutral.in_frag | 24 + .../dot_in/all_amino02.r1/LYS_LYSINE.in_frag | 25 + .../dot_in/all_amino02.r1/MET_METHIONINE.in_frag | 20 + .../all_amino02.r1/NME_N-methyl_all_atom.in_frag | 9 + .../all_amino02.r1/PHE_PHENYLALANINE.in_frag | 23 + .../dot_in/all_amino02.r1/PRO_PROLINE.in_frag | 17 + .../dot_in/all_amino02.r1/SER_SERINE.in_frag | 14 + .../dot_in/all_amino02.r1/THR_THREONINE.in_frag | 17 + .../dot_in/all_amino02.r1/TRP_TRYPTOPHAN.in_frag | 27 + .../dot_in/all_amino02.r1/TYR_TYROSINE.in_frag | 24 + .../dot_in/all_amino02.r1/VAL_VALINE.in_frag | 19 + .../dot_in/all_amino02.r1/all_amino02.r1.in | 1120 ++++++ .../all_amino02/ACE_ACE_BEGINNING_GROUP.in_frag | 9 + .../dot_in/all_amino02/ALA_ALANINE.in_frag | 13 + .../dot_in/all_amino02/ARG_ARGININE.in_frag | 27 + .../dot_in/all_amino02/ASH_ASP_neutral.in_frag | 16 + .../dot_in/all_amino02/ASN_ASPARAGINE.in_frag | 17 + .../dot_in/all_amino02/ASP_ASPARTIC_ACID.in_frag | 15 + .../dot_in/all_amino02/CIM_Chloride_Ion.in_frag | 4 + .../dot_in/all_amino02/CIP_Sodium_Ion.in_frag | 4 + .../CYM_CYSTEINE_with_negative_charge.in_frag | 13 + .../dot_in/all_amino02/CYS_CYSTEINE.in_frag | 14 + .../CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 13 + .../dot_in/all_amino02/GLH_GLU_neutral.in_frag | 19 + .../dot_in/all_amino02/GLN_GLUTAMINE.in_frag | 20 + .../dot_in/all_amino02/GLU_GLUTAMIC_ACID.in_frag | 18 + .../dot_in/all_amino02/GLY_GLYCINE.in_frag | 10 + .../all_amino02/HID_HISTIDINE_DELTAH.in_frag | 20 + .../all_amino02/HIE_HISTIDINE_EPSILONH.in_frag | 20 + .../dot_in/all_amino02/HIP_HISTIDINE_PLUS.in_frag | 21 + .../dot_in/all_amino02/ILE_ISOLEUCINE.in_frag | 22 + .../dot_in/all_amino02/LEU_LEUCINE.in_frag | 22 + .../dot_in/all_amino02/LYN_LYSINE_neutral.in_frag | 24 + .../dot_in/all_amino02/LYS_LYSINE.in_frag | 25 + .../dot_in/all_amino02/MET_METHIONINE.in_frag | 20 + .../all_amino02/NME_N-methyl_all_atom.in_frag | 9 + .../dot_in/all_amino02/PHE_PHENYLALANINE.in_frag | 23 + .../dot_in/all_amino02/PRO_PROLINE.in_frag | 17 + .../dot_in/all_amino02/SER_SERINE.in_frag | 14 + .../dot_in/all_amino02/THR_THREONINE.in_frag | 17 + .../dot_in/all_amino02/TRP_TRYPTOPHAN.in_frag | 27 + .../dot_in/all_amino02/TYR_TYROSINE.in_frag | 24 + .../dot_in/all_amino02/VAL_VALINE.in_frag | 19 + .../dot_in/all_amino02/all_amino02.in | 1095 ++++++ .../all_amino03/ACE_ACE_BEGINNING_GROUP.in_frag | 9 + .../dot_in/all_amino03/ALA_ALANINE.in_frag | 13 + .../dot_in/all_amino03/ARG_ARGININE.in_frag | 27 + .../dot_in/all_amino03/ASH_ASP_neutral.in_frag | 16 + .../dot_in/all_amino03/ASN_ASPARAGINE.in_frag | 17 + .../dot_in/all_amino03/ASP_ASPARTIC_ACID.in_frag | 15 + .../dot_in/all_amino03/CIM_Chloride_Ion.in_frag | 4 + .../dot_in/all_amino03/CIP_Sodium_Ion.in_frag | 4 + .../CYM_CYSTEINE_with_negative_charge.in_frag | 13 + .../dot_in/all_amino03/CYS_CYSTEINE.in_frag | 14 + .../CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 13 + .../dot_in/all_amino03/GLH_GLU_neutral.in_frag | 19 + .../dot_in/all_amino03/GLN_GLUTAMINE.in_frag | 20 + .../dot_in/all_amino03/GLU_GLUTAMIC_ACID.in_frag | 18 + .../dot_in/all_amino03/GLY_GLYCINE.in_frag | 10 + .../all_amino03/HID_HISTIDINE_DELTAH.in_frag | 20 + .../all_amino03/HIE_HISTIDINE_EPSILONH.in_frag | 20 + .../dot_in/all_amino03/HIP_HISTIDINE_PLUS.in_frag | 21 + .../all_amino03/HOH_WATER,_TIP3P_MODEL.in_frag | 6 + .../dot_in/all_amino03/ILE_ISOLEUCINE.in_frag | 22 + .../dot_in/all_amino03/LEU_LEUCINE.in_frag | 22 + .../dot_in/all_amino03/LYN_LYSINE_neutral.in_frag | 24 + .../dot_in/all_amino03/LYS_LYSINE.in_frag | 25 + .../dot_in/all_amino03/MET_METHIONINE.in_frag | 20 + .../all_amino03/NHE_NH2_ENDING_GROUP.in_frag | 6 + .../all_amino03/NME_N-methyl_all_atom.in_frag | 9 + .../dot_in/all_amino03/PHE_PHENYLALANINE.in_frag | 23 + .../dot_in/all_amino03/PRO_PROLINE.in_frag | 17 + .../dot_in/all_amino03/SER_SERINE.in_frag | 14 + .../dot_in/all_amino03/THR_THREONINE.in_frag | 17 + .../dot_in/all_amino03/TRP_TRYPTOPHAN.in_frag | 27 + .../dot_in/all_amino03/TYR_TYROSINE.in_frag | 24 + .../dot_in/all_amino03/VAL_VALINE.in_frag | 19 + .../dot_in/all_amino03/all_amino03.in | 1160 ++++++ .../all_amino94/ACE_ACE_BEGINNING_GROUP.in_frag | 9 + .../dot_in/all_amino94/ALA_ALANINE.in_frag | 13 + .../dot_in/all_amino94/ARG_ARGININE.in_frag | 27 + .../dot_in/all_amino94/ASH_ASP_neutral.in_frag | 16 + .../dot_in/all_amino94/ASN_ASPARAGINE.in_frag | 17 + .../dot_in/all_amino94/ASP_ASPARTIC_ACID.in_frag | 15 + .../dot_in/all_amino94/CIM_Chloride_Ion.in_frag | 4 + .../dot_in/all_amino94/CIP_Sodium_Ion.in_frag | 4 + .../CYM_CYSTEINE_with_negative_charge.in_frag | 13 + .../dot_in/all_amino94/CYS_CYSTEINE.in_frag | 14 + .../CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 13 + .../dot_in/all_amino94/GLH_GLU_neutral.in_frag | 19 + .../dot_in/all_amino94/GLN_GLUTAMINE.in_frag | 20 + .../dot_in/all_amino94/GLU_GLUTAMIC_ACID.in_frag | 18 + .../dot_in/all_amino94/GLY_GLYCINE.in_frag | 10 + .../all_amino94/HID_HISTIDINE_DELTAH.in_frag | 20 + .../all_amino94/HIE_HISTIDINE_EPSILONH.in_frag | 20 + .../dot_in/all_amino94/HIP_HISTIDINE_PLUS.in_frag | 21 + .../dot_in/all_amino94/ILE_ISOLEUCINE.in_frag | 22 + .../dot_in/all_amino94/LEU_LEUCINE.in_frag | 22 + .../dot_in/all_amino94/LYN_LYSINE_neutral.in_frag | 24 + .../dot_in/all_amino94/LYS_LYSINE.in_frag | 25 + .../dot_in/all_amino94/MET_METHIONINE.in_frag | 20 + .../all_amino94/NHE_NH2_ENDING_GROUP.in_frag | 6 + .../all_amino94/NME_N-methyl_all_atom.in_frag | 9 + .../dot_in/all_amino94/PHE_PHENYLALANINE.in_frag | 23 + .../dot_in/all_amino94/PRO_PROLINE.in_frag | 17 + .../dot_in/all_amino94/SER_SERINE.in_frag | 14 + .../dot_in/all_amino94/THR_THREONINE.in_frag | 17 + .../dot_in/all_amino94/TRP_TRYPTOPHAN.in_frag | 27 + .../dot_in/all_amino94/TYR_TYROSINE.in_frag | 24 + .../dot_in/all_amino94/VAL_VALINE.in_frag | 19 + .../dot_in/all_amino94/all_amino94.in | 959 +++++ .../all_aminoct02/ALA_ALANINE_COO-_ANION.in_frag | 14 + .../all_aminoct02/ARG_ARGININE__COO-_ANION.in_frag | 28 + .../ASN_ASPARAGINE____COO-_ANION.in_frag | 18 + .../ASP_ASPARTIC_ACID_COO-_ANION.in_frag | 16 + .../all_aminoct02/CYS_CYSTEINE__COO-_ANION.in_frag | 15 + ...YSTINE_op_S-S_BRIDGE_cp______COO-_ANION.in_frag | 14 + .../GLN_GLUTAMINE_____COO-_ANION.in_frag | 21 + .../GLU_GLUTAMIC_ACID_COO-_ANION.in_frag | 19 + .../all_aminoct02/GLY_GLYCINE_COO-_ANION.in_frag | 11 + .../HID_HISTIDINE_DELTAH_COO-_ANION.in_frag | 21 + .../HIE_HISTIDINE_EPSILON-H___COO-_ANION.in_frag | 21 + .../all_aminoct02/HIP_HISTIDINE_PLUS_COO-.in_frag | 22 + .../ILE_ISOLEUCINE____COO-_ANION.in_frag | 23 + .../all_aminoct02/LEU_LEUCINE__COO-_ANION.in_frag | 23 + .../all_aminoct02/LYS_LYSINE__COO-_ANION.in_frag | 26 + .../MET_METHIONINE____COO-_ANION.in_frag | 21 + .../PHE_PHENYLALANINE_COO-_ANION.in_frag | 24 + .../all_aminoct02/PRO_PROLINE_COO-_ANION.in_frag | 18 + .../all_aminoct02/SER_SERINE__COO-_ANION.in_frag | 15 + .../THR_THREONINE_____COO-_ANION.in_frag | 18 + .../TRP_TRYPTOPHAN____COO-_ANION.in_frag | 28 + .../all_aminoct02/TYR_TYROSINE__COO-_ANION.in_frag | 25 + .../all_aminoct02/VAL_VALINE__COO-_ANION.in_frag | 20 + .../dot_in/all_aminoct02/all_aminoct02.in | 914 +++++ .../all_aminoct03/CALA_ALANINE_COO-_ANION.in_frag | 14 + .../all_aminoct03/CARG_ARGININE_COO-_ANION.in_frag | 28 + .../CASN_ASPARAGINE_COO-_ANION.in_frag | 18 + .../CASP_ASPARTIC_ACID_COO-_ANION.in_frag | 16 + .../all_aminoct03/CCYS_CYSTEINE_COO-_ANION.in_frag | 15 + .../CGLN_GLUTAMINE_COO-_ANION.in_frag | 21 + .../CGLU_GLUTAMIC_ACID_COO-_ANION.in_frag | 19 + .../all_aminoct03/CGLY_GLYCINE_COO-_ANION.in_frag | 11 + .../CHID_HISTIDINE_DELTAH_COO-_ANION.in_frag | 21 + .../CHIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag | 21 + .../CHIP_HISTIDINE_PLUS_COO-_ANION.in_frag | 22 + .../CILE_ISOLEUCINE_COO-_ANION.in_frag | 23 + .../all_aminoct03/CLEU_LEUCINE_COO-_ANION.in_frag | 23 + .../all_aminoct03/CLYS_LYSINE_COO-_ANION.in_frag | 26 + .../CMET_METHIONINE_COO-_ANION.in_frag | 21 + .../CPHE_PHENYLALANINE_COO-_ANION.in_frag | 24 + .../all_aminoct03/CPRO_PROLINE_COO-_ANION.in_frag | 18 + .../all_aminoct03/CSER_SERINE_COO-_ANION.in_frag | 15 + .../CTHR_THREONINE_COO-_ANION.in_frag | 18 + .../CTRP_TRYPTOPHAN_COO-_ANION.in_frag | 28 + .../all_aminoct03/CTYR_TYROSINE_COO-_ANION.in_frag | 25 + .../all_aminoct03/CVAL_VALINE_COO-_ANION.in_frag | 20 + .../dot_in/all_aminoct03/all_aminoct03.in | 733 ++++ .../all_aminoct94/ALA_ALANINE_COO-_ANION.in_frag | 14 + .../all_aminoct94/ARG_ARGININE__COO-_ANION.in_frag | 28 + .../ASN_ASPARAGINE____COO-_ANION.in_frag | 18 + .../ASP_ASPARTIC_ACID_COO-_ANION.in_frag | 16 + .../all_aminoct94/CYS_CYSTEINE__COO-_ANION.in_frag | 15 + ...YSTINE_op_S-S_BRIDGE_cp______COO-_ANION.in_frag | 14 + .../GLN_GLUTAMINE_____COO-_ANION.in_frag | 21 + .../GLU_GLUTAMIC_ACID_COO-_ANION.in_frag | 19 + .../all_aminoct94/GLY_GLYCINE_COO-_ANION.in_frag | 11 + .../HID_HISTIDINE_DELTAH_COO-_ANION.in_frag | 21 + .../HIE_HISTIDINE_EPSILON-H___COO-_ANION.in_frag | 21 + .../all_aminoct94/HIP_HISTIDINE_PLUS_COO-.in_frag | 22 + .../ILE_ISOLEUCINE____COO-_ANION.in_frag | 23 + .../all_aminoct94/LEU_LEUCINE__COO-_ANION.in_frag | 23 + .../all_aminoct94/LYS_LYSINE__COO-_ANION.in_frag | 26 + .../MET_METHIONINE____COO-_ANION.in_frag | 21 + .../PHE_PHENYLALANINE_COO-_ANION.in_frag | 24 + .../all_aminoct94/PRO_PROLINE_COO-_ANION.in_frag | 18 + .../all_aminoct94/SER_SERINE__COO-_ANION.in_frag | 15 + .../THR_THREONINE_____COO-_ANION.in_frag | 18 + .../TRP_TRYPTOPHAN____COO-_ANION.in_frag | 28 + .../all_aminoct94/TYR_TYROSINE__COO-_ANION.in_frag | 25 + .../all_aminoct94/VAL_VALINE__COO-_ANION.in_frag | 20 + .../dot_in/all_aminoct94/all_aminoct94.in | 781 ++++ .../dot_in/all_aminont02/ALA_ALANINE.in_frag | 15 + .../dot_in/all_aminont02/ARG_ARGININE.in_frag | 29 + .../dot_in/all_aminont02/ASN_ASPARAGINE.in_frag | 19 + .../dot_in/all_aminont02/ASP_ASPARTIC_ACID.in_frag | 17 + .../dot_in/all_aminont02/CYS_CYSTEINE.in_frag | 16 + .../CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 15 + .../dot_in/all_aminont02/GLN_GLUTAMINE.in_frag | 22 + .../dot_in/all_aminont02/GLU_GLUTAMIC_ACID.in_frag | 20 + .../dot_in/all_aminont02/GLY_GLYCINE.in_frag | 12 + .../all_aminont02/HID_HISTIDINE_DELTAH.in_frag | 22 + .../all_aminont02/HIE_HISTIDINE_EPSILONH.in_frag | 22 + .../all_aminont02/HIP_HISTIDINE_PLUS.in_frag | 23 + .../dot_in/all_aminont02/ILE_ISOLEUCINE.in_frag | 24 + .../dot_in/all_aminont02/LEU_LEUCINE.in_frag | 24 + .../dot_in/all_aminont02/LYS_LYSINE.in_frag | 27 + .../dot_in/all_aminont02/MET_METHIONINE.in_frag | 22 + .../dot_in/all_aminont02/PHE_PHENYLALANINE.in_frag | 25 + .../dot_in/all_aminont02/PRO_PROLINE.in_frag | 19 + .../dot_in/all_aminont02/SER_SERINE.in_frag | 16 + .../dot_in/all_aminont02/THR_THREONINE.in_frag | 19 + .../dot_in/all_aminont02/TRP_TRYPTOPHAN.in_frag | 29 + .../dot_in/all_aminont02/TYR_TYROSINE.in_frag | 26 + .../dot_in/all_aminont02/VAL_VALINE.in_frag | 21 + .../dot_in/all_aminont02/all_aminont02.in | 922 +++++ .../dot_in/all_aminont03/NALA_ALANINE.in_frag | 15 + .../dot_in/all_aminont03/NARG_ARGININE.in_frag | 29 + .../dot_in/all_aminont03/NASN_ASPARAGINE.in_frag | 19 + .../all_aminont03/NASP_ASPARTIC_ACID.in_frag | 17 + .../dot_in/all_aminont03/NCYS_CYSTEINE.in_frag | 16 + .../dot_in/all_aminont03/NGLN_GLUTAMINE.in_frag | 22 + .../all_aminont03/NGLU_GLUTAMIC_ACID.in_frag | 20 + .../dot_in/all_aminont03/NGLY_GLYCINE.in_frag | 12 + .../all_aminont03/NHID_HISTIDINE_DELTAH.in_frag | 22 + .../all_aminont03/NHIE_HISTIDINE_EPSILONH.in_frag | 22 + .../all_aminont03/NHIP_HISTIDINE_PLUS.in_frag | 23 + .../dot_in/all_aminont03/NILE_ISOLEUCINE.in_frag | 24 + .../dot_in/all_aminont03/NLEU_LEUCINE.in_frag | 24 + .../dot_in/all_aminont03/NLYS_LYSINE.in_frag | 27 + .../dot_in/all_aminont03/NMET_METHIONINE.in_frag | 22 + .../all_aminont03/NPHE_PHENYLALANINE.in_frag | 25 + .../dot_in/all_aminont03/NPRO_PROLINE.in_frag | 19 + .../dot_in/all_aminont03/NSER_SERINE.in_frag | 16 + .../dot_in/all_aminont03/NTHR_THREONINE.in_frag | 19 + .../dot_in/all_aminont03/NTRP_TRYPTOPHAN.in_frag | 29 + .../dot_in/all_aminont03/NTYR_TYROSINE.in_frag | 26 + .../dot_in/all_aminont03/NVAL_VALINE.in_frag | 21 + .../dot_in/all_aminont03/all_aminont03.in | 757 ++++ .../dot_in/all_aminont94/ALA_ALANINE.in_frag | 15 + .../dot_in/all_aminont94/ARG_ARGININE.in_frag | 29 + .../dot_in/all_aminont94/ASN_ASPARAGINE.in_frag | 19 + .../dot_in/all_aminont94/ASP_ASPARTIC_ACID.in_frag | 17 + .../dot_in/all_aminont94/CYS_CYSTEINE.in_frag | 16 + .../CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 15 + .../dot_in/all_aminont94/GLN_GLUTAMINE.in_frag | 22 + .../dot_in/all_aminont94/GLU_GLUTAMIC_ACID.in_frag | 20 + .../dot_in/all_aminont94/GLY_GLYCINE.in_frag | 12 + .../all_aminont94/HID_HISTIDINE_DELTAH.in_frag | 22 + .../all_aminont94/HIE_HISTIDINE_EPSILONH.in_frag | 22 + .../all_aminont94/HIP_HISTIDINE_PLUS.in_frag | 23 + .../dot_in/all_aminont94/ILE_ISOLEUCINE.in_frag | 24 + .../dot_in/all_aminont94/LEU_LEUCINE.in_frag | 24 + .../dot_in/all_aminont94/LYS_LYSINE.in_frag | 27 + .../dot_in/all_aminont94/MET_METHIONINE.in_frag | 22 + .../dot_in/all_aminont94/PHE_PHENYLALANINE.in_frag | 25 + .../dot_in/all_aminont94/PRO_PROLINE.in_frag | 19 + .../dot_in/all_aminont94/SER_SERINE.in_frag | 16 + .../dot_in/all_aminont94/THR_THREONINE.in_frag | 19 + .../dot_in/all_aminont94/TRP_TRYPTOPHAN.in_frag | 29 + .../dot_in/all_aminont94/TYR_TYROSINE.in_frag | 26 + .../dot_in/all_aminont94/VAL_VALINE.in_frag | 21 + .../dot_in/all_aminont94/all_aminont94.in | 782 ++++ .../dot_in/all_nuc02/AME_N-methyl-ADENINE.in_frag | 21 + .../dot_in/all_nuc02/CME_N-methyl-CYTOSINE.in_frag | 19 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 36 + ..._OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag | 33 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 34 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 35 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 34 + ...d_group_and_3_p__-_O_op_minus_cp__group.in_frag | 31 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 32 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 33 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 37 + ...d_group_and_3_p__-_O_op_minus_cp__group.in_frag | 34 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 35 + ...te_group_and_3_p__-_O_op_minus_cp__grou.in_frag | 36 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 36 + ..._OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag | 33 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 34 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 35 + .../dot_in/all_nuc02/GME_N-methyl-GUANINE.in_frag | 22 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 37 + ..._OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag | 34 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 35 + ...te_group_and_3_p__-_O_op_minus_cp__grou.in_frag | 36 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 35 + ...d_group_and_3_p__-_O_op_minus_cp__group.in_frag | 32 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 33 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 34 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 38 + ...d_group_and_3_p__-_O_op_minus_cp__group.in_frag | 35 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 36 + ...te_group_and_3_p__-_O_op_minus_cp__grou.in_frag | 37 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 34 + ..._OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag | 31 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 32 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 33 + .../dot_in/all_nuc02/TME_N-methyl-_THYMINE.in_frag | 21 + .../dot_in/all_nuc02/UME_N-methyl-URACIL.in_frag | 18 + .../dot_in/all_nuc02/all_nuc02.in | 2219 +++++++++++ ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 36 + ..._OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag | 33 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 34 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 35 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 34 + ...d_group_and_3_p__-_O_op_minus_cp__group.in_frag | 31 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 32 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 33 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 37 + ...d_group_and_3_p__-_O_op_minus_cp__group.in_frag | 34 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 35 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 36 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 36 + ..._OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag | 33 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 34 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 35 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 37 + ..._OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag | 34 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 35 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 36 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 35 + ...d_group_and_3_p__-_O_op_minus_cp__group.in_frag | 32 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 33 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 34 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 38 + ...d_group_and_3_p__-_O_op_minus_cp__group.in_frag | 35 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 36 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 37 + ...__-_phosphate_group_and_3_p__-_OH_group.in_frag | 34 + ..._OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag | 31 + ...ith_5_p__-_OH_group_and_3_p__-_OH_group.in_frag | 32 + ...e_group_and_3_p__-_O_op_minus_cp__group.in_frag | 33 + .../dot_in/all_nuc94/all_nuc94.in | 1970 ++++++++++ .../dot_in/allct/ALA_ALANINE_COO-_ANION.in_frag | 14 + .../dot_in/allct/ARG_ARGININE__COO-_ANION.in_frag | 28 + .../allct/ASN_ASPARAGINE____COO-_ANION.in_frag | 18 + .../allct/ASP_ASPARTIC_ACID_COO-_ANION.in_frag | 16 + .../dot_in/allct/CYS_CYSTEINE__COO-_ANION.in_frag | 17 + ...YSTINE_op_S-S_BRIDGE_cp______COO-_ANION.in_frag | 16 + .../allct/GLN_GLUTAMINE_____COO-_ANION.in_frag | 21 + .../allct/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag | 19 + .../dot_in/allct/GLY_GLYCINE_COO-_ANION.in_frag | 11 + .../allct/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag | 21 + .../HIE_HISTIDINE_EPSILON-H___COO-_ANION.in_frag | 21 + .../dot_in/allct/HIP_HISTIDINE_PLUS_COO-.in_frag | 22 + .../allct/ILE_ISOLEUCINE____COO-_ANION.in_frag | 23 + .../dot_in/allct/LEU_LEUCINE__COO-_ANION.in_frag | 23 + .../dot_in/allct/LYS_LYSINE__COO-_ANION.in_frag | 26 + .../allct/MET_METHIONINE____COO-_ANION.in_frag | 23 + .../allct/PHE_PHENYLALANINE_COO-_ANION.in_frag | 24 + .../dot_in/allct/PRO_PROLINE_COO-_ANION.in_frag | 18 + .../dot_in/allct/SER_SERINE__COO-_ANION.in_frag | 15 + .../allct/THR_THREONINE_____COO-_ANION.in_frag | 18 + .../allct/TRP_TRYPTOPHAN____COO-_ANION.in_frag | 28 + .../dot_in/allct/TYR_TYROSINE__COO-_ANION.in_frag | 25 + .../dot_in/allct/VAL_VALINE__COO-_ANION.in_frag | 20 + .../AMBER_test_structures/dot_in/allct/allct.in | 765 ++++ .../dot_in/allnt/ALA_ALANINE.in_frag | 15 + .../dot_in/allnt/ARG_ARGININE.in_frag | 29 + .../dot_in/allnt/ASN_ASPARAGINE.in_frag | 19 + .../dot_in/allnt/ASP_ASPARTIC_ACID.in_frag | 17 + .../dot_in/allnt/CYS_CYSTEINE.in_frag | 18 + .../allnt/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 17 + .../dot_in/allnt/GLN_GLUTAMINE.in_frag | 22 + .../dot_in/allnt/GLU_GLUTAMIC_ACID.in_frag | 20 + .../dot_in/allnt/GLY_GLYCINE.in_frag | 12 + .../dot_in/allnt/HID_HISTIDINE_DELTAH.in_frag | 22 + .../dot_in/allnt/HIE_HISTIDINE_EPSILONH.in_frag | 22 + .../dot_in/allnt/HIP_HISTIDINE_PLUS.in_frag | 23 + .../dot_in/allnt/ILE_ISOLEUCINE.in_frag | 24 + .../dot_in/allnt/LEU_LEUCINE.in_frag | 24 + .../dot_in/allnt/LYS_LYSINE.in_frag | 27 + .../dot_in/allnt/MET_METHIONINE.in_frag | 24 + .../dot_in/allnt/PHE_PHENYLALANINE.in_frag | 25 + .../dot_in/allnt/PRO_PROLINE.in_frag | 19 + .../dot_in/allnt/SER_SERINE.in_frag | 16 + .../dot_in/allnt/THR_THREONINE.in_frag | 19 + .../dot_in/allnt/TRP_TRYPTOPHAN.in_frag | 29 + .../dot_in/allnt/TYR_TYROSINE.in_frag | 26 + .../dot_in/allnt/VAL_VALINE.in_frag | 21 + .../AMBER_test_structures/dot_in/allnt/allnt.in | 766 ++++ .../AMBER_test_structures/dot_in/chcl3/chcl3.in | 18 + cad/tests/AMBER_test_structures/dot_in/ferd | 0 ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 35 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 35 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 35 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 35 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 35 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 35 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 34 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 34 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 34 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 34 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 34 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 34 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 34 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 34 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 34 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 34 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 34 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 34 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 34 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 34 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 34 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 34 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 34 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 34 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 34 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 34 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 34 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 34 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 34 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 34 + ...om_ens_avg_a_s_b-glcgalman_w_s__EPs_cp_.in_frag | 10 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 31 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 31 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 31 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 31 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 31 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 31 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 32 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 32 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 32 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 32 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 32 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 32 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 32 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 32 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 32 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 32 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 32 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 32 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 32 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 32 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 32 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 32 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 32 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 32 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 32 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 32 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 32 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 32 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 32 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 32 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 33 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 33 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 33 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 33 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 33 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 33 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 33 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 33 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 33 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 33 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 33 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 33 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 33 + ...e,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 33 + ...due,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 33 + ..._hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag | 33 + ....,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 33 + ...es.,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag | 33 + ...__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag | 33 + .../dot_in/glycam04EP/glycam04EP.in | 4149 ++++++++++++++++++++ .../AMBER_test_structures/dot_in/meoh/meoh.in | 20 + .../dot_in/opls_nacl/CL_Chloride_Ion.in_frag | 4 + .../dot_in/opls_nacl/NA_Sodium_Ion.in_frag | 4 + .../dot_in/opls_nacl/opls_nacl.in | 25 + .../opls_uni/ACE_ACE_BEGINNING_GROUP.in_frag | 6 + .../dot_in/opls_uni/ALA_ALANINE.in_frag | 9 + .../AME_TERMINAL_METHYL_AMIDE,_OPLS_MODEL.in_frag | 6 + .../dot_in/opls_uni/ARG_ARGININE.in_frag | 20 + .../dot_in/opls_uni/ASN_ASPARAGINE.in_frag | 14 + .../dot_in/opls_uni/ASP_ASPARTIC_ACID.in_frag | 12 + .../dot_in/opls_uni/CYS_CYSTEINE.in_frag | 11 + .../opls_uni/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 10 + .../dot_in/opls_uni/DAL_D-ALANINE.in_frag | 9 + .../dot_in/opls_uni/GLN_GLUTAMINE.in_frag | 15 + .../dot_in/opls_uni/GLU_GLUTAMIC_ACID.in_frag | 13 + .../dot_in/opls_uni/GLY_GLYCINE.in_frag | 8 + ...DELTAH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 15 + ...SILONH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 15 + ...NE_DELTAH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 17 + ..._EPSILONH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 17 + ...DINE_PLUS,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 18 + ...E_PLUS,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 16 + .../dot_in/opls_uni/ILE_ISOLEUCINE.in_frag | 12 + .../dot_in/opls_uni/LEU_LEUCINE.in_frag | 12 + .../dot_in/opls_uni/LYS_LYSINE.in_frag | 16 + .../dot_in/opls_uni/MET_METHIONINE.in_frag | 12 + .../dot_in/opls_uni/OME_O_MINUS_END_ATOM.in_frag | 4 + ...YLALANINE,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 20 + ...LANINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 15 + .../dot_in/opls_uni/PRO_PROLINE.in_frag | 10 + .../dot_in/opls_uni/SER_SERINE.in_frag | 11 + .../dot_in/opls_uni/THR_THREONINE.in_frag | 12 + ...RYPTOPHAN,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 24 + ...TOPHAN,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 19 + ..._TYROSINE,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 21 + ...ROSINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 17 + .../dot_in/opls_uni/VAL_VALINE.in_frag | 11 + .../dot_in/opls_uni/WT3_WATER,_TIP3P_MODEL.in_frag | 6 + .../dot_in/opls_uni/WT4_WATER,_TIP4P_MODEL.in_frag | 7 + .../dot_in/opls_uni/opls_uni.in | 921 +++++ .../opls_unict/ALA_ALANINE_COO-_ANION.in_frag | 10 + .../AME_TERMINAL_METHYL_AMIDE,_OPLS_MODEL.in_frag | 6 + .../opls_unict/ARG_ARGININE_COO-_ANION.in_frag | 21 + .../opls_unict/ASN_ASPARAGINE_COO-_ANION.in_frag | 15 + .../ASP_ASPARTIC_ACID_COO-_ANION.in_frag | 13 + .../opls_unict/CYS_CYSTEINE_COO-_ANION.in_frag | 12 + ...YX_CYSTINE_op_S-S_BRIDGE_cp__COO-_ANION.in_frag | 11 + .../opls_unict/GLN_GLUTAMINE_COO-_ANION.in_frag | 16 + .../GLU_GLUTAMIC_ACID_COO-_ANION.in_frag | 14 + .../opls_unict/GLY_GLYCINE_COO-_ANION.in_frag | 9 + ..._ANION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 16 + ..._ANION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 16 + ...OO-_ANION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 18 + ...OO-_ANION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 18 + ...WITTERION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 19 + ...TERION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 17 + .../opls_unict/ILE_ISOLEUCINE_COO-_ANION.in_frag | 13 + .../opls_unict/LEU_LEUCINE_COO-_ANION.in_frag | 13 + .../opls_unict/LYS_LYSINE_COO-_ANION.in_frag | 17 + .../opls_unict/MET_METHIONINE_COO-_ANION.in_frag | 13 + ...LL_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag | 21 + ...ED_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag | 16 + .../opls_unict/PRO_PROLINE_COO-_ANION.in_frag | 11 + .../opls_unict/SER_SERINE_COO-_ANION.in_frag | 12 + .../opls_unict/THR_THREONINE_COO-_ANION.in_frag | 13 + ...OO-_ANION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 25 + ..._ANION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 20 + ...LL_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag | 22 + ...ED_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag | 18 + .../dot_in/opls_unict/VAL_VALINE.in_frag | 12 + .../dot_in/opls_unict/opls_unict.in | 876 +++++ .../dot_in/opls_unint/ALA_ALANINE.in_frag | 11 + .../dot_in/opls_unint/ARG_ARGININE.in_frag | 22 + .../dot_in/opls_unint/ASN_ASPARAGINE.in_frag | 16 + .../dot_in/opls_unint/ASP_ASPARTIC_ACID.in_frag | 14 + .../dot_in/opls_unint/CYS_CYSTEINE.in_frag | 13 + .../CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 12 + .../dot_in/opls_unint/GLN_GLUTAMINE.in_frag | 17 + .../dot_in/opls_unint/GLU_GLUTAMIC_ACID.in_frag | 15 + .../dot_in/opls_unint/GLY_GLYCINE.in_frag | 10 + ...DELTAH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 17 + ...SILONH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 17 + ...NE_DELTAH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 19 + ..._EPSILONH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 19 + ...DINE_PLUS,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 20 + ...E_PLUS,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 18 + .../dot_in/opls_unint/ILE_ISOLEUCINE.in_frag | 14 + .../dot_in/opls_unint/LEU_LEUCINE.in_frag | 14 + .../dot_in/opls_unint/LYS_LYSINE.in_frag | 18 + .../dot_in/opls_unint/MET_METHIONINE.in_frag | 14 + ...LL_ATOM_AROMATIC_PARAMETERS,_N-TERMINAL.in_frag | 22 + ...LANINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 17 + .../dot_in/opls_unint/PRO_PROLINE.in_frag | 12 + .../dot_in/opls_unint/SER_SERINE.in_frag | 13 + .../dot_in/opls_unint/THR_THREONINE.in_frag | 14 + ...RYPTOPHAN,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag | 26 + ...TOPHAN,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 21 + ...LL_ATOM_AROMATIC_PARAMETERS,_N-TERMINUS.in_frag | 23 + ...ROSINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag | 19 + .../dot_in/opls_unint/VAL_VALINE.in_frag | 13 + .../dot_in/opls_unint/opls_unint.in | 863 ++++ .../ALA_ALANINE_COO-_ANION.in_frag | 10 + .../dot_in/protein.amberua.C/ARG_ARGININE.in_frag | 21 + .../ASN_ASPARAGINE_COO-_ANION.in_frag | 15 + .../ASP_ASPARTIC_ACID_COO-_ANION.in_frag | 13 + .../CYS_CYSTEINE_COO-_ANION.in_frag | 14 + ...YX_CYSTINE_op_S-S_BRIDGE_cp__COO-_ANION.in_frag | 13 + .../GLN_GLUTAMINE_COO-_ANION.in_frag | 16 + .../GLU_GLUTAMIC_ACID_COO-_ANION.in_frag | 14 + .../GLY_GLYCINE_COO-_ANION.in_frag | 9 + .../HID_HISTIDINE_DELTAH_COO-_ANION.in_frag | 16 + .../HIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag | 16 + .../HIP_HISTIDINE_PLUS_ZWITTERION.in_frag | 17 + .../ILE_ISOLEUCINE_COO-_ANION.in_frag | 13 + .../LEU_LEUCINE_COO-_ANION.in_frag | 13 + .../LYS_LYSINE_COO-_ANION.in_frag | 17 + .../MET_METHIONINE_COO-_ANION.in_frag | 15 + .../PHE_PHENYLALANINE_COO-_ANION.in_frag | 16 + .../PRO_PROLINE_COO-_ANION.in_frag | 11 + .../SER_SERINE_COO-_ANION.in_frag | 12 + .../THR_THREONINE_COO-_ANION.in_frag | 13 + .../TRP_TRYPTOPHAN_COO-_ANION.in_frag | 20 + .../TYR_TYROSINE_COO-_ANION.in_frag | 18 + .../dot_in/protein.amberua.C/VAL_VALINE.in_frag | 12 + .../dot_in/protein.amberua.C/protein.amberua.C.in | 645 +++ .../dot_in/protein.amberua.N/ALA_ALANINE.in_frag | 11 + .../dot_in/protein.amberua.N/ARG_ARGININE.in_frag | 22 + .../protein.amberua.N/ASN_ASPARAGINE.in_frag | 16 + .../protein.amberua.N/ASP_ASPARTIC_ACID.in_frag | 14 + .../dot_in/protein.amberua.N/CYS_CYSTEINE.in_frag | 15 + .../CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 14 + .../dot_in/protein.amberua.N/GLN_GLUTAMINE.in_frag | 17 + .../protein.amberua.N/GLU_GLUTAMIC_ACID.in_frag | 15 + .../dot_in/protein.amberua.N/GLY_GLYCINE.in_frag | 10 + .../protein.amberua.N/HID_HISTIDINE_DELTAH.in_frag | 17 + .../HIE_HISTIDINE_EPSILONH.in_frag | 17 + .../protein.amberua.N/HIP_HISTIDINE_PLUS.in_frag | 18 + .../protein.amberua.N/ILE_ISOLEUCINE.in_frag | 14 + .../dot_in/protein.amberua.N/LEU_LEUCINE.in_frag | 14 + .../dot_in/protein.amberua.N/LYS_LYSINE.in_frag | 18 + .../protein.amberua.N/MET_METHIONINE.in_frag | 16 + .../protein.amberua.N/PHE_PHENYLALANINE.in_frag | 17 + .../dot_in/protein.amberua.N/PRO_PROLINE.in_frag | 12 + .../dot_in/protein.amberua.N/SER_SERINE.in_frag | 13 + .../dot_in/protein.amberua.N/THR_THREONINE.in_frag | 14 + .../protein.amberua.N/TRP_TRYPTOPHAN.in_frag | 21 + .../dot_in/protein.amberua.N/TYR_TYROSINE.in_frag | 19 + .../dot_in/protein.amberua.N/VAL_VALINE.in_frag | 13 + .../dot_in/protein.amberua.N/protein.amberua.N.in | 646 +++ .../ACE_ACE_BEGINNING_GROUP.in_frag | 6 + .../dot_in/protein.amberua/ALA_ALANINE.in_frag | 9 + .../dot_in/protein.amberua/ARG_ARGININE.in_frag | 20 + .../dot_in/protein.amberua/ASN_ASPARAGINE.in_frag | 14 + .../protein.amberua/ASP_ASPARTIC_ACID.in_frag | 12 + .../dot_in/protein.amberua/CL_CL__PREP.in_frag | 4 + .../dot_in/protein.amberua/CYS_CYSTEINE.in_frag | 13 + .../CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 12 + .../dot_in/protein.amberua/GLN_GLUTAMINE.in_frag | 15 + .../protein.amberua/GLU_GLUTAMIC_ACID.in_frag | 13 + .../dot_in/protein.amberua/GLY_GLYCINE.in_frag | 8 + .../protein.amberua/HID_HISTIDINE_DELTAH.in_frag | 15 + .../protein.amberua/HIE_HISTIDINE_EPSILONH.in_frag | 15 + .../protein.amberua/HIP_HISTIDINE_PLUS.in_frag | 16 + .../dot_in/protein.amberua/ILE_ISOLEUCINE.in_frag | 12 + .../dot_in/protein.amberua/K_K___PREP.in_frag | 4 + .../dot_in/protein.amberua/LEU_LEUCINE.in_frag | 12 + .../dot_in/protein.amberua/LYS_LYSINE.in_frag | 16 + .../dot_in/protein.amberua/MET_METHIONINE.in_frag | 14 + .../dot_in/protein.amberua/MG_MG__PREP.in_frag | 4 + .../dot_in/protein.amberua/NA_NA__PREP.in_frag | 4 + .../protein.amberua/NME_N-Methyl_end_group.in_frag | 6 + .../protein.amberua/PHE_PHENYLALANINE.in_frag | 15 + .../dot_in/protein.amberua/PRO_PROLINE.in_frag | 10 + .../dot_in/protein.amberua/SER_SERINE.in_frag | 11 + .../dot_in/protein.amberua/THR_THREONINE.in_frag | 12 + .../dot_in/protein.amberua/TRP_TRYPTOPHAN.in_frag | 19 + .../dot_in/protein.amberua/TYR_TYROSINE.in_frag | 17 + .../dot_in/protein.amberua/VAL_VALINE.in_frag | 11 + .../dot_in/protein.amberua/protein.amberua.in | 698 ++++ .../dot_in/uni/ACE_ACE_BEGINNING_GROUP.in_frag | 6 + .../dot_in/uni/ALA_ALANINE.in_frag | 9 + .../dot_in/uni/ARG_ARGININE.in_frag | 20 + .../dot_in/uni/ASN_ASPARAGINE.in_frag | 14 + .../dot_in/uni/ASP_ASPARTIC_ACID.in_frag | 12 + .../dot_in/uni/CL_CL__PREP.in_frag | 4 + .../dot_in/uni/CYS_CYSTEINE.in_frag | 13 + .../uni/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 12 + .../dot_in/uni/DADE_D-ADENOSINE.in_frag | 23 + .../dot_in/uni/DCYT_D-CYTOSINE.in_frag | 21 + .../dot_in/uni/DGUA_D-GUANOSINE.in_frag | 25 + .../dot_in/uni/DOHE_D-OH_END.in_frag | 5 + .../dot_in/uni/DPOM_D_-_PHOSPATE_MINUS.in_frag | 6 + .../dot_in/uni/DTHY_D-THYMINE.in_frag | 21 + .../dot_in/uni/GLN_GLUTAMINE.in_frag | 15 + .../dot_in/uni/GLU_GLUTAMIC_ACID.in_frag | 13 + .../dot_in/uni/GLY_GLYCINE.in_frag | 8 + .../dot_in/uni/HB_H_BEGINNING.in_frag | 4 + .../dot_in/uni/HE_H_END.in_frag | 4 + .../dot_in/uni/HID_HISTIDINE_DELTAH.in_frag | 15 + .../dot_in/uni/HIE_HISTIDINE_EPSILONH.in_frag | 15 + .../dot_in/uni/HIP_HISTIDINE_PLUS.in_frag | 16 + .../dot_in/uni/ILE_ISOLEUCINE.in_frag | 12 + .../dot_in/uni/K_K___PREP.in_frag | 4 + .../dot_in/uni/LEU_LEUCINE.in_frag | 12 + .../dot_in/uni/LYS_LYSINE.in_frag | 16 + .../dot_in/uni/MET_METHIONINE.in_frag | 14 + .../dot_in/uni/MG_MG__PREP.in_frag | 4 + .../dot_in/uni/NA_NA__PREP.in_frag | 4 + .../dot_in/uni/NME_N-Methyl_end_group.in_frag | 6 + .../dot_in/uni/OHB_OH_BEGINNING.in_frag | 5 + .../dot_in/uni/PHE_PHENYLALANINE.in_frag | 15 + .../dot_in/uni/POHE_PROTEIN-OH_END.in_frag | 5 + .../dot_in/uni/PRO_PROLINE.in_frag | 10 + .../dot_in/uni/RADE_R-ADENOSINE.in_frag | 25 + .../dot_in/uni/RCYT_R-CYTOSINE.in_frag | 23 + .../dot_in/uni/RGUA_R-GUANOSINE.in_frag | 27 + .../dot_in/uni/ROHE_R-OH_END.in_frag | 5 + .../dot_in/uni/RPOM_R_-_PHOSPHATE_MINUS.in_frag | 6 + .../dot_in/uni/RURA_R-URACIL.in_frag | 22 + .../dot_in/uni/SER_SERINE.in_frag | 11 + .../dot_in/uni/THR_THREONINE.in_frag | 12 + .../dot_in/uni/TRP_TRYPTOPHAN.in_frag | 19 + .../dot_in/uni/TYR_TYROSINE.in_frag | 17 + .../dot_in/uni/VAL_VALINE.in_frag | 11 + cad/tests/AMBER_test_structures/dot_in/uni/uni.in | 1129 ++++++ .../uni_amino03/ACE_ACE_BEGINNING_GROUP.in_frag | 6 + .../dot_in/uni_amino03/ALA_ALANINE.in_frag | 10 + .../dot_in/uni_amino03/ARG_ARGININE.in_frag | 21 + .../dot_in/uni_amino03/ASN_ASPARAGINE.in_frag | 15 + .../dot_in/uni_amino03/ASP_ASPARTIC_ACID.in_frag | 13 + .../dot_in/uni_amino03/CYS_CYSTEINE.in_frag | 12 + .../CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag | 11 + .../dot_in/uni_amino03/GLN_GLUTAMINE.in_frag | 16 + .../dot_in/uni_amino03/GLU_GLUTAMIC_ACID.in_frag | 14 + .../dot_in/uni_amino03/GLY_GLYCINE.in_frag | 10 + .../uni_amino03/HID_HISTIDINE_DELTAH.in_frag | 18 + .../uni_amino03/HIE_HISTIDINE_EPSILONH.in_frag | 18 + .../dot_in/uni_amino03/HIP_HISTIDINE_PLUS.in_frag | 19 + .../dot_in/uni_amino03/ILE_ISOLEUCINE.in_frag | 13 + .../dot_in/uni_amino03/LEU_LEUCINE.in_frag | 13 + .../dot_in/uni_amino03/LYS_LYSINE.in_frag | 17 + .../dot_in/uni_amino03/MET_METHIONINE.in_frag | 13 + .../uni_amino03/NME_N-methyl_all_atom.in_frag | 6 + .../dot_in/uni_amino03/PHE_PHENYLALANINE.in_frag | 21 + .../dot_in/uni_amino03/PRO_PROLINE.in_frag | 11 + .../dot_in/uni_amino03/SER_SERINE.in_frag | 12 + .../dot_in/uni_amino03/THR_THREONINE.in_frag | 13 + .../dot_in/uni_amino03/TRP_TRYPTOPHAN.in_frag | 25 + .../dot_in/uni_amino03/TYR_TYROSINE.in_frag | 22 + .../dot_in/uni_amino03/VAL_VALINE.in_frag | 12 + .../dot_in/uni_amino03/uni_amino03.in | 701 ++++ .../uni_aminoct03/CALA_ALANINE_COO-_ANION.in_frag | 11 + .../uni_aminoct03/CARG_ARGININE_COO-_ANION.in_frag | 22 + .../CASN_ASPARAGINE_COO-_ANION.in_frag | 16 + .../CASP_ASPARTIC_ACID_COO-_ANION.in_frag | 14 + .../uni_aminoct03/CCYS_CYSTEINE_COO-_ANION.in_frag | 13 + .../CGLN_GLUTAMINE_COO-_ANION.in_frag | 17 + .../CGLU_GLUTAMIC_ACID_COO-_ANION.in_frag | 15 + .../uni_aminoct03/CGLY_GLYCINE_COO-_ANION.in_frag | 11 + .../CHID_HISTIDINE_DELTAH_COO-_ANION.in_frag | 19 + .../CHIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag | 19 + .../CHIP_HISTIDINE_PLUS_COO-_ANION.in_frag | 20 + .../CILE_ISOLEUCINE_COO-_ANION.in_frag | 14 + .../uni_aminoct03/CLEU_LEUCINE_COO-_ANION.in_frag | 14 + .../uni_aminoct03/CLYS_LYSINE_COO-_ANION.in_frag | 18 + .../CMET_METHIONINE_COO-_ANION.in_frag | 14 + .../CPHE_PHENYLALANINE_COO-_ANION.in_frag | 22 + .../uni_aminoct03/CPRO_PROLINE_COO-_ANION.in_frag | 12 + 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cad/tests/AMBER_test_structures/dot_in/unint/HID_HISTIDINE_DELTAH.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/HIE_HISTIDINE_EPSILONH.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/HIP_HISTIDINE_PLUS.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/ILE_ISOLEUCINE.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/LEU_LEUCINE.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/LYS_LYSINE.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/MET_METHIONINE.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/PHE_PHENYLALANINE.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/PRO_PROLINE.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/SER_SERINE.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/THR_THREONINE.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/TRP_TRYPTOPHAN.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/TYR_TYROSINE.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/VAL_VALINE.in_frag create mode 100644 cad/tests/AMBER_test_structures/dot_in/unint/unint.in create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/ALA_ALANINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/ARG_ARGININE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/ASH_ASPARTIC_ACID_neutral.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/ASN_ASPARAGINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/ASP_ASPARTIC_ACID.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/CYM_CYSTEINE_negative.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/CYS_CYSTEINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/CYX_CYSTEINE-S-S-CYSTEINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/GLH_GLUTAMIC_ACID_neutral.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/GLN_GLUTAMINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/GLU_GLUTAMIC_ACID.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/GLY_GLYCINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/HID_HISTIDINE_DELTAH.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/HIE_HISTIDINE_EPSILONH.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/HIP_HISTIDINE_plus.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/ILE_ISOLEUCINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/LEU_LEUCINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/LYN_LYSINE_neutral.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/LYS_LYSINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/MET_METHIONINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/PHE_PHENYLALANINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/PRO_PROLINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/SER_SERINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/THR_THREONINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/TRP_TRYPTOPHAN.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/TYR_TYROSINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/AminoAcids/VAL_VALINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/Nucleotides/DA_D-ADENOSINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/Nucleotides/DC_D-CYTOSINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/Nucleotides/DG_G-GUANOSINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/Nucleotides/DT_D-THYMINE.mmp create mode 100644 cad/tests/AMBER_test_structures/mmp/Nucleotides/RU_R-URACIL.mmp diff --git a/cad/tests/AMBER_test_structures/README.txt b/cad/tests/AMBER_test_structures/README.txt new file mode 100644 index 000000000..f1beb41a2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/README.txt @@ -0,0 +1,40 @@ + +This directory contains structures in two different forms, which are +used to test the pattern matching code for assigning AMBER atom types +to atoms prior to a GROMACS simulation. + +To perform the tests: + +Start NE1. + +Open one of the files under the mmp subdirectory. + +Choose the Tools->Check AMBER AtomTypes menu. Atom type labels should +show up over each atom in the structure. + +File->Import->IN file, and choose the corresponding .in_frag file in +the dot_in subdirectory. + + For mmp files in mmp/AminoAcids, look in dot_in/all_amino02. + For mmp files in mmp/Nucleotides, look in dot_in/all_nuc02. + +A similar structure should be loaded, and annotated with atomtype +labels. Verify that the corresponding atoms in each structure have +the same atom type labels. + +Open a new mmp file and repeat until you have examined all mmp files. + +-- + +There may be some slight differences between the structures, as the +.mmp files are complete molecules, while the .in_frag files are +fragments of molecules, and are designed to be bonded together to form +complete molecules. This changes the type of the Oxygen of the +sugar-phosphate bond on the sugar side of DNA and RNA nucleotides, as +the Phosphorus is replaced by a Hydrogen. + +The .in_frag files do not specify all of the bonds in the structures, +so rings of atoms will remain unclosed. Also, all .in_frag files will +have only single bonds between atoms when imported. Note that running +the Check AMBER AtomTypes menu will not correctly assign types to such +fragments, as the bond information is not complete. diff --git a/cad/tests/AMBER_test_structures/dot_in/all/ACE_ACE_BEGINNING_GROUP.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/ACE_ACE_BEGINNING_GROUP.in_frag new file mode 100644 index 000000000..f4322763a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/ACE_ACE_BEGINNING_GROUP.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H1 HC M 3 2 1 1.000 90.000 180.000 + 5 CH3 CT M 4 3 2 1.090 90.000 180.000 + 6 H2 HC E 5 4 3 1.090 109.500 60.000 + 7 H3 HC E 5 4 3 1.090 109.500 300.000 + 8 C C M 5 4 3 1.530 111.100 180.000 + 9 O O E 8 5 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/ALA_ALANINE.in_frag new file mode 100644 index 000000000..18d955971 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/ALA_ALANINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/ARG_ARGININE.in_frag new file mode 100644 index 000000000..0a32d237e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/ARG_ARGININE.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 + 18 HE H3 E 17 14 11 1.010 118.500 0.000 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 + 21 HH11 H3 E 20 19 17 1.010 119.800 0.000 + 22 HH12 H3 E 20 19 17 1.010 119.800 180.000 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 + 24 HH21 H3 E 23 19 17 1.010 119.800 0.000 + 25 HH22 H3 E 23 19 17 1.010 119.800 180.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O E 26 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/ASH_ASP_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/ASH_ASP_neutral.in_frag new file mode 100644 index 000000000..754ef94b2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/ASH_ASP_neutral.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O E 11 8 6 1.260 117.200 90.000 + 13 OD2 OH S 11 8 6 1.260 117.200 270.000 + 14 HD HO E 13 11 8 0.960 109.500 180.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..ef7cb2053 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/ASN_ASPARAGINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.522 111.100 180.000 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..1263e8651 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..2db0370bc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/CYS_CYSTEINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 SG SH 3 8 6 4 1.810 116.000 180.000 + 12 HG HS E 11 8 6 1.330 96.000 180.000 + 13 LP1 LP E 11 8 6 0.679 96.700 60.000 + 14 LP2 LP E 11 8 6 0.679 96.700 300.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..61de503ed --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 SG S B 8 6 4 1.810 116.000 180.000 + 12 LP1 LP E 11 8 6 0.679 96.700 60.000 + 13 LP2 LP E 11 8 6 0.679 96.700 300.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/D2AP_2-AMINO_PURINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/D2AP_2-AMINO_PURINE.in_frag new file mode 100644 index 000000000..91eea1a54 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/D2AP_2-AMINO_PURINE.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' CT M 4 3 2 1.440 119.000 -39.220 + 6 H5'1 HC E 5 4 3 1.090 109.500 -30.000 + 7 H5'2 HC E 5 4 3 1.090 109.500 90.000 + 8 C4' CT M 5 4 3 1.520 110.000 -151.000 + 9 H4' HC E 8 5 4 1.090 109.500 -200.000 + 10 O1' OS S 8 5 4 1.460 108.860 -86.310 + 11 C1' CT B 10 8 5 1.420 110.040 105.600 + 12 H1' HC E 11 10 8 1.090 109.500 -240.000 + 13 N9 N* S 11 10 8 1.520 109.590 -127.700 + 14 C8 CK B 13 11 10 1.370 131.200 81.590 + 15 H8 HC E 14 13 11 1.080 120.000 0.000 + 16 N7 NB S 14 13 11 1.300 113.930 177.000 + 17 C5 CB S 16 14 13 1.390 104.000 0.000 + 18 C6 CQ B 17 16 14 1.400 132.420 180.000 + 19 H6 HC E 23 22 18 1.080 120.000 180.000 + 20 N1 NC S 18 17 16 1.340 117.430 180.000 + 21 C2 CA B 22 18 17 1.330 118.800 0.000 + 22 N2 N2 B 18 17 16 1.340 123.500 0.000 + 23 H21 H2 E 19 18 17 1.010 120.000 0.000 + 24 H22 H2 E 19 18 17 1.010 120.000 180.000 + 25 N3 NC S 23 22 18 1.320 129.170 0.000 + 26 C4 CB E 25 23 22 1.350 110.800 0.000 + 27 C3' CT M 8 5 4 1.530 115.780 -329.110 + 28 H3' HC E 27 8 5 1.090 109.500 30.000 + 29 C2' CT B 27 8 5 1.530 102.800 -86.300 + 30 H2'1 HC E 29 27 8 1.090 109.500 120.000 + 31 H2'2 HC E 29 27 8 1.090 109.500 240.000 + 32 O3' OS M 27 8 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/DADE_D-ADENOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/DADE_D-ADENOSINE.in_frag new file mode 100644 index 000000000..9b31ca33f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/DADE_D-ADENOSINE.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' CT M 4 3 2 1.440 119.000 -39.220 + 6 H5'1 HC E 5 4 3 1.090 109.500 -30.000 + 7 H5'2 HC E 5 4 3 1.090 109.500 90.000 + 8 C4' CT M 5 4 3 1.520 110.000 -151.000 + 9 H4' HC E 8 5 4 1.090 109.500 -200.000 + 10 O1' OS S 8 5 4 1.460 108.860 -86.310 + 11 C1' CT B 10 8 5 1.420 110.040 105.600 + 12 H1' HC E 11 10 8 1.090 109.500 -240.000 + 13 N9 N* S 11 10 8 1.520 109.590 -127.700 + 14 C8 CK B 13 11 10 1.370 131.200 81.590 + 15 H8 HC E 14 13 11 1.080 120.000 0.000 + 16 N7 NB S 14 13 11 1.300 113.930 177.000 + 17 C5 CB S 16 14 13 1.390 104.000 0.000 + 18 C6 CA B 17 16 14 1.400 132.420 180.000 + 19 N6 N2 B 18 17 16 1.340 123.500 0.000 + 20 H61 H2 E 19 18 17 1.010 120.000 0.000 + 21 H62 H2 E 19 18 17 1.010 120.000 180.000 + 22 N1 NC S 18 17 16 1.340 117.430 180.000 + 23 C2 CQ B 22 18 17 1.330 118.800 0.000 + 24 H2 HC E 23 22 18 1.080 120.000 180.000 + 25 N3 NC S 23 22 18 1.320 129.170 0.000 + 26 C4 CB E 25 23 22 1.350 110.800 0.000 + 27 C3' CT M 8 5 4 1.530 115.780 -329.110 + 28 H3' HC E 27 8 5 1.090 109.500 30.000 + 29 C2' CT B 27 8 5 1.530 102.800 -86.300 + 30 H2'1 HC E 29 27 8 1.090 109.500 120.000 + 31 H2'2 HC E 29 27 8 1.090 109.500 240.000 + 32 O3' OS M 27 8 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/DCYT_D-CYTOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/DCYT_D-CYTOSINE.in_frag new file mode 100644 index 000000000..4a33465db --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/DCYT_D-CYTOSINE.in_frag @@ -0,0 +1,30 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' CT M 4 3 2 1.440 119.000 -39.220 + 6 H5'1 HC E 5 4 3 1.090 109.500 90.000 + 7 H5'2 HC E 5 4 3 1.090 109.500 330.000 + 8 C4' CT M 5 4 3 1.520 110.000 -151.000 + 9 H4' HC E 8 5 4 1.090 109.500 -200.000 + 10 O1' OS S 8 5 4 1.460 108.860 -86.310 + 11 C1' CT B 10 8 5 1.420 110.040 105.600 + 12 H1' HC E 11 10 8 1.090 109.500 -240.000 + 13 N1 N* S 11 10 8 1.490 108.100 -127.700 + 14 C6 CM B 13 11 10 1.360 121.100 81.590 + 15 H6 HC E 14 13 11 1.080 120.000 0.000 + 16 C5 CM B 14 13 11 1.360 121.000 180.000 + 17 H5 HC E 16 14 13 1.090 120.000 180.000 + 18 C4 CA B 16 14 13 1.430 116.900 0.000 + 19 N4 N2 B 18 16 14 1.320 120.100 180.000 + 20 H41 H2 E 19 18 16 1.010 117.700 0.000 + 21 H42 H2 E 19 18 16 1.010 120.270 180.000 + 22 N3 NC S 18 16 14 1.330 121.700 0.000 + 23 C2 C S 22 18 16 1.360 120.500 0.000 + 24 O2 O E 23 22 18 1.240 122.400 180.000 + 25 C3' CT M 8 5 4 1.530 115.780 -329.110 + 26 H3' HC E 25 8 5 1.090 109.500 -320.000 + 27 C2' CT B 25 8 5 1.530 102.800 -86.300 + 28 H2'1 HC E 27 25 8 1.090 109.500 -200.000 + 29 H2'2 HC E 27 25 8 1.090 109.500 -320.000 + 30 O3' OS M 25 8 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/DGUA_D-GUANOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/DGUA_D-GUANOSINE.in_frag new file mode 100644 index 000000000..c333adc97 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/DGUA_D-GUANOSINE.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' CT M 4 3 2 1.440 119.000 -39.220 + 6 H5'1 HC E 5 4 3 1.090 109.500 -30.000 + 7 H5'2 HC E 5 4 3 1.090 109.500 90.000 + 8 C4' CT M 5 4 3 1.520 110.000 -151.000 + 9 H4' HC E 8 5 4 1.090 109.500 -200.000 + 10 O1' OS S 8 5 4 1.460 108.860 -86.310 + 11 C1' CT B 10 8 5 1.420 110.040 105.600 + 12 H1' HC E 11 10 8 1.090 109.500 -240.000 + 13 N9 N* S 11 10 8 1.490 108.060 -127.700 + 14 C8 CK B 13 11 10 1.380 129.200 81.590 + 15 H8 HC E 14 13 11 1.080 120.000 0.000 + 16 N7 NB S 14 13 11 1.310 114.000 -179.900 + 17 C5 CB S 16 14 13 1.390 103.900 0.000 + 18 C6 C B 17 16 14 1.420 130.400 180.000 + 19 O6 O E 18 17 16 1.230 128.800 0.000 + 20 N1 NA B 18 17 16 1.400 111.380 180.000 + 21 H1 H E 20 18 17 1.000 117.360 179.900 + 22 C2 CA B 20 18 17 1.380 125.240 -0.100 + 23 N2 N2 B 22 20 18 1.340 116.020 180.000 + 24 H21 H2 E 23 22 20 1.010 127.000 -0.820 + 25 H22 H2 E 23 22 20 1.010 116.530 -179.440 + 26 N3 NC S 22 20 18 1.330 123.300 0.000 + 27 C4 CB E 26 22 20 1.360 112.200 0.000 + 28 C3' CT M 8 5 4 1.530 115.780 -329.110 + 29 H3' HC E 28 8 5 1.090 109.500 -320.000 + 30 C2' CT B 28 8 5 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 8 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 8 1.090 109.500 240.000 + 33 O3' OS M 28 8 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/DOHE_D-OH_END.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/DOHE_D-OH_END.in_frag new file mode 100644 index 000000000..a45d14691 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/DOHE_D-OH_END.in_frag @@ -0,0 +1,5 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O OH M 3 2 1 1.600 101.430 -98.890 + 5 H HO M 4 3 2 0.960 119.000 -39.220 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/DPOM_PHOSMI_D.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/DPOM_PHOSMI_D.in_frag new file mode 100644 index 000000000..65776e120 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/DPOM_PHOSMI_D.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 -200.850 + 5 OA O2 E 4 3 2 1.480 109.610 -214.890 + 6 OB O2 E 4 3 2 1.480 109.580 -342.910 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/DTHY_D-THY.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/DTHY_D-THY.in_frag new file mode 100644 index 000000000..11774b0c0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/DTHY_D-THY.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' CT M 4 3 2 1.440 119.000 -39.220 + 6 H5'1 HC E 5 4 3 1.090 109.500 -160.000 + 7 H5'2 HC E 5 4 3 1.090 109.500 -280.000 + 8 C4' CT M 5 4 3 1.520 110.000 -151.000 + 9 H4' HC E 8 5 4 1.090 109.500 -200.000 + 10 O1' OS S 8 5 4 1.460 108.860 -86.310 + 11 C1' CT B 10 8 5 1.420 110.040 105.600 + 12 H1' HC E 11 10 8 1.090 109.500 -240.000 + 13 N1 N* S 11 10 8 1.530 109.590 -127.700 + 14 C6 CM B 13 11 10 1.370 123.040 81.590 + 15 H6 HC E 14 13 11 1.080 120.000 0.000 + 16 C5 CM B 14 13 11 1.340 121.220 177.300 + 17 C7 CT 3 16 14 13 1.500 121.630 180.000 + 18 H71 HC E 17 16 14 1.090 109.500 60.000 + 19 H72 HC E 17 16 14 1.090 109.500 180.000 + 20 H73 HC E 17 16 14 1.090 109.500 300.000 + 21 C4 C B 16 14 13 1.440 120.780 0.000 + 22 O4 O E 21 16 14 1.230 125.350 180.000 + 23 N3 NA B 21 16 14 1.380 114.070 0.000 + 24 H3 H E 23 21 16 1.090 116.770 180.000 + 25 C2 C S 23 21 16 1.380 126.460 0.000 + 26 O2 O E 25 23 21 1.220 121.700 180.000 + 27 C3' CT M 8 5 4 1.530 115.780 -329.110 + 28 H3' HC E 27 8 5 1.090 109.500 30.000 + 29 C2' CT B 27 8 5 1.530 102.800 -86.300 + 30 H2'1 HC E 29 27 8 1.090 109.500 120.000 + 31 H2'2 HC E 29 27 8 1.090 109.500 240.000 + 32 O3' OS M 27 8 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/GLH_GLU_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/GLH_GLU_neutral.in_frag new file mode 100644 index 000000000..27e13325e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/GLH_GLU_neutral.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O E 14 11 8 1.260 117.200 90.000 + 16 OE2 OH S 14 11 8 1.260 117.200 270.000 + 17 HE HO E 16 14 11 0.960 109.500 180.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..3bb1200c3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/GLN_GLUTAMINE.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.522 111.100 180.000 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..3b2782f85 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O E 17 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..d5d7e75da --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/GLY_GLYCINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 HC E 6 4 3 1.090 109.500 300.000 + 8 HA3 HC E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O E 9 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/HB_H_BEGINNING.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/HB_H_BEGINNING.in_frag new file mode 100644 index 000000000..ea2ea360e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/HB_H_BEGINNING.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H HO M 3 2 1 1.000 120.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/HE_H_END.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/HE_H_END.in_frag new file mode 100644 index 000000000..b57452ff1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/HE_H_END.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H HO M 3 2 1 0.960 114.970 -211.370 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..6392a9c69 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 HC E 14 12 11 1.090 120.000 180.000 + 16 NE2 NB S 14 12 11 1.310 109.000 0.000 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 + 18 HD2 HC E 17 16 14 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..113d1373d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NB S 11 8 6 1.390 122.000 180.000 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 + 14 HE1 HC E 13 12 11 1.090 120.000 180.000 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 + 18 HD2 HC E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..baf9ce007 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 HC E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD2 HC E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O E 20 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..2982e2149 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..f2268ffa0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/LEU_LEUCINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/LYH_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/LYH_LYSINE.in_frag new file mode 100644 index 000000000..33071e36a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/LYH_LYSINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HC E 17 14 11 1.090 109.500 300.000 + 19 HE3 HC E 17 14 11 1.090 109.500 60.000 + 20 NZ NT B 17 14 11 1.470 109.470 180.000 + 21 HZ1 H2 E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H2 E 20 17 14 1.010 109.470 300.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O E 23 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/LYS_LYSINE.in_frag new file mode 100644 index 000000000..1ef2ec5f2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/LYS_LYSINE.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HC E 17 14 11 1.090 109.500 300.000 + 19 HE3 HC E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 + 21 HZ1 H3 E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H3 E 20 17 14 1.010 109.470 180.000 + 23 HZ3 H3 E 20 17 14 1.010 109.470 300.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O E 24 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/MET_METHIONINE.in_frag new file mode 100644 index 000000000..9bd9b9585 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/MET_METHIONINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 SD S 3 11 8 6 1.810 110.000 180.000 + 15 LP1 LP E 14 11 8 0.679 96.700 60.000 + 16 LP2 LP E 14 11 8 0.679 96.700 300.000 + 17 CE CT 3 14 11 8 1.780 100.000 180.000 + 18 HE1 HC E 17 14 11 1.090 109.500 60.000 + 19 HE2 HC E 17 14 11 1.090 109.500 180.000 + 20 HE3 HC E 17 14 11 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/NHE_NH2_ENDING_GROUP.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/NHE_NH2_ENDING_GROUP.in_frag new file mode 100644 index 000000000..10d8ca029 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/NHE_NH2_ENDING_GROUP.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN1 H E 4 3 2 1.010 119.800 0.000 + 6 HN2 H E 4 3 2 1.010 119.800 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/NME_N-methyl_all_atom.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/NME_N-methyl_all_atom.in_frag new file mode 100644 index 000000000..b23c0a887 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/NME_N-methyl_all_atom.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CT CT M 4 3 2 1.449 121.900 180.000 + 7 HT1 HC E 6 4 3 1.090 109.500 0.000 + 8 HT2 HC E 6 4 3 1.090 109.500 120.000 + 9 HT3 HC E 6 4 3 1.090 109.500 240.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/OHB_OH_BEGINNING.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/OHB_OH_BEGINNING.in_frag new file mode 100644 index 000000000..1b92cda5c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/OHB_OH_BEGINNING.in_frag @@ -0,0 +1,5 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H HO M 3 2 1 1.000 120.000 180.000 + 5 O OH M 4 3 2 0.960 120.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..c515acc67 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 115.000 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HC E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HC E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HC E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HC E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HC E 20 18 16 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O E 22 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/POHE_PROTEIN-OH_END.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/POHE_PROTEIN-OH_END.in_frag new file mode 100644 index 000000000..35c38e0ca --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/POHE_PROTEIN-OH_END.in_frag @@ -0,0 +1,5 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O OH M 3 2 1 1.360 113.000 180.890 + 5 H HO M 4 3 2 0.960 107.000 -39.220 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/PRO_PROLINE.in_frag new file mode 100644 index 000000000..aa93e4896 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/PRO_PROLINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 + 6 HD2 HC E 5 4 3 1.090 109.500 80.000 + 7 HD3 HC E 5 4 3 1.090 109.500 320.000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 + 11 CB CT B 8 5 4 1.510 106.000 338.300 + 12 HB2 HC E 11 8 5 1.090 109.500 136.300 + 13 HB3 HC E 11 8 5 1.090 109.500 256.300 + 14 CA CT M 4 3 2 1.451 120.600 175.200 + 15 HA HC E 14 4 3 1.090 109.500 81.100 + 16 C C M 14 4 3 1.522 111.100 0.000 + 17 O O E 16 14 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/RADE_R-ADENOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/RADE_R-ADENOSINE.in_frag new file mode 100644 index 000000000..7108e4c76 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/RADE_R-ADENOSINE.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' CT M 4 3 2 1.440 119.000 -39.220 + 6 H5'1 HC E 5 4 3 1.090 109.500 -30.000 + 7 H5'2 HC E 5 4 3 1.090 109.500 90.000 + 8 C4' CT M 5 4 3 1.520 110.000 -151.000 + 9 H4' HC E 8 5 4 1.090 109.500 -200.000 + 10 O1' OS S 8 5 4 1.460 108.860 -86.310 + 11 C1' CT B 10 8 5 1.420 110.040 105.600 + 12 H1' HC E 11 10 8 1.090 109.500 -240.000 + 13 N9 N* S 11 10 8 1.520 109.590 -127.700 + 14 C8 CK B 13 11 10 1.370 131.200 81.590 + 15 H8 HC E 14 13 11 1.080 120.000 0.000 + 16 N7 NB S 14 13 11 1.300 113.930 177.000 + 17 C5 CB S 16 14 13 1.390 104.000 0.000 + 18 C6 CA B 17 16 14 1.400 132.420 180.000 + 19 N6 N2 B 18 17 16 1.340 123.500 0.000 + 20 H61 H2 E 19 18 17 1.010 120.000 0.000 + 21 H62 H2 E 19 18 17 1.010 120.000 180.000 + 22 N1 NC S 18 17 16 1.340 117.430 180.000 + 23 C2 CQ B 22 18 17 1.330 118.800 0.000 + 24 H2 HC E 23 22 18 1.080 120.000 180.000 + 25 N3 NC S 23 22 18 1.320 129.170 0.000 + 26 C4 CB E 25 23 22 1.350 110.800 0.000 + 27 C3' CT M 8 5 4 1.530 115.780 -329.110 + 28 H3' HC E 27 8 5 1.090 109.500 -80.000 + 29 C2' CT B 27 8 5 1.530 102.800 -86.300 + 30 H2' HC E 29 27 8 1.090 109.500 120.000 + 31 O2' OH S 29 27 8 1.430 109.500 240.000 + 32 HO2' HO E 31 29 27 0.960 107.000 180.000 + 33 O3' OS M 27 8 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/RCYT_R-CYTOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/RCYT_R-CYTOSINE.in_frag new file mode 100644 index 000000000..4bf5f02fe --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/RCYT_R-CYTOSINE.in_frag @@ -0,0 +1,31 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' CT M 4 3 2 1.440 119.000 -39.220 + 6 H5'1 HC E 5 4 3 1.090 109.500 90.000 + 7 H5'2 HC E 5 4 3 1.090 109.500 330.000 + 8 C4' CT M 5 4 3 1.520 110.000 -151.000 + 9 H4' HC E 8 5 4 1.090 109.500 -200.000 + 10 O1' OS S 8 5 4 1.460 108.860 -86.310 + 11 C1' CT B 10 8 5 1.420 110.040 105.600 + 12 H1' HC E 11 10 8 1.090 109.500 -240.000 + 13 N1 N* S 11 10 8 1.490 108.100 -127.700 + 14 C6 CM B 13 11 10 1.360 121.100 81.590 + 15 H6 HC E 14 13 11 1.080 120.000 0.000 + 16 C5 CM B 14 13 11 1.360 121.000 180.000 + 17 H5 HC E 16 14 13 1.090 120.000 180.000 + 18 C4 CA B 16 14 13 1.430 116.900 0.000 + 19 N4 N2 B 18 16 14 1.320 120.100 180.000 + 20 H41 H2 E 19 18 16 1.010 117.700 0.000 + 21 H42 H2 E 19 18 16 1.010 120.270 180.000 + 22 N3 NC S 18 16 14 1.330 121.700 0.000 + 23 C2 C S 22 18 16 1.360 120.500 0.000 + 24 O2 O E 23 22 18 1.240 122.400 180.000 + 25 C3' CT M 8 5 4 1.530 115.780 -329.110 + 26 H3' HC E 25 8 5 1.090 109.500 -320.000 + 27 C2' CT B 25 8 5 1.530 102.800 -86.300 + 28 H2' HC E 27 25 8 1.090 109.500 120.000 + 29 O2' OH S 27 25 8 1.430 109.500 240.000 + 30 HO2' HO E 29 27 25 0.960 107.000 180.000 + 31 O3' OS M 25 8 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/RGUA_R-GUANOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/RGUA_R-GUANOSINE.in_frag new file mode 100644 index 000000000..1e799fe27 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/RGUA_R-GUANOSINE.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' CT M 4 3 2 1.440 119.000 -39.220 + 6 H5'1 HC E 5 4 3 1.090 109.500 -30.000 + 7 H5'2 HC E 5 4 3 1.090 109.500 90.000 + 8 C4' CT M 5 4 3 1.520 110.000 -151.000 + 9 H4' HC E 8 5 4 1.090 109.500 -200.000 + 10 O1' OS S 8 5 4 1.460 108.860 -86.310 + 11 C1' CT B 10 8 5 1.420 110.040 105.600 + 12 H1' HC E 11 10 8 1.090 109.500 -240.000 + 13 N9 N* S 11 10 8 1.490 108.060 -127.700 + 14 C8 CK B 13 11 10 1.380 129.200 81.590 + 15 H8 HC E 14 13 11 1.080 120.000 0.000 + 16 N7 NB S 14 13 11 1.310 114.000 -179.900 + 17 C5 CB S 16 14 13 1.390 103.900 0.000 + 18 C6 C B 17 16 14 1.420 130.400 180.000 + 19 O6 O E 18 17 16 1.230 128.800 0.000 + 20 N1 NA B 18 17 16 1.400 111.380 180.000 + 21 H1 H E 20 18 17 1.000 117.360 179.900 + 22 C2 CA B 20 18 17 1.380 125.240 -0.100 + 23 N2 N2 B 22 20 18 1.340 116.020 180.000 + 24 H21 H2 E 23 22 20 1.010 127.000 -0.820 + 25 H22 H2 E 23 22 20 1.010 116.530 -179.440 + 26 N3 NC S 22 20 18 1.330 123.300 0.000 + 27 C4 CB E 26 22 20 1.360 112.200 0.000 + 28 C3' CT M 8 5 4 1.530 115.780 -329.110 + 29 H3' HC E 28 8 5 1.090 109.500 -320.000 + 30 C2' CT B 28 8 5 1.530 102.800 -86.300 + 31 H2' HC E 30 28 8 1.090 109.500 120.000 + 32 O2' OH S 30 28 8 1.430 109.500 240.000 + 33 HO2' HO E 32 30 28 0.960 107.000 180.000 + 34 O3' OS M 28 8 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/ROHE_R-OH_END.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/ROHE_R-OH_END.in_frag new file mode 100644 index 000000000..378496e5f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/ROHE_R-OH_END.in_frag @@ -0,0 +1,5 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O OH M 3 2 1 1.600 101.430 -78.600 + 5 H HO M 4 3 2 0.960 119.000 -39.220 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/RPOM_PHOSMI_R.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/RPOM_PHOSMI_R.in_frag new file mode 100644 index 000000000..319ce47eb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/RPOM_PHOSMI_R.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 -213.190 + 5 OA O2 E 4 3 2 1.480 109.580 -194.890 + 6 OB O2 E 4 3 2 1.480 109.650 -332.610 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/RURA_R-URACIL.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/RURA_R-URACIL.in_frag new file mode 100644 index 000000000..01b0de9ba --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/RURA_R-URACIL.in_frag @@ -0,0 +1,30 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' CT M 4 3 2 1.440 119.000 -39.220 + 6 H5'1 HC E 5 4 3 1.090 109.500 -160.000 + 7 H5'2 HC E 5 4 3 1.090 109.500 -280.000 + 8 C4' CT M 5 4 3 1.520 110.000 -151.000 + 9 H4' HC E 8 5 4 1.090 109.500 -200.000 + 10 O1' OS S 8 5 4 1.460 108.860 -86.310 + 11 C1' CT B 10 8 5 1.420 110.040 105.600 + 12 H1' HC E 11 10 8 1.090 109.500 -240.000 + 13 N1 N* S 11 10 8 1.530 109.590 -127.700 + 14 C6 CM B 13 11 10 1.370 123.040 81.590 + 15 H6 HC E 14 13 11 1.080 120.000 0.000 + 16 C5 CM B 14 13 11 1.340 121.220 177.300 + 17 H5 HC E 16 14 13 1.090 120.000 180.000 + 18 C4 C B 16 14 13 1.440 120.780 0.000 + 19 O4 O E 18 16 14 1.230 125.350 180.000 + 20 N3 NA B 18 16 14 1.380 114.070 0.000 + 21 H3 H E 20 18 16 1.090 116.770 180.000 + 22 C2 C S 20 18 16 1.380 126.460 0.000 + 23 O2 O E 22 20 18 1.220 121.700 180.000 + 24 C3' CT M 8 5 4 1.530 115.780 -329.110 + 25 H3' HC E 24 8 5 1.090 109.500 30.000 + 26 C2' CT B 24 8 5 1.530 102.800 -86.300 + 27 H2' HC E 26 24 8 1.090 109.500 120.000 + 28 O2' OH S 26 24 8 1.430 109.500 240.000 + 29 HO2' HO E 28 26 24 0.960 107.000 180.000 + 30 O3' OS M 24 8 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/SER_SERINE.in_frag new file mode 100644 index 000000000..c7933a207 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all/SER_SERINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 OG OH S 8 6 4 1.430 109.470 180.000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all/THR_THREONINE.in_frag new file mode 100644 index 000000000..6b347fe11 --- /dev/null +++ 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128.800 0.000 -0.45800 + 20 N1 NA B 18 17 16 1.400 111.380 180.000 -0.72900 + 21 H1 H E 20 18 17 1.000 117.360 179.900 0.33600 + 22 C2 CA B 20 18 17 1.380 125.240 -0.100 0.87100 + 23 N2 N2 B 22 20 18 1.340 116.020 180.000 -0.77800 + 24 H21 H2 E 23 22 20 1.010 127.000 -0.820 0.32500 + 25 H22 H2 E 23 22 20 1.010 116.530 -179.440 0.33900 + 26 N3 NC S 22 20 18 1.330 123.300 0.000 -0.70900 + 27 C4 CB E 26 22 20 1.360 112.200 0.000 0.39100 + 28 C3' CT M 8 5 4 1.530 115.780 -329.110 0.30300 + 29 H3' HC E 28 8 5 1.090 109.500 -320.000 0.00700 + 30 C2' CT B 28 8 5 1.530 102.800 -86.300 0.10100 + 31 H2' HC E 30 28 8 1.090 109.500 120.000 0.00800 + 32 O2' OH S 30 28 8 1.430 109.500 240.000 -0.54600 + 33 HO2' HO E 32 30 28 0.960 107.000 180.000 0.32400 + 34 O3' OS M 28 8 5 1.420 116.520 -203.470 -0.50900 + +IMPROPER + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + +LOOP + C1' C2' + C4 C5 + C4 N9 + +DONE +D-CYTOSINE + + DCYT INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 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120.270 180.000 0.35100 + 22 N3 NC S 18 16 14 1.330 121.700 0.000 -0.86000 + 23 C2 C S 22 18 16 1.360 120.500 0.000 0.85900 + 24 O2 O E 23 22 18 1.240 122.400 180.000 -0.50800 + 25 C3' CT M 8 5 4 1.530 115.780 -329.110 0.23300 + 26 H3' HC E 25 8 5 1.090 109.500 -320.000 0.02500 + 27 C2' CT B 25 8 5 1.530 102.800 -86.300 -0.30700 + 28 H2'1 HC E 27 25 8 1.090 109.500 -200.000 0.08100 + 29 H2'2 HC E 27 25 8 1.090 109.500 -320.000 0.08100 + 30 O3' OS M 25 8 5 1.420 116.520 -203.470 -0.50900 + +IMPROPER + N1 N3 C2 O2 + C4 H41 N4 H42 + +LOOP + C1' C2' + C2 N1 + +DONE +R-CYTOSINE + + RCYT INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 -0.50900 + 5 C5' CT M 4 3 2 1.440 119.000 -39.220 0.18000 + 6 H5'1 HC E 5 4 3 1.090 109.500 90.000 0.00800 + 7 H5'2 HC E 5 4 3 1.090 109.500 330.000 0.00800 + 8 C4' CT M 5 4 3 1.520 110.000 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H2' HC E 27 25 8 1.090 109.500 120.000 0.00800 + 29 O2' OH S 27 25 8 1.430 109.500 240.000 -0.54600 + 30 HO2' HO E 29 27 25 0.960 107.000 180.000 0.32400 + 31 O3' OS M 25 8 5 1.420 116.520 -203.470 -0.50900 + +IMPROPER + N1 N3 C2 O2 + C4 H41 N4 H42 + +LOOP + C1' C2' + C2 N1 + +DONE + OH BEGINNING + + OHB INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 H HO M 3 2 1 1.000 120.000 180.000 0.24300 + 5 O OH M 4 3 2 0.960 120.000 180.000 -0.57700 + +DONE +D-OH END + + DOHE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 O OH M 3 2 1 1.600 101.430 -98.890 -0.62100 + 5 H HO M 4 3 2 0.960 119.000 -39.220 0.22600 + +DONE +R-OH END + + ROHE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 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3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 -0.01200 + 9 HB HC E 8 6 4 1.090 109.500 300.000 0.02200 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 -0.08500 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 0.02900 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 0.02900 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 0.02900 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 -0.04900 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 0.02700 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 0.02700 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 -0.08500 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 0.02800 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 0.02800 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 0.02800 + 21 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 22 O O E 21 6 4 1.229 120.500 0.000 -0.50400 + 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0.000 -0.00200 + 22 HD2 HC E 21 19 16 1.090 120.000 180.000 0.06400 + 23 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 24 O O E 23 6 4 1.229 120.500 0.000 -0.50400 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + +DONE +GLUTAMIC ACID + + GLU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.18400 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.09200 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.09200 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 -0.39800 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.07100 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.07100 + 14 CD C B 11 8 6 1.527 109.470 180.000 0.71400 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 -0.72100 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 -0.72100 + 17 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 18 O O E 17 6 4 1.229 120.500 0.000 -0.50400 + +IMPROPER + -M CA N H + CA +M C O + CG OE1 CD OE2 + +DONE +ASPARTIC ACID + + ASP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.39800 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.07100 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.07100 + 11 CG C B 8 6 4 1.527 109.470 180.000 0.71400 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 -0.72100 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 -0.72100 + 14 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 15 O O E 14 6 4 1.229 120.500 0.000 -0.50400 + 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HE3 HC E 17 14 11 1.090 109.500 60.000 0.09800 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 -0.13800 + 21 HZ1 H3 E 20 17 14 1.010 109.470 60.000 0.29400 + 22 HZ2 H3 E 20 17 14 1.010 109.470 180.000 0.29400 + 23 HZ3 H3 E 20 17 14 1.010 109.470 300.000 0.29400 + 24 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 25 O O E 24 6 4 1.229 120.500 0.000 -0.50400 + + +IMPROPER + -M CA N H + CA +M C O + +DONE +PROLINE + + PRO INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.337 117.000 180.000 -0.22900 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 -0.01200 + 6 HD2 HC E 5 4 3 1.090 109.500 80.000 0.06000 + 7 HD3 HC E 5 4 3 1.090 109.500 320.000 0.06000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 -0.12100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 0.06300 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 0.06300 + 11 CB CT B 8 5 4 1.510 106.000 338.300 -0.11500 + 12 HB2 HC E 11 8 5 1.090 109.500 136.300 0.06100 + 13 HB3 HC E 11 8 5 1.090 109.500 256.300 0.06100 + 14 CA CT M 4 3 2 1.451 120.600 175.200 0.03500 + 15 HA HC E 14 4 3 1.090 109.500 81.100 0.04800 + 16 C C M 14 4 3 1.522 111.100 0.000 0.52600 + 17 O O E 16 14 4 1.229 120.500 0.000 -0.50000 + +LOOP + CB CA + +IMPROPER + CA +M C O + -M CA N CD + +DONE +CYSTEINE + + CYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.06000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03800 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03800 + 11 SG SH 3 8 6 4 1.810 116.000 180.000 0.82700 + 12 HG HS E 11 8 6 1.330 96.000 180.000 0.13500 + 13 LP1 LP E 11 8 6 0.679 96.700 60.000 -0.48100 + 14 LP2 LP E 11 8 6 0.679 96.700 300.000 -0.48100 + 15 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 16 O O E 15 6 4 1.229 120.500 0.000 -0.50400 + +IMPROPER + -M CA N H + CA +M C O + +DONE +CYSTINE(S-S BRIDGE) + + CYX INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.09800 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04950 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04950 + 11 SG S B 8 6 4 1.810 116.000 180.000 0.82400 + 12 LP1 LP E 11 8 6 0.679 96.700 60.000 -0.40450 + 13 LP2 LP E 11 8 6 0.679 96.700 300.000 -0.40450 + 14 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 15 O O E 14 6 4 1.229 120.500 0.000 -0.50400 + +IMPROPER + -M CA N H + CA +M C O + +DONE +METHIONINE + + MET INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.15100 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.02700 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.02700 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 -0.05400 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.06520 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.06520 + 14 SD S 3 11 8 6 1.810 110.000 180.000 0.73700 + 15 LP1 LP E 14 11 8 0.679 96.700 60.000 -0.38100 + 16 LP2 LP E 14 11 8 0.679 96.700 300.000 -0.38100 + 17 CE CT 3 14 11 8 1.780 100.000 180.000 -0.13400 + 18 HE1 HC E 17 14 11 1.090 109.500 60.000 0.06520 + 19 HE2 HC E 17 14 11 1.090 109.500 180.000 0.06520 + 20 HE3 HC E 17 14 11 1.090 109.500 300.000 0.06520 + 21 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 22 O O E 21 6 4 1.229 120.500 0.000 -0.50400 + +IMPROPER + -M CA N H + CA +M C O + +DONE + ACE BEGINNING GROUP + + ACE INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 H1 HC M 3 2 1 1.000 90.000 180.000 0.01000 + 5 CH3 CT M 4 3 2 1.090 90.000 180.000 -0.14200 + 6 H2 HC E 5 4 3 1.090 109.500 60.000 0.01000 + 7 H3 HC E 5 4 3 1.090 109.500 300.000 0.01000 + 8 C C M 5 4 3 1.530 111.100 180.000 0.61600 + 9 O O E 8 5 4 1.229 120.500 0.000 -0.50400 + +IMPROPER + CH3 +M C O + +DONE + NH2 ENDING GROUP + + NHE INT 1 + CORRECT OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 + 4 N N M 3 2 1 1.3350 116.6000 180.0000 + 5 HN1 H E 4 3 2 1.0100 119.8000 0.0000 + 6 HN2 H E 4 3 2 1.0100 119.8000 180.0000 + +CHARGE + -0.46300 0.23150 0.23150 + +IMPROPER + -M HN1 N HN2 + +DONE +N-methyl all atom + + NME INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CT CT M 4 3 2 1.449 121.900 180.000 0.06700 + 7 HT1 HC E 6 4 3 1.090 109.500 0.000 0.04800 + 8 HT2 HC E 6 4 3 1.090 109.500 120.000 0.04800 + 9 HT3 HC E 6 4 3 1.090 109.500 240.000 0.04800 + +DONE + WATER, TIP3P MODEL +WT3 + WT3 INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 HW1 HW M 3 2 1 1.000 101.430 -98.890 0.41700 + 5 OW OW M 4 3 2 0.9572 104.520 -39.220 -0.83400 + 6 HW2 HW E 5 4 3 0.9572 104.520 -151.000 0.41700 + +LOOP + HW1 HW2 + +DONE +ASP neutral +ASH + ASH INT 0 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.32300 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.13700 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.13700 + 11 CG C B 8 6 4 1.527 109.470 180.000 0.80300 + 12 OD1 O E 11 8 6 1.260 117.200 90.000 -0.47600 + 13 OD2 OH S 11 8 6 1.260 117.200 270.000 -0.63000 + 14 HD HO E 13 11 8 0.96 109.5 180.0 0.36800 + 15 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 16 O O E 15 6 4 1.229 120.500 0.000 -0.50400 + +IMPROPER + -M CA N H + CA +M C O + CB OD1 CG OD2 + +DONE +GLU neutral +GLH + GLH INT 0 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.18400 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.09200 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.09200 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 -0.32300 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.13700 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.13700 + 14 CD C B 11 8 6 1.527 109.470 180.000 0.80300 + 15 OE1 O E 14 11 8 1.260 117.200 90.000 -0.47600 + 16 OE2 OH S 14 11 8 1.260 117.200 270.000 -0.63000 + 17 HE HO E 16 14 11 0.960 109.500 180.000 0.36800 + 18 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 19 O O E 18 6 4 1.229 120.500 0.000 -0.50400 + +IMPROPER + -M CA N H + CA +M C O + CG OE1 CD OE2 + +DONE +LYSINE + + LYH INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.14200 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.06600 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.06600 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 -0.04800 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.02400 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.02400 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 -0.06400 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 0.04000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 0.04000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 0.19600 + 18 HE2 HC E 17 14 11 1.090 109.500 300.000 0.01700 + 19 HE3 HC E 17 14 11 1.090 109.500 60.000 0.01700 + 20 NZ NT B 17 14 11 1.470 109.470 180.000 -0.80000 + 21 HZ1 H2 E 20 17 14 1.010 109.470 60.000 0.29000 + 22 HZ2 H2 E 20 17 14 1.010 109.470 300.000 0.29000 + 23 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 24 O O E 23 6 4 1.229 120.500 0.000 -0.50400 + + +IMPROPER + -M CA N H + CA +M C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ACE_ACE_BEGINNING_GROUP.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ACE_ACE_BEGINNING_GROUP.in_frag new file mode 100644 index 000000000..4b7832b4e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ACE_ACE_BEGINNING_GROUP.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HH31 HC M 3 2 1 1.000 90.000 180.000 + 5 CH3 CT M 4 3 2 1.090 90.000 180.000 + 6 HH32 HC E 5 4 3 1.090 109.500 60.000 + 7 HH33 HC E 5 4 3 1.090 109.500 300.000 + 8 C C M 5 4 3 1.530 111.100 180.000 + 9 O O E 8 5 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ALA_ALANINE.in_frag new file mode 100644 index 000000000..a7bb1df86 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ALA_ALANINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ARG_ARGININE.in_frag new file mode 100644 index 000000000..c81cec911 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ARG_ARGININE.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 H1 E 14 11 8 1.090 109.500 300.000 + 16 HD3 H1 E 14 11 8 1.090 109.500 60.000 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 + 18 HE H E 17 14 11 1.010 118.500 0.000 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 + 21 HH11 H E 20 19 17 1.010 119.800 0.000 + 22 HH12 H E 20 19 17 1.010 119.800 180.000 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 + 24 HH21 H E 23 19 17 1.010 119.800 0.000 + 25 HH22 H E 23 19 17 1.010 119.800 180.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O E 26 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ASH_ASP_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ASH_ASP_neutral.in_frag new file mode 100644 index 000000000..871b86bfb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ASH_ASP_neutral.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O E 11 8 6 1.260 117.200 90.000 + 13 OD2 OH S 11 8 6 1.260 117.200 270.000 + 14 HD2 HO E 13 11 8 0.960 109.500 180.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..923988a6b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ASN_ASPARAGINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.522 111.100 180.000 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..18c0aa80a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CIM_Chloride_Ion.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CIM_Chloride_Ion.in_frag new file mode 100644 index 000000000..b5670775c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CIM_Chloride_Ion.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 CL- IM M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CIP_Sodium_Ion.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CIP_Sodium_Ion.in_frag new file mode 100644 index 000000000..088bc4f00 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CIP_Sodium_Ion.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 NA+ IP M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CYM_CYSTEINE_with_negative_charge.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CYM_CYSTEINE_with_negative_charge.in_frag new file mode 100644 index 000000000..1a6ab8383 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CYM_CYSTEINE_with_negative_charge.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 11 SG SH E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..4c0f31d34 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CYS_CYSTEINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG SH S 8 6 4 1.810 116.000 180.000 + 12 HG HS E 11 8 6 1.330 96.000 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..4bcb8af4c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG S E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GL0_GLYCIN0.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GL0_GLYCIN0.in_frag new file mode 100644 index 000000000..8ac9c1995 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GL0_GLYCIN0.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H0 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H0 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O E 9 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GLH_GLU_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GLH_GLU_neutral.in_frag new file mode 100644 index 000000000..bb692bd02 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GLH_GLU_neutral.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O E 14 11 8 1.260 117.200 90.000 + 16 OE2 OH S 14 11 8 1.260 117.200 270.000 + 17 HE2 HO E 16 14 11 0.960 109.500 180.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..e3905d2e3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GLN_GLUTAMINE.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.522 111.100 180.000 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..9f20f8f01 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O E 17 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..8ac9c1995 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/GLY_GLYCINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H0 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H0 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O E 9 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..47aa5bb10 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NB S 14 12 11 1.310 109.000 0.000 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..10b520062 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NB S 11 8 6 1.390 122.000 180.000 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..0fa584734 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O E 20 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..bca9a78cc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..23b22a7e4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/LEU_LEUCINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/LYN_LYSINE_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/LYN_LYSINE_neutral.in_frag new file mode 100644 index 000000000..ef49d8df9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/LYN_LYSINE_neutral.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 H1 E 17 14 11 1.090 109.500 300.000 + 19 HE3 H1 E 17 14 11 1.090 109.500 60.000 + 20 NZ NT B 17 14 11 1.470 109.470 180.000 + 21 HZ2 H E 20 17 14 1.010 109.470 180.000 + 22 HZ3 H E 20 17 14 1.010 109.470 300.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O E 24 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/LYS_LYSINE.in_frag new file mode 100644 index 000000000..af3f27bf0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/LYS_LYSINE.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 + 21 HZ1 H E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H E 20 17 14 1.010 109.470 180.000 + 23 HZ3 H E 20 17 14 1.010 109.470 300.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O E 24 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/MET_METHIONINE.in_frag new file mode 100644 index 000000000..da19600d3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/MET_METHIONINE.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 + 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 + 14 SD S S 11 8 6 1.810 110.000 180.000 + 15 CE CT 3 14 11 8 1.780 100.000 180.000 + 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 + 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 + 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/NME_N-methyl_all_atom.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/NME_N-methyl_all_atom.in_frag new file mode 100644 index 000000000..aa1758816 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/NME_N-methyl_all_atom.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CH3 CT M 4 3 2 1.449 121.900 180.000 + 7 HH31 H1 E 6 4 3 1.090 109.500 0.000 + 8 HH32 H1 E 6 4 3 1.090 109.500 120.000 + 9 HH33 H1 E 6 4 3 1.090 109.500 240.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..2bb6cdc54 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 115.000 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HA E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HA E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HA E 20 18 16 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O E 22 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/PRO_PROLINE.in_frag new file mode 100644 index 000000000..7c4fada2c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/PRO_PROLINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 + 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 + 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 + 11 CB CT B 8 5 4 1.510 106.000 338.300 + 12 HB2 HC E 11 8 5 1.090 109.500 256.300 + 13 HB3 HC E 11 8 5 1.090 109.500 136.300 + 14 CA CT M 4 3 2 1.451 120.600 175.200 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 + 16 C C M 14 4 3 1.522 109.500 300.000 + 17 O O E 16 14 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/SER_SERINE.in_frag new file mode 100644 index 000000000..5ff430502 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/SER_SERINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 OG OH S 8 6 4 1.430 109.470 180.000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/THR_THREONINE.in_frag new file mode 100644 index 000000000..cf686b69f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/THR_THREONINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB H1 E 8 6 4 1.090 109.500 180.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/TRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/TRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..a7aed5e34 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/TRP_TRYPTOPHAN.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C* S 8 6 4 1.510 115.000 180.000 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 + 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 + 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 + 20 HH2 HA E 19 17 16 1.090 120.000 180.000 + 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 + 22 HZ3 HA E 21 19 17 1.090 120.000 180.000 + 23 CE3 CA B 21 19 17 1.410 122.000 0.000 + 24 HE3 HA E 23 21 19 1.090 120.000 180.000 + 25 CD2 CB E 23 21 19 1.400 117.000 0.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O E 26 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/TYR_TYROSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/TYR_TYROSINE.in_frag new file mode 100644 index 000000000..d3df8e72d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/TYR_TYROSINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 109.470 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 OH OH S 16 14 12 1.360 120.000 180.000 + 18 HH HO E 17 16 14 0.960 113.000 0.000 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 + 20 HE2 HA E 19 16 14 1.090 120.000 180.000 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 + 22 HD2 HA E 21 19 16 1.090 120.000 180.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O E 23 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/VAL_VALINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/VAL_VALINE.in_frag new file mode 100644 index 000000000..6f5affadb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/VAL_VALINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG11 HC E 10 8 6 1.090 109.500 60.000 + 12 HG12 HC E 10 8 6 1.090 109.500 180.000 + 13 HG13 HC E 10 8 6 1.090 109.500 300.000 + 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG21 HC E 14 8 6 1.090 109.500 60.000 + 16 HG22 HC E 14 8 6 1.090 109.500 180.000 + 17 HG23 HC E 14 8 6 1.090 109.500 300.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/all_amino02.r1.in b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/all_amino02.r1.in new file mode 100644 index 000000000..e5c1e690a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02.r1/all_amino02.r1.in @@ -0,0 +1,1120 @@ + 1 1 2 +db2000.dat +ALANINE + + ALA INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0448 .0228 -.0909 + .0425 .0425 .0425 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +GLYCINE + + GLY INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H0 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H0 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O E 9 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0332 .0687 .0687 + .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +GLYCIN0 + + GL0 INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H0 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H0 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O E 9 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0332 .0687 .0687 + .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +SERINE + + SER INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 OG OH S 8 6 4 1.430 109.470 180.000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0717 .0164 .1345 + .0361 .0361 -.5593 .3687 .6731 + -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +THREONINE + + THR INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB H1 E 8 6 4 1.090 109.500 180.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0702 .0164 .4038 + -.0909 -.2117 .0496 .0496 .0496 + -.6375 .4051 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +LEUCINE + + LEU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 + +CHARGE cc-pvt iterated + -.4937 .3018 -.0097 .0432 -.1322 + .0317 .0317 .4429 -.0662 -.4312 + .1042 .1042 .1042 -.4312 .1042 + .1042 .1042 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +ISOLEUCINE + + ILE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 + +CHARGE cc-pvt iterated + -.4937 .3018 -.0257 .0640 .0594 + .0263 -.3030 .0824 .0824 .0824 + -.0214 .0284 .0284 -.0942 .0316 + .0316 .0316 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +VALINE + + VAL INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG11 HC E 10 8 6 1.090 109.500 60.000 + 12 HG12 HC E 10 8 6 1.090 109.500 180.000 + 13 HG13 HC E 10 8 6 1.090 109.500 300.000 + 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG21 HC E 14 8 6 1.090 109.500 60.000 + 16 HG22 HC E 14 8 6 1.090 109.500 180.000 + 17 HG23 HC E 14 8 6 1.090 109.500 300.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0530 .0393 .3674 + -.0145 -.3584 .0803 .0803 .0803 + -.3584 .0803 .0803 .0803 .6731 + -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +ASPARAGINE + + ASN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.522 111.100 180.000 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0551 .0410 -.1944 + .0833 .0833 .6665 -.5754 -.7750 + .3599 .3599 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + CB ND2 CG OD1 + CG HD21 ND2 HD22 + +DONE +GLUTAMINE + + GLN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.522 111.100 180.000 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0299 .0381 .1411 + -.0021 -.0021 -.2820 .1136 .1136 + .7046 -.6162 -.7795 .3525 .3525 + .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + CG NE2 CD OE1 + CD HE21 NE2 HE22 + +DONE +ARGININE + + ARG INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 H1 E 14 11 8 1.090 109.500 300.000 + 16 HD3 H1 E 14 11 8 1.090 109.500 60.000 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 + 18 HE H E 17 14 11 1.010 118.500 0.000 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 + 21 HH11 H E 20 19 17 1.010 119.800 0.000 + 22 HH12 H E 20 19 17 1.010 119.800 180.000 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 + 24 HH21 H E 23 19 17 1.010 119.800 0.000 + 25 HH22 H E 23 19 17 1.010 119.800 180.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O E 26 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0299 .0476 .0040 + .0257 .0257 -.0027 .0314 .0314 + .1008 .0575 .0575 -.5111 .3233 + .8708 -.8348 .4205 .4205 -.8348 + .4205 .4205 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + NE NH1 CZ NH2 + CD CZ NE HE + CZ HH11 NH1 HH12 + CZ HH21 NH2 HH22 + +DONE +HISTIDINE DELTAH + + HID INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NB S 14 12 11 1.310 109.000 0.000 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0860 .0068 -.0602 + .0367 .0367 .0586 -.1647 .2721 + .0985 .1016 -.4715 .0103 .0933 + .6731 -.5854 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE1 ND1 HD1 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +HISTIDINE EPSILONH + + HIE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NB S 11 8 6 1.390 122.000 180.000 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0376 .0217 -.0413 + .0476 .0476 .2502 -.5666 .2311 + .0679 -.2110 .2901 -.2281 .1574 + .6731 -.5854 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +HISTIDINE PLUS + + HIP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O E 20 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .2291 -.0223 -.0362 + .0490 .0490 .0884 -.0188 .2961 + -.0735 .2124 -.0292 .3151 -.1452 + .1903 .6731 -.5854 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE1 ND1 HD1 + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +TRYPTOPHAN + + TRP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C* S 8 6 4 1.510 115.000 180.000 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 + 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 + 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 + 20 HH2 HA E 19 17 16 1.090 120.000 180.000 + 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 + 22 HZ3 HA E 21 19 17 1.090 120.000 180.000 + 23 CE3 CA B 21 19 17 1.410 122.000 0.000 + 24 HE3 HA E 23 21 19 1.090 120.000 180.000 + 25 CD2 CB E 23 21 19 1.400 117.000 0.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O E 26 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0233 .0376 -.0168 + .0307 .0307 -.0988 -.0808 .1434 + -.3542 .3403 .1656 -.2279 .1382 + -.1110 .1076 -.1494 .1087 -.2159 + .1561 .0768 .6731 -.5854 + +LOOP + CG CD2 + CE2 CD2 + +IMPROPER + -M CA N H + CA +M C O + CD1 CE2 NE1 HE1 + CE2 CH2 CZ2 HZ2 + CZ2 CZ3 CH2 HH2 + CH2 CE3 CZ3 HZ3 + CZ3 CD2 CE3 HE3 + CG NE1 CD1 HD1 + CD1 CD2 CG CB + +DONE +PHENYLALANINE + + PHE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 115.000 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HA E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HA E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HA E 20 18 16 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O E 22 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0416 .0184 -.0021 + .0242 .0242 .0293 -.1050 .1123 + -.1506 .1161 -.0770 .1000 -.1506 + .1161 -.1050 .1123 .6731 -.5854 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE2 CD2 HD2 + CD2 CZ CE2 HE2 + CE1 CE2 CZ HZ + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + +DONE +TYROSINE + + TYR INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 109.470 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 OH OH S 16 14 12 1.360 120.000 180.000 + 18 HH HO E 17 16 14 0.960 113.000 0.000 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 + 20 HE2 HA E 19 16 14 1.090 120.000 180.000 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 + 22 HD2 HA E 21 19 16 1.090 120.000 180.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O E 23 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0010 .0556 .0211 + .0225 .0225 -.0017 -.1459 .1195 + -.1848 .1367 .2516 -.4757 .3583 + -.1848 .1367 -.1459 .1195 .6731 + -.5854 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE2 CD2 HD2 + CD2 CZ CE2 HE2 + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + CE1 CE2 CZ OH + +DONE +GLUTAMIC ACID + + GLU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O E 17 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.2384 .0937 .3053 + -.0704 -.0704 -.1671 .0313 .0313 + .6613 -.7362 -.7362 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + CG OE1 CD OE2 + +DONE +ASPARTIC ACID + + ASP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.1667 .0656 .0021 + -.0210 -.0210 .7672 -.7610 -.7610 + .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + CB OD1 CG OD2 + +DONE +LYSINE + + LYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 + 21 HZ1 H E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H E 20 17 14 1.010 109.470 180.000 + 23 HZ3 H E 20 17 14 1.010 109.470 300.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O E 24 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0343 .0464 -.0196 + .0143 .0143 -.0233 .0433 .0433 + -.0574 .0602 .0602 .1461 .0470 + .0470 -.2135 .2872 .2872 .2872 + .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +LYSINE neutral + + LYN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 H1 E 17 14 11 1.090 109.500 300.000 + 19 HE3 H1 E 17 14 11 1.090 109.500 60.000 + 20 NZ NT B 17 14 11 1.470 109.470 180.000 + 21 HZ2 H E 20 17 14 1.010 109.470 180.000 + 22 HZ3 H E 20 17 14 1.010 109.470 300.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O E 24 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0275 .0566 .0084 + -.0011 -.0011 -.0283 .0286 .0286 + -.0800 .0518 .0518 .3329 -.0405 + -.0405 -.8961 .3303 .3303 .6731 + -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +PROLINE + + PRO INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 + 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 + 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 + 11 CB CT B 8 5 4 1.510 106.000 338.300 + 12 HB2 HC E 11 8 5 1.090 109.500 256.300 + 13 HB3 HC E 11 8 5 1.090 109.500 136.300 + 14 CA CT M 4 3 2 1.451 120.600 175.200 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 + 16 C C M 14 4 3 1.522 109.500 300.000 + 17 O O E 16 14 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.2754 .0628 .0273 .0273 .0632 + .0063 .0063 .0262 .0214 .0214 + -.1503 .0758 .6731 -.5854 + +LOOP + CB CA + +IMPROPER + CA +M C O + -M CD N CA + +DONE +CYSTEINE + + CYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG SH S 8 6 4 1.810 116.000 180.000 + 12 HG HS E 11 8 6 1.330 96.000 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0805 .0267 -.0052 + .0448 .0448 -.2429 .1555 .6731 + -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +CYSTEINE with negative charge + + CYM INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 11 SG SH E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.2870 .1203 .0935 + .0125 .0125 -.8476 .6731 -.5854 + +IMPROPER + -M CA N HN + CA +M C O + +DONE +CYSTINE(S-S BRIDGE) + + CYX INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG S E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0599 .0363 .0027 + .0473 .0473 -.0893 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +METHIONINE + + MET INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 + 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 + 14 SD S S 11 8 6 1.810 110.000 180.000 + 15 CE CT 3 14 11 8 1.780 100.000 180.000 + 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 + 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 + 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0110 .0316 .0940 + -.0190 -.0190 -.0130 .0695 .0695 + -.2394 -.0550 .0580 .0580 .0580 + .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE + ACE BEGINNING GROUP + + ACE INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HH31 HC M 3 2 1 1.000 90.000 180.000 + 5 CH3 CT M 4 3 2 1.090 90.000 180.000 + 6 HH32 HC E 5 4 3 1.090 109.500 60.000 + 7 HH33 HC E 5 4 3 1.090 109.500 300.000 + 8 C C M 5 4 3 1.530 111.100 180.000 + 9 O O E 8 5 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1437 -.5188 .1437 .1437 .6731 + -.5854 + +IMPROPER + CH3 +M C O + +DONE +N-methyl all atom + + NME INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CH3 CT M 4 3 2 1.449 121.900 180.000 + 7 HH31 H1 E 6 4 3 1.090 109.500 0.000 + 8 HH32 H1 E 6 4 3 1.090 109.500 120.000 + 9 HH33 H1 E 6 4 3 1.090 109.500 240.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0076 .0665 .0665 + .0665 + +IMPROPER + -M CH3 N H + +DONE +ASP neutral + + ASH INT 0 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O E 11 8 6 1.260 117.200 90.000 + 13 OD2 OH S 11 8 6 1.260 117.200 270.000 + 14 HD2 HO E 13 11 8 0.96 109.5 180.0 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .1120 .0108 -.0417 + .0455 .0455 .6066 -.5440 -.5702 + .4397 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + CB OD1 CG OD2 + +DONE +GLU neutral + + GLH INT 0 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O E 14 11 8 1.260 117.200 90.000 + 16 OE2 OH S 14 11 8 1.260 117.200 270.000 + 17 HE2 HO E 16 14 11 0.960 109.500 180.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0227 .0389 -.0018 + .0278 .0278 -.1054 .0787 .0787 + .6699 -.5729 -.5964 .4362 .6731 + -.5854 + +IMPROPER + -M CA N H + CA +M C O + CG OE1 CD OE2 + +DONE +Sodium Ion +CIP +CIP INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 NA+ IP M 3 2 1 1.0000 90.0000 180.0000 1.000 + +DONE +Chloride Ion +CIM +CIM INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 CL- IM M 3 2 1 1.0000 90.0000 180.0000 -1.000 + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/ACE_ACE_BEGINNING_GROUP.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ACE_ACE_BEGINNING_GROUP.in_frag new file mode 100644 index 000000000..4b7832b4e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ACE_ACE_BEGINNING_GROUP.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HH31 HC M 3 2 1 1.000 90.000 180.000 + 5 CH3 CT M 4 3 2 1.090 90.000 180.000 + 6 HH32 HC E 5 4 3 1.090 109.500 60.000 + 7 HH33 HC E 5 4 3 1.090 109.500 300.000 + 8 C C M 5 4 3 1.530 111.100 180.000 + 9 O O E 8 5 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ALA_ALANINE.in_frag new file mode 100644 index 000000000..a7bb1df86 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ALA_ALANINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ARG_ARGININE.in_frag new file mode 100644 index 000000000..c81cec911 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ARG_ARGININE.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 H1 E 14 11 8 1.090 109.500 300.000 + 16 HD3 H1 E 14 11 8 1.090 109.500 60.000 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 + 18 HE H E 17 14 11 1.010 118.500 0.000 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 + 21 HH11 H E 20 19 17 1.010 119.800 0.000 + 22 HH12 H E 20 19 17 1.010 119.800 180.000 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 + 24 HH21 H E 23 19 17 1.010 119.800 0.000 + 25 HH22 H E 23 19 17 1.010 119.800 180.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O E 26 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/ASH_ASP_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ASH_ASP_neutral.in_frag new file mode 100644 index 000000000..871b86bfb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ASH_ASP_neutral.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O E 11 8 6 1.260 117.200 90.000 + 13 OD2 OH S 11 8 6 1.260 117.200 270.000 + 14 HD2 HO E 13 11 8 0.960 109.500 180.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..923988a6b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ASN_ASPARAGINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.522 111.100 180.000 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..18c0aa80a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/CIM_Chloride_Ion.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/CIM_Chloride_Ion.in_frag new file mode 100644 index 000000000..b5670775c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/CIM_Chloride_Ion.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 CL- IM M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/CIP_Sodium_Ion.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/CIP_Sodium_Ion.in_frag new file mode 100644 index 000000000..088bc4f00 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/CIP_Sodium_Ion.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 NA+ IP M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/CYM_CYSTEINE_with_negative_charge.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/CYM_CYSTEINE_with_negative_charge.in_frag new file mode 100644 index 000000000..1a6ab8383 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/CYM_CYSTEINE_with_negative_charge.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 11 SG SH E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..4c0f31d34 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/CYS_CYSTEINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG SH S 8 6 4 1.810 116.000 180.000 + 12 HG HS E 11 8 6 1.330 96.000 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..4bcb8af4c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG S E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/GLH_GLU_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/GLH_GLU_neutral.in_frag new file mode 100644 index 000000000..bb692bd02 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/GLH_GLU_neutral.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O E 14 11 8 1.260 117.200 90.000 + 16 OE2 OH S 14 11 8 1.260 117.200 270.000 + 17 HE2 HO E 16 14 11 0.960 109.500 180.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..e3905d2e3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/GLN_GLUTAMINE.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.522 111.100 180.000 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..9f20f8f01 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O E 17 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..2b34e89e7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/GLY_GLYCINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H1 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H1 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O E 9 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..47aa5bb10 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NB S 14 12 11 1.310 109.000 0.000 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..10b520062 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NB S 11 8 6 1.390 122.000 180.000 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..0fa584734 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O E 20 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..bca9a78cc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..23b22a7e4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/LEU_LEUCINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/LYN_LYSINE_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/LYN_LYSINE_neutral.in_frag new file mode 100644 index 000000000..ef49d8df9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/LYN_LYSINE_neutral.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 H1 E 17 14 11 1.090 109.500 300.000 + 19 HE3 H1 E 17 14 11 1.090 109.500 60.000 + 20 NZ NT B 17 14 11 1.470 109.470 180.000 + 21 HZ2 H E 20 17 14 1.010 109.470 180.000 + 22 HZ3 H E 20 17 14 1.010 109.470 300.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O E 24 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/LYS_LYSINE.in_frag new file mode 100644 index 000000000..af3f27bf0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/LYS_LYSINE.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 + 21 HZ1 H E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H E 20 17 14 1.010 109.470 180.000 + 23 HZ3 H E 20 17 14 1.010 109.470 300.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O E 24 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/MET_METHIONINE.in_frag new file mode 100644 index 000000000..da19600d3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/MET_METHIONINE.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 + 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 + 14 SD S S 11 8 6 1.810 110.000 180.000 + 15 CE CT 3 14 11 8 1.780 100.000 180.000 + 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 + 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 + 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/NME_N-methyl_all_atom.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/NME_N-methyl_all_atom.in_frag new file mode 100644 index 000000000..aa1758816 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/NME_N-methyl_all_atom.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CH3 CT M 4 3 2 1.449 121.900 180.000 + 7 HH31 H1 E 6 4 3 1.090 109.500 0.000 + 8 HH32 H1 E 6 4 3 1.090 109.500 120.000 + 9 HH33 H1 E 6 4 3 1.090 109.500 240.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..2bb6cdc54 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 115.000 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HA E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HA E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HA E 20 18 16 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O E 22 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/PRO_PROLINE.in_frag new file mode 100644 index 000000000..7c4fada2c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/PRO_PROLINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 + 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 + 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 + 11 CB CT B 8 5 4 1.510 106.000 338.300 + 12 HB2 HC E 11 8 5 1.090 109.500 256.300 + 13 HB3 HC E 11 8 5 1.090 109.500 136.300 + 14 CA CT M 4 3 2 1.451 120.600 175.200 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 + 16 C C M 14 4 3 1.522 109.500 300.000 + 17 O O E 16 14 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/SER_SERINE.in_frag new file mode 100644 index 000000000..5ff430502 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/SER_SERINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 OG OH S 8 6 4 1.430 109.470 180.000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/THR_THREONINE.in_frag new file mode 100644 index 000000000..cf686b69f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/THR_THREONINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB H1 E 8 6 4 1.090 109.500 180.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/TRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/TRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..a7aed5e34 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/TRP_TRYPTOPHAN.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C* S 8 6 4 1.510 115.000 180.000 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 + 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 + 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 + 20 HH2 HA E 19 17 16 1.090 120.000 180.000 + 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 + 22 HZ3 HA E 21 19 17 1.090 120.000 180.000 + 23 CE3 CA B 21 19 17 1.410 122.000 0.000 + 24 HE3 HA E 23 21 19 1.090 120.000 180.000 + 25 CD2 CB E 23 21 19 1.400 117.000 0.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O E 26 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/TYR_TYROSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/TYR_TYROSINE.in_frag new file mode 100644 index 000000000..d3df8e72d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/TYR_TYROSINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 109.470 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 OH OH S 16 14 12 1.360 120.000 180.000 + 18 HH HO E 17 16 14 0.960 113.000 0.000 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 + 20 HE2 HA E 19 16 14 1.090 120.000 180.000 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 + 22 HD2 HA E 21 19 16 1.090 120.000 180.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O E 23 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/VAL_VALINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino02/VAL_VALINE.in_frag new file mode 100644 index 000000000..6f5affadb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/VAL_VALINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG11 HC E 10 8 6 1.090 109.500 60.000 + 12 HG12 HC E 10 8 6 1.090 109.500 180.000 + 13 HG13 HC E 10 8 6 1.090 109.500 300.000 + 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG21 HC E 14 8 6 1.090 109.500 60.000 + 16 HG22 HC E 14 8 6 1.090 109.500 180.000 + 17 HG23 HC E 14 8 6 1.090 109.500 300.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino02/all_amino02.in b/cad/tests/AMBER_test_structures/dot_in/all_amino02/all_amino02.in new file mode 100644 index 000000000..de3c576bd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino02/all_amino02.in @@ -0,0 +1,1095 @@ + 1 1 2 +db2000.dat +ALANINE + + ALA INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0448 .0228 -.0909 + .0425 .0425 .0425 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +GLYCINE + + GLY INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H1 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H1 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O E 9 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0332 .0687 .0687 + .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +SERINE + + SER INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 OG OH S 8 6 4 1.430 109.470 180.000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0717 .0164 .1345 + .0361 .0361 -.5593 .3687 .6731 + -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +THREONINE + + THR INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB H1 E 8 6 4 1.090 109.500 180.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0702 .0164 .4038 + -.0909 -.2117 .0496 .0496 .0496 + -.6375 .4051 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +LEUCINE + + LEU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 + +CHARGE cc-pvt iterated + -.4937 .3018 -.0097 .0432 -.1322 + .0317 .0317 .4429 -.0662 -.4312 + .1042 .1042 .1042 -.4312 .1042 + .1042 .1042 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +ISOLEUCINE + + ILE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 + +CHARGE cc-pvt iterated + -.4937 .3018 -.0257 .0640 .0594 + .0263 -.3030 .0824 .0824 .0824 + -.0214 .0284 .0284 -.0942 .0316 + .0316 .0316 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +VALINE + + VAL INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG11 HC E 10 8 6 1.090 109.500 60.000 + 12 HG12 HC E 10 8 6 1.090 109.500 180.000 + 13 HG13 HC E 10 8 6 1.090 109.500 300.000 + 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG21 HC E 14 8 6 1.090 109.500 60.000 + 16 HG22 HC E 14 8 6 1.090 109.500 180.000 + 17 HG23 HC E 14 8 6 1.090 109.500 300.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0530 .0393 .3674 + -.0145 -.3584 .0803 .0803 .0803 + -.3584 .0803 .0803 .0803 .6731 + -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +ASPARAGINE + + ASN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.522 111.100 180.000 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0551 .0410 -.1944 + .0833 .0833 .6665 -.5754 -.7750 + .3599 .3599 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + CB ND2 CG OD1 + CG HD21 ND2 HD22 + +DONE +GLUTAMINE + + GLN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.522 111.100 180.000 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0299 .0381 .1411 + -.0021 -.0021 -.2820 .1136 .1136 + .7046 -.6162 -.7795 .3525 .3525 + .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + CG NE2 CD OE1 + CD HE21 NE2 HE22 + +DONE +ARGININE + + ARG INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 H1 E 14 11 8 1.090 109.500 300.000 + 16 HD3 H1 E 14 11 8 1.090 109.500 60.000 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 + 18 HE H E 17 14 11 1.010 118.500 0.000 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 + 21 HH11 H E 20 19 17 1.010 119.800 0.000 + 22 HH12 H E 20 19 17 1.010 119.800 180.000 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 + 24 HH21 H E 23 19 17 1.010 119.800 0.000 + 25 HH22 H E 23 19 17 1.010 119.800 180.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O E 26 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0299 .0476 .0040 + .0257 .0257 -.0027 .0314 .0314 + .1008 .0575 .0575 -.5111 .3233 + .8708 -.8348 .4205 .4205 -.8348 + .4205 .4205 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + NE NH1 CZ NH2 + CD CZ NE HE + CZ HH11 NH1 HH12 + CZ HH21 NH2 HH22 + +DONE +HISTIDINE DELTAH + + HID INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NB S 14 12 11 1.310 109.000 0.000 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0860 .0068 -.0602 + .0367 .0367 .0586 -.1647 .2721 + .0985 .1016 -.4715 .0103 .0933 + .6731 -.5854 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE1 ND1 HD1 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +HISTIDINE EPSILONH + + HIE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NB S 11 8 6 1.390 122.000 180.000 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0376 .0217 -.0413 + .0476 .0476 .2502 -.5666 .2311 + .0679 -.2110 .2901 -.2281 .1574 + .6731 -.5854 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +HISTIDINE PLUS + + HIP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O E 20 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .2291 -.0223 -.0362 + .0490 .0490 .0884 -.0188 .2961 + -.0735 .2124 -.0292 .3151 -.1452 + .1903 .6731 -.5854 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE1 ND1 HD1 + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +TRYPTOPHAN + + TRP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C* S 8 6 4 1.510 115.000 180.000 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 + 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 + 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 + 20 HH2 HA E 19 17 16 1.090 120.000 180.000 + 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 + 22 HZ3 HA E 21 19 17 1.090 120.000 180.000 + 23 CE3 CA B 21 19 17 1.410 122.000 0.000 + 24 HE3 HA E 23 21 19 1.090 120.000 180.000 + 25 CD2 CB E 23 21 19 1.400 117.000 0.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O E 26 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0233 .0376 -.0168 + .0307 .0307 -.0988 -.0808 .1434 + -.3542 .3403 .1656 -.2279 .1382 + -.1110 .1076 -.1494 .1087 -.2159 + .1561 .0768 .6731 -.5854 + +LOOP + CG CD2 + CE2 CD2 + +IMPROPER + -M CA N H + CA +M C O + CD1 CE2 NE1 HE1 + CE2 CH2 CZ2 HZ2 + CZ2 CZ3 CH2 HH2 + CH2 CE3 CZ3 HZ3 + CZ3 CD2 CE3 HE3 + CG NE1 CD1 HD1 + CD1 CD2 CG CB + +DONE +PHENYLALANINE + + PHE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 115.000 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HA E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HA E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HA E 20 18 16 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O E 22 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0416 .0184 -.0021 + .0242 .0242 .0293 -.1050 .1123 + -.1506 .1161 -.0770 .1000 -.1506 + .1161 -.1050 .1123 .6731 -.5854 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE2 CD2 HD2 + CD2 CZ CE2 HE2 + CE1 CE2 CZ HZ + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + +DONE +TYROSINE + + TYR INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 109.470 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 OH OH S 16 14 12 1.360 120.000 180.000 + 18 HH HO E 17 16 14 0.960 113.000 0.000 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 + 20 HE2 HA E 19 16 14 1.090 120.000 180.000 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 + 22 HD2 HA E 21 19 16 1.090 120.000 180.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O E 23 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0010 .0556 .0211 + .0225 .0225 -.0017 -.1459 .1195 + -.1848 .1367 .2516 -.4757 .3583 + -.1848 .1367 -.1459 .1195 .6731 + -.5854 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE2 CD2 HD2 + CD2 CZ CE2 HE2 + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + CE1 CE2 CZ OH + +DONE +GLUTAMIC ACID + + GLU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O E 17 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.2384 .0937 .3053 + -.0704 -.0704 -.1671 .0313 .0313 + .6613 -.7362 -.7362 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + CG OE1 CD OE2 + +DONE +ASPARTIC ACID + + ASP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.1667 .0656 .0021 + -.0210 -.0210 .7672 -.7610 -.7610 + .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + CB OD1 CG OD2 + +DONE +LYSINE + + LYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 + 21 HZ1 H E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H E 20 17 14 1.010 109.470 180.000 + 23 HZ3 H E 20 17 14 1.010 109.470 300.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O E 24 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0343 .0464 -.0196 + .0143 .0143 -.0233 .0433 .0433 + -.0574 .0602 .0602 .1461 .0470 + .0470 -.2135 .2872 .2872 .2872 + .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +LYSINE neutral + + LYN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 H1 E 17 14 11 1.090 109.500 300.000 + 19 HE3 H1 E 17 14 11 1.090 109.500 60.000 + 20 NZ NT B 17 14 11 1.470 109.470 180.000 + 21 HZ2 H E 20 17 14 1.010 109.470 180.000 + 22 HZ3 H E 20 17 14 1.010 109.470 300.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O E 24 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0275 .0566 .0084 + -.0011 -.0011 -.0283 .0286 .0286 + -.0800 .0518 .0518 .3329 -.0405 + -.0405 -.8961 .3303 .3303 .6731 + -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +PROLINE + + PRO INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 + 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 + 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 + 11 CB CT B 8 5 4 1.510 106.000 338.300 + 12 HB2 HC E 11 8 5 1.090 109.500 256.300 + 13 HB3 HC E 11 8 5 1.090 109.500 136.300 + 14 CA CT M 4 3 2 1.451 120.600 175.200 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 + 16 C C M 14 4 3 1.522 109.500 300.000 + 17 O O E 16 14 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.2754 .0628 .0273 .0273 .0632 + .0063 .0063 .0262 .0214 .0214 + -.1503 .0758 .6731 -.5854 + +LOOP + CB CA + +IMPROPER + CA +M C O + -M CD N CA + +DONE +CYSTEINE + + CYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG SH S 8 6 4 1.810 116.000 180.000 + 12 HG HS E 11 8 6 1.330 96.000 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0805 .0267 -.0052 + .0448 .0448 -.2429 .1555 .6731 + -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +CYSTEINE with negative charge + + CYM INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 11 SG SH E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.2870 .1203 .0935 + .0125 .0125 -.8476 .6731 -.5854 + +IMPROPER + -M CA N HN + CA +M C O + +DONE +CYSTINE(S-S BRIDGE) + + CYX INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG S E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0599 .0363 .0027 + .0473 .0473 -.0893 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE +METHIONINE + + MET INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 + 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 + 14 SD S S 11 8 6 1.810 110.000 180.000 + 15 CE CT 3 14 11 8 1.780 100.000 180.000 + 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 + 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 + 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0110 .0316 .0940 + -.0190 -.0190 -.0130 .0695 .0695 + -.2394 -.0550 .0580 .0580 .0580 + .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + +DONE + ACE BEGINNING GROUP + + ACE INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HH31 HC M 3 2 1 1.000 90.000 180.000 + 5 CH3 CT M 4 3 2 1.090 90.000 180.000 + 6 HH32 HC E 5 4 3 1.090 109.500 60.000 + 7 HH33 HC E 5 4 3 1.090 109.500 300.000 + 8 C C M 5 4 3 1.530 111.100 180.000 + 9 O O E 8 5 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1437 -.5188 .1437 .1437 .6731 + -.5854 + +IMPROPER + CH3 +M C O + +DONE +N-methyl all atom + + NME INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CH3 CT M 4 3 2 1.449 121.900 180.000 + 7 HH31 H1 E 6 4 3 1.090 109.500 0.000 + 8 HH32 H1 E 6 4 3 1.090 109.500 120.000 + 9 HH33 H1 E 6 4 3 1.090 109.500 240.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 -.0076 .0665 .0665 + .0665 + +IMPROPER + -M CH3 N H + +DONE +ASP neutral + + ASH INT 0 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O E 11 8 6 1.260 117.200 90.000 + 13 OD2 OH S 11 8 6 1.260 117.200 270.000 + 14 HD2 HO E 13 11 8 0.96 109.5 180.0 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .1120 .0108 -.0417 + .0455 .0455 .6066 -.5440 -.5702 + .4397 .6731 -.5854 + +IMPROPER + -M CA N H + CA +M C O + CB OD1 CG OD2 + +DONE +GLU neutral + + GLH INT 0 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O E 14 11 8 1.260 117.200 90.000 + 16 OE2 OH S 14 11 8 1.260 117.200 270.000 + 17 HE2 HO E 16 14 11 0.960 109.500 180.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + -.4937 .3018 .0227 .0389 -.0018 + .0278 .0278 -.1054 .0787 .0787 + .6699 -.5729 -.5964 .4362 .6731 + -.5854 + +IMPROPER + -M CA N H + CA +M C O + CG OE1 CD OE2 + +DONE +Sodium Ion +CIP +CIP INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 NA+ IP M 3 2 1 1.0000 90.0000 180.0000 1.000 + +DONE +Chloride Ion +CIM +CIM INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 CL- IM M 3 2 1 1.0000 90.0000 180.0000 -1.000 + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/ACE_ACE_BEGINNING_GROUP.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ACE_ACE_BEGINNING_GROUP.in_frag new file mode 100644 index 000000000..4b7832b4e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ACE_ACE_BEGINNING_GROUP.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HH31 HC M 3 2 1 1.000 90.000 180.000 + 5 CH3 CT M 4 3 2 1.090 90.000 180.000 + 6 HH32 HC E 5 4 3 1.090 109.500 60.000 + 7 HH33 HC E 5 4 3 1.090 109.500 300.000 + 8 C C M 5 4 3 1.530 111.100 180.000 + 9 O O E 8 5 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ALA_ALANINE.in_frag new file mode 100644 index 000000000..a7bb1df86 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ALA_ALANINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ARG_ARGININE.in_frag new file mode 100644 index 000000000..c81cec911 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ARG_ARGININE.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 H1 E 14 11 8 1.090 109.500 300.000 + 16 HD3 H1 E 14 11 8 1.090 109.500 60.000 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 + 18 HE H E 17 14 11 1.010 118.500 0.000 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 + 21 HH11 H E 20 19 17 1.010 119.800 0.000 + 22 HH12 H E 20 19 17 1.010 119.800 180.000 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 + 24 HH21 H E 23 19 17 1.010 119.800 0.000 + 25 HH22 H E 23 19 17 1.010 119.800 180.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O E 26 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/ASH_ASP_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ASH_ASP_neutral.in_frag new file mode 100644 index 000000000..871b86bfb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ASH_ASP_neutral.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O E 11 8 6 1.260 117.200 90.000 + 13 OD2 OH S 11 8 6 1.260 117.200 270.000 + 14 HD2 HO E 13 11 8 0.960 109.500 180.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..923988a6b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ASN_ASPARAGINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.522 111.100 180.000 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..18c0aa80a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/CIM_Chloride_Ion.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/CIM_Chloride_Ion.in_frag new file mode 100644 index 000000000..b5670775c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/CIM_Chloride_Ion.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 CL- IM M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/CIP_Sodium_Ion.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/CIP_Sodium_Ion.in_frag new file mode 100644 index 000000000..088bc4f00 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/CIP_Sodium_Ion.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 NA+ IP M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/CYM_CYSTEINE_with_negative_charge.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/CYM_CYSTEINE_with_negative_charge.in_frag new file mode 100644 index 000000000..1a6ab8383 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/CYM_CYSTEINE_with_negative_charge.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 11 SG SH E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..4c0f31d34 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/CYS_CYSTEINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG SH S 8 6 4 1.810 116.000 180.000 + 12 HG HS E 11 8 6 1.330 96.000 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..4bcb8af4c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG S E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/GLH_GLU_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/GLH_GLU_neutral.in_frag new file mode 100644 index 000000000..bb692bd02 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/GLH_GLU_neutral.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O E 14 11 8 1.260 117.200 90.000 + 16 OE2 OH S 14 11 8 1.260 117.200 270.000 + 17 HE2 HO E 16 14 11 0.960 109.500 180.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..e3905d2e3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/GLN_GLUTAMINE.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.522 111.100 180.000 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..9f20f8f01 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O E 17 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..8ac9c1995 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/GLY_GLYCINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H0 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H0 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O E 9 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..47aa5bb10 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NB S 14 12 11 1.310 109.000 0.000 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..10b520062 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NB S 11 8 6 1.390 122.000 180.000 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..0fa584734 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O E 20 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/HOH_WATER,_TIP3P_MODEL.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/HOH_WATER,_TIP3P_MODEL.in_frag new file mode 100644 index 000000000..9dc90bca2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/HOH_WATER,_TIP3P_MODEL.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H1 HW M 3 2 1 1.000 101.430 -98.890 + 5 O OW M 4 3 2 0.957 104.520 -39.220 + 6 H2 HW E 5 4 3 0.957 104.520 -151.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..bca9a78cc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..23b22a7e4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/LEU_LEUCINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/LYN_LYSINE_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/LYN_LYSINE_neutral.in_frag new file mode 100644 index 000000000..f4cf643a0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/LYN_LYSINE_neutral.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 B 17 14 11 1.470 109.470 180.000 + 21 HZ2 H E 20 17 14 1.010 109.470 180.000 + 22 HZ3 H E 20 17 14 1.010 109.470 300.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O E 24 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/LYS_LYSINE.in_frag new file mode 100644 index 000000000..af3f27bf0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/LYS_LYSINE.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 + 21 HZ1 H E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H E 20 17 14 1.010 109.470 180.000 + 23 HZ3 H E 20 17 14 1.010 109.470 300.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O E 24 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/MET_METHIONINE.in_frag new file mode 100644 index 000000000..da19600d3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/MET_METHIONINE.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 + 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 + 14 SD S S 11 8 6 1.810 110.000 180.000 + 15 CE CT 3 14 11 8 1.780 100.000 180.000 + 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 + 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 + 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/NHE_NH2_ENDING_GROUP.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/NHE_NH2_ENDING_GROUP.in_frag new file mode 100644 index 000000000..10d8ca029 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/NHE_NH2_ENDING_GROUP.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN1 H E 4 3 2 1.010 119.800 0.000 + 6 HN2 H E 4 3 2 1.010 119.800 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/NME_N-methyl_all_atom.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/NME_N-methyl_all_atom.in_frag new file mode 100644 index 000000000..aa1758816 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/NME_N-methyl_all_atom.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CH3 CT M 4 3 2 1.449 121.900 180.000 + 7 HH31 H1 E 6 4 3 1.090 109.500 0.000 + 8 HH32 H1 E 6 4 3 1.090 109.500 120.000 + 9 HH33 H1 E 6 4 3 1.090 109.500 240.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..2bb6cdc54 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 115.000 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HA E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HA E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HA E 20 18 16 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O E 22 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/PRO_PROLINE.in_frag new file mode 100644 index 000000000..7c4fada2c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/PRO_PROLINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 + 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 + 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 + 11 CB CT B 8 5 4 1.510 106.000 338.300 + 12 HB2 HC E 11 8 5 1.090 109.500 256.300 + 13 HB3 HC E 11 8 5 1.090 109.500 136.300 + 14 CA CT M 4 3 2 1.451 120.600 175.200 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 + 16 C C M 14 4 3 1.522 109.500 300.000 + 17 O O E 16 14 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/SER_SERINE.in_frag new file mode 100644 index 000000000..5ff430502 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/SER_SERINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 OG OH S 8 6 4 1.430 109.470 180.000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/THR_THREONINE.in_frag new file mode 100644 index 000000000..cf686b69f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/THR_THREONINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB H1 E 8 6 4 1.090 109.500 180.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino03/TRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino03/TRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..a7aed5e34 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino03/TRP_TRYPTOPHAN.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C* S 8 6 4 1.510 115.000 180.000 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 + 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 + 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 + 20 HH2 HA E 19 17 16 1.090 120.000 180.000 + 21 CZ3 CA B 19 17 16 1.350 121.000 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4 3 2 1.451 120.600 175.200 -0.034577 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 0.059977 + 16 C C M 14 4 3 1.522 109.500 300.000 0.333720 + 17 O O E 16 14 4 1.229 120.500 0.000 -0.434559 + +CHARGE + -0.088116 -0.011906 0.043951 0.043950 0.013059 + 0.019574 0.019574 -0.003351 0.019352 0.019352 + -0.034577 0.059977 0.333720 -0.434559 + + +LOOP + CB CA + +IMPROPER + CA +M C O + -M CD N CA + +DONE +CYSTEINE + + CYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.396165 + 5 H H E 4 3 2 1.010 119.800 0.000 0.295187 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.073501 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.140510 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.221371 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.146537 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.146537 + 11 SG SH S 8 6 4 1.810 116.000 180.000 -0.285182 + 12 HG HS E 11 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0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 H1 HW M 3 2 1 1.000 101.430 -98.890 0.41700 + 5 O OW M 4 3 2 0.9572 104.520 -39.220 -0.83400 + 6 H2 HW E 5 4 3 0.9572 104.520 -151.000 0.41700 + +LOOP + H1 H2 + +DONE +ASP neutral +ASH + ASH INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.392069 + 5 H H E 4 3 2 1.010 119.800 0.000 0.282413 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.035317 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.094292 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.121405 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.069032 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.069032 + 11 CG C B 8 6 4 1.527 109.470 180.000 0.678640 + 12 OD1 O E 11 8 6 1.260 117.200 90.000 -0.550940 + 13 OD2 OH S 11 8 6 1.260 117.200 270.000 -0.587163 + 14 HD2 HO E 13 11 8 0.96 109.5 180.000 0.438035 + 15 C C M 6 4 3 1.522 111.100 180.000 0.620495 + 16 O O E 15 6 4 1.229 120.500 0.000 -0.565045 + +CHARGE + -0.392069 0.282413 -0.035317 0.094292 -0.121405 + 0.069032 0.069032 0.678640 -0.550940 -0.587163 + 0.438035 0.620495 -0.565045 + + +IMPROPER + -M CA N H + CA +M C O + CB OD1 CG OD2 + +DONE +GLU neutral +GLH + GLH INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.384536 + 5 H H E 4 3 2 1.010 119.800 0.000 0.263963 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.060898 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.109620 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.018753 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.034966 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.034966 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 -0.038364 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.048444 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.048444 + 14 CD C B 11 8 6 1.527 109.470 180.000 0.638937 + 15 OE1 O E 14 11 8 1.260 117.200 90.000 -0.559031 + 16 OE2 OH S 14 11 8 1.260 117.200 270.000 -0.588722 + 17 HE2 HO E 16 14 11 0.960 109.500 180.000 0.447661 + 18 C C M 6 4 3 1.522 111.100 180.000 0.587056 + 19 O O E 18 6 4 1.229 120.500 0.000 -0.563753 + +CHARGE + -0.384536 0.263963 -0.060898 0.109620 -0.018753 + 0.034966 0.034966 -0.038364 0.048444 0.048444 + 0.638937 -0.559031 -0.588722 0.447661 0.587056 + -0.563753 + + +IMPROPER + -M CA N H + CA +M C O + CG OE1 CD OE2 + +DONE +Sodium Ion +CIP + CIP INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 NA+ IP M 3 2 1 1.0000 90.0000 180.0000 1.000 + +DONE +Chloride Ion +CIM + CIM INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 CL- IM M 3 2 1 1.0000 90.0000 180.0000 -1.000 + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/ACE_ACE_BEGINNING_GROUP.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ACE_ACE_BEGINNING_GROUP.in_frag new file mode 100644 index 000000000..4b7832b4e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ACE_ACE_BEGINNING_GROUP.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HH31 HC M 3 2 1 1.000 90.000 180.000 + 5 CH3 CT M 4 3 2 1.090 90.000 180.000 + 6 HH32 HC E 5 4 3 1.090 109.500 60.000 + 7 HH33 HC E 5 4 3 1.090 109.500 300.000 + 8 C C M 5 4 3 1.530 111.100 180.000 + 9 O O E 8 5 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ALA_ALANINE.in_frag new file mode 100644 index 000000000..a7bb1df86 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ALA_ALANINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ARG_ARGININE.in_frag new file mode 100644 index 000000000..c81cec911 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ARG_ARGININE.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 H1 E 14 11 8 1.090 109.500 300.000 + 16 HD3 H1 E 14 11 8 1.090 109.500 60.000 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 + 18 HE H E 17 14 11 1.010 118.500 0.000 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 + 21 HH11 H E 20 19 17 1.010 119.800 0.000 + 22 HH12 H E 20 19 17 1.010 119.800 180.000 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 + 24 HH21 H E 23 19 17 1.010 119.800 0.000 + 25 HH22 H E 23 19 17 1.010 119.800 180.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O E 26 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/ASH_ASP_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ASH_ASP_neutral.in_frag new file mode 100644 index 000000000..871b86bfb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ASH_ASP_neutral.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O E 11 8 6 1.260 117.200 90.000 + 13 OD2 OH S 11 8 6 1.260 117.200 270.000 + 14 HD2 HO E 13 11 8 0.960 109.500 180.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..923988a6b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ASN_ASPARAGINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.522 111.100 180.000 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..18c0aa80a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/CIM_Chloride_Ion.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/CIM_Chloride_Ion.in_frag new file mode 100644 index 000000000..b5670775c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/CIM_Chloride_Ion.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 CL- IM M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/CIP_Sodium_Ion.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/CIP_Sodium_Ion.in_frag new file mode 100644 index 000000000..088bc4f00 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/CIP_Sodium_Ion.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 NA+ IP M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/CYM_CYSTEINE_with_negative_charge.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/CYM_CYSTEINE_with_negative_charge.in_frag new file mode 100644 index 000000000..c4791eff8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/CYM_CYSTEINE_with_negative_charge.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 11 SG SH E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..4c0f31d34 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/CYS_CYSTEINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG SH S 8 6 4 1.810 116.000 180.000 + 12 HG HS E 11 8 6 1.330 96.000 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..4bcb8af4c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG S E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/GLH_GLU_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/GLH_GLU_neutral.in_frag new file mode 100644 index 000000000..bb692bd02 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/GLH_GLU_neutral.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O E 14 11 8 1.260 117.200 90.000 + 16 OE2 OH S 14 11 8 1.260 117.200 270.000 + 17 HE2 HO E 16 14 11 0.960 109.500 180.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..e3905d2e3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/GLN_GLUTAMINE.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.522 111.100 180.000 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..9f20f8f01 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O E 17 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..2b34e89e7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/GLY_GLYCINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H1 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H1 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O E 9 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..47aa5bb10 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NB S 14 12 11 1.310 109.000 0.000 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..10b520062 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NB S 11 8 6 1.390 122.000 180.000 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..0fa584734 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O E 20 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..bca9a78cc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..23b22a7e4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/LEU_LEUCINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/LYN_LYSINE_neutral.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/LYN_LYSINE_neutral.in_frag new file mode 100644 index 000000000..855cd54e2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/LYN_LYSINE_neutral.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 B 17 14 11 1.470 109.470 180.000 + 21 HZ2 H E 20 17 14 1.010 109.470 180.000 + 22 HZ3 H E 20 17 14 1.010 109.470 300.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O E 23 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/LYS_LYSINE.in_frag new file mode 100644 index 000000000..af3f27bf0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/LYS_LYSINE.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 + 21 HZ1 H E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H E 20 17 14 1.010 109.470 180.000 + 23 HZ3 H E 20 17 14 1.010 109.470 300.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O E 24 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/MET_METHIONINE.in_frag new file mode 100644 index 000000000..da19600d3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/MET_METHIONINE.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 + 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 + 14 SD S S 11 8 6 1.810 110.000 180.000 + 15 CE CT 3 14 11 8 1.780 100.000 180.000 + 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 + 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 + 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/NHE_NH2_ENDING_GROUP.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/NHE_NH2_ENDING_GROUP.in_frag new file mode 100644 index 000000000..10d8ca029 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/NHE_NH2_ENDING_GROUP.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN1 H E 4 3 2 1.010 119.800 0.000 + 6 HN2 H E 4 3 2 1.010 119.800 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/NME_N-methyl_all_atom.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/NME_N-methyl_all_atom.in_frag new file mode 100644 index 000000000..aa1758816 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/NME_N-methyl_all_atom.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CH3 CT M 4 3 2 1.449 121.900 180.000 + 7 HH31 H1 E 6 4 3 1.090 109.500 0.000 + 8 HH32 H1 E 6 4 3 1.090 109.500 120.000 + 9 HH33 H1 E 6 4 3 1.090 109.500 240.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..2bb6cdc54 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 115.000 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HA E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HA E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HA E 20 18 16 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O E 22 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/PRO_PROLINE.in_frag new file mode 100644 index 000000000..7c4fada2c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/PRO_PROLINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 + 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 + 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 + 11 CB CT B 8 5 4 1.510 106.000 338.300 + 12 HB2 HC E 11 8 5 1.090 109.500 256.300 + 13 HB3 HC E 11 8 5 1.090 109.500 136.300 + 14 CA CT M 4 3 2 1.451 120.600 175.200 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 + 16 C C M 14 4 3 1.522 109.500 300.000 + 17 O O E 16 14 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/SER_SERINE.in_frag new file mode 100644 index 000000000..5ff430502 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/SER_SERINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 OG OH S 8 6 4 1.430 109.470 180.000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/THR_THREONINE.in_frag new file mode 100644 index 000000000..cf686b69f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/THR_THREONINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB H1 E 8 6 4 1.090 109.500 180.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/TRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/TRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..a7aed5e34 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/TRP_TRYPTOPHAN.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C* S 8 6 4 1.510 115.000 180.000 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 + 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 + 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 + 20 HH2 HA E 19 17 16 1.090 120.000 180.000 + 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 + 22 HZ3 HA E 21 19 17 1.090 120.000 180.000 + 23 CE3 CA B 21 19 17 1.410 122.000 0.000 + 24 HE3 HA E 23 21 19 1.090 120.000 180.000 + 25 CD2 CB E 23 21 19 1.400 117.000 0.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O E 26 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/TYR_TYROSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/TYR_TYROSINE.in_frag new file mode 100644 index 000000000..4da5d8dca --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/TYR_TYROSINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 109.470 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ C B 14 12 11 1.400 120.000 0.000 + 17 OH OH S 16 14 12 1.360 120.000 180.000 + 18 HH HO E 17 16 14 0.960 113.000 0.000 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 + 20 HE2 HA E 19 16 14 1.090 120.000 180.000 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 + 22 HD2 HA E 21 19 16 1.090 120.000 180.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O E 23 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/VAL_VALINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_amino94/VAL_VALINE.in_frag new file mode 100644 index 000000000..6f5affadb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/VAL_VALINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG11 HC E 10 8 6 1.090 109.500 60.000 + 12 HG12 HC E 10 8 6 1.090 109.500 180.000 + 13 HG13 HC E 10 8 6 1.090 109.500 300.000 + 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG21 HC E 14 8 6 1.090 109.500 60.000 + 16 HG22 HC E 14 8 6 1.090 109.500 180.000 + 17 HG23 HC E 14 8 6 1.090 109.500 300.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_amino94/all_amino94.in b/cad/tests/AMBER_test_structures/dot_in/all_amino94/all_amino94.in new file mode 100644 index 000000000..65309f759 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_amino94/all_amino94.in @@ -0,0 +1,959 @@ + 1 1 2 +db94.dat +ALANINE + + ALA INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03370 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08230 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.18250 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 0.06030 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 0.06030 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 0.06030 + 12 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 13 O O E 12 6 4 1.229 120.500 0.000 -0.56790 + +IMPROPER + -M CA N H + CA +M C O + +DONE +GLYCINE + + GLY INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.02520 + 7 HA2 H1 E 6 4 3 1.090 109.500 300.000 0.06980 + 8 HA3 H1 E 6 4 3 1.090 109.500 60.000 0.06980 + 9 C C M 6 4 3 1.522 110.400 180.000 0.59730 + 10 O O E 9 6 4 1.229 120.500 0.000 -0.56790 + +IMPROPER + -M CA N H + CA +M C O + +DONE +SERINE + + SER INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.02490 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08430 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.21170 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.03520 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.03520 + 11 OG OH S 8 6 4 1.430 109.470 180.000 -0.65460 + 12 HG HO E 11 8 6 0.960 109.470 180.000 0.42750 + 13 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 14 O O E 13 6 4 1.229 120.500 0.000 -0.56790 + +IMPROPER + -M CA N H + CA +M C O + +DONE +THREONINE + + THR INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.03890 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.10070 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.36540 + 9 HB H1 E 8 6 4 1.090 109.500 180.000 0.00430 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 -0.24380 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 0.06420 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 0.06420 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 0.06420 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 -0.67610 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 0.41020 + 16 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 17 O O E 16 6 4 1.229 120.500 0.000 -0.56790 + +IMPROPER + -M CA N H + CA +M C O + +DONE +LEUCINE + + LEU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.05180 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.09220 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.11020 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04570 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04570 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.35310 + 12 HG HC E 11 8 6 1.090 109.500 300.000 -0.03610 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 -0.41210 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 0.10000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 0.10000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 0.10000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 -0.41210 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 0.10000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 0.10000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 0.10000 + 21 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 22 O O E 21 6 4 1.229 120.500 0.000 -0.56790 + +IMPROPER + -M CA N H + CA +M C O + +DONE +ISOLEUCINE + + ILE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.05970 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08690 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 0.13030 + 9 HB HC E 8 6 4 1.090 109.500 300.000 0.01870 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 -0.32040 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 0.08820 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 0.08820 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 0.08820 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 -0.04300 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 0.02360 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 0.02360 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 -0.06600 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 0.01860 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 0.01860 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 0.01860 + 21 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 22 O O E 21 6 4 1.229 120.500 0.000 -0.56790 + +IMPROPER + -M CA N H + CA +M C O + +DONE +VALINE + + VAL INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.08750 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.09690 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.29850 + 9 HB HC E 8 6 4 1.090 109.500 300.000 -0.02970 + 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 -0.31920 + 11 HG11 HC E 10 8 6 1.090 109.500 60.000 0.07910 + 12 HG12 HC E 10 8 6 1.090 109.500 180.000 0.07910 + 13 HG13 HC E 10 8 6 1.090 109.500 300.000 0.07910 + 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 -0.31920 + 15 HG21 HC E 14 8 6 1.090 109.500 60.000 0.07910 + 16 HG22 HC E 14 8 6 1.090 109.500 180.000 0.07910 + 17 HG23 HC E 14 8 6 1.090 109.500 300.000 0.07910 + 18 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 19 O O E 18 6 4 1.229 120.500 0.000 -0.56790 + +IMPROPER + -M CA N H + CA +M C O + +DONE +ASPARAGINE + + ASN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.01430 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.10480 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.20410 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.07970 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.07970 + 11 CG C B 8 6 4 1.522 111.100 180.000 0.71300 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 -0.59310 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 -0.91910 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 0.41960 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 0.41960 + 16 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 17 O O E 16 6 4 1.229 120.500 0.000 -0.56790 + +IMPROPER + -M CA N H + CA +M C O + CB ND2 CG OD1 + CG HD21 ND2 HD22 + +DONE +GLUTAMINE + + GLN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.00310 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08500 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00360 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.01710 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.01710 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 -0.06450 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.03520 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.03520 + 14 CD C B 11 8 6 1.522 111.100 180.000 0.69510 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 -0.60860 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 -0.94070 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 0.42510 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 0.42510 + 19 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790 + +IMPROPER + -M CA N H + CA +M C O + CG NE2 CD OE1 + CD HE21 NE2 HE22 + +DONE +ARGININE + + ARG INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.34790 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27470 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.26370 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.15600 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00070 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03270 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03270 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.03900 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.02850 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.02850 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 0.04860 + 15 HD2 H1 E 14 11 8 1.090 109.500 300.000 0.06870 + 16 HD3 H1 E 14 11 8 1.090 109.500 60.000 0.06870 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 -0.52950 + 18 HE H E 17 14 11 1.010 118.500 0.000 0.34560 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 0.80760 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 -0.86270 + 21 HH11 H E 20 19 17 1.010 119.800 0.000 0.44780 + 22 HH12 H E 20 19 17 1.010 119.800 180.000 0.44780 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 -0.86270 + 24 HH21 H E 23 19 17 1.010 119.800 0.000 0.44780 + 25 HH22 H E 23 19 17 1.010 119.800 180.000 0.44780 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16 NE2 NB S 14 12 11 1.310 109.000 0.000 -0.57270 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 0.12920 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 0.11470 + 19 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE1 ND1 HD1 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +HISTIDINE EPSILONH + + HIE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.05810 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13600 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00740 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03670 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03670 + 11 CG CC S 8 6 4 1.510 115.000 180.000 0.18680 + 12 ND1 NB S 11 8 6 1.390 122.000 180.000 -0.54320 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 0.16350 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 0.14350 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 -0.27950 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 0.33390 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 -0.22070 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 0.18620 + 19 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +HISTIDINE PLUS + + HIP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.34790 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27470 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.13540 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.12120 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.04140 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.08100 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.08100 + 11 CG CC S 8 6 4 1.510 115.000 180.000 -0.00120 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 -0.15130 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 0.38660 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 -0.01700 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 0.26810 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 -0.17180 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 0.39110 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 -0.11410 + 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 0.23170 + 20 C C M 6 4 3 1.522 111.100 180.000 0.73410 + 21 O O E 20 6 4 1.229 120.500 0.000 -0.58940 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE1 ND1 HD1 + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +TRYPTOPHAN + + TRP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.02750 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.11230 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00500 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03390 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03390 + 11 CG C* S 8 6 4 1.510 115.000 180.000 -0.14150 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 -0.16380 + 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 0.20620 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 -0.34180 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 0.34120 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 0.13800 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 -0.26010 + 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 0.15720 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 -0.11340 + 20 HH2 HA E 19 17 16 1.090 120.000 180.000 0.14170 + 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 -0.19720 + 22 HZ3 HA E 21 19 17 1.090 120.000 180.000 0.14470 + 23 CE3 CA B 21 19 17 1.410 122.000 0.000 -0.23870 + 24 HE3 HA E 23 21 19 1.090 120.000 180.000 0.17000 + 25 CD2 CB E 23 21 19 1.400 117.000 0.000 0.12430 + 26 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 27 O O E 26 6 4 1.229 120.500 0.000 -0.56790 + +LOOP + CG CD2 + CE2 CD2 + +IMPROPER + -M CA N H + CA +M C O + CD1 CE2 NE1 HE1 + CE2 CH2 CZ2 HZ2 + CZ2 CZ3 CH2 HH2 + CH2 CE3 CZ3 HZ3 + CZ3 CD2 CE3 HE3 + CG NE1 CD1 HD1 + CD1 CD2 CG CB + +DONE +PHENYLALANINE + + PHE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.00240 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.09780 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.03430 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.02950 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.02950 + 11 CG CA S 8 6 4 1.510 115.000 180.000 0.01180 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 -0.12560 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 0.13300 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 -0.17040 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 0.14300 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 -0.10720 + 17 HZ HA E 16 14 12 1.090 120.000 180.000 0.12970 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 -0.17040 + 19 HE2 HA E 18 16 14 1.090 120.000 180.000 0.14300 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 -0.12560 + 21 HD2 HA E 20 18 16 1.090 120.000 180.000 0.13300 + 22 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 23 O O E 22 6 4 1.229 120.500 0.000 -0.56790 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE2 CD2 HD2 + CD2 CZ CE2 HE2 + CE1 CE2 CZ HZ + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + +DONE +TYROSINE + + TYR INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.00140 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08760 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.01520 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.02950 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.02950 + 11 CG CA S 8 6 4 1.510 109.470 180.000 -0.00110 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 -0.19060 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 0.16990 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 -0.23410 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 0.16560 + 16 CZ C B 14 12 11 1.400 120.000 0.000 0.32260 + 17 OH OH S 16 14 12 1.360 120.000 180.000 -0.55790 + 18 HH HO E 17 16 14 0.960 113.000 0.000 0.39920 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 -0.23410 + 20 HE2 HA E 19 16 14 1.090 120.000 180.000 0.16560 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 -0.19060 + 22 HD2 HA E 21 19 16 1.090 120.000 180.000 0.16990 + 23 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 24 O O E 23 6 4 1.229 120.500 0.000 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0 -1 -2 0.0000 0.0000 0.0000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 + 4 N N M 3 2 1 1.3350 116.6000 180.0000 + 5 HN1 H E 4 3 2 1.0100 119.8000 0.0000 + 6 HN2 H E 4 3 2 1.0100 119.8000 180.0000 + +CHARGE + -0.46300 0.23150 0.23150 + +IMPROPER + -M HN1 N HN2 + +DONE +ASP neutral +ASH + ASH INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03410 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08640 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.03160 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04880 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04880 + 11 CG C B 8 6 4 1.527 109.470 180.000 0.64620 + 12 OD1 O E 11 8 6 1.260 117.200 90.000 -0.55540 + 13 OD2 OH S 11 8 6 1.260 117.200 270.000 -0.63760 + 14 HD2 HO E 13 11 8 0.96 109.5 180.000 0.47470 + 15 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 16 O O E 15 6 4 1.229 120.500 0.000 -0.56790 + +IMPROPER + -M CA N H + CA +M C O + CB OD1 CG OD2 + +DONE +GLU neutral +GLH + GLH INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.01450 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.07790 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00710 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.02560 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.02560 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 -0.01740 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.04300 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.04300 + 14 CD C B 11 8 6 1.527 109.470 180.000 0.68010 + 15 OE1 O E 14 11 8 1.260 117.200 90.000 -0.58380 + 16 OE2 OH S 14 11 8 1.260 117.200 270.000 -0.65110 + 17 HE2 HO E 16 14 11 0.960 109.500 180.000 0.46410 + 18 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 19 O O E 18 6 4 1.229 120.500 0.000 -0.56790 + +IMPROPER + -M CA N H + CA +M C O + CG OE1 CD OE2 + +DONE +Sodium Ion +CIP + CIP INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 NA+ IP M 3 2 1 1.0000 90.0000 180.0000 1.000 + +DONE +Chloride Ion +CIM + CIM INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 CL- IM M 3 2 1 1.0000 90.0000 180.0000 -1.000 + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ALA_ALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ALA_ALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..b5292643c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ALA_ALANINE_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ARG_ARGININE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ARG_ARGININE__COO-_ANION.in_frag new file mode 100644 index 000000000..4134efca3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ARG_ARGININE__COO-_ANION.in_frag @@ -0,0 +1,28 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 H1 E 14 11 8 1.090 109.500 300.000 + 16 HD3 H1 E 14 11 8 1.090 109.500 60.000 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 + 18 HE H E 17 14 11 1.010 118.500 0.000 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 + 21 HH11 H E 20 19 17 1.010 119.800 0.000 + 22 HH12 H E 20 19 17 1.010 119.800 180.000 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 + 24 HH21 H E 23 19 17 1.010 119.800 0.000 + 25 HH22 H E 23 19 17 1.010 119.800 180.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O2 E 26 6 4 1.229 120.500 0.000 + 28 OXT O2 E 26 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ASN_ASPARAGINE____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ASN_ASPARAGINE____COO-_ANION.in_frag new file mode 100644 index 000000000..1103e8f02 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ASN_ASPARAGINE____COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.522 111.100 180.000 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ASP_ASPARTIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ASP_ASPARTIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..38ddae5c9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ASP_ASPARTIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/CYS_CYSTEINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/CYS_CYSTEINE__COO-_ANION.in_frag new file mode 100644 index 000000000..d907f763f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/CYS_CYSTEINE__COO-_ANION.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG SH S 8 6 4 1.810 116.000 180.000 + 12 HG HS E 11 8 6 1.330 96.000 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/CYX_CYSTINE_op_S-S_BRIDGE_cp______COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/CYX_CYSTINE_op_S-S_BRIDGE_cp______COO-_ANION.in_frag new file mode 100644 index 000000000..d6fd2c5d8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/CYX_CYSTINE_op_S-S_BRIDGE_cp______COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG S E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/GLN_GLUTAMINE_____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/GLN_GLUTAMINE_____COO-_ANION.in_frag new file mode 100644 index 000000000..1f32b7005 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/GLN_GLUTAMINE_____COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.522 111.100 180.000 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..6b78296d7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O2 E 17 6 4 1.229 120.500 0.000 + 19 OXT O2 E 17 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/GLY_GLYCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/GLY_GLYCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..7fa518f65 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/GLY_GLYCINE_COO-_ANION.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H1 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H1 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O2 E 9 6 4 1.229 120.500 0.000 + 11 OXT O2 E 9 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag new file mode 100644 index 000000000..0a8d923fd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NB S 14 12 11 1.310 109.000 0.000 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/HIE_HISTIDINE_EPSILON-H___COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/HIE_HISTIDINE_EPSILON-H___COO-_ANION.in_frag new file mode 100644 index 000000000..647057964 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/HIE_HISTIDINE_EPSILON-H___COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NB S 11 8 6 1.390 122.000 180.000 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/HIP_HISTIDINE_PLUS_COO-.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/HIP_HISTIDINE_PLUS_COO-.in_frag new file mode 100644 index 000000000..b803ac3e8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/HIP_HISTIDINE_PLUS_COO-.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O2 E 20 6 4 1.229 120.500 0.000 + 22 OXT O2 E 20 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ILE_ISOLEUCINE____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ILE_ISOLEUCINE____COO-_ANION.in_frag new file mode 100644 index 000000000..d10774a63 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/ILE_ISOLEUCINE____COO-_ANION.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O2 E 21 6 4 1.229 120.500 0.000 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/LEU_LEUCINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/LEU_LEUCINE__COO-_ANION.in_frag new file mode 100644 index 000000000..7ae29ba22 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/LEU_LEUCINE__COO-_ANION.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O2 E 21 6 4 1.229 120.500 0.000 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/LYS_LYSINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/LYS_LYSINE__COO-_ANION.in_frag new file mode 100644 index 000000000..56193dcd0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/LYS_LYSINE__COO-_ANION.in_frag @@ -0,0 +1,26 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 + 21 HZ1 H E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H E 20 17 14 1.010 109.470 180.000 + 23 HZ3 H E 20 17 14 1.010 109.470 300.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O2 E 24 6 4 1.229 120.500 0.000 + 26 OXT O2 E 24 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/MET_METHIONINE____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/MET_METHIONINE____COO-_ANION.in_frag new file mode 100644 index 000000000..e82705dcf --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/MET_METHIONINE____COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 + 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 + 14 SD S S 11 8 6 1.810 110.000 180.000 + 15 CE CT 3 14 11 8 1.780 100.000 180.000 + 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 + 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 + 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/PHE_PHENYLALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/PHE_PHENYLALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..a34ed72b9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/PHE_PHENYLALANINE_COO-_ANION.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 115.000 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HA E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HA E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HA E 20 18 16 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O2 E 22 6 4 1.229 120.500 0.000 + 24 OXT O2 E 22 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/PRO_PROLINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/PRO_PROLINE_COO-_ANION.in_frag new file mode 100644 index 000000000..cfec9fc30 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/PRO_PROLINE_COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 + 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 + 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 + 11 CB CT B 8 5 4 1.510 106.000 338.300 + 12 HB2 HC E 11 8 5 1.090 109.500 256.300 + 13 HB3 HC E 11 8 5 1.090 109.500 136.300 + 14 CA CT M 4 3 2 1.451 120.600 175.200 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 + 16 C C M 14 4 3 1.522 109.500 300.000 + 17 O O2 E 16 14 4 1.229 120.500 0.000 + 18 OXT O2 E 16 14 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/SER_SERINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/SER_SERINE__COO-_ANION.in_frag new file mode 100644 index 000000000..2cb07f019 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/SER_SERINE__COO-_ANION.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 OG OH S 8 6 4 1.430 109.470 180.000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/THR_THREONINE_____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/THR_THREONINE_____COO-_ANION.in_frag new file mode 100644 index 000000000..56655d36f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/THR_THREONINE_____COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB H1 E 8 6 4 1.090 109.500 180.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/TRP_TRYPTOPHAN____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/TRP_TRYPTOPHAN____COO-_ANION.in_frag new file mode 100644 index 000000000..a05813d51 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/TRP_TRYPTOPHAN____COO-_ANION.in_frag @@ -0,0 +1,28 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C* S 8 6 4 1.510 115.000 180.000 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 + 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 + 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 + 20 HH2 HA E 19 17 16 1.090 120.000 180.000 + 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 + 22 HZ3 HA E 21 19 17 1.090 120.000 180.000 + 23 CE3 CA B 21 19 17 1.410 122.000 0.000 + 24 HE3 HA E 23 21 19 1.090 120.000 180.000 + 25 CD2 CB E 23 21 19 1.400 117.000 0.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O2 E 26 6 4 1.229 120.500 0.000 + 28 OXT O2 E 26 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/TYR_TYROSINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/TYR_TYROSINE__COO-_ANION.in_frag new file mode 100644 index 000000000..60094dd3d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/TYR_TYROSINE__COO-_ANION.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 109.470 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 OH OH S 16 14 12 1.360 120.000 180.000 + 18 HH HO E 17 16 14 0.960 113.000 0.000 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 + 20 HE2 HA E 19 16 14 1.090 120.000 180.000 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 + 22 HD2 HA E 21 19 16 1.090 120.000 180.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O2 E 23 6 4 1.229 120.500 0.000 + 25 OXT O2 E 23 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/VAL_VALINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/VAL_VALINE__COO-_ANION.in_frag new file mode 100644 index 000000000..376c9d614 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/VAL_VALINE__COO-_ANION.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG11 HC E 10 8 6 1.090 109.500 60.000 + 12 HG12 HC E 10 8 6 1.090 109.500 180.000 + 13 HG13 HC E 10 8 6 1.090 109.500 300.000 + 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG21 HC E 14 8 6 1.090 109.500 60.000 + 16 HG22 HC E 14 8 6 1.090 109.500 180.000 + 17 HG23 HC E 14 8 6 1.090 109.500 300.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O2 E 18 6 4 1.229 120.500 0.000 + 20 OXT O2 E 18 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/all_aminoct02.in b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/all_aminoct02.in new file mode 100644 index 000000000..98e04f9e5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct02/all_aminoct02.in @@ -0,0 +1,914 @@ + 1 1 201 +db2000.dat +ALANINE COO- ANION + + ALA INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.0679 .0708 -.1226 + .0586 .0586 .0586 .5771 -.7432 + -.7432 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +GLYCINE COO- ANION + + GLY INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H1 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H1 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O2 E 9 6 4 1.229 120.500 0.000 + 11 OXT O2 E 9 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.1509 .1035 .1035 + .5771 -.7432 -.7432 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +SERINE COO- ANION + + SER INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 OG OH S 8 6 4 1.430 109.470 180.000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.0356 .0666 .0748 + .0602 .0602 -.5419 .3718 .5771 + -.7432 -.7432 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +THREONINE COO- ANION + + THR INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB H1 E 8 6 4 1.090 109.500 180.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.0138 .0474 .3514 + -.0608 -.1888 .0451 .0451 .0451 + -.6176 .4030 .5771 -.7432 -.7432 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +LEUCINE COO- ANION + + LEU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O2 E 21 6 4 1.229 120.500 0.000 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.1138 .0776 -.1398 + .0480 .0480 .4179 -.0540 -.4091 + .0984 .0984 .0984 -.4091 .0984 + .0984 .0984 .5771 -.7432 -.7432 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +ISOLEUCINE COO- ANION + + ILE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O2 E 21 6 4 1.229 120.500 0.000 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.1622 .1028 .1296 + .0207 -.3021 .0825 .0825 .0825 + -.0335 .0289 .0289 -.0993 .0316 + .0316 .0316 .5771 -.7432 -.7432 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +VALINE COO- ANION + + VAL INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG11 HC E 10 8 6 1.090 109.500 60.000 + 12 HG12 HC E 10 8 6 1.090 109.500 180.000 + 13 HG13 HC E 10 8 6 1.090 109.500 300.000 + 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG21 HC E 14 8 6 1.090 109.500 60.000 + 16 HG22 HC E 14 8 6 1.090 109.500 180.000 + 17 HG23 HC E 14 8 6 1.090 109.500 300.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O2 E 18 6 4 1.229 120.500 0.000 + 20 OXT O2 E 18 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.1531 .0920 .2896 + .0114 -.2902 .0661 .0661 .0661 + -.2902 .0661 .0661 .0661 .5771 + -.7432 -.7432 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +ASPARAGINE COO- ANION + + ASN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.522 111.100 180.000 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.0510 .0810 -.2184 + .1005 .1005 .6838 -.5751 -.7870 + .3609 .3609 .5771 -.7432 -.7432 + +IMPROPER + -M CA N H + CA OXT C O + CB ND2 CG OD1 + CG HD21 ND2 HD22 + +DONE +GLUTAMINE COO- ANION + + GLN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.522 111.100 180.000 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.1222 .0719 .1006 + .0150 .0150 -.2290 .0974 .0974 + .6952 -.6169 -.7851 .3584 .3584 + .5771 -.7432 -.7432 + +IMPROPER + -M CA N H + CA OXT C O + CG NE2 CD OE1 + CD HE21 NE2 HE22 + +DONE +ARGININE COO- ANION + + ARG INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 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13 12 1.010 125.000 180.000 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.0781 .0620 -.0421 + .0604 .0604 .2452 -.5753 .2480 + .0646 -.2343 .2949 -.1936 .1440 + .5771 -.7432 -.7432 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA OXT C O + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +HISTIDINE PLUS COO- + + HIP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O2 E 20 6 4 1.229 120.500 0.000 + 22 OXT O2 E 20 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 .0642 .0453 -.0055 + .0556 .0556 .0948 -.0077 .2872 + -.0740 .2133 -.0432 .3192 -.1224 + .1737 .5771 -.7432 -.7432 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA OXT C O + CG CE1 ND1 HD1 + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +TRYPTOPHAN COO- ANION + + TRP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C* S 8 6 4 1.510 115.000 180.000 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 + 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 + 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 + 20 HH2 HA E 19 17 16 1.090 120.000 180.000 + 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 + 22 HZ3 HA E 21 19 17 1.090 120.000 180.000 + 23 CE3 CA B 21 19 17 1.410 122.000 0.000 + 24 HE3 HA E 23 21 19 1.090 120.000 180.000 + 25 CD2 CB E 23 21 19 1.400 117.000 0.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O2 E 26 6 4 1.229 120.500 0.000 + 28 OXT O2 E 26 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.0713 .0650 -.0149 + .0382 .0382 -.0994 -.0762 .1446 + -.3641 .3426 .1748 -.2311 .1389 + -.1112 .1077 -.1479 .1083 -.2173 + .1556 .0756 .5771 -.7432 -.7432 + +LOOP + CG CD2 + CE2 CD2 + +IMPROPER + -M CA N H + CA OXT C O + CD1 CE2 NE1 HE1 + CE2 CH2 CZ2 HZ2 + CZ2 CZ3 CH2 HH2 + CH2 CE3 CZ3 HZ3 + CZ3 CD2 CE3 HE3 + CG NE1 CD1 HD1 + CD1 CD2 CG CB + +DONE +PHENYLALANINE COO- ANION + + PHE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 115.000 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HA E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HA E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HA E 20 18 16 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O2 E 22 6 4 1.229 120.500 0.000 + 24 OXT O2 E 22 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.0537 .0467 -.0065 + .0340 .0340 .0283 -.1057 .1142 + -.1484 .1146 -.0750 .0989 -.1484 + .1146 -.1057 .1142 .5771 -.7432 + -.7432 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA OXT C O + CG CE2 CD2 HD2 + CD2 CZ CE2 HE2 + CE1 CE2 CZ HZ + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + +DONE +TYROSINE COO- ANION + + TYR INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 109.470 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 OH OH S 16 14 12 1.360 120.000 180.000 + 18 HH HO E 17 16 14 0.960 113.000 0.000 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 + 20 HE2 HA E 19 16 14 1.090 120.000 180.000 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 + 22 HD2 HA E 21 19 16 1.090 120.000 180.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O2 E 23 6 4 1.229 120.500 0.000 + 25 OXT O2 E 23 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.1028 .0905 -.0020 + .0396 .0396 -.0002 -.1421 .1194 + -.1849 .1358 .2534 -.4768 .3584 + -.1849 .1358 -.1421 .1194 .5771 + -.7432 -.7432 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA OXT C O + CG CE2 CD2 HD2 + CD2 CZ CE2 HE2 + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + CE1 CE2 CZ OH + +DONE +GLUTAMIC ACID COO- ANION + + GLU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O2 E 17 6 4 1.229 120.500 0.000 + 19 OXT O2 E 17 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.3065 .1254 .2282 + -.0351 -.0351 -.2150 .0452 .0452 + .6896 -.7429 -.7429 .5771 -.7432 + -.7432 + +IMPROPER + -M CA N H + CA OXT C O + CG OE1 CD OE2 + +DONE +ASPARTIC ACID COO- ANION + + ASP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.2422 .0934 -.0234 + -.0104 -.0104 .7633 -.7571 -.7571 + .5771 -.7432 -.7432 + +IMPROPER + -M CA N H + CA OXT C O + CB OD1 CG OD2 + +DONE +LYSINE COO- ANION + + LYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 + 21 HZ1 H E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H E 20 17 14 1.010 109.470 180.000 + 23 HZ3 H E 20 17 14 1.010 109.470 300.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O2 E 24 6 4 1.229 120.500 0.000 + 26 OXT O2 E 24 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.0882 .0952 -.0277 + .0293 .0293 -.0134 .0387 .0387 + -.0359 .0539 .0539 .1420 .0461 + .0461 -.2099 .2860 .2860 .2860 + .5771 -.7432 -.7432 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +PROLINE COO- ANION + + PRO INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 + 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 + 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 + 11 CB CT B 8 5 4 1.510 106.000 338.300 + 12 HB2 HC E 11 8 5 1.090 109.500 256.300 + 13 HB3 HC E 11 8 5 1.090 109.500 136.300 + 14 CA CT M 4 3 2 1.451 120.600 175.200 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 + 16 C C M 14 4 3 1.522 109.500 300.000 + 17 O O2 E 16 14 4 1.229 120.500 0.000 + 18 OXT O2 E 16 14 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.2667 .0740 .0258 .0258 .0572 + .0068 .0068 .0439 .0233 .0233 + -.2160 .1051 .5771 -.7432 -.7432 + +LOOP + CA CB + +IMPROPER + CA OXT C O + -M CD N CA + +DONE +CYSTEINE COO- ANION + + CYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG SH S 8 6 4 1.810 116.000 180.000 + 12 HG HS E 11 8 6 1.330 96.000 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.0189 .0637 -.0436 + .0709 .0709 -.2446 .1577 .5771 + -.7432 -.7432 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +CYSTINE(S-S BRIDGE) COO- ANION + + CYX INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG S E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.0534 .0794 -.0239 + .0723 .0723 -.0906 .5771 -.7432 + -.7432 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +METHIONINE COO- ANION + + MET INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 + 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 + 14 SD S S 11 8 6 1.810 110.000 180.000 + 15 CE CT 3 14 11 8 1.780 100.000 180.000 + 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 + 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 + 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 + +CHARGE cc-pvtz esp iterated + -.4420 .2952 -.0798 .0614 .0585 + .0042 .0042 -.0227 .0723 .0723 + -.2367 -.0483 .0569 .0569 .0569 + .5771 -.7432 -.7432 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CALA_ALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CALA_ALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..b5292643c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CALA_ALANINE_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CARG_ARGININE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CARG_ARGININE_COO-_ANION.in_frag new file mode 100644 index 000000000..4134efca3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CARG_ARGININE_COO-_ANION.in_frag @@ -0,0 +1,28 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 H1 E 14 11 8 1.090 109.500 300.000 + 16 HD3 H1 E 14 11 8 1.090 109.500 60.000 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 + 18 HE H E 17 14 11 1.010 118.500 0.000 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 + 21 HH11 H E 20 19 17 1.010 119.800 0.000 + 22 HH12 H E 20 19 17 1.010 119.800 180.000 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 + 24 HH21 H E 23 19 17 1.010 119.800 0.000 + 25 HH22 H E 23 19 17 1.010 119.800 180.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O2 E 26 6 4 1.229 120.500 0.000 + 28 OXT O2 E 26 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CASN_ASPARAGINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CASN_ASPARAGINE_COO-_ANION.in_frag new file mode 100644 index 000000000..1103e8f02 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CASN_ASPARAGINE_COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.522 111.100 180.000 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CASP_ASPARTIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CASP_ASPARTIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..38ddae5c9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CASP_ASPARTIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CCYS_CYSTEINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CCYS_CYSTEINE_COO-_ANION.in_frag new file mode 100644 index 000000000..991d40565 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CCYS_CYSTEINE_COO-_ANION.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG SH S 8 6 4 1.810 116.000 180.000 + 12 HG HS E 11 8 6 1.330 96.000 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 15 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CGLN_GLUTAMINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CGLN_GLUTAMINE_COO-_ANION.in_frag new file mode 100644 index 000000000..1f32b7005 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CGLN_GLUTAMINE_COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.522 111.100 180.000 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CGLU_GLUTAMIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CGLU_GLUTAMIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..6b78296d7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CGLU_GLUTAMIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O2 E 17 6 4 1.229 120.500 0.000 + 19 OXT O2 E 17 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CGLY_GLYCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CGLY_GLYCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..7fa518f65 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CGLY_GLYCINE_COO-_ANION.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H1 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H1 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O2 E 9 6 4 1.229 120.500 0.000 + 11 OXT O2 E 9 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CHID_HISTIDINE_DELTAH_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CHID_HISTIDINE_DELTAH_COO-_ANION.in_frag new file mode 100644 index 000000000..0a8d923fd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CHID_HISTIDINE_DELTAH_COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NB S 14 12 11 1.310 109.000 0.000 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CHIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CHIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag new file mode 100644 index 000000000..647057964 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CHIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NB S 11 8 6 1.390 122.000 180.000 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CHIP_HISTIDINE_PLUS_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CHIP_HISTIDINE_PLUS_COO-_ANION.in_frag new file mode 100644 index 000000000..b803ac3e8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CHIP_HISTIDINE_PLUS_COO-_ANION.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O2 E 20 6 4 1.229 120.500 0.000 + 22 OXT O2 E 20 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CILE_ISOLEUCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CILE_ISOLEUCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..d10774a63 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CILE_ISOLEUCINE_COO-_ANION.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O2 E 21 6 4 1.229 120.500 0.000 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CLEU_LEUCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CLEU_LEUCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..7ae29ba22 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CLEU_LEUCINE_COO-_ANION.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O2 E 21 6 4 1.229 120.500 0.000 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CLYS_LYSINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CLYS_LYSINE_COO-_ANION.in_frag new file mode 100644 index 000000000..56193dcd0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CLYS_LYSINE_COO-_ANION.in_frag @@ -0,0 +1,26 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 + 21 HZ1 H E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H E 20 17 14 1.010 109.470 180.000 + 23 HZ3 H E 20 17 14 1.010 109.470 300.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O2 E 24 6 4 1.229 120.500 0.000 + 26 OXT O2 E 24 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CMET_METHIONINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CMET_METHIONINE_COO-_ANION.in_frag new file mode 100644 index 000000000..9c911a130 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CMET_METHIONINE_COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 + 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 + 14 SD S S 11 8 6 1.810 110.000 180.000 + 15 CE CT 3 14 11 8 1.780 100.000 180.000 + 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 + 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 + 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 21 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CPHE_PHENYLALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CPHE_PHENYLALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..a34ed72b9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CPHE_PHENYLALANINE_COO-_ANION.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 115.000 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HA E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HA E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HA E 20 18 16 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O2 E 22 6 4 1.229 120.500 0.000 + 24 OXT O2 E 22 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CPRO_PROLINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CPRO_PROLINE_COO-_ANION.in_frag new file mode 100644 index 000000000..cfec9fc30 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CPRO_PROLINE_COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 + 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 + 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 + 11 CB CT B 8 5 4 1.510 106.000 338.300 + 12 HB2 HC E 11 8 5 1.090 109.500 256.300 + 13 HB3 HC E 11 8 5 1.090 109.500 136.300 + 14 CA CT M 4 3 2 1.451 120.600 175.200 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 + 16 C C M 14 4 3 1.522 109.500 300.000 + 17 O O2 E 16 14 4 1.229 120.500 0.000 + 18 OXT O2 E 16 14 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CSER_SERINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CSER_SERINE_COO-_ANION.in_frag new file mode 100644 index 000000000..2cb07f019 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CSER_SERINE_COO-_ANION.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 OG OH S 8 6 4 1.430 109.470 180.000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CTHR_THREONINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CTHR_THREONINE_COO-_ANION.in_frag new file mode 100644 index 000000000..56655d36f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CTHR_THREONINE_COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB H1 E 8 6 4 1.090 109.500 180.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CTRP_TRYPTOPHAN_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CTRP_TRYPTOPHAN_COO-_ANION.in_frag new file mode 100644 index 000000000..a05813d51 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CTRP_TRYPTOPHAN_COO-_ANION.in_frag @@ -0,0 +1,28 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C* S 8 6 4 1.510 115.000 180.000 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 + 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 + 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 + 20 HH2 HA E 19 17 16 1.090 120.000 180.000 + 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 + 22 HZ3 HA E 21 19 17 1.090 120.000 180.000 + 23 CE3 CA B 21 19 17 1.410 122.000 0.000 + 24 HE3 HA E 23 21 19 1.090 120.000 180.000 + 25 CD2 CB E 23 21 19 1.400 117.000 0.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O2 E 26 6 4 1.229 120.500 0.000 + 28 OXT O2 E 26 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CTYR_TYROSINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CTYR_TYROSINE_COO-_ANION.in_frag new file mode 100644 index 000000000..aff285a28 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CTYR_TYROSINE_COO-_ANION.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 109.470 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ C B 14 12 11 1.400 120.000 0.000 + 17 OH OH S 16 14 12 1.360 120.000 180.000 + 18 HH HO E 17 16 14 0.960 113.000 0.000 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 + 20 HE2 HA E 19 16 14 1.090 120.000 180.000 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 + 22 HD2 HA E 21 19 16 1.090 120.000 180.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O2 E 23 6 4 1.229 120.500 0.000 + 25 OXT O2 E 23 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CVAL_VALINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CVAL_VALINE_COO-_ANION.in_frag new file mode 100644 index 000000000..376c9d614 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/CVAL_VALINE_COO-_ANION.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG11 HC E 10 8 6 1.090 109.500 60.000 + 12 HG12 HC E 10 8 6 1.090 109.500 180.000 + 13 HG13 HC E 10 8 6 1.090 109.500 300.000 + 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG21 HC E 14 8 6 1.090 109.500 60.000 + 16 HG22 HC E 14 8 6 1.090 109.500 180.000 + 17 HG23 HC E 14 8 6 1.090 109.500 300.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O2 E 18 6 4 1.229 120.500 0.000 + 20 OXT O2 E 18 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/all_aminoct03.in b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/all_aminoct03.in new file mode 100644 index 000000000..d4260b1ac --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct03/all_aminoct03.in @@ -0,0 +1,733 @@ + 1 1 2 +db94.dat +ALANINE COO- ANION + +CALA INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.622202 + 5 H H E 4 3 2 1.010 119.800 0.000 0.359784 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.054102 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.123283 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.185718 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 0.069652 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 0.069652 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 0.069652 + 12 C C M 6 4 3 1.522 111.100 180.000 0.664014 + 13 O O2 E 12 6 4 1.229 120.500 0.000 -0.747007 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 -0.747007 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +GLYCINE COO- ANION + +CGLY INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.523362 + 5 H H E 4 3 2 1.010 119.800 0.000 0.349622 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.316659 + 7 HA2 H1 E 6 4 3 1.090 109.500 300.000 0.160200 + 8 HA3 H1 E 6 4 3 1.090 109.500 60.000 0.160200 + 9 C C M 6 4 3 1.522 110.400 180.000 0.661797 + 10 O O2 E 9 6 4 1.229 120.500 0.000 -0.745899 + 11 OXT O2 E 9 6 4 1.229 120.500 180.000 -0.745899 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +SERINE COO- ANION + +CSER INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM 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1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.675628 + 5 H H E 4 3 2 1.010 119.800 0.000 0.350448 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.012728 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.146871 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.058078 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.016619 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.016619 + 11 CG CA S 8 6 4 1.510 109.470 180.000 0.133018 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 -0.194675 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 0.149917 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 -0.218820 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 0.148692 + 16 CZ C B 14 12 11 1.400 120.000 0.000 0.247734 + 17 OH OH S 16 14 12 1.360 120.000 180.000 -0.475120 + 18 HH HO E 17 16 14 0.960 113.000 0.000 0.370016 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 -0.218820 + 20 HE2 HA E 19 16 14 1.090 120.000 180.000 0.148692 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 -0.194675 + 22 HD2 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180.000 0.757964 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 -0.792463 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 -0.792463 + 17 C C M 6 4 3 1.522 111.100 180.000 0.731186 + 18 O O2 E 17 6 4 1.229 120.500 0.000 -0.780593 + 19 OXT O2 E 17 6 4 1.229 120.500 180.000 -0.780593 + +IMPROPER + -M CA N H + CA OXT C O + CG OE1 CD OE2 + +DONE +ASPARTIC ACID COO- ANION + +CASP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.649462 + 5 H H E 4 3 2 1.010 119.800 0.000 0.426853 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.306286 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.183181 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.078986 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.018648 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.018648 + 11 CG C B 8 6 4 1.527 109.470 180.000 0.844830 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 -0.813714 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 -0.813714 + 14 C C M 6 4 3 1.522 111.100 180.000 0.732350 + 15 O O2 E 14 6 4 1.229 120.500 0.000 -0.781175 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 -0.781175 + +IMPROPER + -M CA N H + CA OXT C O + CB OD1 CG OD2 + +DONE +LYSINE COO- ANION + +CLYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.629569 + 5 H H E 4 3 2 1.010 119.800 0.000 0.357460 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.053541 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.138544 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.046022 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.042912 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.042912 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.020231 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.010971 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.010971 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 -0.046165 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 0.061437 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 0.061437 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 -0.032772 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 0.101654 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 0.101654 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 -0.168623 + 21 HZ1 H E 20 17 14 1.010 109.470 60.000 0.285503 + 22 HZ2 H E 20 17 14 1.010 109.470 180.000 0.285503 + 23 HZ3 H E 20 17 14 1.010 109.470 300.000 0.285503 + 24 C C M 6 4 3 1.522 111.100 180.000 0.541818 + 25 O O2 E 24 6 4 1.229 120.500 0.000 -0.685909 + 26 OXT O2 E 24 6 4 1.229 120.500 180.000 -0.685909 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +PROLINE COO- ANION + +CPRO INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.337 117.000 180.000 -0.268742 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 0.062285 + 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 0.034717 + 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 0.034717 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 0.059879 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 0.007548 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 0.007548 + 11 CB CT B 8 5 4 1.510 106.000 338.300 0.065773 + 12 HB2 HC E 11 8 5 1.090 109.500 256.300 0.016889 + 13 HB3 HC E 11 8 5 1.090 109.500 136.300 0.016889 + 14 CA CT M 4 3 2 1.451 120.600 175.200 -0.385442 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 0.177938 + 16 C C M 14 4 3 1.522 109.500 300.000 0.643321 + 17 O O2 E 16 14 4 1.229 120.500 0.000 -0.736661 + 18 OXT O2 E 16 14 4 1.229 120.500 180.000 -0.736661 + +LOOP + CA CB + +IMPROPER + CA OXT C O + -M CA N CD + +DONE +CYSTEINE COO- ANION + +CCYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.555037 + 5 H H E 4 3 2 1.010 119.800 0.000 0.345483 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.110929 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.147206 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.162428 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.131999 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.131999 + 11 SG SH S 8 6 4 1.810 116.000 180.000 -0.290711 + 12 HG HS E 11 8 6 1.330 96.000 180.000 0.192419 + 13 C C M 6 4 3 1.522 111.100 180.000 0.671942 + 14 O O2 E 13 6 4 1.229 120.500 0.000 -0.750971 + 15 OXT O2 E 15 6 4 1.229 120.500 180.000 -0.750971 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +METHIONINE COO- ANION + +CMET INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.564246 + 5 H H E 4 3 2 1.010 119.800 0.000 0.334412 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.159882 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.142833 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.058364 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.052479 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.052479 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 -0.230352 + 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 0.127983 + 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 0.127983 + 14 SD S S 11 8 6 1.810 110.000 180.000 -0.218570 + 15 CE CT 3 14 11 8 1.780 100.000 180.000 -0.262571 + 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 0.123031 + 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 0.123031 + 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 0.123031 + 19 C C M 6 4 3 1.522 111.100 180.000 0.664918 + 20 O O2 E 19 6 4 1.229 120.500 0.000 -0.747459 + 21 OXT O2 E 21 6 4 1.229 120.500 180.000 -0.747459 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ALA_ALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ALA_ALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..b5292643c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ALA_ALANINE_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ARG_ARGININE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ARG_ARGININE__COO-_ANION.in_frag new file mode 100644 index 000000000..4134efca3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ARG_ARGININE__COO-_ANION.in_frag @@ -0,0 +1,28 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 H1 E 14 11 8 1.090 109.500 300.000 + 16 HD3 H1 E 14 11 8 1.090 109.500 60.000 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 + 18 HE H E 17 14 11 1.010 118.500 0.000 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 + 21 HH11 H E 20 19 17 1.010 119.800 0.000 + 22 HH12 H E 20 19 17 1.010 119.800 180.000 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 + 24 HH21 H E 23 19 17 1.010 119.800 0.000 + 25 HH22 H E 23 19 17 1.010 119.800 180.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O2 E 26 6 4 1.229 120.500 0.000 + 28 OXT O2 E 26 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ASN_ASPARAGINE____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ASN_ASPARAGINE____COO-_ANION.in_frag new file mode 100644 index 000000000..1103e8f02 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ASN_ASPARAGINE____COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.522 111.100 180.000 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ASP_ASPARTIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ASP_ASPARTIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..38ddae5c9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ASP_ASPARTIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/CYS_CYSTEINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/CYS_CYSTEINE__COO-_ANION.in_frag new file mode 100644 index 000000000..d907f763f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/CYS_CYSTEINE__COO-_ANION.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG SH S 8 6 4 1.810 116.000 180.000 + 12 HG HS E 11 8 6 1.330 96.000 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/CYX_CYSTINE_op_S-S_BRIDGE_cp______COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/CYX_CYSTINE_op_S-S_BRIDGE_cp______COO-_ANION.in_frag new file mode 100644 index 000000000..d6fd2c5d8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/CYX_CYSTINE_op_S-S_BRIDGE_cp______COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 SG S E 8 6 4 1.810 116.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/GLN_GLUTAMINE_____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/GLN_GLUTAMINE_____COO-_ANION.in_frag new file mode 100644 index 000000000..1f32b7005 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/GLN_GLUTAMINE_____COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.522 111.100 180.000 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..6b78296d7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O2 E 17 6 4 1.229 120.500 0.000 + 19 OXT O2 E 17 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/GLY_GLYCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/GLY_GLYCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..7fa518f65 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/GLY_GLYCINE_COO-_ANION.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H1 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H1 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O2 E 9 6 4 1.229 120.500 0.000 + 11 OXT O2 E 9 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag new file mode 100644 index 000000000..0a8d923fd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NB S 14 12 11 1.310 109.000 0.000 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/HIE_HISTIDINE_EPSILON-H___COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/HIE_HISTIDINE_EPSILON-H___COO-_ANION.in_frag new file mode 100644 index 000000000..647057964 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/HIE_HISTIDINE_EPSILON-H___COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NB S 11 8 6 1.390 122.000 180.000 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/HIP_HISTIDINE_PLUS_COO-.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/HIP_HISTIDINE_PLUS_COO-.in_frag new file mode 100644 index 000000000..b803ac3e8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/HIP_HISTIDINE_PLUS_COO-.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O2 E 20 6 4 1.229 120.500 0.000 + 22 OXT O2 E 20 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ILE_ISOLEUCINE____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ILE_ISOLEUCINE____COO-_ANION.in_frag new file mode 100644 index 000000000..d10774a63 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/ILE_ISOLEUCINE____COO-_ANION.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O2 E 21 6 4 1.229 120.500 0.000 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/LEU_LEUCINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/LEU_LEUCINE__COO-_ANION.in_frag new file mode 100644 index 000000000..7ae29ba22 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/LEU_LEUCINE__COO-_ANION.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O2 E 21 6 4 1.229 120.500 0.000 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/LYS_LYSINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/LYS_LYSINE__COO-_ANION.in_frag new file mode 100644 index 000000000..56193dcd0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/LYS_LYSINE__COO-_ANION.in_frag @@ -0,0 +1,26 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 + 21 HZ1 H E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H E 20 17 14 1.010 109.470 180.000 + 23 HZ3 H E 20 17 14 1.010 109.470 300.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O2 E 24 6 4 1.229 120.500 0.000 + 26 OXT O2 E 24 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/MET_METHIONINE____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/MET_METHIONINE____COO-_ANION.in_frag new file mode 100644 index 000000000..e82705dcf --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/MET_METHIONINE____COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 + 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 + 14 SD S S 11 8 6 1.810 110.000 180.000 + 15 CE CT 3 14 11 8 1.780 100.000 180.000 + 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 + 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 + 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/PHE_PHENYLALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/PHE_PHENYLALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..a34ed72b9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/PHE_PHENYLALANINE_COO-_ANION.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 115.000 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HA E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HA E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HA E 20 18 16 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O2 E 22 6 4 1.229 120.500 0.000 + 24 OXT O2 E 22 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/PRO_PROLINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/PRO_PROLINE_COO-_ANION.in_frag new file mode 100644 index 000000000..cfec9fc30 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/PRO_PROLINE_COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 + 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 + 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 + 11 CB CT B 8 5 4 1.510 106.000 338.300 + 12 HB2 HC E 11 8 5 1.090 109.500 256.300 + 13 HB3 HC E 11 8 5 1.090 109.500 136.300 + 14 CA CT M 4 3 2 1.451 120.600 175.200 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 + 16 C C M 14 4 3 1.522 109.500 300.000 + 17 O O2 E 16 14 4 1.229 120.500 0.000 + 18 OXT O2 E 16 14 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/SER_SERINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/SER_SERINE__COO-_ANION.in_frag new file mode 100644 index 000000000..2cb07f019 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/SER_SERINE__COO-_ANION.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 + 11 OG OH S 8 6 4 1.430 109.470 180.000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/THR_THREONINE_____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/THR_THREONINE_____COO-_ANION.in_frag new file mode 100644 index 000000000..56655d36f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/THR_THREONINE_____COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB H1 E 8 6 4 1.090 109.500 180.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/TRP_TRYPTOPHAN____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/TRP_TRYPTOPHAN____COO-_ANION.in_frag new file mode 100644 index 000000000..a05813d51 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/TRP_TRYPTOPHAN____COO-_ANION.in_frag @@ -0,0 +1,28 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C* S 8 6 4 1.510 115.000 180.000 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 + 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 + 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 + 20 HH2 HA E 19 17 16 1.090 120.000 180.000 + 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 + 22 HZ3 HA E 21 19 17 1.090 120.000 180.000 + 23 CE3 CA B 21 19 17 1.410 122.000 0.000 + 24 HE3 HA E 23 21 19 1.090 120.000 180.000 + 25 CD2 CB E 23 21 19 1.400 117.000 0.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O2 E 26 6 4 1.229 120.500 0.000 + 28 OXT O2 E 26 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/TYR_TYROSINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/TYR_TYROSINE__COO-_ANION.in_frag new file mode 100644 index 000000000..aff285a28 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/TYR_TYROSINE__COO-_ANION.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 109.470 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HA E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ C B 14 12 11 1.400 120.000 0.000 + 17 OH OH S 16 14 12 1.360 120.000 180.000 + 18 HH HO E 17 16 14 0.960 113.000 0.000 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 + 20 HE2 HA E 19 16 14 1.090 120.000 180.000 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 + 22 HD2 HA E 21 19 16 1.090 120.000 180.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O2 E 23 6 4 1.229 120.500 0.000 + 25 OXT O2 E 23 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/VAL_VALINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/VAL_VALINE__COO-_ANION.in_frag new file mode 100644 index 000000000..376c9d614 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/VAL_VALINE__COO-_ANION.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG11 HC E 10 8 6 1.090 109.500 60.000 + 12 HG12 HC E 10 8 6 1.090 109.500 180.000 + 13 HG13 HC E 10 8 6 1.090 109.500 300.000 + 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG21 HC E 14 8 6 1.090 109.500 60.000 + 16 HG22 HC E 14 8 6 1.090 109.500 180.000 + 17 HG23 HC E 14 8 6 1.090 109.500 300.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O2 E 18 6 4 1.229 120.500 0.000 + 20 OXT O2 E 18 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/all_aminoct94.in b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/all_aminoct94.in new file mode 100644 index 000000000..b1565bcd2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminoct94/all_aminoct94.in @@ -0,0 +1,781 @@ + 1 1 201 +db94.dat +ALANINE COO- ANION + + ALA INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 + 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.17470 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.10670 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.20930 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 0.07640 + 10 HB2 HC E 8 6 4 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120.000 180.000 0.16730 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 -0.19220 + 22 HD2 HA E 21 19 16 1.090 120.000 180.000 0.17800 + 23 C C M 6 4 3 1.522 111.100 180.000 0.78170 + 24 O O2 E 23 6 4 1.229 120.500 0.000 -0.80700 + 25 OXT O2 E 23 6 4 1.229 120.500 180.000 -0.80700 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA OXT C O + CG CE2 CD2 HD2 + CD2 CZ CE2 HE2 + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + CE1 CE2 CZ OH + +DONE +GLUTAMIC ACID COO- ANION + + GLU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.51920 + 5 H H E 4 3 2 1.010 119.800 0.000 0.30550 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.20590 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13990 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.00710 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 -0.00780 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 -0.00780 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 0.06750 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 -0.05480 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 -0.05480 + 14 CD C B 11 8 6 1.527 109.470 180.000 0.81830 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 -0.82200 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 -0.82200 + 17 C C M 6 4 3 1.522 111.100 180.000 0.74200 + 18 O O2 E 17 6 4 1.229 120.500 0.000 -0.79300 + 19 OXT O2 E 17 6 4 1.229 120.500 180.000 -0.79300 + +IMPROPER + -M CA N H + CA OXT C O + CG OE1 CD OE2 + +DONE +ASPARTIC ACID COO- ANION + + ASP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.51920 + 5 H H E 4 3 2 1.010 119.800 0.000 0.30550 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.18170 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.10460 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.06770 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 -0.02120 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 -0.02120 + 11 CG C B 8 6 4 1.527 109.470 180.000 0.88510 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 -0.81620 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 -0.81620 + 14 C C M 6 4 3 1.522 111.100 180.000 0.72560 + 15 O O2 E 14 6 4 1.229 120.500 0.000 -0.78870 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 -0.78870 + +IMPROPER + -M CA N H + CA OXT C O + CB OD1 CG OD2 + +DONE +LYSINE COO- ANION + + LYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.34810 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27640 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.29030 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.14380 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.05380 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04820 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04820 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.02270 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.01340 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.01340 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 -0.03920 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 0.06110 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 0.06110 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 -0.01760 + 18 HE2 HP E 17 14 11 1.090 109.500 300.000 0.11210 + 19 HE3 HP E 17 14 11 1.090 109.500 60.000 0.11210 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 -0.37410 + 21 HZ1 H E 20 17 14 1.010 109.470 60.000 0.33740 + 22 HZ2 H E 20 17 14 1.010 109.470 180.000 0.33740 + 23 HZ3 H E 20 17 14 1.010 109.470 300.000 0.33740 + 24 C C M 6 4 3 1.522 111.100 180.000 0.84880 + 25 O O2 E 24 6 4 1.229 120.500 0.000 -0.82520 + 26 OXT O2 E 24 6 4 1.229 120.500 180.000 -0.82520 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +PROLINE COO- ANION + + PRO INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.337 117.000 180.000 -0.28020 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 0.04340 + 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 0.03310 + 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 0.03310 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 0.04660 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 0.01720 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 0.01720 + 11 CB CT B 8 5 4 1.510 106.000 338.300 -0.05430 + 12 HB2 HC E 11 8 5 1.090 109.500 256.300 0.03810 + 13 HB3 HC E 11 8 5 1.090 109.500 136.300 0.03810 + 14 CA CT M 4 3 2 1.451 120.600 175.200 -0.13360 + 15 HA H1 E 14 4 3 1.090 109.500 60.000 0.07760 + 16 C C M 14 4 3 1.522 109.500 300.000 0.66310 + 17 O O2 E 16 14 4 1.229 120.500 0.000 -0.76970 + 18 OXT O2 E 16 14 4 1.229 120.500 180.000 -0.76970 + +LOOP + CA CB + +IMPROPER + CA OXT C O + -M CD N CA + +DONE +CYSTEINE COO- ANION + + CYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 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-0.13180 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.09380 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.19430 + 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.12280 + 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.12280 + 11 SG S E 8 6 4 1.810 116.000 180.000 -0.05290 + 12 C C M 6 4 3 1.522 111.100 180.000 0.76180 + 13 O O2 E 12 6 4 1.229 120.500 0.000 -0.80410 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 -0.80410 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +METHIONINE COO- ANION + + MET INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 + 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.25970 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.12770 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.02360 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04800 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04800 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.04920 + 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 0.03170 + 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 0.03170 + 14 SD S S 11 8 6 1.810 110.000 180.000 -0.26920 + 15 CE CT 3 14 11 8 1.780 100.000 180.000 -0.03760 + 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 0.06250 + 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 0.06250 + 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 0.06250 + 19 C C M 6 4 3 1.522 111.100 180.000 0.80130 + 20 O O2 E 19 6 4 1.229 120.500 0.000 -0.81050 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 -0.81050 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ALA_ALANINE.in_frag new file mode 100644 index 000000000..c2df8a4e2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ALA_ALANINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB1 HC E 10 8 4 1.090 109.500 60.000 + 12 HB2 HC E 10 8 4 1.090 109.500 180.000 + 13 HB3 HC E 10 8 4 1.090 109.500 300.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ARG_ARGININE.in_frag new file mode 100644 index 000000000..490046579 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ARG_ARGININE.in_frag @@ -0,0 +1,29 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD CT 3 13 10 8 1.525 109.470 180.000 + 17 HD2 H1 E 16 13 10 1.090 109.500 300.000 + 18 HD3 H1 E 16 13 10 1.090 109.500 60.000 + 19 NE N2 B 16 13 10 1.480 111.000 180.000 + 20 HE H E 19 16 13 1.010 118.500 0.000 + 21 CZ CA B 19 16 13 1.330 123.000 180.000 + 22 NH1 N2 B 21 19 16 1.330 122.000 0.000 + 23 HH11 H E 22 21 19 1.010 119.800 0.000 + 24 HH12 H E 22 21 19 1.010 119.800 180.000 + 25 NH2 N2 B 21 19 16 1.330 118.000 180.000 + 26 HH21 H E 25 21 19 1.010 119.800 0.000 + 27 HH22 H E 25 21 19 1.010 119.800 180.000 + 28 C C M 8 4 3 1.522 111.100 180.000 + 29 O O E 28 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..75ebc4da3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ASN_ASPARAGINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C B 10 8 4 1.522 111.100 180.000 + 14 OD1 O E 13 10 8 1.229 120.500 0.000 + 15 ND2 N B 13 10 8 1.335 116.600 180.000 + 16 HD21 H E 15 13 10 1.010 119.800 180.000 + 17 HD22 H E 15 13 10 1.010 119.800 0.000 + 18 C C M 8 4 3 1.522 111.100 180.000 + 19 O O E 18 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..de3b9439a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C B 10 8 4 1.527 109.470 180.000 + 14 OD1 O2 E 13 10 8 1.260 117.200 90.000 + 15 OD2 O2 E 13 10 8 1.260 117.200 270.000 + 16 C C M 8 4 3 1.522 111.100 180.000 + 17 O O E 16 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..55155fafc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/CYS_CYSTEINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 + 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 + 13 SG SH S 10 8 4 1.810 116.000 180.000 + 14 HG HS E 13 10 8 1.330 96.000 180.000 + 15 C C M 8 4 3 1.522 111.100 180.000 + 16 O O E 15 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..1b251dd8f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 + 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 + 13 SG S E 10 8 4 1.810 116.000 180.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..772f8ad16 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/GLN_GLUTAMINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD C B 13 10 8 1.522 111.100 180.000 + 17 OE1 O E 16 13 10 1.229 120.500 0.000 + 18 NE2 N B 16 13 10 1.335 116.600 180.000 + 19 HE21 H E 18 16 13 1.010 119.800 180.000 + 20 HE22 H E 18 16 13 1.010 119.800 0.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..5c0db2845 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.510 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD C B 13 10 8 1.527 109.470 180.000 + 17 OE1 O2 E 16 13 10 1.260 117.200 90.000 + 18 OE2 O2 E 16 13 10 1.260 117.200 270.000 + 19 C C M 8 4 3 1.522 111.100 180.000 + 20 O O E 19 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..dd3f61da8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/GLY_GLYCINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA2 HP E 8 4 3 1.090 109.500 300.000 + 10 HA3 HP E 8 4 3 1.090 109.500 60.000 + 11 C C M 8 4 3 1.522 110.400 180.000 + 12 O O E 11 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..f1d09a44c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NA B 13 10 8 1.390 122.000 180.000 + 15 HD1 H E 14 13 10 1.010 126.000 0.000 + 16 CE1 CR B 14 13 10 1.320 108.000 180.000 + 17 HE1 H5 E 16 14 13 1.090 120.000 180.000 + 18 NE2 NB S 16 14 13 1.310 109.000 0.000 + 19 CD2 CV S 18 16 14 1.360 110.000 0.000 + 20 HD2 H4 E 19 18 16 1.090 120.000 180.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..25f6a52ae --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NB S 13 10 8 1.390 122.000 180.000 + 15 CE1 CR B 14 13 10 1.320 108.000 180.000 + 16 HE1 H5 E 15 14 13 1.090 120.000 180.000 + 17 NE2 NA B 15 14 13 1.310 109.000 0.000 + 18 HE2 H E 17 15 14 1.010 125.000 180.000 + 19 CD2 CW S 17 15 14 1.360 110.000 0.000 + 20 HD2 H4 E 19 17 15 1.090 120.000 180.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..17adddb37 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NA B 13 10 8 1.390 122.000 180.000 + 15 HD1 H E 14 13 10 1.010 126.000 0.000 + 16 CE1 CR B 14 13 10 1.320 108.000 180.000 + 17 HE1 H5 E 16 14 13 1.090 120.000 180.000 + 18 NE2 NA B 16 14 13 1.310 109.000 0.000 + 19 HE2 H E 18 16 14 1.010 125.000 180.000 + 20 CD2 CW S 18 16 14 1.360 110.000 0.000 + 21 HD2 H4 E 20 18 16 1.090 120.000 180.000 + 22 C C M 8 4 3 1.522 111.100 180.000 + 23 O O E 22 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..12f5bc278 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 109.470 60.000 + 11 HB HC E 10 8 4 1.090 109.500 300.000 + 12 CG2 CT 3 10 8 4 1.525 109.470 60.000 + 13 HG21 HC E 12 10 8 1.090 109.500 60.000 + 14 HG22 HC E 12 10 8 1.090 109.500 180.000 + 15 HG23 HC E 12 10 8 1.090 109.500 300.000 + 16 CG1 CT 3 10 8 4 1.525 109.470 180.000 + 17 HG12 HC E 16 10 8 1.090 109.500 60.000 + 18 HG13 HC E 16 10 8 1.090 109.500 300.000 + 19 CD1 CT 3 16 10 8 1.525 109.470 180.000 + 20 HD11 HC E 19 16 10 1.090 109.500 60.000 + 21 HD12 HC E 19 16 10 1.090 109.500 180.000 + 22 HD13 HC E 19 16 10 1.090 109.500 300.000 + 23 C C M 8 4 3 1.522 111.100 180.000 + 24 O O E 23 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..12276822e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/LEU_LEUCINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG HC E 13 10 8 1.090 109.500 300.000 + 15 CD1 CT 3 13 10 8 1.525 109.470 60.000 + 16 HD11 HC E 15 13 10 1.090 109.500 60.000 + 17 HD12 HC E 15 13 10 1.090 109.500 180.000 + 18 HD13 HC E 15 13 10 1.090 109.500 300.000 + 19 CD2 CT 3 13 10 8 1.525 109.470 180.000 + 20 HD21 HC E 19 13 10 1.090 109.500 60.000 + 21 HD22 HC E 19 13 10 1.090 109.500 180.000 + 22 HD23 HC E 19 13 10 1.090 109.500 300.000 + 23 C C M 8 4 3 1.522 111.100 180.000 + 24 O O E 23 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/LYS_LYSINE.in_frag new file mode 100644 index 000000000..cefb647ec --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/LYS_LYSINE.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD CT 3 13 10 8 1.525 109.470 180.000 + 17 HD2 HC E 16 13 10 1.090 109.500 300.000 + 18 HD3 HC E 16 13 10 1.090 109.500 60.000 + 19 CE CT 3 16 13 10 1.525 109.470 180.000 + 20 HE2 HP E 19 16 13 1.090 109.500 300.000 + 21 HE3 HP E 19 16 13 1.090 109.500 60.000 + 22 NZ N3 3 19 16 13 1.470 109.470 180.000 + 23 HZ1 H E 22 19 16 1.010 109.470 60.000 + 24 HZ2 H E 22 19 16 1.010 109.470 180.000 + 25 HZ3 H E 22 19 16 1.010 109.470 300.000 + 26 C C M 8 4 3 1.522 111.100 180.000 + 27 O O E 26 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/MET_METHIONINE.in_frag new file mode 100644 index 000000000..8fd74e252 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/MET_METHIONINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 H1 E 13 10 8 1.090 109.500 300.000 + 15 HG3 H1 E 13 10 8 1.090 109.500 60.000 + 16 SD S S 13 10 8 1.810 110.000 180.000 + 17 CE CT 3 16 13 10 1.780 100.000 180.000 + 18 HE1 H1 E 17 16 13 1.090 109.500 60.000 + 19 HE2 H1 E 17 16 13 1.090 109.500 180.000 + 20 HE3 H1 E 17 16 13 1.090 109.500 300.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..6833d9ea9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CA S 10 8 4 1.510 115.000 180.000 + 14 CD1 CA B 13 10 8 1.400 120.000 180.000 + 15 HD1 HA E 14 13 10 1.090 120.000 0.000 + 16 CE1 CA B 14 13 10 1.400 120.000 180.000 + 17 HE1 HA E 16 14 13 1.090 120.000 180.000 + 18 CZ CA B 16 14 13 1.400 120.000 0.000 + 19 HZ HA E 18 16 14 1.090 120.000 180.000 + 20 CE2 CA B 18 16 14 1.400 120.000 0.000 + 21 HE2 HA E 20 18 16 1.090 120.000 180.000 + 22 CD2 CA S 20 18 16 1.400 120.000 0.000 + 23 HD2 HA E 22 20 18 1.090 120.000 180.000 + 24 C C M 8 4 3 1.522 111.100 180.000 + 25 O O E 24 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/PRO_PROLINE.in_frag new file mode 100644 index 000000000..5d19530db --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/PRO_PROLINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H2 H E 4 3 2 1.010 60.000 90.000 + 6 H3 H E 4 3 2 1.010 60.000 -90.000 + 7 CD CT 3 4 3 2 1.458 126.100 356.100 + 8 HD2 HP E 7 4 3 1.090 109.500 80.000 + 9 HD3 HP E 7 4 3 1.090 109.500 320.000 + 10 CG CT 3 7 4 3 1.500 103.200 200.100 + 11 HG2 HC E 10 7 4 1.090 109.500 218.000 + 12 HG3 HC E 10 7 4 1.090 109.500 98.000 + 13 CB CT B 10 7 4 1.510 106.000 338.300 + 14 HB2 HC E 13 10 7 1.090 109.500 256.300 + 15 HB3 HC E 13 10 7 1.090 109.500 136.300 + 16 CA CT M 4 3 2 1.451 120.600 175.200 + 17 HA HP E 16 4 3 1.090 109.500 60.000 + 18 C C M 16 4 3 1.522 109.500 300.000 + 19 O O E 18 16 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/SER_SERINE.in_frag new file mode 100644 index 000000000..768186cb8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/SER_SERINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 + 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 + 13 OG OH S 10 8 4 1.430 109.470 180.000 + 14 HG HO E 13 10 8 0.960 109.470 180.000 + 15 C C M 8 4 3 1.522 111.100 180.000 + 16 O O E 15 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/THR_THREONINE.in_frag new file mode 100644 index 000000000..6871bde84 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/THR_THREONINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB H1 E 10 8 4 1.090 109.500 180.000 + 12 CG2 CT 3 10 8 4 1.525 109.470 300.000 + 13 HG21 HC E 12 10 8 1.090 109.500 60.000 + 14 HG22 HC E 12 10 8 1.090 109.500 180.000 + 15 HG23 HC E 12 10 8 1.090 109.500 300.000 + 16 OG1 OH S 10 8 4 1.430 109.470 60.000 + 17 HG1 HO E 16 10 8 0.960 109.470 180.000 + 18 C C M 8 4 3 1.522 111.100 180.000 + 19 O O E 18 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/TRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/TRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..56fd0dd42 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/TRP_TRYPTOPHAN.in_frag @@ -0,0 +1,29 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C* S 10 8 4 1.510 115.000 180.000 + 14 CD1 CW B 13 10 8 1.340 127.000 180.000 + 15 HD1 H4 E 14 13 10 1.090 120.000 0.000 + 16 NE1 NA B 14 13 10 1.430 107.000 180.000 + 17 HE1 H E 16 14 13 1.010 125.500 180.000 + 18 CE2 CN S 16 14 13 1.310 109.000 0.000 + 19 CZ2 CA B 18 16 14 1.400 128.000 180.000 + 20 HZ2 HA E 19 18 16 1.090 120.000 0.000 + 21 CH2 CA B 19 18 16 1.390 116.000 180.000 + 22 HH2 HA E 21 19 18 1.090 120.000 180.000 + 23 CZ3 CA B 21 19 18 1.350 121.000 0.000 + 24 HZ3 HA E 23 21 19 1.090 120.000 180.000 + 25 CE3 CA B 23 21 19 1.410 122.000 0.000 + 26 HE3 HA E 25 23 21 1.090 120.000 180.000 + 27 CD2 CB E 25 23 21 1.400 117.000 0.000 + 28 C C M 8 4 3 1.522 111.100 180.000 + 29 O O E 28 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/TYR_TYROSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/TYR_TYROSINE.in_frag new file mode 100644 index 000000000..6d62c97a2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/TYR_TYROSINE.in_frag @@ -0,0 +1,26 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CA S 10 8 4 1.510 109.470 180.000 + 14 CD1 CA B 13 10 8 1.400 120.000 180.000 + 15 HD1 HA E 14 13 10 1.090 120.000 0.000 + 16 CE1 CA B 14 13 10 1.400 120.000 180.000 + 17 HE1 HA E 16 14 13 1.090 120.000 180.000 + 18 CZ CA B 16 14 13 1.400 120.000 0.000 + 19 OH OH S 18 16 14 1.360 120.000 180.000 + 20 HH HO E 19 18 16 0.960 113.000 0.000 + 21 CE2 CA B 18 16 14 1.400 120.000 0.000 + 22 HE2 HA E 21 18 16 1.090 120.000 180.000 + 23 CD2 CA S 21 18 16 1.400 120.000 0.000 + 24 HD2 HA E 23 21 18 1.090 120.000 180.000 + 25 C C M 8 4 3 1.522 111.100 180.000 + 26 O O E 25 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/VAL_VALINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/VAL_VALINE.in_frag new file mode 100644 index 000000000..fa2527771 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/VAL_VALINE.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB HC E 10 8 4 1.090 109.500 300.000 + 12 CG1 CT 3 10 8 4 1.525 109.470 60.000 + 13 HG11 HC E 12 10 8 1.090 109.500 60.000 + 14 HG12 HC E 12 10 8 1.090 109.500 180.000 + 15 HG13 HC E 12 10 8 1.090 109.500 300.000 + 16 CG2 CT 3 10 8 4 1.525 109.470 180.000 + 17 HG21 HC E 16 10 8 1.090 109.500 60.000 + 18 HG22 HC E 16 10 8 1.090 109.500 180.000 + 19 HG23 HC E 16 10 8 1.090 109.500 300.000 + 20 C C M 8 4 3 1.522 111.100 180.000 + 21 O O E 20 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont02/all_aminont02.in b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/all_aminont02.in new file mode 100644 index 000000000..b043696c4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont02/all_aminont02.in @@ -0,0 +1,922 @@ + 1 1 200 +db2000.dat +ALANINE + + ALA INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB1 HC E 10 8 4 1.090 109.500 60.000 + 12 HB2 HC E 10 8 4 1.090 109.500 180.000 + 13 HB3 HC E 10 8 4 1.090 109.500 300.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 .0040 + .0430 -.0968 .0470 .0470 .0470 + .6837 -.5819 + +IMPROPER + CA +M C O + +DONE +GLYCINE + + GLY INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA2 HP E 8 4 3 1.090 109.500 300.000 + 10 HA3 HP E 8 4 3 1.090 109.500 60.000 + 11 C C M 8 4 3 1.522 110.400 180.000 + 12 O O E 11 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0766 + .0839 .0839 .6837 -.5819 + +IMPROPER + CA +M C O + +DONE +SERINE + + SER INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 + 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 + 13 OG OH S 10 8 4 1.430 109.470 180.000 + 14 HG HO E 13 10 8 0.960 109.470 180.000 + 15 C C M 8 4 3 1.522 111.100 180.000 + 16 O O E 15 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 .0528 + .0220 .1146 .0482 .0482 -.5676 + .3730 .6837 -.5819 + +IMPROPER + CA +M C O + +DONE +THREONINE + + THR INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB H1 E 10 8 4 1.090 109.500 180.000 + 12 CG2 CT 3 10 8 4 1.525 109.470 300.000 + 13 HG21 HC E 12 10 8 1.090 109.500 60.000 + 14 HG22 HC E 12 10 8 1.090 109.500 180.000 + 15 HG23 HC E 12 10 8 1.090 109.500 300.000 + 16 OG1 OH S 10 8 4 1.430 109.470 60.000 + 17 HG1 HO E 16 10 8 0.960 109.470 180.000 + 18 C C M 8 4 3 1.522 111.100 180.000 + 19 O O E 18 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 .0051 + .0448 .3997 -.0804 -.2169 .0535 + .0535 .0535 -.6238 .4022 .6837 + -.5819 + +IMPROPER + CA +M C O + +DONE +LEUCINE + + LEU INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG HC E 13 10 8 1.090 109.500 300.000 + 15 CD1 CT 3 13 10 8 1.525 109.470 60.000 + 16 HD11 HC E 15 13 10 1.090 109.500 60.000 + 17 HD12 HC E 15 13 10 1.090 109.500 180.000 + 18 HD13 HC E 15 13 10 1.090 109.500 300.000 + 19 CD2 CT 3 13 10 8 1.525 109.470 180.000 + 20 HD21 HC E 19 13 10 1.090 109.500 60.000 + 21 HD22 HC E 19 13 10 1.090 109.500 180.000 + 22 HD23 HC E 19 13 10 1.090 109.500 300.000 + 23 C C M 8 4 3 1.522 111.100 180.000 + 24 O O E 23 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0529 + .0574 -.1221 .0335 .0335 .4490 + -.0664 -.4399 .1065 .1065 .1065 + -.4399 .1065 .1065 .1065 .6837 + -.5819 + +IMPROPER + CA +M C O + +DONE +ISOLEUCINE + + ILE INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 109.470 60.000 + 11 HB HC E 10 8 4 1.090 109.500 300.000 + 12 CG2 CT 3 10 8 4 1.525 109.470 60.000 + 13 HG21 HC E 12 10 8 1.090 109.500 60.000 + 14 HG22 HC E 12 10 8 1.090 109.500 180.000 + 15 HG23 HC E 12 10 8 1.090 109.500 300.000 + 16 CG1 CT 3 10 8 4 1.525 109.470 180.000 + 17 HG12 HC E 16 10 8 1.090 109.500 60.000 + 18 HG13 HC E 16 10 8 1.090 109.500 300.000 + 19 CD1 CT 3 16 10 8 1.525 109.470 180.000 + 20 HD11 HC E 19 16 10 1.090 109.500 60.000 + 21 HD12 HC E 19 16 10 1.090 109.500 180.000 + 22 HD13 HC E 19 16 10 1.090 109.500 300.000 + 23 C C M 8 4 3 1.522 111.100 180.000 + 24 O O E 23 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0434 + .0668 .0569 .0223 -.2829 .0775 + .0775 .0775 -.0244 .0328 .0328 + -.1102 .0360 .0360 .0360 .6837 + -.5819 + +IMPROPER + CA +M C O + +DONE +VALINE + + VAL INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB HC E 10 8 4 1.090 109.500 300.000 + 12 CG1 CT 3 10 8 4 1.525 109.470 60.000 + 13 HG11 HC E 12 10 8 1.090 109.500 60.000 + 14 HG12 HC E 12 10 8 1.090 109.500 180.000 + 15 HG13 HC E 12 10 8 1.090 109.500 300.000 + 16 CG2 CT 3 10 8 4 1.525 109.470 180.000 + 17 HG21 HC E 16 10 8 1.090 109.500 60.000 + 18 HG22 HC E 16 10 8 1.090 109.500 180.000 + 19 HG23 HC E 16 10 8 1.090 109.500 300.000 + 20 C C M 8 4 3 1.522 111.100 180.000 + 21 O O E 20 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0769 + .0502 .3476 .0011 -.3620 .0822 + .0822 .0822 -.3620 .0822 .0822 + .0822 .6837 -.5819 + +IMPROPER + CA +M C O + +DONE +ASPARAGINE + + ASN INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C B 10 8 4 1.522 111.100 180.000 + 14 OD1 O E 13 10 8 1.229 120.500 0.000 + 15 ND2 N B 13 10 8 1.335 116.600 180.000 + 16 HD21 H E 15 13 10 1.010 119.800 180.000 + 17 HD22 H E 15 13 10 1.010 119.800 0.000 + 18 C C M 8 4 3 1.522 111.100 180.000 + 19 O O E 18 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 .0059 + .0645 -.2021 .0905 .0905 .6724 + -.5761 -.7770 .3613 .3613 .6837 + -.5819 + +IMPROPER + CA +M C O + CB ND2 CG OD1 + CG HD21 ND2 HD22 + +DONE +GLUTAMINE + + GLN INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD C B 13 10 8 1.522 111.100 180.000 + 17 OE1 O E 16 13 10 1.229 120.500 0.000 + 18 NE2 N B 16 13 10 1.335 116.600 180.000 + 19 HE21 H E 18 16 13 1.010 119.800 180.000 + 20 HE22 H E 18 16 13 1.010 119.800 0.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0874 + .0661 .1263 .0130 .0130 -.2997 + .1196 .1196 .7233 -.6218 -.7926 + .3559 .3559 .6837 -.5819 + +IMPROPER + CA +M C O + CG NE2 CD OE1 + CD HE21 NE2 HE22 + +DONE +ARGININE + + ARG INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD CT 3 13 10 8 1.525 109.470 180.000 + 17 HD2 H1 E 16 13 10 1.090 109.500 300.000 + 18 HD3 H1 E 16 13 10 1.090 109.500 60.000 + 19 NE N2 B 16 13 10 1.480 111.000 180.000 + 20 HE H E 19 16 13 1.010 118.500 0.000 + 21 CZ CA B 19 16 13 1.330 123.000 180.000 + 22 NH1 N2 B 21 19 16 1.330 122.000 0.000 + 23 HH11 H E 22 21 19 1.010 119.800 0.000 + 24 HH12 H E 22 21 19 1.010 119.800 180.000 + 25 NH2 N2 B 21 19 16 1.330 118.000 180.000 + 26 HH21 H E 25 21 19 1.010 119.800 0.000 + 27 HH22 H E 25 21 19 1.010 119.800 180.000 + 28 C C M 8 4 3 1.522 111.100 180.000 + 29 O O E 28 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0389 + .0692 .0290 .0341 .0341 .0003 + .0304 .0304 .0966 .0585 .0585 + -.5249 .3258 .8813 -.8376 .4205 + .4205 -.8376 .4205 .4205 .6837 + -.5819 + +IMPROPER + CA +M C O + NE NH1 CZ NH2 + CD CZ NE HE + CZ HH11 NH1 HH12 + CZ HH21 NH2 HH22 + +DONE +HISTIDINE DELTAH + + HID INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NA B 13 10 8 1.390 122.000 180.000 + 15 HD1 H E 14 13 10 1.010 126.000 0.000 + 16 CE1 CR B 14 13 10 1.320 108.000 180.000 + 17 HE1 H5 E 16 14 13 1.090 120.000 180.000 + 18 NE2 NB S 16 14 13 1.310 109.000 0.000 + 19 CD2 CV S 18 16 14 1.360 110.000 0.000 + 20 HD2 H4 E 19 18 16 1.090 120.000 180.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 .0189 + .0370 -.0356 .0393 .0393 .0471 + -.1644 .2712 .1023 .1006 -.4742 + .0182 .0915 .6837 -.5819 + +LOOP + CG CD2 + +IMPROPER + CA +M C O + CG CE1 ND1 HD1 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +HISTIDINE EPSILONH + + HIE INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NB S 13 10 8 1.390 122.000 180.000 + 15 CE1 CR B 14 13 10 1.320 108.000 180.000 + 16 HE1 H5 E 15 14 13 1.090 120.000 180.000 + 17 NE2 NA B 15 14 13 1.310 109.000 0.000 + 18 HE2 H E 17 15 14 1.010 125.000 180.000 + 19 CD2 CW S 17 15 14 1.360 110.000 0.000 + 20 HD2 H4 E 19 17 15 1.090 120.000 180.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0047 + .0393 -.0485 .0512 .0512 .2683 + -.5675 .2272 .0692 -.2130 .2911 + -.2292 .1566 .6837 -.5819 + +LOOP + CG CD2 + +IMPROPER + CA +M C O + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +HISTIDINE PLUS + + HIP INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NA B 13 10 8 1.390 122.000 180.000 + 15 HD1 H E 14 13 10 1.010 126.000 0.000 + 16 CE1 CR B 14 13 10 1.320 108.000 180.000 + 17 HE1 H5 E 16 14 13 1.090 120.000 180.000 + 18 NE2 NA B 16 14 13 1.310 109.000 0.000 + 19 HE2 H E 18 16 14 1.010 125.000 180.000 + 20 CD2 CW S 18 16 14 1.360 110.000 0.000 + 21 HD2 H4 E 20 18 16 1.090 120.000 180.000 + 22 C C M 8 4 3 1.522 111.100 180.000 + 23 O O E 22 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 .1381 + .0003 .0296 .0569 .0569 .0591 + -.0008 .2806 -.0677 .2108 -.0391 + .3178 -.1262 .1749 .6837 -.5819 + +LOOP + CG CD2 + +IMPROPER + CA +M C O + CG CE1 ND1 HD1 + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +TRYPTOPHAN + + TRP INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C* S 10 8 4 1.510 115.000 180.000 + 14 CD1 CW B 13 10 8 1.340 127.000 180.000 + 15 HD1 H4 E 14 13 10 1.090 120.000 0.000 + 16 NE1 NA B 14 13 10 1.430 107.000 180.000 + 17 HE1 H E 16 14 13 1.010 125.500 180.000 + 18 CE2 CN S 16 14 13 1.310 109.000 0.000 + 19 CZ2 CA B 18 16 14 1.400 128.000 180.000 + 20 HZ2 HA E 19 18 16 1.090 120.000 0.000 + 21 CH2 CA B 19 18 16 1.390 116.000 180.000 + 22 HH2 HA E 21 19 18 1.090 120.000 180.000 + 23 CZ3 CA B 21 19 18 1.350 121.000 0.000 + 24 HZ3 HA E 23 21 19 1.090 120.000 180.000 + 25 CE3 CA B 23 21 19 1.410 122.000 0.000 + 26 HE3 HA E 25 23 21 1.090 120.000 180.000 + 27 CD2 CB E 25 23 21 1.400 117.000 0.000 + 28 C C M 8 4 3 1.522 111.100 180.000 + 29 O O E 28 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0188 + .0543 -.0111 .0328 .0328 -.0973 + -.0798 .1437 -.3581 .3411 .1680 + -.2298 .1385 -.1089 .1066 -.1461 + .1078 -.2304 .1627 .0832 .6837 + -.5819 + +LOOP + CG CD2 + CE2 CD2 + +IMPROPER + CA +M C O + CD1 CE2 NE1 HE1 + CE2 CH2 CZ2 HZ2 + CZ2 CZ3 CH2 HH2 + CH2 CE3 CZ3 HZ3 + CZ3 CD2 CE3 HE3 + CG NE1 CD1 HD1 + CD1 CD2 CG CB + +DONE +PHENYLALANINE + + PHE INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CA S 10 8 4 1.510 115.000 180.000 + 14 CD1 CA B 13 10 8 1.400 120.000 180.000 + 15 HD1 HA E 14 13 10 1.090 120.000 0.000 + 16 CE1 CA B 14 13 10 1.400 120.000 180.000 + 17 HE1 HA E 16 14 13 1.090 120.000 180.000 + 18 CZ CA B 16 14 13 1.400 120.000 0.000 + 19 HZ HA E 18 16 14 1.090 120.000 180.000 + 20 CE2 CA B 18 16 14 1.400 120.000 0.000 + 21 HE2 HA E 20 18 16 1.090 120.000 180.000 + 22 CD2 CA S 20 18 16 1.400 120.000 0.000 + 23 HD2 HA E 22 20 18 1.090 120.000 180.000 + 24 C C M 8 4 3 1.522 111.100 180.000 + 25 O O E 24 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0022 + .0381 -.0053 .0289 .0289 .0358 + -.1078 .1140 -.1503 .1153 -.0744 + .0990 -.1503 .1153 -.1078 .1140 + .6837 -.5819 + +LOOP + CG CD2 + +IMPROPER + CA +M C O + CG CE2 CD2 HD2 + CD2 CZ CE2 HE2 + CE1 CE2 CZ HZ + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + +DONE +TYROSINE + + TYR INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CA S 10 8 4 1.510 109.470 180.000 + 14 CD1 CA B 13 10 8 1.400 120.000 180.000 + 15 HD1 HA E 14 13 10 1.090 120.000 0.000 + 16 CE1 CA B 14 13 10 1.400 120.000 180.000 + 17 HE1 HA E 16 14 13 1.090 120.000 180.000 + 18 CZ CA B 16 14 13 1.400 120.000 0.000 + 19 OH OH S 18 16 14 1.360 120.000 180.000 + 20 HH HO E 19 18 16 0.960 113.000 0.000 + 21 CE2 CA B 18 16 14 1.400 120.000 0.000 + 22 HE2 HA E 21 18 16 1.090 120.000 180.000 + 23 CD2 CA S 21 18 16 1.400 120.000 0.000 + 24 HD2 HA E 23 21 18 1.090 120.000 180.000 + 25 C C M 8 4 3 1.522 111.100 180.000 + 26 O O E 25 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0426 + .0724 .0085 .0313 .0313 .0005 + -.1423 .1204 -.1892 .1368 .2570 + -.4770 .3584 -.1892 .1368 -.1423 + .1204 .6837 -.5819 + +LOOP + CG CD2 + +IMPROPER + CA +M C O + CG CE2 CD2 HD2 + CD2 CZ CE2 HE2 + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + CE1 CE2 CZ OH + + +DONE +GLUTAMIC ACID + + GLU INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.510 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD C B 13 10 8 1.527 109.470 180.000 + 17 OE1 O2 E 16 13 10 1.260 117.200 90.000 + 18 OE2 O2 E 16 13 10 1.260 117.200 270.000 + 19 C C M 8 4 3 1.522 111.100 180.000 + 20 O O E 19 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.2418 + .0961 .2765 -.0627 -.0627 -.1881 + .0410 .0410 .6733 -.7407 -.7407 + .6837 -.5819 + +IMPROPER + CA +M C O + CG OE1 CD OE2 + +DONE +ASPARTIC ACID + + ASP INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C B 10 8 4 1.527 109.470 180.000 + 14 OD1 O2 E 13 10 8 1.260 117.200 90.000 + 15 OD2 O2 E 13 10 8 1.260 117.200 270.000 + 16 C C M 8 4 3 1.522 111.100 180.000 + 17 O O E 16 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.1523 + .0664 -.0383 -.0197 -.0197 .7630 + -.7541 -.7541 .6837 -.5819 + +IMPROPER + CA +M C O + CB OD1 CG OD2 + +DONE +LYSINE + + LYS INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD CT 3 13 10 8 1.525 109.470 180.000 + 17 HD2 HC E 16 13 10 1.090 109.500 300.000 + 18 HD3 HC E 16 13 10 1.090 109.500 60.000 + 19 CE CT 3 16 13 10 1.525 109.470 180.000 + 20 HE2 HP E 19 16 13 1.090 109.500 300.000 + 21 HE3 HP E 19 16 13 1.090 109.500 60.000 + 22 NZ N3 3 19 16 13 1.470 109.470 180.000 + 23 HZ1 H E 22 19 16 1.010 109.470 60.000 + 24 HZ2 H E 22 19 16 1.010 109.470 180.000 + 25 HZ3 H E 22 19 16 1.010 109.470 300.000 + 26 C C M 8 4 3 1.522 111.100 180.000 + 27 O O E 26 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0269 + .0709 -.0348 .0323 .0323 -.0231 + .0449 .0449 -.0433 .0550 .0550 + .1380 .0472 .0472 -.2004 .2840 + .2840 .2840 .6837 -.5819 + +IMPROPER + CA +M C O + +DONE +PROLINE + + PRO INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H2 H E 4 3 2 1.010 60.000 90.000 + 6 H3 H E 4 3 2 1.010 60.000 -90.000 + 7 CD CT 3 4 3 2 1.458 126.100 356.100 + 8 HD2 HP E 7 4 3 1.090 109.500 80.000 + 9 HD3 HP E 7 4 3 1.090 109.500 320.000 + 10 CG CT 3 7 4 3 1.500 103.200 200.100 + 11 HG2 HC E 10 7 4 1.090 109.500 218.000 + 12 HG3 HC E 10 7 4 1.090 109.500 98.000 + 13 CB CT B 10 7 4 1.510 106.000 338.300 + 14 HB2 HC E 13 10 7 1.090 109.500 256.300 + 15 HB3 HC E 13 10 7 1.090 109.500 136.300 + 16 CA CT M 4 3 2 1.451 120.600 175.200 + 17 HA HP E 16 4 3 1.090 109.500 60.000 + 18 C C M 16 4 3 1.522 109.500 300.000 + 19 O O E 18 16 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .0365 .2080 .2080 .0280 .0654 + .0654 .0299 .0210 .0210 -.0206 + .0391 .0391 .1718 -.0144 .6837 + -.5819 + +LOOP + CB CA + +IMPROPER + CA +M C O + +DONE +CYSTEINE + + CYS INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 + 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 + 13 SG SH S 10 8 4 1.810 116.000 180.000 + 14 HG HS E 13 10 8 1.330 96.000 180.000 + 15 C C M 8 4 3 1.522 111.100 180.000 + 16 O O E 15 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 .0213 + .0578 -.0316 .0655 .0655 -.2464 + .1591 .6837 -.5819 + +IMPROPER + CA +M C O + +DONE +CYSTINE(S-S BRIDGE) + + CYX INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 + 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 + 13 SG S E 10 8 4 1.810 116.000 180.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0005 + .0649 -.0084 .0634 .0634 -.0916 + .6837 -.5819 + +IMPROPER + CA +M C O + +DONE +METHIONINE + + MET INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 H1 E 13 10 8 1.090 109.500 300.000 + 15 HG3 H1 E 13 10 8 1.090 109.500 60.000 + 16 SD S S 13 10 8 1.810 110.000 180.000 + 17 CE CT 3 16 13 10 1.780 100.000 180.000 + 18 HE1 H1 E 17 16 13 1.090 109.500 60.000 + 19 HE2 H1 E 17 16 13 1.090 109.500 180.000 + 20 HE3 H1 E 17 16 13 1.090 109.500 300.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 + +CHARGE cc-pvtz esp iterated + .1902 .2056 .2056 .2056 -.0377 + .0516 .0828 -.0060 -.0060 -.0162 + .0722 .0722 -.2381 -.0585 .0583 + .0583 .0583 .6837 -.5819 + +IMPROPER + CA +M C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NALA_ALANINE.in_frag new file mode 100644 index 000000000..c2df8a4e2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NALA_ALANINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB1 HC E 10 8 4 1.090 109.500 60.000 + 12 HB2 HC E 10 8 4 1.090 109.500 180.000 + 13 HB3 HC E 10 8 4 1.090 109.500 300.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NARG_ARGININE.in_frag new file mode 100644 index 000000000..490046579 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NARG_ARGININE.in_frag @@ -0,0 +1,29 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD CT 3 13 10 8 1.525 109.470 180.000 + 17 HD2 H1 E 16 13 10 1.090 109.500 300.000 + 18 HD3 H1 E 16 13 10 1.090 109.500 60.000 + 19 NE N2 B 16 13 10 1.480 111.000 180.000 + 20 HE H E 19 16 13 1.010 118.500 0.000 + 21 CZ CA B 19 16 13 1.330 123.000 180.000 + 22 NH1 N2 B 21 19 16 1.330 122.000 0.000 + 23 HH11 H E 22 21 19 1.010 119.800 0.000 + 24 HH12 H E 22 21 19 1.010 119.800 180.000 + 25 NH2 N2 B 21 19 16 1.330 118.000 180.000 + 26 HH21 H E 25 21 19 1.010 119.800 0.000 + 27 HH22 H E 25 21 19 1.010 119.800 180.000 + 28 C C M 8 4 3 1.522 111.100 180.000 + 29 O O E 28 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..75ebc4da3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NASN_ASPARAGINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C B 10 8 4 1.522 111.100 180.000 + 14 OD1 O E 13 10 8 1.229 120.500 0.000 + 15 ND2 N B 13 10 8 1.335 116.600 180.000 + 16 HD21 H E 15 13 10 1.010 119.800 180.000 + 17 HD22 H E 15 13 10 1.010 119.800 0.000 + 18 C C M 8 4 3 1.522 111.100 180.000 + 19 O O E 18 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..de3b9439a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C B 10 8 4 1.527 109.470 180.000 + 14 OD1 O2 E 13 10 8 1.260 117.200 90.000 + 15 OD2 O2 E 13 10 8 1.260 117.200 270.000 + 16 C C M 8 4 3 1.522 111.100 180.000 + 17 O O E 16 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NCYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NCYS_CYSTEINE.in_frag new file mode 100644 index 000000000..55155fafc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NCYS_CYSTEINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 + 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 + 13 SG SH S 10 8 4 1.810 116.000 180.000 + 14 HG HS E 13 10 8 1.330 96.000 180.000 + 15 C C M 8 4 3 1.522 111.100 180.000 + 16 O O E 15 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NGLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NGLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..772f8ad16 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NGLN_GLUTAMINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD C B 13 10 8 1.522 111.100 180.000 + 17 OE1 O E 16 13 10 1.229 120.500 0.000 + 18 NE2 N B 16 13 10 1.335 116.600 180.000 + 19 HE21 H E 18 16 13 1.010 119.800 180.000 + 20 HE22 H E 18 16 13 1.010 119.800 0.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NGLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NGLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..5c0db2845 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NGLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.510 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD C B 13 10 8 1.527 109.470 180.000 + 17 OE1 O2 E 16 13 10 1.260 117.200 90.000 + 18 OE2 O2 E 16 13 10 1.260 117.200 270.000 + 19 C C M 8 4 3 1.522 111.100 180.000 + 20 O O E 19 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NGLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NGLY_GLYCINE.in_frag new file mode 100644 index 000000000..dd3f61da8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NGLY_GLYCINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA2 HP E 8 4 3 1.090 109.500 300.000 + 10 HA3 HP E 8 4 3 1.090 109.500 60.000 + 11 C C M 8 4 3 1.522 110.400 180.000 + 12 O O E 11 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NHID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NHID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..f1d09a44c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NHID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NA B 13 10 8 1.390 122.000 180.000 + 15 HD1 H E 14 13 10 1.010 126.000 0.000 + 16 CE1 CR B 14 13 10 1.320 108.000 180.000 + 17 HE1 H5 E 16 14 13 1.090 120.000 180.000 + 18 NE2 NB S 16 14 13 1.310 109.000 0.000 + 19 CD2 CV S 18 16 14 1.360 110.000 0.000 + 20 HD2 H4 E 19 18 16 1.090 120.000 180.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NHIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NHIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..25f6a52ae --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NHIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NB S 13 10 8 1.390 122.000 180.000 + 15 CE1 CR B 14 13 10 1.320 108.000 180.000 + 16 HE1 H5 E 15 14 13 1.090 120.000 180.000 + 17 NE2 NA B 15 14 13 1.310 109.000 0.000 + 18 HE2 H E 17 15 14 1.010 125.000 180.000 + 19 CD2 CW S 17 15 14 1.360 110.000 0.000 + 20 HD2 H4 E 19 17 15 1.090 120.000 180.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NHIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NHIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..17adddb37 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NHIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NA B 13 10 8 1.390 122.000 180.000 + 15 HD1 H E 14 13 10 1.010 126.000 0.000 + 16 CE1 CR B 14 13 10 1.320 108.000 180.000 + 17 HE1 H5 E 16 14 13 1.090 120.000 180.000 + 18 NE2 NA B 16 14 13 1.310 109.000 0.000 + 19 HE2 H E 18 16 14 1.010 125.000 180.000 + 20 CD2 CW S 18 16 14 1.360 110.000 0.000 + 21 HD2 H4 E 20 18 16 1.090 120.000 180.000 + 22 C C M 8 4 3 1.522 111.100 180.000 + 23 O O E 22 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..12f5bc278 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NILE_ISOLEUCINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 109.470 60.000 + 11 HB HC E 10 8 4 1.090 109.500 300.000 + 12 CG2 CT 3 10 8 4 1.525 109.470 60.000 + 13 HG21 HC E 12 10 8 1.090 109.500 60.000 + 14 HG22 HC E 12 10 8 1.090 109.500 180.000 + 15 HG23 HC E 12 10 8 1.090 109.500 300.000 + 16 CG1 CT 3 10 8 4 1.525 109.470 180.000 + 17 HG12 HC E 16 10 8 1.090 109.500 60.000 + 18 HG13 HC E 16 10 8 1.090 109.500 300.000 + 19 CD1 CT 3 16 10 8 1.525 109.470 180.000 + 20 HD11 HC E 19 16 10 1.090 109.500 60.000 + 21 HD12 HC E 19 16 10 1.090 109.500 180.000 + 22 HD13 HC E 19 16 10 1.090 109.500 300.000 + 23 C C M 8 4 3 1.522 111.100 180.000 + 24 O O E 23 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NLEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NLEU_LEUCINE.in_frag new file mode 100644 index 000000000..12276822e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NLEU_LEUCINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG HC E 13 10 8 1.090 109.500 300.000 + 15 CD1 CT 3 13 10 8 1.525 109.470 60.000 + 16 HD11 HC E 15 13 10 1.090 109.500 60.000 + 17 HD12 HC E 15 13 10 1.090 109.500 180.000 + 18 HD13 HC E 15 13 10 1.090 109.500 300.000 + 19 CD2 CT 3 13 10 8 1.525 109.470 180.000 + 20 HD21 HC E 19 13 10 1.090 109.500 60.000 + 21 HD22 HC E 19 13 10 1.090 109.500 180.000 + 22 HD23 HC E 19 13 10 1.090 109.500 300.000 + 23 C C M 8 4 3 1.522 111.100 180.000 + 24 O O E 23 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NLYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NLYS_LYSINE.in_frag new file mode 100644 index 000000000..cefb647ec --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NLYS_LYSINE.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD CT 3 13 10 8 1.525 109.470 180.000 + 17 HD2 HC E 16 13 10 1.090 109.500 300.000 + 18 HD3 HC E 16 13 10 1.090 109.500 60.000 + 19 CE CT 3 16 13 10 1.525 109.470 180.000 + 20 HE2 HP E 19 16 13 1.090 109.500 300.000 + 21 HE3 HP E 19 16 13 1.090 109.500 60.000 + 22 NZ N3 3 19 16 13 1.470 109.470 180.000 + 23 HZ1 H E 22 19 16 1.010 109.470 60.000 + 24 HZ2 H E 22 19 16 1.010 109.470 180.000 + 25 HZ3 H E 22 19 16 1.010 109.470 300.000 + 26 C C M 8 4 3 1.522 111.100 180.000 + 27 O O E 26 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NMET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NMET_METHIONINE.in_frag new file mode 100644 index 000000000..8fd74e252 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NMET_METHIONINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 H1 E 13 10 8 1.090 109.500 300.000 + 15 HG3 H1 E 13 10 8 1.090 109.500 60.000 + 16 SD S S 13 10 8 1.810 110.000 180.000 + 17 CE CT 3 16 13 10 1.780 100.000 180.000 + 18 HE1 H1 E 17 16 13 1.090 109.500 60.000 + 19 HE2 H1 E 17 16 13 1.090 109.500 180.000 + 20 HE3 H1 E 17 16 13 1.090 109.500 300.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NPHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NPHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..6833d9ea9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NPHE_PHENYLALANINE.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CA S 10 8 4 1.510 115.000 180.000 + 14 CD1 CA B 13 10 8 1.400 120.000 180.000 + 15 HD1 HA E 14 13 10 1.090 120.000 0.000 + 16 CE1 CA B 14 13 10 1.400 120.000 180.000 + 17 HE1 HA E 16 14 13 1.090 120.000 180.000 + 18 CZ CA B 16 14 13 1.400 120.000 0.000 + 19 HZ HA E 18 16 14 1.090 120.000 180.000 + 20 CE2 CA B 18 16 14 1.400 120.000 0.000 + 21 HE2 HA E 20 18 16 1.090 120.000 180.000 + 22 CD2 CA S 20 18 16 1.400 120.000 0.000 + 23 HD2 HA E 22 20 18 1.090 120.000 180.000 + 24 C C M 8 4 3 1.522 111.100 180.000 + 25 O O E 24 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NPRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NPRO_PROLINE.in_frag new file mode 100644 index 000000000..5d19530db --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NPRO_PROLINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H2 H E 4 3 2 1.010 60.000 90.000 + 6 H3 H E 4 3 2 1.010 60.000 -90.000 + 7 CD CT 3 4 3 2 1.458 126.100 356.100 + 8 HD2 HP E 7 4 3 1.090 109.500 80.000 + 9 HD3 HP E 7 4 3 1.090 109.500 320.000 + 10 CG CT 3 7 4 3 1.500 103.200 200.100 + 11 HG2 HC E 10 7 4 1.090 109.500 218.000 + 12 HG3 HC E 10 7 4 1.090 109.500 98.000 + 13 CB CT B 10 7 4 1.510 106.000 338.300 + 14 HB2 HC E 13 10 7 1.090 109.500 256.300 + 15 HB3 HC E 13 10 7 1.090 109.500 136.300 + 16 CA CT M 4 3 2 1.451 120.600 175.200 + 17 HA HP E 16 4 3 1.090 109.500 60.000 + 18 C C M 16 4 3 1.522 109.500 300.000 + 19 O O E 18 16 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NSER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NSER_SERINE.in_frag new file mode 100644 index 000000000..768186cb8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NSER_SERINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 + 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 + 13 OG OH S 10 8 4 1.430 109.470 180.000 + 14 HG HO E 13 10 8 0.960 109.470 180.000 + 15 C C M 8 4 3 1.522 111.100 180.000 + 16 O O E 15 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NTHR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NTHR_THREONINE.in_frag new file mode 100644 index 000000000..6871bde84 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NTHR_THREONINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB H1 E 10 8 4 1.090 109.500 180.000 + 12 CG2 CT 3 10 8 4 1.525 109.470 300.000 + 13 HG21 HC E 12 10 8 1.090 109.500 60.000 + 14 HG22 HC E 12 10 8 1.090 109.500 180.000 + 15 HG23 HC E 12 10 8 1.090 109.500 300.000 + 16 OG1 OH S 10 8 4 1.430 109.470 60.000 + 17 HG1 HO E 16 10 8 0.960 109.470 180.000 + 18 C C M 8 4 3 1.522 111.100 180.000 + 19 O O E 18 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NTRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NTRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..56fd0dd42 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NTRP_TRYPTOPHAN.in_frag @@ -0,0 +1,29 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C* S 10 8 4 1.510 115.000 180.000 + 14 CD1 CW B 13 10 8 1.340 127.000 180.000 + 15 HD1 H4 E 14 13 10 1.090 120.000 0.000 + 16 NE1 NA B 14 13 10 1.430 107.000 180.000 + 17 HE1 H E 16 14 13 1.010 125.500 180.000 + 18 CE2 CN S 16 14 13 1.310 109.000 0.000 + 19 CZ2 CA B 18 16 14 1.400 128.000 180.000 + 20 HZ2 HA E 19 18 16 1.090 120.000 0.000 + 21 CH2 CA B 19 18 16 1.390 116.000 180.000 + 22 HH2 HA E 21 19 18 1.090 120.000 180.000 + 23 CZ3 CA B 21 19 18 1.350 121.000 0.000 + 24 HZ3 HA E 23 21 19 1.090 120.000 180.000 + 25 CE3 CA B 23 21 19 1.410 122.000 0.000 + 26 HE3 HA E 25 23 21 1.090 120.000 180.000 + 27 CD2 CB E 25 23 21 1.400 117.000 0.000 + 28 C C M 8 4 3 1.522 111.100 180.000 + 29 O O E 28 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NTYR_TYROSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NTYR_TYROSINE.in_frag new file mode 100644 index 000000000..81db6af2a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NTYR_TYROSINE.in_frag @@ -0,0 +1,26 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CA S 10 8 4 1.510 109.470 180.000 + 14 CD1 CA B 13 10 8 1.400 120.000 180.000 + 15 HD1 HA E 14 13 10 1.090 120.000 0.000 + 16 CE1 CA B 14 13 10 1.400 120.000 180.000 + 17 HE1 HA E 16 14 13 1.090 120.000 180.000 + 18 CZ C B 16 14 13 1.400 120.000 0.000 + 19 OH OH S 18 16 14 1.360 120.000 180.000 + 20 HH HO E 19 18 16 0.960 113.000 0.000 + 21 CE2 CA B 18 16 14 1.400 120.000 0.000 + 22 HE2 HA E 21 18 16 1.090 120.000 180.000 + 23 CD2 CA S 21 18 16 1.400 120.000 0.000 + 24 HD2 HA E 23 21 18 1.090 120.000 180.000 + 25 C C M 8 4 3 1.522 111.100 180.000 + 26 O O E 25 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NVAL_VALINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NVAL_VALINE.in_frag new file mode 100644 index 000000000..fa2527771 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/NVAL_VALINE.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB HC E 10 8 4 1.090 109.500 300.000 + 12 CG1 CT 3 10 8 4 1.525 109.470 60.000 + 13 HG11 HC E 12 10 8 1.090 109.500 60.000 + 14 HG12 HC E 12 10 8 1.090 109.500 180.000 + 15 HG13 HC E 12 10 8 1.090 109.500 300.000 + 16 CG2 CT 3 10 8 4 1.525 109.470 180.000 + 17 HG21 HC E 16 10 8 1.090 109.500 60.000 + 18 HG22 HC E 16 10 8 1.090 109.500 180.000 + 19 HG23 HC E 16 10 8 1.090 109.500 300.000 + 20 C C M 8 4 3 1.522 111.100 180.000 + 21 O O E 20 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont03/all_aminont03.in b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/all_aminont03.in new file mode 100644 index 000000000..1f60a831f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont03/all_aminont03.in @@ -0,0 +1,757 @@ + 1 1 200 +db94.dat +ALANINE + + NALA INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.589266 + 5 H1 H E 4 3 2 1.010 130.000 0.000 0.446422 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.446422 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.446422 + 8 CA CT 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0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.570235 + 5 H1 H E 4 3 2 1.010 130.000 0.000 0.440078 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.440078 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.440078 + 8 CA CT M 4 3 2 1.449 121.900 180.000 0.028754 + 9 HA HP E 8 4 3 1.090 109.500 300.000 0.078538 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.270941 + 11 HB H1 E 10 8 4 1.090 109.500 180.000 -0.014476 + 12 CG2 CT 3 10 8 4 1.525 109.470 300.000 -0.160657 + 13 HG21 HC E 12 10 8 1.090 109.500 60.000 0.053833 + 14 HG22 HC E 12 10 8 1.090 109.500 180.000 0.053833 + 15 HG23 HC E 12 10 8 1.090 109.500 300.000 0.053833 + 16 OG1 OH S 10 8 4 1.430 109.470 60.000 -0.621934 + 17 HG1 HO E 16 10 8 0.960 109.470 180.000 0.409167 + 18 C C M 8 4 3 1.522 111.100 180.000 0.709968 + 19 O O E 18 8 4 1.229 120.500 0.000 -0.611797 + +IMPROPER + CA +M C O + +DONE +LEUCINE + + NLEU INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.624705 + 5 H1 H E 4 3 2 1.010 130.000 0.000 0.458235 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.458235 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.458235 + 8 CA CT M 4 3 2 1.449 121.900 180.000 0.069804 + 9 HA HP E 8 4 3 1.090 109.500 300.000 0.092394 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 -0.118019 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.037615 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.037615 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 0.177099 + 14 HG HC E 13 10 8 1.090 109.500 300.000 0.013272 + 15 CD1 CT 3 13 10 8 1.525 109.470 60.000 -0.157414 + 16 HD11 HC E 15 13 10 1.090 109.500 60.000 0.031964 + 17 HD12 HC E 15 13 10 1.090 109.500 180.000 0.031964 + 18 HD13 HC E 15 13 10 1.090 109.500 300.000 0.031964 + 19 CD2 CT 3 13 10 8 1.525 109.470 180.000 -0.157414 + 20 HD21 HC E 19 13 10 1.090 109.500 60.000 0.031964 + 21 HD22 HC E 19 13 10 1.090 109.500 180.000 0.031964 + 22 HD23 HC E 19 13 10 1.090 109.500 300.000 0.031964 + 23 C C M 8 4 3 1.522 111.100 180.000 0.656583 + 24 O O E 23 8 4 1.229 120.500 0.000 -0.593318 + +IMPROPER + CA +M C O + +DONE +ISOLEUCINE + + NILE INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.605757 + 5 H1 H E 4 3 2 1.010 130.000 0.000 0.451919 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.451919 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.451919 + 8 CA CT M 4 3 2 1.449 121.900 180.000 0.025768 + 9 HA HP E 8 4 3 1.090 109.500 300.000 0.062754 + 10 CB CT 3 8 4 3 1.525 109.470 60.000 0.044198 + 11 HB HC E 10 8 4 1.090 109.500 300.000 0.038704 + 12 CG2 CT 3 10 8 4 1.525 109.470 60.000 -0.172672 + 13 HG21 HC E 12 10 8 1.090 109.500 60.000 0.038544 + 14 HG22 HC E 12 10 8 1.090 109.500 180.000 0.038544 + 15 HG23 HC E 12 10 8 1.090 109.500 300.000 0.038544 + 16 CG1 CT 3 10 8 4 1.525 109.470 180.000 0.058447 + 17 HG12 HC E 16 10 8 1.090 109.500 60.000 0.003617 + 18 HG13 HC E 16 10 8 1.090 109.500 300.000 0.003617 + 19 CD1 CT 3 16 10 8 1.525 109.470 180.000 -0.111609 + 20 HD11 HC E 19 16 10 1.090 109.500 60.000 0.025639 + 21 HD12 HC E 19 16 10 1.090 109.500 180.000 0.025639 + 22 HD13 HC E 19 16 10 1.090 109.500 300.000 0.025639 + 23 C C M 8 4 3 1.522 111.100 180.000 0.733445 + 24 O O E 23 8 4 1.229 120.500 0.000 -0.628820 + +IMPROPER + CA +M C O + +DONE +VALINE + + NVAL INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.737450 + 5 H1 H E 4 3 2 1.010 130.000 0.000 0.495817 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.495817 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.495817 + 8 CA CT M 4 3 2 1.449 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1.010 130.000 0.000 0.473035 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.473035 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.473035 + 8 CA CT M 4 3 2 1.449 121.900 180.000 0.256684 + 9 HA HP E 8 4 3 1.090 109.500 300.000 0.013306 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 -0.062106 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.038289 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.038289 + 13 CG C B 10 8 4 1.522 111.100 180.000 0.554932 + 14 OD1 O E 13 10 8 1.229 120.500 0.000 -0.568797 + 15 ND2 N B 13 10 8 1.335 116.600 180.000 -0.784547 + 16 HD21 H E 15 13 10 1.010 119.800 180.000 0.372344 + 17 HD22 H E 15 13 10 1.010 119.800 0.000 0.372344 + 18 C C M 8 4 3 1.522 111.100 180.000 0.602554 + 19 O O E 18 8 4 1.229 120.500 0.000 -0.583293 + +IMPROPER + CA +M C O + CB ND2 CG OD1 + CG HD21 ND2 HD22 + +DONE +GLUTAMINE + + NGLN INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.603779 + 5 H1 H E 4 3 2 1.010 130.000 0.000 0.451260 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.451260 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.451260 + 8 CA CT M 4 3 2 1.449 121.900 180.000 0.201127 + 9 HA HP E 8 4 3 1.090 109.500 300.000 0.028930 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 -0.013277 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.001827 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.001827 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 -0.030707 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 0.024665 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 0.024665 + 16 CD C B 13 10 8 1.522 111.100 180.000 0.669568 + 17 OE1 O E 16 13 10 1.229 120.500 0.000 -0.585802 + 18 NE2 N B 16 13 10 1.335 116.600 180.000 -0.889652 + 19 HE21 H E 18 16 13 1.010 119.800 180.000 0.397306 + 20 HE22 H E 18 16 13 1.010 119.800 0.000 0.397306 + 21 C C M 8 4 3 1.522 111.100 180.000 0.606634 + 22 O O E 21 8 4 1.229 120.500 0.000 -0.584415 + +IMPROPER + CA +M C O + CG NE2 CD OE1 + CD HE21 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-0.592849 + 5 H1 H E 4 3 2 1.010 130.000 0.000 0.447616 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.447616 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.447616 + 8 CA CT M 4 3 2 1.449 121.900 180.000 0.090652 + 9 HA HP E 8 4 3 1.090 109.500 300.000 0.113265 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 -0.050705 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.006441 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.006441 + 13 CG CA S 10 8 4 1.510 109.470 180.000 0.130909 + 14 CD1 CA B 13 10 8 1.400 120.000 180.000 -0.198282 + 15 HD1 HA E 14 13 10 1.090 120.000 0.000 0.148246 + 16 CE1 CA B 14 13 10 1.400 120.000 180.000 -0.213863 + 17 HE1 HA E 16 14 13 1.090 120.000 180.000 0.148090 + 18 CZ C B 16 14 13 1.400 120.000 0.000 0.242629 + 19 OH OH S 18 16 14 1.360 120.000 180.000 -0.475387 + 20 HH HO E 19 18 16 0.960 113.000 0.000 0.370782 + 21 CE2 CA B 18 16 14 1.400 120.000 0.000 -0.213863 + 22 HE2 HA E 21 18 16 1.090 120.000 180.000 0.148090 + 23 CD2 CA S 21 18 16 1.400 120.000 0.000 -0.198282 + 24 HD2 HA E 23 21 18 1.090 120.000 180.000 0.148246 + 25 C C M 8 4 3 1.522 111.100 180.000 0.620893 + 26 O O E 25 8 4 1.229 120.500 0.000 -0.574301 + +LOOP + CG CD2 + +IMPROPER + CA +M C O + CG CE2 CD2 HD2 + CD2 CZ CE2 HE2 + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + CE1 CE2 CZ OH + + +DONE +GLUTAMIC ACID + + NGLU INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.465328 + 5 H1 H E 4 3 2 1.010 130.000 0.000 0.405109 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.405109 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.405109 + 8 CA CT M 4 3 2 1.449 121.900 180.000 0.127199 + 9 HA HP E 8 4 3 1.090 109.500 300.000 0.023038 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.088282 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 -0.034219 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 -0.034219 + 13 CG CT 3 10 8 4 1.510 109.470 180.000 -0.009673 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 -0.021524 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 -0.021524 + 16 CD C B 13 10 8 1.527 109.470 180.000 0.740015 + 17 OE1 O2 E 16 13 10 1.260 117.200 90.000 -0.780545 + 18 OE2 O2 E 16 13 10 1.260 117.200 270.000 -0.780545 + 19 C C M 8 4 3 1.522 111.100 180.000 0.552551 + 20 O O E 19 8 4 1.229 120.500 0.000 -0.598835 + +IMPROPER + CA +M C O + CG OE1 CD OE2 + +DONE +ASPARTIC ACID + + NASP INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.588807 + 5 H1 H E 4 3 2 1.010 130.000 0.000 0.446269 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.446269 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.446269 + 8 CA CT M 4 3 2 1.449 121.900 180.000 0.015024 + 9 HA HP E 8 4 3 1.090 109.500 300.000 0.090798 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 -0.071792 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.002802 + 12 HB3 HC E 10 8 4 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1.335 116.600 180.000 -0.421739 + 5 H2 H E 4 3 2 1.010 60.000 90.000 0.421870 + 6 H3 H E 4 3 2 1.010 60.000 -90.000 0.421870 + 7 CD CT 3 4 3 2 1.458 126.100 356.100 0.048486 + 8 HD2 HP E 7 4 3 1.090 109.500 80.000 0.039901 + 9 HD3 HP E 7 4 3 1.090 109.500 320.000 0.039901 + 10 CG CT 3 7 4 3 1.500 103.200 200.100 0.106081 + 11 HG2 HC E 10 7 4 1.090 109.500 218.000 -0.000632 + 12 HG3 HC E 10 7 4 1.090 109.500 98.000 -0.000632 + 13 CB CT B 10 7 4 1.510 106.000 338.300 -0.123305 + 14 HB2 HC E 13 10 7 1.090 109.500 256.300 0.028355 + 15 HB3 HC E 13 10 7 1.090 109.500 136.300 0.028355 + 16 CA CT M 4 3 2 1.451 120.600 175.200 0.251986 + 17 HA HP E 16 4 3 1.090 109.500 60.000 -0.021715 + 18 C C M 16 4 3 1.522 109.500 300.000 0.680470 + 19 O O E 18 16 4 1.229 120.500 0.000 -0.599226 + +LOOP + CB CA + +IMPROPER + CA +M C O + +DONE +CYSTEINE + + NCYS INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.610355 + 5 H1 H E 4 3 2 1.010 130.000 0.000 0.453452 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.453452 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.453452 + 8 CA CT M 4 3 2 1.449 121.900 180.000 0.072150 + 9 HA HP E 8 4 3 1.090 109.500 300.000 0.083203 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 -0.155113 + 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 0.113742 + 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 0.113742 + 13 SG SH S 10 8 4 1.810 116.000 180.000 -0.293380 + 14 HG HS E 13 10 8 1.330 96.000 180.000 0.190705 + 15 C C M 8 4 3 1.522 111.100 180.000 0.747857 + 16 O O E 15 8 4 1.229 120.500 0.000 -0.622908 + +IMPROPER + CA +M C O + +DONE +METHIONINE + + NMET INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.597213 + 5 H1 H E 4 3 2 1.010 130.000 0.000 0.449071 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.449071 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.449071 + 8 CA CT M 4 3 2 1.449 121.900 180.000 0.060906 + 9 HA HP E 8 4 3 1.090 109.500 300.000 0.075421 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.051523 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.038926 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.038926 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 -0.254386 + 14 HG2 H1 E 13 10 8 1.090 109.500 300.000 0.129517 + 15 HG3 H1 E 13 10 8 1.090 109.500 60.000 0.129517 + 16 SD S S 13 10 8 1.810 110.000 180.000 -0.206852 + 17 CE CT 3 16 13 10 1.780 100.000 180.000 -0.284358 + 18 HE1 H1 E 17 16 13 1.090 109.500 60.000 0.128754 + 19 HE2 H1 E 17 16 13 1.090 109.500 180.000 0.128754 + 20 HE3 H1 E 17 16 13 1.090 109.500 300.000 0.128754 + 21 C C M 8 4 3 1.522 111.100 180.000 0.683639 + 22 O O E 21 8 4 1.229 120.500 0.000 -0.599042 + +IMPROPER + CA +M C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ALA_ALANINE.in_frag new file mode 100644 index 000000000..c2df8a4e2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ALA_ALANINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB1 HC E 10 8 4 1.090 109.500 60.000 + 12 HB2 HC E 10 8 4 1.090 109.500 180.000 + 13 HB3 HC E 10 8 4 1.090 109.500 300.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ARG_ARGININE.in_frag new file mode 100644 index 000000000..490046579 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ARG_ARGININE.in_frag @@ -0,0 +1,29 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD CT 3 13 10 8 1.525 109.470 180.000 + 17 HD2 H1 E 16 13 10 1.090 109.500 300.000 + 18 HD3 H1 E 16 13 10 1.090 109.500 60.000 + 19 NE N2 B 16 13 10 1.480 111.000 180.000 + 20 HE H E 19 16 13 1.010 118.500 0.000 + 21 CZ CA B 19 16 13 1.330 123.000 180.000 + 22 NH1 N2 B 21 19 16 1.330 122.000 0.000 + 23 HH11 H E 22 21 19 1.010 119.800 0.000 + 24 HH12 H E 22 21 19 1.010 119.800 180.000 + 25 NH2 N2 B 21 19 16 1.330 118.000 180.000 + 26 HH21 H E 25 21 19 1.010 119.800 0.000 + 27 HH22 H E 25 21 19 1.010 119.800 180.000 + 28 C C M 8 4 3 1.522 111.100 180.000 + 29 O O E 28 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..75ebc4da3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ASN_ASPARAGINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C B 10 8 4 1.522 111.100 180.000 + 14 OD1 O E 13 10 8 1.229 120.500 0.000 + 15 ND2 N B 13 10 8 1.335 116.600 180.000 + 16 HD21 H E 15 13 10 1.010 119.800 180.000 + 17 HD22 H E 15 13 10 1.010 119.800 0.000 + 18 C C M 8 4 3 1.522 111.100 180.000 + 19 O O E 18 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..de3b9439a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C B 10 8 4 1.527 109.470 180.000 + 14 OD1 O2 E 13 10 8 1.260 117.200 90.000 + 15 OD2 O2 E 13 10 8 1.260 117.200 270.000 + 16 C C M 8 4 3 1.522 111.100 180.000 + 17 O O E 16 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..55155fafc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/CYS_CYSTEINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 + 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 + 13 SG SH S 10 8 4 1.810 116.000 180.000 + 14 HG HS E 13 10 8 1.330 96.000 180.000 + 15 C C M 8 4 3 1.522 111.100 180.000 + 16 O O E 15 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..1b251dd8f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 + 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 + 13 SG S E 10 8 4 1.810 116.000 180.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..772f8ad16 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/GLN_GLUTAMINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD C B 13 10 8 1.522 111.100 180.000 + 17 OE1 O E 16 13 10 1.229 120.500 0.000 + 18 NE2 N B 16 13 10 1.335 116.600 180.000 + 19 HE21 H E 18 16 13 1.010 119.800 180.000 + 20 HE22 H E 18 16 13 1.010 119.800 0.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..5c0db2845 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.510 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD C B 13 10 8 1.527 109.470 180.000 + 17 OE1 O2 E 16 13 10 1.260 117.200 90.000 + 18 OE2 O2 E 16 13 10 1.260 117.200 270.000 + 19 C C M 8 4 3 1.522 111.100 180.000 + 20 O O E 19 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..dd3f61da8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/GLY_GLYCINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA2 HP E 8 4 3 1.090 109.500 300.000 + 10 HA3 HP E 8 4 3 1.090 109.500 60.000 + 11 C C M 8 4 3 1.522 110.400 180.000 + 12 O O E 11 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..f1d09a44c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NA B 13 10 8 1.390 122.000 180.000 + 15 HD1 H E 14 13 10 1.010 126.000 0.000 + 16 CE1 CR B 14 13 10 1.320 108.000 180.000 + 17 HE1 H5 E 16 14 13 1.090 120.000 180.000 + 18 NE2 NB S 16 14 13 1.310 109.000 0.000 + 19 CD2 CV S 18 16 14 1.360 110.000 0.000 + 20 HD2 H4 E 19 18 16 1.090 120.000 180.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..25f6a52ae --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NB S 13 10 8 1.390 122.000 180.000 + 15 CE1 CR B 14 13 10 1.320 108.000 180.000 + 16 HE1 H5 E 15 14 13 1.090 120.000 180.000 + 17 NE2 NA B 15 14 13 1.310 109.000 0.000 + 18 HE2 H E 17 15 14 1.010 125.000 180.000 + 19 CD2 CW S 17 15 14 1.360 110.000 0.000 + 20 HD2 H4 E 19 17 15 1.090 120.000 180.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..17adddb37 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NA B 13 10 8 1.390 122.000 180.000 + 15 HD1 H E 14 13 10 1.010 126.000 0.000 + 16 CE1 CR B 14 13 10 1.320 108.000 180.000 + 17 HE1 H5 E 16 14 13 1.090 120.000 180.000 + 18 NE2 NA B 16 14 13 1.310 109.000 0.000 + 19 HE2 H E 18 16 14 1.010 125.000 180.000 + 20 CD2 CW S 18 16 14 1.360 110.000 0.000 + 21 HD2 H4 E 20 18 16 1.090 120.000 180.000 + 22 C C M 8 4 3 1.522 111.100 180.000 + 23 O O E 22 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..12f5bc278 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 109.470 60.000 + 11 HB HC E 10 8 4 1.090 109.500 300.000 + 12 CG2 CT 3 10 8 4 1.525 109.470 60.000 + 13 HG21 HC E 12 10 8 1.090 109.500 60.000 + 14 HG22 HC E 12 10 8 1.090 109.500 180.000 + 15 HG23 HC E 12 10 8 1.090 109.500 300.000 + 16 CG1 CT 3 10 8 4 1.525 109.470 180.000 + 17 HG12 HC E 16 10 8 1.090 109.500 60.000 + 18 HG13 HC E 16 10 8 1.090 109.500 300.000 + 19 CD1 CT 3 16 10 8 1.525 109.470 180.000 + 20 HD11 HC E 19 16 10 1.090 109.500 60.000 + 21 HD12 HC E 19 16 10 1.090 109.500 180.000 + 22 HD13 HC E 19 16 10 1.090 109.500 300.000 + 23 C C M 8 4 3 1.522 111.100 180.000 + 24 O O E 23 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..12276822e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/LEU_LEUCINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG HC E 13 10 8 1.090 109.500 300.000 + 15 CD1 CT 3 13 10 8 1.525 109.470 60.000 + 16 HD11 HC E 15 13 10 1.090 109.500 60.000 + 17 HD12 HC E 15 13 10 1.090 109.500 180.000 + 18 HD13 HC E 15 13 10 1.090 109.500 300.000 + 19 CD2 CT 3 13 10 8 1.525 109.470 180.000 + 20 HD21 HC E 19 13 10 1.090 109.500 60.000 + 21 HD22 HC E 19 13 10 1.090 109.500 180.000 + 22 HD23 HC E 19 13 10 1.090 109.500 300.000 + 23 C C M 8 4 3 1.522 111.100 180.000 + 24 O O E 23 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/LYS_LYSINE.in_frag new file mode 100644 index 000000000..cefb647ec --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/LYS_LYSINE.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD CT 3 13 10 8 1.525 109.470 180.000 + 17 HD2 HC E 16 13 10 1.090 109.500 300.000 + 18 HD3 HC E 16 13 10 1.090 109.500 60.000 + 19 CE CT 3 16 13 10 1.525 109.470 180.000 + 20 HE2 HP E 19 16 13 1.090 109.500 300.000 + 21 HE3 HP E 19 16 13 1.090 109.500 60.000 + 22 NZ N3 3 19 16 13 1.470 109.470 180.000 + 23 HZ1 H E 22 19 16 1.010 109.470 60.000 + 24 HZ2 H E 22 19 16 1.010 109.470 180.000 + 25 HZ3 H E 22 19 16 1.010 109.470 300.000 + 26 C C M 8 4 3 1.522 111.100 180.000 + 27 O O E 26 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/MET_METHIONINE.in_frag new file mode 100644 index 000000000..8fd74e252 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/MET_METHIONINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 H1 E 13 10 8 1.090 109.500 300.000 + 15 HG3 H1 E 13 10 8 1.090 109.500 60.000 + 16 SD S S 13 10 8 1.810 110.000 180.000 + 17 CE CT 3 16 13 10 1.780 100.000 180.000 + 18 HE1 H1 E 17 16 13 1.090 109.500 60.000 + 19 HE2 H1 E 17 16 13 1.090 109.500 180.000 + 20 HE3 H1 E 17 16 13 1.090 109.500 300.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..6833d9ea9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CA S 10 8 4 1.510 115.000 180.000 + 14 CD1 CA B 13 10 8 1.400 120.000 180.000 + 15 HD1 HA E 14 13 10 1.090 120.000 0.000 + 16 CE1 CA B 14 13 10 1.400 120.000 180.000 + 17 HE1 HA E 16 14 13 1.090 120.000 180.000 + 18 CZ CA B 16 14 13 1.400 120.000 0.000 + 19 HZ HA E 18 16 14 1.090 120.000 180.000 + 20 CE2 CA B 18 16 14 1.400 120.000 0.000 + 21 HE2 HA E 20 18 16 1.090 120.000 180.000 + 22 CD2 CA S 20 18 16 1.400 120.000 0.000 + 23 HD2 HA E 22 20 18 1.090 120.000 180.000 + 24 C C M 8 4 3 1.522 111.100 180.000 + 25 O O E 24 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/PRO_PROLINE.in_frag new file mode 100644 index 000000000..5d19530db --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/PRO_PROLINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H2 H E 4 3 2 1.010 60.000 90.000 + 6 H3 H E 4 3 2 1.010 60.000 -90.000 + 7 CD CT 3 4 3 2 1.458 126.100 356.100 + 8 HD2 HP E 7 4 3 1.090 109.500 80.000 + 9 HD3 HP E 7 4 3 1.090 109.500 320.000 + 10 CG CT 3 7 4 3 1.500 103.200 200.100 + 11 HG2 HC E 10 7 4 1.090 109.500 218.000 + 12 HG3 HC E 10 7 4 1.090 109.500 98.000 + 13 CB CT B 10 7 4 1.510 106.000 338.300 + 14 HB2 HC E 13 10 7 1.090 109.500 256.300 + 15 HB3 HC E 13 10 7 1.090 109.500 136.300 + 16 CA CT M 4 3 2 1.451 120.600 175.200 + 17 HA HP E 16 4 3 1.090 109.500 60.000 + 18 C C M 16 4 3 1.522 109.500 300.000 + 19 O O E 18 16 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/SER_SERINE.in_frag new file mode 100644 index 000000000..768186cb8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/SER_SERINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 + 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 + 13 OG OH S 10 8 4 1.430 109.470 180.000 + 14 HG HO E 13 10 8 0.960 109.470 180.000 + 15 C C M 8 4 3 1.522 111.100 180.000 + 16 O O E 15 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/THR_THREONINE.in_frag new file mode 100644 index 000000000..6871bde84 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/THR_THREONINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB H1 E 10 8 4 1.090 109.500 180.000 + 12 CG2 CT 3 10 8 4 1.525 109.470 300.000 + 13 HG21 HC E 12 10 8 1.090 109.500 60.000 + 14 HG22 HC E 12 10 8 1.090 109.500 180.000 + 15 HG23 HC E 12 10 8 1.090 109.500 300.000 + 16 OG1 OH S 10 8 4 1.430 109.470 60.000 + 17 HG1 HO E 16 10 8 0.960 109.470 180.000 + 18 C C M 8 4 3 1.522 111.100 180.000 + 19 O O E 18 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/TRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/TRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..56fd0dd42 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/TRP_TRYPTOPHAN.in_frag @@ -0,0 +1,29 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HP E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C* S 10 8 4 1.510 115.000 180.000 + 14 CD1 CW B 13 10 8 1.340 127.000 180.000 + 15 HD1 H4 E 14 13 10 1.090 120.000 0.000 + 16 NE1 NA B 14 13 10 1.430 107.000 180.000 + 17 HE1 H E 16 14 13 1.010 125.500 180.000 + 18 CE2 CN S 16 14 13 1.310 109.000 0.000 + 19 CZ2 CA B 18 16 14 1.400 128.000 180.000 + 20 HZ2 HA E 19 18 16 1.090 120.000 0.000 + 21 CH2 CA B 19 18 16 1.390 116.000 180.000 + 22 HH2 HA E 21 19 18 1.090 120.000 180.000 + 23 CZ3 CA B 21 19 18 1.350 121.000 0.000 + 24 HZ3 HA E 23 21 19 1.090 120.000 180.000 + 25 CE3 CA B 23 21 19 1.410 122.000 0.000 + 26 HE3 HA E 25 23 21 1.090 120.000 180.000 + 27 CD2 CB E 25 23 21 1.400 117.000 0.000 + 28 C C M 8 4 3 1.522 111.100 180.000 + 29 O O E 28 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_aminont94/TYR_TYROSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_aminont94/TYR_TYROSINE.in_frag new file mode 100644 index 000000000..81db6af2a --- /dev/null +++ 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CB CT 3 8 4 3 1.525 111.100 60.000 0.06590 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.01020 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.01020 + 13 CG CA S 10 8 4 1.510 109.470 180.000 -0.02050 + 14 CD1 CA B 13 10 8 1.400 120.000 180.000 -0.20020 + 15 HD1 HA E 14 13 10 1.090 120.000 0.000 0.17200 + 16 CE1 CA B 14 13 10 1.400 120.000 180.000 -0.22390 + 17 HE1 HA E 16 14 13 1.090 120.000 180.000 0.16500 + 18 CZ C B 16 14 13 1.400 120.000 0.000 0.31390 + 19 OH OH S 18 16 14 1.360 120.000 180.000 -0.55780 + 20 HH HO E 19 18 16 0.960 113.000 0.000 0.40010 + 21 CE2 CA B 18 16 14 1.400 120.000 0.000 -0.22390 + 22 HE2 HA E 21 18 16 1.090 120.000 180.000 0.16500 + 23 CD2 CA S 21 18 16 1.400 120.000 0.000 -0.20020 + 24 HD2 HA E 23 21 18 1.090 120.000 180.000 0.17200 + 25 C C M 8 4 3 1.522 111.100 180.000 0.61230 + 26 O O E 25 8 4 1.229 120.500 0.000 -0.57130 + +LOOP + CG CD2 + +IMPROPER + CA +M C O + CG CE2 CD2 HD2 + CD2 CZ CE2 HE2 + CD1 CZ CE1 HE1 + CG CE1 CD1 HD1 + CD1 CD2 CG CB + CE1 CE2 CZ 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180.000 -0.01810 + 20 HE2 HP E 19 16 13 1.090 109.500 300.000 0.11710 + 21 HE3 HP E 19 16 13 1.090 109.500 60.000 0.11710 + 22 NZ N3 3 19 16 13 1.470 109.470 180.000 -0.37640 + 23 HZ1 H E 22 19 16 1.010 109.470 60.000 0.33820 + 24 HZ2 H E 22 19 16 1.010 109.470 180.000 0.33820 + 25 HZ3 H E 22 19 16 1.010 109.470 300.000 0.33820 + 26 C C M 8 4 3 1.522 111.100 180.000 0.72140 + 27 O O E 26 8 4 1.229 120.500 0.000 -0.60130 + +IMPROPER + CA +M C O + +DONE +PROLINE + + PRO INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.20200 + 5 H2 H E 4 3 2 1.010 60.000 90.000 0.31200 + 6 H3 H E 4 3 2 1.010 60.000 -90.000 0.31200 + 7 CD CT 3 4 3 2 1.458 126.100 356.100 -0.01200 + 8 HD2 HP E 7 4 3 1.090 109.500 80.000 0.10000 + 9 HD3 HP E 7 4 3 1.090 109.500 320.000 0.10000 + 10 CG CT 3 7 4 3 1.500 103.200 200.100 -0.12100 + 11 HG2 HC E 10 7 4 1.090 109.500 218.000 0.10000 + 12 HG3 HC E 10 7 4 1.090 109.500 98.000 0.10000 + 13 CB CT B 10 7 4 1.510 106.000 338.300 -0.11500 + 14 HB2 HC E 13 10 7 1.090 109.500 256.300 0.10000 + 15 HB3 HC E 13 10 7 1.090 109.500 136.300 0.10000 + 16 CA CT M 4 3 2 1.451 120.600 175.200 0.10000 + 17 HA HP E 16 4 3 1.090 109.500 60.000 0.10000 + 18 C C M 16 4 3 1.522 109.500 300.000 0.52600 + 19 O O E 18 16 4 1.229 120.500 0.000 -0.50000 + +LOOP + CB CA + +IMPROPER + CA +M C O + +DONE +CYSTEINE + + CYS INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 0.13250 + 5 H1 H E 4 3 2 1.010 130.000 0.000 0.20230 + 6 H2 H E 4 3 2 1.010 60.000 90.000 0.20230 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.20230 + 8 CA CT M 4 3 2 1.449 121.900 180.000 0.09270 + 9 HA HP E 8 4 3 1.090 109.500 300.000 0.14110 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 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10 1.780 100.000 180.000 -0.03410 + 18 HE1 H1 E 17 16 13 1.090 109.500 60.000 0.05970 + 19 HE2 H1 E 17 16 13 1.090 109.500 180.000 0.05970 + 20 HE3 H1 E 17 16 13 1.090 109.500 300.000 0.05970 + 21 C C M 8 4 3 1.522 111.100 180.000 0.61230 + 22 O O E 21 8 4 1.229 120.500 0.000 -0.57130 + +IMPROPER + CA +M C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/AME_N-methyl-ADENINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/AME_N-methyl-ADENINE.in_frag new file mode 100644 index 000000000..7325e7ba3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/AME_N-methyl-ADENINE.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H11' H1 M 3 2 1 3.886 92.507 92.096 + 5 C1' CT M 4 3 2 1.090 102.037 71.294 + 6 H12' H1 E 5 4 3 1.090 109.478 183.234 + 7 H13' H1 E 5 4 3 1.090 107.820 59.290 + 8 N9 N* M 5 4 3 1.521 109.603 295.536 + 9 C8 CK M 8 5 4 1.370 131.187 81.607 + 10 H8 H5 E 9 8 5 1.080 120.006 0.005 + 11 N7 NB M 9 8 5 1.300 113.887 177.020 + 12 C5 CB M 11 9 8 1.389 104.039 0.004 + 13 C6 CA M 12 11 9 1.400 132.429 180.043 + 14 N6 N2 B 13 12 11 1.340 123.498 359.961 + 15 H61 H E 14 13 12 1.010 119.942 180.044 + 16 H62 H E 14 13 12 1.010 120.005 0.006 + 17 N1 NC M 13 12 11 1.340 117.408 179.960 + 18 C2 CQ M 17 13 12 1.330 118.832 0.008 + 19 H2 H5 E 18 17 13 1.080 120.013 179.993 + 20 N3 NC M 18 17 13 1.319 129.149 359.931 + 21 C4 CB M 20 18 17 1.350 110.830 0.083 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/CME_N-methyl-CYTOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/CME_N-methyl-CYTOSINE.in_frag new file mode 100644 index 000000000..9cc870683 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/CME_N-methyl-CYTOSINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H11' H1 M 3 2 1 3.886 92.507 92.096 + 5 C1' CT M 4 3 2 1.090 102.037 71.294 + 6 H12' H1 E 5 4 3 1.090 109.478 183.234 + 7 H13' H1 E 5 4 3 1.090 107.820 59.290 + 8 N1 N* M 5 4 3 1.490 108.119 295.550 + 9 C6 CM M 8 5 4 1.360 121.134 81.573 + 10 H6 H4 E 9 8 5 1.080 119.949 0.042 + 11 C5 CM M 9 8 5 1.360 121.029 180.041 + 12 H5 HA E 11 9 8 1.090 119.994 180.067 + 13 C4 CA M 11 9 8 1.430 116.875 359.972 + 14 N4 N2 B 13 11 9 1.319 120.077 179.993 + 15 H41 H E 14 13 11 1.010 117.746 180.030 + 16 H42 H E 14 13 11 1.010 120.295 0.061 + 17 N3 NC M 13 11 9 1.330 121.703 0.075 + 18 C2 C M 17 13 11 1.360 120.533 359.923 + 19 O2 O E 18 17 13 1.239 122.457 180.051 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DA3_D-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DA3_D-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..d7c8041d1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DA3_D-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,36 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.520 109.590 -127.700 + 17 C8 CK B 16 14 13 1.370 131.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.300 113.930 177.000 + 20 C5 CB S 19 17 16 1.390 104.000 0.000 + 21 C6 CA B 20 19 17 1.400 132.420 180.000 + 22 N6 N2 B 21 20 19 1.340 123.500 0.000 + 23 H61 H E 22 21 20 1.010 120.000 180.000 + 24 H62 H E 22 21 20 1.010 120.000 0.000 + 25 N1 NC S 21 20 19 1.340 117.430 180.000 + 26 C2 CQ B 25 21 20 1.330 118.800 0.000 + 27 H2 H5 E 26 25 21 1.080 120.000 180.000 + 28 N3 NC S 26 25 21 1.320 129.170 0.000 + 29 C4 CB E 28 26 25 1.350 110.800 0.000 + 30 C3' CT M 11 8 7 1.530 115.780 -329.110 + 31 H3' H1 E 30 11 8 1.090 109.500 30.000 + 32 C2' CT B 30 11 8 1.530 102.800 -86.300 + 33 H2'1 HC E 32 30 11 1.090 109.500 120.000 + 34 H2'2 HC E 32 30 11 1.090 109.500 240.000 + 35 O3' OH M 30 11 8 1.420 116.520 -203.470 + 36 H3T HO M 35 30 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DA5_D-ADENOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DA5_D-ADENOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag new file mode 100644 index 000000000..b017a823c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DA5_D-ADENOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.520 109.590 -127.700 + 15 C8 CK B 14 12 11 1.370 131.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.300 113.930 177.000 + 18 C5 CB S 17 15 14 1.390 104.000 0.000 + 19 C6 CA B 18 17 15 1.400 132.420 180.000 + 20 N6 N2 B 19 18 17 1.340 123.500 0.000 + 21 H61 H E 20 19 18 1.010 120.000 180.000 + 22 H62 H E 20 19 18 1.010 120.000 0.000 + 23 N1 NC S 19 18 17 1.340 117.430 180.000 + 24 C2 CQ B 23 19 18 1.330 118.800 0.000 + 25 H2 H5 E 24 23 19 1.080 120.000 180.000 + 26 N3 NC S 24 23 19 1.320 129.170 0.000 + 27 C4 CB E 26 24 23 1.350 110.800 0.000 + 28 C3' CT M 9 6 5 1.530 115.780 -329.110 + 29 H3' H1 E 28 9 6 1.090 109.500 30.000 + 30 C2' CT B 28 9 6 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 9 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 9 1.090 109.500 240.000 + 33 O3' OS M 28 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DAN_D-ADENOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DAN_D-ADENOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..07eaa1462 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DAN_D-ADENOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.520 109.590 -127.700 + 15 C8 CK B 14 12 11 1.370 131.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.300 113.930 177.000 + 18 C5 CB S 17 15 14 1.390 104.000 0.000 + 19 C6 CA B 18 17 15 1.400 132.420 180.000 + 20 N6 N2 B 19 18 17 1.340 123.500 0.000 + 21 H61 H E 20 19 18 1.010 120.000 180.000 + 22 H62 H E 20 19 18 1.010 120.000 0.000 + 23 N1 NC S 19 18 17 1.340 117.430 180.000 + 24 C2 CQ B 23 19 18 1.330 118.800 0.000 + 25 H2 H5 E 24 23 19 1.080 120.000 180.000 + 26 N3 NC S 24 23 19 1.320 129.170 0.000 + 27 C4 CB E 26 24 23 1.350 110.800 0.000 + 28 C3' CT M 9 6 5 1.530 115.780 -329.110 + 29 H3' H1 E 28 9 6 1.090 109.500 30.000 + 30 C2' CT B 28 9 6 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 9 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 9 1.090 109.500 240.000 + 33 O3' OH M 28 9 6 1.420 116.520 -203.470 + 34 H3T HO M 33 28 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DA_D-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DA_D-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..47683c43b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DA_D-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.520 109.590 -127.700 + 17 C8 CK B 16 14 13 1.370 131.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.300 113.930 177.000 + 20 C5 CB S 19 17 16 1.390 104.000 0.000 + 21 C6 CA B 20 19 17 1.400 132.420 180.000 + 22 N6 N2 B 21 20 19 1.340 123.500 0.000 + 23 H61 H E 22 21 20 1.010 120.000 180.000 + 24 H62 H E 22 21 20 1.010 120.000 0.000 + 25 N1 NC S 21 20 19 1.340 117.430 180.000 + 26 C2 CQ B 25 21 20 1.330 118.800 0.000 + 27 H2 H5 E 26 25 21 1.080 120.000 180.000 + 28 N3 NC S 26 25 21 1.320 129.170 0.000 + 29 C4 CB E 28 26 25 1.350 110.800 0.000 + 30 C3' CT M 11 8 7 1.530 115.780 -329.110 + 31 H3' H1 E 30 11 8 1.090 109.500 30.000 + 32 C2' CT B 30 11 8 1.530 102.800 -86.300 + 33 H2'1 HC E 32 30 11 1.090 109.500 120.000 + 34 H2'2 HC E 32 30 11 1.090 109.500 240.000 + 35 O3' OS M 30 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DC3_D-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DC3_D-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..4db0b10ec --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DC3_D-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.490 108.100 -127.700 + 17 C6 CM B 16 14 13 1.360 121.100 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.360 121.000 180.000 + 20 H5 HA E 19 17 16 1.090 120.000 180.000 + 21 C4 CA B 19 17 16 1.430 116.900 0.000 + 22 N4 N2 B 21 19 17 1.320 120.100 180.000 + 23 H41 H E 22 21 19 1.010 117.700 180.000 + 24 H42 H E 22 21 19 1.010 120.270 0.000 + 25 N3 NC S 21 19 17 1.330 121.700 0.000 + 26 C2 C S 25 21 19 1.360 120.500 0.000 + 27 O2 O E 26 25 21 1.240 122.400 180.000 + 28 C3' CT M 11 8 7 1.530 115.780 -329.110 + 29 H3' H1 E 28 11 8 1.090 109.500 30.000 + 30 C2' CT B 28 11 8 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 11 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 11 1.090 109.500 240.000 + 33 O3' OH M 28 11 8 1.420 116.520 -203.470 + 34 H3T HO M 30 25 8 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DC5_D-CYTOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DC5_D-CYTOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..4c8f63c17 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DC5_D-CYTOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,31 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.490 108.100 -127.700 + 15 C6 CM B 14 12 11 1.360 121.100 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.360 121.000 180.000 + 18 H5 HA E 17 15 14 1.090 120.000 180.000 + 19 C4 CA B 17 15 14 1.430 116.900 0.000 + 20 N4 N2 B 19 17 15 1.320 120.100 180.000 + 21 H41 H E 20 19 17 1.010 117.700 180.000 + 22 H42 H E 20 19 17 1.010 120.270 0.000 + 23 N3 NC S 19 17 15 1.330 121.700 0.000 + 24 C2 C S 23 19 17 1.360 120.500 0.000 + 25 O2 O E 24 23 19 1.240 122.400 180.000 + 26 C3' CT M 9 6 5 1.530 115.780 -329.110 + 27 H3' H1 E 26 9 6 1.090 109.500 30.000 + 28 C2' CT B 26 9 6 1.530 102.800 -86.300 + 29 H2'1 HC E 28 26 9 1.090 109.500 120.000 + 30 H2'2 HC E 28 26 9 1.090 109.500 240.000 + 31 O3' OS M 26 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DCN_D-CYTOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DCN_D-CYTOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..cc05558b3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DCN_D-CYTOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.490 108.100 -127.700 + 15 C6 CM B 14 12 11 1.360 121.100 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.360 121.000 180.000 + 18 H5 HA E 17 15 14 1.090 120.000 180.000 + 19 C4 CA B 17 15 14 1.430 116.900 0.000 + 20 N4 N2 B 19 17 15 1.320 120.100 180.000 + 21 H41 H E 20 19 17 1.010 117.700 180.000 + 22 H42 H E 20 19 17 1.010 120.270 0.000 + 23 N3 NC S 19 17 15 1.330 121.700 0.000 + 24 C2 C S 23 19 17 1.360 120.500 0.000 + 25 O2 O E 24 23 19 1.240 122.400 180.000 + 26 C3' CT M 9 6 5 1.530 115.780 -329.110 + 27 H3' H1 E 26 9 6 1.090 109.500 30.000 + 28 C2' CT B 26 9 6 1.530 102.800 -86.300 + 29 H2'1 HC E 28 26 9 1.090 109.500 120.000 + 30 H2'2 HC E 28 26 9 1.090 109.500 240.000 + 31 O3' OH M 26 9 6 1.420 116.520 -203.470 + 32 H3T HO M 31 26 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DC_D-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DC_D-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..8d0b26c2b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DC_D-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.490 108.100 -127.700 + 17 C6 CM B 16 14 13 1.360 121.100 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.360 121.000 180.000 + 20 H5 HA E 19 17 16 1.090 120.000 180.000 + 21 C4 CA B 19 17 16 1.430 116.900 0.000 + 22 N4 N2 B 21 19 17 1.320 120.100 180.000 + 23 H41 H E 22 21 19 1.010 117.700 180.000 + 24 H42 H E 22 21 19 1.010 120.270 0.000 + 25 N3 NC S 21 19 17 1.330 121.700 0.000 + 26 C2 C S 25 21 19 1.360 120.500 0.000 + 27 O2 O E 26 25 21 1.240 122.400 180.000 + 28 C3' CT M 11 8 7 1.530 115.780 -329.110 + 29 H3' H1 E 28 11 8 1.090 109.500 30.000 + 30 C2' CT B 28 11 8 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 11 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 11 1.090 109.500 240.000 + 33 O3' OS M 28 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DG3_D-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DG3_D-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..cf83eb63c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DG3_D-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,37 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.490 108.060 -127.700 + 17 C8 CK B 16 14 13 1.380 129.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.310 114.000 -179.900 + 20 C5 CB S 19 17 16 1.390 103.900 0.000 + 21 C6 C B 20 19 17 1.420 130.400 180.000 + 22 O6 O E 21 20 19 1.230 128.800 0.000 + 23 N1 NA B 21 20 19 1.400 111.380 180.000 + 24 H1 H E 23 21 20 1.000 117.360 179.900 + 25 C2 CA B 23 21 20 1.380 125.240 -0.100 + 26 N2 N2 B 25 23 21 1.340 116.020 180.000 + 27 H21 H E 26 25 23 1.010 127.000 -0.820 + 28 H22 H E 26 25 23 1.010 116.530 -179.440 + 29 N3 NC S 25 23 21 1.330 123.300 0.000 + 30 C4 CB E 29 25 23 1.360 112.200 0.000 + 31 C3' CT M 11 8 7 1.530 115.780 -329.110 + 32 H3' H1 E 31 11 8 1.090 109.500 30.000 + 33 C2' CT B 31 11 8 1.530 102.800 -86.300 + 34 H2'1 HC E 33 31 11 1.090 109.500 120.000 + 35 H2'2 HC E 33 31 11 1.090 109.500 240.000 + 36 O3' OH M 31 11 8 1.420 116.520 -203.470 + 37 H3T HO M 36 31 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DG5_D-GUANOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DG5_D-GUANOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..0997610b6 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DG5_D-GUANOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.490 108.060 -127.700 + 15 C8 CK B 14 12 11 1.380 129.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.310 114.000 -179.900 + 18 C5 CB S 17 15 14 1.390 103.900 0.000 + 19 C6 C B 18 17 15 1.420 130.400 180.000 + 20 O6 O E 19 18 17 1.230 128.800 0.000 + 21 N1 NA B 19 18 17 1.400 111.380 180.000 + 22 H1 H E 21 19 18 1.000 117.360 179.900 + 23 C2 CA B 21 19 18 1.380 125.240 -0.100 + 24 N2 N2 B 23 21 19 1.340 116.020 180.000 + 25 H21 H E 24 23 21 1.010 127.000 -0.820 + 26 H22 H E 24 23 21 1.010 116.530 -179.440 + 27 N3 NC S 23 21 19 1.330 123.300 0.000 + 28 C4 CB E 27 23 21 1.360 112.200 0.000 + 29 C3' CT M 9 6 5 1.530 115.780 -329.110 + 30 H3' H1 E 29 9 6 1.090 109.500 30.000 + 31 C2' CT B 29 9 6 1.530 102.800 -86.300 + 32 H2'1 HC E 31 29 9 1.090 109.500 120.000 + 33 H2'2 HC E 31 29 9 1.090 109.500 240.000 + 34 O3' OS M 29 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DGN_D-GUANOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DGN_D-GUANOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..56185415a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DGN_D-GUANOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.490 108.060 -127.700 + 15 C8 CK B 14 12 11 1.380 129.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.310 114.000 -179.900 + 18 C5 CB S 17 15 14 1.390 103.900 0.000 + 19 C6 C B 18 17 15 1.420 130.400 180.000 + 20 O6 O E 19 18 17 1.230 128.800 0.000 + 21 N1 NA B 19 18 17 1.400 111.380 180.000 + 22 H1 H E 21 19 18 1.000 117.360 179.900 + 23 C2 CA B 21 19 18 1.380 125.240 -0.100 + 24 N2 N2 B 23 21 19 1.340 116.020 180.000 + 25 H21 H E 24 23 21 1.010 127.000 -0.820 + 26 H22 H E 24 23 21 1.010 116.530 -179.440 + 27 N3 NC S 23 21 19 1.330 123.300 0.000 + 28 C4 CB E 27 23 21 1.360 112.200 0.000 + 29 C3' CT M 9 6 5 1.530 115.780 -329.110 + 30 H3' H1 E 29 9 6 1.090 109.500 30.000 + 31 C2' CT B 29 9 6 1.530 102.800 -86.300 + 32 H2'1 HC E 31 29 9 1.090 109.500 120.000 + 33 H2'2 HC E 31 29 9 1.090 109.500 240.000 + 34 O3' OH M 29 9 6 1.420 116.520 -203.470 + 35 H3T HO M 34 29 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DG_D-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__grou.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DG_D-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__grou.in_frag new file mode 100644 index 000000000..acf8f7bb5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DG_D-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__grou.in_frag @@ -0,0 +1,36 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.490 108.060 -127.700 + 17 C8 CK B 16 14 13 1.380 129.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.310 114.000 -179.900 + 20 C5 CB S 19 17 16 1.390 103.900 0.000 + 21 C6 C B 20 19 17 1.420 130.400 180.000 + 22 O6 O E 21 20 19 1.230 128.800 0.000 + 23 N1 NA B 21 20 19 1.400 111.380 180.000 + 24 H1 H E 23 21 20 1.000 117.360 179.900 + 25 C2 CA B 23 21 20 1.380 125.240 -0.100 + 26 N2 N2 B 25 23 21 1.340 116.020 180.000 + 27 H21 H E 26 25 23 1.010 127.000 -0.820 + 28 H22 H E 26 25 23 1.010 116.530 -179.440 + 29 N3 NC S 25 23 21 1.330 123.300 0.000 + 30 C4 CB E 29 25 23 1.360 112.200 0.000 + 31 C3' CT M 11 8 7 1.530 115.780 -329.110 + 32 H3' H1 E 31 11 8 1.090 109.500 30.000 + 33 C2' CT B 31 11 8 1.530 102.800 -86.300 + 34 H2'1 HC E 33 31 11 1.090 109.500 120.000 + 35 H2'2 HC E 33 31 11 1.090 109.500 240.000 + 36 O3' OS M 31 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DT3_D-THYMINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DT3_D-THYMINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..c83118990 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DT3_D-THYMINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,36 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.530 109.590 -127.700 + 17 C6 CM B 16 14 13 1.370 123.040 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.340 121.220 177.300 + 20 C7 CT 3 19 17 16 1.500 121.630 180.000 + 21 H71 HC E 20 19 17 1.090 109.500 60.000 + 22 H72 HC E 20 19 17 1.090 109.500 180.000 + 23 H73 HC E 20 19 17 1.090 109.500 300.000 + 24 C4 C B 19 17 16 1.440 120.780 0.000 + 25 O4 O E 24 19 17 1.230 125.350 180.000 + 26 N3 NA B 24 19 17 1.380 114.070 0.000 + 27 H3 H E 26 24 19 1.090 116.770 180.000 + 28 C2 C S 26 24 19 1.380 126.460 0.000 + 29 O2 O E 28 26 24 1.220 121.700 180.000 + 30 C3' CT M 11 8 7 1.530 115.780 -329.110 + 31 H3' H1 E 30 11 8 1.090 109.500 30.000 + 32 C2' CT B 30 11 8 1.530 102.800 -86.300 + 33 H2'1 HC E 32 30 11 1.090 109.500 120.000 + 34 H2'2 HC E 32 30 11 1.090 109.500 240.000 + 35 O3' OH M 30 11 8 1.420 116.520 -203.470 + 36 H3T HO M 35 30 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DT5_D-THYMINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DT5_D-THYMINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag new file mode 100644 index 000000000..cd4ef1061 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DT5_D-THYMINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.530 109.590 -127.700 + 15 C6 CM B 14 12 11 1.370 123.040 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.340 121.220 177.300 + 18 C7 CT 3 17 15 14 1.500 121.630 180.000 + 19 H71 HC E 18 17 15 1.090 109.500 60.000 + 20 H72 HC E 18 17 15 1.090 109.500 180.000 + 21 H73 HC E 18 17 15 1.090 109.500 300.000 + 22 C4 C B 17 15 14 1.440 120.780 0.000 + 23 O4 O E 22 17 15 1.230 125.350 180.000 + 24 N3 NA B 22 17 15 1.380 114.070 0.000 + 25 H3 H E 24 22 17 1.090 116.770 180.000 + 26 C2 C S 24 22 17 1.380 126.460 0.000 + 27 O2 O E 26 24 22 1.220 121.700 180.000 + 28 C3' CT M 9 6 5 1.530 115.780 -329.110 + 29 H3' H1 E 28 9 6 1.090 109.500 30.000 + 30 C2' CT B 28 9 6 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 9 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 9 1.090 109.500 240.000 + 33 O3' OS M 28 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DTN_D-THYMINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DTN_D-THYMINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..37948bad6 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DTN_D-THYMINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.530 109.590 -127.700 + 15 C6 CM B 14 12 11 1.370 123.040 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.340 121.220 177.300 + 18 C7 CT 3 17 15 14 1.500 121.630 180.000 + 19 H71 HC E 18 17 15 1.090 109.500 60.000 + 20 H72 HC E 18 17 15 1.090 109.500 180.000 + 21 H73 HC E 18 17 15 1.090 109.500 300.000 + 22 C4 C B 17 15 14 1.440 120.780 0.000 + 23 O4 O E 22 17 15 1.230 125.350 180.000 + 24 N3 NA B 22 17 15 1.380 114.070 0.000 + 25 H3 H E 24 22 17 1.090 116.770 180.000 + 26 C2 C S 24 22 17 1.380 126.460 0.000 + 27 O2 O E 26 24 22 1.220 121.700 180.000 + 28 C3' CT M 9 6 5 1.530 115.780 -329.110 + 29 H3' H1 E 28 9 6 1.090 109.500 30.000 + 30 C2' CT B 28 9 6 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 9 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 9 1.090 109.500 240.000 + 33 O3' OH M 28 9 6 1.420 116.520 -203.470 + 34 H3T HO M 33 28 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DT_D-THYMINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DT_D-THYMINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..0aafac705 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/DT_D-THYMINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.530 109.590 -127.700 + 17 C6 CM B 16 14 13 1.370 123.040 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.340 121.220 177.300 + 20 C7 CT 3 19 17 16 1.500 121.630 180.000 + 21 H71 HC E 20 19 17 1.090 109.500 60.000 + 22 H72 HC E 20 19 17 1.090 109.500 180.000 + 23 H73 HC E 20 19 17 1.090 109.500 300.000 + 24 C4 C B 19 17 16 1.440 120.780 0.000 + 25 O4 O E 24 19 17 1.230 125.350 180.000 + 26 N3 NA B 24 19 17 1.380 114.070 0.000 + 27 H3 H E 26 24 19 1.090 116.770 180.000 + 28 C2 C S 26 24 19 1.380 126.460 0.000 + 29 O2 O E 28 26 24 1.220 121.700 180.000 + 30 C3' CT M 11 8 7 1.530 115.780 -329.110 + 31 H3' H1 E 30 11 8 1.090 109.500 30.000 + 32 C2' CT B 30 11 8 1.530 102.800 -86.300 + 33 H2'1 HC E 32 30 11 1.090 109.500 120.000 + 34 H2'2 HC E 32 30 11 1.090 109.500 240.000 + 35 O3' OS M 30 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/GME_N-methyl-GUANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/GME_N-methyl-GUANINE.in_frag new file mode 100644 index 000000000..3276b2e47 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/GME_N-methyl-GUANINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H11' H1 M 3 2 1 3.886 92.507 92.096 + 5 C1' CT M 4 3 2 1.090 102.037 71.294 + 6 H12' H1 E 5 4 3 1.090 109.478 183.234 + 7 H13' H1 E 5 4 3 1.090 107.820 59.290 + 8 N9 N* M 5 4 3 1.490 108.083 295.538 + 9 C8 CK M 8 5 4 1.380 129.207 81.569 + 10 H8 H5 E 9 8 5 1.080 119.990 0.059 + 11 N7 NB M 9 8 5 1.310 114.017 180.107 + 12 C5 CB M 11 9 8 1.390 103.895 0.035 + 13 C6 C M 12 11 9 1.420 130.429 179.953 + 14 O6 O E 13 12 11 1.231 128.783 0.029 + 15 N1 NA M 13 12 11 1.400 111.406 180.017 + 16 H1 H E 15 13 12 1.001 117.361 179.931 + 17 C2 CA M 15 13 12 1.380 125.226 359.894 + 18 N2 N2 B 17 15 13 1.341 116.036 180.023 + 19 H21 H E 18 17 15 1.010 126.957 359.196 + 20 H22 H E 18 17 15 1.010 116.558 180.562 + 21 N3 NC M 17 15 13 1.330 123.346 0.013 + 22 C4 CB M 21 17 15 1.360 112.160 359.998 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RA3_R-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RA3_R-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..0f484cfc7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RA3_R-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,37 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.520 109.590 -127.700 + 17 C8 CK B 16 14 13 1.370 131.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.300 113.930 177.000 + 20 C5 CB S 19 17 16 1.390 104.000 0.000 + 21 C6 CA B 20 19 17 1.400 132.420 180.000 + 22 N6 N2 B 21 20 19 1.340 123.500 0.000 + 23 H61 H E 22 21 20 1.010 120.000 180.000 + 24 H62 H E 22 21 20 1.010 120.000 0.000 + 25 N1 NC S 21 20 19 1.340 117.430 180.000 + 26 C2 CQ B 25 21 20 1.330 118.800 0.000 + 27 H2 H5 E 26 25 21 1.080 120.000 180.000 + 28 N3 NC S 26 25 21 1.320 129.170 0.000 + 29 C4 CB E 28 26 25 1.350 110.800 0.000 + 30 C3' CT M 11 8 7 1.530 115.780 -329.110 + 31 H3' H1 E 30 11 8 1.090 109.500 30.000 + 32 C2' CT B 30 11 8 1.530 102.800 -86.300 + 33 H2'1 H1 E 32 30 11 1.090 109.500 120.000 + 34 O2' OH S 32 30 11 1.430 109.500 240.000 + 35 HO'2 HO E 34 32 30 0.960 107.000 180.000 + 36 O3' OH M 30 11 8 1.420 116.520 -203.470 + 37 H3T HO M 36 30 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RA5_R-ADENOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RA5_R-ADENOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag new file mode 100644 index 000000000..3366e1f81 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RA5_R-ADENOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.520 109.590 -127.700 + 15 C8 CK B 14 12 11 1.370 131.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.300 113.930 177.000 + 18 C5 CB S 17 15 14 1.390 104.000 0.000 + 19 C6 CA B 18 17 15 1.400 132.420 180.000 + 20 N6 N2 B 19 18 17 1.340 123.500 0.000 + 21 H61 H E 20 19 18 1.010 120.000 180.000 + 22 H62 H E 20 19 18 1.010 120.000 0.000 + 23 N1 NC S 19 18 17 1.340 117.430 180.000 + 24 C2 CQ B 23 19 18 1.330 118.800 0.000 + 25 H2 H5 E 24 23 19 1.080 120.000 180.000 + 26 N3 NC S 24 23 19 1.320 129.170 0.000 + 27 C4 CB E 26 24 23 1.350 110.800 0.000 + 28 C3' CT M 9 6 5 1.530 115.780 -329.110 + 29 H3' H1 E 28 9 6 1.090 109.500 30.000 + 30 C2' CT B 28 9 6 1.530 102.800 -86.300 + 31 H2'1 H1 E 30 28 9 1.090 109.500 120.000 + 32 O2' OH S 30 28 9 1.430 109.500 240.000 + 33 HO'2 HO E 32 30 28 0.960 107.000 180.000 + 34 O3' OS M 28 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RAN_R-ADENOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RAN_R-ADENOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..b14a4b407 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RAN_R-ADENOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.520 109.590 -127.700 + 15 C8 CK B 14 12 11 1.370 131.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.300 113.930 177.000 + 18 C5 CB S 17 15 14 1.390 104.000 0.000 + 19 C6 CA B 18 17 15 1.400 132.420 180.000 + 20 N6 N2 B 19 18 17 1.340 123.500 0.000 + 21 H61 H E 20 19 18 1.010 120.000 180.000 + 22 H62 H E 20 19 18 1.010 120.000 0.000 + 23 N1 NC S 19 18 17 1.340 117.430 180.000 + 24 C2 CQ B 23 19 18 1.330 118.800 0.000 + 25 H2 H5 E 24 23 19 1.080 120.000 180.000 + 26 N3 NC S 24 23 19 1.320 129.170 0.000 + 27 C4 CB E 26 24 23 1.350 110.800 0.000 + 28 C3' CT M 9 6 5 1.530 115.780 -329.110 + 29 H3' H1 E 28 9 6 1.090 109.500 30.000 + 30 C2' CT B 28 9 6 1.530 102.800 -86.300 + 31 H2'1 H1 E 30 28 9 1.090 109.500 120.000 + 32 O2' OH S 30 28 9 1.430 109.500 240.000 + 33 HO'2 HO E 32 30 28 0.960 107.000 180.000 + 34 O3' OH M 28 9 6 1.420 116.520 -203.470 + 35 H3T HO M 34 28 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RA_R-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__grou.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RA_R-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__grou.in_frag new file mode 100644 index 000000000..fbae9a960 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RA_R-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__grou.in_frag @@ -0,0 +1,36 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.520 109.590 -127.700 + 17 C8 CK B 16 14 13 1.370 131.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.300 113.930 177.000 + 20 C5 CB S 19 17 16 1.390 104.000 0.000 + 21 C6 CA B 20 19 17 1.400 132.420 180.000 + 22 N6 N2 B 21 20 19 1.340 123.500 0.000 + 23 H61 H E 22 21 20 1.010 120.000 180.000 + 24 H62 H E 22 21 20 1.010 120.000 0.000 + 25 N1 NC S 21 20 19 1.340 117.430 180.000 + 26 C2 CQ B 25 21 20 1.330 118.800 0.000 + 27 H2 H5 E 26 25 21 1.080 120.000 180.000 + 28 N3 NC S 26 25 21 1.320 129.170 0.000 + 29 C4 CB E 28 26 25 1.350 110.800 0.000 + 30 C3' CT M 11 8 7 1.530 115.780 -329.110 + 31 H3' H1 E 30 11 8 1.090 109.500 30.000 + 32 C2' CT B 30 11 8 1.530 102.800 -86.300 + 33 H2'1 H1 E 32 30 11 1.090 109.500 120.000 + 34 O2' OH S 32 30 11 1.430 109.500 240.000 + 35 HO'2 HO E 34 32 30 0.960 107.000 180.000 + 36 O3' OS M 30 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RC3_R-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RC3_R-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..dd226e8cb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RC3_R-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.490 108.100 -127.700 + 17 C6 CM B 16 14 13 1.360 121.100 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.360 121.000 180.000 + 20 H5 HA E 19 17 16 1.090 120.000 180.000 + 21 C4 CA B 19 17 16 1.430 116.900 0.000 + 22 N4 N2 B 21 19 17 1.320 120.100 180.000 + 23 H41 H E 22 21 19 1.010 117.700 180.000 + 24 H42 H E 22 21 19 1.010 120.270 0.000 + 25 N3 NC S 21 19 17 1.330 121.700 0.000 + 26 C2 C S 25 21 19 1.360 120.500 0.000 + 27 O2 O E 26 25 21 1.240 122.400 180.000 + 28 C3' CT M 11 8 7 1.530 115.780 -329.110 + 29 H3' H1 E 28 11 8 1.090 109.500 30.000 + 30 C2' CT B 28 11 8 1.530 102.800 -86.300 + 31 H2'1 H1 E 30 28 11 1.090 109.500 120.000 + 32 O2' OH S 30 28 11 1.430 109.500 240.000 + 33 HO'2 HO E 32 30 28 0.960 107.000 180.000 + 34 O3' OH M 28 11 8 1.420 116.520 -203.470 + 35 H3T HO M 34 28 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RC5_R-CYTOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RC5_R-CYTOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..310fb25e0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RC5_R-CYTOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.490 108.100 -127.700 + 15 C6 CM B 14 12 11 1.360 121.100 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.360 121.000 180.000 + 18 H5 HA E 17 15 14 1.090 120.000 180.000 + 19 C4 CA B 17 15 14 1.430 116.900 0.000 + 20 N4 N2 B 19 17 15 1.320 120.100 180.000 + 21 H41 H E 20 19 17 1.010 117.700 180.000 + 22 H42 H E 20 19 17 1.010 120.270 0.000 + 23 N3 NC S 19 17 15 1.330 121.700 0.000 + 24 C2 C S 23 19 17 1.360 120.500 0.000 + 25 O2 O E 24 23 19 1.240 122.400 180.000 + 26 C3' CT M 9 6 5 1.530 115.780 -329.110 + 27 H3' H1 E 26 9 6 1.090 109.500 30.000 + 28 C2' CT B 26 9 6 1.530 102.800 -86.300 + 29 H2'1 H1 E 28 26 9 1.090 109.500 120.000 + 30 O2' OH S 28 26 9 1.430 109.500 240.000 + 31 HO'2 HO E 30 28 26 0.960 107.000 180.000 + 32 O3' OS M 26 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RCN_R-CYTOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RCN_R-CYTOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..1ca2447df --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RCN_R-CYTOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.490 108.100 -127.700 + 15 C6 CM B 14 12 11 1.360 121.100 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.360 121.000 180.000 + 18 H5 HA E 17 15 14 1.090 120.000 180.000 + 19 C4 CA B 17 15 14 1.430 116.900 0.000 + 20 N4 N2 B 19 17 15 1.320 120.100 180.000 + 21 H41 H E 20 19 17 1.010 117.700 180.000 + 22 H42 H E 20 19 17 1.010 120.270 0.000 + 23 N3 NC S 19 17 15 1.330 121.700 0.000 + 24 C2 C S 23 19 17 1.360 120.500 0.000 + 25 O2 O E 24 23 19 1.240 122.400 180.000 + 26 C3' CT M 9 6 5 1.530 115.780 -329.110 + 27 H3' H1 E 26 9 6 1.090 109.500 30.000 + 28 C2' CT B 26 9 6 1.530 102.800 -86.300 + 29 H2'1 H1 E 28 26 9 1.090 109.500 120.000 + 30 O2' OH S 28 26 9 1.430 109.500 240.000 + 31 HO'2 HO E 30 28 26 0.960 107.000 180.000 + 32 O3' OH M 26 9 6 1.420 116.520 -203.470 + 33 H3T HO M 32 26 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RC_R-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RC_R-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..89a342595 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RC_R-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.490 108.100 -127.700 + 17 C6 CM B 16 14 13 1.360 121.100 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.360 121.000 180.000 + 20 H5 HA E 19 17 16 1.090 120.000 180.000 + 21 C4 CA B 19 17 16 1.430 116.900 0.000 + 22 N4 N2 B 21 19 17 1.320 120.100 180.000 + 23 H41 H E 22 21 19 1.010 117.700 180.000 + 24 H42 H E 22 21 19 1.010 120.270 0.000 + 25 N3 NC S 21 19 17 1.330 121.700 0.000 + 26 C2 C S 25 21 19 1.360 120.500 0.000 + 27 O2 O E 26 25 21 1.240 122.400 180.000 + 28 C3' CT M 11 8 7 1.530 115.780 -329.110 + 29 H3' H1 E 28 11 8 1.090 109.500 30.000 + 30 C2' CT B 28 11 8 1.530 102.800 -86.300 + 31 H2'1 H1 E 30 28 11 1.090 109.500 120.000 + 32 O2' OH S 30 28 11 1.430 109.500 240.000 + 33 HO'2 HO E 32 30 28 0.960 107.000 180.000 + 34 O3' OS M 28 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RG3_R-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RG3_R-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..d8281d3ef --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RG3_R-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,38 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.490 108.060 -127.700 + 17 C8 CK B 16 14 13 1.380 129.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.310 114.000 -179.900 + 20 C5 CB S 19 17 16 1.390 103.900 0.000 + 21 C6 C B 20 19 17 1.420 130.400 180.000 + 22 O6 O E 21 20 19 1.230 128.800 0.000 + 23 N1 NA B 21 20 19 1.400 111.380 180.000 + 24 H1 H E 23 21 20 1.000 117.360 179.900 + 25 C2 CA B 23 21 20 1.380 125.240 -0.100 + 26 N2 N2 B 25 23 21 1.340 116.020 180.000 + 27 H21 H E 26 25 23 1.010 127.000 -0.820 + 28 H22 H E 26 25 23 1.010 116.530 -179.440 + 29 N3 NC S 25 23 21 1.330 123.300 0.000 + 30 C4 CB E 29 25 23 1.360 112.200 0.000 + 31 C3' CT M 11 8 7 1.530 115.780 -329.110 + 32 H3' H1 E 31 11 8 1.090 109.500 30.000 + 33 C2' CT B 31 11 8 1.530 102.800 -86.300 + 34 H2'1 H1 E 33 31 11 1.090 109.500 120.000 + 35 O2' OH S 33 31 11 1.430 109.500 240.000 + 36 HO'2 HO E 35 33 31 0.960 107.000 180.000 + 37 O3' OH M 31 11 8 1.420 116.520 -203.470 + 38 H3T HO M 37 31 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RG5_R-GUANOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RG5_R-GUANOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..3642f293f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RG5_R-GUANOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.490 108.060 -127.700 + 15 C8 CK B 14 12 11 1.380 129.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.310 114.000 -179.900 + 18 C5 CB S 17 15 14 1.390 103.900 0.000 + 19 C6 C B 18 17 15 1.420 130.400 180.000 + 20 O6 O E 19 18 17 1.230 128.800 0.000 + 21 N1 NA B 19 18 17 1.400 111.380 180.000 + 22 H1 H E 21 19 18 1.000 117.360 179.900 + 23 C2 CA B 21 19 18 1.380 125.240 -0.100 + 24 N2 N2 B 23 21 19 1.340 116.020 180.000 + 25 H21 H E 24 23 21 1.010 127.000 -0.820 + 26 H22 H E 24 23 21 1.010 116.530 -179.440 + 27 N3 NC S 23 21 19 1.330 123.300 0.000 + 28 C4 CB E 27 23 21 1.360 112.200 0.000 + 29 C3' CT M 9 6 5 1.530 115.780 -329.110 + 30 H3' H1 E 29 9 6 1.090 109.500 30.000 + 31 C2' CT B 29 9 6 1.530 102.800 -86.300 + 32 H2'1 H1 E 31 29 9 1.090 109.500 120.000 + 33 O2' OH S 31 29 9 1.430 109.500 240.000 + 34 HO'2 HO E 33 31 29 0.960 107.000 180.000 + 35 O3' OS M 29 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RGN_R-GUANOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RGN_R-GUANOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..250669a6f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RGN_R-GUANOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,36 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.490 108.060 -127.700 + 15 C8 CK B 14 12 11 1.380 129.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.310 114.000 -179.900 + 18 C5 CB S 17 15 14 1.390 103.900 0.000 + 19 C6 C B 18 17 15 1.420 130.400 180.000 + 20 O6 O E 19 18 17 1.230 128.800 0.000 + 21 N1 NA B 19 18 17 1.400 111.380 180.000 + 22 H1 H E 21 19 18 1.000 117.360 179.900 + 23 C2 CA B 21 19 18 1.380 125.240 -0.100 + 24 N2 N2 B 23 21 19 1.340 116.020 180.000 + 25 H21 H E 24 23 21 1.010 127.000 -0.820 + 26 H22 H E 24 23 21 1.010 116.530 -179.440 + 27 N3 NC S 23 21 19 1.330 123.300 0.000 + 28 C4 CB E 27 23 21 1.360 112.200 0.000 + 29 C3' CT M 9 6 5 1.530 115.780 -329.110 + 30 H3' H1 E 29 9 6 1.090 109.500 30.000 + 31 C2' CT B 29 9 6 1.530 102.800 -86.300 + 32 H2'1 H1 E 31 29 9 1.090 109.500 120.000 + 33 O2' OH S 31 29 9 1.430 109.500 240.000 + 34 HO'2 HO E 33 31 29 0.960 107.000 180.000 + 35 O3' OH M 29 9 6 1.420 116.520 -203.470 + 36 H3T HO M 35 29 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RG_R-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__grou.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RG_R-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__grou.in_frag new file mode 100644 index 000000000..b70ca087e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RG_R-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__grou.in_frag @@ -0,0 +1,37 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.490 108.060 -127.700 + 17 C8 CK B 16 14 13 1.380 129.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.310 114.000 -179.900 + 20 C5 CB S 19 17 16 1.390 103.900 0.000 + 21 C6 C B 20 19 17 1.420 130.400 180.000 + 22 O6 O E 21 20 19 1.230 128.800 0.000 + 23 N1 NA B 21 20 19 1.400 111.380 180.000 + 24 H1 H E 23 21 20 1.000 117.360 179.900 + 25 C2 CA B 23 21 20 1.380 125.240 -0.100 + 26 N2 N2 B 25 23 21 1.340 116.020 180.000 + 27 H21 H E 26 25 23 1.010 127.000 -0.820 + 28 H22 H E 26 25 23 1.010 116.530 -179.440 + 29 N3 NC S 25 23 21 1.330 123.300 0.000 + 30 C4 CB E 29 25 23 1.360 112.200 0.000 + 31 C3' CT M 11 8 7 1.530 115.780 -329.110 + 32 H3' H1 E 31 11 8 1.090 109.500 30.000 + 33 C2' CT B 31 11 8 1.530 102.800 -86.300 + 34 H2'1 H1 E 33 31 11 1.090 109.500 120.000 + 35 O2' OH S 33 31 11 1.430 109.500 240.000 + 36 HO'2 HO E 35 33 31 0.960 107.000 180.000 + 37 O3' OS M 31 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RU3_R-URACIL_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RU3_R-URACIL_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..0370f880a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RU3_R-URACIL_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.530 109.590 -127.700 + 17 C6 CM B 16 14 13 1.370 123.040 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.340 121.220 177.300 + 20 H5 HA E 19 17 16 1.090 120.000 180.000 + 21 C4 C B 19 17 16 1.440 120.780 0.000 + 22 O4 O E 21 19 17 1.230 125.350 180.000 + 23 N3 NA B 21 19 17 1.380 114.070 0.000 + 24 H3 H E 23 21 19 1.090 116.770 180.000 + 25 C2 C S 23 21 19 1.380 126.460 0.000 + 26 O2 O E 25 23 21 1.220 121.700 180.000 + 27 C3' CT M 11 8 7 1.530 115.780 -329.110 + 28 H3' H1 E 27 11 8 1.090 109.500 30.000 + 29 C2' CT B 27 11 8 1.530 102.800 -86.300 + 30 H2'1 H1 E 29 27 11 1.090 109.500 120.000 + 31 O2' OH S 29 27 11 1.430 109.500 240.000 + 32 HO'2 HO E 31 29 27 0.960 107.000 180.000 + 33 O3' OH M 27 11 8 1.420 116.520 -203.470 + 34 H3T HO M 33 27 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RU5_R-URACIL_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RU5_R-URACIL_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag new file mode 100644 index 000000000..e61651431 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RU5_R-URACIL_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag @@ -0,0 +1,31 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.530 109.590 -127.700 + 15 C6 CM B 14 12 11 1.370 123.040 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.340 121.220 177.300 + 18 H5 HA E 17 15 14 1.090 120.000 180.000 + 19 C4 C B 17 15 14 1.440 120.780 0.000 + 20 O4 O E 19 17 15 1.230 125.350 180.000 + 21 N3 NA B 19 17 15 1.380 114.070 0.000 + 22 H3 H E 21 19 17 1.090 116.770 180.000 + 23 C2 C S 21 19 17 1.380 126.460 0.000 + 24 O2 O E 23 21 19 1.220 121.700 180.000 + 25 C3' CT M 9 6 5 1.530 115.780 -329.110 + 26 H3' H1 E 25 9 6 1.090 109.500 30.000 + 27 C2' CT B 25 9 6 1.530 102.800 -86.300 + 28 H2'1 H1 E 27 25 9 1.090 109.500 120.000 + 29 O2' OH S 27 25 9 1.430 109.500 240.000 + 30 HO'2 HO E 29 27 25 0.960 107.000 180.000 + 31 O3' OS M 25 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RUN_R-URACIL_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RUN_R-URACIL_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..bddd84d94 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RUN_R-URACIL_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.530 109.590 -127.700 + 15 C6 CM B 14 12 11 1.370 123.040 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.340 121.220 177.300 + 18 H5 HA E 17 15 14 1.090 120.000 180.000 + 19 C4 C B 17 15 14 1.440 120.780 0.000 + 20 O4 O E 19 17 15 1.230 125.350 180.000 + 21 N3 NA B 19 17 15 1.380 114.070 0.000 + 22 H3 H E 21 19 17 1.090 116.770 180.000 + 23 C2 C S 21 19 17 1.380 126.460 0.000 + 24 O2 O E 23 21 19 1.220 121.700 180.000 + 25 C3' CT M 9 6 5 1.530 115.780 -329.110 + 26 H3' H1 E 25 9 6 1.090 109.500 30.000 + 27 C2' CT B 25 9 6 1.530 102.800 -86.300 + 28 H2'1 H1 E 27 25 9 1.090 109.500 120.000 + 29 O2' OH S 27 25 9 1.430 109.500 240.000 + 30 HO'2 HO E 29 27 25 0.960 107.000 180.000 + 31 O3' OH M 25 9 6 1.420 116.520 -203.470 + 32 H3T HO M 31 25 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RU_R-URACIL_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RU_R-URACIL_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..c81a03314 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/RU_R-URACIL_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.530 109.590 -127.700 + 17 C6 CM B 16 14 13 1.370 123.040 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.340 121.220 177.300 + 20 H5 HA E 19 17 16 1.090 120.000 180.000 + 21 C4 C B 19 17 16 1.440 120.780 0.000 + 22 O4 O E 21 19 17 1.230 125.350 180.000 + 23 N3 NA B 21 19 17 1.380 114.070 0.000 + 24 H3 H E 23 21 19 1.090 116.770 180.000 + 25 C2 C S 23 21 19 1.380 126.460 0.000 + 26 O2 O E 25 23 21 1.220 121.700 180.000 + 27 C3' CT M 11 8 7 1.530 115.780 -329.110 + 28 H3' H1 E 27 11 8 1.090 109.500 30.000 + 29 C2' CT B 27 11 8 1.530 102.800 -86.300 + 30 H2'1 H1 E 29 27 11 1.090 109.500 120.000 + 31 O2' OH S 29 27 11 1.430 109.500 240.000 + 32 HO'2 HO E 31 29 27 0.960 107.000 180.000 + 33 O3' OS M 27 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/TME_N-methyl-_THYMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/TME_N-methyl-_THYMINE.in_frag new file mode 100644 index 000000000..0cf1d1fee --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/TME_N-methyl-_THYMINE.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H11' H1 M 3 2 1 1.100 92.507 92.096 + 5 C1' CT M 4 3 2 1.090 102.037 71.294 + 6 H12' H1 E 5 4 3 1.090 109.478 183.234 + 7 H13' H1 E 5 4 3 1.090 107.820 59.290 + 8 N1 N* M 5 4 3 1.530 109.599 295.545 + 9 C6 CM M 8 5 4 1.369 123.065 81.617 + 10 H6 H4 E 9 8 5 1.081 120.003 359.961 + 11 C5 CM M 9 8 5 1.340 121.249 177.325 + 12 C7 CT 3 11 9 8 1.500 121.661 179.962 + 13 H71 HC E 12 11 9 1.090 109.500 59.987 + 14 H72 HC E 12 11 9 1.089 109.504 179.953 + 15 H73 HC E 12 11 9 1.090 109.522 300.024 + 16 C4 C M 11 9 8 1.440 120.750 359.957 + 17 O4 O E 16 11 9 1.230 125.346 180.004 + 18 N3 NA M 16 11 9 1.380 114.100 0.044 + 19 H3 H E 18 16 11 1.089 116.782 180.040 + 20 C2 C M 18 16 11 1.380 126.403 359.936 + 21 O2 O E 20 18 16 1.221 121.639 179.980 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/UME_N-methyl-URACIL.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/UME_N-methyl-URACIL.in_frag new file mode 100644 index 000000000..495182132 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/UME_N-methyl-URACIL.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H11' H1 M 3 2 1 3.886 92.507 92.096 + 5 C1' CT M 4 3 2 1.090 102.037 71.294 + 6 H12' H1 E 5 4 3 1.090 109.478 183.234 + 7 H13' H1 E 5 4 3 1.090 107.820 59.290 + 8 N1 N* M 5 4 3 1.530 109.599 295.545 + 9 C6 CM M 8 5 4 1.369 123.065 81.617 + 10 H6 H4 E 9 8 5 1.081 120.003 359.961 + 11 C5 CM M 9 8 5 1.340 121.249 177.325 + 12 H5 HA E 11 9 8 1.091 120.029 179.993 + 13 C4 C M 11 9 8 1.440 120.750 359.957 + 14 O4 O E 13 11 9 1.230 125.346 180.004 + 15 N3 NA M 13 11 9 1.380 114.100 0.044 + 16 H3 H E 15 13 11 1.089 116.782 180.040 + 17 C2 C M 15 13 11 1.380 126.403 359.936 + 18 O2 O E 17 15 13 1.221 121.639 179.980 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc02/all_nuc02.in b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/all_nuc02.in new file mode 100644 index 000000000..b75afc725 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc02/all_nuc02.in @@ -0,0 +1,2219 @@ + 1 0 2 +db2000.dat +D-ADENOSINE - with 5' - OH end group and 3' - O(minus) + + DA5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 + 9 C4' CT M 6 5 4 1.52 110.00 180.00 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 + 12 C1' CT B 11 9 6 1.42 110.04 105.60 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 + 14 N9 N* S 12 11 9 1.52 109.59 -127.70 + 15 C8 CK B 14 12 11 1.37 131.20 81.59 + 16 H8 H5 E 15 14 12 1.08 120.00 0.00 + 17 N7 NB S 15 14 12 1.30 113.93 177.00 + 18 C5 CB S 17 15 14 1.39 104.00 0.00 + 19 C6 CA B 18 17 15 1.40 132.42 180.00 + 20 N6 N2 B 19 18 17 1.34 123.50 0.00 + 21 H61 H E 20 19 18 1.01 120.00 180.00 + 22 H62 H E 20 19 18 1.01 120.00 0.00 + 23 N1 NC S 19 18 17 1.34 117.43 180.00 + 24 C2 CQ B 23 19 18 1.33 118.80 0.00 + 25 H2 H5 E 24 23 19 1.08 120.00 180.00 + 26 N3 NC S 24 23 19 1.32 129.17 0.00 + 27 C4 CB E 26 24 23 1.35 110.80 0.00 + 28 C3' CT M 9 6 5 1.53 115.78 -329.11 + 29 H3' H1 E 28 9 6 1.09 109.50 30.00 + 30 C2' CT B 28 9 6 1.53 102.80 -86.30 + 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 + 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 + 33 O3' OS M 28 9 6 1.42 116.52 -203.47 + +CHARGE A5E, dft/cc-pVTZ, polarization corrected + .4109 -.5671 -.0111 .0662 .0662 + .0721 .0887 -.3124 .1680 .1024 + -.1692 .2153 .1451 -.5436 -.0475 + .6038 -.7136 .3558 .3558 -.7313 + .5726 .0119 -.7649 .5499 .1645 + .0623 -.0561 .0486 .0486 -.4998 + +IMPROPER + C8 C4 N9 C1' + C6 H61 N6 H62 + N7 N9 C8 H8 + N1 N3 C2 H2 + C5 N1 C6 N6 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +D-ADENOSINE - with 5' - phosphate group and 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3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 + 9 C4' CT M 6 5 4 1.52 110.00 180.00 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 + 12 C1' CT B 11 9 6 1.42 110.04 105.60 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 + 14 N9 N* S 12 11 9 1.52 109.59 -127.70 + 15 C8 CK B 14 12 11 1.37 131.20 81.59 + 16 H8 H5 E 15 14 12 1.08 120.00 0.00 + 17 N7 NB S 15 14 12 1.30 113.93 177.00 + 18 C5 CB S 17 15 14 1.39 104.00 0.00 + 19 C6 CA B 18 17 15 1.40 132.42 180.00 + 20 N6 N2 B 19 18 17 1.34 123.50 0.00 + 21 H61 H E 20 19 18 1.01 120.00 180.00 + 22 H62 H E 20 19 18 1.01 120.00 0.00 + 23 N1 NC S 19 18 17 1.34 117.43 180.00 + 24 C2 CQ B 23 19 18 1.33 118.80 0.00 + 25 H2 H5 E 24 23 19 1.08 120.00 180.00 + 26 N3 NC S 24 23 19 1.32 129.17 0.00 + 27 C4 CB E 26 24 23 1.35 110.80 0.00 + 28 C3' CT M 9 6 5 1.53 115.78 -329.11 + 29 H3' H1 E 28 9 6 1.09 109.50 30.00 + 30 C2' CT B 28 9 6 1.53 102.80 -86.30 + 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 + 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 + 33 O3' OH M 28 9 6 1.42 116.52 -203.47 + 34 H3T HO M 33 28 9 0.96 114.97 180.00 + +CHARGE ADE resp, dft/cc-pvtz, polarization corrected + .4109 -.5671 -.0111 .0662 .0662 + .0721 .0887 -.3124 .1680 .1024 + -.1692 .2153 .1451 -.5436 -.0475 + .6038 -.7136 .3558 .3558 -.7313 + .5726 .0119 -.7649 .5499 .1645 + .0623 -.0561 .0486 .0486 -.5918 + .3999 + +IMPROPER + C8 C4 N9 C1' + C6 H61 N6 H62 + N7 N9 C8 H8 + N1 N3 C2 H2 + C5 N1 C6 N6 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +R-ADENOSINE - with 5' - OH end group and 3' - O(minus) + + RA5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 + 9 C4' CT M 6 5 4 1.52 110.00 180.00 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 + 12 C1' CT B 11 9 6 1.42 110.04 105.60 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 + 14 N9 N* S 12 11 9 1.52 109.59 -127.70 + 15 C8 CK B 14 12 11 1.37 131.20 81.59 + 16 H8 H5 E 15 14 12 1.08 120.00 0.00 + 17 N7 NB S 15 14 12 1.30 113.93 177.00 + 18 C5 CB S 17 15 14 1.39 104.00 0.00 + 19 C6 CA B 18 17 15 1.40 132.42 180.00 + 20 N6 N2 B 19 18 17 1.34 123.50 0.00 + 21 H61 H E 20 19 18 1.01 120.00 180.00 + 22 H62 H E 20 19 18 1.01 120.00 0.00 + 23 N1 NC S 19 18 17 1.34 117.43 180.00 + 24 C2 CQ B 23 19 18 1.33 118.80 0.00 + 25 H2 H5 E 24 23 19 1.08 120.00 180.00 + 26 N3 NC S 24 23 19 1.32 129.17 0.00 + 27 C4 CB E 26 24 23 1.35 110.80 0.00 + 28 C3' CT M 9 6 5 1.53 115.78 -329.11 + 29 H3' H1 E 28 9 6 1.09 109.50 30.00 + 30 C2' CT B 28 9 6 1.53 102.80 -86.30 + 31 H2'1 H1 E 30 28 9 1.09 109.50 120.00 + 32 O2' OH S 30 28 9 1.43 109.50 240.00 + 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 + 34 O3' OS M 28 9 6 1.42 116.52 -203.47 + +CHARGE RA5E, dft/cc-pvtz, polarization corrected + .4086 -.5634 .0556 .0602 .0602 + .0219 .1055 -.2599 .0264 .1660 + -.0994 .2280 .1154 -.5462 -.0196 + .5848 -.6928 .3475 .3475 -.7181 + .5805 .0031 -.7390 .4398 .2522 + .0191 .0041 .1033 -.4963 .3720 + -.4749 + +IMPROPER + C8 C4 N9 C1' + C6 H61 N6 H62 + N7 N9 C8 H8 + N1 N3 C2 H2 + C5 N1 C6 N6 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +R-ADENOSINE - with 5' - phosphate group and 3' - O(minus) grou + + RA INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 P P M 3 2 1 1.60 119.04 200.00 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 + 16 N9 N* S 14 13 11 1.52 109.59 -127.70 + 17 C8 CK B 16 14 13 1.37 131.20 81.59 + 18 H8 H5 E 17 16 14 1.08 120.00 0.00 + 19 N7 NB S 17 16 14 1.30 113.93 177.00 + 20 C5 CB S 19 17 16 1.39 104.00 0.00 + 21 C6 CA B 20 19 17 1.40 132.42 180.00 + 22 N6 N2 B 21 20 19 1.34 123.50 0.00 + 23 H61 H E 22 21 20 1.01 120.00 180.00 + 24 H62 H E 22 21 20 1.01 120.00 0.00 + 25 N1 NC S 21 20 19 1.34 117.43 180.00 + 26 C2 CQ B 25 21 20 1.33 118.80 0.00 + 27 H2 H5 E 26 25 21 1.08 120.00 180.00 + 28 N3 NC S 26 25 21 1.32 129.17 0.00 + 29 C4 CB E 28 26 25 1.35 110.80 0.00 + 30 C3' CT M 11 8 7 1.53 115.78 -329.11 + 31 H3' H1 E 30 11 8 1.09 109.50 30.00 + 32 C2' CT B 30 11 8 1.53 102.80 -86.30 + 33 H2'1 H1 E 32 30 11 1.09 109.50 120.00 + 34 O2' OH S 32 30 11 1.43 109.50 240.00 + 35 HO'2 HO E 34 32 30 0.96 107.00 180.00 + 36 O3' OS M 30 11 8 1.42 116.52 -203.47 + +CHARGE RA, dft/cc-pvtz, polarization corrected + 1.0720 -.7552 -.7552 -.4085 .0556 + .0602 .0602 .0219 .1055 -.2599 + .0264 .1660 -.0994 .2280 .1154 + -.5462 -.0196 .5848 -.6928 .3475 + .3475 -.7181 .5805 .0031 -.7390 + .4398 .2522 .0191 .0041 .1033 + -.4963 .3720 -.4749 + +IMPROPER + C8 C4 N9 C1' + C6 H61 N6 H62 + N7 N9 C8 H8 + N1 N3 C2 H2 + C5 N1 C6 N6 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +R-ADENOSINE - with 5' - phosphate group and 3' - OH group + + RA3 INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 P P M 3 2 1 1.60 119.04 200.00 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 + 16 N9 N* S 14 13 11 1.52 109.59 -127.70 + 17 C8 CK B 16 14 13 1.37 131.20 81.59 + 18 H8 H5 E 17 16 14 1.08 120.00 0.00 + 19 N7 NB S 17 16 14 1.30 113.93 177.00 + 20 C5 CB S 19 17 16 1.39 104.00 0.00 + 21 C6 CA B 20 19 17 1.40 132.42 180.00 + 22 N6 N2 B 21 20 19 1.34 123.50 0.00 + 23 H61 H E 22 21 20 1.01 120.00 180.00 + 24 H62 H E 22 21 20 1.01 120.00 0.00 + 25 N1 NC S 21 20 19 1.34 117.43 180.00 + 26 C2 CQ B 25 21 20 1.33 118.80 0.00 + 27 H2 H5 E 26 25 21 1.08 120.00 180.00 + 28 N3 NC S 26 25 21 1.32 129.17 0.00 + 29 C4 CB E 28 26 25 1.35 110.80 0.00 + 30 C3' CT M 11 8 7 1.53 115.78 -329.11 + 31 H3' H1 E 30 11 8 1.09 109.50 30.00 + 32 C2' CT B 30 11 8 1.53 102.80 -86.30 + 33 H2'1 H1 E 32 30 11 1.09 109.50 120.00 + 34 O2' OH S 32 30 11 1.43 109.50 240.00 + 35 HO'2 HO E 34 32 30 0.96 107.00 180.00 + 36 O3' OH M 30 11 8 1.42 116.52 -203.47 + 37 H3T HO M 36 30 11 0.96 114.97 180.00 + +CHARGE RA3E, cc-pvtz, polarization corrected + 1.0720 -.7552 -.7552 -.4085 .0556 + .0602 .0602 .0219 .1055 -.2599 + .0264 .1660 -.0994 .2280 .1154 + -.5462 -.0196 .5848 -.6928 .3475 + .3475 -.7181 .5805 .0031 -.7390 + .4398 .2522 .0191 .0041 .1033 + -.4963 .3720 -.5798 .4128 + +IMPROPER + C8 C4 N9 C1' + C6 H61 N6 H62 + N7 N9 C8 H8 + N1 N3 C2 H2 + C5 N1 C6 N6 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +R-ADENOSINE - with 5' - OH group and 3' - OH group + + RAN INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 + 9 C4' CT M 6 5 4 1.52 110.00 180.00 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 + 12 C1' CT B 11 9 6 1.42 110.04 105.60 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 + 14 N9 N* S 12 11 9 1.52 109.59 -127.70 + 15 C8 CK B 14 12 11 1.37 131.20 81.59 + 16 H8 H5 E 15 14 12 1.08 120.00 0.00 + 17 N7 NB S 15 14 12 1.30 113.93 177.00 + 18 C5 CB S 17 15 14 1.39 104.00 0.00 + 19 C6 CA B 18 17 15 1.40 132.42 180.00 + 20 N6 N2 B 19 18 17 1.34 123.50 0.00 + 21 H61 H E 20 19 18 1.01 120.00 180.00 + 22 H62 H E 20 19 18 1.01 120.00 0.00 + 23 N1 NC S 19 18 17 1.34 117.43 180.00 + 24 C2 CQ B 23 19 18 1.33 118.80 0.00 + 25 H2 H5 E 24 23 19 1.08 120.00 180.00 + 26 N3 NC S 24 23 19 1.32 129.17 0.00 + 27 C4 CB E 26 24 23 1.35 110.80 0.00 + 28 C3' CT M 9 6 5 1.53 115.78 -329.11 + 29 H3' H1 E 28 9 6 1.09 109.50 30.00 + 30 C2' CT B 28 9 6 1.53 102.80 -86.30 + 31 H2'1 H1 E 30 28 9 1.09 109.50 120.00 + 32 O2' OH S 30 28 9 1.43 109.50 240.00 + 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 + 34 O3' OH M 28 9 6 1.42 116.52 -203.47 + 35 H3T HO M 34 28 9 0.96 114.97 180.00 + +CHARGE resp RADE, dft/cc-pvtz, polarization corrected + .4086 -.5634 .0556 .0602 .0602 + .0219 .1055 -.2599 .0264 .1660 + -.0994 .2280 .1154 -.5462 -.0196 + .5848 -.6928 .3475 .3475 -.7181 + .5805 .0031 -.7390 .4398 .2522 + .0191 .0041 .1033 -.4963 .3720 + -.5798 .4128 + +IMPROPER + C8 C4 N9 C1' + C6 H61 N6 H62 + N7 N9 C8 H8 + N1 N3 C2 H2 + C5 N1 C6 N6 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +D-THYMINE - with 5' - OH end group and 3' - O(minus) + + DT5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 + 12 C1' CT B 11 9 6 1.42 110.04 105.60 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 + 14 N1 N* S 12 11 9 1.53 109.59 -127.70 + 15 C6 CM B 14 12 11 1.37 123.04 81.59 + 16 H6 H4 E 15 14 12 1.08 120.00 0.00 + 17 C5 CM B 15 14 12 1.34 121.22 177.30 + 18 C7 CT 3 17 15 14 1.50 121.63 180.00 + 19 H71 HC E 18 17 15 1.09 109.50 60.00 + 20 H72 HC E 18 17 15 1.09 109.50 180.00 + 21 H73 HC E 18 17 15 1.09 109.50 300.00 + 22 C4 C B 17 15 14 1.44 120.78 0.00 + 23 O4 O E 22 17 15 1.23 125.35 180.00 + 24 N3 NA B 22 17 15 1.38 114.07 0.00 + 25 H3 H E 24 22 17 1.09 116.77 180.00 + 26 C2 C S 24 22 17 1.38 126.46 0.00 + 27 O2 O E 26 24 22 1.22 121.70 180.00 + 28 C3' CT M 9 6 5 1.53 115.78 -329.11 + 29 H3' H1 E 28 9 6 1.09 109.50 30.00 + 30 C2' CT B 28 9 6 1.53 102.80 -86.30 + 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 + 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 + 33 O3' OS M 28 9 6 1.42 116.52 -203.47 + +CHARGE T5 dft/cc-pvtz, polarization corrected + .4109 -.5671 -.0111 .0662 .0662 + .0721 .0887 -.3124 .1082 .1074 + -.0282 -.2552 .2796 -.0388 -.1326 + .0606 .0606 .0606 .5608 -.5455 + -.4824 .3542 .5892 -.5880 .1645 + .0623 -.0561 .0486 .0486 -.4998 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +D-THYMINE - with 5' - phosphate group and 3' - O(minus) group + + DT INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 P P M 3 2 1 1.60 119.04 200.00 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 + 16 N1 N* S 14 13 11 1.53 109.59 -127.70 + 17 C6 CM B 16 14 13 1.37 123.04 81.59 + 18 H6 H4 E 17 16 14 1.08 120.00 0.00 + 19 C5 CM B 17 16 14 1.34 121.22 177.30 + 20 C7 CT 3 19 17 16 1.50 121.63 180.00 + 21 H71 HC E 20 19 17 1.09 109.50 60.00 + 22 H72 HC E 20 19 17 1.09 109.50 180.00 + 23 H73 HC E 20 19 17 1.09 109.50 300.00 + 24 C4 C B 19 17 16 1.44 120.78 0.00 + 25 O4 O E 24 19 17 1.23 125.35 180.00 + 26 N3 NA B 24 19 17 1.38 114.07 0.00 + 27 H3 H E 26 24 19 1.09 116.77 180.00 + 28 C2 C S 26 24 19 1.38 126.46 0.00 + 29 O2 O E 28 26 24 1.22 121.70 180.00 + 30 C3' CT M 11 8 7 1.53 115.78 -329.11 + 31 H3' H1 E 30 11 8 1.09 109.50 30.00 + 32 C2' CT B 30 11 8 1.53 102.80 -86.30 + 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 + 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 + 35 O3' OS M 30 11 8 1.42 116.52 -203.47 + +CHARGE deoxy -resp T, dft/cc-pvtz, polarization corrected + 1.0735 -.7545 -.7545 -.4128 -.0111 + .0662 .0662 .0721 .0887 -.3124 + .1082 .1074 -.0282 -.2552 .2796 + -.0388 -.1326 .0606 .0606 .0606 + .5608 -.5455 -.4824 .3542 .5892 + -.5880 .1645 .0623 -.0561 .0486 + .0486 -.4998 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +D-THYMINE - with 5' - phosphate group and 3' - OH group + + DT3 INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 P P M 3 2 1 1.60 119.04 200.00 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 + 16 N1 N* S 14 13 11 1.53 109.59 -127.70 + 17 C6 CM B 16 14 13 1.37 123.04 81.59 + 18 H6 H4 E 17 16 14 1.08 120.00 0.00 + 19 C5 CM B 17 16 14 1.34 121.22 177.30 + 20 C7 CT 3 19 17 16 1.50 121.63 180.00 + 21 H71 HC E 20 19 17 1.09 109.50 60.00 + 22 H72 HC E 20 19 17 1.09 109.50 180.00 + 23 H73 HC E 20 19 17 1.09 109.50 300.00 + 24 C4 C B 19 17 16 1.44 120.78 0.00 + 25 O4 O E 24 19 17 1.23 125.35 180.00 + 26 N3 NA B 24 19 17 1.38 114.07 0.00 + 27 H3 H E 26 24 19 1.09 116.77 180.00 + 28 C2 C S 26 24 19 1.38 126.46 0.00 + 29 O2 O E 28 26 24 1.22 121.70 180.00 + 30 C3' CT M 11 8 7 1.53 115.78 -329.11 + 31 H3' H1 E 30 11 8 1.09 109.50 30.00 + 32 C2' CT B 30 11 8 1.53 102.80 -86.30 + 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 + 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 + 35 O3' OH M 30 11 8 1.42 116.52 -203.47 + 36 H3T HO M 35 30 11 0.96 114.97 180.00 + +CHARGE T3, dft/cc-pvtz, polarization corrected + 1.0735 -.7545 -.7545 -.4128 -.0111 + .0662 .0662 .0721 .0887 -.3124 + .1082 .1074 -.0282 -.2552 .2796 + -.0388 -.1326 .0606 .0606 .0606 + .5608 -.5455 -.4824 .3542 .5892 + -.5880 .1645 .0623 -.0561 .0486 + .0486 -.5918 .3999 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +D-THYMINE - with 5' - OH group and 3' - OH group + + DTN INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 + 12 C1' CT B 11 9 6 1.42 110.04 105.60 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 + 14 N1 N* S 12 11 9 1.53 109.59 -127.70 + 15 C6 CM B 14 12 11 1.37 123.04 81.59 + 16 H6 H4 E 15 14 12 1.08 120.00 0.00 + 17 C5 CM B 15 14 12 1.34 121.22 177.30 + 18 C7 CT 3 17 15 14 1.50 121.63 180.00 + 19 H71 HC E 18 17 15 1.09 109.50 60.00 + 20 H72 HC E 18 17 15 1.09 109.50 180.00 + 21 H73 HC E 18 17 15 1.09 109.50 300.00 + 22 C4 C B 17 15 14 1.44 120.78 0.00 + 23 O4 O E 22 17 15 1.23 125.35 180.00 + 24 N3 NA B 22 17 15 1.38 114.07 0.00 + 25 H3 H E 24 22 17 1.09 116.77 180.00 + 26 C2 C S 24 22 17 1.38 126.46 0.00 + 27 O2 O E 26 24 22 1.22 121.70 180.00 + 28 C3' CT M 9 6 5 1.53 115.78 -329.11 + 29 H3' H1 E 28 9 6 1.09 109.50 30.00 + 30 C2' CT B 28 9 6 1.53 102.80 -86.30 + 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 + 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 + 33 O3' OH M 28 9 6 1.42 116.52 -203.47 + 34 H3T HO M 33 28 9 0.96 114.97 180.00 + +CHARGE deoxy-THY-B, dft/cc-pvtz, polarization corrected + .4109 -.5671 -.0111 .0662 .0662 + .0721 .0887 -.3124 .1082 .1074 + -.0282 -.2552 .2796 -.0388 -.1326 + .0606 .0606 .0606 .5608 -.5455 + -.4824 .3542 .5892 -.5880 .1645 + .0623 -.0561 .0486 .0486 -.5918 + .3999 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +R-URACIL - with 5' - OH end group and 3' - O(minus) + + RU5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 + 12 C1' CT B 11 9 6 1.42 110.04 105.60 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 + 14 N1 N* S 12 11 9 1.53 109.59 -127.70 + 15 C6 CM B 14 12 11 1.37 123.04 81.59 + 16 H6 H4 E 15 14 12 1.08 120.00 0.00 + 17 C5 CM B 15 14 12 1.34 121.22 177.30 + 18 H5 HA E 17 15 14 1.09 120.00 180.00 + 19 C4 C B 17 15 14 1.44 120.78 0.00 + 20 O4 O E 19 17 15 1.23 125.35 180.00 + 21 N3 NA B 19 17 15 1.38 114.07 0.00 + 22 H3 H E 21 19 17 1.09 116.77 180.00 + 23 C2 C S 21 19 17 1.38 126.46 0.00 + 24 O2 O E 23 21 19 1.22 121.70 180.00 + 25 C3' CT M 9 6 5 1.53 115.78 -329.11 + 26 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21 1.34 116.02 180.00 + 27 H21 H E 26 25 23 1.01 127.00 -0.82 + 28 H22 H E 26 25 23 1.01 116.53 -179.44 + 29 N3 NC S 25 23 21 1.33 123.30 0.00 + 30 C4 CB E 29 25 23 1.36 112.20 0.00 + 31 C3' CT M 11 8 7 1.53 115.78 -329.11 + 32 H3' H1 E 31 11 8 1.09 109.50 30.00 + 33 C2' CT B 31 11 8 1.53 102.80 -86.30 + 34 H2'1 HC E 33 31 11 1.09 109.50 120.00 + 35 H2'2 HC E 33 31 11 1.09 109.50 240.00 + 36 O3' OH M 31 11 8 1.42 116.52 -203.47 + 37 H3T HO M 36 31 11 0.96 114.97 180.00 + +CHARGE gua, dft/cc-pvtz, polarization corrected + 1.0735 -.7545 -.7545 -.4128 -.0111 + .0662 .0662 .0721 .0887 -.3124 + .1557 .0886 -.0379 .1353 .1508 + -.5139 .0585 .5071 -.5301 -.5405 + .3750 .6834 -.7508 .3443 .3443 + -.6502 .2909 .1645 .0623 -.0561 + .0486 .0486 -.5918 .3999 + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +D-GUANOSINE - with 5' - OH group and 3' - OH group + + DGN INT 1 + CORRECT NOMIT DU 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H E 24 23 21 1.01 116.53 -179.44 + 27 N3 NC S 23 21 19 1.33 123.30 0.00 + 28 C4 CB E 27 23 21 1.36 112.20 0.00 + 29 C3' CT M 9 6 5 1.53 115.78 -329.11 + 30 H3' H1 E 29 9 6 1.09 109.50 30.00 + 31 C2' CT B 29 9 6 1.53 102.80 -86.30 + 32 H2'1 HC E 31 29 9 1.09 109.50 120.00 + 33 H2'2 HC E 31 29 9 1.09 109.50 240.00 + 34 O3' OH M 29 9 6 1.42 116.52 -203.47 + 35 H3T HO M 34 29 9 0.96 114.97 180.00 + +CHARGE deoxy-GUA-B, dft/cc-pvtz, polarization corrected + .4109 -.5671 -.0111 .0662 .0662 + .0721 .0887 -.3124 .1557 .0886 + -.0379 .1353 .1508 -.5139 .0585 + .5071 -.5301 -.5405 .3750 .6834 + -.7508 .3443 .3443 -.6502 .2909 + .1645 .0623 -.0561 .0486 .0486 + -.5918 .3999 + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +R-GUANOSINE - with 5' - OH end group and 3' - O(minus) group + + RG5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 + 12 C1' CT B 11 9 5 1.42 110.04 105.60 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 + 14 N9 N* S 12 11 9 1.49 108.06 -127.70 + 15 C8 CK B 14 12 11 1.38 129.20 81.59 + 16 H8 H5 E 15 14 12 1.08 120.00 0.00 + 17 N7 NB S 15 14 12 1.31 114.00 -179.90 + 18 C5 CB S 17 15 14 1.39 103.90 0.00 + 19 C6 C B 18 17 15 1.42 130.40 180.00 + 20 O6 O E 19 18 17 1.23 128.80 0.00 + 21 N1 NA B 19 18 17 1.40 111.38 180.00 + 22 H1 H E 21 19 18 1.00 117.36 179.90 + 23 C2 CA B 21 19 18 1.38 125.24 -0.10 + 24 N2 N2 B 23 21 19 1.34 116.02 180.00 + 25 H21 H E 24 23 21 1.01 127.00 -0.82 + 26 H22 H E 24 23 21 1.01 116.53 -179.44 + 27 N3 NC S 23 21 19 1.33 123.30 0.00 + 28 C4 CB E 27 23 21 1.36 112.20 0.00 + 29 C3' CT M 9 6 5 1.53 115.78 -329.11 + 30 H3' H1 E 29 9 6 1.09 109.50 30.00 + 31 C2' CT B 29 9 6 1.53 102.80 -86.30 + 32 H2'1 H1 E 31 29 9 1.09 109.50 120.00 + 33 O2' OH S 31 29 9 1.43 109.50 240.00 + 34 HO'2 HO E 33 31 29 0.96 107.00 180.00 + 35 O3' OS M 29 9 6 1.42 116.52 -203.47 + +CHARGE RG5E, cc-pvtz, polarization corrected + .4086 -.5634 .0556 .0602 .0602 + .0219 .1055 -.2599 .1132 .1019 + -.0871 .1966 .1168 -.5279 .0827 + .4649 -.5150 -.4848 .3601 .6423 + -.7501 .3488 .3488 -.6313 .2440 + .2522 .0191 .0041 .1033 -.4963 + .3720 -.4749 + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +R-GUANOSINE - with 5' - phosphate group and 3' - O(minus) grou + + RG INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 P P M 3 2 1 1.60 119.04 200.00 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 + 16 N9 N* S 14 13 11 1.49 108.06 -127.70 + 17 C8 CK B 16 14 13 1.38 129.20 81.59 + 18 H8 H5 E 17 16 14 1.08 120.00 0.00 + 19 N7 NB S 17 16 14 1.31 114.00 -179.90 + 20 C5 CB S 19 17 16 1.39 103.90 0.00 + 21 C6 C B 20 19 17 1.42 130.40 180.00 + 22 O6 O E 21 20 19 1.23 128.80 0.00 + 23 N1 NA B 21 20 19 1.40 111.38 180.00 + 24 H1 H E 23 21 20 1.00 117.36 179.90 + 25 C2 CA B 23 21 20 1.38 125.24 -0.10 + 26 N2 N2 B 25 23 21 1.34 116.02 180.00 + 27 H21 H E 26 25 23 1.01 127.00 -0.82 + 28 H22 H E 26 25 23 1.01 116.53 -179.44 + 29 N3 NC S 25 23 21 1.33 123.30 0.00 + 30 C4 CB E 29 25 23 1.36 112.20 0.00 + 31 C3' CT M 11 8 7 1.53 115.78 -329.11 + 32 H3' H1 E 31 11 8 1.09 109.50 30.00 + 33 C2' CT B 31 11 8 1.53 102.80 -86.30 + 34 H2'1 H1 E 33 31 11 1.09 109.50 120.00 + 35 O2' OH S 33 31 11 1.43 109.50 240.00 + 36 HO'2 HO E 35 33 31 0.96 107.00 180.00 + 37 O3' OS M 31 11 8 1.42 116.52 -203.47 + +CHARGE RG, dft/cc-pvtz, polarization corrected + 1.0720 -.7552 -.7552 -.4085 .0556 + .0602 .0602 .0219 .1055 -.2599 + .1132 .1019 -.0871 .1966 .1168 + -.5279 .0827 .4649 -.5150 -.4848 + .3601 .6423 -.7501 .3488 .3488 + -.6313 .2440 .2522 .0191 .0041 + .1033 -.4963 .3720 -.4749 + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +R-GUANOSINE - with 5' - phosphate group and 3' - OH group + + RG3 INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 P P M 3 2 1 1.60 119.04 200.00 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 + 16 N9 N* S 14 13 11 1.49 108.06 -127.70 + 17 C8 CK B 16 14 13 1.38 129.20 81.59 + 18 H8 H5 E 17 16 14 1.08 120.00 0.00 + 19 N7 NB S 17 16 14 1.31 114.00 -179.90 + 20 C5 CB S 19 17 16 1.39 103.90 0.00 + 21 C6 C B 20 19 17 1.42 130.40 180.00 + 22 O6 O E 21 20 19 1.23 128.80 0.00 + 23 N1 NA B 21 20 19 1.40 111.38 180.00 + 24 H1 H E 23 21 20 1.00 117.36 179.90 + 25 C2 CA B 23 21 20 1.38 125.24 -0.10 + 26 N2 N2 B 25 23 21 1.34 116.02 180.00 + 27 H21 H E 26 25 23 1.01 127.00 -0.82 + 28 H22 H E 26 25 23 1.01 116.53 -179.44 + 29 N3 NC S 25 23 21 1.33 123.30 0.00 + 30 C4 CB E 29 25 23 1.36 112.20 0.00 + 31 C3' CT M 11 8 7 1.53 115.78 -329.11 + 32 H3' H1 E 31 11 8 1.09 109.50 30.00 + 33 C2' CT B 31 11 8 1.53 102.80 -86.30 + 34 H2'1 H1 E 33 31 11 1.09 109.50 120.00 + 35 O2' OH S 33 31 11 1.43 109.50 240.00 + 36 HO'2 HO E 35 33 31 0.96 107.00 180.00 + 37 O3' OH M 31 11 8 1.42 116.52 -203.47 + 38 H3T HO M 37 31 11 0.96 114.97 180.00 + +CHARGE RG3E, dft/cc-pvtz, polarization corrected + 1.0720 -.7552 -.7552 -.4085 .0556 + .0602 .0602 .0219 .1055 -.2599 + .1132 .1019 -.0871 .1966 .1168 + -.5279 .0827 .4649 -.5150 -.4848 + .3601 .6423 -.7501 .3488 .3488 + -.6313 .2440 .2522 .0191 .0041 + .1033 -.4963 .3720 -.5798 .4128 + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +R-GUANOSINE - with 5' - OH group and 3' - OH group + + RGN INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 + 12 C1' CT B 11 9 5 1.42 110.04 105.60 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 + 14 N9 N* S 12 11 9 1.49 108.06 -127.70 + 15 C8 CK B 14 12 11 1.38 129.20 81.59 + 16 H8 H5 E 15 14 12 1.08 120.00 0.00 + 17 N7 NB S 15 14 12 1.31 114.00 -179.90 + 18 C5 CB S 17 15 14 1.39 103.90 0.00 + 19 C6 C B 18 17 15 1.42 130.40 180.00 + 20 O6 O E 19 18 17 1.23 128.80 0.00 + 21 N1 NA B 19 18 17 1.40 111.38 180.00 + 22 H1 H E 21 19 18 1.00 117.36 179.90 + 23 C2 CA B 21 19 18 1.38 125.24 -0.10 + 24 N2 N2 B 23 21 19 1.34 116.02 180.00 + 25 H21 H E 24 23 21 1.01 127.00 -0.82 + 26 H22 H E 24 23 21 1.01 116.53 -179.44 + 27 N3 NC S 23 21 19 1.33 123.30 0.00 + 28 C4 CB E 27 23 21 1.36 112.20 0.00 + 29 C3' CT M 9 6 5 1.53 115.78 -329.11 + 30 H3' H1 E 29 9 6 1.09 109.50 30.00 + 31 C2' CT B 29 9 6 1.53 102.80 -86.30 + 32 H2'1 H1 E 31 29 9 1.09 109.50 120.00 + 33 O2' OH S 31 29 9 1.43 109.50 240.00 + 34 HO'2 HO E 33 31 29 0.96 107.00 180.00 + 35 O3' OH M 29 9 6 1.42 116.52 -203.47 + 36 H3T HO M 35 29 9 0.96 114.97 180.00 + +CHARGE resp RGUA, dft/cc-pvtz, polarization corrected + .4086 -.5634 .0556 .0602 .0602 + .0219 .1055 -.2599 .1132 .1019 + -.0871 .1966 .1168 -.5279 .0827 + .4649 -.5150 -.4848 .3601 .6423 + -.7501 .3488 .3488 -.6313 .2440 + .2522 .0191 .0041 .1033 -.4963 + .3720 -.5798 .4128 + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +D-CYTOSINE - with 5' - OH end group and 3' - O(minus) group + + DC5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 + 12 C1' CT B 11 9 5 1.42 110.04 105.60 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 + 14 N1 N* S 12 11 9 1.49 108.10 -127.70 + 15 C6 CM B 14 12 11 1.36 121.10 81.59 + 16 H6 H4 E 15 14 12 1.08 120.00 0.00 + 17 C5 CM B 15 14 12 1.36 121.00 180.00 + 18 H5 HA E 17 15 14 1.09 120.00 180.00 + 19 C4 CA B 17 15 14 1.43 116.90 0.00 + 20 N4 N2 B 19 17 15 1.32 120.10 180.00 + 21 H41 H E 20 19 17 1.01 117.70 180.00 + 22 H42 H E 20 19 17 1.01 120.27 0.00 + 23 N3 NC S 19 17 15 1.33 121.70 0.00 + 24 C2 C S 23 19 17 1.36 120.50 0.00 + 25 O2 O E 24 23 19 1.24 122.40 180.00 + 26 C3' CT M 9 6 5 1.53 115.78 -329.11 + 27 H3' H1 E 26 9 6 1.09 109.50 30.00 + 28 C2' CT B 26 9 6 1.53 102.80 -86.30 + 29 H2'1 HC E 28 26 9 1.09 109.50 120.00 + 30 H2'2 HC E 28 26 9 1.09 109.50 240.00 + 31 O3' OS M 26 9 6 1.42 116.52 -203.47 + +CHARGE C5E, cc-pvtz, polarization corected + .4109 -.5671 -.0111 .0662 .0662 + .0721 .0887 -.3124 .1421 .0851 + -.1318 -.0115 .2099 -.4696 .1833 + .7010 -.7417 .3526 .3526 -.7555 + .8464 -.6524 .1645 .0623 -.0561 + .0486 .0486 -.4998 + +IMPROPER + C6 C2 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + N3 C5 C4 N4 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +D-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group + + DC INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 P P M 3 2 1 1.60 119.04 200.00 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 + 16 N1 N* S 14 13 11 1.49 108.10 -127.70 + 17 C6 CM B 16 14 13 1.36 121.10 81.59 + 18 H6 H4 E 17 16 14 1.08 120.00 0.00 + 19 C5 CM B 17 16 14 1.36 121.00 180.00 + 20 H5 HA E 19 17 16 1.09 120.00 180.00 + 21 C4 CA B 19 17 16 1.43 116.90 0.00 + 22 N4 N2 B 21 19 17 1.32 120.10 180.00 + 23 H41 H E 22 21 19 1.01 117.70 180.00 + 24 H42 H E 22 21 19 1.01 120.27 0.00 + 25 N3 NC S 21 19 17 1.33 121.70 0.00 + 26 C2 C S 25 21 19 1.36 120.50 0.00 + 27 O2 O E 26 25 21 1.24 122.40 180.00 + 28 C3' CT M 11 8 7 1.53 115.78 -329.11 + 29 H3' H1 E 28 11 8 1.09 109.50 30.00 + 30 C2' CT B 28 11 8 1.53 102.80 -86.30 + 31 H2'1 HC E 30 28 11 1.09 109.50 120.00 + 32 H2'2 HC E 30 28 11 1.09 109.50 240.00 + 33 O3' OS M 28 11 8 1.42 116.52 -203.47 + +CHARGE deoxy -resp C, dft/cc-pvtz, polarization corrected + 1.0735 -.7545 -.7545 -.4128 -.0111 + .0662 .0662 .0721 .0887 -.3124 + .1421 .0851 -.1318 -.0115 .2099 + -.4696 .1833 .7010 -.7417 .3526 + .3526 -.7555 .8464 -.6524 .1645 + .0623 -.0561 .0486 .0486 -.4998 + +IMPROPER + C6 C2 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + N3 C5 C4 N4 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +D-CYTOSINE - with 5' - phosphate group and 3' - OH group + + DC3 INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 P P M 3 2 1 1.60 119.04 200.00 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 + 16 N1 N* S 14 13 11 1.49 108.10 -127.70 + 17 C6 CM B 16 14 13 1.36 121.10 81.59 + 18 H6 H4 E 17 16 14 1.08 120.00 0.00 + 19 C5 CM B 17 16 14 1.36 121.00 180.00 + 20 H5 HA E 19 17 16 1.09 120.00 180.00 + 21 C4 CA B 19 17 16 1.43 116.90 0.00 + 22 N4 N2 B 21 19 17 1.32 120.10 180.00 + 23 H41 H E 22 21 19 1.01 117.70 180.00 + 24 H42 H E 22 21 19 1.01 120.27 0.00 + 25 N3 NC S 21 19 17 1.33 121.70 0.00 + 26 C2 C S 25 21 19 1.36 120.50 0.00 + 27 O2 O E 26 25 21 1.24 122.40 180.00 + 28 C3' CT M 11 8 7 1.53 115.78 -329.11 + 29 H3' H1 E 28 11 8 1.09 109.50 30.00 + 30 C2' CT B 28 11 8 1.53 102.80 -86.30 + 31 H2'1 HC E 30 28 11 1.09 109.50 120.00 + 32 H2'2 HC E 30 28 11 1.09 109.50 240.00 + 33 O3' OH M 28 11 8 1.42 116.52 -203.47 + 34 H3T HO M 30 25 8 0.96 114.97 180.00 + +CHARGE deoxy -resp C, dft/cc-pvtz, polarization corrected + 1.0735 -.7545 -.7545 -.4128 -.0111 + .0662 .0662 .0721 .0887 -.3124 + .1421 .0851 -.1318 -.0115 .2099 + -.4696 .1833 .7010 -.7417 .3526 + .3526 -.7555 .8464 -.6524 .1645 + .0623 -.0561 .0486 .0486 -.5918 + .3999 + +IMPROPER + C6 C2 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + N3 C5 C4 N4 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +D-CYTOSINE - with 5' - OH group and 3' - OH group + + DCN INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 + 12 C1' CT B 11 9 5 1.42 110.04 105.60 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 + 14 N1 N* S 12 11 9 1.49 108.10 -127.70 + 15 C6 CM B 14 12 11 1.36 121.10 81.59 + 16 H6 H4 E 15 14 12 1.08 120.00 0.00 + 17 C5 CM B 15 14 12 1.36 121.00 180.00 + 18 H5 HA E 17 15 14 1.09 120.00 180.00 + 19 C4 CA B 17 15 14 1.43 116.90 0.00 + 20 N4 N2 B 19 17 15 1.32 120.10 180.00 + 21 H41 H E 20 19 17 1.01 117.70 180.00 + 22 H42 H E 20 19 17 1.01 120.27 0.00 + 23 N3 NC S 19 17 15 1.33 121.70 0.00 + 24 C2 C S 23 19 17 1.36 120.50 0.00 + 25 O2 O E 24 23 19 1.24 122.40 180.00 + 26 C3' CT M 9 6 5 1.53 115.78 -329.11 + 27 H3' H1 E 26 9 6 1.09 109.50 30.00 + 28 C2' CT B 26 9 6 1.53 102.80 -86.30 + 29 H2'1 HC E 28 26 9 1.09 109.50 120.00 + 30 H2'2 HC E 28 26 9 1.09 109.50 240.00 + 31 O3' OH M 26 9 6 1.42 116.52 -203.47 + 32 H3T HO M 31 26 9 0.96 114.97 180.00 + +CHARGE deoxy-CYT-B: CYT, df/cc-pvtz, polarization corrected + .4109 -.5671 -.0111 .0662 .0662 + .0721 .0887 -.3124 .1421 .0851 + -.1318 -.0115 .2099 -.4696 .1833 + .7010 -.7417 .3526 .3526 -.7555 + .8464 -.6524 .1645 .0623 -.0561 + .0486 .0486 -.5918 .3999 + +IMPROPER + C6 C2 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + N3 C5 C4 N4 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +R-CYTOSINE - with 5' 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17 1.36 120.50 0.00 + 25 O2 O E 24 23 19 1.24 122.40 180.00 + 26 C3' CT M 9 6 5 1.53 115.78 -329.11 + 27 H3' H1 E 26 9 6 1.09 109.50 30.00 + 28 C2' CT B 26 9 6 1.53 102.80 -86.30 + 29 H2'1 H1 E 28 26 9 1.09 109.50 120.00 + 30 O2' OH S 28 26 9 1.43 109.50 240.00 + 31 HO'2 HO E 30 28 26 0.96 107.00 180.00 + 32 O3' OS M 26 9 6 1.42 116.52 -203.47 + +CHARGE RC5E , dft/cc-pvtz, polarization corrected + .4086 -.5634 .0556 .0602 .0602 + .0219 .1055 -.2599 .0175 .1427 + -.0827 -.0403 .2017 -.4449 .1759 + .6770 -.7460 .3542 .3542 -.7264 + .8021 -.6611 .2522 .0191 .0041 + .1033 -.4963 .3720 -.4749 + +IMPROPER + C6 C2 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + N3 C5 C4 N4 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +R-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group + + RC INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 P P M 3 2 1 1.60 119.04 200.00 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 + 16 N1 N* S 14 13 11 1.49 108.10 -127.70 + 17 C6 CM B 16 14 13 1.36 121.10 81.59 + 18 H6 H4 E 17 16 14 1.08 120.00 0.00 + 19 C5 CM B 17 16 14 1.36 121.00 180.00 + 20 H5 HA E 19 17 16 1.09 120.00 180.00 + 21 C4 CA B 19 17 16 1.43 116.90 0.00 + 22 N4 N2 B 21 19 17 1.32 120.10 180.00 + 23 H41 H E 22 21 19 1.01 117.70 180.00 + 24 H42 H E 22 21 19 1.01 120.27 0.00 + 25 N3 NC S 21 19 17 1.33 121.70 0.00 + 26 C2 C S 25 21 19 1.36 120.50 0.00 + 27 O2 O E 26 25 21 1.24 122.40 180.00 + 28 C3' CT M 11 8 7 1.53 115.78 -329.11 + 29 H3' H1 E 28 11 8 1.09 109.50 30.00 + 30 C2' CT B 28 11 8 1.53 102.80 -86.30 + 31 H2'1 H1 E 30 28 11 1.09 109.50 120.00 + 32 O2' OH S 30 28 11 1.43 109.50 240.00 + 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 + 34 O3' OS M 28 11 8 1.42 116.52 -203.47 + +CHARGE RC, dft/cc-pvtz, polarization corrected + 1.0720 -.7552 -.7552 -.4085 .0556 + .0602 .0602 .0219 .1055 -.2599 + .0175 .1427 -.0827 -.0403 .2017 + -.4449 .1759 .6770 -.7460 .3542 + .3542 -.7264 .8021 -.6611 .2522 + .0191 .0041 .1033 -.4963 .3720 + -.4749 + +IMPROPER + C6 C2 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + N3 C5 C4 N4 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +R-CYTOSINE - with 5' - phosphate group and 3' - OH group + + RC3 INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 P P M 3 2 1 1.60 119.04 200.00 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 + 16 N1 N* S 14 13 11 1.49 108.10 -127.70 + 17 C6 CM B 16 14 13 1.36 121.10 81.59 + 18 H6 H4 E 17 16 14 1.08 120.00 0.00 + 19 C5 CM B 17 16 14 1.36 121.00 180.00 + 20 H5 HA E 19 17 16 1.09 120.00 180.00 + 21 C4 CA B 19 17 16 1.43 116.90 0.00 + 22 N4 N2 B 21 19 17 1.32 120.10 180.00 + 23 H41 H E 22 21 19 1.01 117.70 180.00 + 24 H42 H E 22 21 19 1.01 120.27 0.00 + 25 N3 NC S 21 19 17 1.33 121.70 0.00 + 26 C2 C S 25 21 19 1.36 120.50 0.00 + 27 O2 O E 26 25 21 1.24 122.40 180.00 + 28 C3' CT M 11 8 7 1.53 115.78 -329.11 + 29 H3' H1 E 28 11 8 1.09 109.50 30.00 + 30 C2' CT B 28 11 8 1.53 102.80 -86.30 + 31 H2'1 H1 E 30 28 11 1.09 109.50 120.00 + 32 O2' OH S 30 28 11 1.43 109.50 240.00 + 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 + 34 O3' OH M 28 11 8 1.42 116.52 -203.47 + 35 H3T HO M 34 28 11 0.96 114.97 180.00 + +CHARGE RC3E, dft/cc-pvtz, polarization corrected + 1.0720 -.7552 -.7552 -.4085 .0556 + .0602 .0602 .0219 .1055 -.2599 + .0175 .1427 -.0827 -.0403 .2017 + -.4449 .1759 .6770 -.7460 .3542 + .3542 -.7264 .8021 -.6611 .2522 + .0191 .0041 .1033 -.4963 .3720 + -.5798 .4128 + +IMPROPER + C6 C2 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + N3 C5 C4 N4 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +R-CYTOSINE - with 5' - OH group and 3' - OH group + + RCN INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 + 12 C1' CT B 11 9 5 1.42 110.04 105.60 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 + 14 N1 N* S 12 11 9 1.49 108.10 -127.70 + 15 C6 CM B 14 12 11 1.36 121.10 81.59 + 16 H6 H4 E 15 14 12 1.08 120.00 0.00 + 17 C5 CM B 15 14 12 1.36 121.00 180.00 + 18 H5 HA E 17 15 14 1.09 120.00 180.00 + 19 C4 CA B 17 15 14 1.43 116.90 0.00 + 20 N4 N2 B 19 17 15 1.32 120.10 180.00 + 21 H41 H E 20 19 17 1.01 117.70 180.00 + 22 H42 H E 20 19 17 1.01 120.27 0.00 + 23 N3 NC S 19 17 15 1.33 121.70 0.00 + 24 C2 C S 23 19 17 1.36 120.50 0.00 + 25 O2 O E 24 23 19 1.24 122.40 180.00 + 26 C3' CT M 9 6 5 1.53 115.78 -329.11 + 27 H3' H1 E 26 9 6 1.09 109.50 30.00 + 28 C2' CT B 26 9 6 1.53 102.80 -86.30 + 29 H2'1 H1 E 28 26 9 1.09 109.50 120.00 + 30 O2' OH S 28 26 9 1.43 109.50 240.00 + 31 HO'2 HO E 30 28 26 0.96 107.00 180.00 + 32 O3' OH M 26 9 6 1.42 116.52 -203.47 + 33 H3T HO M 32 26 9 0.96 114.97 180.00 + +CHARGE resp RCYT, dft/cc-pvtz, polarization corrected + .4086 -.5634 .0556 .0602 .0602 + .0219 .1055 -.2599 .0175 .1427 + -.0827 -.0403 .2017 -.4449 .1759 + .6770 -.7460 .3542 .3542 -.7264 + .8021 -.6611 .2522 .0191 .0041 + .1033 -.4963 .3720 -.5798 .4128 + +IMPROPER + C6 C2 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + N3 C5 C4 N4 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +N-methyl-ADENINE + +AME INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 .00000 .0000 .0000 + 2 DUMM DU M 1 0 -1 1.00000 .0000 .0000 + 3 DUMM DU M 2 1 0 1.00000 90.0000 .0000 + 4 H11' H1 M 3 2 1 3.88600 92.5070 92.0960 + 5 C1' CT M 4 3 2 1.09000 102.0370 71.2940 + 6 H12' H1 E 5 4 3 1.09000 109.4780 183.2340 + 7 H13' H1 E 5 4 3 1.09000 107.8200 59.2900 + 8 N9 N* M 5 4 3 1.52100 109.6030 295.5360 + 9 C8 CK M 8 5 4 1.37000 131.1870 81.6070 + 10 H8 H5 E 9 8 5 1.08000 120.0060 .0050 + 11 N7 NB M 9 8 5 1.30000 113.8870 177.0200 + 12 C5 CB M 11 9 8 1.38900 104.0390 .0040 + 13 C6 CA M 12 11 9 1.40000 132.4290 180.0430 + 14 N6 N2 B 13 12 11 1.34000 123.4980 359.9610 + 15 H61 H E 14 13 12 1.01000 119.9420 180.0440 + 16 H62 H E 14 13 12 1.01000 120.0050 .0060 + 17 N1 NC M 13 12 11 1.34000 117.4080 179.9600 + 18 C2 CQ M 17 13 12 1.33000 118.8320 .0080 + 19 H2 H5 E 18 17 13 1.08000 120.0130 179.9930 + 20 N3 NC M 18 17 13 1.31900 129.1490 359.9310 + 21 C4 CB M 20 18 17 1.35000 110.8300 .0830 + +CHARGE + ADE new-resp polarization corrected, dft/cc-pvtz + .110341 -.178023 .110341 .110341 -.078080 + .105117 .145537 -.513780 -.017376 .581790 + -.751139 .379088 .379088 -.725359 .566714 + .019429 -.748533 .504503 + +IMPROPER + C8 C4 N9 C1' + C6 H61 N6 H62 + N7 N9 C8 H8 + N1 N3 C2 H2 + C5 N1 C6 N6 + +LOOP CLOSING EXPLICIT + C4 C5 + C4 N9 + +DONE +N-methyl-CYTOSINE + +CME INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 .00000 .0000 .0000 .0000 + 2 DUMM DU M 1 0 -1 1.00000 .0000 .0000 .0000 + 3 DUMM DU M 2 1 0 1.00000 90.0000 .0000 .0000 + 4 H11' H1 M 3 2 1 3.88600 92.5070 92.0960 .0000 + 5 C1' CT M 4 3 2 1.09000 102.0370 71.2940 .0000 + 6 H12' H1 E 5 4 3 1.09000 109.4780 183.2340 .0000 + 7 H13' H1 E 5 4 3 1.09000 107.8200 59.2900 .0000 + 8 N1 N* M 5 4 3 1.49000 108.1190 295.5500 .0000 + 9 C6 CM M 8 5 4 1.36000 121.1340 81.5730 .0000 + 10 H6 H4 E 9 8 5 1.08000 119.9490 .0420 .0000 + 11 C5 CM M 9 8 5 1.36000 121.0290 180.0410 .0000 + 12 H5 HA E 11 9 8 1.09000 119.9940 180.0670 .0000 + 13 C4 CA M 11 9 8 1.43000 116.8750 359.9720 .0000 + 14 N4 N2 B 13 11 9 1.31900 120.0770 179.9930 .0000 + 15 H41 H E 14 13 11 1.01000 117.7460 180.0300 .0000 + 16 H42 H E 14 13 11 1.01000 120.2950 .0610 .0000 + 17 N3 NC M 13 11 9 1.33000 121.7030 .0750 .0000 + 18 C2 C M 17 13 11 1.36000 120.5330 359.9230 .0000 + 19 O2 O E 18 17 13 1.23900 122.4570 180.0510 .0000 + +CHARGE + deoxy-CYT-B: polarization corrected charges, CYT, df/cc-pvtz + .072305 -.066987 .072305 .072305 -.120009 + -.022683 .170764 -.534862 .199549 .852027 + -.917553 .409639 .409639 -.787560 .816641 + -.625521 + +IMPROPER + C6 C2 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + N3 C5 C4 N4 + +LOOP CLOSING EXPLICIT + C2 N1 + +DONE +N-methyl-GUANINE + +GME INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 .00000 .0000 .0000 + 2 DUMM DU M 1 0 -1 1.00000 .0000 .0000 + 3 DUMM DU M 2 1 0 1.00000 90.0000 .0000 + 4 H11' H1 M 3 2 1 3.88600 92.5070 92.0960 + 5 C1' CT M 4 3 2 1.09000 102.0370 71.2940 + 6 H12' H1 E 5 4 3 1.09000 109.4780 183.2340 + 7 H13' H1 E 5 4 3 1.09000 107.8200 59.2900 + 8 N9 N* M 5 4 3 1.49000 108.0830 295.5380 + 9 C8 CK M 8 5 4 1.38000 129.2070 81.5690 + 10 H8 H5 E 9 8 5 1.08000 119.9900 .0590 + 11 N7 NB M 9 8 5 1.31000 114.0170 180.1070 + 12 C5 CB M 11 9 8 1.39000 103.8950 .0350 + 13 C6 C M 12 11 9 1.42000 130.4290 179.9530 + 14 O6 O E 13 12 11 1.23100 128.7830 .0290 + 15 N1 NA M 13 12 11 1.40000 111.4060 180.0170 + 16 H1 H E 15 13 12 1.00100 117.3610 179.9310 + 17 C2 CA M 15 13 12 1.38000 125.2260 359.8940 + 18 N2 N2 B 17 15 13 1.34100 116.0360 180.0230 + 19 H21 H E 18 17 15 1.01000 126.9570 359.1960 + 20 H22 H E 18 17 15 1.01000 116.5580 180.5620 + 21 N3 NC M 17 15 13 1.33000 123.3460 .0130 + 22 C4 CB M 21 17 15 1.36000 112.1600 359.9980 + +CHARGE + deoxy-GUA-B, polarization corrected, dft/cc-pvtz + .101967 -.155686 .101967 .101967 -.055116 + .086175 .140052 -.473394 -.023631 .540370 + -.534593 -.550934 .374369 .645312 -.692954 + .331359 .331359 -.683661 .415072 + + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C4 C5 + C4 N9 + +DONE +N-methyl- THYMINE + +TME INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 .00000 .0000 .0000 + 2 DUMM DU M 1 0 -1 1.00000 .0000 .0000 + 3 DUMM DU M 2 1 0 1.00000 90.0000 .0000 + 4 H11' H1 M 3 2 1 1.10000 92.5070 92.0960 + 5 C1' CT M 4 3 2 1.09000 102.0370 71.2940 + 6 H12' H1 E 5 4 3 1.09000 109.4780 183.2340 + 7 H13' H1 E 5 4 3 1.09000 107.8200 59.2900 + 8 N1 N* M 5 4 3 1.53000 109.5990 295.5450 + 9 C6 CM M 8 5 4 1.36900 123.0650 81.6170 + 10 H6 H4 E 9 8 5 1.08100 120.0030 359.9610 + 11 C5 CM M 9 8 5 1.34000 121.2490 177.3250 + 12 C7 CT 3 11 9 8 1.50000 121.6610 179.9620 + 13 H71 HC E 12 11 9 1.09000 109.5000 59.9870 + 14 H72 HC E 12 11 9 1.08900 109.5040 179.9530 + 15 H73 HC E 12 11 9 1.09000 109.5220 300.0240 + 16 C4 C M 11 9 8 1.44000 120.7500 359.9570 + 17 O4 O E 16 11 9 1.23000 125.3460 180.0040 + 18 N3 NA M 16 11 9 1.38000 114.1000 .0440 + 19 H3 H E 18 16 11 1.08900 116.7820 180.0400 + 20 C2 C M 18 16 11 1.38000 126.4030 359.9360 + 21 O2 O E 20 18 16 1.22100 121.6390 179.9800 + +CHARGE + THY dft/cc-pvtz, polarization corrected + .074001 -.067546 .074001 .074001 -.031294 + -.189777 .194132 -.030526 -.231950 .089475 + .089475 .089475 .547155 -.539763 -.438227 + .339487 .485470 -.527589 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C2 N1 + +DONE +N-methyl-URACIL + +UME INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 .00000 .0000 .0000 + 2 DUMM DU M 1 0 -1 1.00000 .0000 .0000 + 3 DUMM DU M 2 1 0 1.00000 90.0000 .0000 + 4 H11' H1 M 3 2 1 3.88600 92.5070 92.0960 + 5 C1' CT M 4 3 2 1.09000 102.0370 71.2940 + 6 H12' H1 E 5 4 3 1.09000 109.4780 183.2340 + 7 H13' H1 E 5 4 3 1.09000 107.8200 59.2900 + 8 N1 N* M 5 4 3 1.53000 109.5990 295.5450 + 9 C6 CM M 8 5 4 1.36900 123.0650 81.6170 + 10 H6 H4 E 9 8 5 1.08100 120.0030 359.9610 + 11 C5 CM M 9 8 5 1.34000 121.2490 177.3250 + 12 H5 HA E 11 9 8 1.09100 120.0290 179.9930 + 13 C4 C M 11 9 8 1.44000 120.7500 359.9570 + 14 O4 O E 13 11 9 1.23000 125.3460 180.0040 + 15 N3 NA M 13 11 9 1.38000 114.1000 .0440 + 16 H3 H E 15 13 11 1.08900 116.7820 180.0400 + 17 C2 C M 15 13 11 1.38000 126.4030 359.9360 + 18 O2 O E 17 15 13 1.22100 121.6390 179.9800 + +CHARGE + URA dft/cc-pvtz, polarization corrected + .078008 -.082649 .078008 .078008 -.006301 + -.113902 .190428 -.361481 .177457 .646954 + -.569023 -.440391 .326261 .549017 -.550394 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 H5 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C2 N1 + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DA3_D-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DA3_D-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..d7c8041d1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DA3_D-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,36 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.520 109.590 -127.700 + 17 C8 CK B 16 14 13 1.370 131.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.300 113.930 177.000 + 20 C5 CB S 19 17 16 1.390 104.000 0.000 + 21 C6 CA B 20 19 17 1.400 132.420 180.000 + 22 N6 N2 B 21 20 19 1.340 123.500 0.000 + 23 H61 H E 22 21 20 1.010 120.000 180.000 + 24 H62 H E 22 21 20 1.010 120.000 0.000 + 25 N1 NC S 21 20 19 1.340 117.430 180.000 + 26 C2 CQ B 25 21 20 1.330 118.800 0.000 + 27 H2 H5 E 26 25 21 1.080 120.000 180.000 + 28 N3 NC S 26 25 21 1.320 129.170 0.000 + 29 C4 CB E 28 26 25 1.350 110.800 0.000 + 30 C3' CT M 11 8 7 1.530 115.780 -329.110 + 31 H3' H1 E 30 11 8 1.090 109.500 30.000 + 32 C2' CT B 30 11 8 1.530 102.800 -86.300 + 33 H2'1 HC E 32 30 11 1.090 109.500 120.000 + 34 H2'2 HC E 32 30 11 1.090 109.500 240.000 + 35 O3' OH M 30 11 8 1.420 116.520 -203.470 + 36 H3T HO M 35 30 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DA5_D-ADENOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DA5_D-ADENOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag new file mode 100644 index 000000000..b017a823c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DA5_D-ADENOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.520 109.590 -127.700 + 15 C8 CK B 14 12 11 1.370 131.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.300 113.930 177.000 + 18 C5 CB S 17 15 14 1.390 104.000 0.000 + 19 C6 CA B 18 17 15 1.400 132.420 180.000 + 20 N6 N2 B 19 18 17 1.340 123.500 0.000 + 21 H61 H E 20 19 18 1.010 120.000 180.000 + 22 H62 H E 20 19 18 1.010 120.000 0.000 + 23 N1 NC S 19 18 17 1.340 117.430 180.000 + 24 C2 CQ B 23 19 18 1.330 118.800 0.000 + 25 H2 H5 E 24 23 19 1.080 120.000 180.000 + 26 N3 NC S 24 23 19 1.320 129.170 0.000 + 27 C4 CB E 26 24 23 1.350 110.800 0.000 + 28 C3' CT M 9 6 5 1.530 115.780 -329.110 + 29 H3' H1 E 28 9 6 1.090 109.500 30.000 + 30 C2' CT B 28 9 6 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 9 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 9 1.090 109.500 240.000 + 33 O3' OS M 28 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DAN_D-ADENOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DAN_D-ADENOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..07eaa1462 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DAN_D-ADENOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.520 109.590 -127.700 + 15 C8 CK B 14 12 11 1.370 131.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.300 113.930 177.000 + 18 C5 CB S 17 15 14 1.390 104.000 0.000 + 19 C6 CA B 18 17 15 1.400 132.420 180.000 + 20 N6 N2 B 19 18 17 1.340 123.500 0.000 + 21 H61 H E 20 19 18 1.010 120.000 180.000 + 22 H62 H E 20 19 18 1.010 120.000 0.000 + 23 N1 NC S 19 18 17 1.340 117.430 180.000 + 24 C2 CQ B 23 19 18 1.330 118.800 0.000 + 25 H2 H5 E 24 23 19 1.080 120.000 180.000 + 26 N3 NC S 24 23 19 1.320 129.170 0.000 + 27 C4 CB E 26 24 23 1.350 110.800 0.000 + 28 C3' CT M 9 6 5 1.530 115.780 -329.110 + 29 H3' H1 E 28 9 6 1.090 109.500 30.000 + 30 C2' CT B 28 9 6 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 9 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 9 1.090 109.500 240.000 + 33 O3' OH M 28 9 6 1.420 116.520 -203.470 + 34 H3T HO M 33 28 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DA_D-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DA_D-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..47683c43b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DA_D-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.520 109.590 -127.700 + 17 C8 CK B 16 14 13 1.370 131.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.300 113.930 177.000 + 20 C5 CB S 19 17 16 1.390 104.000 0.000 + 21 C6 CA B 20 19 17 1.400 132.420 180.000 + 22 N6 N2 B 21 20 19 1.340 123.500 0.000 + 23 H61 H E 22 21 20 1.010 120.000 180.000 + 24 H62 H E 22 21 20 1.010 120.000 0.000 + 25 N1 NC S 21 20 19 1.340 117.430 180.000 + 26 C2 CQ B 25 21 20 1.330 118.800 0.000 + 27 H2 H5 E 26 25 21 1.080 120.000 180.000 + 28 N3 NC S 26 25 21 1.320 129.170 0.000 + 29 C4 CB E 28 26 25 1.350 110.800 0.000 + 30 C3' CT M 11 8 7 1.530 115.780 -329.110 + 31 H3' H1 E 30 11 8 1.090 109.500 30.000 + 32 C2' CT B 30 11 8 1.530 102.800 -86.300 + 33 H2'1 HC E 32 30 11 1.090 109.500 120.000 + 34 H2'2 HC E 32 30 11 1.090 109.500 240.000 + 35 O3' OS M 30 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DC3_D-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DC3_D-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..4db0b10ec --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DC3_D-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.490 108.100 -127.700 + 17 C6 CM B 16 14 13 1.360 121.100 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.360 121.000 180.000 + 20 H5 HA E 19 17 16 1.090 120.000 180.000 + 21 C4 CA B 19 17 16 1.430 116.900 0.000 + 22 N4 N2 B 21 19 17 1.320 120.100 180.000 + 23 H41 H E 22 21 19 1.010 117.700 180.000 + 24 H42 H E 22 21 19 1.010 120.270 0.000 + 25 N3 NC S 21 19 17 1.330 121.700 0.000 + 26 C2 C S 25 21 19 1.360 120.500 0.000 + 27 O2 O E 26 25 21 1.240 122.400 180.000 + 28 C3' CT M 11 8 7 1.530 115.780 -329.110 + 29 H3' H1 E 28 11 8 1.090 109.500 30.000 + 30 C2' CT B 28 11 8 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 11 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 11 1.090 109.500 240.000 + 33 O3' OH M 28 11 8 1.420 116.520 -203.470 + 34 H3T HO M 30 25 8 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DC5_D-CYTOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DC5_D-CYTOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..4c8f63c17 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DC5_D-CYTOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,31 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.490 108.100 -127.700 + 15 C6 CM B 14 12 11 1.360 121.100 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.360 121.000 180.000 + 18 H5 HA E 17 15 14 1.090 120.000 180.000 + 19 C4 CA B 17 15 14 1.430 116.900 0.000 + 20 N4 N2 B 19 17 15 1.320 120.100 180.000 + 21 H41 H E 20 19 17 1.010 117.700 180.000 + 22 H42 H E 20 19 17 1.010 120.270 0.000 + 23 N3 NC S 19 17 15 1.330 121.700 0.000 + 24 C2 C S 23 19 17 1.360 120.500 0.000 + 25 O2 O E 24 23 19 1.240 122.400 180.000 + 26 C3' CT M 9 6 5 1.530 115.780 -329.110 + 27 H3' H1 E 26 9 6 1.090 109.500 30.000 + 28 C2' CT B 26 9 6 1.530 102.800 -86.300 + 29 H2'1 HC E 28 26 9 1.090 109.500 120.000 + 30 H2'2 HC E 28 26 9 1.090 109.500 240.000 + 31 O3' OS M 26 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DCN_D-CYTOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DCN_D-CYTOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..cc05558b3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DCN_D-CYTOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.490 108.100 -127.700 + 15 C6 CM B 14 12 11 1.360 121.100 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.360 121.000 180.000 + 18 H5 HA E 17 15 14 1.090 120.000 180.000 + 19 C4 CA B 17 15 14 1.430 116.900 0.000 + 20 N4 N2 B 19 17 15 1.320 120.100 180.000 + 21 H41 H E 20 19 17 1.010 117.700 180.000 + 22 H42 H E 20 19 17 1.010 120.270 0.000 + 23 N3 NC S 19 17 15 1.330 121.700 0.000 + 24 C2 C S 23 19 17 1.360 120.500 0.000 + 25 O2 O E 24 23 19 1.240 122.400 180.000 + 26 C3' CT M 9 6 5 1.530 115.780 -329.110 + 27 H3' H1 E 26 9 6 1.090 109.500 30.000 + 28 C2' CT B 26 9 6 1.530 102.800 -86.300 + 29 H2'1 HC E 28 26 9 1.090 109.500 120.000 + 30 H2'2 HC E 28 26 9 1.090 109.500 240.000 + 31 O3' OH M 26 9 6 1.420 116.520 -203.470 + 32 H3T HO M 31 26 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DC_D-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DC_D-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..8d0b26c2b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DC_D-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.490 108.100 -127.700 + 17 C6 CM B 16 14 13 1.360 121.100 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.360 121.000 180.000 + 20 H5 HA E 19 17 16 1.090 120.000 180.000 + 21 C4 CA B 19 17 16 1.430 116.900 0.000 + 22 N4 N2 B 21 19 17 1.320 120.100 180.000 + 23 H41 H E 22 21 19 1.010 117.700 180.000 + 24 H42 H E 22 21 19 1.010 120.270 0.000 + 25 N3 NC S 21 19 17 1.330 121.700 0.000 + 26 C2 C S 25 21 19 1.360 120.500 0.000 + 27 O2 O E 26 25 21 1.240 122.400 180.000 + 28 C3' CT M 11 8 7 1.530 115.780 -329.110 + 29 H3' H1 E 28 11 8 1.090 109.500 30.000 + 30 C2' CT B 28 11 8 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 11 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 11 1.090 109.500 240.000 + 33 O3' OS M 28 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DG3_D-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DG3_D-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..cf83eb63c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DG3_D-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,37 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.490 108.060 -127.700 + 17 C8 CK B 16 14 13 1.380 129.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.310 114.000 -179.900 + 20 C5 CB S 19 17 16 1.390 103.900 0.000 + 21 C6 C B 20 19 17 1.420 130.400 180.000 + 22 O6 O E 21 20 19 1.230 128.800 0.000 + 23 N1 NA B 21 20 19 1.400 111.380 180.000 + 24 H1 H E 23 21 20 1.000 117.360 179.900 + 25 C2 CA B 23 21 20 1.380 125.240 -0.100 + 26 N2 N2 B 25 23 21 1.340 116.020 180.000 + 27 H21 H E 26 25 23 1.010 127.000 -0.820 + 28 H22 H E 26 25 23 1.010 116.530 -179.440 + 29 N3 NC S 25 23 21 1.330 123.300 0.000 + 30 C4 CB E 29 25 23 1.360 112.200 0.000 + 31 C3' CT M 11 8 7 1.530 115.780 -329.110 + 32 H3' H1 E 31 11 8 1.090 109.500 30.000 + 33 C2' CT B 31 11 8 1.530 102.800 -86.300 + 34 H2'1 HC E 33 31 11 1.090 109.500 120.000 + 35 H2'2 HC E 33 31 11 1.090 109.500 240.000 + 36 O3' OH M 31 11 8 1.420 116.520 -203.470 + 37 H3T HO M 36 31 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DG5_D-GUANOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DG5_D-GUANOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..0997610b6 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DG5_D-GUANOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.490 108.060 -127.700 + 15 C8 CK B 14 12 11 1.380 129.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.310 114.000 -179.900 + 18 C5 CB S 17 15 14 1.390 103.900 0.000 + 19 C6 C B 18 17 15 1.420 130.400 180.000 + 20 O6 O E 19 18 17 1.230 128.800 0.000 + 21 N1 NA B 19 18 17 1.400 111.380 180.000 + 22 H1 H E 21 19 18 1.000 117.360 179.900 + 23 C2 CA B 21 19 18 1.380 125.240 -0.100 + 24 N2 N2 B 23 21 19 1.340 116.020 180.000 + 25 H21 H E 24 23 21 1.010 127.000 -0.820 + 26 H22 H E 24 23 21 1.010 116.530 -179.440 + 27 N3 NC S 23 21 19 1.330 123.300 0.000 + 28 C4 CB E 27 23 21 1.360 112.200 0.000 + 29 C3' CT M 9 6 5 1.530 115.780 -329.110 + 30 H3' H1 E 29 9 6 1.090 109.500 30.000 + 31 C2' CT B 29 9 6 1.530 102.800 -86.300 + 32 H2'1 HC E 31 29 9 1.090 109.500 120.000 + 33 H2'2 HC E 31 29 9 1.090 109.500 240.000 + 34 O3' OS M 29 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DGN_D-GUANOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DGN_D-GUANOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..56185415a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DGN_D-GUANOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.490 108.060 -127.700 + 15 C8 CK B 14 12 11 1.380 129.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.310 114.000 -179.900 + 18 C5 CB S 17 15 14 1.390 103.900 0.000 + 19 C6 C B 18 17 15 1.420 130.400 180.000 + 20 O6 O E 19 18 17 1.230 128.800 0.000 + 21 N1 NA B 19 18 17 1.400 111.380 180.000 + 22 H1 H E 21 19 18 1.000 117.360 179.900 + 23 C2 CA B 21 19 18 1.380 125.240 -0.100 + 24 N2 N2 B 23 21 19 1.340 116.020 180.000 + 25 H21 H E 24 23 21 1.010 127.000 -0.820 + 26 H22 H E 24 23 21 1.010 116.530 -179.440 + 27 N3 NC S 23 21 19 1.330 123.300 0.000 + 28 C4 CB E 27 23 21 1.360 112.200 0.000 + 29 C3' CT M 9 6 5 1.530 115.780 -329.110 + 30 H3' H1 E 29 9 6 1.090 109.500 30.000 + 31 C2' CT B 29 9 6 1.530 102.800 -86.300 + 32 H2'1 HC E 31 29 9 1.090 109.500 120.000 + 33 H2'2 HC E 31 29 9 1.090 109.500 240.000 + 34 O3' OH M 29 9 6 1.420 116.520 -203.470 + 35 H3T HO M 34 29 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DG_D-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DG_D-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..acf8f7bb5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DG_D-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,36 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.490 108.060 -127.700 + 17 C8 CK B 16 14 13 1.380 129.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.310 114.000 -179.900 + 20 C5 CB S 19 17 16 1.390 103.900 0.000 + 21 C6 C B 20 19 17 1.420 130.400 180.000 + 22 O6 O E 21 20 19 1.230 128.800 0.000 + 23 N1 NA B 21 20 19 1.400 111.380 180.000 + 24 H1 H E 23 21 20 1.000 117.360 179.900 + 25 C2 CA B 23 21 20 1.380 125.240 -0.100 + 26 N2 N2 B 25 23 21 1.340 116.020 180.000 + 27 H21 H E 26 25 23 1.010 127.000 -0.820 + 28 H22 H E 26 25 23 1.010 116.530 -179.440 + 29 N3 NC S 25 23 21 1.330 123.300 0.000 + 30 C4 CB E 29 25 23 1.360 112.200 0.000 + 31 C3' CT M 11 8 7 1.530 115.780 -329.110 + 32 H3' H1 E 31 11 8 1.090 109.500 30.000 + 33 C2' CT B 31 11 8 1.530 102.800 -86.300 + 34 H2'1 HC E 33 31 11 1.090 109.500 120.000 + 35 H2'2 HC E 33 31 11 1.090 109.500 240.000 + 36 O3' OS M 31 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DT3_D-THYMINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DT3_D-THYMINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..c83118990 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DT3_D-THYMINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,36 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.530 109.590 -127.700 + 17 C6 CM B 16 14 13 1.370 123.040 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.340 121.220 177.300 + 20 C7 CT 3 19 17 16 1.500 121.630 180.000 + 21 H71 HC E 20 19 17 1.090 109.500 60.000 + 22 H72 HC E 20 19 17 1.090 109.500 180.000 + 23 H73 HC E 20 19 17 1.090 109.500 300.000 + 24 C4 C B 19 17 16 1.440 120.780 0.000 + 25 O4 O E 24 19 17 1.230 125.350 180.000 + 26 N3 NA B 24 19 17 1.380 114.070 0.000 + 27 H3 H E 26 24 19 1.090 116.770 180.000 + 28 C2 C S 26 24 19 1.380 126.460 0.000 + 29 O2 O E 28 26 24 1.220 121.700 180.000 + 30 C3' CT M 11 8 7 1.530 115.780 -329.110 + 31 H3' H1 E 30 11 8 1.090 109.500 30.000 + 32 C2' CT B 30 11 8 1.530 102.800 -86.300 + 33 H2'1 HC E 32 30 11 1.090 109.500 120.000 + 34 H2'2 HC E 32 30 11 1.090 109.500 240.000 + 35 O3' OH M 30 11 8 1.420 116.520 -203.470 + 36 H3T HO M 35 30 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DT5_D-THYMINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DT5_D-THYMINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag new file mode 100644 index 000000000..cd4ef1061 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DT5_D-THYMINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.530 109.590 -127.700 + 15 C6 CM B 14 12 11 1.370 123.040 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.340 121.220 177.300 + 18 C7 CT 3 17 15 14 1.500 121.630 180.000 + 19 H71 HC E 18 17 15 1.090 109.500 60.000 + 20 H72 HC E 18 17 15 1.090 109.500 180.000 + 21 H73 HC E 18 17 15 1.090 109.500 300.000 + 22 C4 C B 17 15 14 1.440 120.780 0.000 + 23 O4 O E 22 17 15 1.230 125.350 180.000 + 24 N3 NA B 22 17 15 1.380 114.070 0.000 + 25 H3 H E 24 22 17 1.090 116.770 180.000 + 26 C2 C S 24 22 17 1.380 126.460 0.000 + 27 O2 O E 26 24 22 1.220 121.700 180.000 + 28 C3' CT M 9 6 5 1.530 115.780 -329.110 + 29 H3' H1 E 28 9 6 1.090 109.500 30.000 + 30 C2' CT B 28 9 6 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 9 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 9 1.090 109.500 240.000 + 33 O3' OS M 28 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DTN_D-THYMINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DTN_D-THYMINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..37948bad6 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DTN_D-THYMINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.530 109.590 -127.700 + 15 C6 CM B 14 12 11 1.370 123.040 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.340 121.220 177.300 + 18 C7 CT 3 17 15 14 1.500 121.630 180.000 + 19 H71 HC E 18 17 15 1.090 109.500 60.000 + 20 H72 HC E 18 17 15 1.090 109.500 180.000 + 21 H73 HC E 18 17 15 1.090 109.500 300.000 + 22 C4 C B 17 15 14 1.440 120.780 0.000 + 23 O4 O E 22 17 15 1.230 125.350 180.000 + 24 N3 NA B 22 17 15 1.380 114.070 0.000 + 25 H3 H E 24 22 17 1.090 116.770 180.000 + 26 C2 C S 24 22 17 1.380 126.460 0.000 + 27 O2 O E 26 24 22 1.220 121.700 180.000 + 28 C3' CT M 9 6 5 1.530 115.780 -329.110 + 29 H3' H1 E 28 9 6 1.090 109.500 30.000 + 30 C2' CT B 28 9 6 1.530 102.800 -86.300 + 31 H2'1 HC E 30 28 9 1.090 109.500 120.000 + 32 H2'2 HC E 30 28 9 1.090 109.500 240.000 + 33 O3' OH M 28 9 6 1.420 116.520 -203.470 + 34 H3T HO M 33 28 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DT_D-THYMINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DT_D-THYMINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..0aafac705 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/DT_D-THYMINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.530 109.590 -127.700 + 17 C6 CM B 16 14 13 1.370 123.040 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.340 121.220 177.300 + 20 C7 CT 3 19 17 16 1.500 121.630 180.000 + 21 H71 HC E 20 19 17 1.090 109.500 60.000 + 22 H72 HC E 20 19 17 1.090 109.500 180.000 + 23 H73 HC E 20 19 17 1.090 109.500 300.000 + 24 C4 C B 19 17 16 1.440 120.780 0.000 + 25 O4 O E 24 19 17 1.230 125.350 180.000 + 26 N3 NA B 24 19 17 1.380 114.070 0.000 + 27 H3 H E 26 24 19 1.090 116.770 180.000 + 28 C2 C S 26 24 19 1.380 126.460 0.000 + 29 O2 O E 28 26 24 1.220 121.700 180.000 + 30 C3' CT M 11 8 7 1.530 115.780 -329.110 + 31 H3' H1 E 30 11 8 1.090 109.500 30.000 + 32 C2' CT B 30 11 8 1.530 102.800 -86.300 + 33 H2'1 HC E 32 30 11 1.090 109.500 120.000 + 34 H2'2 HC E 32 30 11 1.090 109.500 240.000 + 35 O3' OS M 30 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RA3_R-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RA3_R-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..0f484cfc7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RA3_R-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,37 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.520 109.590 -127.700 + 17 C8 CK B 16 14 13 1.370 131.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.300 113.930 177.000 + 20 C5 CB S 19 17 16 1.390 104.000 0.000 + 21 C6 CA B 20 19 17 1.400 132.420 180.000 + 22 N6 N2 B 21 20 19 1.340 123.500 0.000 + 23 H61 H E 22 21 20 1.010 120.000 180.000 + 24 H62 H E 22 21 20 1.010 120.000 0.000 + 25 N1 NC S 21 20 19 1.340 117.430 180.000 + 26 C2 CQ B 25 21 20 1.330 118.800 0.000 + 27 H2 H5 E 26 25 21 1.080 120.000 180.000 + 28 N3 NC S 26 25 21 1.320 129.170 0.000 + 29 C4 CB E 28 26 25 1.350 110.800 0.000 + 30 C3' CT M 11 8 7 1.530 115.780 -329.110 + 31 H3' H1 E 30 11 8 1.090 109.500 30.000 + 32 C2' CT B 30 11 8 1.530 102.800 -86.300 + 33 H2'1 H1 E 32 30 11 1.090 109.500 120.000 + 34 O2' OH S 32 30 11 1.430 109.500 240.000 + 35 HO'2 HO E 34 32 30 0.960 107.000 180.000 + 36 O3' OH M 30 11 8 1.420 116.520 -203.470 + 37 H3T HO M 36 30 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RA5_R-ADENOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RA5_R-ADENOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag new file mode 100644 index 000000000..3366e1f81 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RA5_R-ADENOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.520 109.590 -127.700 + 15 C8 CK B 14 12 11 1.370 131.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.300 113.930 177.000 + 18 C5 CB S 17 15 14 1.390 104.000 0.000 + 19 C6 CA B 18 17 15 1.400 132.420 180.000 + 20 N6 N2 B 19 18 17 1.340 123.500 0.000 + 21 H61 H E 20 19 18 1.010 120.000 180.000 + 22 H62 H E 20 19 18 1.010 120.000 0.000 + 23 N1 NC S 19 18 17 1.340 117.430 180.000 + 24 C2 CQ B 23 19 18 1.330 118.800 0.000 + 25 H2 H5 E 24 23 19 1.080 120.000 180.000 + 26 N3 NC S 24 23 19 1.320 129.170 0.000 + 27 C4 CB E 26 24 23 1.350 110.800 0.000 + 28 C3' CT M 9 6 5 1.530 115.780 -329.110 + 29 H3' H1 E 28 9 6 1.090 109.500 30.000 + 30 C2' CT B 28 9 6 1.530 102.800 -86.300 + 31 H2'1 H1 E 30 28 9 1.090 109.500 120.000 + 32 O2' OH S 30 28 9 1.430 109.500 240.000 + 33 HO'2 HO E 32 30 28 0.960 107.000 180.000 + 34 O3' OS M 28 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RAN_R-ADENOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RAN_R-ADENOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..b14a4b407 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RAN_R-ADENOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.520 109.590 -127.700 + 15 C8 CK B 14 12 11 1.370 131.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.300 113.930 177.000 + 18 C5 CB S 17 15 14 1.390 104.000 0.000 + 19 C6 CA B 18 17 15 1.400 132.420 180.000 + 20 N6 N2 B 19 18 17 1.340 123.500 0.000 + 21 H61 H E 20 19 18 1.010 120.000 180.000 + 22 H62 H E 20 19 18 1.010 120.000 0.000 + 23 N1 NC S 19 18 17 1.340 117.430 180.000 + 24 C2 CQ B 23 19 18 1.330 118.800 0.000 + 25 H2 H5 E 24 23 19 1.080 120.000 180.000 + 26 N3 NC S 24 23 19 1.320 129.170 0.000 + 27 C4 CB E 26 24 23 1.350 110.800 0.000 + 28 C3' CT M 9 6 5 1.530 115.780 -329.110 + 29 H3' H1 E 28 9 6 1.090 109.500 30.000 + 30 C2' CT B 28 9 6 1.530 102.800 -86.300 + 31 H2'1 H1 E 30 28 9 1.090 109.500 120.000 + 32 O2' OH S 30 28 9 1.430 109.500 240.000 + 33 HO'2 HO E 32 30 28 0.960 107.000 180.000 + 34 O3' OH M 28 9 6 1.420 116.520 -203.470 + 35 H3T HO M 34 28 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RA_R-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RA_R-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..fbae9a960 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RA_R-ADENOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,36 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.520 109.590 -127.700 + 17 C8 CK B 16 14 13 1.370 131.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.300 113.930 177.000 + 20 C5 CB S 19 17 16 1.390 104.000 0.000 + 21 C6 CA B 20 19 17 1.400 132.420 180.000 + 22 N6 N2 B 21 20 19 1.340 123.500 0.000 + 23 H61 H E 22 21 20 1.010 120.000 180.000 + 24 H62 H E 22 21 20 1.010 120.000 0.000 + 25 N1 NC S 21 20 19 1.340 117.430 180.000 + 26 C2 CQ B 25 21 20 1.330 118.800 0.000 + 27 H2 H5 E 26 25 21 1.080 120.000 180.000 + 28 N3 NC S 26 25 21 1.320 129.170 0.000 + 29 C4 CB E 28 26 25 1.350 110.800 0.000 + 30 C3' CT M 11 8 7 1.530 115.780 -329.110 + 31 H3' H1 E 30 11 8 1.090 109.500 30.000 + 32 C2' CT B 30 11 8 1.530 102.800 -86.300 + 33 H2'1 H1 E 32 30 11 1.090 109.500 120.000 + 34 O2' OH S 32 30 11 1.430 109.500 240.000 + 35 HO'2 HO E 34 32 30 0.960 107.000 180.000 + 36 O3' OS M 30 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RC3_R-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RC3_R-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..dd226e8cb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RC3_R-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.490 108.100 -127.700 + 17 C6 CM B 16 14 13 1.360 121.100 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.360 121.000 180.000 + 20 H5 HA E 19 17 16 1.090 120.000 180.000 + 21 C4 CA B 19 17 16 1.430 116.900 0.000 + 22 N4 N2 B 21 19 17 1.320 120.100 180.000 + 23 H41 H E 22 21 19 1.010 117.700 180.000 + 24 H42 H E 22 21 19 1.010 120.270 0.000 + 25 N3 NC S 21 19 17 1.330 121.700 0.000 + 26 C2 C S 25 21 19 1.360 120.500 0.000 + 27 O2 O E 26 25 21 1.240 122.400 180.000 + 28 C3' CT M 11 8 7 1.530 115.780 -329.110 + 29 H3' H1 E 28 11 8 1.090 109.500 30.000 + 30 C2' CT B 28 11 8 1.530 102.800 -86.300 + 31 H2'1 H1 E 30 28 11 1.090 109.500 120.000 + 32 O2' OH S 30 28 11 1.430 109.500 240.000 + 33 HO'2 HO E 32 30 28 0.960 107.000 180.000 + 34 O3' OH M 28 11 8 1.420 116.520 -203.470 + 35 H3T HO M 34 28 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RC5_R-CYTOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RC5_R-CYTOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..310fb25e0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RC5_R-CYTOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.490 108.100 -127.700 + 15 C6 CM B 14 12 11 1.360 121.100 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.360 121.000 180.000 + 18 H5 HA E 17 15 14 1.090 120.000 180.000 + 19 C4 CA B 17 15 14 1.430 116.900 0.000 + 20 N4 N2 B 19 17 15 1.320 120.100 180.000 + 21 H41 H E 20 19 17 1.010 117.700 180.000 + 22 H42 H E 20 19 17 1.010 120.270 0.000 + 23 N3 NC S 19 17 15 1.330 121.700 0.000 + 24 C2 C S 23 19 17 1.360 120.500 0.000 + 25 O2 O E 24 23 19 1.240 122.400 180.000 + 26 C3' CT M 9 6 5 1.530 115.780 -329.110 + 27 H3' H1 E 26 9 6 1.090 109.500 30.000 + 28 C2' CT B 26 9 6 1.530 102.800 -86.300 + 29 H2'1 H1 E 28 26 9 1.090 109.500 120.000 + 30 O2' OH S 28 26 9 1.430 109.500 240.000 + 31 HO'2 HO E 30 28 26 0.960 107.000 180.000 + 32 O3' OS M 26 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RCN_R-CYTOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RCN_R-CYTOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..1ca2447df --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RCN_R-CYTOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.490 108.100 -127.700 + 15 C6 CM B 14 12 11 1.360 121.100 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.360 121.000 180.000 + 18 H5 HA E 17 15 14 1.090 120.000 180.000 + 19 C4 CA B 17 15 14 1.430 116.900 0.000 + 20 N4 N2 B 19 17 15 1.320 120.100 180.000 + 21 H41 H E 20 19 17 1.010 117.700 180.000 + 22 H42 H E 20 19 17 1.010 120.270 0.000 + 23 N3 NC S 19 17 15 1.330 121.700 0.000 + 24 C2 C S 23 19 17 1.360 120.500 0.000 + 25 O2 O E 24 23 19 1.240 122.400 180.000 + 26 C3' CT M 9 6 5 1.530 115.780 -329.110 + 27 H3' H1 E 26 9 6 1.090 109.500 30.000 + 28 C2' CT B 26 9 6 1.530 102.800 -86.300 + 29 H2'1 H1 E 28 26 9 1.090 109.500 120.000 + 30 O2' OH S 28 26 9 1.430 109.500 240.000 + 31 HO'2 HO E 30 28 26 0.960 107.000 180.000 + 32 O3' OH M 26 9 6 1.420 116.520 -203.470 + 33 H3T HO M 32 26 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RC_R-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RC_R-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..89a342595 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RC_R-CYTOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.490 108.100 -127.700 + 17 C6 CM B 16 14 13 1.360 121.100 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.360 121.000 180.000 + 20 H5 HA E 19 17 16 1.090 120.000 180.000 + 21 C4 CA B 19 17 16 1.430 116.900 0.000 + 22 N4 N2 B 21 19 17 1.320 120.100 180.000 + 23 H41 H E 22 21 19 1.010 117.700 180.000 + 24 H42 H E 22 21 19 1.010 120.270 0.000 + 25 N3 NC S 21 19 17 1.330 121.700 0.000 + 26 C2 C S 25 21 19 1.360 120.500 0.000 + 27 O2 O E 26 25 21 1.240 122.400 180.000 + 28 C3' CT M 11 8 7 1.530 115.780 -329.110 + 29 H3' H1 E 28 11 8 1.090 109.500 30.000 + 30 C2' CT B 28 11 8 1.530 102.800 -86.300 + 31 H2'1 H1 E 30 28 11 1.090 109.500 120.000 + 32 O2' OH S 30 28 11 1.430 109.500 240.000 + 33 HO'2 HO E 32 30 28 0.960 107.000 180.000 + 34 O3' OS M 28 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RG3_R-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RG3_R-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..d8281d3ef --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RG3_R-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,38 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.490 108.060 -127.700 + 17 C8 CK B 16 14 13 1.380 129.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.310 114.000 -179.900 + 20 C5 CB S 19 17 16 1.390 103.900 0.000 + 21 C6 C B 20 19 17 1.420 130.400 180.000 + 22 O6 O E 21 20 19 1.230 128.800 0.000 + 23 N1 NA B 21 20 19 1.400 111.380 180.000 + 24 H1 H E 23 21 20 1.000 117.360 179.900 + 25 C2 CA B 23 21 20 1.380 125.240 -0.100 + 26 N2 N2 B 25 23 21 1.340 116.020 180.000 + 27 H21 H E 26 25 23 1.010 127.000 -0.820 + 28 H22 H E 26 25 23 1.010 116.530 -179.440 + 29 N3 NC S 25 23 21 1.330 123.300 0.000 + 30 C4 CB E 29 25 23 1.360 112.200 0.000 + 31 C3' CT M 11 8 7 1.530 115.780 -329.110 + 32 H3' H1 E 31 11 8 1.090 109.500 30.000 + 33 C2' CT B 31 11 8 1.530 102.800 -86.300 + 34 H2'1 H1 E 33 31 11 1.090 109.500 120.000 + 35 O2' OH S 33 31 11 1.430 109.500 240.000 + 36 HO'2 HO E 35 33 31 0.960 107.000 180.000 + 37 O3' OH M 31 11 8 1.420 116.520 -203.470 + 38 H3T HO M 37 31 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RG5_R-GUANOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RG5_R-GUANOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..3642f293f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RG5_R-GUANOSINE_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.490 108.060 -127.700 + 15 C8 CK B 14 12 11 1.380 129.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.310 114.000 -179.900 + 18 C5 CB S 17 15 14 1.390 103.900 0.000 + 19 C6 C B 18 17 15 1.420 130.400 180.000 + 20 O6 O E 19 18 17 1.230 128.800 0.000 + 21 N1 NA B 19 18 17 1.400 111.380 180.000 + 22 H1 H E 21 19 18 1.000 117.360 179.900 + 23 C2 CA B 21 19 18 1.380 125.240 -0.100 + 24 N2 N2 B 23 21 19 1.340 116.020 180.000 + 25 H21 H E 24 23 21 1.010 127.000 -0.820 + 26 H22 H E 24 23 21 1.010 116.530 -179.440 + 27 N3 NC S 23 21 19 1.330 123.300 0.000 + 28 C4 CB E 27 23 21 1.360 112.200 0.000 + 29 C3' CT M 9 6 5 1.530 115.780 -329.110 + 30 H3' H1 E 29 9 6 1.090 109.500 30.000 + 31 C2' CT B 29 9 6 1.530 102.800 -86.300 + 32 H2'1 H1 E 31 29 9 1.090 109.500 120.000 + 33 O2' OH S 31 29 9 1.430 109.500 240.000 + 34 HO'2 HO E 33 31 29 0.960 107.000 180.000 + 35 O3' OS M 29 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RGN_R-GUANOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RGN_R-GUANOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..250669a6f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RGN_R-GUANOSINE_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,36 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 5 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N9 N* S 12 11 9 1.490 108.060 -127.700 + 15 C8 CK B 14 12 11 1.380 129.200 81.590 + 16 H8 H5 E 15 14 12 1.080 120.000 0.000 + 17 N7 NB S 15 14 12 1.310 114.000 -179.900 + 18 C5 CB S 17 15 14 1.390 103.900 0.000 + 19 C6 C B 18 17 15 1.420 130.400 180.000 + 20 O6 O E 19 18 17 1.230 128.800 0.000 + 21 N1 NA B 19 18 17 1.400 111.380 180.000 + 22 H1 H E 21 19 18 1.000 117.360 179.900 + 23 C2 CA B 21 19 18 1.380 125.240 -0.100 + 24 N2 N2 B 23 21 19 1.340 116.020 180.000 + 25 H21 H E 24 23 21 1.010 127.000 -0.820 + 26 H22 H E 24 23 21 1.010 116.530 -179.440 + 27 N3 NC S 23 21 19 1.330 123.300 0.000 + 28 C4 CB E 27 23 21 1.360 112.200 0.000 + 29 C3' CT M 9 6 5 1.530 115.780 -329.110 + 30 H3' H1 E 29 9 6 1.090 109.500 30.000 + 31 C2' CT B 29 9 6 1.530 102.800 -86.300 + 32 H2'1 H1 E 31 29 9 1.090 109.500 120.000 + 33 O2' OH S 31 29 9 1.430 109.500 240.000 + 34 HO'2 HO E 33 31 29 0.960 107.000 180.000 + 35 O3' OH M 29 9 6 1.420 116.520 -203.470 + 36 H3T HO M 35 29 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RG_R-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RG_R-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..b70ca087e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RG_R-GUANOSINE_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,37 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N9 N* S 14 13 11 1.490 108.060 -127.700 + 17 C8 CK B 16 14 13 1.380 129.200 81.590 + 18 H8 H5 E 17 16 14 1.080 120.000 0.000 + 19 N7 NB S 17 16 14 1.310 114.000 -179.900 + 20 C5 CB S 19 17 16 1.390 103.900 0.000 + 21 C6 C B 20 19 17 1.420 130.400 180.000 + 22 O6 O E 21 20 19 1.230 128.800 0.000 + 23 N1 NA B 21 20 19 1.400 111.380 180.000 + 24 H1 H E 23 21 20 1.000 117.360 179.900 + 25 C2 CA B 23 21 20 1.380 125.240 -0.100 + 26 N2 N2 B 25 23 21 1.340 116.020 180.000 + 27 H21 H E 26 25 23 1.010 127.000 -0.820 + 28 H22 H E 26 25 23 1.010 116.530 -179.440 + 29 N3 NC S 25 23 21 1.330 123.300 0.000 + 30 C4 CB E 29 25 23 1.360 112.200 0.000 + 31 C3' CT M 11 8 7 1.530 115.780 -329.110 + 32 H3' H1 E 31 11 8 1.090 109.500 30.000 + 33 C2' CT B 31 11 8 1.530 102.800 -86.300 + 34 H2'1 H1 E 33 31 11 1.090 109.500 120.000 + 35 O2' OH S 33 31 11 1.430 109.500 240.000 + 36 HO'2 HO E 35 33 31 0.960 107.000 180.000 + 37 O3' OS M 31 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RU3_R-URACIL_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RU3_R-URACIL_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..0370f880a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RU3_R-URACIL_-_with_5_p__-_phosphate_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.530 109.590 -127.700 + 17 C6 CM B 16 14 13 1.370 123.040 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.340 121.220 177.300 + 20 H5 HA E 19 17 16 1.090 120.000 180.000 + 21 C4 C B 19 17 16 1.440 120.780 0.000 + 22 O4 O E 21 19 17 1.230 125.350 180.000 + 23 N3 NA B 21 19 17 1.380 114.070 0.000 + 24 H3 H E 23 21 19 1.090 116.770 180.000 + 25 C2 C S 23 21 19 1.380 126.460 0.000 + 26 O2 O E 25 23 21 1.220 121.700 180.000 + 27 C3' CT M 11 8 7 1.530 115.780 -329.110 + 28 H3' H1 E 27 11 8 1.090 109.500 30.000 + 29 C2' CT B 27 11 8 1.530 102.800 -86.300 + 30 H2'1 H1 E 29 27 11 1.090 109.500 120.000 + 31 O2' OH S 29 27 11 1.430 109.500 240.000 + 32 HO'2 HO E 31 29 27 0.960 107.000 180.000 + 33 O3' OH M 27 11 8 1.420 116.520 -203.470 + 34 H3T HO M 33 27 11 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RU5_R-URACIL_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RU5_R-URACIL_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag new file mode 100644 index 000000000..e61651431 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RU5_R-URACIL_-_with_5_p__-_OH_end_group_and_3_p__-_O_op_minus_cp_.in_frag @@ -0,0 +1,31 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.530 109.590 -127.700 + 15 C6 CM B 14 12 11 1.370 123.040 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.340 121.220 177.300 + 18 H5 HA E 17 15 14 1.090 120.000 180.000 + 19 C4 C B 17 15 14 1.440 120.780 0.000 + 20 O4 O E 19 17 15 1.230 125.350 180.000 + 21 N3 NA B 19 17 15 1.380 114.070 0.000 + 22 H3 H E 21 19 17 1.090 116.770 180.000 + 23 C2 C S 21 19 17 1.380 126.460 0.000 + 24 O2 O E 23 21 19 1.220 121.700 180.000 + 25 C3' CT M 9 6 5 1.530 115.780 -329.110 + 26 H3' H1 E 25 9 6 1.090 109.500 30.000 + 27 C2' CT B 25 9 6 1.530 102.800 -86.300 + 28 H2'1 H1 E 27 25 9 1.090 109.500 120.000 + 29 O2' OH S 27 25 9 1.430 109.500 240.000 + 30 HO'2 HO E 29 27 25 0.960 107.000 180.000 + 31 O3' OS M 25 9 6 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RUN_R-URACIL_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RUN_R-URACIL_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag new file mode 100644 index 000000000..bddd84d94 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RUN_R-URACIL_-_with_5_p__-_OH_group_and_3_p__-_OH_group.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H5T HO M 3 2 1 1.000 120.000 180.000 + 5 O5' OH M 4 3 2 0.960 101.430 -98.890 + 6 C5' CT M 5 4 3 1.440 119.000 -39.220 + 7 H5'1 H1 E 6 5 4 1.090 109.500 60.000 + 8 H5'2 H1 E 6 5 4 1.090 109.500 -60.000 + 9 C4' CT M 6 5 4 1.520 110.000 -180.000 + 10 H4' H1 E 9 6 5 1.090 109.500 -200.000 + 11 O4' OS S 9 6 5 1.460 108.860 -86.310 + 12 C1' CT B 11 9 6 1.420 110.040 105.600 + 13 H1' H2 E 12 11 9 1.090 109.500 -240.000 + 14 N1 N* S 12 11 9 1.530 109.590 -127.700 + 15 C6 CM B 14 12 11 1.370 123.040 81.590 + 16 H6 H4 E 15 14 12 1.080 120.000 0.000 + 17 C5 CM B 15 14 12 1.340 121.220 177.300 + 18 H5 HA E 17 15 14 1.090 120.000 180.000 + 19 C4 C B 17 15 14 1.440 120.780 0.000 + 20 O4 O E 19 17 15 1.230 125.350 180.000 + 21 N3 NA B 19 17 15 1.380 114.070 0.000 + 22 H3 H E 21 19 17 1.090 116.770 180.000 + 23 C2 C S 21 19 17 1.380 126.460 0.000 + 24 O2 O E 23 21 19 1.220 121.700 180.000 + 25 C3' CT M 9 6 5 1.530 115.780 -329.110 + 26 H3' H1 E 25 9 6 1.090 109.500 30.000 + 27 C2' CT B 25 9 6 1.530 102.800 -86.300 + 28 H2'1 H1 E 27 25 9 1.090 109.500 120.000 + 29 O2' OH S 27 25 9 1.430 109.500 240.000 + 30 HO'2 HO E 29 27 25 0.960 107.000 180.000 + 31 O3' OH M 25 9 6 1.420 116.520 -203.470 + 32 H3T HO M 31 25 9 0.960 114.970 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RU_R-URACIL_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RU_R-URACIL_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag new file mode 100644 index 000000000..c81a03314 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/RU_R-URACIL_-_with_5_p__-_phosphate_group_and_3_p__-_O_op_minus_cp__group.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 200.000 + 5 O1P O2 E 4 3 2 1.480 109.610 150.000 + 6 O2P O2 E 4 3 2 1.480 109.580 20.000 + 7 O5' OS M 4 3 2 1.600 101.430 -98.890 + 8 C5' CT M 7 4 3 1.440 119.000 -39.220 + 9 H5'1 H1 E 8 7 4 1.090 109.500 60.000 + 10 H5'2 H1 E 8 7 4 1.090 109.500 -60.000 + 11 C4' CT M 8 7 4 1.520 110.000 180.000 + 12 H4' H1 E 11 8 7 1.090 109.500 -200.000 + 13 O4' OS S 11 8 7 1.460 108.860 -86.310 + 14 C1' CT B 13 11 8 1.420 110.040 105.600 + 15 H1' H2 E 14 13 11 1.090 109.500 -240.000 + 16 N1 N* S 14 13 11 1.530 109.590 -127.700 + 17 C6 CM B 16 14 13 1.370 123.040 81.590 + 18 H6 H4 E 17 16 14 1.080 120.000 0.000 + 19 C5 CM B 17 16 14 1.340 121.220 177.300 + 20 H5 HA E 19 17 16 1.090 120.000 180.000 + 21 C4 C B 19 17 16 1.440 120.780 0.000 + 22 O4 O E 21 19 17 1.230 125.350 180.000 + 23 N3 NA B 21 19 17 1.380 114.070 0.000 + 24 H3 H E 23 21 19 1.090 116.770 180.000 + 25 C2 C S 23 21 19 1.380 126.460 0.000 + 26 O2 O E 25 23 21 1.220 121.700 180.000 + 27 C3' CT M 11 8 7 1.530 115.780 -329.110 + 28 H3' H1 E 27 11 8 1.090 109.500 30.000 + 29 C2' CT B 27 11 8 1.530 102.800 -86.300 + 30 H2'1 H1 E 29 27 11 1.090 109.500 120.000 + 31 O2' OH S 29 27 11 1.430 109.500 240.000 + 32 HO'2 HO E 31 29 27 0.960 107.000 180.000 + 33 O3' OS M 27 11 8 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/all_nuc94/all_nuc94.in b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/all_nuc94.in new file mode 100644 index 000000000..e4672f404 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/all_nuc94/all_nuc94.in @@ -0,0 +1,1970 @@ + 1 0 2 +db94.dat +D-ADENOSINE - with 5' - OH end group and 3' - O(minus) + + DA5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 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H3' H1 E 30 11 8 1.09 109.50 30.00 0.0615 + 32 C2' CT B 30 11 8 1.53 102.80 -86.30 0.0670 + 33 H2'1 H1 E 32 30 11 1.09 109.50 120.00 0.0972 + 34 O2' OH S 32 30 11 1.43 109.50 240.00 -0.6139 + 35 HO'2 HO E 34 32 30 0.96 107.00 180.00 0.4186 + 36 O3' OS M 30 11 8 1.42 116.52 -203.47 -0.5246 + +CHARGE RA + 1.1662 -0.7760 -0.7760 -0.4989 0.0558 + 0.0679 0.0679 0.1065 0.1174 -0.3548 + 0.0394 0.2007 -0.0251 0.2006 0.1553 + -0.6073 0.0515 0.7009 -0.9019 0.4115 + 0.4115 -0.7615 0.5875 0.0473 -0.6997 + 0.3053 0.2022 0.0615 0.0670 0.0972 + -0.6139 0.4186 -0.5246 + +IMPROPER + C8 C4 N9 C1' + C6 H61 N6 H62 + N7 N9 C8 H8 + N1 N3 C2 H2 + C5 N1 C6 N6 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +R-ADENOSINE - with 5' - phosphate group and 3' - OH group + + RA3 INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0394 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2007 + 16 N9 N* S 14 13 11 1.52 109.59 -127.70 -0.0251 + 17 C8 CK B 16 14 13 1.37 131.20 81.59 0.2006 + 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1553 + 19 N7 NB S 17 16 14 1.30 113.93 177.00 -0.6073 + 20 C5 CB S 19 17 16 1.39 104.00 0.00 0.0515 + 21 C6 CA B 20 19 17 1.40 132.42 180.00 0.7009 + 22 N6 N2 B 21 20 19 1.34 123.50 0.00 -0.9019 + 23 H61 H E 22 21 20 1.01 120.00 180.00 0.4115 + 24 H62 H E 22 21 20 1.01 120.00 0.00 0.4115 + 25 N1 NC S 21 20 19 1.34 117.43 180.00 -0.7615 + 26 C2 CQ B 25 21 20 1.33 118.80 0.00 0.5875 + 27 H2 H5 E 26 25 21 1.08 120.00 180.00 0.0473 + 28 N3 NC S 26 25 21 1.32 129.17 0.00 -0.6997 + 29 C4 CB E 28 26 25 1.35 110.80 0.00 0.3053 + 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 + 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0615 + 32 C2' CT B 30 11 8 1.53 102.80 -86.30 0.0670 + 33 H2'1 H1 E 32 30 11 1.09 109.50 120.00 0.0972 + 34 O2' OH S 32 30 11 1.43 109.50 240.00 -0.6139 + 35 HO'2 HO E 34 32 30 0.96 107.00 180.00 0.4186 + 36 O3' OH M 30 11 8 1.42 116.52 -203.47 -0.6541 + 37 H3T HO M 36 30 11 0.96 114.97 180.00 0.4376 + +CHARGE RA3E + 1.1662 -0.7760 -0.7760 -0.4989 0.0558 + 0.0679 0.0679 0.1065 0.1174 -0.3548 + 0.0394 0.2007 -0.0251 0.2006 0.1553 + -0.6073 0.0515 0.7009 -0.9019 0.4115 + 0.4115 -0.7615 0.5875 0.0473 -0.6997 + 0.3053 0.2022 0.0615 0.0670 0.0972 + -0.6139 0.4186 -0.6541 0.4376 + +IMPROPER + C8 C4 N9 C1' + C6 H61 N6 H62 + N7 N9 C8 H8 + N1 N3 C2 H2 + C5 N1 C6 N6 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +R-ADENOSINE - with 5' - OH group and 3' - OH group + + RAN INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 + 9 C4' CT M 6 5 4 1.52 110.00 180.00 0.1065 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 + 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0394 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2007 + 14 N9 N* S 12 11 9 1.52 109.59 -127.70 -0.0251 + 15 C8 CK B 14 12 11 1.37 131.20 81.59 0.2006 + 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1553 + 17 N7 NB S 15 14 12 1.30 113.93 177.00 -0.6073 + 18 C5 CB S 17 15 14 1.39 104.00 0.00 0.0515 + 19 C6 CA B 18 17 15 1.40 132.42 180.00 0.7009 + 20 N6 N2 B 19 18 17 1.34 123.50 0.00 -0.9019 + 21 H61 H E 20 19 18 1.01 120.00 180.00 0.4115 + 22 H62 H E 20 19 18 1.01 120.00 0.00 0.4115 + 23 N1 NC S 19 18 17 1.34 117.43 180.00 -0.7615 + 24 C2 CQ B 23 19 18 1.33 118.80 0.00 0.5875 + 25 H2 H5 E 24 23 19 1.08 120.00 180.00 0.0473 + 26 N3 NC S 24 23 19 1.32 129.17 0.00 -0.6997 + 27 C4 CB E 26 24 23 1.35 110.80 0.00 0.3053 + 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 + 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0615 + 30 C2' CT B 28 9 6 1.53 102.80 -86.30 0.0670 + 31 H2'1 H1 E 30 28 9 1.09 109.50 120.00 0.0972 + 32 O2' OH S 30 28 9 1.43 109.50 240.00 -0.6139 + 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 0.4186 + 34 O3' OH M 28 9 6 1.42 116.52 -203.47 -0.6541 + 35 H3T HO M 34 28 9 0.96 114.97 180.00 0.4376 + +CHARGE resp RADE + 0.4295 -0.6223 0.0558 0.0679 0.0679 + 0.1065 0.1174 -0.3548 0.0394 0.2007 + -0.0251 0.2006 0.1553 -0.6073 0.0515 + 0.7009 -0.9019 0.4115 0.4115 -0.7615 + 0.5875 0.0473 -0.6997 0.3053 0.2022 + 0.0615 0.0670 0.0972 -0.6139 0.4186 + -0.6541 0.4376 + +IMPROPER + C8 C4 N9 C1' + C6 H61 N6 H62 + N7 N9 C8 H8 + N1 N3 C2 H2 + C5 N1 C6 N6 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +D-THYMINE - with 5' - OH end group and 3' - O(minus) + + DT5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 + 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0680 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1804 + 14 N1 N* S 12 11 9 1.53 109.59 -127.70 -0.0239 + 15 C6 CM B 14 12 11 1.37 123.04 81.59 -0.2209 + 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2607 + 17 C5 CM B 15 14 12 1.34 121.22 177.30 0.0025 + 18 C7 CT 3 17 15 14 1.50 121.63 180.00 -0.2269 + 19 H71 HC E 18 17 15 1.09 109.50 60.00 0.0770 + 20 H72 HC E 18 17 15 1.09 109.50 180.00 0.0770 + 21 H73 HC E 18 17 15 1.09 109.50 300.00 0.0770 + 22 C4 C B 17 15 14 1.44 120.78 0.00 0.5194 + 23 O4 O E 22 17 15 1.23 125.35 180.00 -0.5563 + 24 N3 NA B 22 17 15 1.38 114.07 0.00 -0.4340 + 25 H3 H E 24 22 17 1.09 116.77 180.00 0.3420 + 26 C2 C S 24 22 17 1.38 126.46 0.00 0.5677 + 27 O2 O E 26 24 22 1.22 121.70 180.00 -0.5881 + 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 + 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0985 + 30 C2' CT B 28 9 6 1.53 102.80 -86.30 -0.0854 + 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 0.0718 + 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 0.0718 + 33 O3' OS M 28 9 6 1.42 116.52 -203.47 -0.5232 + +CHARGE T5E + 0.4422 -0.6318 -0.0069 0.0754 0.0754 + 0.1629 0.1176 -0.3691 0.0680 0.1804 + -0.0239 -0.2209 0.2607 0.0025 -0.2269 + 0.0770 0.0770 0.0770 0.5194 -0.5563 + -0.4340 0.3420 0.5677 -0.5881 0.0713 + 0.0985 -0.0854 0.0718 0.0718 -0.5232 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +D-THYMINE - with 5' - phosphate group and 3' - O(minus) group + + DT INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0680 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1804 + 16 N1 N* S 14 13 11 1.53 109.59 -127.70 -0.0239 + 17 C6 CM B 16 14 13 1.37 123.04 81.59 -0.2209 + 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2607 + 19 C5 CM B 17 16 14 1.34 121.22 177.30 0.0025 + 20 C7 CT 3 19 17 16 1.50 121.63 180.00 -0.2269 + 21 H71 HC E 20 19 17 1.09 109.50 60.00 0.0770 + 22 H72 HC E 20 19 17 1.09 109.50 180.00 0.0770 + 23 H73 HC E 20 19 17 1.09 109.50 300.00 0.0770 + 24 C4 C B 19 17 16 1.44 120.78 0.00 0.5194 + 25 O4 O E 24 19 17 1.23 125.35 180.00 -0.5563 + 26 N3 NA B 24 19 17 1.38 114.07 0.00 -0.4340 + 27 H3 H E 26 24 19 1.09 116.77 180.00 0.3420 + 28 C2 C S 26 24 19 1.38 126.46 0.00 0.5677 + 29 O2 O E 28 26 24 1.22 121.70 180.00 -0.5881 + 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 + 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0985 + 32 C2' CT B 30 11 8 1.53 102.80 -86.30 -0.0854 + 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 0.0718 + 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 0.0718 + 35 O3' OS M 30 11 8 1.42 116.52 -203.47 -0.5232 + +CHARGE deoxy -resp T + 1.1659 -0.7761 -0.7761 -0.4954 -0.0069 + 0.0754 0.0754 0.1629 0.1176 -0.3691 + 0.0680 0.1804 -0.0239 -0.2209 0.2607 + 0.0025 -0.2269 0.0770 0.0770 0.0770 + 0.5194 -0.5563 -0.4340 0.3420 0.5677 + -0.5881 0.0713 0.0985 -0.0854 0.0718 + 0.0718 -0.5232 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +D-THYMINE - with 5' - phosphate group and 3' - OH group + + DT3 INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0680 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1804 + 16 N1 N* S 14 13 11 1.53 109.59 -127.70 -0.0239 + 17 C6 CM B 16 14 13 1.37 123.04 81.59 -0.2209 + 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2607 + 19 C5 CM B 17 16 14 1.34 121.22 177.30 0.0025 + 20 C7 CT 3 19 17 16 1.50 121.63 180.00 -0.2269 + 21 H71 HC E 20 19 17 1.09 109.50 60.00 0.0770 + 22 H72 HC E 20 19 17 1.09 109.50 180.00 0.0770 + 23 H73 HC E 20 19 17 1.09 109.50 300.00 0.0770 + 24 C4 C B 19 17 16 1.44 120.78 0.00 0.5194 + 25 O4 O E 24 19 17 1.23 125.35 180.00 -0.5563 + 26 N3 NA B 24 19 17 1.38 114.07 0.00 -0.4340 + 27 H3 H E 26 24 19 1.09 116.77 180.00 0.3420 + 28 C2 C S 26 24 19 1.38 126.46 0.00 0.5677 + 29 O2 O E 28 26 24 1.22 121.70 180.00 -0.5881 + 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 + 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0985 + 32 C2' CT B 30 11 8 1.53 102.80 -86.30 -0.0854 + 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 0.0718 + 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 0.0718 + 35 O3' OH M 30 11 8 1.42 116.52 -203.47 -0.6549 + 36 H3T HO M 35 30 11 0.96 114.97 180.00 0.4396 + +CHARGE T3E + 1.1659 -0.7761 -0.7761 -0.4954 -0.0069 + 0.0754 0.0754 0.1629 0.1176 -0.3691 + 0.0680 0.1804 -0.0239 -0.2209 0.2607 + 0.0025 -0.2269 0.0770 0.0770 0.0770 + 0.5194 -0.5563 -0.4340 0.3420 0.5677 + -0.5881 0.0713 0.0985 -0.0854 0.0718 + 0.0718 -0.6549 0.4396 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +D-THYMINE - with 5' - OH group and 3' - OH group + + DTN INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 + 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0680 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1804 + 14 N1 N* S 12 11 9 1.53 109.59 -127.70 -0.0239 + 15 C6 CM B 14 12 11 1.37 123.04 81.59 -0.2209 + 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2607 + 17 C5 CM B 15 14 12 1.34 121.22 177.30 0.0025 + 18 C7 CT 3 17 15 14 1.50 121.63 180.00 -0.2269 + 19 H71 HC E 18 17 15 1.09 109.50 60.00 0.0770 + 20 H72 HC E 18 17 15 1.09 109.50 180.00 0.0770 + 21 H73 HC E 18 17 15 1.09 109.50 300.00 0.0770 + 22 C4 C B 17 15 14 1.44 120.78 0.00 0.5194 + 23 O4 O E 22 17 15 1.23 125.35 180.00 -0.5563 + 24 N3 NA B 22 17 15 1.38 114.07 0.00 -0.4340 + 25 H3 H E 24 22 17 1.09 116.77 180.00 0.3420 + 26 C2 C S 24 22 17 1.38 126.46 0.00 0.5677 + 27 O2 O E 26 24 22 1.22 121.70 180.00 -0.5881 + 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 + 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0985 + 30 C2' CT B 28 9 6 1.53 102.80 -86.30 -0.0854 + 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 0.0718 + 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 0.0718 + 33 O3' OH M 28 9 6 1.42 116.52 -203.47 -0.6549 + 34 H3T HO M 33 28 9 0.96 114.97 180.00 0.4396 + +CHARGE deoxy-THY-B: + 0.4422 -0.6318 -0.0069 0.0754 0.0754 + 0.1629 0.1176 -0.3691 0.0680 0.1804 + -0.0239 -0.2209 0.2607 0.0025 -0.2269 + 0.0770 0.0770 0.0770 0.5194 -0.5563 + -0.4340 0.3420 0.5677 -0.5881 0.0713 + 0.0985 -0.0854 0.0718 0.0718 -0.6549 + 0.4396 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 C7 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +R-URACIL - with 5' - OH end group and 3' - O(minus) + + RU5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1065 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 + 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0674 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1824 + 14 N1 N* S 12 11 9 1.53 109.59 -127.70 0.0418 + 15 C6 CM B 14 12 11 1.37 123.04 81.59 -0.1126 + 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2188 + 17 C5 CM B 15 14 12 1.34 121.22 177.30 -0.3635 + 18 H5 HA E 17 15 14 1.09 120.00 180.00 0.1811 + 19 C4 C B 17 15 14 1.44 120.78 0.00 0.5952 + 20 O4 O E 19 17 15 1.23 125.35 180.00 -0.5761 + 21 N3 NA B 19 17 15 1.38 114.07 0.00 -0.3549 + 22 H3 H E 21 19 17 1.09 116.77 180.00 0.3154 + 23 C2 C S 21 19 17 1.38 126.46 0.00 0.4687 + 24 O2 O E 23 21 19 1.22 121.70 180.00 -0.5477 + 25 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 + 26 H3' H1 E 25 9 6 1.09 109.50 30.00 0.0615 + 27 C2' CT B 25 9 6 1.53 102.80 -86.30 0.0670 + 28 H2'1 H1 E 27 25 9 1.09 109.50 120.00 0.0972 + 29 O2' OH S 27 25 9 1.43 109.50 240.00 -0.6139 + 30 HO'2 HO E 29 27 25 0.96 107.00 180.00 0.4186 + 31 O3' OS M 25 9 6 1.42 116.52 -203.47 -0.5246 + +CHARGE RU5E + 0.4295 -0.6223 0.0558 0.0679 0.0679 + 0.1065 0.1174 -0.3548 0.0674 0.1824 + 0.0418 -0.1126 0.2188 -0.3635 0.1811 + 0.5952 -0.5761 -0.3549 0.3154 0.4687 + -0.5477 0.2022 0.0615 0.0670 0.0972 + -0.6139 0.4186 -0.5246 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 H5 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +R-URACIL - with 5' - phosphate group and 3' - O(minus) group + + RU INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0674 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1824 + 16 N1 N* S 14 13 11 1.53 109.59 -127.70 0.0418 + 17 C6 CM B 16 14 13 1.37 123.04 81.59 -0.1126 + 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2188 + 19 C5 CM B 17 16 14 1.34 121.22 177.30 -0.3635 + 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1811 + 21 C4 C B 19 17 16 1.44 120.78 0.00 0.5952 + 22 O4 O E 21 19 17 1.23 125.35 180.00 -0.5761 + 23 N3 NA B 21 19 17 1.38 114.07 0.00 -0.3549 + 24 H3 H E 23 21 19 1.09 116.77 180.00 0.3154 + 25 C2 C S 23 21 19 1.38 126.46 0.00 0.4687 + 26 O2 O E 25 23 21 1.22 121.70 180.00 -0.5477 + 27 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 + 28 H3' H1 E 27 11 8 1.09 109.50 30.00 0.0615 + 29 C2' CT B 27 11 8 1.53 102.80 -86.30 0.0670 + 30 H2'1 H1 E 29 27 11 1.09 109.50 120.00 0.0972 + 31 O2' OH S 29 27 11 1.43 109.50 240.00 -0.6139 + 32 HO'2 HO E 31 29 27 0.96 107.00 180.00 0.4186 + 33 O3' OS M 27 11 8 1.42 116.52 -203.47 -0.5246 + +CHARGE RU + 1.1662 -0.7760 -0.7760 -0.4989 0.0558 + 0.0679 0.0679 0.1065 0.1174 -0.3548 + 0.0674 0.1824 0.0418 -0.1126 0.2188 + -0.3635 0.1811 0.5952 -0.5761 -0.3549 + 0.3154 0.4687 -0.5477 0.2022 0.0615 + 0.0670 0.0972 -0.6139 0.4186 -0.5246 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 H5 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +R-URACIL - with 5' - phosphate group and 3' - OH group + + RU3 INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0674 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1824 + 16 N1 N* S 14 13 11 1.53 109.59 -127.70 0.0418 + 17 C6 CM B 16 14 13 1.37 123.04 81.59 -0.1126 + 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2188 + 19 C5 CM B 17 16 14 1.34 121.22 177.30 -0.3635 + 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1811 + 21 C4 C B 19 17 16 1.44 120.78 0.00 0.5952 + 22 O4 O E 21 19 17 1.23 125.35 180.00 -0.5761 + 23 N3 NA B 21 19 17 1.38 114.07 0.00 -0.3549 + 24 H3 H E 23 21 19 1.09 116.77 180.00 0.3154 + 25 C2 C S 23 21 19 1.38 126.46 0.00 0.4687 + 26 O2 O E 25 23 21 1.22 121.70 180.00 -0.5477 + 27 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 + 28 H3' H1 E 27 11 8 1.09 109.50 30.00 0.0615 + 29 C2' CT B 27 11 8 1.53 102.80 -86.30 0.0670 + 30 H2'1 H1 E 29 27 11 1.09 109.50 120.00 0.0972 + 31 O2' OH S 29 27 11 1.43 109.50 240.00 -0.6139 + 32 HO'2 HO E 31 29 27 0.96 107.00 180.00 0.4186 + 33 O3' OH M 27 11 8 1.42 116.52 -203.47 -0.6541 + 34 H3T HO M 33 27 11 0.96 114.97 180.00 0.4376 + +CHARGE RU3E + 1.1662 -0.7760 -0.7760 -0.4989 0.0558 + 0.0679 0.0679 0.1065 0.1174 -0.3548 + 0.0674 0.1824 0.0418 -0.1126 0.2188 + -0.3635 0.1811 0.5952 -0.5761 -0.3549 + 0.3154 0.4687 -0.5477 0.2022 0.0615 + 0.0670 0.0972 -0.6139 0.4186 -0.6541 + 0.4376 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 H5 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +R-URACIL - with 5' - OH group and 3' - OH group + + RUN INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1065 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 + 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0674 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1824 + 14 N1 N* S 12 11 9 1.53 109.59 -127.70 0.0418 + 15 C6 CM B 14 12 11 1.37 123.04 81.59 -0.1126 + 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2188 + 17 C5 CM B 15 14 12 1.34 121.22 177.30 -0.3635 + 18 H5 HA E 17 15 14 1.09 120.00 180.00 0.1811 + 19 C4 C B 17 15 14 1.44 120.78 0.00 0.5952 + 20 O4 O E 19 17 15 1.23 125.35 180.00 -0.5761 + 21 N3 NA B 19 17 15 1.38 114.07 0.00 -0.3549 + 22 H3 H E 21 19 17 1.09 116.77 180.00 0.3154 + 23 C2 C S 21 19 17 1.38 126.46 0.00 0.4687 + 24 O2 O E 23 21 19 1.22 121.70 180.00 -0.5477 + 25 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 + 26 H3' H1 E 25 9 6 1.09 109.50 30.00 0.0615 + 27 C2' CT B 25 9 6 1.53 102.80 -86.30 0.0670 + 28 H2'1 H1 E 27 25 9 1.09 109.50 120.00 0.0972 + 29 O2' OH S 27 25 9 1.43 109.50 240.00 -0.6139 + 30 HO'2 HO E 29 27 25 0.96 107.00 180.00 0.4186 + 31 O3' OH M 25 9 6 1.42 116.52 -203.47 -0.6541 + 32 H3T HO M 31 25 9 0.96 114.97 180.00 0.4376 + +CHARGE resp RURA + 0.4295 -0.6223 0.0558 0.0679 0.0679 + 0.1065 0.1174 -0.3548 0.0674 0.1824 + 0.0418 -0.1126 0.2188 -0.3635 0.1811 + 0.5952 -0.5761 -0.3549 0.3154 0.4687 + -0.5477 0.2022 0.0615 0.0670 0.0972 + -0.6139 0.4186 -0.6541 0.4376 + +IMPROPER + C6 C2 N1 C1' + C4 C6 C5 H5 + N1 N3 C2 O2 + C5 N3 C4 O4 + C2 C4 N3 H3 + N1 C5 C6 H6 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +D-GUANOSINE - with 5' - OH end group and 3' - O(minus) group + + DG5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 + 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0358 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1746 + 14 N9 N* S 12 11 9 1.49 108.06 -127.70 0.0577 + 15 C8 CK B 14 12 11 1.38 129.20 81.59 0.0736 + 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1997 + 17 N7 NB S 15 14 12 1.31 114.00 -179.90 -0.5725 + 18 C5 CB S 17 15 14 1.39 103.90 0.00 0.1991 + 19 C6 C B 18 17 15 1.42 130.40 180.00 0.4918 + 20 O6 O E 19 18 17 1.23 128.80 0.00 -0.5699 + 21 N1 NA B 19 18 17 1.40 111.38 180.00 -0.5053 + 22 H1 H E 21 19 18 1.00 117.36 179.90 0.3520 + 23 C2 CA B 21 19 18 1.38 125.24 -0.10 0.7432 + 24 N2 N2 B 23 21 19 1.34 116.02 180.00 -0.9230 + 25 H21 H E 24 23 21 1.01 127.00 -0.82 0.4235 + 26 H22 H E 24 23 21 1.01 116.53 -179.44 0.4235 + 27 N3 NC S 23 21 19 1.33 123.30 0.00 -0.6636 + 28 C4 CB E 27 23 21 1.36 112.20 0.00 0.1814 + 29 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 + 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0985 + 31 C2' CT B 29 9 6 1.53 102.80 -86.30 -0.0854 + 32 H2'1 HC E 31 29 9 1.09 109.50 120.00 0.0718 + 33 H2'2 HC E 31 29 9 1.09 109.50 240.00 0.0718 + 34 O3' OS M 29 9 6 1.42 116.52 -203.47 -0.5232 + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +D-GUANOSINE - with 5' - phosphate group and 3' - O(minus) group + + DG INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0358 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1746 + 16 N9 N* S 14 13 11 1.49 108.06 -127.70 0.0577 + 17 C8 CK B 16 14 13 1.38 129.20 81.59 0.0736 + 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1997 + 19 N7 NB S 17 16 14 1.31 114.00 -179.90 -0.5725 + 20 C5 CB S 19 17 16 1.39 103.90 0.00 0.1991 + 21 C6 C B 20 19 17 1.42 130.40 180.00 0.4918 + 22 O6 O E 21 20 19 1.23 128.80 0.00 -0.5699 + 23 N1 NA B 21 20 19 1.40 111.38 180.00 -0.5053 + 24 H1 H E 23 21 20 1.00 117.36 179.90 0.3520 + 25 C2 CA B 23 21 20 1.38 125.24 -0.10 0.7432 + 26 N2 N2 B 25 23 21 1.34 116.02 180.00 -0.9230 + 27 H21 H E 26 25 23 1.01 127.00 -0.82 0.4235 + 28 H22 H E 26 25 23 1.01 116.53 -179.44 0.4235 + 29 N3 NC S 25 23 21 1.33 123.30 0.00 -0.6636 + 30 C4 CB E 29 25 23 1.36 112.20 0.00 0.1814 + 31 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 + 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0985 + 33 C2' CT B 31 11 8 1.53 102.80 -86.30 -0.0854 + 34 H2'1 HC E 33 31 11 1.09 109.50 120.00 0.0718 + 35 H2'2 HC E 33 31 11 1.09 109.50 240.00 0.0718 + 36 O3' OS M 31 11 8 1.42 116.52 -203.47 -0.5232 + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +D-GUANOSINE - with 5' - phosphate group and 3' - OH group + + DG3 INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0358 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1746 + 16 N9 N* S 14 13 11 1.49 108.06 -127.70 0.0577 + 17 C8 CK B 16 14 13 1.38 129.20 81.59 0.0736 + 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1997 + 19 N7 NB S 17 16 14 1.31 114.00 -179.90 -0.5725 + 20 C5 CB S 19 17 16 1.39 103.90 0.00 0.1991 + 21 C6 C B 20 19 17 1.42 130.40 180.00 0.4918 + 22 O6 O E 21 20 19 1.23 128.80 0.00 -0.5699 + 23 N1 NA B 21 20 19 1.40 111.38 180.00 -0.5053 + 24 H1 H E 23 21 20 1.00 117.36 179.90 0.3520 + 25 C2 CA B 23 21 20 1.38 125.24 -0.10 0.7432 + 26 N2 N2 B 25 23 21 1.34 116.02 180.00 -0.9230 + 27 H21 H E 26 25 23 1.01 127.00 -0.82 0.4235 + 28 H22 H E 26 25 23 1.01 116.53 -179.44 0.4235 + 29 N3 NC S 25 23 21 1.33 123.30 0.00 -0.6636 + 30 C4 CB E 29 25 23 1.36 112.20 0.00 0.1814 + 31 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 + 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0985 + 33 C2' CT B 31 11 8 1.53 102.80 -86.30 -0.0854 + 34 H2'1 HC E 33 31 11 1.09 109.50 120.00 0.0718 + 35 H2'2 HC E 33 31 11 1.09 109.50 240.00 0.0718 + 36 O3' OH M 31 11 8 1.42 116.52 -203.47 -0.6549 + 37 H3T HO M 36 31 11 0.96 114.97 180.00 0.4396 + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +D-GUANOSINE - with 5' - OH group and 3' - OH group + + DGN INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 + 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0358 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1746 + 14 N9 N* S 12 11 9 1.49 108.06 -127.70 0.0577 + 15 C8 CK B 14 12 11 1.38 129.20 81.59 0.0736 + 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1997 + 17 N7 NB S 15 14 12 1.31 114.00 -179.90 -0.5725 + 18 C5 CB S 17 15 14 1.39 103.90 0.00 0.1991 + 19 C6 C B 18 17 15 1.42 130.40 180.00 0.4918 + 20 O6 O E 19 18 17 1.23 128.80 0.00 -0.5699 + 21 N1 NA B 19 18 17 1.40 111.38 180.00 -0.5053 + 22 H1 H E 21 19 18 1.00 117.36 179.90 0.3520 + 23 C2 CA B 21 19 18 1.38 125.24 -0.10 0.7432 + 24 N2 N2 B 23 21 19 1.34 116.02 180.00 -0.9230 + 25 H21 H E 24 23 21 1.01 127.00 -0.82 0.4235 + 26 H22 H E 24 23 21 1.01 116.53 -179.44 0.4235 + 27 N3 NC S 23 21 19 1.33 123.30 0.00 -0.6636 + 28 C4 CB E 27 23 21 1.36 112.20 0.00 0.1814 + 29 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 + 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0985 + 31 C2' CT B 29 9 6 1.53 102.80 -86.30 -0.0854 + 32 H2'1 HC E 31 29 9 1.09 109.50 120.00 0.0718 + 33 H2'2 HC E 31 29 9 1.09 109.50 240.00 0.0718 + 34 O3' OH M 29 9 6 1.42 116.52 -203.47 -0.6549 + 35 H3T HO M 34 29 9 0.96 114.97 180.00 0.4396 + +CHARGE deoxy-GUA-B: + 0.4422 -0.6318 -0.0069 0.0754 0.0754 + 0.1629 0.1176 -0.3691 0.0358 0.1746 + 0.0577 0.0736 0.1997 -0.5725 0.1991 + 0.4918 -0.5699 -0.5053 0.3520 0.7432 + -0.9230 0.4235 0.4235 -0.6636 0.1814 + 0.0713 0.0985 -0.0854 0.0718 0.0718 + -0.6549 0.4396 + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +R-GUANOSINE - with 5' - OH end group and 3' - O(minus) group + + RG5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1065 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 + 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0191 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2006 + 14 N9 N* S 12 11 9 1.49 108.06 -127.70 0.0492 + 15 C8 CK B 14 12 11 1.38 129.20 81.59 0.1374 + 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1640 + 17 N7 NB S 15 14 12 1.31 114.00 -179.90 -0.5709 + 18 C5 CB S 17 15 14 1.39 103.90 0.00 0.1744 + 19 C6 C B 18 17 15 1.42 130.40 180.00 0.4770 + 20 O6 O E 19 18 17 1.23 128.80 0.00 -0.5597 + 21 N1 NA B 19 18 17 1.40 111.38 180.00 -0.4787 + 22 H1 H E 21 19 18 1.00 117.36 179.90 0.3424 + 23 C2 CA B 21 19 18 1.38 125.24 -0.10 0.7657 + 24 N2 N2 B 23 21 19 1.34 116.02 180.00 -0.9672 + 25 H21 H E 24 23 21 1.01 127.00 -0.82 0.4364 + 26 H22 H E 24 23 21 1.01 116.53 -179.44 0.4364 + 27 N3 NC S 23 21 19 1.33 123.30 0.00 -0.6323 + 28 C4 CB E 27 23 21 1.36 112.20 0.00 0.1222 + 29 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 + 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0615 + 31 C2' CT B 29 9 6 1.53 102.80 -86.30 0.0670 + 32 H2'1 H1 E 31 29 9 1.09 109.50 120.00 0.0972 + 33 O2' OH S 31 29 9 1.43 109.50 240.00 -0.6139 + 34 HO'2 HO E 33 31 29 0.96 107.00 180.00 0.4186 + 35 O3' OS M 29 9 6 1.42 116.52 -203.47 -0.5246 + +CHARGE RG5E + 0.4295 -0.6223 0.0558 0.0679 0.0679 + 0.1065 0.1174 -0.3548 0.0191 0.2006 + 0.0492 0.1374 0.1640 -0.5709 0.1744 + 0.4770 -0.5597 -0.4787 0.3424 0.7657 + -0.9672 0.4364 0.4364 -0.6323 0.1222 + 0.2022 0.0615 0.0670 0.0972 -0.6139 + 0.4186 -0.5246 + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +R-GUANOSINE - with 5' - phosphate group and 3' - O(minus) group + + RG INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0191 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2006 + 16 N9 N* S 14 13 11 1.49 108.06 -127.70 0.0492 + 17 C8 CK B 16 14 13 1.38 129.20 81.59 0.1374 + 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1640 + 19 N7 NB S 17 16 14 1.31 114.00 -179.90 -0.5709 + 20 C5 CB S 19 17 16 1.39 103.90 0.00 0.1744 + 21 C6 C B 20 19 17 1.42 130.40 180.00 0.4770 + 22 O6 O E 21 20 19 1.23 128.80 0.00 -0.5597 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C8 CK B 16 14 13 1.38 129.20 81.59 0.1374 + 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1640 + 19 N7 NB S 17 16 14 1.31 114.00 -179.90 -0.5709 + 20 C5 CB S 19 17 16 1.39 103.90 0.00 0.1744 + 21 C6 C B 20 19 17 1.42 130.40 180.00 0.4770 + 22 O6 O E 21 20 19 1.23 128.80 0.00 -0.5597 + 23 N1 NA B 21 20 19 1.40 111.38 180.00 -0.4787 + 24 H1 H E 23 21 20 1.00 117.36 179.90 0.3424 + 25 C2 CA B 23 21 20 1.38 125.24 -0.10 0.7657 + 26 N2 N2 B 25 23 21 1.34 116.02 180.00 -0.9672 + 27 H21 H E 26 25 23 1.01 127.00 -0.82 0.4364 + 28 H22 H E 26 25 23 1.01 116.53 -179.44 0.4364 + 29 N3 NC S 25 23 21 1.33 123.30 0.00 -0.6323 + 30 C4 CB E 29 25 23 1.36 112.20 0.00 0.1222 + 31 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 + 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0615 + 33 C2' CT B 31 11 8 1.53 102.80 -86.30 0.0670 + 34 H2'1 H1 E 33 31 11 1.09 109.50 120.00 0.0972 + 35 O2' OH S 33 31 11 1.43 109.50 240.00 -0.6139 + 36 HO'2 HO E 35 33 31 0.96 107.00 180.00 0.4186 + 37 O3' OH M 31 11 8 1.42 116.52 -203.47 -0.6541 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H1 E 9 6 5 1.09 109.50 -200.00 0.1174 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 + 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0191 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2006 + 14 N9 N* S 12 11 9 1.49 108.06 -127.70 0.0492 + 15 C8 CK B 14 12 11 1.38 129.20 81.59 0.1374 + 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1640 + 17 N7 NB S 15 14 12 1.31 114.00 -179.90 -0.5709 + 18 C5 CB S 17 15 14 1.39 103.90 0.00 0.1744 + 19 C6 C B 18 17 15 1.42 130.40 180.00 0.4770 + 20 O6 O E 19 18 17 1.23 128.80 0.00 -0.5597 + 21 N1 NA B 19 18 17 1.40 111.38 180.00 -0.4787 + 22 H1 H E 21 19 18 1.00 117.36 179.90 0.3424 + 23 C2 CA B 21 19 18 1.38 125.24 -0.10 0.7657 + 24 N2 N2 B 23 21 19 1.34 116.02 180.00 -0.9672 + 25 H21 H E 24 23 21 1.01 127.00 -0.82 0.4364 + 26 H22 H E 24 23 21 1.01 116.53 -179.44 0.4364 + 27 N3 NC S 23 21 19 1.33 123.30 0.00 -0.6323 + 28 C4 CB E 27 23 21 1.36 112.20 0.00 0.1222 + 29 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 + 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0615 + 31 C2' CT B 29 9 6 1.53 102.80 -86.30 0.0670 + 32 H2'1 H1 E 31 29 9 1.09 109.50 120.00 0.0972 + 33 O2' OH S 31 29 9 1.43 109.50 240.00 -0.6139 + 34 HO'2 HO E 33 31 29 0.96 107.00 180.00 0.4186 + 35 O3' OH M 29 9 6 1.42 116.52 -203.47 -0.6541 + 36 H3T HO M 35 29 9 0.96 114.97 180.00 0.4376 + +CHARGE resp RGUA + 0.4295 -0.6223 0.0558 0.0679 0.0679 + 0.1065 0.1174 -0.3548 0.0191 0.2006 + 0.0492 0.1374 0.1640 -0.5709 0.1744 + 0.4770 -0.5597 -0.4787 0.3424 0.7657 + -0.9672 0.4364 0.4364 -0.6323 0.1222 + 0.2022 0.0615 0.0670 0.0972 -0.6139 + 0.4186 -0.6541 0.4376 + +IMPROPER + C8 C4 N9 C1' + C5 N1 C6 O6 + C6 C2 N1 H1 + C2 H21 N2 H22 + N7 N9 C8 H8 + N1 N3 C2 N2 + +LOOP CLOSING EXPLICIT + C1' C2' + C4 C5 + C4 N9 + +DONE +D-CYTOSINE - with 5' - OH end group and 3' - O(minus) group + + DC5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 + 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 + 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 + 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 + 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 + 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 + 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 + 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 + 12 C1' CT B 11 9 5 1.42 110.04 105.60 -0.0116 + 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1963 + 14 N1 N* S 12 11 9 1.49 108.10 -127.70 -0.0339 + 15 C6 CM B 14 12 11 1.36 121.10 81.59 -0.0183 + 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2293 + 17 C5 CM B 15 14 12 1.36 121.00 180.00 -0.5222 + 18 H5 HA E 17 15 14 1.09 120.00 180.00 0.1863 + 19 C4 CA B 17 15 14 1.43 116.90 0.00 0.8439 + 20 N4 N2 B 19 17 15 1.32 120.10 180.00 -0.9773 + 21 H41 H E 20 19 17 1.01 117.70 180.00 0.4314 + 22 H42 H E 20 19 17 1.01 120.27 0.00 0.4314 + 23 N3 NC S 19 17 15 1.33 121.70 0.00 -0.7748 + 24 C2 C S 23 19 17 1.36 120.50 0.00 0.7959 + 25 O2 O E 24 23 19 1.24 122.40 180.00 -0.6548 + 26 C3' CT M 9 6 5 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109.58 20.00 -0.7761 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 -0.0116 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1963 + 16 N1 N* S 14 13 11 1.49 108.10 -127.70 -0.0339 + 17 C6 CM B 16 14 13 1.36 121.10 81.59 -0.0183 + 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2293 + 19 C5 CM B 17 16 14 1.36 121.00 180.00 -0.5222 + 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1863 + 21 C4 CA B 19 17 16 1.43 116.90 0.00 0.8439 + 22 N4 N2 B 21 19 17 1.32 120.10 180.00 -0.9773 + 23 H41 H E 22 21 19 1.01 117.70 180.00 0.4314 + 24 H42 H E 22 21 19 1.01 120.27 0.00 0.4314 + 25 N3 NC S 21 19 17 1.33 121.70 0.00 -0.7748 + 26 C2 C S 25 21 19 1.36 120.50 0.00 0.7959 + 27 O2 O E 26 25 21 1.24 122.40 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C2 C S 23 19 17 1.36 120.50 0.00 0.7959 + 25 O2 O E 24 23 19 1.24 122.40 180.00 -0.6548 + 26 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 + 27 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0985 + 28 C2' CT B 26 9 6 1.53 102.80 -86.30 -0.0854 + 29 H2'1 HC E 28 26 9 1.09 109.50 120.00 0.0718 + 30 H2'2 HC E 28 26 9 1.09 109.50 240.00 0.0718 + 31 O3' OH M 26 9 6 1.42 116.52 -203.47 -0.6549 + 32 H3T HO M 31 26 9 0.96 114.97 180.00 0.4396 + +CHARGE deoxy-CYT-B: CYT + 0.4422 -0.6318 -0.0069 0.0754 0.0754 + 0.1629 0.1176 -0.3691 -0.0116 0.1963 + -0.0339 -0.0183 0.2293 -0.5222 0.1863 + 0.8439 -0.9773 0.4314 0.4314 -0.7748 + 0.7959 -0.6548 0.0713 0.0985 -0.0854 + 0.0718 0.0718 -0.6549 0.4396 + +IMPROPER + C6 C2 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + N3 C5 C4 N4 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +R-CYTOSINE - with 5' - OH end group and 3' - O(minus) group + + RC5 INT 1 + CORRECT NOMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 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+ RC3 INT 1 + CORRECT OMIT DU BEG + 0.0 + 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 + 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 + 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 + 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 + 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 + 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 + 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 + 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 + 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 + 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 + 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 + 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 + 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 + 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0066 + 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2029 + 16 N1 N* S 14 13 11 1.49 108.10 -127.70 -0.0484 + 17 C6 CM B 16 14 13 1.36 121.10 81.59 0.0053 + 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.1958 + 19 C5 CM B 17 16 14 1.36 121.00 180.00 -0.5215 + 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1928 + 21 C4 CA B 19 17 16 1.43 116.90 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1.09 120.00 180.00 0.1928 + 19 C4 CA B 17 15 14 1.43 116.90 0.00 0.8185 + 20 N4 N2 B 19 17 15 1.32 120.10 180.00 -0.9530 + 21 H41 H E 20 19 17 1.01 117.70 180.00 0.4234 + 22 H42 H E 20 19 17 1.01 120.27 0.00 0.4234 + 23 N3 NC S 19 17 15 1.33 121.70 0.00 -0.7584 + 24 C2 C S 23 19 17 1.36 120.50 0.00 0.7538 + 25 O2 O E 24 23 19 1.24 122.40 180.00 -0.6252 + 26 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 + 27 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0615 + 28 C2' CT B 26 9 6 1.53 102.80 -86.30 0.0670 + 29 H2'1 H1 E 28 26 9 1.09 109.50 120.00 0.0972 + 30 O2' OH S 28 26 9 1.43 109.50 240.00 -0.6139 + 31 HO'2 HO E 30 28 26 0.96 107.00 180.00 0.4186 + 32 O3' OH M 26 9 6 1.42 116.52 -203.47 -0.6541 + 33 H3T HO M 32 26 9 0.96 114.97 180.00 0.4376 + +CHARGE resp RCYT + 0.4295 -0.6223 0.0558 0.0679 0.0679 + 0.1065 0.1174 -0.3548 0.0066 0.2029 + -0.0484 0.0053 0.1958 -0.5215 0.1928 + 0.8185 -0.9530 0.4234 0.4234 -0.7584 + 0.7538 -0.6252 0.2022 0.0615 0.0670 + 0.0972 -0.6139 0.4186 -0.6541 0.4376 + +IMPROPER + C6 C2 N1 C1' + N1 N3 C2 O2 + C4 H41 N4 H42 + N1 C5 C6 H6 + C6 C4 C5 H5 + N3 C5 C4 N4 + +LOOP CLOSING EXPLICIT + C1' C2' + C2 N1 + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/ALA_ALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/ALA_ALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..c699daffd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/ALA_ALANINE_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/ARG_ARGININE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/ARG_ARGININE__COO-_ANION.in_frag new file mode 100644 index 000000000..81def524a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/ARG_ARGININE__COO-_ANION.in_frag @@ -0,0 +1,28 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 + 18 HE H3 E 17 14 11 1.010 118.500 0.000 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 + 21 HH11 H3 E 20 19 17 1.010 119.800 0.000 + 22 HH12 H3 E 20 19 17 1.010 119.800 180.000 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 + 24 HH21 H3 E 23 19 17 1.010 119.800 0.000 + 25 HH22 H3 E 23 19 17 1.010 119.800 180.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O2 E 26 6 4 1.229 120.500 0.000 + 28 OXT O2 E 26 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/ASN_ASPARAGINE____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/ASN_ASPARAGINE____COO-_ANION.in_frag new file mode 100644 index 000000000..db277ad64 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/ASN_ASPARAGINE____COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.522 111.100 180.000 + 12 OD1 O E 11 8 6 1.229 120.500 0.000 + 13 ND2 N B 11 8 6 1.335 116.600 180.000 + 14 HD21 H E 13 11 8 1.010 119.800 180.000 + 15 HD22 H E 13 11 8 1.010 119.800 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/ASP_ASPARTIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/ASP_ASPARTIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..7eaa3e4f2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/ASP_ASPARTIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C B 8 6 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/CYS_CYSTEINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/CYS_CYSTEINE__COO-_ANION.in_frag new file mode 100644 index 000000000..1c9f44426 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/CYS_CYSTEINE__COO-_ANION.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 SG SH 3 8 6 4 1.810 116.000 180.000 + 12 HG HS E 11 8 6 1.330 96.000 180.000 + 13 LP1 LP E 11 8 6 0.679 96.700 60.000 + 14 LP2 LP E 11 8 6 0.679 96.700 300.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O2 E 15 6 4 1.229 120.500 0.000 + 17 OXT O2 E 15 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/CYX_CYSTINE_op_S-S_BRIDGE_cp______COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/CYX_CYSTINE_op_S-S_BRIDGE_cp______COO-_ANION.in_frag new file mode 100644 index 000000000..9216f5503 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/CYX_CYSTINE_op_S-S_BRIDGE_cp______COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 SG S B 8 6 4 1.810 116.000 180.000 + 12 LP1 LP E 11 8 6 0.679 96.700 60.000 + 13 LP2 LP E 11 8 6 0.679 96.700 300.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/GLN_GLUTAMINE_____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/GLN_GLUTAMINE_____COO-_ANION.in_frag new file mode 100644 index 000000000..68af5f9ca --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/GLN_GLUTAMINE_____COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.522 111.100 180.000 + 15 OE1 O E 14 11 8 1.229 120.500 0.000 + 16 NE2 N B 14 11 8 1.335 116.600 180.000 + 17 HE21 H E 16 14 11 1.010 119.800 180.000 + 18 HE22 H E 16 14 11 1.010 119.800 0.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..de08fa814 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD C B 11 8 6 1.527 109.470 180.000 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O2 E 17 6 4 1.229 120.500 0.000 + 19 OXT O2 E 17 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/GLY_GLYCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/GLY_GLYCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..026e70cdb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/GLY_GLYCINE_COO-_ANION.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 HC E 6 4 3 1.090 109.500 300.000 + 8 HA3 HC E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O2 E 9 6 4 1.229 120.500 0.000 + 11 OXT O2 E 9 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag new file mode 100644 index 000000000..6e4119f8c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE HC E 14 12 11 1.090 120.000 180.000 + 16 NE2 NB S 14 12 11 1.310 109.000 0.000 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 + 18 HD HC E 17 16 14 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/HIE_HISTIDINE_EPSILON-H___COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/HIE_HISTIDINE_EPSILON-H___COO-_ANION.in_frag new file mode 100644 index 000000000..b8eaf8a4d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/HIE_HISTIDINE_EPSILON-H___COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NB S 11 8 6 1.390 122.000 180.000 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 + 14 HE HC E 13 12 11 1.090 120.000 180.000 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 + 18 HD HC E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/HIP_HISTIDINE_PLUS_COO-.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/HIP_HISTIDINE_PLUS_COO-.in_frag new file mode 100644 index 000000000..59d029b95 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/HIP_HISTIDINE_PLUS_COO-.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CC S 8 6 4 1.510 115.000 180.000 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 + 15 HE HC E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD HC E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O2 E 20 6 4 1.229 120.500 0.000 + 22 OXT O2 E 20 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/ILE_ISOLEUCINE____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/ILE_ISOLEUCINE____COO-_ANION.in_frag new file mode 100644 index 000000000..769dcba5b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/ILE_ISOLEUCINE____COO-_ANION.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 109.470 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG12 HC E 14 8 6 1.090 109.500 300.000 + 16 HG13 HC E 14 8 6 1.090 109.500 60.000 + 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 + 18 HD11 HC E 17 14 8 1.090 109.500 60.000 + 19 HD12 HC E 17 14 8 1.090 109.500 180.000 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O2 E 21 6 4 1.229 120.500 0.000 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/LEU_LEUCINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/LEU_LEUCINE__COO-_ANION.in_frag new file mode 100644 index 000000000..43982d7f7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/LEU_LEUCINE__COO-_ANION.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O2 E 21 6 4 1.229 120.500 0.000 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/LYS_LYSINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/LYS_LYSINE__COO-_ANION.in_frag new file mode 100644 index 000000000..564c3dc26 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/LYS_LYSINE__COO-_ANION.in_frag @@ -0,0 +1,26 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 + 17 CE CT 3 14 11 8 1.525 109.470 180.000 + 18 HE2 HC E 17 14 11 1.090 109.500 300.000 + 19 HE3 HC E 17 14 11 1.090 109.500 60.000 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 + 21 HZ1 H3 E 20 17 14 1.010 109.470 60.000 + 22 HZ2 H3 E 20 17 14 1.010 109.470 180.000 + 23 HZ3 H3 E 20 17 14 1.010 109.470 300.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O2 E 24 6 4 1.229 120.500 0.000 + 26 OXT O2 E 24 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/MET_METHIONINE____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/MET_METHIONINE____COO-_ANION.in_frag new file mode 100644 index 000000000..2094bcc89 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/MET_METHIONINE____COO-_ANION.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 + 14 SD S 3 11 8 6 1.810 110.000 180.000 + 15 LP1 LP E 14 11 8 0.679 96.700 60.000 + 16 LP2 LP E 14 11 8 0.679 96.700 300.000 + 17 CE CT 3 14 11 8 1.780 100.000 180.000 + 18 HE1 HC E 17 14 11 1.090 109.500 60.000 + 19 HE2 HC E 17 14 11 1.090 109.500 180.000 + 20 HE3 HC E 17 14 11 1.090 109.500 300.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O2 E 21 6 4 1.229 120.500 0.000 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/PHE_PHENYLALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/PHE_PHENYLALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..078c3c4f2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/PHE_PHENYLALANINE_COO-_ANION.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 115.000 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HC E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HC E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HC E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HC E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HC E 20 18 16 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O2 E 22 6 4 1.229 120.500 0.000 + 24 OXT O2 E 22 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/PRO_PROLINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/PRO_PROLINE_COO-_ANION.in_frag new file mode 100644 index 000000000..88ff4ebb2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/PRO_PROLINE_COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 + 6 HD2 HC E 5 4 3 1.090 109.500 80.000 + 7 HD3 HC E 5 4 3 1.090 109.500 320.000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 + 11 CB CT B 8 5 4 1.510 106.000 338.300 + 12 HB2 HC E 11 8 5 1.090 109.500 136.300 + 13 HB3 HC E 11 8 5 1.090 109.500 256.300 + 14 CA CT M 4 3 2 1.451 120.600 175.200 + 15 HA HC E 14 4 3 1.090 109.500 81.100 + 16 C C M 14 4 3 1.522 111.100 0.000 + 17 O O2 E 16 14 4 1.229 120.500 0.000 + 18 OXT O2 E 16 14 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/SER_SERINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/SER_SERINE__COO-_ANION.in_frag new file mode 100644 index 000000000..8fa1fcca6 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/SER_SERINE__COO-_ANION.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 OG OH S 8 6 4 1.430 109.470 180.000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/THR_THREONINE_____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/THR_THREONINE_____COO-_ANION.in_frag new file mode 100644 index 000000000..b796d35f0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/THR_THREONINE_____COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB HC E 8 6 4 1.090 109.500 180.000 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/TRP_TRYPTOPHAN____COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/TRP_TRYPTOPHAN____COO-_ANION.in_frag new file mode 100644 index 000000000..72404375f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/TRP_TRYPTOPHAN____COO-_ANION.in_frag @@ -0,0 +1,28 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG C* S 8 6 4 1.510 115.000 180.000 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 + 13 HD1 HC E 12 11 8 1.090 120.000 0.000 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 + 18 HZ2 HC E 17 16 14 1.090 120.000 0.000 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 + 20 HH2 HC E 19 17 16 1.090 120.000 180.000 + 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 + 22 HZ3 HC E 21 19 17 1.090 120.000 180.000 + 23 CE3 CA B 21 19 17 1.410 122.000 0.000 + 24 HE3 HC E 23 21 19 1.090 120.000 180.000 + 25 CD2 CB E 23 21 19 1.400 117.000 0.000 + 26 C C M 6 4 3 1.522 111.100 180.000 + 27 O O2 E 26 6 4 1.229 120.500 0.000 + 28 OXT O2 E 26 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/TYR_TYROSINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/TYR_TYROSINE__COO-_ANION.in_frag new file mode 100644 index 000000000..7476bb176 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/TYR_TYROSINE__COO-_ANION.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 + 11 CG CA S 8 6 4 1.510 109.470 180.000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 + 13 HD1 HC E 12 11 8 1.090 120.000 0.000 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 + 15 HE1 HC E 14 12 11 1.090 120.000 180.000 + 16 CZ C B 14 12 11 1.400 120.000 0.000 + 17 OH OH S 16 14 12 1.360 120.000 180.000 + 18 HH HO E 17 16 14 0.960 113.000 0.000 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 + 20 HE2 HC E 19 16 14 1.090 120.000 180.000 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 + 22 HD2 HC E 21 19 16 1.090 120.000 180.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O2 E 23 6 4 1.229 120.500 0.000 + 25 OXT O2 E 23 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/VAL_VALINE__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/allct/VAL_VALINE__COO-_ANION.in_frag new file mode 100644 index 000000000..5971607a4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/VAL_VALINE__COO-_ANION.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA HC E 6 4 3 1.090 109.500 300.000 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 + 9 HB HC E 8 6 4 1.090 109.500 300.000 + 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 + 11 HG11 HC E 10 8 6 1.090 109.500 60.000 + 12 HG12 HC E 10 8 6 1.090 109.500 180.000 + 13 HG13 HC E 10 8 6 1.090 109.500 300.000 + 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 + 15 HG21 HC E 14 8 6 1.090 109.500 60.000 + 16 HG22 HC E 14 8 6 1.090 109.500 180.000 + 17 HG23 HC E 14 8 6 1.090 109.500 300.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O2 E 18 6 4 1.229 120.500 0.000 + 20 OXT O2 E 18 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allct/allct.in b/cad/tests/AMBER_test_structures/dot_in/allct/allct.in new file mode 100644 index 000000000..19ddae62c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allct/allct.in @@ -0,0 +1,765 @@ + 1 1 201 +db4.dat +ALANINE COO- ANION + + ALA INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.09800 + 9 HB1 HC E 8 6 4 1.090 109.500 60.000 0.03800 + 10 HB2 HC E 8 6 4 1.090 109.500 180.000 0.03800 + 11 HB3 HC E 8 6 4 1.090 109.500 300.000 0.03800 + 12 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 13 O O2 E 12 6 4 1.229 120.500 0.000 -0.70600 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +GLYCINE COO- ANION + + GLY INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA2 HC E 6 4 3 1.090 109.500 300.000 0.03200 + 8 HA3 HC E 6 4 3 1.090 109.500 60.000 0.03200 + 9 C C M 6 4 3 1.522 110.400 180.000 0.52400 + 10 O O2 E 9 6 4 1.229 120.500 0.000 -0.70600 + 11 OXT O2 E 9 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +SERINE COO- ANION + + SER INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.01800 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.11900 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.11900 + 11 OG OH S 8 6 4 1.430 109.470 180.000 -0.55000 + 12 HG HO E 11 8 6 0.960 109.470 180.000 0.31000 + 13 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 14 O O2 E 13 6 4 1.229 120.500 0.000 -0.70600 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +THREONINE COO- ANION + + THR INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.17000 + 9 HB HC E 8 6 4 1.090 109.500 180.000 0.08200 + 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 -0.19100 + 11 HG21 HC E 10 8 6 1.090 109.500 60.000 0.06500 + 12 HG22 HC E 10 8 6 1.090 109.500 180.000 0.06500 + 13 HG23 HC E 10 8 6 1.090 109.500 300.000 0.06500 + 14 OG1 OH S 8 6 4 1.430 109.470 60.000 -0.55000 + 15 HG1 HO E 14 8 6 0.960 109.470 180.000 0.31000 + 16 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 17 O O2 E 16 6 4 1.229 120.500 0.000 -0.70600 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +LEUCINE COO- ANION + + LEU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.06100 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03300 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03300 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 -0.01000 + 12 HG HC E 11 8 6 1.090 109.500 300.000 0.03100 + 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 -0.10700 + 14 HD11 HC E 13 11 8 1.090 109.500 60.000 0.03400 + 15 HD12 HC E 13 11 8 1.090 109.500 180.000 0.03400 + 16 HD13 HC E 13 11 8 1.090 109.500 300.000 0.03400 + 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 -0.10700 + 18 HD21 HC E 17 11 8 1.090 109.500 60.000 0.03400 + 19 HD22 HC E 17 11 8 1.090 109.500 180.000 0.03400 + 20 HD23 HC E 17 11 8 1.090 109.500 300.000 0.03400 + 21 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 22 O O2 E 21 6 4 1.229 120.500 0.000 -0.70600 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 -0.70600 + 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19 HD12 HC E 17 14 8 1.090 109.500 180.000 0.02800 + 20 HD13 HC E 17 14 8 1.090 109.500 300.000 0.02800 + 21 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 22 O O2 E 21 6 4 1.229 120.500 0.000 -0.70600 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +VALINE COO- ANION + + VAL INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.01200 + 9 HB HC E 8 6 4 1.090 109.500 300.000 0.02400 + 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 -0.09100 + 11 HG11 HC E 10 8 6 1.090 109.500 60.000 0.03100 + 12 HG12 HC E 10 8 6 1.090 109.500 180.000 0.03100 + 13 HG13 HC E 10 8 6 1.090 109.500 300.000 0.03100 + 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 -0.09100 + 15 HG21 HC E 14 8 6 1.090 109.500 60.000 0.03100 + 16 HG22 HC E 14 8 6 1.090 109.500 180.000 0.03100 + 17 HG23 HC E 14 8 6 1.090 109.500 300.000 0.03100 + 18 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 19 O O2 E 18 6 4 1.229 120.500 0.000 -0.70600 + 20 OXT O2 E 18 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +ASPARAGINE COO- ANION + + ASN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.08600 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03800 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03800 + 11 CG C B 8 6 4 1.522 111.100 180.000 0.67500 + 12 OD1 O E 11 8 6 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111.100 60.000 -0.08000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.05600 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.05600 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 -0.10300 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.07400 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.07400 + 14 CD CT 3 11 8 6 1.525 109.470 180.000 -0.22800 + 15 HD2 HC E 14 11 8 1.090 109.500 300.000 0.13300 + 16 HD3 HC E 14 11 8 1.090 109.500 60.000 0.13300 + 17 NE N2 B 14 11 8 1.480 111.000 180.000 -0.32400 + 18 HE H3 E 17 14 11 1.010 118.500 0.000 0.26900 + 19 CZ CA B 17 14 11 1.330 123.000 180.000 0.76000 + 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 -0.62400 + 21 HH11 H3 E 20 19 17 1.010 119.800 0.000 0.36100 + 22 HH12 H3 E 20 19 17 1.010 119.800 180.000 0.36100 + 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 -0.62400 + 24 HH21 H3 E 23 19 17 1.010 119.800 0.000 0.36100 + 25 HH22 H3 E 23 19 17 1.010 119.800 180.000 0.36100 + 26 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 27 O O2 E 26 6 4 1.229 120.500 0.000 -0.70600 + 28 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CE1 CR B 12 11 8 1.320 108.000 180.000 0.24100 + 14 HE HC E 13 12 11 1.090 120.000 180.000 0.03600 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 -0.14600 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 0.22800 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 -0.18400 + 18 HD HC E 17 15 13 1.090 120.000 180.000 0.11400 + 19 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 20 O O2 E 19 6 4 1.229 120.500 0.000 -0.70600 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 -0.70600 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA OXT C O + CE1 CD2 NE2 HE2 + +DONE +HISTIDINE PLUS COO- + + HIP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.09800 + 9 HB2 HC E 8 6 4 1.090 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2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.09800 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03800 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03800 + 11 CG C* S 8 6 4 1.510 115.000 180.000 -0.13500 + 12 CD1 CW B 11 8 6 1.340 127.000 180.000 0.04400 + 13 HD1 HC E 12 11 8 1.090 120.000 0.000 0.09300 + 14 NE1 NA B 12 11 8 1.430 107.000 180.000 -0.35200 + 15 HE1 H E 14 12 11 1.010 125.500 180.000 0.27100 + 16 CE2 CN S 14 12 11 1.310 109.000 0.000 0.15400 + 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 -0.16800 + 18 HZ2 HC E 17 16 14 1.090 120.000 0.000 0.08400 + 19 CH2 CA B 17 16 14 1.390 116.000 180.000 -0.07700 + 20 HH2 HC E 19 17 16 1.090 120.000 180.000 0.07400 + 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 -0.06600 + 22 HZ3 HC E 21 19 17 1.090 120.000 180.000 0.05700 + 23 CE3 CA B 21 19 17 1.410 122.000 0.000 -0.17300 + 24 HE3 HC E 23 21 19 1.090 120.000 180.000 0.08600 + 25 CD2 CB E 23 21 19 1.400 117.000 0.000 0.14600 + 26 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 27 O O2 E 26 6 4 1.229 120.500 0.000 -0.70600 + 28 OXT O2 E 26 6 4 1.229 120.500 180.000 -0.70600 + +LOOP + CG CD2 + CE2 CD2 + +IMPROPER + -M CA N H + CA OXT C O + CD1 CE2 NE1 HE1 + CE2 CH2 CZ2 HZ2 + CZ2 CZ3 CH2 HH2 + CH2 CE3 CZ3 HZ3 + CZ3 CD2 CE3 HE3 + +DONE +PHENYLALANINE COO- ANION + + PHE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.09800 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03800 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03800 + 11 CG CA S 8 6 4 1.510 115.000 180.000 0.05500 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 -0.06900 + 13 HD1 HC E 12 11 8 1.090 120.000 0.000 0.05800 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 -0.05900 + 15 HE1 HC E 14 12 11 1.090 120.000 180.000 0.06300 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 -0.06500 + 17 HZ HC E 16 14 12 1.090 120.000 180.000 0.06200 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 -0.05900 + 19 HE2 HC E 18 16 14 1.090 120.000 180.000 0.06300 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 -0.06900 + 21 HD2 HC E 20 18 16 1.090 120.000 180.000 0.05800 + 22 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 23 O O2 E 22 6 4 1.229 120.500 0.000 -0.70600 + 24 OXT O2 E 22 6 4 1.229 120.500 180.000 -0.70600 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +TYROSINE COO- ANION + + TYR INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.09800 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03800 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03800 + 11 CG CA S 8 6 4 1.510 109.470 180.000 -0.03000 + 12 CD1 CA B 11 8 6 1.400 120.000 180.000 -0.00200 + 13 HD1 HC E 12 11 8 1.090 120.000 0.000 0.06400 + 14 CE1 CA B 12 11 8 1.400 120.000 180.000 -0.26400 + 15 HE1 HC E 14 12 11 1.090 120.000 180.000 0.10200 + 16 CZ C B 14 12 11 1.400 120.000 0.000 0.46200 + 17 OH OH S 16 14 12 1.360 120.000 180.000 -0.52800 + 18 HH HO E 17 16 14 0.960 113.000 0.000 0.33400 + 19 CE2 CA B 16 14 12 1.400 120.000 0.000 -0.26400 + 20 HE2 HC E 19 16 14 1.090 120.000 180.000 0.10200 + 21 CD2 CA S 19 16 14 1.400 120.000 0.000 -0.00200 + 22 HD2 HC E 21 19 16 1.090 120.000 180.000 0.06400 + 23 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 24 O O2 E 23 6 4 1.229 120.500 0.000 -0.70600 + 25 OXT O2 E 23 6 4 1.229 120.500 180.000 -0.70600 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +GLUTAMIC ACID COO- ANION + + GLU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.18400 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.09200 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.09200 + 11 CG CT 3 8 6 4 1.510 109.470 180.000 -0.39800 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.07100 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.07100 + 14 CD C B 11 8 6 1.527 109.470 180.000 0.71400 + 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 -0.72100 + 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 -0.72100 + 17 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 18 O O2 E 17 6 4 1.229 120.500 0.000 -0.70600 + 19 OXT O2 E 17 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N H + CA OXT C O + CG OE1 CD OE2 + +DONE +ASPARTIC ACID COO- ANION + + ASP INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.39800 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.07100 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.07100 + 11 CG C B 8 6 4 1.527 109.470 180.000 0.71400 + 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 -0.72100 + 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 -0.72100 + 14 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 15 O O2 E 14 6 4 1.229 120.500 0.000 -0.70600 + 16 OXT O2 E 14 6 4 1.229 120.500 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1.090 109.500 300.000 0.09800 + 19 HE3 HC E 17 14 11 1.090 109.500 60.000 0.09800 + 20 NZ N3 3 17 14 11 1.470 109.470 180.000 -0.13800 + 21 HZ1 H3 E 20 17 14 1.010 109.470 60.000 0.29400 + 22 HZ2 H3 E 20 17 14 1.010 109.470 180.000 0.29400 + 23 HZ3 H3 E 20 17 14 1.010 109.470 300.000 0.29400 + 24 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 25 O O2 E 24 6 4 1.229 120.500 0.000 -0.70600 + 26 OXT O2 E 24 6 4 1.229 120.500 180.000 -0.70600 + + +IMPROPER + -M CA N H + CA OXT C O + +DONE +PROLINE COO- ANION + + PRO INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.337 117.000 180.000 -0.22900 + 5 CD CT 3 4 3 2 1.458 126.100 356.100 -0.01200 + 6 HD2 HC E 5 4 3 1.090 109.500 80.000 0.06000 + 7 HD3 HC E 5 4 3 1.090 109.500 320.000 0.06000 + 8 CG CT 3 5 4 3 1.500 103.200 200.100 -0.12100 + 9 HG2 HC E 8 5 4 1.090 109.500 218.000 0.06300 + 10 HG3 HC E 8 5 4 1.090 109.500 98.000 0.06300 + 11 CB CT B 8 5 4 1.510 106.000 338.300 -0.11500 + 12 HB2 HC E 11 8 5 1.090 109.500 136.300 0.06100 + 13 HB3 HC E 11 8 5 1.090 109.500 256.300 0.06100 + 14 CA CT M 4 3 2 1.451 120.600 175.200 0.03500 + 15 HA HC E 14 4 3 1.090 109.500 81.100 0.04800 + 16 C C M 14 4 3 1.522 111.100 0.000 0.43800 + 17 O O2 E 16 14 4 1.229 120.500 0.000 -0.70600 + 18 OXT O2 E 16 14 4 1.229 120.500 180.000 -0.70600 + +LOOP + CA CB + +IMPROPER + CA OXT C O + -M CA N CD + +DONE +CYSTEINE COO- ANION + + CYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.06000 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03800 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03800 + 11 SG SH 3 8 6 4 1.810 116.000 180.000 0.82700 + 12 HG HS E 11 8 6 1.330 96.000 180.000 0.13500 + 13 LP1 LP E 11 8 6 0.679 96.700 60.000 -0.48100 + 14 LP2 LP E 11 8 6 0.679 96.700 300.000 -0.48100 + 15 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 16 O O2 E 15 6 4 1.229 120.500 0.000 -0.70600 + 17 OXT O2 E 15 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +CYSTINE(S-S BRIDGE) COO- ANION + + CYX INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.09800 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04950 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04950 + 11 SG S B 8 6 4 1.810 116.000 180.000 0.82400 + 12 LP1 LP E 11 8 6 0.679 96.700 60.000 -0.40450 + 13 LP2 LP E 11 8 6 0.679 96.700 300.000 -0.40450 + 14 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 15 O O2 E 14 6 4 1.229 120.500 0.000 -0.70600 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +METHIONINE COO- ANION + + MET INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 H H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA HC E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.15100 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.02700 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.02700 + 11 CG CT 3 8 6 4 1.525 109.470 180.000 -0.05400 + 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.06520 + 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.06520 + 14 SD S 3 11 8 6 1.810 110.000 180.000 0.73700 + 15 LP1 LP E 14 11 8 0.679 96.700 60.000 -0.38100 + 16 LP2 LP E 14 11 8 0.679 96.700 300.000 -0.38100 + 17 CE CT 3 14 11 8 1.780 100.000 180.000 -0.13400 + 18 HE1 HC E 17 14 11 1.090 109.500 60.000 0.06520 + 19 HE2 HC E 17 14 11 1.090 109.500 180.000 0.06520 + 20 HE3 HC E 17 14 11 1.090 109.500 300.000 0.06520 + 21 C C M 6 4 3 1.522 111.100 180.000 0.52400 + 22 O O2 E 21 6 4 1.229 120.500 0.000 -0.70600 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/ALA_ALANINE.in_frag new file mode 100644 index 000000000..a78ec7789 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/ALA_ALANINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB1 HC E 10 8 4 1.090 109.500 60.000 + 12 HB2 HC E 10 8 4 1.090 109.500 180.000 + 13 HB3 HC E 10 8 4 1.090 109.500 300.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/ARG_ARGININE.in_frag new file mode 100644 index 000000000..4f4c18a34 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/ARG_ARGININE.in_frag @@ -0,0 +1,29 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD CT 3 13 10 8 1.525 109.470 180.000 + 17 HD2 HC E 16 13 10 1.090 109.500 300.000 + 18 HD3 HC E 16 13 10 1.090 109.500 60.000 + 19 NE N2 B 16 13 10 1.480 111.000 180.000 + 20 HE H3 E 19 16 13 1.010 118.500 0.000 + 21 CZ CA B 19 16 13 1.330 123.000 180.000 + 22 NH1 N2 B 21 19 16 1.330 122.000 0.000 + 23 HH11 H3 E 22 21 19 1.010 119.800 0.000 + 24 HH12 H3 E 22 21 19 1.010 119.800 180.000 + 25 NH2 N2 B 21 19 16 1.330 118.000 180.000 + 26 HH21 H3 E 25 21 19 1.010 119.800 0.000 + 27 HH22 H3 E 25 21 19 1.010 119.800 180.000 + 28 C C M 8 4 3 1.522 111.100 180.000 + 29 O O E 28 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..5c984b90b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/ASN_ASPARAGINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C B 10 8 4 1.522 111.100 180.000 + 14 OD1 O E 13 10 8 1.229 120.500 0.000 + 15 ND2 N B 13 10 8 1.335 116.600 180.000 + 16 HD21 H E 15 13 10 1.010 119.800 180.000 + 17 HD22 H E 15 13 10 1.010 119.800 0.000 + 18 C C M 8 4 3 1.522 111.100 180.000 + 19 O O E 18 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..4e0d0ce9e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C B 10 8 4 1.527 109.470 180.000 + 14 OD1 O2 E 13 10 8 1.260 117.200 90.000 + 15 OD2 O2 E 13 10 8 1.260 117.200 270.000 + 16 C C M 8 4 3 1.522 111.100 180.000 + 17 O O E 16 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..73d3ce095 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/CYS_CYSTEINE.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 SG SH 3 10 8 4 1.810 116.000 180.000 + 14 HG HS E 13 10 8 1.330 96.000 180.000 + 15 LP1 LP E 13 10 8 0.679 96.700 60.000 + 16 LP2 LP E 13 10 8 0.679 96.700 300.000 + 17 C C M 8 4 3 1.522 111.100 180.000 + 18 O O E 17 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..1b3e85475 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 SG S B 10 8 4 1.810 116.000 180.000 + 14 LP1 LP E 13 10 8 0.679 96.700 60.000 + 15 LP2 LP E 13 10 8 0.679 96.700 300.000 + 16 C C M 8 4 3 1.522 111.100 180.000 + 17 O O E 16 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..3b895343f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/GLN_GLUTAMINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD C B 13 10 8 1.522 111.100 180.000 + 17 OE1 O E 16 13 10 1.229 120.500 0.000 + 18 NE2 N B 16 13 10 1.335 116.600 180.000 + 19 HE21 H E 18 16 13 1.010 119.800 180.000 + 20 HE22 H E 18 16 13 1.010 119.800 0.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..33c4b359f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.510 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD C B 13 10 8 1.527 109.470 180.000 + 17 OE1 O2 E 16 13 10 1.260 117.200 90.000 + 18 OE2 O2 E 16 13 10 1.260 117.200 270.000 + 19 C C M 8 4 3 1.522 111.100 180.000 + 20 O O E 19 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..a0303ff38 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/GLY_GLYCINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA2 HC E 8 4 3 1.090 109.500 300.000 + 10 HA3 HC E 8 4 3 1.090 109.500 60.000 + 11 C C M 8 4 3 1.522 110.400 180.000 + 12 O O E 11 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..e3015d6e0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NA B 13 10 8 1.390 122.000 180.000 + 15 HD1 H E 14 13 10 1.010 126.000 0.000 + 16 CE1 CR B 14 13 10 1.320 108.000 180.000 + 17 HE HC E 16 14 13 1.090 120.000 180.000 + 18 NE2 NB S 16 14 13 1.310 109.000 0.000 + 19 CD2 CV S 18 16 14 1.360 110.000 0.000 + 20 HD HC E 19 18 16 1.090 120.000 180.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..f63ecec7b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NB S 13 10 8 1.390 122.000 180.000 + 15 CE1 CR B 14 13 10 1.320 108.000 180.000 + 16 HE HC E 15 14 13 1.090 120.000 180.000 + 17 NE2 NA B 15 14 13 1.310 109.000 0.000 + 18 HE2 H E 17 15 14 1.010 125.000 180.000 + 19 CD2 CW S 17 15 14 1.360 110.000 0.000 + 20 HD HC E 19 17 15 1.090 120.000 180.000 + 21 C C M 8 4 3 1.522 111.100 180.000 + 22 O O E 21 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..8f90f95ca --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CC S 10 8 4 1.510 115.000 180.000 + 14 ND1 NA B 13 10 8 1.390 122.000 180.000 + 15 HD1 H E 14 13 10 1.010 126.000 0.000 + 16 CE1 CR B 14 13 10 1.320 108.000 180.000 + 17 HE HC E 16 14 13 1.090 120.000 180.000 + 18 NE2 NA B 16 14 13 1.310 109.000 0.000 + 19 HE2 H E 18 16 14 1.010 125.000 180.000 + 20 CD2 CW S 18 16 14 1.360 110.000 0.000 + 21 HD HC E 20 18 16 1.090 120.000 180.000 + 22 C C M 8 4 3 1.522 111.100 180.000 + 23 O O E 22 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..338b7f23b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 109.470 60.000 + 11 HB HC E 10 8 4 1.090 109.500 300.000 + 12 CG2 CT 3 10 8 4 1.525 109.470 60.000 + 13 HG21 HC E 12 10 8 1.090 109.500 60.000 + 14 HG22 HC E 12 10 8 1.090 109.500 180.000 + 15 HG23 HC E 12 10 8 1.090 109.500 300.000 + 16 CG1 CT 3 10 8 4 1.525 109.470 180.000 + 17 HG12 HC E 16 10 8 1.090 109.500 60.000 + 18 HG13 HC E 16 10 8 1.090 109.500 300.000 + 19 CD1 CT 3 16 10 8 1.525 109.470 180.000 + 20 HD11 HC E 19 16 10 1.090 109.500 60.000 + 21 HD12 HC E 19 16 10 1.090 109.500 180.000 + 22 HD13 HC E 19 16 10 1.090 109.500 300.000 + 23 C C M 8 4 3 1.522 111.100 180.000 + 24 O O E 23 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..3800fd7db --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/LEU_LEUCINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG HC E 13 10 8 1.090 109.500 300.000 + 15 CD1 CT 3 13 10 8 1.525 109.470 60.000 + 16 HD11 HC E 15 13 10 1.090 109.500 60.000 + 17 HD12 HC E 15 13 10 1.090 109.500 180.000 + 18 HD13 HC E 15 13 10 1.090 109.500 300.000 + 19 CD2 CT 3 13 10 8 1.525 109.470 180.000 + 20 HD21 HC E 19 13 10 1.090 109.500 60.000 + 21 HD22 HC E 19 13 10 1.090 109.500 180.000 + 22 HD23 HC E 19 13 10 1.090 109.500 300.000 + 23 C C M 8 4 3 1.522 111.100 180.000 + 24 O O E 23 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/LYS_LYSINE.in_frag new file mode 100644 index 000000000..ba9682b81 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/LYS_LYSINE.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 CD CT 3 13 10 8 1.525 109.470 180.000 + 17 HD2 HC E 16 13 10 1.090 109.500 300.000 + 18 HD3 HC E 16 13 10 1.090 109.500 60.000 + 19 CE CT 3 16 13 10 1.525 109.470 180.000 + 20 HE2 HC E 19 16 13 1.090 109.500 300.000 + 21 HE3 HC E 19 16 13 1.090 109.500 60.000 + 22 NZ N3 3 19 16 13 1.470 109.470 180.000 + 23 HZ1 H3 E 22 19 16 1.010 109.470 60.000 + 24 HZ2 H3 E 22 19 16 1.010 109.470 180.000 + 25 HZ3 H3 E 22 19 16 1.010 109.470 300.000 + 26 C C M 8 4 3 1.522 111.100 180.000 + 27 O O E 26 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/MET_METHIONINE.in_frag new file mode 100644 index 000000000..2d0d4603e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/MET_METHIONINE.in_frag @@ -0,0 +1,24 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CT 3 10 8 4 1.525 109.470 180.000 + 14 HG2 HC E 13 10 8 1.090 109.500 300.000 + 15 HG3 HC E 13 10 8 1.090 109.500 60.000 + 16 SD S 3 13 10 8 1.810 110.000 180.000 + 17 LP1 LP E 16 13 10 0.679 96.700 60.000 + 18 LP2 LP E 16 13 10 0.679 96.700 300.000 + 19 CE CT 3 16 13 10 1.780 100.000 180.000 + 20 HE1 HC E 19 16 13 1.090 109.500 60.000 + 21 HE2 HC E 19 16 13 1.090 109.500 180.000 + 22 HE3 HC E 19 16 13 1.090 109.500 300.000 + 23 C C M 8 4 3 1.522 111.100 180.000 + 24 O O E 23 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..913243b8e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CA S 10 8 4 1.510 115.000 180.000 + 14 CD1 CA B 13 10 8 1.400 120.000 180.000 + 15 HD1 HC E 14 13 10 1.090 120.000 0.000 + 16 CE1 CA B 14 13 10 1.400 120.000 180.000 + 17 HE1 HC E 16 14 13 1.090 120.000 180.000 + 18 CZ CA B 16 14 13 1.400 120.000 0.000 + 19 HZ HC E 18 16 14 1.090 120.000 180.000 + 20 CE2 CA B 18 16 14 1.400 120.000 0.000 + 21 HE2 HC E 20 18 16 1.090 120.000 180.000 + 22 CD2 CA S 20 18 16 1.400 120.000 0.000 + 23 HD2 HC E 22 20 18 1.090 120.000 180.000 + 24 C C M 8 4 3 1.522 111.100 180.000 + 25 O O E 24 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/PRO_PROLINE.in_frag new file mode 100644 index 000000000..ce89d8606 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/PRO_PROLINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H2 H3 E 4 3 2 1.010 119.800 120.000 + 6 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 7 CD CT 3 4 3 2 1.458 126.100 356.100 + 8 HD2 HC E 7 4 3 1.090 109.500 80.000 + 9 HD3 HC E 7 4 3 1.090 109.500 320.000 + 10 CG CT 3 7 4 3 1.500 103.200 200.100 + 11 HG2 HC E 10 7 4 1.090 109.500 218.000 + 12 HG3 HC E 10 7 4 1.090 109.500 98.000 + 13 CB CT B 10 7 4 1.510 106.000 338.300 + 14 HB2 HC E 13 10 7 1.090 109.500 136.300 + 15 HB3 HC E 13 10 7 1.090 109.500 256.300 + 16 CA CT M 4 3 2 1.451 120.600 175.200 + 17 HA HC E 16 4 3 1.090 109.500 81.100 + 18 C C M 16 4 3 1.522 111.100 0.000 + 19 O O E 18 16 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/SER_SERINE.in_frag new file mode 100644 index 000000000..7bb0fe841 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/SER_SERINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 OG OH S 10 8 4 1.430 109.470 180.000 + 14 HG HO E 13 10 8 0.960 109.470 180.000 + 15 C C M 8 4 3 1.522 111.100 180.000 + 16 O O E 15 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/THR_THREONINE.in_frag new file mode 100644 index 000000000..bc972a7e8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/THR_THREONINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB HC E 10 8 4 1.090 109.500 180.000 + 12 CG2 CT 3 10 8 4 1.525 109.470 300.000 + 13 HG21 HC E 12 10 8 1.090 109.500 60.000 + 14 HG22 HC E 12 10 8 1.090 109.500 180.000 + 15 HG23 HC E 12 10 8 1.090 109.500 300.000 + 16 OG1 OH S 10 8 4 1.430 109.470 60.000 + 17 HG1 HO E 16 10 8 0.960 109.470 180.000 + 18 C C M 8 4 3 1.522 111.100 180.000 + 19 O O E 18 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/TRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/TRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..4fcb424e9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/TRP_TRYPTOPHAN.in_frag @@ -0,0 +1,29 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG C* S 10 8 4 1.510 115.000 180.000 + 14 CD1 CW B 13 10 8 1.340 127.000 180.000 + 15 HD HC E 14 13 10 1.090 120.000 0.000 + 16 NE1 NA B 14 13 10 1.430 107.000 180.000 + 17 HE1 H E 16 14 13 1.010 125.500 180.000 + 18 CE2 CN S 16 14 13 1.310 109.000 0.000 + 19 CZ2 CA B 18 16 14 1.400 128.000 180.000 + 20 HZ2 HC E 19 18 16 1.090 120.000 0.000 + 21 CH2 CA B 19 18 16 1.390 116.000 180.000 + 22 HH2 HC E 21 19 18 1.090 120.000 180.000 + 23 CZ3 CA B 21 19 18 1.350 121.000 0.000 + 24 HZ3 HC E 23 21 19 1.090 120.000 180.000 + 25 CE3 CA B 23 21 19 1.410 122.000 0.000 + 26 HE3 HC E 25 23 21 1.090 120.000 180.000 + 27 CD2 CB E 25 23 21 1.400 117.000 0.000 + 28 C C M 8 4 3 1.522 111.100 180.000 + 29 O O E 28 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/TYR_TYROSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/TYR_TYROSINE.in_frag new file mode 100644 index 000000000..de0157d68 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/TYR_TYROSINE.in_frag @@ -0,0 +1,26 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB2 HC E 10 8 4 1.090 109.500 300.000 + 12 HB3 HC E 10 8 4 1.090 109.500 60.000 + 13 CG CA S 10 8 4 1.510 109.470 180.000 + 14 CD1 CA B 13 10 8 1.400 120.000 180.000 + 15 HD1 HC E 14 13 10 1.090 120.000 0.000 + 16 CE1 CA B 14 13 10 1.400 120.000 180.000 + 17 HE1 HC E 16 14 13 1.090 120.000 180.000 + 18 CZ C B 16 14 13 1.400 120.000 0.000 + 19 OH OH S 18 16 14 1.360 120.000 180.000 + 20 HH HO E 19 18 16 0.960 113.000 0.000 + 21 CE2 CA B 18 16 14 1.400 120.000 0.000 + 22 HE2 HC E 21 18 16 1.090 120.000 180.000 + 23 CD2 CA S 21 18 16 1.400 120.000 0.000 + 24 HD2 HC E 23 21 18 1.090 120.000 180.000 + 25 C C M 8 4 3 1.522 111.100 180.000 + 26 O O E 25 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/VAL_VALINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/allnt/VAL_VALINE.in_frag new file mode 100644 index 000000000..532cf57be --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/VAL_VALINE.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA HC E 8 4 3 1.090 109.500 300.000 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 + 11 HB HC E 10 8 4 1.090 109.500 300.000 + 12 CG1 CT 3 10 8 4 1.525 109.470 60.000 + 13 HG11 HC E 12 10 8 1.090 109.500 60.000 + 14 HG12 HC E 12 10 8 1.090 109.500 180.000 + 15 HG13 HC E 12 10 8 1.090 109.500 300.000 + 16 CG2 CT 3 10 8 4 1.525 109.470 180.000 + 17 HG21 HC E 16 10 8 1.090 109.500 60.000 + 18 HG22 HC E 16 10 8 1.090 109.500 180.000 + 19 HG23 HC E 16 10 8 1.090 109.500 300.000 + 20 C C M 8 4 3 1.522 111.100 180.000 + 21 O O E 20 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/allnt/allnt.in b/cad/tests/AMBER_test_structures/dot_in/allnt/allnt.in new file mode 100644 index 000000000..06274f33a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/allnt/allnt.in @@ -0,0 +1,766 @@ + 1 1 200 +db4.dat +ALANINE + + ALA INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.26300 + 5 H1 H3 E 4 3 2 1.010 119.800 0.000 0.31200 + 6 H2 H3 E 4 3 2 1.010 119.800 120.000 0.31200 + 7 H3 H3 E 4 3 2 1.010 119.800 -120.000 0.31200 + 8 CA CT M 4 3 2 1.449 121.900 180.000 0.15100 + 9 HA HC E 8 4 3 1.090 109.500 300.000 0.04800 + 10 CB CT 3 8 4 3 1.525 111.100 60.000 -0.09800 + 11 HB1 HC E 10 8 4 1.090 109.500 60.000 0.03800 + 12 HB2 HC E 10 8 4 1.090 109.500 180.000 0.03800 + 13 HB3 HC E 10 8 4 1.090 109.500 300.000 0.03800 + 14 C C M 8 4 3 1.522 111.100 180.000 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0.000 -0.50400 + +IMPROPER + CA +M C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/chcl3/chcl3.in b/cad/tests/AMBER_test_structures/dot_in/chcl3/chcl3.in new file mode 100644 index 000000000..71ac077f9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/chcl3/chcl3.in @@ -0,0 +1,18 @@ + 0 0 2 + +chloroform + +CL3 INT 0 +CORRECT OMIT DU BEG +0.0 +1 DUMM DU M 0 0 0 0. +2 DUMM DU M 0 0 0 1.000 +3 DUMM DU M 0 0 0 1.000 90. +4 H1 HZ M 0 0 0 1.0 90. 180. 0.2659 +5 C1 CZ M 0 0 0 1.0 109.5 180. -.3847 +6 CL1 CL E 0 0 0 1.4 109.5 60. 0.0396 +7 CL2 CL E 0 0 0 1.4 109.5 -60. 0.0396 +8 CL3 CL M 0 0 0 1.4 109.5 180. 0.0396 + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/ferd b/cad/tests/AMBER_test_structures/dot_in/ferd new file mode 100644 index 000000000..e69de29bb diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1GA_A-D-GLUCOPYRANOS_terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1GA_A-D-GLUCOPYRANOS_terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..91516eedc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1GA_A-D-GLUCOPYRANOS_terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OH 3 12 6 4 1.421 109.900 -173.300 + 15 H3O HO E 14 12 6 0.976 108.500 -141.400 + 16 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 17 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 18 C4 CG M 12 6 4 1.519 110.600 -53.300 + 19 H4 H1 E 18 12 6 1.100 109.600 -68.100 + 20 O4 OH 3 18 12 6 1.430 109.600 171.400 + 21 H4O HO E 20 18 12 0.958 109.200 59.600 + 22 EP+4 EP E 20 18 12 0.700 109.500 179.600 + 23 EP-4 EP E 20 18 12 0.700 109.500 -59.600 + 24 C5 CG M 18 12 6 1.528 110.100 52.800 + 25 H5 H1 E 24 18 12 1.105 108.800 65.600 + 26 O5 OS B 24 18 12 1.435 110.800 -54.400 + 27 EP+5 EP E 26 24 18 0.700 109.500 178.300 + 28 EP-5 EP E 26 24 18 0.700 109.500 -63.800 + 29 C6 CG M 24 18 12 1.517 113.300 -174.200 + 30 H61 H1 E 29 24 18 1.092 108.300 -55.800 + 31 H62 H1 E 29 24 18 1.093 108.800 63.200 + 32 O6 OH M 29 24 18 1.413 112.700 -172.600 + 33 H6O HO E 32 29 24 0.955 108.100 -87.200 + 34 EP+6 EP E 32 29 24 0.700 109.500 42.800 + 35 EP-6 EP E 32 29 24 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1GB_B-D-GLUCOPYRANO_terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1GB_B-D-GLUCOPYRANO_terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..c75ec61da --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1GB_B-D-GLUCOPYRANO_terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 O4 OH 3 18 9 6 1.430 107.900 -174.000 + 21 H4O HO E 20 18 9 0.958 109.200 -139.600 + 22 EP+4 EP E 20 18 9 0.700 109.500 -19.600 + 23 EP-4 EP E 20 18 9 0.700 109.500 100.400 + 24 C3 CG M 18 9 6 1.519 110.100 -54.400 + 25 H3 H1 E 24 18 9 1.101 108.400 -66.700 + 26 O3 OH 3 24 18 9 1.421 108.700 173.500 + 27 H30 HO E 26 24 18 0.976 108.500 51.300 + 28 EP+3 EP E 26 24 18 0.700 109.500 171.300 + 29 EP-3 EP E 26 24 18 0.700 109.500 -68.700 + 30 C2 CG M 24 18 9 1.529 110.600 52.800 + 31 H2 H1 E 30 24 18 1.105 104.400 63.400 + 32 O2 OH M 30 24 18 1.415 109.500 -174.500 + 33 H2O HO E 32 30 24 0.957 110.000 -149.400 + 34 EP+2 EP E 32 30 24 0.700 109.500 -29.400 + 35 EP-2 EP E 32 30 24 0.700 109.500 90.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1LA_A-D-GALACTO-_terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1LA_A-D-GALACTO-_terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..06b9bfca1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1LA_A-D-GALACTO-_terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OH 3 12 6 4 1.421 109.900 -173.300 + 15 H3O HO E 14 12 6 0.976 108.500 -141.400 + 16 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 17 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 18 C4 CG M 12 6 4 1.519 110.600 -53.300 + 19 H4 H1 E 18 12 6 1.100 109.600 173.600 + 20 O4 OH 3 18 12 6 1.430 109.600 -63.800 + 21 H4O HO E 20 18 12 0.958 109.200 59.600 + 22 EP+4 EP E 20 18 12 0.700 109.500 179.600 + 23 EP-4 EP E 20 18 12 0.700 109.500 -59.600 + 24 C5 CG M 18 12 6 1.528 110.100 52.800 + 25 H5 H1 E 24 18 12 1.105 108.800 65.600 + 26 O5 OS B 24 18 12 1.435 110.800 -54.400 + 27 EP+5 EP E 26 24 18 0.700 109.500 178.300 + 28 EP-5 EP E 26 24 18 0.700 109.500 -63.800 + 29 C6 CG M 24 18 12 1.517 113.300 -174.200 + 30 H61 H1 E 29 24 18 1.092 108.300 -55.800 + 31 H62 H1 E 29 24 18 1.093 108.800 63.200 + 32 O6 OH M 29 24 18 1.413 112.700 -172.600 + 33 H6O HO E 32 29 24 0.955 108.100 -87.200 + 34 EP+6 EP E 32 29 24 0.700 109.500 42.800 + 35 EP-6 EP E 32 29 24 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1LB_B-D-GALACTO_terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1LB_B-D-GALACTO_terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..df5952992 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1LB_B-D-GALACTO_terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 107.500 -173.800 + 20 O4 OH 3 18 9 6 1.430 111.700 67.600 + 21 H4O HO E 20 18 9 0.958 109.200 -21.800 + 22 EP+4 EP E 20 18 9 0.700 109.500 -141.800 + 23 EP-4 EP E 20 18 9 0.700 109.500 98.200 + 24 C3 CG M 18 9 6 1.519 110.100 -54.400 + 25 H3 H1 E 24 18 9 1.101 108.400 -66.700 + 26 O3 OH 3 24 18 9 1.421 108.700 173.500 + 27 H30 HO E 26 24 18 0.976 108.500 51.300 + 28 EP+3 EP E 26 24 18 0.700 109.500 171.300 + 29 EP-3 EP E 26 24 18 0.700 109.500 -68.700 + 30 C2 CG M 24 18 9 1.529 110.600 52.800 + 31 H2 H1 E 30 24 18 1.105 104.400 63.400 + 32 O2 OH M 30 24 18 1.415 109.500 -174.500 + 33 H2O HO E 32 30 24 0.957 110.000 -149.400 + 34 EP+2 EP E 32 30 24 0.700 109.500 -29.400 + 35 EP-2 EP E 32 30 24 0.700 109.500 90.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1MA_A-D-MANNO-_terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1MA_A-D-MANNO-_terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..f2d606b78 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1MA_A-D-MANNO-_terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OH 3 6 4 3 1.415 106.300 171.500 + 9 H2O HO E 8 6 4 0.957 110.000 167.900 + 10 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 11 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OH 3 12 6 4 1.421 109.900 -173.300 + 15 H3O HO E 14 12 6 0.976 108.500 -70.100 + 16 EP+3 EP E 14 12 6 0.700 109.500 49.900 + 17 EP-3 EP E 14 12 6 0.700 109.500 169.900 + 18 C4 CG M 12 6 4 1.519 110.600 -53.300 + 19 H4 H1 E 18 12 6 1.100 109.600 -68.100 + 20 O4 OH 3 18 12 6 1.430 109.600 171.400 + 21 H4O HO E 20 18 12 0.958 109.200 115.200 + 22 EP+4 EP E 20 18 12 0.700 109.500 -124.800 + 23 EP-4 EP E 20 18 12 0.700 109.500 -4.800 + 24 C5 CG M 18 12 6 1.528 110.100 52.800 + 25 H5 H1 E 24 18 12 1.105 108.800 65.600 + 26 O5 OS B 24 18 12 1.435 110.800 -54.400 + 27 EP+5 EP E 26 24 18 0.700 109.500 -174.400 + 28 EP-5 EP E 26 24 18 0.700 109.500 -65.600 + 29 C6 CG M 24 18 12 1.517 113.300 -174.200 + 30 H61 H1 E 29 24 18 1.092 108.300 57.100 + 31 H62 H1 E 29 24 18 1.093 108.800 -54.900 + 32 O6 OH M 29 24 18 1.413 112.700 178.900 + 33 H6O HO E 32 29 24 0.955 108.100 96.000 + 34 EP+6 EP E 32 29 24 0.700 109.500 -24.000 + 35 EP-6 EP E 32 29 24 0.700 109.500 -144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1MB_B-D-MANNO_terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1MB_B-D-MANNO_terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..d255f5605 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/1MB_B-D-MANNO_terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,35 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 179.300 + 13 H62 H1 E 11 9 6 1.093 108.800 62.900 + 14 O6 OH 3 11 9 6 1.413 112.700 -65.100 + 15 H6O HO E 14 11 9 0.955 108.100 -96.000 + 16 EP+6 EP E 14 11 9 0.700 109.500 24.000 + 17 EP-6 EP E 14 11 9 0.700 109.500 144.000 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 O4 OH 3 18 9 6 1.430 107.900 -174.000 + 21 H4O HO E 20 18 9 0.958 109.200 -124.900 + 22 EP+4 EP E 20 18 9 0.700 109.500 -4.900 + 23 EP-4 EP E 20 18 9 0.700 109.500 115.100 + 24 C3 CG M 18 9 6 1.519 110.100 -54.400 + 25 H3 H1 E 24 18 9 1.101 108.400 -66.700 + 26 O3 OH 3 24 18 9 1.421 108.700 173.500 + 27 H30 HO E 26 24 18 0.976 108.500 168.700 + 28 EP+3 EP E 26 24 18 0.700 109.500 48.700 + 29 EP-3 EP E 26 24 18 0.700 109.500 -71.300 + 30 C2 CG M 24 18 9 1.529 110.600 52.800 + 31 H2 H1 E 30 24 18 1.105 106.200 -171.000 + 32 O2 OH M 30 24 18 1.415 113.900 66.100 + 33 H2O HO E 32 30 24 0.957 110.000 46.300 + 34 EP+2 EP E 32 30 24 0.700 109.500 166.300 + 35 EP-2 EP E 32 30 24 0.700 109.500 -73.700 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2GA_2-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2GA_2-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..4add0fdf7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2GA_2-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 C3 CG 3 6 4 3 1.529 110.300 -67.600 + 9 H3 H1 E 8 6 4 1.101 109.000 65.800 + 10 O3 OH 3 8 6 4 1.421 109.900 -173.300 + 11 H3O HO E 10 8 6 0.976 108.500 -141.400 + 12 EP+3 EP E 10 8 6 0.700 109.500 -21.400 + 13 EP-3 EP E 10 8 6 0.700 109.500 98.600 + 14 C4 CG 3 8 6 4 1.519 110.600 -53.300 + 15 H4 H1 E 14 8 6 1.100 109.600 -68.100 + 16 O4 OH 3 14 8 6 1.430 109.600 171.400 + 17 H4O HO E 16 14 8 0.958 109.200 59.600 + 18 EP+4 EP E 16 14 8 0.700 109.500 179.600 + 19 EP-4 EP E 16 14 8 0.700 109.500 -59.600 + 20 C5 CG 3 14 8 6 1.528 110.100 52.800 + 21 H5 H1 E 20 14 8 1.105 108.800 65.600 + 22 O5 OS B 20 14 8 1.435 110.800 -54.400 + 23 EP+5 EP E 22 20 14 0.700 109.500 178.300 + 24 EP-5 EP E 22 20 14 0.700 109.500 -63.800 + 25 C6 CG 3 20 14 8 1.517 113.300 -174.200 + 26 H61 H1 E 25 20 14 1.092 108.300 -55.800 + 27 H62 H1 E 25 20 14 1.093 108.800 63.200 + 28 O6 OH 3 25 20 14 1.413 112.700 -172.600 + 29 H6O HO E 28 25 20 0.955 108.100 -87.200 + 30 EP+6 EP E 28 25 20 0.700 109.500 42.800 + 31 EP-6 EP E 28 25 20 0.700 109.500 162.800 + 32 O2 OS M 6 4 3 1.415 110.000 52.100 + 33 EP+2 EP E 32 6 4 0.700 109.500 43.300 + 34 EP-2 EP E 32 6 4 0.700 109.500 163.300 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2GB_2-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2GB_2-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..979199dc1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2GB_2-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 O4 OH 3 18 9 6 1.430 107.900 -174.000 + 21 H4O HO E 20 18 9 0.958 109.200 -139.600 + 22 EP+4 EP E 20 18 9 0.700 109.500 -19.600 + 23 EP-4 EP E 20 18 9 0.700 109.500 100.400 + 24 C3 CG M 18 9 6 1.519 110.100 -54.400 + 25 H3 H1 E 24 18 9 1.101 108.400 -66.700 + 26 O3 OH 3 24 18 9 1.421 108.700 173.500 + 27 H30 HO E 26 24 18 0.976 108.500 51.300 + 28 EP+3 EP E 26 24 18 0.700 109.500 171.300 + 29 EP-3 EP E 26 24 18 0.700 109.500 -68.700 + 30 C2 CG M 24 18 9 1.529 110.600 52.800 + 31 H2 H1 E 30 24 18 1.105 104.400 63.400 + 32 O2 OS M 30 24 18 1.415 109.500 -174.500 + 33 EP+2 EP E 32 30 24 0.700 109.500 -29.400 + 34 EP-2 EP E 32 30 24 0.700 109.500 90.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2LA_2-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2LA_2-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..31c249043 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2LA_2-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 C3 CG 3 6 4 3 1.529 110.300 -67.600 + 9 H3 H1 E 8 6 4 1.101 109.000 65.800 + 10 O3 OH 3 8 6 4 1.421 109.900 -173.300 + 11 H3O HO E 10 8 6 0.976 108.500 -141.400 + 12 EP+3 EP E 10 8 6 0.700 109.500 -21.400 + 13 EP-3 EP E 10 8 6 0.700 109.500 98.600 + 14 C4 CG 3 8 6 4 1.519 110.600 -53.300 + 15 H4 H1 E 14 8 6 1.100 109.600 173.600 + 16 O4 OH 3 14 8 6 1.430 109.600 -63.800 + 17 H4O HO E 16 14 8 0.958 109.200 59.600 + 18 EP+4 EP E 16 14 8 0.700 109.500 179.600 + 19 EP-4 EP E 16 14 8 0.700 109.500 -59.600 + 20 C5 CG 3 14 8 6 1.528 110.100 52.800 + 21 H5 H1 E 20 14 8 1.105 108.800 65.600 + 22 O5 OS B 20 14 8 1.435 110.800 -54.400 + 23 EP+5 EP E 22 20 14 0.700 109.500 178.300 + 24 EP-5 EP E 22 20 14 0.700 109.500 -63.800 + 25 C6 CG 3 20 14 8 1.517 113.300 -174.200 + 26 H61 H1 E 25 20 14 1.092 108.300 -55.800 + 27 H62 H1 E 25 20 14 1.093 108.800 63.200 + 28 O6 OH 3 25 20 14 1.413 112.700 -172.600 + 29 H6O HO E 28 25 20 0.955 108.100 -87.200 + 30 EP+6 EP E 28 25 20 0.700 109.500 42.800 + 31 EP-6 EP E 28 25 20 0.700 109.500 162.800 + 32 O2 OS M 6 4 3 1.415 110.000 52.100 + 33 EP+2 EP E 32 6 4 0.700 109.500 43.300 + 34 EP-2 EP E 32 6 4 0.700 109.500 163.300 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2LB_2-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2LB_2-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..992380ca3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2LB_2-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 107.500 -173.800 + 20 O4 OH 3 18 9 6 1.430 111.700 67.600 + 21 H4O HO E 20 18 9 0.958 109.200 -21.800 + 22 EP+4 EP E 20 18 9 0.700 109.500 -141.800 + 23 EP-4 EP E 20 18 9 0.700 109.500 98.200 + 24 C3 CG M 18 9 6 1.519 110.100 -54.400 + 25 H3 H1 E 24 18 9 1.101 108.400 -66.700 + 26 O3 OH 3 24 18 9 1.421 108.700 173.500 + 27 H30 HO E 26 24 18 0.976 108.500 51.300 + 28 EP+3 EP E 26 24 18 0.700 109.500 171.300 + 29 EP-3 EP E 26 24 18 0.700 109.500 -68.700 + 30 C2 CG M 24 18 9 1.529 110.600 52.800 + 31 H2 H1 E 30 24 18 1.105 104.400 63.400 + 32 O2 OS M 30 24 18 1.415 109.500 -174.500 + 33 EP+2 EP E 32 30 24 0.700 109.500 -29.400 + 34 EP-2 EP E 32 30 24 0.700 109.500 90.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2MA_2-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2MA_2-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..dedcf5c8f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2MA_2-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 C3 CG 3 6 4 3 1.529 110.300 -67.600 + 9 H3 H1 E 8 6 4 1.101 109.000 65.800 + 10 O3 OH 3 8 6 4 1.421 109.900 -173.300 + 11 H3O HO E 10 8 6 0.976 108.500 -70.100 + 12 EP+3 EP E 10 8 6 0.700 109.500 49.900 + 13 EP-3 EP E 10 8 6 0.700 109.500 169.900 + 14 C4 CG 3 8 6 4 1.519 110.600 -53.300 + 15 H4 H1 E 14 8 6 1.100 109.600 -68.100 + 16 O4 OH 3 14 8 6 1.430 109.600 171.400 + 17 H4O HO E 16 14 8 0.958 109.200 115.200 + 18 EP+4 EP E 16 14 8 0.700 109.500 -124.800 + 19 EP-4 EP E 16 14 8 0.700 109.500 -4.800 + 20 C5 CG 3 14 8 6 1.528 110.100 52.800 + 21 H5 H1 E 20 14 8 1.105 108.800 65.600 + 22 O5 OS B 20 14 8 1.435 110.800 -54.400 + 23 EP+5 EP E 22 20 14 0.700 109.500 -174.400 + 24 EP-5 EP E 22 20 14 0.700 109.500 -65.600 + 25 C6 CG 3 20 14 8 1.517 113.300 -174.200 + 26 H61 H1 E 25 20 14 1.092 108.300 57.100 + 27 H62 H1 E 25 20 14 1.093 108.800 -54.900 + 28 O6 OH 3 25 20 14 1.413 112.700 178.900 + 29 H6O HO E 28 25 20 0.955 108.100 96.000 + 30 EP+6 EP E 28 25 20 0.700 109.500 -24.000 + 31 EP-6 EP E 28 25 20 0.700 109.500 -144.000 + 32 O2 OS M 6 4 3 1.415 106.300 171.500 + 33 EP+2 EP E 32 6 4 0.700 109.500 47.900 + 34 EP-2 EP E 32 6 4 0.700 109.500 -72.100 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2MB_2-_os_B-D-MANNO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2MB_2-_os_B-D-MANNO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..a7f18742f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/2MB_2-_os_B-D-MANNO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 179.300 + 13 H62 H1 E 11 9 6 1.093 108.800 62.900 + 14 O6 OH 3 11 9 6 1.413 112.700 -65.100 + 15 H6O HO E 14 11 9 0.955 108.100 -96.000 + 16 EP+6 EP E 14 11 9 0.700 109.500 24.000 + 17 EP-6 EP E 14 11 9 0.700 109.500 144.000 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 O4 OH 3 18 9 6 1.430 107.900 -174.000 + 21 H4O HO E 20 18 9 0.958 109.200 -124.900 + 22 EP+4 EP E 20 18 9 0.700 109.500 -4.900 + 23 EP-4 EP E 20 18 9 0.700 109.500 115.100 + 24 C3 CG M 18 9 6 1.519 110.100 -54.400 + 25 H3 H1 E 24 18 9 1.101 108.400 -66.700 + 26 O3 OH 3 24 18 9 1.421 108.700 173.500 + 27 H30 HO E 26 24 18 0.976 108.500 168.700 + 28 EP+3 EP E 26 24 18 0.700 109.500 48.700 + 29 EP-3 EP E 26 24 18 0.700 109.500 -71.300 + 30 C2 CG M 24 18 9 1.529 110.600 52.800 + 31 H2 H1 E 30 24 18 1.105 106.200 -171.000 + 32 O2 OS M 30 24 18 1.415 113.900 66.100 + 33 EP+2 EP E 32 30 24 0.700 109.500 166.300 + 34 EP-2 EP E 32 30 24 0.700 109.500 -73.700 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3GA_3-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3GA_3-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..fb73f4dbd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3GA_3-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 C4 CG 3 12 6 4 1.519 110.600 -53.300 + 15 H4 H1 E 14 12 6 1.100 109.600 -68.100 + 16 O4 OH 3 14 12 6 1.430 109.600 171.400 + 17 H4O HO E 16 14 12 0.958 109.200 59.600 + 18 EP+4 EP E 16 14 12 0.700 109.500 179.600 + 19 EP-4 EP E 16 14 12 0.700 109.500 -59.600 + 20 C5 CG 3 14 12 6 1.528 110.100 52.800 + 21 H5 H1 E 20 14 12 1.105 108.800 65.600 + 22 O5 OS B 20 14 12 1.435 110.800 -54.400 + 23 EP+5 EP E 22 20 14 0.700 109.500 178.300 + 24 EP-5 EP E 22 20 14 0.700 109.500 -63.800 + 25 C6 CG 3 20 14 12 1.517 113.300 -174.200 + 26 H61 H1 E 25 20 14 1.092 108.300 -55.800 + 27 H62 H1 E 25 20 14 1.093 108.800 63.200 + 28 O6 OH 3 25 20 14 1.413 112.700 -172.600 + 29 H6O HO E 28 25 20 0.955 108.100 -87.200 + 30 EP+6 EP E 28 25 20 0.700 109.500 42.800 + 31 EP-6 EP E 28 25 20 0.700 109.500 162.800 + 32 O3 OS M 12 6 4 1.421 109.900 -173.300 + 33 EP+3 EP E 32 12 6 0.700 109.500 -21.400 + 34 EP-3 EP E 32 12 6 0.700 109.500 98.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3GB_3-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3GB_3-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..b18e39608 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3GB_3-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 O4 OH 3 18 9 6 1.430 107.900 -174.000 + 21 H4O HO E 20 18 9 0.958 109.200 -139.600 + 22 EP+4 EP E 20 18 9 0.700 109.500 -19.600 + 23 EP-4 EP E 20 18 9 0.700 109.500 100.400 + 24 C3 CG M 18 9 6 1.519 110.100 -54.400 + 25 H3 H1 E 24 18 9 1.101 108.400 -66.700 + 26 C2 CG B 24 18 9 1.529 110.600 52.800 + 27 H2 H1 E 26 24 18 1.105 104.400 63.400 + 28 O2 OH 3 26 24 18 1.415 109.500 -174.500 + 29 H2O HO E 28 26 24 0.957 110.000 -149.400 + 30 EP+2 EP E 28 26 24 0.700 109.500 -29.400 + 31 EP-2 EP E 28 26 24 0.700 109.500 90.600 + 32 O3 OS M 24 18 9 1.421 108.700 173.500 + 33 EP+3 EP E 32 24 18 0.700 109.500 171.300 + 34 EP-3 EP E 32 24 18 0.700 109.500 -68.700 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3LA_3-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3LA_3-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..aa8f90e4b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3LA_3-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 C4 CG 3 12 6 4 1.519 110.600 -53.300 + 15 H4 H1 E 14 12 6 1.100 109.600 173.600 + 16 O4 OH 3 14 12 6 1.430 109.600 -63.800 + 17 H4O HO E 16 14 12 0.958 109.200 59.600 + 18 EP+4 EP E 16 14 12 0.700 109.500 179.600 + 19 EP-4 EP E 16 14 12 0.700 109.500 -59.600 + 20 C5 CG 3 14 12 6 1.528 110.100 52.800 + 21 H5 H1 E 20 14 12 1.105 108.800 65.600 + 22 O5 OS B 20 14 12 1.435 110.800 -54.400 + 23 EP+5 EP E 22 20 14 0.700 109.500 178.300 + 24 EP-5 EP E 22 20 14 0.700 109.500 -63.800 + 25 C6 CG 3 20 14 12 1.517 113.300 -174.200 + 26 H61 H1 E 25 20 14 1.092 108.300 -55.800 + 27 H62 H1 E 25 20 14 1.093 108.800 63.200 + 28 O6 OH 3 25 20 14 1.413 112.700 -172.600 + 29 H6O HO E 28 25 20 0.955 108.100 -87.200 + 30 EP+6 EP E 28 25 20 0.700 109.500 42.800 + 31 EP-6 EP E 28 25 20 0.700 109.500 162.800 + 32 O3 OS M 12 6 4 1.421 109.900 -173.300 + 33 EP+3 EP E 32 12 6 0.700 109.500 -21.400 + 34 EP-3 EP E 32 12 6 0.700 109.500 98.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3LB_3-_os_B-D-GALACTO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3LB_3-_os_B-D-GALACTO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..cbdd8413a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3LB_3-_os_B-D-GALACTO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 107.500 -173.800 + 20 O4 OH 3 18 9 6 1.430 111.700 67.600 + 21 H4O HO E 20 18 9 0.958 109.200 -21.800 + 22 EP+4 EP E 20 18 9 0.700 109.500 -141.800 + 23 EP-4 EP E 20 18 9 0.700 109.500 98.200 + 24 C3 CG M 18 9 6 1.519 110.100 -54.400 + 25 H3 H1 E 24 18 9 1.101 108.400 -66.700 + 26 C2 CG B 24 18 9 1.529 110.600 52.800 + 27 H2 H1 E 26 24 18 1.105 104.400 63.400 + 28 O2 OH 3 26 24 18 1.415 109.500 -174.500 + 29 H2O HO E 28 26 24 0.957 110.000 -149.400 + 30 EP+2 EP E 28 26 24 0.700 109.500 -29.400 + 31 EP-2 EP E 28 26 24 0.700 109.500 90.600 + 32 O3 OS M 24 18 9 1.421 108.700 173.500 + 33 EP+3 EP E 32 24 18 0.700 109.500 171.300 + 34 EP-3 EP E 32 24 18 0.700 109.500 -68.700 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3MA_3-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3MA_3-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..1c3add8e5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3MA_3-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OH 3 6 4 3 1.415 106.300 171.500 + 9 H2O HO E 8 6 4 0.957 110.000 167.900 + 10 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 11 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 C4 CG 3 12 6 4 1.519 110.600 -53.300 + 15 H4 H1 E 14 12 6 1.100 109.600 -68.100 + 16 O4 OH 3 14 12 6 1.430 109.600 171.400 + 17 H4O HO E 16 14 12 0.958 109.200 115.200 + 18 EP+4 EP E 16 14 12 0.700 109.500 -124.800 + 19 EP-4 EP E 16 14 12 0.700 109.500 -4.800 + 20 C5 CG 3 14 12 6 1.528 110.100 52.800 + 21 H5 H1 E 20 14 12 1.105 108.800 65.600 + 22 O5 OS B 20 14 12 1.435 110.800 -54.400 + 23 EP+5 EP E 22 20 14 0.700 109.500 -174.400 + 24 EP-5 EP E 22 20 14 0.700 109.500 -65.600 + 25 C6 CG 3 20 14 12 1.517 113.300 -174.200 + 26 H61 H1 E 25 20 14 1.092 108.300 57.100 + 27 H62 H1 E 25 20 14 1.093 108.800 -54.900 + 28 O6 OH 3 25 20 14 1.413 112.700 178.900 + 29 H6O HO E 28 25 20 0.955 108.100 96.000 + 30 EP+6 EP E 28 25 20 0.700 109.500 -24.000 + 31 EP-6 EP E 28 25 20 0.700 109.500 -144.000 + 32 O3 OS M 12 6 4 1.421 109.900 -173.300 + 33 EP+3 EP E 32 12 6 0.700 109.500 49.900 + 34 EP-3 EP E 32 12 6 0.700 109.500 169.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3MB_3-_os_B-D-MANNO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3MB_3-_os_B-D-MANNO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..55924a0da --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/3MB_3-_os_B-D-MANNO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 179.300 + 13 H62 H1 E 11 9 6 1.093 108.800 62.900 + 14 O6 OH 3 11 9 6 1.413 112.700 -65.100 + 15 H6O HO E 14 11 9 0.955 108.100 -96.000 + 16 EP+6 EP E 14 11 9 0.700 109.500 24.000 + 17 EP-6 EP E 14 11 9 0.700 109.500 144.000 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 O4 OH 3 18 9 6 1.430 107.900 -174.000 + 21 H4O HO E 20 18 9 0.958 109.200 -124.900 + 22 EP+4 EP E 20 18 9 0.700 109.500 -4.900 + 23 EP-4 EP E 20 18 9 0.700 109.500 115.100 + 24 C3 CG M 18 9 6 1.519 110.100 -54.400 + 25 H3 H1 E 24 18 9 1.101 108.400 -66.700 + 26 C2 CG B 24 18 9 1.529 110.600 52.800 + 27 H2 H1 E 26 24 18 1.105 106.200 -171.000 + 28 O2 OH 3 26 24 18 1.415 113.900 66.100 + 29 H2O HO E 28 26 24 0.957 110.000 46.300 + 30 EP+2 EP E 28 26 24 0.700 109.500 166.300 + 31 EP-2 EP E 28 26 24 0.700 109.500 -73.700 + 32 O3 OS M 24 18 9 1.421 108.700 173.500 + 33 EP+3 EP E 32 24 18 0.700 109.500 48.700 + 34 EP-3 EP E 32 24 18 0.700 109.500 -71.300 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4GA_4-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4GA_4-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..4e4014cf7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4GA_4-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OH 3 12 6 4 1.421 109.900 -173.300 + 15 H3O HO E 14 12 6 0.976 108.500 -141.400 + 16 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 17 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 18 C4 CG M 12 6 4 1.519 110.600 -53.300 + 19 H4 H1 E 18 12 6 1.100 109.600 -68.100 + 20 C5 CG 3 18 12 6 1.528 110.100 52.800 + 21 H5 H1 E 20 18 12 1.105 108.800 65.600 + 22 O5 OS B 20 18 12 1.435 110.800 -54.400 + 23 EP+5 EP E 22 20 18 0.700 109.500 178.300 + 24 EP-5 EP E 22 20 18 0.700 109.500 -63.800 + 25 C6 CG 3 20 18 12 1.517 113.300 -174.200 + 26 H61 H1 E 25 20 18 1.092 108.300 -55.800 + 27 H62 H1 E 25 20 18 1.093 108.800 63.200 + 28 O6 OH 3 25 20 18 1.413 112.700 -172.600 + 29 H6O HO E 28 25 20 0.955 108.100 -87.200 + 30 EP+6 EP E 28 25 20 0.700 109.500 42.800 + 31 EP-6 EP E 28 25 20 0.700 109.500 162.800 + 32 O4 OS M 18 12 6 1.430 109.600 171.400 + 33 EP+4 EP E 32 18 12 0.700 109.500 179.600 + 34 EP-4 EP E 32 18 12 0.700 109.500 -59.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4GB_4-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4GB_4-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..250d09296 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4GB_4-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 C3 CG 3 18 9 6 1.519 110.100 -54.400 + 21 H3 H1 E 20 18 9 1.101 108.400 -66.700 + 22 O3 OH 3 20 18 9 1.421 108.700 173.500 + 23 H30 HO E 22 20 18 0.976 108.500 51.300 + 24 EP+3 EP E 22 20 18 0.700 109.500 171.300 + 25 EP-3 EP E 22 20 18 0.700 109.500 -68.700 + 26 C2 CG B 20 18 9 1.529 110.600 52.800 + 27 H2 H1 E 26 20 18 1.105 104.400 63.400 + 28 O2 OH 3 26 20 18 1.415 109.500 -174.500 + 29 H2O HO E 28 26 20 0.957 110.000 -149.400 + 30 EP+2 EP E 28 26 20 0.700 109.500 -29.400 + 31 EP-2 EP E 28 26 20 0.700 109.500 90.600 + 32 O4 OS M 18 9 6 1.430 107.900 -174.000 + 33 EP+4 EP E 32 18 9 0.700 109.500 -19.600 + 34 EP-4 EP E 32 18 9 0.700 109.500 100.400 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4LA_4-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4LA_4-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..bd8144979 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4LA_4-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OH 3 12 6 4 1.421 109.900 -173.300 + 15 H3O HO E 14 12 6 0.976 108.500 -141.400 + 16 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 17 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 18 C4 CG M 12 6 4 1.519 110.600 -53.300 + 19 H4 H1 E 18 12 6 1.100 109.600 173.600 + 20 C5 CG 3 18 12 6 1.528 110.100 52.800 + 21 H5 H1 E 20 18 12 1.105 108.800 65.600 + 22 O5 OS B 20 18 12 1.435 110.800 -54.400 + 23 EP+5 EP E 22 20 18 0.700 109.500 178.300 + 24 EP-5 EP E 22 20 18 0.700 109.500 -63.800 + 25 C6 CG 3 20 18 12 1.517 113.300 -174.200 + 26 H61 H1 E 25 20 18 1.092 108.300 -55.800 + 27 H62 H1 E 25 20 18 1.093 108.800 63.200 + 28 O6 OH 3 25 20 18 1.413 112.700 -172.600 + 29 H6O HO E 28 25 20 0.955 108.100 -87.200 + 30 EP+6 EP E 28 25 20 0.700 109.500 42.800 + 31 EP-6 EP E 28 25 20 0.700 109.500 162.800 + 32 O4 OS M 18 12 6 1.430 109.600 -63.800 + 33 EP+4 EP E 32 18 12 0.700 109.500 179.600 + 34 EP-4 EP E 32 18 12 0.700 109.500 -59.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4LB_4-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4LB_4-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..d613d3a41 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4LB_4-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 107.500 -173.800 + 20 C3 CG 3 18 9 6 1.519 110.100 -54.400 + 21 H3 H1 E 20 18 9 1.101 108.400 -66.700 + 22 O3 OH 3 20 18 9 1.421 108.700 173.500 + 23 H30 HO E 22 20 18 0.976 108.500 51.300 + 24 EP+3 EP E 22 20 18 0.700 109.500 171.300 + 25 EP-3 EP E 22 20 18 0.700 109.500 -68.700 + 26 C2 CG B 20 18 9 1.529 110.600 52.800 + 27 H2 H1 E 26 20 18 1.105 104.400 63.400 + 28 O2 OH 3 26 20 18 1.415 109.500 -174.500 + 29 H2O HO E 28 26 20 0.957 110.000 -149.400 + 30 EP+2 EP E 28 26 20 0.700 109.500 -29.400 + 31 EP-2 EP E 28 26 20 0.700 109.500 90.600 + 32 O4 OS M 18 9 6 1.430 111.700 67.600 + 33 EP+4 EP E 32 18 9 0.700 109.500 -141.800 + 34 EP-4 EP E 32 18 9 0.700 109.500 98.200 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4MA_4-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4MA_4-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..8ff8643df --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4MA_4-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OH 3 6 4 3 1.415 106.300 171.500 + 9 H2O HO E 8 6 4 0.957 110.000 167.900 + 10 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 11 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OH 3 12 6 4 1.421 109.900 -173.300 + 15 H3O HO E 14 12 6 0.976 108.500 -70.100 + 16 EP+3 EP E 14 12 6 0.700 109.500 49.900 + 17 EP-3 EP E 14 12 6 0.700 109.500 169.900 + 18 C4 CG M 12 6 4 1.519 110.600 -53.300 + 19 H4 H1 E 18 12 6 1.100 109.600 -68.100 + 20 C5 CG 3 18 12 6 1.528 110.100 52.800 + 21 H5 H1 E 20 18 12 1.105 108.800 65.600 + 22 O5 OS B 20 18 12 1.435 110.800 -54.400 + 23 EP+5 EP E 22 20 18 0.700 109.500 -174.400 + 24 EP-5 EP E 22 20 18 0.700 109.500 -65.600 + 25 C6 CG 3 20 18 12 1.517 113.300 -174.200 + 26 H61 H1 E 25 20 18 1.092 108.300 57.100 + 27 H62 H1 E 25 20 18 1.093 108.800 -54.900 + 28 O6 OH 3 25 20 18 1.413 112.700 178.900 + 29 H6O HO E 28 25 20 0.955 108.100 96.000 + 30 EP+6 EP E 28 25 20 0.700 109.500 -24.000 + 31 EP-6 EP E 28 25 20 0.700 109.500 -144.000 + 32 O4 OS M 18 12 6 1.430 109.600 171.400 + 33 EP+4 EP E 32 18 12 0.700 109.500 -124.800 + 34 EP-4 EP E 32 18 12 0.700 109.500 -4.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4MB_4-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4MB_4-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..12c8837ce --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/4MB_4-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 179.300 + 13 H62 H1 E 11 9 6 1.093 108.800 62.900 + 14 O6 OH 3 11 9 6 1.413 112.700 -65.100 + 15 H6O HO E 14 11 9 0.955 108.100 -96.000 + 16 EP+6 EP E 14 11 9 0.700 109.500 24.000 + 17 EP-6 EP E 14 11 9 0.700 109.500 144.000 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 C3 CG 3 18 9 6 1.519 110.100 -54.400 + 21 H3 H1 E 20 18 9 1.101 108.400 -66.700 + 22 O3 OH 3 20 18 9 1.421 108.700 173.500 + 23 H30 HO E 22 20 18 0.976 108.500 168.700 + 24 EP+3 EP E 22 20 18 0.700 109.500 48.700 + 25 EP-3 EP E 22 20 18 0.700 109.500 -71.300 + 26 C2 CG B 20 18 9 1.529 110.600 52.800 + 27 H2 H1 E 26 20 18 1.105 106.200 -171.000 + 28 O2 OH 3 26 20 18 1.415 113.900 66.100 + 29 H2O HO E 28 26 20 0.957 110.000 46.300 + 30 EP+2 EP E 28 26 20 0.700 109.500 166.300 + 31 EP-2 EP E 28 26 20 0.700 109.500 -73.700 + 32 O4 OS M 18 9 6 1.430 107.900 -174.000 + 33 EP+4 EP E 32 18 9 0.700 109.500 -4.900 + 34 EP-4 EP E 32 18 9 0.700 109.500 115.100 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6GA_6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6GA_6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..9a25aa15e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6GA_6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OH 3 12 6 4 1.421 109.900 -173.300 + 15 H3O HO E 14 12 6 0.976 108.500 -141.400 + 16 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 17 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 18 C4 CG M 12 6 4 1.519 110.600 -53.300 + 19 H4 H1 E 18 12 6 1.100 109.600 -68.100 + 20 O4 OH 3 18 12 6 1.430 109.600 171.400 + 21 H4O HO E 20 18 12 0.958 109.200 59.600 + 22 EP+4 EP E 20 18 12 0.700 109.500 179.600 + 23 EP-4 EP E 20 18 12 0.700 109.500 -59.600 + 24 C5 CG M 18 12 6 1.528 110.100 52.800 + 25 H5 H1 E 24 18 12 1.105 108.800 65.600 + 26 O5 OS B 24 18 12 1.435 110.800 -54.400 + 27 EP+5 EP E 26 24 18 0.700 109.500 178.300 + 28 EP-5 EP E 26 24 18 0.700 109.500 -63.800 + 29 C6 CG M 24 18 12 1.517 113.300 -174.200 + 30 H61 H1 E 29 24 18 1.092 108.300 -55.800 + 31 H62 H1 E 29 24 18 1.093 108.800 63.200 + 32 O6 OS M 29 24 18 1.413 112.700 -172.600 + 33 EP+6 EP E 32 29 24 0.700 109.500 42.800 + 34 EP-6 EP E 32 29 24 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6GB_6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6GB_6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..deeeaa7cd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6GB_6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS M 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OH 3 11 9 6 1.430 107.900 -174.000 + 14 H4O HO E 13 11 9 0.958 109.200 -139.600 + 15 EP+4 EP E 13 11 9 0.700 109.500 -19.600 + 16 EP-4 EP E 13 11 9 0.700 109.500 100.400 + 17 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 18 H3 H1 E 17 11 9 1.101 108.400 -66.700 + 19 O3 OH 3 17 11 9 1.421 108.700 173.500 + 20 H30 HO E 19 17 11 0.976 108.500 51.300 + 21 EP+3 EP E 19 17 11 0.700 109.500 171.300 + 22 EP-3 EP E 19 17 11 0.700 109.500 -68.700 + 23 C2 CG B 17 11 9 1.529 110.600 52.800 + 24 H2 H1 E 23 17 11 1.105 104.400 63.400 + 25 O2 OH 3 23 17 11 1.415 109.500 -174.500 + 26 H2O HO E 25 23 17 0.957 110.000 -149.400 + 27 EP+2 EP E 25 23 17 0.700 109.500 -29.400 + 28 EP-2 EP E 25 23 17 0.700 109.500 90.600 + 29 C6 CG M 9 6 4 1.517 106.600 -177.200 + 30 H61 H1 E 29 9 6 1.092 108.300 -178.000 + 31 H62 H1 E 29 9 6 1.093 108.800 -59.000 + 32 O6 OS M 29 9 6 1.413 112.700 65.200 + 33 EP+6 EP E 32 29 9 0.700 109.500 178.100 + 34 EP-6 EP E 32 29 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6LA_6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6LA_6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..dc21d03f3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6LA_6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OH 3 12 6 4 1.421 109.900 -173.300 + 15 H3O HO E 14 12 6 0.976 108.500 -141.400 + 16 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 17 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 18 C4 CG M 12 6 4 1.519 110.600 -53.300 + 19 H4 H1 E 18 12 6 1.100 109.600 173.600 + 20 O4 OH 3 18 12 6 1.430 109.600 -63.800 + 21 H4O HO E 20 18 12 0.958 109.200 59.600 + 22 EP+4 EP E 20 18 12 0.700 109.500 179.600 + 23 EP-4 EP E 20 18 12 0.700 109.500 -59.600 + 24 C5 CG M 18 12 6 1.528 110.100 52.800 + 25 H5 H1 E 24 18 12 1.105 108.800 65.600 + 26 O5 OS B 24 18 12 1.435 110.800 -54.400 + 27 EP+5 EP E 26 24 18 0.700 109.500 178.300 + 28 EP-5 EP E 26 24 18 0.700 109.500 -63.800 + 29 C6 CG M 24 18 12 1.517 113.300 -174.200 + 30 H61 H1 E 29 24 18 1.092 108.300 -55.800 + 31 H62 H1 E 29 24 18 1.093 108.800 63.200 + 32 O6 OS M 29 24 18 1.413 112.700 -172.600 + 33 EP+6 EP E 32 29 24 0.700 109.500 42.800 + 34 EP-6 EP E 32 29 24 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6LB_6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6LB_6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..896adeb5f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6LB_6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 107.500 -173.800 + 13 O4 OH 3 11 9 6 1.430 111.700 67.600 + 14 H4O HO E 13 11 9 0.958 109.200 -21.800 + 15 EP+4 EP E 13 11 9 0.700 109.500 -141.800 + 16 EP-4 EP E 13 11 9 0.700 109.500 98.200 + 17 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 18 H3 H1 E 17 11 9 1.101 108.400 -66.700 + 19 O3 OH 3 17 11 9 1.421 108.700 173.500 + 20 H30 HO E 19 17 11 0.976 108.500 51.300 + 21 EP+3 EP E 19 17 11 0.700 109.500 171.300 + 22 EP-3 EP E 19 17 11 0.700 109.500 -68.700 + 23 C2 CG B 17 11 9 1.529 110.600 52.800 + 24 H2 H1 E 23 17 11 1.105 104.400 63.400 + 25 O2 OH 3 23 17 11 1.415 109.500 -174.500 + 26 H2O HO E 25 23 17 0.957 110.000 -149.400 + 27 EP+2 EP E 25 23 17 0.700 109.500 -29.400 + 28 EP-2 EP E 25 23 17 0.700 109.500 90.600 + 29 C6 CG M 9 6 4 1.517 106.600 -177.200 + 30 H61 H1 E 29 9 6 1.092 108.300 -178.000 + 31 H62 H1 E 29 9 6 1.093 108.800 -59.000 + 32 O6 OS M 29 9 6 1.413 112.700 65.200 + 33 EP+6 EP E 32 29 9 0.700 109.500 178.100 + 34 EP-6 EP E 32 29 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6MA_6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6MA_6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..911de9cf7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6MA_6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OH 3 6 4 3 1.415 106.300 171.500 + 9 H2O HO E 8 6 4 0.957 110.000 167.900 + 10 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 11 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OH 3 12 6 4 1.421 109.900 -173.300 + 15 H3O HO E 14 12 6 0.976 108.500 -70.100 + 16 EP+3 EP E 14 12 6 0.700 109.500 49.900 + 17 EP-3 EP E 14 12 6 0.700 109.500 169.900 + 18 C4 CG M 12 6 4 1.519 110.600 -53.300 + 19 H4 H1 E 18 12 6 1.100 109.600 -68.100 + 20 O4 OH 3 18 12 6 1.430 109.600 171.400 + 21 H4O HO E 20 18 12 0.958 109.200 115.200 + 22 EP+4 EP E 20 18 12 0.700 109.500 -124.800 + 23 EP-4 EP E 20 18 12 0.700 109.500 -4.800 + 24 C5 CG M 18 12 6 1.528 110.100 52.800 + 25 H5 H1 E 24 18 12 1.105 108.800 65.600 + 26 O5 OS B 24 18 12 1.435 110.800 -54.400 + 27 EP+5 EP E 26 24 18 0.700 109.500 -174.400 + 28 EP-5 EP E 26 24 18 0.700 109.500 -65.600 + 29 C6 CG M 24 18 12 1.517 113.300 -174.200 + 30 H61 H1 E 29 24 18 1.092 108.300 57.100 + 31 H62 H1 E 29 24 18 1.093 108.800 -54.900 + 32 O6 OS M 29 24 18 1.413 112.700 178.900 + 33 EP+6 EP E 32 29 24 0.700 109.500 -24.000 + 34 EP-6 EP E 32 29 24 0.700 109.500 -144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6MB_6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6MB_6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..1e735e9ac --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/6MB_6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,34 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OH 3 11 9 6 1.430 107.900 -174.000 + 14 H4O HO E 13 11 9 0.958 109.200 -124.900 + 15 EP+4 EP E 13 11 9 0.700 109.500 -4.900 + 16 EP-4 EP E 13 11 9 0.700 109.500 115.100 + 17 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 18 H3 H1 E 17 11 9 1.101 108.400 -66.700 + 19 O3 OH 3 17 11 9 1.421 108.700 173.500 + 20 H30 HO E 19 17 11 0.976 108.500 168.700 + 21 EP+3 EP E 19 17 11 0.700 109.500 48.700 + 22 EP-3 EP E 19 17 11 0.700 109.500 -71.300 + 23 C2 CG B 17 11 9 1.529 110.600 52.800 + 24 H2 H1 E 23 17 11 1.105 106.200 -171.000 + 25 O2 OH 3 23 17 11 1.415 113.900 66.100 + 26 H2O HO E 25 23 17 0.957 110.000 46.300 + 27 EP+2 EP E 25 23 17 0.700 109.500 166.300 + 28 EP-2 EP E 25 23 17 0.700 109.500 -73.700 + 29 C6 CG M 9 6 4 1.517 106.600 -177.200 + 30 H61 H1 E 29 9 6 1.092 108.300 179.300 + 31 H62 H1 E 29 9 6 1.093 108.800 62.900 + 32 O6 OS M 29 9 6 1.413 112.700 -65.100 + 33 EP+6 EP E 32 29 9 0.700 109.500 24.000 + 34 EP-6 EP E 32 29 9 0.700 109.500 144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/OME_o-methyl_for_glycon_RESP_0.010__op_avg._from_ens_avg_a_s_b-glcgalman_w_s__EPs_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/OME_o-methyl_for_glycon_RESP_0.010__op_avg._from_ens_avg_a_s_b-glcgalman_w_s__EPs_cp_.in_frag new file mode 100644 index 000000000..8768ac734 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/OME_o-methyl_for_glycon_RESP_0.010__op_avg._from_ens_avg_a_s_b-glcgalman_w_s__EPs_cp_.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H1 H1 M 3 2 1 1.000 90.000 180.000 + 5 CH3 CG M 4 3 2 1.085 109.500 180.000 + 6 H2 H1 E 5 4 3 1.085 111.400 60.000 + 7 H3 H1 E 5 4 3 1.085 111.400 -60.000 + 8 O OS M 5 4 3 1.399 107.000 180.000 + 9 EP+1 EP E 8 5 4 0.700 109.500 60.000 + 10 EP-1 EP E 8 5 4 0.700 109.500 -60.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PGA_2,3,4,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PGA_2,3,4,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..5427287e1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PGA_2,3,4,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,31 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OS B 11 6 4 1.421 109.900 -173.300 + 14 EP+3 EP E 13 11 6 0.700 109.500 -21.400 + 15 EP-3 EP E 13 11 6 0.700 109.500 98.600 + 16 C4 CG M 11 6 4 1.519 110.600 -53.300 + 17 H4 H1 E 16 11 6 1.100 109.600 -68.100 + 18 O4 OS B 16 11 6 1.430 109.600 171.400 + 19 EP+4 EP E 18 16 11 0.700 109.500 179.600 + 20 EP-4 EP E 18 16 11 0.700 109.500 -59.600 + 21 C5 CG M 16 11 6 1.528 110.100 52.800 + 22 H5 H1 E 21 16 11 1.105 108.800 65.600 + 23 O5 OS B 21 16 11 1.435 110.800 -54.400 + 24 EP+5 EP E 23 22 16 0.700 109.500 178.300 + 25 EP-5 EP E 22 23 16 0.700 109.500 -63.800 + 26 C6 CG M 22 16 11 1.517 113.300 -174.200 + 27 H61 H1 E 26 22 16 1.092 108.300 -55.800 + 28 H62 H1 E 26 22 16 1.093 108.800 63.200 + 29 O6 OS M 26 22 16 1.413 112.700 -172.600 + 30 EP+6 EP E 29 26 22 0.700 109.500 42.800 + 31 EP-6 EP E 29 26 22 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PGB_2,3,4,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PGB_2,3,4,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..93613956b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PGB_2,3,4,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,31 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS M 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OS B 11 9 6 1.430 107.900 -174.000 + 14 EP+4 EP E 13 11 9 0.700 109.500 -19.600 + 15 EP-4 EP E 13 11 9 0.700 109.500 100.400 + 16 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 17 H3 H1 E 16 11 9 1.101 108.400 -66.700 + 18 O3 OS B 16 11 9 1.421 108.700 173.500 + 19 EP+3 EP E 18 16 11 0.700 109.500 171.300 + 20 EP-3 EP E 18 16 11 0.700 109.500 -68.700 + 21 C2 CG B 16 14 9 1.529 110.600 52.800 + 22 H2 H1 E 21 16 11 1.105 104.400 63.400 + 23 O2 OS B 21 16 11 1.415 109.500 -174.500 + 24 EP+2 EP E 23 21 16 0.700 109.500 -29.400 + 25 EP-2 EP E 23 21 16 0.700 109.500 90.600 + 26 C6 CG M 9 6 4 1.517 106.600 -177.200 + 27 H61 H1 E 26 9 6 1.092 108.300 -178.000 + 28 H62 H1 E 26 9 6 1.093 108.800 -59.000 + 29 O6 OS M 26 9 6 1.413 112.700 65.200 + 30 EP+6 EP E 29 26 9 0.700 109.500 178.100 + 31 EP-6 EP E 29 26 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PLA_2,3,4,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PLA_2,3,4,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..ce7c7e510 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PLA_2,3,4,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,31 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OS B 11 6 4 1.421 109.900 -173.300 + 14 EP+3 EP E 13 11 6 0.700 109.500 -21.400 + 15 EP-3 EP E 13 11 6 0.700 109.500 98.600 + 16 C4 CG M 11 6 4 1.519 110.600 -53.300 + 17 H4 H1 E 16 11 6 1.100 109.600 173.600 + 18 O4 OS B 16 11 6 1.430 109.600 -63.800 + 19 EP+4 EP E 18 16 11 0.700 109.500 179.600 + 20 EP-4 EP E 18 16 11 0.700 109.500 -59.600 + 21 C5 CG M 16 11 6 1.528 110.100 52.800 + 22 H5 H1 E 22 16 11 1.105 108.800 65.600 + 23 O5 OS B 22 16 11 1.435 110.800 -54.400 + 24 EP+5 EP E 24 22 16 0.700 109.500 178.300 + 25 EP-5 EP E 24 22 16 0.700 109.500 -63.800 + 26 C6 CG M 22 16 11 1.517 113.300 -174.200 + 27 H61 H1 E 27 22 16 1.092 108.300 -55.800 + 28 H62 H1 E 27 22 16 1.093 108.800 63.200 + 29 O6 OS M 27 22 16 1.413 112.700 -172.600 + 30 EP+6 EP E 30 27 22 0.700 109.500 42.800 + 31 EP-6 EP E 30 27 22 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PLB_2,3,4,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PLB_2,3,4,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..5fa27cd1c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PLB_2,3,4,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,31 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 107.500 -173.800 + 13 O4 OS B 11 9 6 1.430 111.700 67.600 + 14 EP+4 EP E 13 11 9 0.700 109.500 -141.800 + 15 EP-4 EP E 13 11 9 0.700 109.500 98.200 + 16 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 17 H3 H1 E 16 11 9 1.101 108.400 -66.700 + 18 O3 OS B 16 11 9 1.421 108.700 173.500 + 19 EP+3 EP E 18 16 11 0.700 109.500 171.300 + 20 EP-3 EP E 18 16 11 0.700 109.500 -68.700 + 21 C2 CG B 16 11 9 1.529 110.600 52.800 + 22 H2 H1 E 21 16 11 1.105 104.400 63.400 + 23 O2 OS B 21 16 11 1.415 109.500 -174.500 + 24 EP+2 EP E 23 21 16 0.700 109.500 -29.400 + 25 EP-2 EP E 23 21 16 0.700 109.500 90.600 + 26 C6 CG M 9 6 4 1.517 106.600 -177.200 + 27 H61 H1 E 26 9 6 1.092 108.300 -178.000 + 28 H62 H1 E 26 9 6 1.093 108.800 -59.000 + 29 O6 OS M 26 9 6 1.413 112.700 65.200 + 30 EP+6 EP E 29 26 9 0.700 109.500 178.100 + 31 EP-6 EP E 29 26 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PMA_2,3,4,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PMA_2,3,4,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..d459e2f86 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PMA_2,3,4,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,31 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OS B 6 4 3 1.415 106.300 171.500 + 9 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 10 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OS B 11 6 4 1.421 109.900 -173.300 + 14 EP+3 EP E 13 11 6 0.700 109.500 49.900 + 15 EP-3 EP E 13 11 6 0.700 109.500 169.900 + 16 C4 CG M 11 6 4 1.519 110.600 -53.300 + 17 H4 H1 E 16 11 6 1.100 109.600 -68.100 + 18 O4 OS B 16 11 6 1.430 109.600 171.400 + 19 EP+4 EP E 18 16 11 0.700 109.500 -124.800 + 20 EP-4 EP E 18 16 11 0.700 109.500 -4.800 + 21 C5 CG M 16 11 6 1.528 110.100 52.800 + 22 H5 H1 E 21 16 11 1.105 108.800 65.600 + 23 O5 OS B 21 16 11 1.435 110.800 -54.400 + 24 EP+5 EP E 23 21 16 0.700 109.500 -174.400 + 25 EP-5 EP E 23 21 16 0.700 109.500 -65.600 + 26 C6 CG M 21 16 11 1.517 113.300 -174.200 + 27 H61 H1 E 26 21 16 1.092 108.300 57.100 + 28 H62 H1 E 26 21 16 1.093 108.800 -54.900 + 29 O6 OS M 26 21 16 1.413 112.700 178.900 + 30 EP+6 EP E 29 26 21 0.700 109.500 -24.000 + 31 EP-6 EP E 29 26 21 0.700 109.500 -144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PMB_2,3,4,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PMB_2,3,4,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..3f3fa2fec --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/PMB_2,3,4,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,31 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OS B 11 9 6 1.430 107.900 -174.000 + 14 EP+4 EP E 13 11 9 0.700 109.500 -4.900 + 15 EP-4 EP E 13 11 9 0.700 109.500 115.100 + 16 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 17 H3 H1 E 16 11 9 1.101 108.400 -66.700 + 18 O3 OS B 16 11 9 1.421 108.700 173.500 + 19 EP+3 EP E 18 16 11 0.700 109.500 48.700 + 20 EP-3 EP E 18 16 11 0.700 109.500 -71.300 + 21 C2 CG B 16 11 9 1.529 110.600 52.800 + 22 H2 H1 E 22 16 11 1.105 106.200 -171.000 + 23 O2 OS B 22 16 11 1.415 113.900 66.100 + 24 EP+2 EP E 24 22 16 0.700 109.500 166.300 + 25 EP-2 EP E 24 22 16 0.700 109.500 -73.700 + 26 C6 CG M 9 6 4 1.517 106.600 -177.200 + 27 H61 H1 E 26 9 6 1.092 108.300 179.300 + 28 H62 H1 E 26 9 6 1.093 108.800 62.900 + 29 O6 OS M 26 9 6 1.413 112.700 -65.100 + 30 EP+6 EP E 29 26 9 0.700 109.500 24.000 + 31 EP-6 EP E 29 26 9 0.700 109.500 144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QGA_3,4,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QGA_3,4,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..dda38389e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QGA_3,4,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OS B 12 6 4 1.421 109.900 -173.300 + 15 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 16 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 17 C4 CG M 12 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 12 6 1.100 109.600 -68.100 + 19 O4 OS B 17 12 6 1.430 109.600 171.400 + 20 EP+4 EP E 19 17 12 0.700 109.500 179.600 + 21 EP-4 EP E 19 17 12 0.700 109.500 -59.600 + 22 C5 CG M 17 12 6 1.528 110.100 52.800 + 23 H5 H1 E 22 17 12 1.105 108.800 65.600 + 24 O5 OS B 22 17 12 1.435 110.800 -54.400 + 25 EP+5 EP E 24 22 17 0.700 109.500 178.300 + 26 EP-5 EP E 24 22 17 0.700 109.500 -63.800 + 27 C6 CG M 22 17 12 1.517 113.300 -174.200 + 28 H61 H1 E 27 22 17 1.092 108.300 -55.800 + 29 H62 H1 E 27 22 17 1.093 108.800 63.200 + 30 O6 OS M 27 22 17 1.413 112.700 -172.600 + 31 EP+6 EP E 30 27 22 0.700 109.500 42.800 + 32 EP-6 EP E 30 27 22 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QGB_3,4,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QGB_3,4,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..2f1cb9c97 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QGB_3,4,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS M 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OS B 11 9 6 1.430 107.900 -174.000 + 14 EP+4 EP E 13 11 9 0.700 109.500 -19.600 + 15 EP-4 EP E 13 11 9 0.700 109.500 100.400 + 16 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 17 H3 H1 E 16 11 9 1.101 108.400 -66.700 + 18 O3 OS B 16 11 9 1.421 108.700 173.500 + 19 EP+3 EP E 18 16 11 0.700 109.500 171.300 + 20 EP-3 EP E 18 16 11 0.700 109.500 -68.700 + 21 C2 CG B 16 14 9 1.529 110.600 52.800 + 22 H2 H1 E 21 16 11 1.105 104.400 63.400 + 23 O2 OH 3 21 16 11 1.415 109.500 -174.500 + 24 H2O HO E 23 21 16 0.957 110.000 -149.400 + 25 EP+2 EP E 23 21 16 0.700 109.500 -29.400 + 26 EP-2 EP E 23 21 16 0.700 109.500 90.600 + 27 C6 CG M 9 6 4 1.517 106.600 -177.200 + 28 H61 H1 E 27 9 6 1.092 108.300 -178.000 + 29 H62 H1 E 27 9 6 1.093 108.800 -59.000 + 30 O6 OS M 27 9 6 1.413 112.700 65.200 + 31 EP+6 EP E 30 27 9 0.700 109.500 178.100 + 32 EP-6 EP E 30 27 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QLA_3,4,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QLA_3,4,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..5e59f487f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QLA_3,4,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OS B 12 6 4 1.421 109.900 -173.300 + 15 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 16 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 17 C4 CG M 12 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 12 6 1.100 109.600 173.600 + 19 O4 OS B 17 12 6 1.430 109.600 -63.800 + 20 EP+4 EP E 19 17 12 0.700 109.500 179.600 + 21 EP-4 EP E 19 17 12 0.700 109.500 -59.600 + 22 C5 CG M 17 12 6 1.528 110.100 52.800 + 23 H5 H1 E 22 17 12 1.105 108.800 65.600 + 24 O5 OS B 22 17 12 1.435 110.800 -54.400 + 25 EP+5 EP E 24 22 17 0.700 109.500 178.300 + 26 EP-5 EP E 24 22 17 0.700 109.500 -63.800 + 27 C6 CG M 22 17 12 1.517 113.300 -174.200 + 28 H61 H1 E 27 22 18 1.092 108.300 -55.800 + 29 H62 H1 E 27 22 18 1.093 108.800 63.200 + 30 O6 OS M 27 22 18 1.413 112.700 -172.600 + 31 EP+6 EP E 30 27 22 0.700 109.500 42.800 + 32 EP-6 EP E 30 27 22 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QLB_3,4,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QLB_3,4,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..b63fdaf52 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QLB_3,4,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 107.500 -173.800 + 13 O4 OS B 11 9 6 1.430 111.700 67.600 + 14 EP+4 EP E 13 11 9 0.700 109.500 -141.800 + 15 EP-4 EP E 13 11 9 0.700 109.500 98.200 + 16 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 17 H3 H1 E 16 11 9 1.101 108.400 -66.700 + 18 O3 OS B 16 11 9 1.421 108.700 173.500 + 19 EP+3 EP E 18 16 11 0.700 109.500 171.300 + 20 EP-3 EP E 18 16 11 0.700 109.500 -68.700 + 21 C2 CG B 16 11 9 1.529 110.600 52.800 + 22 H2 H1 E 21 16 11 1.105 104.400 63.400 + 23 O2 OH 3 21 16 11 1.415 109.500 -174.500 + 24 H2O HO E 23 21 16 0.957 110.000 -149.400 + 25 EP+2 EP E 23 21 16 0.700 109.500 -29.400 + 26 EP-2 EP E 23 21 16 0.700 109.500 90.600 + 27 C6 CG M 9 6 4 1.517 106.600 -177.200 + 28 H61 H1 E 27 9 6 1.092 108.300 -178.000 + 29 H62 H1 E 27 9 6 1.093 108.800 -59.000 + 30 O6 OS M 27 9 6 1.413 112.700 65.200 + 31 EP+6 EP E 30 27 9 0.700 109.500 178.100 + 32 EP-6 EP E 30 27 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QMA_3,4,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QMA_3,4,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..31e8d6038 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QMA_3,4,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OH 3 6 4 3 1.415 106.300 171.500 + 9 H2O HO E 8 6 4 0.957 110.000 167.900 + 10 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 11 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OS B 12 6 4 1.421 109.900 -173.300 + 15 EP+3 EP E 14 12 6 0.700 109.500 49.900 + 16 EP-3 EP E 14 12 6 0.700 109.500 169.900 + 17 C4 CG M 12 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 12 6 1.100 109.600 -68.100 + 19 O4 OS B 17 12 6 1.430 109.600 171.400 + 20 EP+4 EP E 19 17 12 0.700 109.500 -124.800 + 21 EP-4 EP E 19 17 12 0.700 109.500 -4.800 + 22 C5 CG M 17 12 6 1.528 110.100 52.800 + 23 H5 H1 E 22 17 12 1.105 108.800 65.600 + 24 O5 OS B 22 17 12 1.435 110.800 -54.400 + 25 EP+5 EP E 24 22 17 0.700 109.500 -174.400 + 26 EP-5 EP E 24 22 17 0.700 109.500 -65.600 + 27 C6 CG M 22 17 12 1.517 113.300 -174.200 + 28 H61 H1 E 27 22 17 1.092 108.300 57.100 + 29 H62 H1 E 27 22 17 1.093 108.800 -54.900 + 30 O6 OS M 27 22 17 1.413 112.700 178.900 + 31 EP+6 EP E 30 27 22 0.700 109.500 -24.000 + 32 EP-6 EP E 30 27 22 0.700 109.500 -144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QMB_3,4,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QMB_3,4,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..87dc057ca --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/QMB_3,4,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OS B 11 9 6 1.430 107.900 -174.000 + 14 EP+4 EP E 13 11 9 0.700 109.500 -4.900 + 15 EP-4 EP E 13 11 9 0.700 109.500 115.100 + 16 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 17 H3 H1 E 16 11 9 1.101 108.400 -66.700 + 18 O3 OS B 16 11 9 1.421 108.700 173.500 + 19 EP+3 EP E 18 16 11 0.700 109.500 48.700 + 20 EP-3 EP E 18 16 11 0.700 109.500 -71.300 + 21 C2 CG B 16 11 9 1.529 110.600 52.800 + 22 H2 H1 E 22 16 11 1.105 106.200 -171.000 + 23 O2 OH 3 22 16 11 1.415 113.900 66.100 + 24 H2O HO E 24 22 16 0.957 110.000 46.300 + 25 EP+2 EP E 24 22 16 0.700 109.500 166.300 + 26 EP-2 EP E 24 22 16 0.700 109.500 -73.700 + 27 C6 CG M 9 6 4 1.517 106.600 -177.200 + 28 H61 H1 E 27 9 6 1.092 108.300 179.300 + 29 H62 H1 E 27 9 6 1.093 108.800 62.900 + 30 O6 OS M 27 9 6 1.413 112.700 -65.100 + 31 EP+6 EP E 30 27 9 0.700 109.500 24.000 + 32 EP-6 EP E 30 27 9 0.700 109.500 144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RGA_2,4,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RGA_2,4,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..5bb166cd5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RGA_2,4,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OH 3 11 6 4 1.421 109.900 -173.300 + 14 H3O HO E 13 11 6 0.976 108.500 -141.400 + 15 EP+3 EP E 13 11 6 0.700 109.500 -21.400 + 16 EP-3 EP E 13 11 6 0.700 109.500 98.600 + 17 C4 CG M 11 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 11 6 1.100 109.600 -68.100 + 19 O4 OS B 17 11 6 1.430 109.600 171.400 + 20 EP+4 EP E 19 17 11 0.700 109.500 179.600 + 21 EP-4 EP E 19 17 11 0.700 109.500 -59.600 + 22 C5 CG M 17 11 6 1.528 110.100 52.800 + 23 H5 H1 E 22 17 11 1.105 108.800 65.600 + 24 O5 OS B 22 17 11 1.435 110.800 -54.400 + 25 EP+5 EP E 24 22 17 0.700 109.500 178.300 + 26 EP-5 EP E 24 22 17 0.700 109.500 -63.800 + 27 C6 CG M 22 17 11 1.517 113.300 -174.200 + 28 H61 H1 E 27 22 17 1.092 108.300 -55.800 + 29 H62 H1 E 27 22 17 1.093 108.800 63.200 + 30 O6 OS M 27 22 17 1.413 112.700 -172.600 + 31 EP+6 EP E 30 27 22 0.700 109.500 42.800 + 32 EP-6 EP E 30 27 22 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RGB_2,4,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RGB_2,4,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..4f8c13db8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RGB_2,4,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS M 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OS B 11 9 6 1.430 107.900 -174.000 + 14 EP+4 EP E 13 11 9 0.700 109.500 -19.600 + 15 EP-4 EP E 13 11 9 0.700 109.500 100.400 + 16 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 17 H3 H1 E 16 11 9 1.101 108.400 -66.700 + 18 O3 OH 3 16 11 9 1.421 108.700 173.500 + 19 H30 HO E 18 16 11 0.976 108.500 51.300 + 20 EP+3 EP E 18 16 11 0.700 109.500 171.300 + 21 EP-3 EP E 18 16 11 0.700 109.500 -68.700 + 22 C2 CG B 16 14 9 1.529 110.600 52.800 + 23 H2 H1 E 22 16 11 1.105 104.400 63.400 + 24 O2 OS B 22 16 11 1.415 109.500 -174.500 + 25 EP+2 EP E 24 22 16 0.700 109.500 -29.400 + 26 EP-2 EP E 24 22 16 0.700 109.500 90.600 + 27 C6 CG M 9 6 4 1.517 106.600 -177.200 + 28 H61 H1 E 27 9 6 1.092 108.300 -178.000 + 29 H62 H1 E 27 9 6 1.093 108.800 -59.000 + 30 O6 OS M 27 9 6 1.413 112.700 65.200 + 31 EP+6 EP E 30 27 9 0.700 109.500 178.100 + 32 EP-6 EP E 30 27 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RLA_2,4,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RLA_2,4,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..3cc8e1a42 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RLA_2,4,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OH 3 11 6 4 1.421 109.900 -173.300 + 14 H3O HO E 13 11 6 0.976 108.500 -141.400 + 15 EP+3 EP E 13 11 6 0.700 109.500 -21.400 + 16 EP-3 EP E 13 11 6 0.700 109.500 98.600 + 17 C4 CG M 11 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 11 6 1.100 109.600 173.600 + 19 O4 OS B 17 11 6 1.430 109.600 -63.800 + 20 EP+4 EP E 19 17 11 0.700 109.500 179.600 + 21 EP-4 EP E 19 17 11 0.700 109.500 -59.600 + 22 C5 CG M 17 11 6 1.528 110.100 52.800 + 23 H5 H1 E 23 17 11 1.105 108.800 65.600 + 24 O5 OS B 23 17 11 1.435 110.800 -54.400 + 25 EP+5 EP E 25 23 17 0.700 109.500 178.300 + 26 EP-5 EP E 25 23 17 0.700 109.500 -63.800 + 27 C6 CG M 23 17 11 1.517 113.300 -174.200 + 28 H61 H1 E 28 23 17 1.092 108.300 -55.800 + 29 H62 H1 E 28 23 17 1.093 108.800 63.200 + 30 O6 OS M 28 23 17 1.413 112.700 -172.600 + 31 EP+6 EP E 31 28 23 0.700 109.500 42.800 + 32 EP-6 EP E 31 28 23 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RLB_2,4,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RLB_2,4,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..fb648823d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RLB_2,4,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 107.500 -173.800 + 13 O4 OS B 11 9 6 1.430 111.700 67.600 + 14 EP+4 EP E 13 11 9 0.700 109.500 -141.800 + 15 EP-4 EP E 13 11 9 0.700 109.500 98.200 + 16 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 17 H3 H1 E 16 11 9 1.101 108.400 -66.700 + 18 O3 OH 3 16 11 9 1.421 108.700 173.500 + 19 H30 HO E 18 16 11 0.976 108.500 51.300 + 20 EP+3 EP E 18 16 11 0.700 109.500 171.300 + 21 EP-3 EP E 18 16 11 0.700 109.500 -68.700 + 22 C2 CG B 16 11 9 1.529 110.600 52.800 + 23 H2 H1 E 22 16 11 1.105 104.400 63.400 + 24 O2 OS B 22 16 11 1.415 109.500 -174.500 + 25 EP+2 EP E 24 22 16 0.700 109.500 -29.400 + 26 EP-2 EP E 24 22 16 0.700 109.500 90.600 + 27 C6 CG M 9 6 4 1.517 106.600 -177.200 + 28 H61 H1 E 27 9 6 1.092 108.300 -178.000 + 29 H62 H1 E 27 9 6 1.093 108.800 -59.000 + 30 O6 OS M 27 9 6 1.413 112.700 65.200 + 31 EP+6 EP E 30 27 9 0.700 109.500 178.100 + 32 EP-6 EP E 30 27 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RMA_2,4,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RMA_2,4,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..17ef14f05 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RMA_2,4,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OS B 6 4 3 1.415 106.300 171.500 + 9 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 10 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OH 3 11 6 4 1.421 109.900 -173.300 + 14 H3O HO E 13 11 6 0.976 108.500 -70.100 + 15 EP+3 EP E 13 11 6 0.700 109.500 49.900 + 16 EP-3 EP E 13 11 6 0.700 109.500 169.900 + 17 C4 CG M 11 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 11 6 1.100 109.600 -68.100 + 19 O4 OS B 17 11 6 1.430 109.600 171.400 + 20 EP+4 EP E 19 17 11 0.700 109.500 -124.800 + 21 EP-4 EP E 19 17 11 0.700 109.500 -4.800 + 22 C5 CG M 17 11 6 1.528 110.100 52.800 + 23 H5 H1 E 22 17 11 1.105 108.800 65.600 + 24 O5 OS B 22 17 11 1.435 110.800 -54.400 + 25 EP+5 EP E 24 22 17 0.700 109.500 -174.400 + 26 EP-5 EP E 24 22 17 0.700 109.500 -65.600 + 27 C6 CG M 22 17 11 1.517 113.300 -174.200 + 28 H61 H1 E 27 22 17 1.092 108.300 57.100 + 29 H62 H1 E 27 22 17 1.093 108.800 -54.900 + 30 O6 OS M 27 22 17 1.413 112.700 178.900 + 31 EP+6 EP E 30 27 22 0.700 109.500 -24.000 + 32 EP-6 EP E 30 27 22 0.700 109.500 -144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RMB_2,4,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RMB_2,4,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..0ff94862b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/RMB_2,4,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OS B 11 9 6 1.430 107.900 -174.000 + 14 EP+4 EP E 13 11 9 0.700 109.500 -4.900 + 15 EP-4 EP E 13 11 9 0.700 109.500 115.100 + 16 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 17 H3 H1 E 16 11 9 1.101 108.400 -66.700 + 18 O3 OH 3 16 11 9 1.421 108.700 173.500 + 19 H30 HO E 18 16 11 0.976 108.500 168.700 + 20 EP+3 EP E 18 16 11 0.700 109.500 48.700 + 21 EP-3 EP E 18 16 11 0.700 109.500 -71.300 + 22 C2 CG B 16 11 9 1.529 110.600 52.800 + 23 H2 H1 E 22 16 11 1.105 106.200 -171.000 + 24 O2 OS B 22 16 11 1.415 113.900 66.100 + 25 EP+2 EP E 24 22 16 0.700 109.500 166.300 + 26 EP-2 EP E 24 22 16 0.700 109.500 -73.700 + 27 C6 CG M 9 6 4 1.517 106.600 -177.200 + 28 H61 H1 E 27 9 6 1.092 108.300 179.300 + 29 H62 H1 E 27 9 6 1.093 108.800 62.900 + 30 O6 OS M 27 9 6 1.413 112.700 -65.100 + 31 EP+6 EP E 30 27 9 0.700 109.500 24.000 + 32 EP-6 EP E 30 27 9 0.700 109.500 144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SGA_2,3,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SGA_2,3,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..ef6561ee2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SGA_2,3,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OS B 11 6 4 1.421 109.900 -173.300 + 14 EP+3 EP E 13 11 6 0.700 109.500 -21.400 + 15 EP-3 EP E 13 11 6 0.700 109.500 98.600 + 16 C4 CG M 11 6 4 1.519 110.600 -53.300 + 17 H4 H1 E 16 11 6 1.100 109.600 -68.100 + 18 O4 OH 3 16 11 6 1.430 109.600 171.400 + 19 H4O HO E 18 16 11 0.958 109.200 59.600 + 20 EP+4 EP E 18 16 11 0.700 109.500 179.600 + 21 EP-4 EP E 18 16 11 0.700 109.500 -59.600 + 22 C5 CG M 16 11 6 1.528 110.100 52.800 + 23 H5 H1 E 22 16 11 1.105 108.800 65.600 + 24 O5 OS B 22 16 11 1.435 110.800 -54.400 + 25 EP+5 EP E 24 23 16 0.700 109.500 178.300 + 26 EP-5 EP E 24 23 16 0.700 109.500 -63.800 + 27 C6 CG M 23 16 11 1.517 113.300 -174.200 + 28 H61 H1 E 27 23 16 1.092 108.300 -55.800 + 29 H62 H1 E 27 23 16 1.093 108.800 63.200 + 30 O6 OS M 27 23 16 1.413 112.700 -172.600 + 31 EP+6 EP E 30 27 23 0.700 109.500 42.800 + 32 EP-6 EP E 30 27 23 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SGB_2,3,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SGB_2,3,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..bf8d47da1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SGB_2,3,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS M 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OH 3 11 9 6 1.430 107.900 -174.000 + 14 H4O HO E 16 11 9 0.958 109.200 -139.600 + 15 EP+4 EP E 16 11 9 0.700 109.500 -19.600 + 16 EP-4 EP E 16 11 9 0.700 109.500 100.400 + 17 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 18 H3 H1 E 17 11 9 1.101 108.400 -66.700 + 19 O3 OS B 17 11 9 1.421 108.700 173.500 + 20 EP+3 EP E 19 17 11 0.700 109.500 171.300 + 21 EP-3 EP E 19 17 11 0.700 109.500 -68.700 + 22 C2 CG B 17 11 9 1.529 110.600 52.800 + 23 H2 H1 E 22 17 11 1.105 104.400 63.400 + 24 O2 OS B 22 17 11 1.415 109.500 -174.500 + 25 EP+2 EP E 24 22 17 0.700 109.500 -29.400 + 26 EP-2 EP E 24 22 17 0.700 109.500 90.600 + 27 C6 CG M 9 6 4 1.517 106.600 -177.200 + 28 H61 H1 E 27 9 6 1.092 108.300 -178.000 + 29 H62 H1 E 27 9 6 1.093 108.800 -59.000 + 30 O6 OS M 27 9 6 1.413 112.700 65.200 + 31 EP+6 EP E 30 27 9 0.700 109.500 178.100 + 32 EP-6 EP E 30 27 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SLA_2,3,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SLA_2,3,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..b45147e86 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SLA_2,3,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OS B 11 6 4 1.421 109.900 -173.300 + 14 EP+3 EP E 13 11 6 0.700 109.500 -21.400 + 15 EP-3 EP E 13 11 6 0.700 109.500 98.600 + 16 C4 CG M 11 6 4 1.519 110.600 -53.300 + 17 H4 H1 E 16 11 6 1.100 109.600 173.600 + 18 O4 OH 3 16 11 6 1.430 109.600 -63.800 + 19 H4O HO E 18 16 11 0.958 109.200 59.600 + 20 EP+4 EP E 18 16 11 0.700 109.500 179.600 + 21 EP-4 EP E 18 16 11 0.700 109.500 -59.600 + 22 C5 CG M 16 11 6 1.528 110.100 52.800 + 23 H5 H1 E 22 16 11 1.105 108.800 65.600 + 24 O5 OS B 22 16 11 1.435 110.800 -54.400 + 25 EP+5 EP E 24 22 16 0.700 109.500 178.300 + 26 EP-5 EP E 24 22 16 0.700 109.500 -63.800 + 27 C6 CG M 22 16 11 1.517 113.300 -174.200 + 28 H61 H1 E 27 22 16 1.092 108.300 -55.800 + 29 H62 H1 E 27 22 16 1.093 108.800 63.200 + 30 O6 OS M 27 22 16 1.413 112.700 -172.600 + 31 EP+6 EP E 30 27 22 0.700 109.500 42.800 + 32 EP-6 EP E 30 27 22 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SLB_2,3,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SLB_2,3,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..25ed5e2c6 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SLB_2,3,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 107.500 -173.800 + 13 O4 OH 3 11 9 6 1.430 111.700 67.600 + 14 H4O HO E 13 11 9 0.958 109.200 -21.800 + 15 EP+4 EP E 13 11 9 0.700 109.500 -141.800 + 16 EP-4 EP E 13 11 9 0.700 109.500 98.200 + 17 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 18 H3 H1 E 17 11 9 1.101 108.400 -66.700 + 19 O3 OS B 17 11 9 1.421 108.700 173.500 + 20 EP+3 EP E 19 17 11 0.700 109.500 171.300 + 21 EP-3 EP E 19 17 11 0.700 109.500 -68.700 + 22 C2 CG B 17 11 9 1.529 110.600 52.800 + 23 H2 H1 E 22 17 11 1.105 104.400 63.400 + 24 O2 OS B 22 17 11 1.415 109.500 -174.500 + 25 EP+2 EP E 24 22 17 0.700 109.500 -29.400 + 26 EP-2 EP E 24 22 17 0.700 109.500 90.600 + 27 C6 CG M 9 6 4 1.517 106.600 -177.200 + 28 H61 H1 E 27 9 6 1.092 108.300 -178.000 + 29 H62 H1 E 27 9 6 1.093 108.800 -59.000 + 30 O6 OS M 27 9 6 1.413 112.700 65.200 + 31 EP+6 EP E 30 27 9 0.700 109.500 178.100 + 32 EP-6 EP E 30 27 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SMA_2,3,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SMA_2,3,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..060e784c4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SMA_2,3,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OS B 6 4 3 1.415 106.300 171.500 + 9 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 10 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OS B 11 6 4 1.421 109.900 -173.300 + 14 EP+3 EP E 13 11 6 0.700 109.500 49.900 + 15 EP-3 EP E 13 11 6 0.700 109.500 169.900 + 16 C4 CG M 11 6 4 1.519 110.600 -53.300 + 17 H4 H1 E 16 11 6 1.100 109.600 -68.100 + 18 O4 OH 3 16 11 6 1.430 109.600 171.400 + 19 H4O HO E 18 16 11 0.958 109.200 115.200 + 20 EP+4 EP E 18 16 11 0.700 109.500 -124.800 + 21 EP-4 EP E 18 16 11 0.700 109.500 -4.800 + 22 C5 CG M 16 11 6 1.528 110.100 52.800 + 23 H5 H1 E 22 16 11 1.105 108.800 65.600 + 24 O5 OS B 22 16 11 1.435 110.800 -54.400 + 25 EP+5 EP E 24 22 16 0.700 109.500 -174.400 + 26 EP-5 EP E 24 22 16 0.700 109.500 -65.600 + 27 C6 CG M 22 16 11 1.517 113.300 -174.200 + 28 H61 H1 E 27 22 16 1.092 108.300 57.100 + 29 H62 H1 E 27 22 16 1.093 108.800 -54.900 + 30 O6 OS M 27 22 16 1.413 112.700 178.900 + 31 EP+6 EP E 30 27 22 0.700 109.500 -24.000 + 32 EP-6 EP E 30 27 22 0.700 109.500 -144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SMB_2,3,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SMB_2,3,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..3e174d1a8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/SMB_2,3,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OH 3 11 9 6 1.430 107.900 -174.000 + 14 H4O HO E 13 11 9 0.958 109.200 -124.900 + 15 EP+4 EP E 13 11 9 0.700 109.500 -4.900 + 16 EP-4 EP E 13 11 9 0.700 109.500 115.100 + 17 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 18 H3 H1 E 17 11 9 1.101 108.400 -66.700 + 19 O3 OS B 17 11 9 1.421 108.700 173.500 + 20 EP+3 EP E 19 17 11 0.700 109.500 48.700 + 21 EP-3 EP E 19 17 11 0.700 109.500 -71.300 + 22 C2 CG B 17 11 9 1.529 110.600 52.800 + 23 H2 H1 E 22 17 11 1.105 106.200 -171.000 + 24 O2 OS B 22 17 11 1.415 113.900 66.100 + 25 EP+2 EP E 24 22 17 0.700 109.500 166.300 + 26 EP-2 EP E 24 22 17 0.700 109.500 -73.700 + 27 C6 CG M 9 6 4 1.517 106.600 -177.200 + 28 H61 H1 E 27 9 6 1.092 108.300 179.300 + 29 H62 H1 E 27 9 6 1.093 108.800 62.900 + 30 O6 OS M 27 9 6 1.413 112.700 -65.100 + 31 EP+6 EP E 30 27 9 0.700 109.500 24.000 + 32 EP-6 EP E 30 27 9 0.700 109.500 144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TGA_2,3,4-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TGA_2,3,4-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..05df8ba3b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TGA_2,3,4-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OS B 11 6 4 1.421 109.900 -173.300 + 14 EP+3 EP E 13 11 6 0.700 109.500 -21.400 + 15 EP-3 EP E 13 11 6 0.700 109.500 98.600 + 16 C4 CG M 11 6 4 1.519 110.600 -53.300 + 17 H4 H1 E 16 11 6 1.100 109.600 -68.100 + 18 C5 CG 3 16 11 6 1.528 110.100 52.800 + 19 H5 H1 E 18 16 11 1.105 108.800 65.600 + 20 O5 OS B 18 16 11 1.435 110.800 -54.400 + 21 EP+5 EP E 20 18 16 0.700 109.500 178.300 + 22 EP-5 EP E 20 18 16 0.700 109.500 -63.800 + 23 C6 CG 3 18 16 11 1.517 113.300 -174.200 + 24 H61 H1 E 23 18 16 1.092 108.300 -55.800 + 25 H62 H1 E 23 18 16 1.093 108.800 63.200 + 26 O6 OH 3 23 18 16 1.413 112.700 -172.600 + 27 H6O HO E 26 23 18 0.955 108.100 -87.200 + 28 EP+6 EP E 26 23 18 0.700 109.500 42.800 + 29 EP-6 EP E 26 23 18 0.700 109.500 162.800 + 30 O4 OS M 16 11 6 1.430 109.600 171.400 + 31 EP+4 EP E 30 16 11 0.700 109.500 179.600 + 32 EP-4 EP E 30 16 11 0.700 109.500 -59.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TGB_2,3,4-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TGB_2,3,4-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..ec1fb0314 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TGB_2,3,4-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 C3 CG 3 18 9 6 1.519 110.100 -54.400 + 21 H3 H1 E 20 18 9 1.101 108.400 -66.700 + 22 O3 OS B 20 18 9 1.421 108.700 173.500 + 23 EP+3 EP E 22 20 18 0.700 109.500 171.300 + 24 EP-3 EP E 22 20 18 0.700 109.500 -68.700 + 25 C2 CG B 20 18 9 1.529 110.600 52.800 + 26 H2 H1 E 25 20 18 1.105 104.400 63.400 + 27 O2 OS B 25 20 18 1.415 109.500 -174.500 + 28 EP+2 EP E 27 25 20 0.700 109.500 -29.400 + 29 EP-2 EP E 27 25 20 0.700 109.500 90.600 + 30 O4 OS M 18 9 6 1.430 107.900 -174.000 + 31 EP+4 EP E 30 18 9 0.700 109.500 -19.600 + 32 EP-4 EP E 30 18 9 0.700 109.500 100.400 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TLA_2,3,4-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TLA_2,3,4-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..95d1ff30c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TLA_2,3,4-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OS B 11 6 4 1.421 109.900 -173.300 + 14 EP+3 EP E 13 11 6 0.700 109.500 -21.400 + 15 EP-3 EP E 13 11 6 0.700 109.500 98.600 + 16 C4 CG M 11 6 4 1.519 110.600 -53.300 + 17 H4 H1 E 16 11 6 1.100 109.600 173.600 + 18 C5 CG 3 16 11 6 1.528 110.100 52.800 + 19 H5 H1 E 18 16 11 1.105 108.800 65.600 + 20 O5 OS B 18 16 11 1.435 110.800 -54.400 + 21 EP+5 EP E 20 18 16 0.700 109.500 178.300 + 22 EP-5 EP E 20 18 16 0.700 109.500 -63.800 + 23 C6 CG 3 18 16 11 1.517 113.300 -174.200 + 24 H61 H1 E 23 18 16 1.092 108.300 -55.800 + 25 H62 H1 E 23 18 16 1.093 108.800 63.200 + 26 O6 OH 3 23 18 16 1.413 112.700 -172.600 + 27 H6O HO E 26 23 18 0.955 108.100 -87.200 + 28 EP+6 EP E 26 23 18 0.700 109.500 42.800 + 29 EP-6 EP E 26 23 18 0.700 109.500 162.800 + 30 O4 OS M 16 11 6 1.430 109.600 -63.800 + 31 EP+4 EP E 30 16 11 0.700 109.500 179.600 + 32 EP-4 EP E 30 16 11 0.700 109.500 -59.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TLB_2,3,4-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TLB_2,3,4-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..d847c0bd7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TLB_2,3,4-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 107.500 -173.800 + 20 C3 CG 3 18 9 6 1.519 110.100 -54.400 + 21 H3 H1 E 20 18 9 1.101 108.400 -66.700 + 22 O3 OS B 20 18 9 1.421 108.700 173.500 + 23 EP+3 EP E 22 20 18 0.700 109.500 171.300 + 24 EP-3 EP E 22 20 18 0.700 109.500 -68.700 + 25 C2 CG B 20 18 9 1.529 110.600 52.800 + 26 H2 H1 E 25 20 18 1.105 104.400 63.400 + 27 O2 OS B 25 20 18 1.415 109.500 -174.500 + 28 EP+2 EP E 27 25 20 0.700 109.500 -29.400 + 29 EP-2 EP E 27 25 20 0.700 109.500 90.600 + 30 O4 OS M 18 9 6 1.430 111.700 67.600 + 31 EP+4 EP E 30 18 9 0.700 109.500 -141.800 + 32 EP-4 EP E 30 18 9 0.700 109.500 98.200 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TMA_2,3,4-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TMA_2,3,4-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..093240bbb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TMA_2,3,4-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OS B 6 4 3 1.415 106.300 171.500 + 9 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 10 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OS B 11 6 4 1.421 109.900 -173.300 + 14 EP+3 EP E 13 11 6 0.700 109.500 49.900 + 15 EP-3 EP E 13 11 6 0.700 109.500 169.900 + 16 C4 CG M 11 6 4 1.519 110.600 -53.300 + 17 H4 H1 E 16 11 6 1.100 109.600 -68.100 + 18 C5 CG 3 16 11 6 1.528 110.100 52.800 + 19 H5 H1 E 18 16 11 1.105 108.800 65.600 + 20 O5 OS B 18 16 11 1.435 110.800 -54.400 + 21 EP+5 EP E 20 18 16 0.700 109.500 -174.400 + 22 EP-5 EP E 20 18 16 0.700 109.500 -65.600 + 23 C6 CG 3 18 16 11 1.517 113.300 -174.200 + 24 H61 H1 E 23 18 16 1.092 108.300 57.100 + 25 H62 H1 E 23 18 16 1.093 108.800 -54.900 + 26 O6 OH 3 23 18 16 1.413 112.700 178.900 + 27 H6O HO E 26 23 18 0.955 108.100 96.000 + 28 EP+6 EP E 26 23 18 0.700 109.500 -24.000 + 29 EP-6 EP E 26 23 18 0.700 109.500 -144.000 + 30 O4 OS M 16 11 6 1.430 109.600 171.400 + 31 EP+4 EP E 30 16 11 0.700 109.500 -124.800 + 32 EP-4 EP E 30 16 11 0.700 109.500 -4.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TMB_2,3,4-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TMB_2,3,4-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..46857332e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/TMB_2,3,4-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,32 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 179.300 + 13 H62 H1 E 11 9 6 1.093 108.800 62.900 + 14 O6 OH 3 11 9 6 1.413 112.700 -65.100 + 15 H6O HO E 14 11 9 0.955 108.100 -96.000 + 16 EP+6 EP E 14 11 9 0.700 109.500 24.000 + 17 EP-6 EP E 14 11 9 0.700 109.500 144.000 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 C3 CG 3 18 9 6 1.519 110.100 -54.400 + 21 H3 H1 E 20 18 9 1.101 108.400 -66.700 + 22 O3 OS B 20 18 9 1.421 108.700 173.500 + 23 EP+3 EP E 22 20 18 0.700 109.500 48.700 + 24 EP-3 EP E 22 20 18 0.700 109.500 -71.300 + 25 C2 CG B 20 18 9 1.529 110.600 52.800 + 26 H2 H1 E 25 20 18 1.105 106.200 -171.000 + 27 O2 OS B 25 20 18 1.415 113.900 66.100 + 28 EP+2 EP E 27 25 20 0.700 109.500 166.300 + 29 EP-2 EP E 27 25 20 0.700 109.500 -73.700 + 30 O4 OS M 18 9 6 1.430 107.900 -174.000 + 31 EP+4 EP E 30 18 9 0.700 109.500 -4.900 + 32 EP-4 EP E 30 18 9 0.700 109.500 115.100 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/UGA_4,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/UGA_4,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..ac63af1c1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/UGA_4,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OH 3 12 6 4 1.421 109.900 -173.300 + 15 H3O HO E 14 12 6 0.976 108.500 -141.400 + 16 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 17 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 18 C4 CG M 12 6 4 1.519 110.600 -53.300 + 19 H4 H1 E 18 12 6 1.100 109.600 -68.100 + 20 O4 OS B 18 12 6 1.430 109.600 171.400 + 21 EP+4 EP E 20 18 12 0.700 109.500 179.600 + 22 EP-4 EP E 20 18 12 0.700 109.500 -59.600 + 23 C5 CG M 18 12 6 1.528 110.100 52.800 + 24 H5 H1 E 23 18 12 1.105 108.800 65.600 + 25 O5 OS B 23 18 12 1.435 110.800 -54.400 + 26 EP+5 EP E 25 23 18 0.700 109.500 178.300 + 27 EP-5 EP E 25 23 18 0.700 109.500 -63.800 + 28 C6 CG M 23 18 12 1.517 113.300 -174.200 + 29 H61 H1 E 28 23 18 1.092 108.300 -55.800 + 30 H62 H1 E 28 23 18 1.093 108.800 63.200 + 31 O6 OS M 28 23 18 1.413 112.700 -172.600 + 32 EP+6 EP E 31 28 23 0.700 109.500 42.800 + 33 EP-6 EP E 31 28 23 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/UGB_4,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/UGB_4,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..8c2abe6ef --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/UGB_4,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS M 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OS B 11 9 6 1.430 107.900 -174.000 + 14 EP+4 EP E 13 11 9 0.700 109.500 -19.600 + 15 EP-4 EP E 13 11 9 0.700 109.500 100.400 + 16 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 17 H3 H1 E 16 11 9 1.101 108.400 -66.700 + 18 O3 OH 3 16 11 9 1.421 108.700 173.500 + 19 H30 HO E 18 16 11 0.976 108.500 51.300 + 20 EP+3 EP E 18 16 11 0.700 109.500 171.300 + 21 EP-3 EP E 18 16 11 0.700 109.500 -68.700 + 22 C2 CG B 16 14 9 1.529 110.600 52.800 + 23 H2 H1 E 22 16 11 1.105 104.400 63.400 + 24 O2 OH 3 22 16 11 1.415 109.500 -174.500 + 25 H2O HO E 24 22 16 0.957 110.000 -149.400 + 26 EP+2 EP E 24 22 16 0.700 109.500 -29.400 + 27 EP-2 EP E 24 22 16 0.700 109.500 90.600 + 28 C6 CG M 9 6 4 1.517 106.600 -177.200 + 29 H61 H1 E 28 9 6 1.092 108.300 -178.000 + 30 H62 H1 E 28 9 6 1.093 108.800 -59.000 + 31 O6 OS M 28 9 6 1.413 112.700 65.200 + 32 EP+6 EP E 31 28 9 0.700 109.500 178.100 + 33 EP-6 EP E 31 28 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ULA_4,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ULA_4,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..4c70f3795 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ULA_4,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OH 3 12 6 4 1.421 109.900 -173.300 + 15 H3O HO E 14 12 6 0.976 108.500 -141.400 + 16 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 17 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 18 C4 CG M 12 6 4 1.519 110.600 -53.300 + 19 H4 H1 E 18 12 6 1.100 109.600 173.600 + 20 O4 OS B 18 12 6 1.430 109.600 -63.800 + 21 EP+4 EP E 20 18 12 0.700 109.500 179.600 + 22 EP-4 EP E 20 18 12 0.700 109.500 -59.600 + 23 C5 CG M 18 12 6 1.528 110.100 52.800 + 24 H5 H1 E 23 18 12 1.105 108.800 65.600 + 25 O5 OS B 23 18 12 1.435 110.800 -54.400 + 26 EP+5 EP E 25 23 18 0.700 109.500 178.300 + 27 EP-5 EP E 25 23 18 0.700 109.500 -63.800 + 28 C6 CG M 23 18 12 1.517 113.300 -174.200 + 29 H61 H1 E 28 23 18 1.092 108.300 -55.800 + 30 H62 H1 E 28 23 18 1.093 108.800 63.200 + 31 O6 OS M 28 23 18 1.413 112.700 -172.600 + 32 EP+6 EP E 31 28 23 0.700 109.500 42.800 + 33 EP-6 EP E 31 28 23 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ULB_4,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ULB_4,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..8d8d02736 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ULB_4,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 107.500 -173.800 + 13 O4 OS B 11 9 6 1.430 111.700 67.600 + 14 EP+4 EP E 13 11 9 0.700 109.500 -141.800 + 15 EP-4 EP E 13 11 9 0.700 109.500 98.200 + 16 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 17 H3 H1 E 16 11 9 1.101 108.400 -66.700 + 18 O3 OH 3 16 11 9 1.421 108.700 173.500 + 19 H30 HO E 18 16 11 0.976 108.500 51.300 + 20 EP+3 EP E 18 16 11 0.700 109.500 171.300 + 21 EP-3 EP E 18 16 11 0.700 109.500 -68.700 + 22 C2 CG B 16 11 9 1.529 110.600 52.800 + 23 H2 H1 E 22 16 11 1.105 104.400 63.400 + 24 O2 OH 3 22 16 11 1.415 109.500 -174.500 + 25 H2O HO E 24 22 16 0.957 110.000 -149.400 + 26 EP+2 EP E 24 22 16 0.700 109.500 -29.400 + 27 EP-2 EP E 24 22 16 0.700 109.500 90.600 + 28 C6 CG M 9 6 4 1.517 106.600 -177.200 + 29 H61 H1 E 28 9 6 1.092 108.300 -178.000 + 30 H62 H1 E 28 9 6 1.093 108.800 -59.000 + 31 O6 OS M 28 9 6 1.413 112.700 65.200 + 32 EP+6 EP E 31 28 9 0.700 109.500 178.100 + 33 EP-6 EP E 31 28 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/UMA_4,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/UMA_4,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..d6a1a13e1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/UMA_4,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OH 3 6 4 3 1.415 106.300 171.500 + 9 H2O HO E 8 6 4 0.957 110.000 167.900 + 10 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 11 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OH 3 12 6 4 1.421 109.900 -173.300 + 15 H3O HO E 14 12 6 0.976 108.500 -70.100 + 16 EP+3 EP E 14 12 6 0.700 109.500 49.900 + 17 EP-3 EP E 14 12 6 0.700 109.500 169.900 + 18 C4 CG M 12 6 4 1.519 110.600 -53.300 + 19 H4 H1 E 18 12 6 1.100 109.600 -68.100 + 20 O4 OS B 18 12 6 1.430 109.600 171.400 + 21 EP+4 EP E 20 18 12 0.700 109.500 -124.800 + 22 EP-4 EP E 20 18 12 0.700 109.500 -4.800 + 23 C5 CG M 18 12 6 1.528 110.100 52.800 + 24 H5 H1 E 23 18 12 1.105 108.800 65.600 + 25 O5 OS B 23 18 12 1.435 110.800 -54.400 + 26 EP+5 EP E 25 23 18 0.700 109.500 -174.400 + 27 EP-5 EP E 25 23 18 0.700 109.500 -65.600 + 28 C6 CG M 23 18 12 1.517 113.300 -174.200 + 29 H61 H1 E 28 23 18 1.092 108.300 57.100 + 30 H62 H1 E 28 23 18 1.093 108.800 -54.900 + 31 O6 OS M 28 23 18 1.413 112.700 178.900 + 32 EP+6 EP E 31 28 23 0.700 109.500 -24.000 + 33 EP-6 EP E 31 28 23 0.700 109.500 -144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/UMB_4,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/UMB_4,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..16bae073d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/UMB_4,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OS B 11 9 6 1.430 107.900 -174.000 + 14 EP+4 EP E 13 11 9 0.700 109.500 -4.900 + 15 EP-4 EP E 13 11 9 0.700 109.500 115.100 + 16 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 17 H3 H1 E 16 11 9 1.101 108.400 -66.700 + 18 O3 OH 3 16 11 9 1.421 108.700 173.500 + 19 H30 HO E 18 16 11 0.976 108.500 168.700 + 20 EP+3 EP E 18 16 11 0.700 109.500 48.700 + 21 EP-3 EP E 18 16 11 0.700 109.500 -71.300 + 22 C2 CG B 16 11 9 1.529 110.600 52.800 + 23 H2 H1 E 22 16 11 1.105 106.200 -171.000 + 24 O2 OH 3 22 16 11 1.415 113.900 66.100 + 25 H2O HO E 24 22 16 0.957 110.000 46.300 + 26 EP+2 EP E 24 22 16 0.700 109.500 166.300 + 27 EP-2 EP E 24 22 16 0.700 109.500 -73.700 + 28 C6 CG M 9 6 4 1.517 106.600 -177.200 + 29 H61 H1 E 28 9 6 1.092 108.300 179.300 + 30 H62 H1 E 28 9 6 1.093 108.800 62.900 + 31 O6 OS M 28 9 6 1.413 112.700 -65.100 + 32 EP+6 EP E 31 28 9 0.700 109.500 24.000 + 33 EP-6 EP E 31 28 9 0.700 109.500 144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VGA_3,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VGA_3,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..1786c8b5e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VGA_3,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OS B 12 6 4 1.421 109.900 -173.300 + 15 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 16 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 17 C4 CG M 12 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 12 6 1.100 109.600 -68.100 + 19 O4 OH 3 17 12 6 1.430 109.600 171.400 + 20 H4O HO E 19 17 12 0.958 109.200 59.600 + 21 EP+4 EP E 19 17 12 0.700 109.500 179.600 + 22 EP-4 EP E 19 17 12 0.700 109.500 -59.600 + 23 C5 CG M 17 12 6 1.528 110.100 52.800 + 24 H5 H1 E 23 17 12 1.105 108.800 65.600 + 25 O5 OS B 23 17 12 1.435 110.800 -54.400 + 26 EP+5 EP E 25 23 17 0.700 109.500 178.300 + 27 EP-5 EP E 25 23 17 0.700 109.500 -63.800 + 28 C6 CG M 23 17 12 1.517 113.300 -174.200 + 29 H61 H1 E 28 23 17 1.092 108.300 -55.800 + 30 H62 H1 E 28 23 17 1.093 108.800 63.200 + 31 O6 OS M 28 23 17 1.413 112.700 -172.600 + 32 EP+6 EP E 31 28 23 0.700 109.500 42.800 + 33 EP-6 EP E 31 28 23 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VGB_3,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VGB_3,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..adfb1665f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VGB_3,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS M 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OH 3 11 9 6 1.430 107.900 -174.000 + 14 H4O HO E 16 11 9 0.958 109.200 -139.600 + 15 EP+4 EP E 16 11 9 0.700 109.500 -19.600 + 16 EP-4 EP E 16 11 9 0.700 109.500 100.400 + 17 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 18 H3 H1 E 17 11 9 1.101 108.400 -66.700 + 19 O3 OS B 17 11 9 1.421 108.700 173.500 + 20 EP+3 EP E 19 17 11 0.700 109.500 171.300 + 21 EP-3 EP E 19 17 11 0.700 109.500 -68.700 + 22 C2 CG B 17 11 9 1.529 110.600 52.800 + 23 H2 H1 E 22 17 11 1.105 104.400 63.400 + 24 O2 OH 3 22 17 11 1.415 109.500 -174.500 + 25 H2O HO E 24 22 17 0.957 110.000 -149.400 + 26 EP+2 EP E 24 22 17 0.700 109.500 -29.400 + 27 EP-2 EP E 24 22 17 0.700 109.500 90.600 + 28 C6 CG M 9 6 4 1.517 106.600 -177.200 + 29 H61 H1 E 28 9 6 1.092 108.300 -178.000 + 30 H62 H1 E 28 9 6 1.093 108.800 -59.000 + 31 O6 OS M 28 9 6 1.413 112.700 65.200 + 32 EP+6 EP E 31 28 9 0.700 109.500 178.100 + 33 EP-6 EP E 31 28 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VLA_3,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VLA_3,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..1152a9e93 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VLA_3,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OS B 12 6 4 1.421 109.900 -173.300 + 15 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 16 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 17 C4 CG M 12 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 12 6 1.100 109.600 173.600 + 19 O4 OH 3 17 12 6 1.430 109.600 -63.800 + 20 H4O HO E 19 17 12 0.958 109.200 59.600 + 21 EP+4 EP E 19 17 12 0.700 109.500 179.600 + 22 EP-4 EP E 19 17 12 0.700 109.500 -59.600 + 23 C5 CG M 17 12 6 1.528 110.100 52.800 + 24 H5 H1 E 23 17 12 1.105 108.800 65.600 + 25 O5 OS B 23 17 12 1.435 110.800 -54.400 + 26 EP+5 EP E 25 23 17 0.700 109.500 178.300 + 27 EP-5 EP E 25 23 17 0.700 109.500 -63.800 + 28 C6 CG M 23 17 12 1.517 113.300 -174.200 + 29 H61 H1 E 28 23 18 1.092 108.300 -55.800 + 30 H62 H1 E 28 23 18 1.093 108.800 63.200 + 31 O6 OS M 28 23 18 1.413 112.700 -172.600 + 32 EP+6 EP E 31 28 23 0.700 109.500 42.800 + 33 EP-6 EP E 31 28 23 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VLB_3,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VLB_3,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..a51adad76 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VLB_3,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 107.500 -173.800 + 13 O4 OH 3 11 9 6 1.430 111.700 67.600 + 14 H4O HO E 13 11 9 0.958 109.200 -21.800 + 15 EP+4 EP E 13 11 9 0.700 109.500 -141.800 + 16 EP-4 EP E 13 11 9 0.700 109.500 98.200 + 17 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 18 H3 H1 E 17 11 9 1.101 108.400 -66.700 + 19 O3 OS B 17 11 9 1.421 108.700 173.500 + 20 EP+3 EP E 19 17 11 0.700 109.500 171.300 + 21 EP-3 EP E 19 17 11 0.700 109.500 -68.700 + 22 C2 CG B 17 11 9 1.529 110.600 52.800 + 23 H2 H1 E 22 17 11 1.105 104.400 63.400 + 24 O2 OH 3 22 17 11 1.415 109.500 -174.500 + 25 H2O HO E 24 22 17 0.957 110.000 -149.400 + 26 EP+2 EP E 24 22 17 0.700 109.500 -29.400 + 27 EP-2 EP E 24 22 17 0.700 109.500 90.600 + 28 C6 CG M 9 6 4 1.517 106.600 -177.200 + 29 H61 H1 E 28 9 6 1.092 108.300 -178.000 + 30 H62 H1 E 28 9 6 1.093 108.800 -59.000 + 31 O6 OS M 28 9 6 1.413 112.700 65.200 + 32 EP+6 EP E 31 28 9 0.700 109.500 178.100 + 33 EP-6 EP E 31 28 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VMA_3,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VMA_3,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..70c7dd47d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VMA_3,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OH 3 6 4 3 1.415 106.300 171.500 + 9 H2O HO E 8 6 4 0.957 110.000 167.900 + 10 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 11 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OS B 12 6 4 1.421 109.900 -173.300 + 15 EP+3 EP E 14 12 6 0.700 109.500 49.900 + 16 EP-3 EP E 14 12 6 0.700 109.500 169.900 + 17 C4 CG M 12 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 12 6 1.100 109.600 -68.100 + 19 O4 OH 3 17 12 6 1.430 109.600 171.400 + 20 H4O HO E 19 17 12 0.958 109.200 115.200 + 21 EP+4 EP E 19 17 12 0.700 109.500 -124.800 + 22 EP-4 EP E 19 17 12 0.700 109.500 -4.800 + 23 C5 CG M 17 12 6 1.528 110.100 52.800 + 24 H5 H1 E 23 17 12 1.105 108.800 65.600 + 25 O5 OS B 23 17 12 1.435 110.800 -54.400 + 26 EP+5 EP E 25 23 17 0.700 109.500 -174.400 + 27 EP-5 EP E 25 23 17 0.700 109.500 -65.600 + 28 C6 CG M 23 17 12 1.517 113.300 -174.200 + 29 H61 H1 E 28 23 17 1.092 108.300 57.100 + 30 H62 H1 E 28 23 17 1.093 108.800 -54.900 + 31 O6 OS M 28 23 17 1.413 112.700 178.900 + 32 EP+6 EP E 31 28 23 0.700 109.500 -24.000 + 33 EP-6 EP E 31 28 23 0.700 109.500 -144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VMB_3,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VMB_3,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..c76c4f02a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/VMB_3,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OH 3 11 9 6 1.430 107.900 -174.000 + 14 H4O HO E 13 11 9 0.958 109.200 -124.900 + 15 EP+4 EP E 13 11 9 0.700 109.500 -4.900 + 16 EP-4 EP E 13 11 9 0.700 109.500 115.100 + 17 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 18 H3 H1 E 17 11 9 1.101 108.400 -66.700 + 19 O3 OS B 17 11 9 1.421 108.700 173.500 + 20 EP+3 EP E 19 17 11 0.700 109.500 48.700 + 21 EP-3 EP E 19 17 11 0.700 109.500 -71.300 + 22 C2 CG B 17 11 9 1.529 110.600 52.800 + 23 H2 H1 E 22 17 11 1.105 106.200 -171.000 + 24 O2 OH 3 22 17 11 1.415 113.900 66.100 + 25 H2O HO E 24 22 17 0.957 110.000 46.300 + 26 EP+2 EP E 24 22 17 0.700 109.500 166.300 + 27 EP-2 EP E 24 22 17 0.700 109.500 -73.700 + 28 C6 CG M 9 6 4 1.517 106.600 -177.200 + 29 H61 H1 E 28 9 6 1.092 108.300 179.300 + 30 H62 H1 E 28 9 6 1.093 108.800 62.900 + 31 O6 OS M 28 9 6 1.413 112.700 -65.100 + 32 EP+6 EP E 31 28 9 0.700 109.500 24.000 + 33 EP-6 EP E 31 28 9 0.700 109.500 144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WGA_3,4-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WGA_3,4-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..adfd58244 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WGA_3,4-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OS B 12 6 4 1.421 109.900 -173.300 + 15 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 16 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 17 C4 CG M 12 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 12 6 1.100 109.600 -68.100 + 19 C5 CG 3 17 12 6 1.528 110.100 52.800 + 20 H5 H1 E 19 17 12 1.105 108.800 65.600 + 21 O5 OS B 19 17 12 1.435 110.800 -54.400 + 22 EP+5 EP E 21 19 17 0.700 109.500 178.300 + 23 EP-5 EP E 21 19 17 0.700 109.500 -63.800 + 24 C6 CG 3 19 17 12 1.517 113.300 -174.200 + 25 H61 H1 E 24 19 17 1.092 108.300 -55.800 + 26 H62 H1 E 24 19 17 1.093 108.800 63.200 + 27 O6 OH 3 24 19 17 1.413 112.700 -172.600 + 28 H6O HO E 27 24 19 0.955 108.100 -87.200 + 29 EP+6 EP E 27 24 19 0.700 109.500 42.800 + 30 EP-6 EP E 27 24 19 0.700 109.500 162.800 + 31 O4 OS M 17 12 6 1.430 109.600 171.400 + 32 EP+4 EP E 31 17 12 0.700 109.500 179.600 + 33 EP-4 EP E 31 17 12 0.700 109.500 -59.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WGB_3,4-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WGB_3,4-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..c55caec04 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WGB_3,4-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 C3 CG 3 18 9 6 1.519 110.100 -54.400 + 21 H3 H1 E 20 18 9 1.101 108.400 -66.700 + 22 O3 OS B 20 18 9 1.421 108.700 173.500 + 23 EP+3 EP E 22 20 18 0.700 109.500 171.300 + 24 EP-3 EP E 22 20 18 0.700 109.500 -68.700 + 25 C2 CG B 20 18 9 1.529 110.600 52.800 + 26 H2 H1 E 25 20 18 1.105 104.400 63.400 + 27 O2 OH 3 25 20 18 1.415 109.500 -174.500 + 28 H2O HO E 27 25 20 0.957 110.000 -149.400 + 29 EP+2 EP E 27 25 20 0.700 109.500 -29.400 + 30 EP-2 EP E 27 25 20 0.700 109.500 90.600 + 31 O4 OS M 18 9 6 1.430 107.900 -174.000 + 32 EP+4 EP E 31 18 9 0.700 109.500 -19.600 + 33 EP-4 EP E 31 18 9 0.700 109.500 100.400 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WLA_3,4-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WLA_3,4-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..a37e733ef --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WLA_3,4-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OH 3 6 4 3 1.415 110.000 52.100 + 9 H2O HO E 8 6 4 0.957 110.000 -74.700 + 10 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 11 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OS B 12 6 4 1.421 109.900 -173.300 + 15 EP+3 EP E 14 12 6 0.700 109.500 -21.400 + 16 EP-3 EP E 14 12 6 0.700 109.500 98.600 + 17 C4 CG M 12 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 12 6 1.100 109.600 173.600 + 19 C5 CG 3 17 12 6 1.528 110.100 52.800 + 20 H5 H1 E 19 17 12 1.105 108.800 65.600 + 21 O5 OS B 19 17 12 1.435 110.800 -54.400 + 22 EP+5 EP E 21 19 17 0.700 109.500 178.300 + 23 EP-5 EP E 21 19 17 0.700 109.500 -63.800 + 24 C6 CG 3 19 17 12 1.517 113.300 -174.200 + 25 H61 H1 E 24 19 17 1.092 108.300 -55.800 + 26 H62 H1 E 24 19 17 1.093 108.800 63.200 + 27 O6 OH 3 24 19 17 1.413 112.700 -172.600 + 28 H6O HO E 27 24 19 0.955 108.100 -87.200 + 29 EP+6 EP E 27 24 19 0.700 109.500 42.800 + 30 EP-6 EP E 27 24 19 0.700 109.500 162.800 + 31 O4 OS M 17 12 6 1.430 109.600 -63.800 + 32 EP+4 EP E 31 17 12 0.700 109.500 179.600 + 33 EP-4 EP E 31 17 12 0.700 109.500 -59.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WLB_3,4-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WLB_3,4-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..b1d6750ce --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WLB_3,4-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 107.500 -173.800 + 20 C3 CG 3 18 9 6 1.519 110.100 -54.400 + 21 H3 H1 E 20 18 9 1.101 108.400 -66.700 + 22 O3 OS B 20 18 9 1.421 108.700 173.500 + 23 EP+3 EP E 22 20 18 0.700 109.500 171.300 + 24 EP-3 EP E 22 20 18 0.700 109.500 -68.700 + 25 C2 CG B 20 18 9 1.529 110.600 52.800 + 26 H2 H1 E 25 20 18 1.105 104.400 63.400 + 27 O2 OH 3 25 20 18 1.415 109.500 -174.500 + 28 H2O HO E 27 25 20 0.957 110.000 -149.400 + 29 EP+2 EP E 27 25 20 0.700 109.500 -29.400 + 30 EP-2 EP E 27 25 20 0.700 109.500 90.600 + 31 O4 OS M 18 9 6 1.430 111.700 67.600 + 32 EP+4 EP E 31 18 9 0.700 109.500 -141.800 + 33 EP-4 EP E 31 18 9 0.700 109.500 98.200 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WMA_3,4-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WMA_3,4-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..2cd87d2bf --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WMA_3,4-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OH 3 6 4 3 1.415 106.300 171.500 + 9 H2O HO E 8 6 4 0.957 110.000 167.900 + 10 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 11 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 12 C3 CG M 6 4 3 1.529 110.300 -67.600 + 13 H3 H1 E 12 6 4 1.101 109.000 65.800 + 14 O3 OS B 12 6 4 1.421 109.900 -173.300 + 15 EP+3 EP E 14 12 6 0.700 109.500 49.900 + 16 EP-3 EP E 14 12 6 0.700 109.500 169.900 + 17 C4 CG M 12 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 12 6 1.100 109.600 -68.100 + 19 C5 CG 3 17 12 6 1.528 110.100 52.800 + 20 H5 H1 E 19 17 12 1.105 108.800 65.600 + 21 O5 OS B 19 17 12 1.435 110.800 -54.400 + 22 EP+5 EP E 21 19 17 0.700 109.500 -174.400 + 23 EP-5 EP E 21 19 17 0.700 109.500 -65.600 + 24 C6 CG 3 19 17 12 1.517 113.300 -174.200 + 25 H61 H1 E 24 19 17 1.092 108.300 57.100 + 26 H62 H1 E 24 19 17 1.093 108.800 -54.900 + 27 O6 OH 3 24 19 17 1.413 112.700 178.900 + 28 H6O HO E 27 24 19 0.955 108.100 96.000 + 29 EP+6 EP E 27 24 19 0.700 109.500 -24.000 + 30 EP-6 EP E 27 24 19 0.700 109.500 -144.000 + 31 O4 OS M 17 12 6 1.430 109.600 171.400 + 32 EP+4 EP E 32 17 12 0.700 109.500 -124.800 + 33 EP-4 EP E 32 17 12 0.700 109.500 -4.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WMB_3,4-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WMB_3,4-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..89a6697cd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/WMB_3,4-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 179.300 + 13 H62 H1 E 11 9 6 1.093 108.800 62.900 + 14 O6 OH 3 11 9 6 1.413 112.700 -65.100 + 15 H6O HO E 14 11 9 0.955 108.100 -96.000 + 16 EP+6 EP E 14 11 9 0.700 109.500 24.000 + 17 EP-6 EP E 14 11 9 0.700 109.500 144.000 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 C3 CG 3 18 9 6 1.519 110.100 -54.400 + 21 H3 H1 E 20 18 9 1.101 108.400 -66.700 + 22 O3 OS B 20 18 9 1.421 108.700 173.500 + 23 EP+3 EP E 22 20 18 0.700 109.500 48.700 + 24 EP-3 EP E 22 20 18 0.700 109.500 -71.300 + 25 C2 CG B 20 18 9 1.529 110.600 52.800 + 26 H2 H1 E 25 20 18 1.105 106.200 -171.000 + 27 O2 OH 3 25 20 18 1.415 113.900 66.100 + 28 H2O HO E 27 25 20 0.957 110.000 46.300 + 29 EP+2 EP E 27 25 20 0.700 109.500 166.300 + 30 EP-2 EP E 27 25 20 0.700 109.500 -73.700 + 31 O4 OS M 18 9 6 1.430 107.900 -174.000 + 32 EP+4 EP E 31 18 9 0.700 109.500 -4.900 + 33 EP-4 EP E 31 18 9 0.700 109.500 115.100 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XGA_2,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XGA_2,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..d1cb479a9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XGA_2,6-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OH 3 11 6 4 1.421 109.900 -173.300 + 14 H3O HO E 13 11 6 0.976 108.500 -141.400 + 15 EP+3 EP E 13 11 6 0.700 109.500 -21.400 + 16 EP-3 EP E 13 11 6 0.700 109.500 98.600 + 17 C4 CG M 11 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 11 6 1.100 109.600 -68.100 + 19 O4 OH 3 17 11 6 1.430 109.600 171.400 + 20 H4O HO E 19 17 11 0.958 109.200 59.600 + 21 EP+4 EP E 19 17 11 0.700 109.500 179.600 + 22 EP-4 EP E 19 17 11 0.700 109.500 -59.600 + 23 C5 CG M 17 11 6 1.528 110.100 52.800 + 24 H5 H1 E 23 17 11 1.105 108.800 65.600 + 25 O5 OS B 23 17 11 1.435 110.800 -54.400 + 26 EP+5 EP E 25 23 17 0.700 109.500 178.300 + 27 EP-5 EP E 25 23 17 0.700 109.500 -63.800 + 28 C6 CG M 23 17 11 1.517 113.300 -174.200 + 29 H61 H1 E 28 23 17 1.092 108.300 -55.800 + 30 H62 H1 E 28 23 17 1.093 108.800 63.200 + 31 O6 OS M 28 23 17 1.413 112.700 -172.600 + 32 EP+6 EP E 31 28 23 0.700 109.500 42.800 + 33 EP-6 EP E 31 28 23 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XGB_2,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XGB_2,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..dbd93c3b5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XGB_2,6-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS M 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OH 3 11 9 6 1.430 107.900 -174.000 + 14 H4O HO E 13 11 9 0.958 109.200 -139.600 + 15 EP+4 EP E 13 11 9 0.700 109.500 -19.600 + 16 EP-4 EP E 13 11 9 0.700 109.500 100.400 + 17 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 18 H3 H1 E 17 11 9 1.101 108.400 -66.700 + 19 O3 OH 3 17 11 9 1.421 108.700 173.500 + 20 H30 HO E 19 17 11 0.976 108.500 51.300 + 21 EP+3 EP E 19 17 11 0.700 109.500 171.300 + 22 EP-3 EP E 19 17 11 0.700 109.500 -68.700 + 23 C2 CG B 17 11 9 1.529 110.600 52.800 + 24 H2 H1 E 23 17 11 1.105 104.400 63.400 + 25 O2 OS B 23 17 11 1.415 109.500 -174.500 + 26 EP+2 EP E 25 23 17 0.700 109.500 -29.400 + 27 EP-2 EP E 25 23 17 0.700 109.500 90.600 + 28 C6 CG M 9 6 4 1.517 106.600 -177.200 + 29 H61 H1 E 28 9 6 1.092 108.300 -178.000 + 30 H62 H1 E 28 9 6 1.093 108.800 -59.000 + 31 O6 OS M 28 9 6 1.413 112.700 65.200 + 32 EP+6 EP E 31 28 9 0.700 109.500 178.100 + 33 EP-6 EP E 31 28 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XLA_2,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XLA_2,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..ed23945f4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XLA_2,6-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OH 3 11 6 4 1.421 109.900 -173.300 + 14 H3O HO E 13 11 6 0.976 108.500 -141.400 + 15 EP+3 EP E 13 11 6 0.700 109.500 -21.400 + 16 EP-3 EP E 13 11 6 0.700 109.500 98.600 + 17 C4 CG M 11 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 11 6 1.100 109.600 173.600 + 19 O4 OH 3 17 11 6 1.430 109.600 -63.800 + 20 H4O HO E 19 17 11 0.958 109.200 59.600 + 21 EP+4 EP E 19 17 11 0.700 109.500 179.600 + 22 EP-4 EP E 19 17 11 0.700 109.500 -59.600 + 23 C5 CG M 17 11 6 1.528 110.100 52.800 + 24 H5 H1 E 23 17 11 1.105 108.800 65.600 + 25 O5 OS B 23 17 11 1.435 110.800 -54.400 + 26 EP+5 EP E 25 23 17 0.700 109.500 178.300 + 27 EP-5 EP E 25 23 17 0.700 109.500 -63.800 + 28 C6 CG M 23 17 11 1.517 113.300 -174.200 + 29 H61 H1 E 28 23 17 1.092 108.300 -55.800 + 30 H62 H1 E 28 23 17 1.093 108.800 63.200 + 31 O6 OS M 28 23 17 1.413 112.700 -172.600 + 32 EP+6 EP E 31 28 23 0.700 109.500 42.800 + 33 EP-6 EP E 31 28 23 0.700 109.500 162.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XLB_2,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XLB_2,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..0dc017c6b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XLB_2,6-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 107.500 -173.800 + 13 O4 OH 3 11 9 6 1.430 111.700 67.600 + 14 H4O HO E 13 11 9 0.958 109.200 -21.800 + 15 EP+4 EP E 13 11 9 0.700 109.500 -141.800 + 16 EP-4 EP E 13 11 9 0.700 109.500 98.200 + 17 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 18 H3 H1 E 17 11 9 1.101 108.400 -66.700 + 19 O3 OH 3 17 11 9 1.421 108.700 173.500 + 20 H30 HO E 19 17 11 0.976 108.500 51.300 + 21 EP+3 EP E 19 17 11 0.700 109.500 171.300 + 22 EP-3 EP E 19 17 11 0.700 109.500 -68.700 + 23 C2 CG B 17 11 9 1.529 110.600 52.800 + 24 H2 H1 E 23 17 11 1.105 104.400 63.400 + 25 O2 OS B 23 17 11 1.415 109.500 -174.500 + 26 EP+2 EP E 25 23 17 0.700 109.500 -29.400 + 27 EP-2 EP E 25 23 17 0.700 109.500 90.600 + 28 C6 CG M 9 6 4 1.517 106.600 -177.200 + 29 H61 H1 E 28 9 6 1.092 108.300 -178.000 + 30 H62 H1 E 28 9 6 1.093 108.800 -59.000 + 31 O6 OS M 28 9 6 1.413 112.700 65.200 + 32 EP+6 EP E 31 28 9 0.700 109.500 178.100 + 33 EP-6 EP E 31 28 9 0.700 109.500 61.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XMA_2,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XMA_2,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..4ae1af9e9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XMA_2,6-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OS B 6 4 3 1.415 106.300 171.500 + 9 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 10 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OH 3 11 6 4 1.421 109.900 -173.300 + 14 H3O HO E 13 11 6 0.976 108.500 -70.100 + 15 EP+3 EP E 13 11 6 0.700 109.500 49.900 + 16 EP-3 EP E 13 11 6 0.700 109.500 169.900 + 17 C4 CG M 11 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 11 6 1.100 109.600 -68.100 + 19 O4 OH 3 17 11 6 1.430 109.600 171.400 + 20 H4O HO E 19 17 11 0.958 109.200 115.200 + 21 EP+4 EP E 19 17 11 0.700 109.500 -124.800 + 22 EP-4 EP E 19 17 11 0.700 109.500 -4.800 + 23 C5 CG M 17 11 6 1.528 110.100 52.800 + 24 H5 H1 E 23 17 11 1.105 108.800 65.600 + 25 O5 OS B 23 17 11 1.435 110.800 -54.400 + 26 EP+5 EP E 25 23 17 0.700 109.500 -174.400 + 27 EP-5 EP E 25 23 17 0.700 109.500 -65.600 + 28 C6 CG M 23 17 11 1.517 113.300 -174.200 + 29 H61 H1 E 28 23 17 1.092 108.300 57.100 + 30 H62 H1 E 28 23 17 1.093 108.800 -54.900 + 31 O6 OS M 28 23 17 1.413 112.700 178.900 + 32 EP+6 EP E 31 28 23 0.700 109.500 -24.000 + 33 EP-6 EP E 31 28 23 0.700 109.500 -144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XMB_2,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XMB_2,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..d63029f38 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/XMB_2,6-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C4 CG 3 9 6 4 1.528 110.800 59.100 + 12 H4 H1 E 11 9 6 1.100 109.800 66.400 + 13 O4 OH 3 11 9 6 1.430 107.900 -174.000 + 14 H4O HO E 13 11 9 0.958 109.200 -124.900 + 15 EP+4 EP E 13 11 9 0.700 109.500 -4.900 + 16 EP-4 EP E 13 11 9 0.700 109.500 115.100 + 17 C3 CG 3 11 9 6 1.519 110.100 -54.400 + 18 H3 H1 E 17 11 9 1.101 108.400 -66.700 + 19 O3 OH 3 17 11 9 1.421 108.700 173.500 + 20 H30 HO E 19 17 11 0.976 108.500 168.700 + 21 EP+3 EP E 19 17 11 0.700 109.500 48.700 + 22 EP-3 EP E 19 17 11 0.700 109.500 -71.300 + 23 C2 CG B 17 11 9 1.529 110.600 52.800 + 24 H2 H1 E 23 17 11 1.105 106.200 -171.000 + 25 O2 OS B 23 17 11 1.415 113.900 66.100 + 26 EP+2 EP E 25 23 17 0.700 109.500 166.300 + 27 EP-2 EP E 25 23 17 0.700 109.500 -73.700 + 28 C6 CG M 9 6 4 1.517 106.600 -177.200 + 29 H61 H1 E 28 9 6 1.092 108.300 179.300 + 30 H62 H1 E 28 9 6 1.093 108.800 62.900 + 31 O6 OS M 28 9 6 1.413 112.700 -65.100 + 32 EP+6 EP E 31 28 9 0.700 109.500 24.000 + 33 EP-6 EP E 31 28 9 0.700 109.500 144.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YGA_2,4-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YGA_2,4-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..5f5ca6135 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YGA_2,4-_os_A-D-GLUCOPYRANO-_cs__non-terminal_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OH 3 11 6 4 1.421 109.900 -173.300 + 14 H3O HO E 13 11 6 0.976 108.500 -141.400 + 15 EP+3 EP E 13 11 6 0.700 109.500 -21.400 + 16 EP-3 EP E 13 11 6 0.700 109.500 98.600 + 17 C4 CG M 11 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 11 6 1.100 109.600 -68.100 + 19 C5 CG 3 17 11 6 1.528 110.100 52.800 + 20 H5 H1 E 19 17 11 1.105 108.800 65.600 + 21 O5 OS B 19 17 11 1.435 110.800 -54.400 + 22 EP+5 EP E 21 19 17 0.700 109.500 178.300 + 23 EP-5 EP E 21 19 17 0.700 109.500 -63.800 + 24 C6 CG 3 19 17 11 1.517 113.300 -174.200 + 25 H61 H1 E 24 19 17 1.092 108.300 -55.800 + 26 H62 H1 E 24 19 17 1.093 108.800 63.200 + 27 O6 OH 3 24 19 17 1.413 112.700 -172.600 + 28 H6O HO E 27 24 19 0.955 108.100 -87.200 + 29 EP+6 EP E 27 24 19 0.700 109.500 42.800 + 30 EP-6 EP E 27 24 19 0.700 109.500 162.800 + 31 O4 OS M 17 11 6 1.430 109.600 171.400 + 32 EP+4 EP E 31 17 11 0.700 109.500 179.600 + 33 EP-4 EP E 31 17 11 0.700 109.500 -59.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YGB_2,4-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YGB_2,4-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..0ce07e007 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YGB_2,4-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 C3 CG 3 18 9 6 1.519 110.100 -54.400 + 21 H3 H1 E 20 18 9 1.101 108.400 -66.700 + 22 O3 OH 3 20 18 9 1.421 108.700 173.500 + 23 H30 HO E 22 20 18 0.976 108.500 51.300 + 24 EP+3 EP E 22 20 18 0.700 109.500 171.300 + 25 EP-3 EP E 22 20 18 0.700 109.500 -68.700 + 26 C2 CG B 20 18 9 1.529 110.600 52.800 + 27 H2 H1 E 26 20 18 1.105 104.400 63.400 + 28 O2 OS B 26 20 18 1.415 109.500 -174.500 + 29 EP+2 EP E 28 26 20 0.700 109.500 -29.400 + 30 EP-2 EP E 28 26 20 0.700 109.500 90.600 + 31 O4 OS M 18 9 6 1.430 107.900 -174.000 + 32 EP+4 EP E 31 18 9 0.700 109.500 -19.600 + 33 EP-4 EP E 31 18 9 0.700 109.500 100.400 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YLA_2,4-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YLA_2,4-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..60d4f2ff1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YLA_2,4-_os_A-D-GALACTO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OH 3 11 6 4 1.421 109.900 -173.300 + 14 H3O HO E 13 11 6 0.976 108.500 -141.400 + 15 EP+3 EP E 13 11 6 0.700 109.500 -21.400 + 16 EP-3 EP E 13 11 6 0.700 109.500 98.600 + 17 C4 CG M 11 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 11 6 1.100 109.600 173.600 + 19 C5 CG 3 17 11 6 1.528 110.100 52.800 + 20 H5 H1 E 19 17 11 1.105 108.800 65.600 + 21 O5 OS B 19 17 11 1.435 110.800 -54.400 + 22 EP+5 EP E 21 19 17 0.700 109.500 178.300 + 23 EP-5 EP E 21 19 17 0.700 109.500 -63.800 + 24 C6 CG 3 19 17 11 1.517 113.300 -174.200 + 25 H61 H1 E 24 19 17 1.092 108.300 -55.800 + 26 H62 H1 E 24 19 17 1.093 108.800 63.200 + 27 O6 OH 3 24 19 17 1.413 112.700 -172.600 + 28 H6O HO E 27 24 19 0.955 108.100 -87.200 + 29 EP+6 EP E 27 24 19 0.700 109.500 42.800 + 30 EP-6 EP E 27 24 19 0.700 109.500 162.800 + 31 O4 OS M 17 11 6 1.430 109.600 -63.800 + 32 EP+4 EP E 31 17 11 0.700 109.500 179.600 + 33 EP-4 EP E 31 17 11 0.700 109.500 -59.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YLB_2,4-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YLB_2,4-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..a2c44c472 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YLB_2,4-_os_B-D-GALACTO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 107.500 -173.800 + 20 C3 CG 3 18 9 6 1.519 110.100 -54.400 + 21 H3 H1 E 20 18 9 1.101 108.400 -66.700 + 22 O3 OH 3 20 18 9 1.421 108.700 173.500 + 23 H30 HO E 22 20 18 0.976 108.500 51.300 + 24 EP+3 EP E 22 20 18 0.700 109.500 171.300 + 25 EP-3 EP E 22 20 18 0.700 109.500 -68.700 + 26 C2 CG B 20 18 9 1.529 110.600 52.800 + 27 H2 H1 E 26 20 18 1.105 104.400 63.400 + 28 O2 OS B 26 20 18 1.415 109.500 -174.500 + 29 EP+2 EP E 28 26 20 0.700 109.500 -29.400 + 30 EP-2 EP E 28 26 20 0.700 109.500 90.600 + 31 O4 OS M 18 9 6 1.430 111.700 67.600 + 32 EP+4 EP E 31 18 9 0.700 109.500 -141.800 + 33 EP-4 EP E 31 18 9 0.700 109.500 98.200 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YMA_2,4-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YMA_2,4-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..9501bbb0f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YMA_2,4-_os_A-D-MANNO-_cs__non-terminal_residue,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OS B 6 4 3 1.415 106.300 171.500 + 9 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 10 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 O3 OH 3 11 6 4 1.421 109.900 -173.300 + 14 H3O HO E 13 11 6 0.976 108.500 -70.100 + 15 EP+3 EP E 13 11 6 0.700 109.500 49.900 + 16 EP-3 EP E 13 11 6 0.700 109.500 169.900 + 17 C4 CG M 11 6 4 1.519 110.600 -53.300 + 18 H4 H1 E 17 11 6 1.100 109.600 -68.100 + 19 C5 CG 3 17 11 6 1.528 110.100 52.800 + 20 H5 H1 E 19 17 11 1.105 108.800 65.600 + 21 O5 OS B 19 17 11 1.435 110.800 -54.400 + 22 EP+5 EP E 21 19 17 0.700 109.500 -174.400 + 23 EP-5 EP E 21 19 17 0.700 109.500 -65.600 + 24 C6 CG 3 19 17 11 1.517 113.300 -174.200 + 25 H61 H1 E 24 19 17 1.092 108.300 57.100 + 26 H62 H1 E 24 19 17 1.093 108.800 -54.900 + 27 O6 OH 3 24 19 17 1.413 112.700 178.900 + 28 H6O HO E 27 24 19 0.955 108.100 96.000 + 29 EP+6 EP E 27 24 19 0.700 109.500 -24.000 + 30 EP-6 EP E 27 24 19 0.700 109.500 -144.000 + 31 O4 OS M 17 11 6 1.430 109.600 171.400 + 32 EP+4 EP E 31 17 11 0.700 109.500 -124.800 + 33 EP-4 EP E 31 17 11 0.700 109.500 -4.800 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YMB_2,4-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YMB_2,4-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..9798bcc09 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/YMB_2,4-_os_B-D-MANNO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 179.300 + 13 H62 H1 E 11 9 6 1.093 108.800 62.900 + 14 O6 OH 3 11 9 6 1.413 112.700 -65.100 + 15 H6O HO E 14 11 9 0.955 108.100 -96.000 + 16 EP+6 EP E 14 11 9 0.700 109.500 24.000 + 17 EP-6 EP E 14 11 9 0.700 109.500 144.000 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 C3 CG 3 18 9 6 1.519 110.100 -54.400 + 21 H3 H1 E 20 18 9 1.101 108.400 -66.700 + 22 O3 OH 3 20 18 9 1.421 108.700 173.500 + 23 H30 HO E 22 20 18 0.976 108.500 168.700 + 24 EP+3 EP E 22 20 18 0.700 109.500 48.700 + 25 EP-3 EP E 22 20 18 0.700 109.500 -71.300 + 26 C2 CG B 20 18 9 1.529 110.600 52.800 + 27 H2 H1 E 26 20 18 1.105 106.200 -171.000 + 28 O2 OS B 26 20 18 1.415 113.900 66.100 + 29 EP+2 EP E 28 26 20 0.700 109.500 166.300 + 30 EP-2 EP E 28 26 20 0.700 109.500 -73.700 + 31 O4 OS M 18 9 6 1.430 107.900 -174.000 + 32 EP+4 EP E 31 18 9 0.700 109.500 -4.900 + 33 EP-4 EP E 31 18 9 0.700 109.500 115.100 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZGA_2,3-_os_A-D-GLUCOPYRANO-_cs__branched_res_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZGA_2,3-_os_A-D-GLUCOPYRANO-_cs__branched_res_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag new file mode 100644 index 000000000..dc9138586 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZGA_2,3-_os_A-D-GLUCOPYRANO-_cs__branched_res_ESP_hf_s_6-31G_x__RESP_010_ENS_AVG_and_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -169.200 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 C4 CG 3 11 6 4 1.519 110.600 -53.300 + 14 H4 H1 E 13 11 6 1.100 109.600 -68.100 + 15 O4 OH 3 13 11 6 1.430 109.600 171.400 + 16 H4O HO E 15 13 11 0.958 109.200 59.600 + 17 EP+4 EP E 15 13 11 0.700 109.500 179.600 + 18 EP-4 EP E 15 13 11 0.700 109.500 -59.600 + 19 C5 CG 3 13 11 6 1.528 110.100 52.800 + 20 H5 H1 E 19 13 11 1.105 108.800 65.600 + 21 O5 OS B 19 13 11 1.435 110.800 -54.400 + 22 EP+5 EP E 21 19 13 0.700 109.500 178.300 + 23 EP-5 EP E 21 19 13 0.700 109.500 -63.800 + 24 C6 CG 3 19 13 11 1.517 113.300 -174.200 + 25 H61 H1 E 24 19 13 1.092 108.300 -55.800 + 26 H62 H1 E 24 19 13 1.093 108.800 63.200 + 27 O6 OH 3 24 19 13 1.413 112.700 -172.600 + 28 H6O HO E 27 24 19 0.955 108.100 -87.200 + 29 EP+6 EP E 27 24 19 0.700 109.500 42.800 + 30 EP-6 EP E 27 24 19 0.700 109.500 162.800 + 31 O3 OS M 11 6 4 1.421 109.900 -173.300 + 32 EP+3 EP E 31 11 6 0.700 109.500 -21.400 + 33 EP-3 EP E 31 11 6 0.700 109.500 98.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZGB_2,3-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZGB_2,3-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag new file mode 100644 index 000000000..46c1edda7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZGB_2,3-_os_B-D-GLUCOPYRANO-_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPS.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 60.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 O4 OH 3 18 9 6 1.430 107.900 -174.000 + 21 H4O HO E 20 18 9 0.958 109.200 -139.600 + 22 EP+4 EP E 20 18 9 0.700 109.500 -19.600 + 23 EP-4 EP E 20 18 9 0.700 109.500 100.400 + 24 C3 CG M 18 9 6 1.519 110.100 -54.400 + 25 H3 H1 E 24 18 9 1.101 108.400 -66.700 + 26 C2 CG B 24 18 9 1.529 110.600 52.800 + 27 H2 H1 E 26 24 18 1.105 104.400 63.400 + 28 O2 OS B 26 24 18 1.415 109.500 -174.500 + 29 EP+2 EP E 28 26 24 0.700 109.500 -29.400 + 30 EP-2 EP E 28 26 24 0.700 109.500 90.600 + 31 O3 OS M 24 18 9 1.421 108.700 173.500 + 32 EP+3 EP E 31 24 18 0.700 109.500 171.300 + 33 EP-3 EP E 31 24 18 0.700 109.500 -68.700 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZLA_2,3-_os_A-D-GALACTO-_cs_branched_res.,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZLA_2,3-_os_A-D-GALACTO-_cs_branched_res.,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..da533ad1e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZLA_2,3-_os_A-D-GALACTO-_cs_branched_res.,_hf_s_6-31g_x__RESP0.010__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 171.500 + 8 O2 OS B 6 4 3 1.415 110.000 52.100 + 9 EP+2 EP E 8 6 4 0.700 109.500 43.300 + 10 EP-2 EP E 8 6 4 0.700 109.500 163.300 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 C4 CG 3 11 6 4 1.519 110.600 -53.300 + 14 H4 H1 E 13 11 6 1.100 109.600 173.600 + 15 O4 OH 3 13 11 6 1.430 109.600 -63.800 + 16 H4O HO E 15 13 11 0.958 109.200 59.600 + 17 EP+4 EP E 15 13 11 0.700 109.500 179.600 + 18 EP-4 EP E 15 13 11 0.700 109.500 -59.600 + 19 C5 CG 3 13 11 6 1.528 110.100 52.800 + 20 H5 H1 E 19 13 11 1.105 108.800 65.600 + 21 O5 OS B 19 13 11 1.435 110.800 -54.400 + 22 EP+5 EP E 21 19 13 0.700 109.500 178.300 + 23 EP-5 EP E 21 19 13 0.700 109.500 -63.800 + 24 C6 CG 3 19 13 11 1.517 113.300 -174.200 + 25 H61 H1 E 24 19 13 1.092 108.300 -55.800 + 26 H62 H1 E 24 19 13 1.093 108.800 63.200 + 27 O6 OH 3 24 19 13 1.413 112.700 -172.600 + 28 H6O HO E 27 24 19 0.955 108.100 -87.200 + 29 EP+6 EP E 27 24 19 0.700 109.500 42.800 + 30 EP-6 EP E 27 24 19 0.700 109.500 162.800 + 31 O3 OS M 11 6 4 1.421 109.900 -173.300 + 32 EP+3 EP E 31 11 6 0.700 109.500 -21.400 + 33 EP-3 EP E 31 11 6 0.700 109.500 98.600 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZLB_2,3-_os_B-D-GALACTO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZLB_2,3-_os_B-D-GALACTO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..4326a334b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZLB_2,3-_os_B-D-GALACTO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 -178.000 + 13 H62 H1 E 11 9 6 1.093 108.800 -59.000 + 14 O6 OH 3 11 9 6 1.413 112.700 65.200 + 15 H6O HO E 14 11 9 0.955 108.100 -58.100 + 16 EP+6 EP E 14 11 9 0.700 109.500 178.100 + 17 EP-6 EP E 14 11 9 0.700 109.500 61.900 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 107.500 -173.800 + 20 O4 OH 3 18 9 6 1.430 111.700 67.600 + 21 H4O HO E 20 18 9 0.958 109.200 -21.800 + 22 EP+4 EP E 20 18 9 0.700 109.500 -141.800 + 23 EP-4 EP E 20 18 9 0.700 109.500 98.200 + 24 C3 CG M 18 9 6 1.519 110.100 -54.400 + 25 H3 H1 E 24 18 9 1.101 108.400 -66.700 + 26 C2 CG B 24 18 9 1.529 110.600 52.800 + 27 H2 H1 E 26 24 18 1.105 104.400 63.400 + 28 O2 OS B 26 24 18 1.415 109.500 -174.500 + 29 EP+2 EP E 28 26 24 0.700 109.500 -29.400 + 30 EP-2 EP E 28 26 24 0.700 109.500 90.600 + 31 O3 OS M 24 18 9 1.421 108.700 173.500 + 32 EP+3 EP E 31 24 18 0.700 109.500 171.300 + 33 EP-3 EP E 31 24 18 0.700 109.500 -68.700 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZMA_2,3-_os_A-D-MANNO-_cs__branched_res.,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZMA_2,3-_os_A-D-MANNO-_cs__branched_res.,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..92242fb96 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZMA_2,3-_os_A-D-MANNO-_cs__branched_res.,_hf_s_6-31g_x__RESP_010_ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.900 -40.000 + 5 H1 H2 E 4 3 2 1.102 110.700 -56.200 + 6 C2 CG M 4 3 2 1.524 107.400 -177.700 + 7 H2 H1 E 6 4 3 1.105 108.800 52.100 + 8 O2 OS B 6 4 3 1.415 106.300 171.500 + 9 EP+2 EP E 8 6 4 0.700 109.500 47.900 + 10 EP-2 EP E 8 6 4 0.700 109.500 -72.100 + 11 C3 CG M 6 4 3 1.529 110.300 -67.600 + 12 H3 H1 E 11 6 4 1.101 109.000 65.800 + 13 C4 CG 3 11 6 4 1.519 110.600 -53.300 + 14 H4 H1 E 13 11 6 1.100 109.600 -68.100 + 15 O4 OH 3 13 11 6 1.430 109.600 171.400 + 16 H4O HO E 15 13 11 0.958 109.200 115.200 + 17 EP+4 EP E 15 13 11 0.700 109.500 -124.800 + 18 EP-4 EP E 15 13 11 0.700 109.500 -4.800 + 19 C5 CG 3 13 11 6 1.528 110.100 52.800 + 20 H5 H1 E 19 13 11 1.105 108.800 65.600 + 21 O5 OS B 19 13 11 1.435 110.800 -54.400 + 22 EP+5 EP E 21 19 13 0.700 109.500 -174.400 + 23 EP-5 EP E 21 19 13 0.700 109.500 -65.600 + 24 C6 CG 3 19 13 11 1.517 113.300 -174.200 + 25 H61 H1 E 24 19 13 1.092 108.300 57.100 + 26 H62 H1 E 24 19 13 1.093 108.800 -54.900 + 27 O6 OH 3 24 19 13 1.413 112.700 178.900 + 28 H6O HO E 27 24 19 0.955 108.100 96.000 + 29 EP+6 EP E 27 24 19 0.700 109.500 -24.000 + 30 EP-6 EP E 27 24 19 0.700 109.500 -144.000 + 31 O3 OS M 11 6 4 1.421 109.900 -173.300 + 32 EP+3 EP E 31 11 6 0.700 109.500 49.900 + 33 EP-3 EP E 31 11 6 0.700 109.500 169.900 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZMB_2,3-_os_B-D-MANNO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZMB_2,3-_os_B-D-MANNO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag new file mode 100644 index 000000000..fe74870d2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/ZMB_2,3-_os_B-D-MANNO_cs__non-terminal__RESP010_ESP_hf_s_6-31G_x__ENS_AVG_EPs.in_frag @@ -0,0 +1,33 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.522 0.000 0.000 + 3 DUMM DU M 2 1 0 1.422 109.500 0.000 + 4 C1 CG M 3 2 1 1.400 113.300 180.000 + 5 H1 H2 E 4 3 2 1.102 111.600 56.200 + 6 O5 OS 3 4 3 2 1.412 112.900 -68.700 + 7 EP+5 EP E 6 4 3 0.700 109.500 -59.700 + 8 EP-5 EP E 6 4 3 0.700 109.500 60.300 + 9 C5 CG M 6 4 3 1.435 114.300 -179.700 + 10 H5 H1 E 9 6 4 1.105 109.100 -60.700 + 11 C6 CG 3 9 6 4 1.517 106.600 -177.200 + 12 H61 H1 E 11 9 6 1.092 108.300 179.300 + 13 H62 H1 E 11 9 6 1.093 108.800 62.900 + 14 O6 OH 3 11 9 6 1.413 112.700 -65.100 + 15 H6O HO E 14 11 9 0.955 108.100 -96.000 + 16 EP+6 EP E 14 11 9 0.700 109.500 24.000 + 17 EP-6 EP E 14 11 9 0.700 109.500 144.000 + 18 C4 CG M 9 6 4 1.528 110.800 59.100 + 19 H4 H1 E 18 9 6 1.100 109.800 66.400 + 20 O4 OH 3 18 9 6 1.430 107.900 -174.000 + 21 H4O HO E 20 18 9 0.958 109.200 -124.900 + 22 EP+4 EP E 20 18 9 0.700 109.500 -4.900 + 23 EP-4 EP E 20 18 9 0.700 109.500 115.100 + 24 C3 CG M 18 9 6 1.519 110.100 -54.400 + 25 H3 H1 E 24 18 9 1.101 108.400 -66.700 + 26 C2 CG B 24 18 9 1.529 110.600 52.800 + 27 H2 H1 E 26 24 18 1.105 106.200 -171.000 + 28 O2 OS B 26 24 18 1.415 113.900 66.100 + 29 EP+2 EP E 28 26 24 0.700 109.500 166.300 + 30 EP-2 EP E 28 26 24 0.700 109.500 -73.700 + 31 O3 OS M 24 18 9 1.421 108.700 173.500 + 32 EP+3 EP E 31 24 18 0.700 109.500 48.700 + 33 EP-3 EP E 31 24 18 0.700 109.500 -71.300 diff --git a/cad/tests/AMBER_test_structures/dot_in/glycam04EP/glycam04EP.in b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/glycam04EP.in new file mode 100644 index 000000000..9a17ce1bd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/glycam04EP/glycam04EP.in @@ -0,0 +1,4149 @@ + 0 0 2 +Carbohydrate_04EP.dat +2,3,4,6-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +2346ga.dat +PGA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.134 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.134 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.110 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OS B 11 6 4 1.421 109.9 -173.3 0.000 +14 EP+3 EP E 13 11 6 0.700 109.5 -21.4 -0.132 +15 EP-3 EP E 13 11 6 0.700 109.5 98.6 -0.132 +16 C4 CG M 11 6 4 1.519 110.6 -53.3 0.147 +17 H4 H1 E 16 11 6 1.100 109.6 -68.1 0.000 +18 O4 OS B 16 11 6 1.430 109.6 171.4 0.000 +19 EP+4 EP E 18 16 11 0.700 109.5 179.6 -0.132 +20 EP-4 EP E 18 16 11 0.700 109.5 -59.6 -0.132 +21 C5 CG M 16 11 6 1.528 110.1 52.8 0.227 +22 H5 H1 E 21 16 11 1.105 108.8 65.6 0.000 +23 O5 OS B 21 16 11 1.435 110.8 -54.4 0.000 +24 EP+5 EP E 23 22 16 0.700 109.5 178.3 -0.183 +25 EP-5 EP E 22 23 16 0.700 109.5 -63.8 -0.183 +26 C6 CG M 22 16 11 1.517 113.3 -174.2 0.139 +27 H61 H1 E 26 22 16 1.092 108.3 -55.8 0.000 +28 H62 H1 E 26 22 16 1.093 108.8 63.2 0.000 +29 O6 OS M 26 22 16 1.413 112.7 -172.6 0.000 +30 EP+6 EP E 29 26 22 0.700 109.5 42.8 -0.131 +31 EP-6 EP E 29 26 22 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +2,3,4,6-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +2346la.dat +PLA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.139 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.139 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OS B 11 6 4 1.421 109.9 -173.3 0.000 +14 EP+3 EP E 13 11 6 0.700 109.5 -21.4 -0.134 +15 EP-3 EP E 13 11 6 0.700 109.5 98.6 -0.134 +16 C4 CG M 11 6 4 1.519 110.6 -53.3 0.099 +17 H4 H1 E 16 11 6 1.100 109.6 173.6 0.000 +18 O4 OS B 16 11 6 1.430 109.6 -63.8 0.000 +19 EP+4 EP E 18 16 11 0.700 109.5 179.6 -0.118 +20 EP-4 EP E 18 16 11 0.700 109.5 -59.6 -0.118 +21 C5 CG M 16 11 6 1.528 110.1 52.8 0.172 +22 H5 H1 E 22 16 11 1.105 108.8 65.6 0.000 +23 O5 OS B 22 16 11 1.435 110.8 -54.4 0.000 +24 EP+5 EP E 24 22 16 0.700 109.5 178.3 -0.169 +25 EP-5 EP E 24 22 16 0.700 109.5 -63.8 -0.169 +26 C6 CG M 22 16 11 1.517 113.3 -174.2 0.162 +27 H61 H1 E 27 22 16 1.092 108.3 -55.8 0.000 +28 H62 H1 E 27 22 16 1.093 108.8 63.2 0.000 +29 O6 OS M 27 22 16 1.413 112.7 -172.6 0.000 +30 EP+6 EP E 30 27 22 0.700 109.5 42.8 -0.131 +31 EP-6 EP E 30 27 22 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +2,3,4,6-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +2346ma.dat +PMA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OS B 6 4 3 1.415 106.3 171.5 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.127 +10 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.127 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OS B 11 6 4 1.421 109.9 -173.3 0.000 +14 EP+3 EP E 13 11 6 0.700 109.5 49.9 -0.134 +15 EP-3 EP E 13 11 6 0.700 109.5 169.9 -0.134 +16 C4 CG M 11 6 4 1.519 110.6 -53.3 0.183 +17 H4 H1 E 16 11 6 1.100 109.6 -68.1 0.000 +18 O4 OS B 16 11 6 1.430 109.6 171.4 0.000 +19 EP+4 EP E 18 16 11 0.700 109.5 -124.8 -0.139 +20 EP-4 EP E 18 16 11 0.700 109.5 -4.8 -0.139 +21 C5 CG M 16 11 6 1.528 110.1 52.8 0.228 +22 H5 H1 E 21 16 11 1.105 108.8 65.6 0.000 +23 O5 OS B 21 16 11 1.435 110.8 -54.4 0.000 +24 EP+5 EP E 23 21 16 0.700 109.5 -174.4 -0.167 +25 EP-5 EP E 23 21 16 0.700 109.5 -65.6 -0.167 +26 C6 CG M 21 16 11 1.517 113.3 -174.2 0.132 +27 H61 H1 E 26 21 16 1.092 108.3 57.1 0.000 +28 H62 H1 E 26 21 16 1.093 108.8 -54.9 0.000 +29 O6 OS M 26 21 16 1.413 112.7 178.9 0.000 +30 EP+6 EP E 29 26 21 0.700 109.5 -24.0 -0.131 +31 EP-6 EP E 29 26 21 0.700 109.5 -144.0 -0.131 + +LOOP +O5 C1 + +DONE +2,3,4-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +234ga.dat +TGA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.134 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.134 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.110 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OS B 11 6 4 1.421 109.9 -173.3 0.000 +14 EP+3 EP E 13 11 6 0.700 109.5 -21.4 -0.132 +15 EP-3 EP E 13 11 6 0.700 109.5 98.6 -0.132 +16 C4 CG M 11 6 4 1.519 110.6 -53.3 0.147 +17 H4 H1 E 16 11 6 1.100 109.6 -68.1 0.000 +18 C5 CG 3 16 11 6 1.528 110.1 52.8 0.227 +19 H5 H1 E 18 16 11 1.105 108.8 65.6 0.000 +20 O5 OS B 18 16 11 1.435 110.8 -54.4 0.000 +21 EP+5 EP E 20 18 16 0.700 109.5 178.3 -0.183 +22 EP-5 EP E 20 18 16 0.700 109.5 -63.8 -0.183 +23 C6 CG 3 18 16 11 1.517 113.3 -174.2 0.138 +24 H61 H1 E 23 18 16 1.092 108.3 -55.8 0.000 +25 H62 H1 E 23 18 16 1.093 108.8 63.2 0.000 +26 O6 OH 3 23 18 16 1.413 112.7 -172.6 0.000 +27 H6O HO E 26 23 18 0.955 108.1 -87.2 0.272 +28 EP+6 EP E 26 23 18 0.700 109.5 42.8 -0.210 +29 EP-6 EP E 26 23 18 0.700 109.5 162.8 -0.210 +30 O4 OS M 16 11 6 1.430 109.6 171.4 0.000 +31 EP+4 EP E 30 16 11 0.700 109.5 179.6 -0.132 +32 EP-4 EP E 30 16 11 0.700 109.5 -59.6 -0.132 + +LOOP +O5 C1 + +DONE +2,3,4-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +234la.dat +TLA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.139 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.139 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OS B 11 6 4 1.421 109.9 -173.3 0.000 +14 EP+3 EP E 13 11 6 0.700 109.5 -21.4 -0.134 +15 EP-3 EP E 13 11 6 0.700 109.5 98.6 -0.134 +16 C4 CG M 11 6 4 1.519 110.6 -53.3 0.099 +17 H4 H1 E 16 11 6 1.100 109.6 173.6 0.000 +18 C5 CG 3 16 11 6 1.528 110.1 52.8 0.172 +19 H5 H1 E 18 16 11 1.105 108.8 65.6 0.000 +20 O5 OS B 18 16 11 1.435 110.8 -54.4 0.000 +21 EP+5 EP E 20 18 16 0.700 109.5 178.3 -0.169 +22 EP-5 EP E 20 18 16 0.700 109.5 -63.8 -0.169 +23 C6 CG 3 18 16 11 1.517 113.3 -174.2 0.161 +24 H61 H1 E 23 18 16 1.092 108.3 -55.8 0.000 +25 H62 H1 E 23 18 16 1.093 108.8 63.2 0.000 +26 O6 OH 3 23 18 16 1.413 112.7 -172.6 0.000 +27 H6O HO E 26 23 18 0.955 108.1 -87.2 0.272 +28 EP+6 EP E 26 23 18 0.700 109.5 42.8 -0.210 +29 EP-6 EP E 26 23 18 0.700 109.5 162.8 -0.210 +30 O4 OS M 16 11 6 1.430 109.6 -63.8 0.000 +31 EP+4 EP E 30 16 11 0.700 109.5 179.6 -0.118 +32 EP-4 EP E 30 16 11 0.700 109.5 -59.6 -0.118 + +LOOP +O5 C1 + +DONE +2,3,4-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +234ma.dat +TMA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OS B 6 4 3 1.415 106.3 171.5 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.127 +10 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.127 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OS B 11 6 4 1.421 109.9 -173.3 0.000 +14 EP+3 EP E 13 11 6 0.700 109.5 49.9 -0.134 +15 EP-3 EP E 13 11 6 0.700 109.5 169.9 -0.134 +16 C4 CG M 11 6 4 1.519 110.6 -53.3 0.183 +17 H4 H1 E 16 11 6 1.100 109.6 -68.1 0.000 +18 C5 CG 3 16 11 6 1.528 110.1 52.8 0.228 +19 H5 H1 E 18 16 11 1.105 108.8 65.6 0.000 +20 O5 OS B 18 16 11 1.435 110.8 -54.4 0.000 +21 EP+5 EP E 20 18 16 0.700 109.5 -174.4 -0.167 +22 EP-5 EP E 20 18 16 0.700 109.5 -65.6 -0.167 +23 C6 CG 3 18 16 11 1.517 113.3 -174.2 0.131 +24 H61 H1 E 23 18 16 1.092 108.3 57.1 0.000 +25 H62 H1 E 23 18 16 1.093 108.8 -54.9 0.000 +26 O6 OH 3 23 18 16 1.413 112.7 178.9 0.000 +27 H6O HO E 26 23 18 0.955 108.1 96.0 0.274 +28 EP+6 EP E 26 23 18 0.700 109.5 -24.0 -0.211 +29 EP-6 EP E 26 23 18 0.700 109.5 -144.0 -0.211 +30 O4 OS M 16 11 6 1.430 109.6 171.4 0.000 +31 EP+4 EP E 30 16 11 0.700 109.5 -124.8 -0.139 +32 EP-4 EP E 30 16 11 0.700 109.5 -4.8 -0.139 + +LOOP +O5 C1 + +DONE +2,3,6-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +236ga.dat +SGA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.134 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.134 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.110 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OS B 11 6 4 1.421 109.9 -173.3 0.000 +14 EP+3 EP E 13 11 6 0.700 109.5 -21.4 -0.132 +15 EP-3 EP E 13 11 6 0.700 109.5 98.6 -0.132 +16 C4 CG M 11 6 4 1.519 110.6 -53.3 0.146 +17 H4 H1 E 16 11 6 1.100 109.6 -68.1 0.000 +18 O4 OH 3 16 11 6 1.430 109.6 171.4 0.000 +19 H4O HO E 18 16 11 0.958 109.2 59.6 0.278 +20 EP+4 EP E 18 16 11 0.700 109.5 179.6 -0.214 +21 EP-4 EP E 18 16 11 0.700 109.5 -59.6 -0.214 +22 C5 CG M 16 11 6 1.528 110.1 52.8 0.227 +23 H5 H1 E 22 16 11 1.105 108.8 65.6 0.000 +24 O5 OS B 22 16 11 1.435 110.8 -54.4 0.000 +25 EP+5 EP E 24 23 16 0.700 109.5 178.3 -0.183 +26 EP-5 EP E 24 23 16 0.700 109.5 -63.8 -0.183 +27 C6 CG M 23 16 11 1.517 113.3 -174.2 0.139 +28 H61 H1 E 27 23 16 1.092 108.3 -55.8 0.000 +29 H62 H1 E 27 23 16 1.093 108.8 63.2 0.000 +30 O6 OS M 27 23 16 1.413 112.7 -172.6 0.000 +31 EP+6 EP E 30 27 23 0.700 109.5 42.8 -0.131 +32 EP-6 EP E 30 27 23 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +2,3,6-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +236la.dat +SLA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.139 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.139 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OS B 11 6 4 1.421 109.9 -173.3 0.000 +14 EP+3 EP E 13 11 6 0.700 109.5 -21.4 -0.134 +15 EP-3 EP E 13 11 6 0.700 109.5 98.6 -0.134 +16 C4 CG M 11 6 4 1.519 110.6 -53.3 0.099 +17 H4 H1 E 16 11 6 1.100 109.6 173.6 0.000 +18 O4 OH 3 16 11 6 1.430 109.6 -63.8 0.000 +19 H4O HO E 18 16 11 0.958 109.2 59.6 0.287 +20 EP+4 EP E 18 16 11 0.700 109.5 179.6 -0.205 +21 EP-4 EP E 18 16 11 0.700 109.5 -59.6 -0.205 +22 C5 CG M 16 11 6 1.528 110.1 52.8 0.172 +23 H5 H1 E 22 16 11 1.105 108.8 65.6 0.000 +24 O5 OS B 22 16 11 1.435 110.8 -54.4 0.000 +25 EP+5 EP E 24 22 16 0.700 109.5 178.3 -0.169 +26 EP-5 EP E 24 22 16 0.700 109.5 -63.8 -0.169 +27 C6 CG M 22 16 11 1.517 113.3 -174.2 0.162 +28 H61 H1 E 27 22 16 1.092 108.3 -55.8 0.000 +29 H62 H1 E 27 22 16 1.093 108.8 63.2 0.000 +30 O6 OS M 27 22 16 1.413 112.7 -172.6 0.000 +31 EP+6 EP E 30 27 22 0.700 109.5 42.8 -0.131 +32 EP-6 EP E 30 27 22 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +2,3,6-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +236ma.dat +SMA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OS B 6 4 3 1.415 106.3 171.5 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.127 +10 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.127 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OS B 11 6 4 1.421 109.9 -173.3 0.000 +14 EP+3 EP E 13 11 6 0.700 109.5 49.9 -0.134 +15 EP-3 EP E 13 11 6 0.700 109.5 169.9 -0.134 +16 C4 CG M 11 6 4 1.519 110.6 -53.3 0.182 +17 H4 H1 E 16 11 6 1.100 109.6 -68.1 0.000 +18 O4 OH 3 16 11 6 1.430 109.6 171.4 0.000 +19 H4O HO E 18 16 11 0.958 109.2 115.2 0.276 +20 EP+4 EP E 18 16 11 0.700 109.5 -124.8 -0.220 +21 EP-4 EP E 18 16 11 0.700 109.5 -4.8 -0.220 +22 C5 CG M 16 11 6 1.528 110.1 52.8 0.228 +23 H5 H1 E 22 16 11 1.105 108.8 65.6 0.000 +24 O5 OS B 22 16 11 1.435 110.8 -54.4 0.000 +25 EP+5 EP E 24 22 16 0.700 109.5 -174.4 -0.167 +26 EP-5 EP E 24 22 16 0.700 109.5 -65.6 -0.167 +27 C6 CG M 22 16 11 1.517 113.3 -174.2 0.132 +28 H61 H1 E 27 22 16 1.092 108.3 57.1 0.000 +29 H62 H1 E 27 22 16 1.093 108.8 -54.9 0.000 +30 O6 OS M 27 22 16 1.413 112.7 178.9 0.000 +31 EP+6 EP E 30 27 22 0.700 109.5 -24.0 -0.131 +32 EP-6 EP E 30 27 22 0.700 109.5 -144.0 -0.131 + +LOOP +O5 C1 + +DONE +2,3-[A-D-GLUCOPYRANO-] branched res ESP hf/6-31G* RESP 010 ENS AVG and EPs +23ga.dat +ZGA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.134 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.134 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.110 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 C4 CG 3 11 6 4 1.519 110.6 -53.3 0.146 +14 H4 H1 E 13 11 6 1.100 109.6 -68.1 0.000 +15 O4 OH 3 13 11 6 1.430 109.6 171.4 0.000 +16 H4O HO E 15 13 11 0.958 109.2 59.6 0.278 +17 EP+4 EP E 15 13 11 0.700 109.5 179.6 -0.214 +18 EP-4 EP E 15 13 11 0.700 109.5 -59.6 -0.214 +19 C5 CG 3 13 11 6 1.528 110.1 52.8 0.227 +20 H5 H1 E 19 13 11 1.105 108.8 65.6 0.000 +21 O5 OS B 19 13 11 1.435 110.8 -54.4 0.000 +22 EP+5 EP E 21 19 13 0.700 109.5 178.3 -0.183 +23 EP-5 EP E 21 19 13 0.700 109.5 -63.8 -0.183 +24 C6 CG 3 19 13 11 1.517 113.3 -174.2 0.138 +25 H61 H1 E 24 19 13 1.092 108.3 -55.8 0.000 +26 H62 H1 E 24 19 13 1.093 108.8 63.2 0.000 +27 O6 OH 3 24 19 13 1.413 112.7 -172.6 0.000 +28 H6O HO E 27 24 19 0.955 108.1 -87.2 0.272 +29 EP+6 EP E 27 24 19 0.700 109.5 42.8 -0.210 +30 EP-6 EP E 27 24 19 0.700 109.5 162.8 -0.210 +31 O3 OS M 11 6 4 1.421 109.9 -173.3 0.000 +32 EP+3 EP E 31 11 6 0.700 109.5 -21.4 -0.132 +33 EP-3 EP E 31 11 6 0.700 109.5 98.6 -0.132 + +LOOP +O5 C1 + +DONE +2,3-[A-D-GALACTO-]branched res., hf/6-31g* RESP0.010 ENS AVG EPs +23la.dat +ZLA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.139 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.139 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 C4 CG 3 11 6 4 1.519 110.6 -53.3 0.099 +14 H4 H1 E 13 11 6 1.100 109.6 173.6 0.000 +15 O4 OH 3 13 11 6 1.430 109.6 -63.8 0.000 +16 H4O HO E 15 13 11 0.958 109.2 59.6 0.287 +17 EP+4 EP E 15 13 11 0.700 109.5 179.6 -0.205 +18 EP-4 EP E 15 13 11 0.700 109.5 -59.6 -0.205 +19 C5 CG 3 13 11 6 1.528 110.1 52.8 0.172 +20 H5 H1 E 19 13 11 1.105 108.8 65.6 0.000 +21 O5 OS B 19 13 11 1.435 110.8 -54.4 0.000 +22 EP+5 EP E 21 19 13 0.700 109.5 178.3 -0.169 +23 EP-5 EP E 21 19 13 0.700 109.5 -63.8 -0.169 +24 C6 CG 3 19 13 11 1.517 113.3 -174.2 0.161 +25 H61 H1 E 24 19 13 1.092 108.3 -55.8 0.000 +26 H62 H1 E 24 19 13 1.093 108.8 63.2 0.000 +27 O6 OH 3 24 19 13 1.413 112.7 -172.6 0.000 +28 H6O HO E 27 24 19 0.955 108.1 -87.2 0.272 +29 EP+6 EP E 27 24 19 0.700 109.5 42.8 -0.210 +30 EP-6 EP E 27 24 19 0.700 109.5 162.8 -0.210 +31 O3 OS M 11 6 4 1.421 109.9 -173.3 0.000 +32 EP+3 EP E 31 11 6 0.700 109.5 -21.4 -0.134 +33 EP-3 EP E 31 11 6 0.700 109.5 98.6 -0.134 + +LOOP +O5 C1 + +DONE +2,3-[A-D-MANNO-] branched res., hf/6-31g* RESP 010 ENS AVG EPs +23ma.dat +ZMA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OS B 6 4 3 1.415 106.3 171.5 0.000 +10 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.127 +11 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.127 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +13 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +14 C4 CG 3 11 6 4 1.519 110.6 -53.3 0.182 +15 H4 H1 E 13 11 6 1.100 109.6 -68.1 0.000 +16 O4 OH 3 13 11 6 1.430 109.6 171.4 0.000 +17 H4O HO E 15 13 11 0.958 109.2 115.2 0.276 +18 EP+4 EP E 15 13 11 0.700 109.5 -124.8 -0.220 +19 EP-4 EP E 15 13 11 0.700 109.5 -4.8 -0.220 +20 C5 CG 3 13 11 6 1.528 110.1 52.8 0.228 +21 H5 H1 E 19 13 11 1.105 108.8 65.6 0.000 +22 O5 OS B 19 13 11 1.435 110.8 -54.4 0.000 +23 EP+5 EP E 21 19 13 0.700 109.5 -174.4 -0.167 +24 EP-5 EP E 21 19 13 0.700 109.5 -65.6 -0.167 +25 C6 CG 3 19 13 11 1.517 113.3 -174.2 0.131 +26 H61 H1 E 24 19 13 1.092 108.3 57.1 0.000 +27 H62 H1 E 24 19 13 1.093 108.8 -54.9 0.000 +28 O6 OH 3 24 19 13 1.413 112.7 178.9 0.000 +29 H6O HO E 27 24 19 0.955 108.1 96.0 0.274 +30 EP+6 EP E 27 24 19 0.700 109.5 -24.0 -0.211 +31 EP-6 EP E 27 24 19 0.700 109.5 -144.0 -0.211 +32 O3 OS M 11 6 4 1.421 109.9 -173.3 0.000 +33 EP+3 EP E 31 11 6 0.700 109.5 49.9 -0.134 +34 EP-3 EP E 31 11 6 0.700 109.5 169.9 -0.134 + +LOOP +O5 C1 + +DONE +2,4,6-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +246ga.dat +RGA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.134 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.134 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.109 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OH 3 11 6 4 1.421 109.9 -173.3 0.000 +14 H3O HO E 13 11 6 0.976 108.5 -141.4 0.280 +15 EP+3 EP E 13 11 6 0.700 109.5 -21.4 -0.215 +16 EP-3 EP E 13 11 6 0.700 109.5 98.6 -0.215 +17 C4 CG M 11 6 4 1.519 110.6 -53.3 0.147 +18 H4 H1 E 17 11 6 1.100 109.6 -68.1 0.000 +19 O4 OS B 17 11 6 1.430 109.6 171.4 0.000 +20 EP+4 EP E 19 17 11 0.700 109.5 179.6 -0.132 +21 EP-4 EP E 19 17 11 0.700 109.5 -59.6 -0.132 +22 C5 CG M 17 11 6 1.528 110.1 52.8 0.227 +23 H5 H1 E 22 17 11 1.105 108.8 65.6 0.000 +24 O5 OS B 22 17 11 1.435 110.8 -54.4 0.000 +25 EP+5 EP E 24 22 17 0.700 109.5 178.3 -0.183 +26 EP-5 EP E 24 22 17 0.700 109.5 -63.8 -0.183 +27 C6 CG M 22 17 11 1.517 113.3 -174.2 0.139 +28 H61 H1 E 27 22 17 1.092 108.3 -55.8 0.000 +29 H62 H1 E 27 22 17 1.093 108.8 63.2 0.000 +30 O6 OS M 27 22 17 1.413 112.7 -172.6 0.000 +31 EP+6 EP E 30 27 22 0.700 109.5 42.8 -0.131 +32 EP-6 EP E 30 27 22 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +2,4,6-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +246la.dat +RLA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.139 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.139 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OH 3 11 6 4 1.421 109.9 -173.3 0.000 +14 H3O HO E 13 11 6 0.976 108.5 -141.4 0.283 +15 EP+3 EP E 13 11 6 0.700 109.5 -21.4 -0.219 +16 EP-3 EP E 13 11 6 0.700 109.5 98.6 -0.219 +17 C4 CG M 11 6 4 1.519 110.6 -53.3 0.099 +18 H4 H1 E 17 11 6 1.100 109.6 173.6 0.000 +19 O4 OS B 17 11 6 1.430 109.6 -63.8 0.000 +20 EP+4 EP E 19 17 11 0.700 109.5 179.6 -0.118 +21 EP-4 EP E 19 17 11 0.700 109.5 -59.6 -0.118 +22 C5 CG M 17 11 6 1.528 110.1 52.8 0.172 +23 H5 H1 E 23 17 11 1.105 108.8 65.6 0.000 +24 O5 OS B 23 17 11 1.435 110.8 -54.4 0.000 +25 EP+5 EP E 25 23 17 0.700 109.5 178.3 -0.169 +26 EP-5 EP E 25 23 17 0.700 109.5 -63.8 -0.169 +27 C6 CG M 23 17 11 1.517 113.3 -174.2 0.162 +28 H61 H1 E 28 23 17 1.092 108.3 -55.8 0.000 +29 H62 H1 E 28 23 17 1.093 108.8 63.2 0.000 +30 O6 OS M 28 23 17 1.413 112.7 -172.6 0.000 +31 EP+6 EP E 31 28 23 0.700 109.5 42.8 -0.131 +32 EP-6 EP E 31 28 23 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +2,4,6-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +246ma.dat +RMA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OS B 6 4 3 1.415 106.3 171.5 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.127 +10 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.127 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OH 3 11 6 4 1.421 109.9 -173.3 0.000 +14 H3O HO E 13 11 6 0.976 108.5 -70.1 0.279 +15 EP+3 EP E 13 11 6 0.700 109.5 49.9 -0.217 +16 EP-3 EP E 13 11 6 0.700 109.5 169.9 -0.217 +17 C4 CG M 11 6 4 1.519 110.6 -53.3 0.183 +18 H4 H1 E 17 11 6 1.100 109.6 -68.1 0.000 +19 O4 OS B 17 11 6 1.430 109.6 171.4 0.000 +20 EP+4 EP E 19 17 11 0.700 109.5 -124.8 -0.139 +21 EP-4 EP E 19 17 11 0.700 109.5 -4.8 -0.139 +22 C5 CG M 17 11 6 1.528 110.1 52.8 0.228 +23 H5 H1 E 22 17 11 1.105 108.8 65.6 0.000 +24 O5 OS B 22 17 11 1.435 110.8 -54.4 0.000 +25 EP+5 EP E 24 22 17 0.700 109.5 -174.4 -0.167 +26 EP-5 EP E 24 22 17 0.700 109.5 -65.6 -0.167 +27 C6 CG M 22 17 11 1.517 113.3 -174.2 0.132 +28 H61 H1 E 27 22 17 1.092 108.3 57.1 0.000 +29 H62 H1 E 27 22 17 1.093 108.8 -54.9 0.000 +30 O6 OS M 27 22 17 1.413 112.7 178.9 0.000 +31 EP+6 EP E 30 27 22 0.700 109.5 -24.0 -0.131 +32 EP-6 EP E 30 27 22 0.700 109.5 -144.0 -0.131 + +LOOP +O5 C1 + +DONE +2,4-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +24ga.dat +YGA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.134 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.134 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.109 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OH 3 11 6 4 1.421 109.9 -173.3 0.000 +14 H3O HO E 13 11 6 0.976 108.5 -141.4 0.280 +15 EP+3 EP E 13 11 6 0.700 109.5 -21.4 -0.215 +16 EP-3 EP E 13 11 6 0.700 109.5 98.6 -0.215 +17 C4 CG M 11 6 4 1.519 110.6 -53.3 0.147 +18 H4 H1 E 17 11 6 1.100 109.6 -68.1 0.000 +19 C5 CG 3 17 11 6 1.528 110.1 52.8 0.227 +20 H5 H1 E 19 17 11 1.105 108.8 65.6 0.000 +21 O5 OS B 19 17 11 1.435 110.8 -54.4 0.000 +22 EP+5 EP E 21 19 17 0.700 109.5 178.3 -0.183 +23 EP-5 EP E 21 19 17 0.700 109.5 -63.8 -0.183 +24 C6 CG 3 19 17 11 1.517 113.3 -174.2 0.138 +25 H61 H1 E 24 19 17 1.092 108.3 -55.8 0.000 +26 H62 H1 E 24 19 17 1.093 108.8 63.2 0.000 +27 O6 OH 3 24 19 17 1.413 112.7 -172.6 0.000 +28 H6O HO E 27 24 19 0.955 108.1 -87.2 0.272 +29 EP+6 EP E 27 24 19 0.700 109.5 42.8 -0.210 +30 EP-6 EP E 27 24 19 0.700 109.5 162.8 -0.210 +31 O4 OS M 17 11 6 1.430 109.6 171.4 0.000 +32 EP+4 EP E 31 17 11 0.700 109.5 179.6 -0.132 +33 EP-4 EP E 31 17 11 0.700 109.5 -59.6 -0.132 + +LOOP +O5 C1 + +DONE +2,4-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +24la.dat +YLA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.139 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.139 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OH 3 11 6 4 1.421 109.9 -173.3 0.000 +14 H3O HO E 13 11 6 0.976 108.5 -141.4 0.283 +15 EP+3 EP E 13 11 6 0.700 109.5 -21.4 -0.219 +16 EP-3 EP E 13 11 6 0.700 109.5 98.6 -0.219 +17 C4 CG M 11 6 4 1.519 110.6 -53.3 0.099 +18 H4 H1 E 17 11 6 1.100 109.6 173.6 0.000 +19 C5 CG 3 17 11 6 1.528 110.1 52.8 0.172 +20 H5 H1 E 19 17 11 1.105 108.8 65.6 0.000 +21 O5 OS B 19 17 11 1.435 110.8 -54.4 0.000 +22 EP+5 EP E 21 19 17 0.700 109.5 178.3 -0.169 +23 EP-5 EP E 21 19 17 0.700 109.5 -63.8 -0.169 +24 C6 CG 3 19 17 11 1.517 113.3 -174.2 0.161 +25 H61 H1 E 24 19 17 1.092 108.3 -55.8 0.000 +26 H62 H1 E 24 19 17 1.093 108.8 63.2 0.000 +27 O6 OH 3 24 19 17 1.413 112.7 -172.6 0.000 +28 H6O HO E 27 24 19 0.955 108.1 -87.2 0.272 +29 EP+6 EP E 27 24 19 0.700 109.5 42.8 -0.210 +30 EP-6 EP E 27 24 19 0.700 109.5 162.8 -0.210 +31 O4 OS M 17 11 6 1.430 109.6 -63.8 0.000 +32 EP+4 EP E 31 17 11 0.700 109.5 179.6 -0.118 +33 EP-4 EP E 31 17 11 0.700 109.5 -59.6 -0.118 + +LOOP +O5 C1 + +DONE +2,4-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +24ma.dat +YMA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OS B 6 4 3 1.415 106.3 171.5 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.127 +10 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.127 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OH 3 11 6 4 1.421 109.9 -173.3 0.000 +14 H3O HO E 13 11 6 0.976 108.5 -70.1 0.279 +15 EP+3 EP E 13 11 6 0.700 109.5 49.9 -0.217 +16 EP-3 EP E 13 11 6 0.700 109.5 169.9 -0.217 +17 C4 CG M 11 6 4 1.519 110.6 -53.3 0.183 +18 H4 H1 E 17 11 6 1.100 109.6 -68.1 0.000 +19 C5 CG 3 17 11 6 1.528 110.1 52.8 0.228 +20 H5 H1 E 19 17 11 1.105 108.8 65.6 0.000 +21 O5 OS B 19 17 11 1.435 110.8 -54.4 0.000 +22 EP+5 EP E 21 19 17 0.700 109.5 -174.4 -0.167 +23 EP-5 EP E 21 19 17 0.700 109.5 -65.6 -0.167 +24 C6 CG 3 19 17 11 1.517 113.3 -174.2 0.131 +25 H61 H1 E 24 19 17 1.092 108.3 57.1 0.000 +26 H62 H1 E 24 19 17 1.093 108.8 -54.9 0.000 +27 O6 OH 3 24 19 17 1.413 112.7 178.9 0.000 +28 H6O HO E 27 24 19 0.955 108.1 96.0 0.274 +29 EP+6 EP E 27 24 19 0.700 109.5 -24.0 -0.211 +30 EP-6 EP E 27 24 19 0.700 109.5 -144.0 -0.211 +31 O4 OS M 17 11 6 1.430 109.6 171.4 0.000 +32 EP+4 EP E 31 17 11 0.700 109.5 -124.8 -0.139 +33 EP-4 EP E 31 17 11 0.700 109.5 -4.8 -0.139 + +LOOP +O5 C1 + +DONE +2,6-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +26ga.dat +XGA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.134 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.134 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.109 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OH 3 11 6 4 1.421 109.9 -173.3 0.000 +14 H3O HO E 13 11 6 0.976 108.5 -141.4 0.280 +15 EP+3 EP E 13 11 6 0.700 109.5 -21.4 -0.215 +16 EP-3 EP E 13 11 6 0.700 109.5 98.6 -0.215 +17 C4 CG M 11 6 4 1.519 110.6 -53.3 0.146 +18 H4 H1 E 17 11 6 1.100 109.6 -68.1 0.000 +19 O4 OH 3 17 11 6 1.430 109.6 171.4 0.000 +20 H4O HO E 19 17 11 0.958 109.2 59.6 0.278 +21 EP+4 EP E 19 17 11 0.700 109.5 179.6 -0.214 +22 EP-4 EP E 19 17 11 0.700 109.5 -59.6 -0.214 +23 C5 CG M 17 11 6 1.528 110.1 52.8 0.227 +24 H5 H1 E 23 17 11 1.105 108.8 65.6 0.000 +25 O5 OS B 23 17 11 1.435 110.8 -54.4 0.000 +26 EP+5 EP E 25 23 17 0.700 109.5 178.3 -0.183 +27 EP-5 EP E 25 23 17 0.700 109.5 -63.8 -0.183 +28 C6 CG M 23 17 11 1.517 113.3 -174.2 0.139 +29 H61 H1 E 28 23 17 1.092 108.3 -55.8 0.000 +30 H62 H1 E 28 23 17 1.093 108.8 63.2 0.000 +31 O6 OS M 28 23 17 1.413 112.7 -172.6 0.000 +32 EP+6 EP E 31 28 23 0.700 109.5 42.8 -0.131 +33 EP-6 EP E 31 28 23 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +2,6-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +26la.dat +XLA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OS B 6 4 3 1.415 110.0 52.1 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.139 +10 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.139 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OH 3 11 6 4 1.421 109.9 -173.3 0.000 +14 H3O HO E 13 11 6 0.976 108.5 -141.4 0.283 +15 EP+3 EP E 13 11 6 0.700 109.5 -21.4 -0.219 +16 EP-3 EP E 13 11 6 0.700 109.5 98.6 -0.219 +17 C4 CG M 11 6 4 1.519 110.6 -53.3 0.099 +18 H4 H1 E 17 11 6 1.100 109.6 173.6 0.000 +19 O4 OH 3 17 11 6 1.430 109.6 -63.8 0.000 +20 H4O HO E 19 17 11 0.958 109.2 59.6 0.287 +21 EP+4 EP E 19 17 11 0.700 109.5 179.6 -0.205 +22 EP-4 EP E 19 17 11 0.700 109.5 -59.6 -0.205 +23 C5 CG M 17 11 6 1.528 110.1 52.8 0.172 +24 H5 H1 E 23 17 11 1.105 108.8 65.6 0.000 +25 O5 OS B 23 17 11 1.435 110.8 -54.4 0.000 +26 EP+5 EP E 25 23 17 0.700 109.5 178.3 -0.169 +27 EP-5 EP E 25 23 17 0.700 109.5 -63.8 -0.169 +28 C6 CG M 23 17 11 1.517 113.3 -174.2 0.162 +29 H61 H1 E 28 23 17 1.092 108.3 -55.8 0.000 +30 H62 H1 E 28 23 17 1.093 108.8 63.2 0.000 +31 O6 OS M 28 23 17 1.413 112.7 -172.6 0.000 +32 EP+6 EP E 31 28 23 0.700 109.5 42.8 -0.131 +33 EP-6 EP E 31 28 23 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +2,6-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +26ma.dat +XMA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OS B 6 4 3 1.415 106.3 171.5 0.000 + 9 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.127 +10 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.127 +11 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +12 H3 H1 E 11 6 4 1.101 109.0 65.8 0.000 +13 O3 OH 3 11 6 4 1.421 109.9 -173.3 0.000 +14 H3O HO E 13 11 6 0.976 108.5 -70.1 0.279 +15 EP+3 EP E 13 11 6 0.700 109.5 49.9 -0.217 +16 EP-3 EP E 13 11 6 0.700 109.5 169.9 -0.217 +17 C4 CG M 11 6 4 1.519 110.6 -53.3 0.182 +18 H4 H1 E 17 11 6 1.100 109.6 -68.1 0.000 +19 O4 OH 3 17 11 6 1.430 109.6 171.4 0.000 +20 H4O HO E 19 17 11 0.958 109.2 115.2 0.276 +21 EP+4 EP E 19 17 11 0.700 109.5 -124.8 -0.220 +22 EP-4 EP E 19 17 11 0.700 109.5 -4.8 -0.220 +23 C5 CG M 17 11 6 1.528 110.1 52.8 0.228 +24 H5 H1 E 23 17 11 1.105 108.8 65.6 0.000 +25 O5 OS B 23 17 11 1.435 110.8 -54.4 0.000 +26 EP+5 EP E 25 23 17 0.700 109.5 -174.4 -0.167 +27 EP-5 EP E 25 23 17 0.700 109.5 -65.6 -0.167 +28 C6 CG M 23 17 11 1.517 113.3 -174.2 0.132 +29 H61 H1 E 28 23 17 1.092 108.3 57.1 0.000 +30 H62 H1 E 28 23 17 1.093 108.8 -54.9 0.000 +31 O6 OS M 28 23 17 1.413 112.7 178.9 0.000 +32 EP+6 EP E 31 28 23 0.700 109.5 -24.0 -0.131 +33 EP-6 EP E 31 28 23 0.700 109.5 -144.0 -0.131 + +LOOP +O5 C1 + +DONE +2-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +2ga.dat +2GA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 C3 CG 3 6 4 3 1.529 110.3 -67.6 0.109 + 9 H3 H1 E 8 6 4 1.101 109.0 65.8 0.000 +10 O3 OH 3 8 6 4 1.421 109.9 -173.3 0.000 +11 H3O HO E 10 8 6 0.976 108.5 -141.4 0.280 +12 EP+3 EP E 10 8 6 0.700 109.5 -21.4 -0.215 +13 EP-3 EP E 10 8 6 0.700 109.5 98.6 -0.215 +14 C4 CG 3 8 6 4 1.519 110.6 -53.3 0.146 +15 H4 H1 E 14 8 6 1.100 109.6 -68.1 0.000 +16 O4 OH 3 14 8 6 1.430 109.6 171.4 0.000 +17 H4O HO E 16 14 8 0.958 109.2 59.6 0.278 +18 EP+4 EP E 16 14 8 0.700 109.5 179.6 -0.214 +19 EP-4 EP E 16 14 8 0.700 109.5 -59.6 -0.214 +20 C5 CG 3 14 8 6 1.528 110.1 52.8 0.227 +21 H5 H1 E 20 14 8 1.105 108.8 65.6 0.000 +22 O5 OS B 20 14 8 1.435 110.8 -54.4 0.000 +23 EP+5 EP E 22 20 14 0.700 109.5 178.3 -0.183 +24 EP-5 EP E 22 20 14 0.700 109.5 -63.8 -0.183 +25 C6 CG 3 20 14 8 1.517 113.3 -174.2 0.138 +26 H61 H1 E 25 20 14 1.092 108.3 -55.8 0.000 +27 H62 H1 E 25 20 14 1.093 108.8 63.2 0.000 +28 O6 OH 3 25 20 14 1.413 112.7 -172.6 0.000 +29 H6O HO E 28 25 20 0.955 108.1 -87.2 0.272 +30 EP+6 EP E 28 25 20 0.700 109.5 42.8 -0.210 +31 EP-6 EP E 28 25 20 0.700 109.5 162.8 -0.210 +32 O2 OS M 6 4 3 1.415 110.0 52.1 0.000 +33 EP+2 EP E 32 6 4 0.700 109.5 43.3 -0.134 +34 EP-2 EP E 32 6 4 0.700 109.5 163.3 -0.134 + +LOOP +O5 C1 + +DONE +2-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +2la.dat +2LA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 C3 CG 3 6 4 3 1.529 110.3 -67.6 0.118 + 9 H3 H1 E 8 6 4 1.101 109.0 65.8 0.000 +10 O3 OH 3 8 6 4 1.421 109.9 -173.3 0.000 +11 H3O HO E 10 8 6 0.976 108.5 -141.4 0.283 +12 EP+3 EP E 10 8 6 0.700 109.5 -21.4 -0.219 +13 EP-3 EP E 10 8 6 0.700 109.5 98.6 -0.219 +14 C4 CG 3 8 6 4 1.519 110.6 -53.3 0.099 +15 H4 H1 E 14 8 6 1.100 109.6 173.6 0.000 +16 O4 OH 3 14 8 6 1.430 109.6 -63.8 0.000 +17 H4O HO E 16 14 8 0.958 109.2 59.6 0.287 +18 EP+4 EP E 16 14 8 0.700 109.5 179.6 -0.205 +19 EP-4 EP E 16 14 8 0.700 109.5 -59.6 -0.205 +20 C5 CG 3 14 8 6 1.528 110.1 52.8 0.172 +21 H5 H1 E 20 14 8 1.105 108.8 65.6 0.000 +22 O5 OS B 20 14 8 1.435 110.8 -54.4 0.000 +23 EP+5 EP E 22 20 14 0.700 109.5 178.3 -0.169 +24 EP-5 EP E 22 20 14 0.700 109.5 -63.8 -0.169 +25 C6 CG 3 20 14 8 1.517 113.3 -174.2 0.161 +26 H61 H1 E 25 20 14 1.092 108.3 -55.8 0.000 +27 H62 H1 E 25 20 14 1.093 108.8 63.2 0.000 +28 O6 OH 3 25 20 14 1.413 112.7 -172.6 0.000 +29 H6O HO E 28 25 20 0.955 108.1 -87.2 0.272 +30 EP+6 EP E 28 25 20 0.700 109.5 42.8 -0.210 +31 EP-6 EP E 28 25 20 0.700 109.5 162.8 -0.210 +32 O2 OS M 6 4 3 1.415 110.0 52.1 0.000 +33 EP+2 EP E 32 6 4 0.700 109.5 43.3 -0.139 +34 EP-2 EP E 32 6 4 0.700 109.5 163.3 -0.139 + +LOOP +O5 C1 + +DONE +2-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +2ma.dat +2MA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 C3 CG 3 6 4 3 1.529 110.3 -67.6 0.130 + 9 H3 H1 E 8 6 4 1.101 109.0 65.8 0.000 +10 O3 OH 3 8 6 4 1.421 109.9 -173.3 0.000 +11 H3O HO E 10 8 6 0.976 108.5 -70.1 0.279 +12 EP+3 EP E 10 8 6 0.700 109.5 49.9 -0.217 +13 EP-3 EP E 10 8 6 0.700 109.5 169.9 -0.217 +14 C4 CG 3 8 6 4 1.519 110.6 -53.3 0.182 +15 H4 H1 E 14 8 6 1.100 109.6 -68.1 0.000 +16 O4 OH 3 14 8 6 1.430 109.6 171.4 0.000 +17 H4O HO E 16 14 8 0.958 109.2 115.2 0.276 +18 EP+4 EP E 16 14 8 0.700 109.5 -124.8 -0.220 +19 EP-4 EP E 16 14 8 0.700 109.5 -4.8 -0.220 +20 C5 CG 3 14 8 6 1.528 110.1 52.8 0.228 +21 H5 H1 E 20 14 8 1.105 108.8 65.6 0.000 +22 O5 OS B 20 14 8 1.435 110.8 -54.4 0.000 +23 EP+5 EP E 22 20 14 0.700 109.5 -174.4 -0.167 +24 EP-5 EP E 22 20 14 0.700 109.5 -65.6 -0.167 +25 C6 CG 3 20 14 8 1.517 113.3 -174.2 0.131 +26 H61 H1 E 25 20 14 1.092 108.3 57.1 0.000 +27 H62 H1 E 25 20 14 1.093 108.8 -54.9 0.000 +28 O6 OH 3 25 20 14 1.413 112.7 178.9 0.000 +29 H6O HO E 28 25 20 0.955 108.1 96.0 0.274 +30 EP+6 EP E 28 25 20 0.700 109.5 -24.0 -0.211 +31 EP-6 EP E 28 25 20 0.700 109.5 -144.0 -0.211 +32 O2 OS M 6 4 3 1.415 106.3 171.5 0.000 +33 EP+2 EP E 32 6 4 0.700 109.5 47.9 -0.127 +34 EP-2 EP E 32 6 4 0.700 109.5 -72.1 -0.127 + +LOOP +O5 C1 + +DONE +3,4,6-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +346ga.dat +QGA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.281 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.218 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.218 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.110 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OS B 12 6 4 1.421 109.9 -173.3 0.000 +15 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.132 +16 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.132 +17 C4 CG M 12 6 4 1.519 110.6 -53.3 0.147 +18 H4 H1 E 17 12 6 1.100 109.6 -68.1 0.000 +19 O4 OS B 17 12 6 1.430 109.6 171.4 0.000 +20 EP+4 EP E 19 17 12 0.700 109.5 179.6 -0.132 +21 EP-4 EP E 19 17 12 0.700 109.5 -59.6 -0.132 +22 C5 CG M 17 12 6 1.528 110.1 52.8 0.227 +23 H5 H1 E 22 17 12 1.105 108.8 65.6 0.000 +24 O5 OS B 22 17 12 1.435 110.8 -54.4 0.000 +25 EP+5 EP E 24 22 17 0.700 109.5 178.3 -0.183 +26 EP-5 EP E 24 22 17 0.700 109.5 -63.8 -0.183 +27 C6 CG M 22 17 12 1.517 113.3 -174.2 0.139 +28 H61 H1 E 27 22 17 1.092 108.3 -55.8 0.000 +29 H62 H1 E 27 22 17 1.093 108.8 63.2 0.000 +30 O6 OS M 27 22 17 1.413 112.7 -172.6 0.000 +31 EP+6 EP E 30 27 22 0.700 109.5 42.8 -0.131 +32 EP-6 EP E 30 27 22 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +3,4,6-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +346la.dat +QLA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.275 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.220 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.220 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OS B 12 6 4 1.421 109.9 -173.3 0.000 +15 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.134 +16 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.134 +17 C4 CG M 12 6 4 1.519 110.6 -53.3 0.099 +18 H4 H1 E 17 12 6 1.100 109.6 173.6 0.000 +19 O4 OS B 17 12 6 1.430 109.6 -63.8 0.000 +20 EP+4 EP E 19 17 12 0.700 109.5 179.6 -0.118 +21 EP-4 EP E 19 17 12 0.700 109.5 -59.6 -0.118 +22 C5 CG M 17 12 6 1.528 110.1 52.8 0.172 +23 H5 H1 E 22 17 12 1.105 108.8 65.6 0.000 +24 O5 OS B 22 17 12 1.435 110.8 -54.4 0.000 +25 EP+5 EP E 24 22 17 0.700 109.5 178.3 -0.169 +26 EP-5 EP E 24 22 17 0.700 109.5 -63.8 -0.169 +27 C6 CG M 22 17 12 1.517 113.3 -174.2 0.162 +28 H61 H1 E 27 22 18 1.092 108.3 -55.8 0.000 +29 H62 H1 E 27 22 18 1.093 108.8 63.2 0.000 +30 O6 OS M 27 22 18 1.413 112.7 -172.6 0.000 +31 EP+6 EP E 30 27 22 0.700 109.5 42.8 -0.131 +32 EP-6 EP E 30 27 22 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +3,4,6-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +346ma.dat +QMA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OH 3 6 4 3 1.415 106.3 171.5 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 167.9 0.289 +10 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.215 +11 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.215 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OS B 12 6 4 1.421 109.9 -173.3 0.000 +15 EP+3 EP E 14 12 6 0.700 109.5 49.9 -0.134 +16 EP-3 EP E 14 12 6 0.700 109.5 169.9 -0.134 +17 C4 CG M 12 6 4 1.519 110.6 -53.3 0.183 +18 H4 H1 E 17 12 6 1.100 109.6 -68.1 0.000 +19 O4 OS B 17 12 6 1.430 109.6 171.4 0.000 +20 EP+4 EP E 19 17 12 0.700 109.5 -124.8 -0.139 +21 EP-4 EP E 19 17 12 0.700 109.5 -4.8 -0.139 +22 C5 CG M 17 12 6 1.528 110.1 52.8 0.228 +23 H5 H1 E 22 17 12 1.105 108.8 65.6 0.000 +24 O5 OS B 22 17 12 1.435 110.8 -54.4 0.000 +25 EP+5 EP E 24 22 17 0.700 109.5 -174.4 -0.167 +26 EP-5 EP E 24 22 17 0.700 109.5 -65.6 -0.167 +27 C6 CG M 22 17 12 1.517 113.3 -174.2 0.132 +28 H61 H1 E 27 22 17 1.092 108.3 57.1 0.000 +29 H62 H1 E 27 22 17 1.093 108.8 -54.9 0.000 +30 O6 OS M 27 22 17 1.413 112.7 178.9 0.000 +31 EP+6 EP E 30 27 22 0.700 109.5 -24.0 -0.131 +32 EP-6 EP E 30 27 22 0.700 109.5 -144.0 -0.131 + +LOOP +O5 C1 + +DONE +3,4-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +34ga.dat +WGA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.281 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.218 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.218 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.110 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OS B 12 6 4 1.421 109.9 -173.3 0.000 +15 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.132 +16 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.132 +17 C4 CG M 12 6 4 1.519 110.6 -53.3 0.147 +18 H4 H1 E 17 12 6 1.100 109.6 -68.1 0.000 +19 C5 CG 3 17 12 6 1.528 110.1 52.8 0.227 +20 H5 H1 E 19 17 12 1.105 108.8 65.6 0.000 +21 O5 OS B 19 17 12 1.435 110.8 -54.4 0.000 +22 EP+5 EP E 21 19 17 0.700 109.5 178.3 -0.183 +23 EP-5 EP E 21 19 17 0.700 109.5 -63.8 -0.183 +24 C6 CG 3 19 17 12 1.517 113.3 -174.2 0.138 +25 H61 H1 E 24 19 17 1.092 108.3 -55.8 0.000 +26 H62 H1 E 24 19 17 1.093 108.8 63.2 0.000 +27 O6 OH 3 24 19 17 1.413 112.7 -172.6 0.000 +28 H6O HO E 27 24 19 0.955 108.1 -87.2 0.272 +29 EP+6 EP E 27 24 19 0.700 109.5 42.8 -0.210 +30 EP-6 EP E 27 24 19 0.700 109.5 162.8 -0.210 +31 O4 OS M 17 12 6 1.430 109.6 171.4 0.000 +32 EP+4 EP E 31 17 12 0.700 109.5 179.6 -0.132 +33 EP-4 EP E 31 17 12 0.700 109.5 -59.6 -0.132 + +LOOP +O5 C1 + +DONE +3,4-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +34la.dat +WLA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.275 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.220 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.220 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OS B 12 6 4 1.421 109.9 -173.3 0.000 +15 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.134 +16 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.134 +17 C4 CG M 12 6 4 1.519 110.6 -53.3 0.099 +18 H4 H1 E 17 12 6 1.100 109.6 173.6 0.000 +19 C5 CG 3 17 12 6 1.528 110.1 52.8 0.172 +20 H5 H1 E 19 17 12 1.105 108.8 65.6 0.000 +21 O5 OS B 19 17 12 1.435 110.8 -54.4 0.000 +22 EP+5 EP E 21 19 17 0.700 109.5 178.3 -0.169 +23 EP-5 EP E 21 19 17 0.700 109.5 -63.8 -0.169 +24 C6 CG 3 19 17 12 1.517 113.3 -174.2 0.161 +25 H61 H1 E 24 19 17 1.092 108.3 -55.8 0.000 +26 H62 H1 E 24 19 17 1.093 108.8 63.2 0.000 +27 O6 OH 3 24 19 17 1.413 112.7 -172.6 0.000 +28 H6O HO E 27 24 19 0.955 108.1 -87.2 0.272 +29 EP+6 EP E 27 24 19 0.700 109.5 42.8 -0.210 +30 EP-6 EP E 27 24 19 0.700 109.5 162.8 -0.210 +31 O4 OS M 17 12 6 1.430 109.6 -63.8 0.000 +32 EP+4 EP E 31 17 12 0.700 109.5 179.6 -0.118 +33 EP-4 EP E 31 17 12 0.700 109.5 -59.6 -0.118 + +LOOP +O5 C1 + +DONE +3,4-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +34ma.dat +WMA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OH 3 6 4 3 1.415 106.3 171.5 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 167.9 0.289 +10 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.215 +11 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.215 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OS B 12 6 4 1.421 109.9 -173.3 0.000 +15 EP+3 EP E 14 12 6 0.700 109.5 49.9 -0.134 +16 EP-3 EP E 14 12 6 0.700 109.5 169.9 -0.134 +17 C4 CG M 12 6 4 1.519 110.6 -53.3 0.183 +18 H4 H1 E 17 12 6 1.100 109.6 -68.1 0.000 +19 C5 CG 3 17 12 6 1.528 110.1 52.8 0.228 +20 H5 H1 E 19 17 12 1.105 108.8 65.6 0.000 +21 O5 OS B 19 17 12 1.435 110.8 -54.4 0.000 +22 EP+5 EP E 21 19 17 0.700 109.5 -174.4 -0.167 +23 EP-5 EP E 21 19 17 0.700 109.5 -65.6 -0.167 +24 C6 CG 3 19 17 12 1.517 113.3 -174.2 0.131 +25 H61 H1 E 24 19 17 1.092 108.3 57.1 0.000 +26 H62 H1 E 24 19 17 1.093 108.8 -54.9 0.000 +27 O6 OH 3 24 19 17 1.413 112.7 178.9 0.000 +28 H6O HO E 27 24 19 0.955 108.1 96.0 0.274 +29 EP+6 EP E 27 24 19 0.700 109.5 -24.0 -0.211 +30 EP-6 EP E 27 24 19 0.700 109.5 -144.0 -0.211 +31 O4 OS M 17 12 6 1.430 109.6 171.4 0.000 +32 EP+4 EP E 32 17 12 0.700 109.5 -124.8 -0.139 +33 EP-4 EP E 32 17 12 0.700 109.5 -4.8 -0.139 + +LOOP +O5 C1 + +DONE +3,6-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +36ga.dat +VGA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.281 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.218 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.218 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.110 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OS B 12 6 4 1.421 109.9 -173.3 0.000 +15 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.132 +16 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.132 +17 C4 CG M 12 6 4 1.519 110.6 -53.3 0.146 +18 H4 H1 E 17 12 6 1.100 109.6 -68.1 0.000 +19 O4 OH 3 17 12 6 1.430 109.6 171.4 0.000 +20 H4O HO E 19 17 12 0.958 109.2 59.6 0.278 +21 EP+4 EP E 19 17 12 0.700 109.5 179.6 -0.214 +22 EP-4 EP E 19 17 12 0.700 109.5 -59.6 -0.214 +23 C5 CG M 17 12 6 1.528 110.1 52.8 0.227 +24 H5 H1 E 23 17 12 1.105 108.8 65.6 0.000 +25 O5 OS B 23 17 12 1.435 110.8 -54.4 0.000 +26 EP+5 EP E 25 23 17 0.700 109.5 178.3 -0.183 +27 EP-5 EP E 25 23 17 0.700 109.5 -63.8 -0.183 +28 C6 CG M 23 17 12 1.517 113.3 -174.2 0.139 +29 H61 H1 E 28 23 17 1.092 108.3 -55.8 0.000 +30 H62 H1 E 28 23 17 1.093 108.8 63.2 0.000 +31 O6 OS M 28 23 17 1.413 112.7 -172.6 0.000 +32 EP+6 EP E 31 28 23 0.700 109.5 42.8 -0.131 +33 EP-6 EP E 31 28 23 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +3,6-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +36la.dat +VLA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.275 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.220 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.220 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OS B 12 6 4 1.421 109.9 -173.3 0.000 +15 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.134 +16 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.134 +17 C4 CG M 12 6 4 1.519 110.6 -53.3 0.099 +18 H4 H1 E 17 12 6 1.100 109.6 173.6 0.000 +19 O4 OH 3 17 12 6 1.430 109.6 -63.8 0.000 +20 H4O HO E 19 17 12 0.958 109.2 59.6 0.287 +21 EP+4 EP E 19 17 12 0.700 109.5 179.6 -0.205 +22 EP-4 EP E 19 17 12 0.700 109.5 -59.6 -0.205 +23 C5 CG M 17 12 6 1.528 110.1 52.8 0.172 +24 H5 H1 E 23 17 12 1.105 108.8 65.6 0.000 +25 O5 OS B 23 17 12 1.435 110.8 -54.4 0.000 +26 EP+5 EP E 25 23 17 0.700 109.5 178.3 -0.169 +27 EP-5 EP E 25 23 17 0.700 109.5 -63.8 -0.169 +28 C6 CG M 23 17 12 1.517 113.3 -174.2 0.162 +29 H61 H1 E 28 23 18 1.092 108.3 -55.8 0.000 +30 H62 H1 E 28 23 18 1.093 108.8 63.2 0.000 +31 O6 OS M 28 23 18 1.413 112.7 -172.6 0.000 +32 EP+6 EP E 31 28 23 0.700 109.5 42.8 -0.131 +33 EP-6 EP E 31 28 23 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +3,6-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +36ma.dat +VMA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OH 3 6 4 3 1.415 106.3 171.5 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 167.9 0.289 +10 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.215 +11 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.215 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OS B 12 6 4 1.421 109.9 -173.3 0.000 +15 EP+3 EP E 14 12 6 0.700 109.5 49.9 -0.134 +16 EP-3 EP E 14 12 6 0.700 109.5 169.9 -0.134 +17 C4 CG M 12 6 4 1.519 110.6 -53.3 0.182 +18 H4 H1 E 17 12 6 1.100 109.6 -68.1 0.000 +19 O4 OH 3 17 12 6 1.430 109.6 171.4 0.000 +20 H4O HO E 19 17 12 0.958 109.2 115.2 0.276 +21 EP+4 EP E 19 17 12 0.700 109.5 -124.8 -0.220 +22 EP-4 EP E 19 17 12 0.700 109.5 -4.8 -0.220 +23 C5 CG M 17 12 6 1.528 110.1 52.8 0.228 +24 H5 H1 E 23 17 12 1.105 108.8 65.6 0.000 +25 O5 OS B 23 17 12 1.435 110.8 -54.4 0.000 +26 EP+5 EP E 25 23 17 0.700 109.5 -174.4 -0.167 +27 EP-5 EP E 25 23 17 0.700 109.5 -65.6 -0.167 +28 C6 CG M 23 17 12 1.517 113.3 -174.2 0.132 +29 H61 H1 E 28 23 17 1.092 108.3 57.1 0.000 +30 H62 H1 E 28 23 17 1.093 108.8 -54.9 0.000 +31 O6 OS M 28 23 17 1.413 112.7 178.9 0.000 +32 EP+6 EP E 31 28 23 0.700 109.5 -24.0 -0.131 +33 EP-6 EP E 31 28 23 0.700 109.5 -144.0 -0.131 + +LOOP +O5 C1 + +DONE +3-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +3ga.dat +3GA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.281 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.218 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.218 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.110 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 C4 CG 3 12 6 4 1.519 110.6 -53.3 0.146 +15 H4 H1 E 14 12 6 1.100 109.6 -68.1 0.000 +16 O4 OH 3 14 12 6 1.430 109.6 171.4 0.000 +17 H4O HO E 16 14 12 0.958 109.2 59.6 0.278 +18 EP+4 EP E 16 14 12 0.700 109.5 179.6 -0.214 +19 EP-4 EP E 16 14 12 0.700 109.5 -59.6 -0.214 +20 C5 CG 3 14 12 6 1.528 110.1 52.8 0.227 +21 H5 H1 E 20 14 12 1.105 108.8 65.6 0.000 +22 O5 OS B 20 14 12 1.435 110.8 -54.4 0.000 +23 EP+5 EP E 22 20 14 0.700 109.5 178.3 -0.183 +24 EP-5 EP E 22 20 14 0.700 109.5 -63.8 -0.183 +25 C6 CG 3 20 14 12 1.517 113.3 -174.2 0.138 +26 H61 H1 E 25 20 14 1.092 108.3 -55.8 0.000 +27 H62 H1 E 25 20 14 1.093 108.8 63.2 0.000 +28 O6 OH 3 25 20 14 1.413 112.7 -172.6 0.000 +29 H6O HO E 28 25 20 0.955 108.1 -87.2 0.272 +30 EP+6 EP E 28 25 20 0.700 109.5 42.8 -0.210 +31 EP-6 EP E 28 25 20 0.700 109.5 162.8 -0.210 +32 O3 OS M 12 6 4 1.421 109.9 -173.3 0.000 +33 EP+3 EP E 32 12 6 0.700 109.5 -21.4 -0.132 +34 EP-3 EP E 32 12 6 0.700 109.5 98.6 -0.132 + +LOOP +O5 C1 + +DONE +3-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +3la.dat +3LA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.275 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.220 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.220 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 C4 CG 3 12 6 4 1.519 110.6 -53.3 0.099 +15 H4 H1 E 14 12 6 1.100 109.6 173.6 0.000 +16 O4 OH 3 14 12 6 1.430 109.6 -63.8 0.000 +17 H4O HO E 16 14 12 0.958 109.2 59.6 0.287 +18 EP+4 EP E 16 14 12 0.700 109.5 179.6 -0.205 +19 EP-4 EP E 16 14 12 0.700 109.5 -59.6 -0.205 +20 C5 CG 3 14 12 6 1.528 110.1 52.8 0.172 +21 H5 H1 E 20 14 12 1.105 108.8 65.6 0.000 +22 O5 OS B 20 14 12 1.435 110.8 -54.4 0.000 +23 EP+5 EP E 22 20 14 0.700 109.5 178.3 -0.169 +24 EP-5 EP E 22 20 14 0.700 109.5 -63.8 -0.169 +25 C6 CG 3 20 14 12 1.517 113.3 -174.2 0.161 +26 H61 H1 E 25 20 14 1.092 108.3 -55.8 0.000 +27 H62 H1 E 25 20 14 1.093 108.8 63.2 0.000 +28 O6 OH 3 25 20 14 1.413 112.7 -172.6 0.000 +29 H6O HO E 28 25 20 0.955 108.1 -87.2 0.272 +30 EP+6 EP E 28 25 20 0.700 109.5 42.8 -0.210 +31 EP-6 EP E 28 25 20 0.700 109.5 162.8 -0.210 +32 O3 OS M 12 6 4 1.421 109.9 -173.3 0.000 +33 EP+3 EP E 32 12 6 0.700 109.5 -21.4 -0.134 +34 EP-3 EP E 32 12 6 0.700 109.5 98.6 -0.134 + +LOOP +O5 C1 + +DONE +3-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +3ma.dat +3MA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OH 3 6 4 3 1.415 106.3 171.5 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 167.9 0.289 +10 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.215 +11 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.215 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 C4 CG 3 12 6 4 1.519 110.6 -53.3 0.182 +15 H4 H1 E 14 12 6 1.100 109.6 -68.1 0.000 +16 O4 OH 3 14 12 6 1.430 109.6 171.4 0.000 +17 H4O HO E 16 14 12 0.958 109.2 115.2 0.276 +18 EP+4 EP E 16 14 12 0.700 109.5 -124.8 -0.220 +19 EP-4 EP E 16 14 12 0.700 109.5 -4.8 -0.220 +20 C5 CG 3 14 12 6 1.528 110.1 52.8 0.228 +21 H5 H1 E 20 14 12 1.105 108.8 65.6 0.000 +22 O5 OS B 20 14 12 1.435 110.8 -54.4 0.000 +23 EP+5 EP E 22 20 14 0.700 109.5 -174.4 -0.167 +24 EP-5 EP E 22 20 14 0.700 109.5 -65.6 -0.167 +25 C6 CG 3 20 14 12 1.517 113.3 -174.2 0.131 +26 H61 H1 E 25 20 14 1.092 108.3 57.1 0.000 +27 H62 H1 E 25 20 14 1.093 108.8 -54.9 0.000 +28 O6 OH 3 25 20 14 1.413 112.7 178.9 0.000 +29 H6O HO E 28 25 20 0.955 108.1 96.0 0.274 +30 EP+6 EP E 28 25 20 0.700 109.5 -24.0 -0.211 +31 EP-6 EP E 28 25 20 0.700 109.5 -144.0 -0.211 +32 O3 OS M 12 6 4 1.421 109.9 -173.3 0.000 +33 EP+3 EP E 32 12 6 0.700 109.5 49.9 -0.134 +34 EP-3 EP E 32 12 6 0.700 109.5 169.9 -0.134 + +LOOP +O5 C1 + +DONE +4,6-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +46ga.dat +UGA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.281 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.218 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.218 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.109 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OH 3 12 6 4 1.421 109.9 -173.3 0.000 +15 H3O HO E 14 12 6 0.976 108.5 -141.4 0.280 +16 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.215 +17 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.215 +18 C4 CG M 12 6 4 1.519 110.6 -53.3 0.147 +19 H4 H1 E 18 12 6 1.100 109.6 -68.1 0.000 +20 O4 OS B 18 12 6 1.430 109.6 171.4 0.000 +21 EP+4 EP E 20 18 12 0.700 109.5 179.6 -0.132 +22 EP-4 EP E 20 18 12 0.700 109.5 -59.6 -0.132 +23 C5 CG M 18 12 6 1.528 110.1 52.8 0.227 +24 H5 H1 E 23 18 12 1.105 108.8 65.6 0.000 +25 O5 OS B 23 18 12 1.435 110.8 -54.4 0.000 +26 EP+5 EP E 25 23 18 0.700 109.5 178.3 -0.183 +27 EP-5 EP E 25 23 18 0.700 109.5 -63.8 -0.183 +28 C6 CG M 23 18 12 1.517 113.3 -174.2 0.139 +29 H61 H1 E 28 23 18 1.092 108.3 -55.8 0.000 +30 H62 H1 E 28 23 18 1.093 108.8 63.2 0.000 +31 O6 OS M 28 23 18 1.413 112.7 -172.6 0.000 +32 EP+6 EP E 31 28 23 0.700 109.5 42.8 -0.131 +33 EP-6 EP E 31 28 23 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +4,6-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +46la.dat +ULA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.275 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.220 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.220 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OH 3 12 6 4 1.421 109.9 -173.3 0.000 +15 H3O HO E 14 12 6 0.976 108.5 -141.4 0.283 +16 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.219 +17 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.219 +18 C4 CG M 12 6 4 1.519 110.6 -53.3 0.099 +19 H4 H1 E 18 12 6 1.100 109.6 173.6 0.000 +20 O4 OS B 18 12 6 1.430 109.6 -63.8 0.000 +21 EP+4 EP E 20 18 12 0.700 109.5 179.6 -0.118 +22 EP-4 EP E 20 18 12 0.700 109.5 -59.6 -0.118 +23 C5 CG M 18 12 6 1.528 110.1 52.8 0.172 +24 H5 H1 E 23 18 12 1.105 108.8 65.6 0.000 +25 O5 OS B 23 18 12 1.435 110.8 -54.4 0.000 +26 EP+5 EP E 25 23 18 0.700 109.5 178.3 -0.169 +27 EP-5 EP E 25 23 18 0.700 109.5 -63.8 -0.169 +28 C6 CG M 23 18 12 1.517 113.3 -174.2 0.162 +29 H61 H1 E 28 23 18 1.092 108.3 -55.8 0.000 +30 H62 H1 E 28 23 18 1.093 108.8 63.2 0.000 +31 O6 OS M 28 23 18 1.413 112.7 -172.6 0.000 +32 EP+6 EP E 31 28 23 0.700 109.5 42.8 -0.131 +33 EP-6 EP E 31 28 23 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +4,6-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +46ma.dat +UMA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OH 3 6 4 3 1.415 106.3 171.5 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 167.9 0.289 +10 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.215 +11 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.215 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OH 3 12 6 4 1.421 109.9 -173.3 0.000 +15 H3O HO E 14 12 6 0.976 108.5 -70.1 0.279 +16 EP+3 EP E 14 12 6 0.700 109.5 49.9 -0.217 +17 EP-3 EP E 14 12 6 0.700 109.5 169.9 -0.217 +18 C4 CG M 12 6 4 1.519 110.6 -53.3 0.183 +19 H4 H1 E 18 12 6 1.100 109.6 -68.1 0.000 +20 O4 OS B 18 12 6 1.430 109.6 171.4 0.000 +21 EP+4 EP E 20 18 12 0.700 109.5 -124.8 -0.139 +22 EP-4 EP E 20 18 12 0.700 109.5 -4.8 -0.139 +23 C5 CG M 18 12 6 1.528 110.1 52.8 0.228 +24 H5 H1 E 23 18 12 1.105 108.8 65.6 0.000 +25 O5 OS B 23 18 12 1.435 110.8 -54.4 0.000 +26 EP+5 EP E 25 23 18 0.700 109.5 -174.4 -0.167 +27 EP-5 EP E 25 23 18 0.700 109.5 -65.6 -0.167 +28 C6 CG M 23 18 12 1.517 113.3 -174.2 0.132 +29 H61 H1 E 28 23 18 1.092 108.3 57.1 0.000 +30 H62 H1 E 28 23 18 1.093 108.8 -54.9 0.000 +31 O6 OS M 28 23 18 1.413 112.7 178.9 0.000 +32 EP+6 EP E 31 28 23 0.700 109.5 -24.0 -0.131 +33 EP-6 EP E 31 28 23 0.700 109.5 -144.0 -0.131 + +LOOP +O5 C1 + +DONE +4-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +4ga.dat +4GA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.281 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.218 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.218 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.109 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OH 3 12 6 4 1.421 109.9 -173.3 0.000 +15 H3O HO E 14 12 6 0.976 108.5 -141.4 0.280 +16 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.215 +17 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.215 +18 C4 CG M 12 6 4 1.519 110.6 -53.3 0.147 +19 H4 H1 E 18 12 6 1.100 109.6 -68.1 0.000 +20 C5 CG 3 18 12 6 1.528 110.1 52.8 0.227 +21 H5 H1 E 20 18 12 1.105 108.8 65.6 0.000 +22 O5 OS B 20 18 12 1.435 110.8 -54.4 0.000 +23 EP+5 EP E 22 20 18 0.700 109.5 178.3 -0.183 +24 EP-5 EP E 22 20 18 0.700 109.5 -63.8 -0.183 +25 C6 CG 3 20 18 12 1.517 113.3 -174.2 0.138 +26 H61 H1 E 25 20 18 1.092 108.3 -55.8 0.000 +27 H62 H1 E 25 20 18 1.093 108.8 63.2 0.000 +28 O6 OH 3 25 20 18 1.413 112.7 -172.6 0.000 +29 H6O HO E 28 25 20 0.955 108.1 -87.2 0.272 +30 EP+6 EP E 28 25 20 0.700 109.5 42.8 -0.210 +31 EP-6 EP E 28 25 20 0.700 109.5 162.8 -0.210 +32 O4 OS M 18 12 6 1.430 109.6 171.4 0.000 +33 EP+4 EP E 32 18 12 0.700 109.5 179.6 -0.132 +34 EP-4 EP E 32 18 12 0.700 109.5 -59.6 -0.132 + +LOOP +O5 C1 + +DONE +4-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +4la.dat +4LA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.275 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.220 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.220 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OH 3 12 6 4 1.421 109.9 -173.3 0.000 +15 H3O HO E 14 12 6 0.976 108.5 -141.4 0.283 +16 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.219 +17 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.219 +18 C4 CG M 12 6 4 1.519 110.6 -53.3 0.099 +19 H4 H1 E 18 12 6 1.100 109.6 173.6 0.000 +20 C5 CG 3 18 12 6 1.528 110.1 52.8 0.172 +21 H5 H1 E 20 18 12 1.105 108.8 65.6 0.000 +22 O5 OS B 20 18 12 1.435 110.8 -54.4 0.000 +23 EP+5 EP E 22 20 18 0.700 109.5 178.3 -0.169 +24 EP-5 EP E 22 20 18 0.700 109.5 -63.8 -0.169 +25 C6 CG 3 20 18 12 1.517 113.3 -174.2 0.161 +26 H61 H1 E 25 20 18 1.092 108.3 -55.8 0.000 +27 H62 H1 E 25 20 18 1.093 108.8 63.2 0.000 +28 O6 OH 3 25 20 18 1.413 112.7 -172.6 0.000 +29 H6O HO E 28 25 20 0.955 108.1 -87.2 0.272 +30 EP+6 EP E 28 25 20 0.700 109.5 42.8 -0.210 +31 EP-6 EP E 28 25 20 0.700 109.5 162.8 -0.210 +32 O4 OS M 18 12 6 1.430 109.6 -63.8 0.000 +33 EP+4 EP E 32 18 12 0.700 109.5 179.6 -0.118 +34 EP-4 EP E 32 18 12 0.700 109.5 -59.6 -0.118 + +LOOP +O5 C1 + +DONE +4-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +4ma.dat +4MA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OH 3 6 4 3 1.415 106.3 171.5 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 167.9 0.289 +10 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.215 +11 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.215 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OH 3 12 6 4 1.421 109.9 -173.3 0.000 +15 H3O HO E 14 12 6 0.976 108.5 -70.1 0.279 +16 EP+3 EP E 14 12 6 0.700 109.5 49.9 -0.217 +17 EP-3 EP E 14 12 6 0.700 109.5 169.9 -0.217 +18 C4 CG M 12 6 4 1.519 110.6 -53.3 0.183 +19 H4 H1 E 18 12 6 1.100 109.6 -68.1 0.000 +20 C5 CG 3 18 12 6 1.528 110.1 52.8 0.228 +21 H5 H1 E 20 18 12 1.105 108.8 65.6 0.000 +22 O5 OS B 20 18 12 1.435 110.8 -54.4 0.000 +23 EP+5 EP E 22 20 18 0.700 109.5 -174.4 -0.167 +24 EP-5 EP E 22 20 18 0.700 109.5 -65.6 -0.167 +25 C6 CG 3 20 18 12 1.517 113.3 -174.2 0.131 +26 H61 H1 E 25 20 18 1.092 108.3 57.1 0.000 +27 H62 H1 E 25 20 18 1.093 108.8 -54.9 0.000 +28 O6 OH 3 25 20 18 1.413 112.7 178.9 0.000 +29 H6O HO E 28 25 20 0.955 108.1 96.0 0.274 +30 EP+6 EP E 28 25 20 0.700 109.5 -24.0 -0.211 +31 EP-6 EP E 28 25 20 0.700 109.5 -144.0 -0.211 +32 O4 OS M 18 12 6 1.430 109.6 171.4 0.000 +33 EP+4 EP E 32 18 12 0.700 109.5 -124.8 -0.139 +34 EP-4 EP E 32 18 12 0.700 109.5 -4.8 -0.139 + +LOOP +O5 C1 + +DONE +6-[A-D-GLUCOPYRANO-] non-terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +6ga.dat +6GA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.281 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.218 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.218 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.109 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OH 3 12 6 4 1.421 109.9 -173.3 0.000 +15 H3O HO E 14 12 6 0.976 108.5 -141.4 0.280 +16 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.215 +17 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.215 +18 C4 CG M 12 6 4 1.519 110.6 -53.3 0.146 +19 H4 H1 E 18 12 6 1.100 109.6 -68.1 0.000 +20 O4 OH 3 18 12 6 1.430 109.6 171.4 0.000 +21 H4O HO E 20 18 12 0.958 109.2 59.6 0.278 +22 EP+4 EP E 20 18 12 0.700 109.5 179.6 -0.214 +23 EP-4 EP E 20 18 12 0.700 109.5 -59.6 -0.214 +24 C5 CG M 18 12 6 1.528 110.1 52.8 0.227 +25 H5 H1 E 24 18 12 1.105 108.8 65.6 0.000 +26 O5 OS B 24 18 12 1.435 110.8 -54.4 0.000 +27 EP+5 EP E 26 24 18 0.700 109.5 178.3 -0.183 +28 EP-5 EP E 26 24 18 0.700 109.5 -63.8 -0.183 +29 C6 CG M 24 18 12 1.517 113.3 -174.2 0.139 +30 H61 H1 E 29 24 18 1.092 108.3 -55.8 0.000 +31 H62 H1 E 29 24 18 1.093 108.8 63.2 0.000 +32 O6 OS M 29 24 18 1.413 112.7 -172.6 0.000 +33 EP+6 EP E 32 29 24 0.700 109.5 42.8 -0.131 +34 EP-6 EP E 32 29 24 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +6-[A-D-GALACTO-] non-terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +6la.dat +6LA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.275 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.220 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.220 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OH 3 12 6 4 1.421 109.9 -173.3 0.000 +15 H3O HO E 14 12 6 0.976 108.5 -141.4 0.283 +16 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.219 +17 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.219 +18 C4 CG M 12 6 4 1.519 110.6 -53.3 0.099 +19 H4 H1 E 18 12 6 1.100 109.6 173.6 0.000 +20 O4 OH 3 18 12 6 1.430 109.6 -63.8 0.000 +21 H4O HO E 20 18 12 0.958 109.2 59.6 0.287 +22 EP+4 EP E 20 18 12 0.700 109.5 179.6 -0.205 +23 EP-4 EP E 20 18 12 0.700 109.5 -59.6 -0.205 +24 C5 CG M 18 12 6 1.528 110.1 52.8 0.172 +25 H5 H1 E 24 18 12 1.105 108.8 65.6 0.000 +26 O5 OS B 24 18 12 1.435 110.8 -54.4 0.000 +27 EP+5 EP E 26 24 18 0.700 109.5 178.3 -0.169 +28 EP-5 EP E 26 24 18 0.700 109.5 -63.8 -0.169 +29 C6 CG M 24 18 12 1.517 113.3 -174.2 0.162 +30 H61 H1 E 29 24 18 1.092 108.3 -55.8 0.000 +31 H62 H1 E 29 24 18 1.093 108.8 63.2 0.000 +32 O6 OS M 29 24 18 1.413 112.7 -172.6 0.000 +34 EP+6 EP E 32 29 24 0.700 109.5 42.8 -0.131 +35 EP-6 EP E 32 29 24 0.700 109.5 162.8 -0.131 + +LOOP +O5 C1 + +DONE +6-[A-D-MANNO-] non-terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +6ma.dat +6MA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OH 3 6 4 3 1.415 106.3 171.5 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 167.9 0.289 +10 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.215 +11 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.215 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OH 3 12 6 4 1.421 109.9 -173.3 0.000 +15 H3O HO E 14 12 6 0.976 108.5 -70.1 0.279 +16 EP+3 EP E 14 12 6 0.700 109.5 49.9 -0.217 +17 EP-3 EP E 14 12 6 0.700 109.5 169.9 -0.217 +18 C4 CG M 12 6 4 1.519 110.6 -53.3 0.182 +19 H4 H1 E 18 12 6 1.100 109.6 -68.1 0.000 +20 O4 OH 3 18 12 6 1.430 109.6 171.4 0.000 +21 H4O HO E 20 18 12 0.958 109.2 115.2 0.276 +22 EP+4 EP E 20 18 12 0.700 109.5 -124.8 -0.220 +23 EP-4 EP E 20 18 12 0.700 109.5 -4.8 -0.220 +24 C5 CG M 18 12 6 1.528 110.1 52.8 0.228 +25 H5 H1 E 24 18 12 1.105 108.8 65.6 0.000 +26 O5 OS B 24 18 12 1.435 110.8 -54.4 0.000 +27 EP+5 EP E 26 24 18 0.700 109.5 -174.4 -0.167 +28 EP-5 EP E 26 24 18 0.700 109.5 -65.6 -0.167 +29 C6 CG M 24 18 12 1.517 113.3 -174.2 0.132 +30 H61 H1 E 29 24 18 1.092 108.3 57.1 0.000 +31 H62 H1 E 29 24 18 1.093 108.8 -54.9 0.000 +32 O6 OS M 29 24 18 1.413 112.7 178.9 0.000 +33 EP+6 EP E 32 29 24 0.700 109.5 -24.0 -0.131 +34 EP-6 EP E 32 29 24 0.700 109.5 -144.0 -0.131 + +LOOP +O5 C1 + +DONE +A-D-GLUCOPYRANOS terminal ESP hf/6-31G* RESP 010 ENS AVG and EPs +ga.dat +1GA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.292 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -169.2 0.170 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.281 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.218 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.218 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.109 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OH 3 12 6 4 1.421 109.9 -173.3 0.000 +15 H3O HO E 14 12 6 0.976 108.5 -141.4 0.280 +16 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.215 +17 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.215 +18 C4 CG M 12 6 4 1.519 110.6 -53.3 0.146 +19 H4 H1 E 18 12 6 1.100 109.6 -68.1 0.000 +20 O4 OH 3 18 12 6 1.430 109.6 171.4 0.000 +21 H4O HO E 20 18 12 0.958 109.2 59.6 0.278 +22 EP+4 EP E 20 18 12 0.700 109.5 179.6 -0.214 +23 EP-4 EP E 20 18 12 0.700 109.5 -59.6 -0.214 +24 C5 CG M 18 12 6 1.528 110.1 52.8 0.227 +25 H5 H1 E 24 18 12 1.105 108.8 65.6 0.000 +26 O5 OS B 24 18 12 1.435 110.8 -54.4 0.000 +27 EP+5 EP E 26 24 18 0.700 109.5 178.3 -0.183 +28 EP-5 EP E 26 24 18 0.700 109.5 -63.8 -0.183 +29 C6 CG M 24 18 12 1.517 113.3 -174.2 0.138 +30 H61 H1 E 29 24 18 1.092 108.3 -55.8 0.000 +31 H62 H1 E 29 24 18 1.093 108.8 63.2 0.000 +32 O6 OH M 29 24 18 1.413 112.7 -172.6 0.000 +33 H6O HO E 32 29 24 0.955 108.1 -87.2 0.272 +34 EP+6 EP E 32 29 24 0.700 109.5 42.8 -0.210 +35 EP-6 EP E 32 29 24 0.700 109.5 162.8 -0.210 + +LOOP +O5 C1 + +DONE +A-D-GALACTO- terminal residue, hf/6-31g* RESP0.010 ENS AVG EPs +la.dat +1LA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.270 + 5 H1 H2 E 4 3 2 1.102 111.6 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.222 + 7 H2 H1 E 6 4 3 1.105 108.8 171.5 0.000 + 8 O2 OH 3 6 4 3 1.415 110.0 52.1 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 -74.7 0.275 +10 EP+2 EP E 8 6 4 0.700 109.5 43.3 -0.220 +11 EP-2 EP E 8 6 4 0.700 109.5 163.3 -0.220 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.118 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OH 3 12 6 4 1.421 109.9 -173.3 0.000 +15 H3O HO E 14 12 6 0.976 108.5 -141.4 0.283 +16 EP+3 EP E 14 12 6 0.700 109.5 -21.4 -0.219 +17 EP-3 EP E 14 12 6 0.700 109.5 98.6 -0.219 +18 C4 CG M 12 6 4 1.519 110.6 -53.3 0.099 +19 H4 H1 E 18 12 6 1.100 109.6 173.6 0.000 +20 O4 OH 3 18 12 6 1.430 109.6 -63.8 0.000 +21 H4O HO E 20 18 12 0.958 109.2 59.6 0.287 +22 EP+4 EP E 20 18 12 0.700 109.5 179.6 -0.205 +23 EP-4 EP E 20 18 12 0.700 109.5 -59.6 -0.205 +24 C5 CG M 18 12 6 1.528 110.1 52.8 0.172 +25 H5 H1 E 24 18 12 1.105 108.8 65.6 0.000 +26 O5 OS B 24 18 12 1.435 110.8 -54.4 0.000 +27 EP+5 EP E 26 24 18 0.700 109.5 178.3 -0.169 +28 EP-5 EP E 26 24 18 0.700 109.5 -63.8 -0.169 +29 C6 CG M 24 18 12 1.517 113.3 -174.2 0.161 +30 H61 H1 E 29 24 18 1.092 108.3 -55.8 0.000 +31 H62 H1 E 29 24 18 1.093 108.8 63.2 0.000 +32 O6 OH M 29 24 18 1.413 112.7 -172.6 0.000 +33 H6O HO E 32 29 24 0.955 108.1 -87.2 0.272 +34 EP+6 EP E 32 29 24 0.700 109.5 42.8 -0.210 +35 EP-6 EP E 32 29 24 0.700 109.5 162.8 -0.210 + +LOOP +O5 C1 + +DONE +A-D-MANNO- terminal residue, hf/6-31g* RESP 010 ENS AVG EPs +ma.dat +1MA INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.9 -40.0 0.251 + 5 H1 H2 E 4 3 2 1.102 110.7 -56.2 0.000 + 6 C2 CG M 4 3 2 1.524 107.4 -177.7 0.133 + 7 H2 H1 E 6 4 3 1.105 108.8 52.1 0.000 + 8 O2 OH 3 6 4 3 1.415 106.3 171.5 0.000 + 9 H2O HO E 8 6 4 0.957 110.0 167.9 0.289 +10 EP+2 EP E 8 6 4 0.700 109.5 47.9 -0.215 +11 EP-2 EP E 8 6 4 0.700 109.5 -72.1 -0.215 +12 C3 CG M 6 4 3 1.529 110.3 -67.6 0.130 +13 H3 H1 E 12 6 4 1.101 109.0 65.8 0.000 +14 O3 OH 3 12 6 4 1.421 109.9 -173.3 0.000 +15 H3O HO E 14 12 6 0.976 108.5 -70.1 0.279 +16 EP+3 EP E 14 12 6 0.700 109.5 49.9 -0.217 +17 EP-3 EP E 14 12 6 0.700 109.5 169.9 -0.217 +18 C4 CG M 12 6 4 1.519 110.6 -53.3 0.182 +19 H4 H1 E 18 12 6 1.100 109.6 -68.1 0.000 +20 O4 OH 3 18 12 6 1.430 109.6 171.4 0.000 +21 H4O HO E 20 18 12 0.958 109.2 115.2 0.276 +22 EP+4 EP E 20 18 12 0.700 109.5 -124.8 -0.220 +23 EP-4 EP E 20 18 12 0.700 109.5 -4.8 -0.220 +24 C5 CG M 18 12 6 1.528 110.1 52.8 0.228 +25 H5 H1 E 24 18 12 1.105 108.8 65.6 0.000 +26 O5 OS B 24 18 12 1.435 110.8 -54.4 0.000 +27 EP+5 EP E 26 24 18 0.700 109.5 -174.4 -0.167 +28 EP-5 EP E 26 24 18 0.700 109.5 -65.6 -0.167 +29 C6 CG M 24 18 12 1.517 113.3 -174.2 0.131 +30 H61 H1 E 29 24 18 1.092 108.3 57.1 0.000 +31 H62 H1 E 29 24 18 1.093 108.8 -54.9 0.000 +32 O6 OH M 29 24 18 1.413 112.7 178.9 0.000 +33 H6O HO E 32 29 24 0.955 108.1 96.0 0.274 +34 EP+6 EP E 32 29 24 0.700 109.5 -24.0 -0.211 +35 EP-6 EP E 32 29 24 0.700 109.5 -144.0 -0.211 + +LOOP +O5 C1 + +DONE +2,3-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +23gb.dat +ZGB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.143 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.277 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.212 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.212 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.178 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 O4 OH 3 18 9 6 1.430 107.9 -174.0 0.000 +21 H4O HO E 20 18 9 0.958 109.2 -139.6 0.281 +22 EP+4 EP E 20 18 9 0.700 109.5 -19.6 -0.217 +23 EP-4 EP E 20 18 9 0.700 109.5 100.4 -0.217 +24 C3 CG M 18 9 6 1.519 110.1 -54.4 0.113 +25 H3 H1 E 24 18 9 1.101 108.4 -66.7 0.000 +26 C2 CG B 24 18 9 1.529 110.6 52.8 0.231 +27 H2 H1 E 26 24 18 1.105 104.4 63.4 0.000 +28 O2 OS B 26 24 18 1.415 109.5 -174.5 0.000 +29 EP+2 EP E 28 26 24 0.700 109.5 -29.4 -0.137 +30 EP-2 EP E 28 26 24 0.700 109.5 90.6 -0.137 +31 O3 OS M 24 18 9 1.421 108.7 173.5 0.000 +32 EP+3 EP E 31 24 18 0.700 109.5 171.3 -0.135 +33 EP-3 EP E 31 24 18 0.700 109.5 -68.7 -0.135 + +LOOP +C2 C1 + +DONE +2,3-[B-D-GALACTO] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +23lb.dat +ZLB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.173 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.213 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.213 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.094 +19 H4 H1 E 18 9 6 1.100 107.5 -173.8 0.000 +20 O4 OH 3 18 9 6 1.430 111.7 67.6 0.000 +21 H4O HO E 20 18 9 0.958 109.2 -21.8 0.292 +22 EP+4 EP E 20 18 9 0.700 109.5 -141.8 -0.202 +23 EP-4 EP E 20 18 9 0.700 109.5 98.2 -0.202 +24 C3 CG M 18 9 6 1.519 110.1 -54.4 0.139 +25 H3 H1 E 24 18 9 1.101 108.4 -66.7 0.000 +26 C2 CG B 24 18 9 1.529 110.6 52.8 0.231 +27 H2 H1 E 26 24 18 1.105 104.4 63.4 0.000 +28 O2 OS B 26 24 18 1.415 109.5 -174.5 0.000 +29 EP+2 EP E 28 26 24 0.700 109.5 -29.4 -0.140 +30 EP-2 EP E 28 26 24 0.700 109.5 90.6 -0.140 +31 O3 OS M 24 18 9 1.421 108.7 173.5 0.000 +32 EP+3 EP E 31 24 18 0.700 109.5 171.3 -0.133 +33 EP-3 EP E 31 24 18 0.700 109.5 -68.7 -0.133 + +LOOP +C2 C1 + +DONE +2,3-[B-D-MANNO] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +23mb.dat +ZMB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.144 +12 H61 H1 E 11 9 6 1.092 108.3 179.3 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 62.9 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 -65.1 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -96.0 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 24.0 -0.209 +17 EP-6 EP E 14 11 9 0.700 109.5 144.0 -0.209 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.196 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 O4 OH 3 18 9 6 1.430 107.9 -174.0 0.000 +21 H4O HO E 20 18 9 0.958 109.2 -124.9 0.279 +22 EP+4 EP E 20 18 9 0.700 109.5 -4.9 -0.224 +23 EP-4 EP E 20 18 9 0.700 109.5 115.1 -0.224 +24 C3 CG M 18 9 6 1.519 110.1 -54.4 0.144 +25 H3 H1 E 24 18 9 1.101 108.4 -66.7 0.000 +26 C2 CG B 24 18 9 1.529 110.6 52.8 0.138 +27 H2 H1 E 26 24 18 1.105 106.2 -171.0 0.000 +28 O2 OS B 26 24 18 1.415 113.9 66.1 0.000 +29 EP+2 EP E 28 26 24 0.700 109.5 166.3 -0.114 +30 EP-2 EP E 28 26 24 0.700 109.5 -73.7 -0.114 +31 O3 OS M 24 18 9 1.421 108.7 173.5 0.000 +32 EP+3 EP E 31 24 18 0.700 109.5 48.7 -0.132 +33 EP-3 EP E 31 24 18 0.700 109.5 -71.3 -0.132 + +LOOP +C2 C1 + +DONE +2,4-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +24gb.dat +YGB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.143 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.277 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.212 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.212 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.178 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 C3 CG 3 18 9 6 1.519 110.1 -54.4 0.112 +21 H3 H1 E 20 18 9 1.101 108.4 -66.7 0.000 +22 O3 OH 3 20 18 9 1.421 108.7 173.5 0.000 +23 H30 HO E 22 20 18 0.976 108.5 51.3 0.282 +24 EP+3 EP E 22 20 18 0.700 109.5 171.3 -0.219 +25 EP-3 EP E 22 20 18 0.700 109.5 -68.7 -0.219 +26 C2 CG B 20 18 9 1.529 110.6 52.8 0.231 +27 H2 H1 E 26 20 18 1.105 104.4 63.4 0.000 +28 O2 OS B 26 20 18 1.415 109.5 -174.5 0.000 +29 EP+2 EP E 28 26 20 0.700 109.5 -29.4 -0.137 +30 EP-2 EP E 28 26 20 0.700 109.5 90.6 -0.137 +31 O4 OS M 18 9 6 1.430 107.9 -174.0 0.000 +32 EP+4 EP E 31 18 9 0.700 109.5 -19.6 -0.133 +33 EP-4 EP E 31 18 9 0.700 109.5 100.4 -0.133 + +LOOP +C2 C1 + +DONE +2,4-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +24lb.dat +YLB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.173 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.213 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.213 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.095 +19 H4 H1 E 18 9 6 1.100 107.5 -173.8 0.000 +20 C3 CG 3 18 9 6 1.519 110.1 -54.4 0.139 +21 H3 H1 E 20 18 9 1.101 108.4 -66.7 0.000 +22 O3 OH 3 20 18 9 1.421 108.7 173.5 0.000 +23 H30 HO E 22 20 18 0.976 108.5 51.3 0.281 +24 EP+3 EP E 22 20 18 0.700 109.5 171.3 -0.217 +25 EP-3 EP E 22 20 18 0.700 109.5 -68.7 -0.217 +26 C2 CG B 20 18 9 1.529 110.6 52.8 0.231 +27 H2 H1 E 26 20 18 1.105 104.4 63.4 0.000 +28 O2 OS B 26 20 18 1.415 109.5 -174.5 0.000 +29 EP+2 EP E 28 26 20 0.700 109.5 -29.4 -0.140 +30 EP-2 EP E 28 26 20 0.700 109.5 90.6 -0.140 +31 O4 OS M 18 9 6 1.430 111.7 67.6 0.000 +32 EP+4 EP E 31 18 9 0.700 109.5 -141.8 -0.113 +33 EP-4 EP E 31 18 9 0.700 109.5 98.2 -0.113 + +LOOP +C2 C1 + +DONE +2,4-[B-D-MANNO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +24mb.dat +YMB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.144 +12 H61 H1 E 11 9 6 1.092 108.3 179.3 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 62.9 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 -65.1 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -96.0 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 24.0 -0.209 +17 EP-6 EP E 14 11 9 0.700 109.5 144.0 -0.209 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.196 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 C3 CG 3 18 9 6 1.519 110.1 -54.4 0.143 +21 H3 H1 E 20 18 9 1.101 108.4 -66.7 0.000 +22 O3 OH 3 20 18 9 1.421 108.7 173.5 0.000 +23 H30 HO E 22 20 18 0.976 108.5 168.7 0.278 +24 EP+3 EP E 22 20 18 0.700 109.5 48.7 -0.214 +25 EP-3 EP E 22 20 18 0.700 109.5 -71.3 -0.214 +26 C2 CG B 20 18 9 1.529 110.6 52.8 0.138 +27 H2 H1 E 26 20 18 1.105 106.2 -171.0 0.000 +28 O2 OS B 26 20 18 1.415 113.9 66.1 0.000 +29 EP+2 EP E 28 26 20 0.700 109.5 166.3 -0.114 +30 EP-2 EP E 28 26 20 0.700 109.5 -73.7 -0.114 +31 O4 OS M 18 9 6 1.430 107.9 -174.0 0.000 +32 EP+4 EP E 31 18 9 0.700 109.5 -4.9 -0.141 +33 EP-4 EP E 31 18 9 0.700 109.5 115.1 -0.141 + +LOOP +C2 C1 + +DONE +2,6-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +26gb.dat +XGB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS M 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.178 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OH 3 11 9 6 1.430 107.9 -174.0 0.000 +14 H4O HO E 13 11 9 0.958 109.2 -139.6 0.281 +15 EP+4 EP E 13 11 9 0.700 109.5 -19.6 -0.217 +16 EP-4 EP E 13 11 9 0.700 109.5 100.4 -0.217 +17 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.112 +18 H3 H1 E 17 11 9 1.101 108.4 -66.7 0.000 +19 O3 OH 3 17 11 9 1.421 108.7 173.5 0.000 +20 H30 HO E 19 17 11 0.976 108.5 51.3 0.282 +21 EP+3 EP E 19 17 11 0.700 109.5 171.3 -0.219 +22 EP-3 EP E 19 17 11 0.700 109.5 -68.7 -0.219 +23 C2 CG B 17 11 9 1.529 110.6 52.8 0.231 +24 H2 H1 E 23 17 11 1.105 104.4 63.4 0.000 +25 O2 OS B 23 17 11 1.415 109.5 -174.5 0.000 +26 EP+2 EP E 25 23 17 0.700 109.5 -29.4 -0.137 +27 EP-2 EP E 25 23 17 0.700 109.5 90.6 -0.137 +28 C6 CG M 9 6 4 1.517 106.6 -177.2 0.143 +29 H61 H1 E 28 9 6 1.092 108.3 -178.0 0.000 +30 H62 H1 E 28 9 6 1.093 108.8 -59.0 0.000 +31 O6 OS M 28 9 6 1.413 112.7 65.2 0.000 +32 EP+6 EP E 31 28 9 0.700 109.5 178.1 -0.130 +33 EP-6 EP E 31 28 9 0.700 109.5 61.9 -0.130 + +LOOP +C2 C1 + +DONE +2,6-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +26lb.dat +XLB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.094 +12 H4 H1 E 11 9 6 1.100 107.5 -173.8 0.000 +13 O4 OH 3 11 9 6 1.430 111.7 67.6 0.000 +14 H4O HO E 13 11 9 0.958 109.2 -21.8 0.292 +15 EP+4 EP E 13 11 9 0.700 109.5 -141.8 -0.202 +16 EP-4 EP E 13 11 9 0.700 109.5 98.2 -0.202 +17 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.139 +18 H3 H1 E 17 11 9 1.101 108.4 -66.7 0.000 +19 O3 OH 3 17 11 9 1.421 108.7 173.5 0.000 +20 H30 HO E 19 17 11 0.976 108.5 51.3 0.281 +21 EP+3 EP E 19 17 11 0.700 109.5 171.3 -0.217 +22 EP-3 EP E 19 17 11 0.700 109.5 -68.7 -0.217 +23 C2 CG B 17 11 9 1.529 110.6 52.8 0.231 +24 H2 H1 E 23 17 11 1.105 104.4 63.4 0.000 +25 O2 OS B 23 17 11 1.415 109.5 -174.5 0.000 +26 EP+2 EP E 25 23 17 0.700 109.5 -29.4 -0.140 +27 EP-2 EP E 25 23 17 0.700 109.5 90.6 -0.140 +28 C6 CG M 9 6 4 1.517 106.6 -177.2 0.173 +29 H61 H1 E 28 9 6 1.092 108.3 -178.0 0.000 +30 H62 H1 E 28 9 6 1.093 108.8 -59.0 0.000 +31 O6 OS M 28 9 6 1.413 112.7 65.2 0.000 +32 EP+6 EP E 31 28 9 0.700 109.5 178.1 -0.133 +33 EP-6 EP E 31 28 9 0.700 109.5 61.9 -0.133 + +LOOP +C2 C1 + +DONE +2,6-[B-D-MANNO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +26mb.dat +XMB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.196 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OH 3 11 9 6 1.430 107.9 -174.0 0.000 +14 H4O HO E 13 11 9 0.958 109.2 -124.9 0.279 +15 EP+4 EP E 13 11 9 0.700 109.5 -4.9 -0.224 +16 EP-4 EP E 13 11 9 0.700 109.5 115.1 -0.224 +17 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.143 +18 H3 H1 E 17 11 9 1.101 108.4 -66.7 0.000 +19 O3 OH 3 17 11 9 1.421 108.7 173.5 0.000 +20 H30 HO E 19 17 11 0.976 108.5 168.7 0.278 +21 EP+3 EP E 19 17 11 0.700 109.5 48.7 -0.214 +22 EP-3 EP E 19 17 11 0.700 109.5 -71.3 -0.214 +23 C2 CG B 17 11 9 1.529 110.6 52.8 0.138 +24 H2 H1 E 23 17 11 1.105 106.2 -171.0 0.000 +25 O2 OS B 23 17 11 1.415 113.9 66.1 0.000 +26 EP+2 EP E 25 23 17 0.700 109.5 166.3 -0.114 +27 EP-2 EP E 25 23 17 0.700 109.5 -73.7 -0.114 +28 C6 CG M 9 6 4 1.517 106.6 -177.2 0.144 +29 H61 H1 E 28 9 6 1.092 108.3 179.3 0.000 +30 H62 H1 E 28 9 6 1.093 108.8 62.9 0.000 +31 O6 OS M 28 9 6 1.413 112.7 -65.1 0.000 +32 EP+6 EP E 31 28 9 0.700 109.5 24.0 -0.129 +33 EP-6 EP E 31 28 9 0.700 109.5 144.0 -0.129 + +LOOP +C2 C1 + +DONE +2-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +2gb.dat +2GB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.143 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.277 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.212 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.212 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.178 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 O4 OH 3 18 9 6 1.430 107.9 -174.0 0.000 +21 H4O HO E 20 18 9 0.958 109.2 -139.6 0.281 +22 EP+4 EP E 20 18 9 0.700 109.5 -19.6 -0.217 +23 EP-4 EP E 20 18 9 0.700 109.5 100.4 -0.217 +24 C3 CG M 18 9 6 1.519 110.1 -54.4 0.112 +25 H3 H1 E 24 18 9 1.101 108.4 -66.7 0.000 +26 O3 OH 3 24 18 9 1.421 108.7 173.5 0.000 +27 H30 HO E 26 24 18 0.976 108.5 51.3 0.282 +28 EP+3 EP E 26 24 18 0.700 109.5 171.3 -0.219 +29 EP-3 EP E 26 24 18 0.700 109.5 -68.7 -0.219 +30 C2 CG M 24 18 9 1.529 110.6 52.8 0.231 +31 H2 H1 E 30 24 18 1.105 104.4 63.4 0.000 +32 O2 OS M 30 24 18 1.415 109.5 -174.5 0.000 +33 EP+2 EP E 32 30 24 0.700 109.5 -29.4 -0.137 +34 EP-2 EP E 32 30 24 0.700 109.5 90.6 -0.137 + +LOOP +C2 C1 + +DONE +2-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +2lb.dat +2LB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.173 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.213 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.213 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.094 +19 H4 H1 E 18 9 6 1.100 107.5 -173.8 0.000 +20 O4 OH 3 18 9 6 1.430 111.7 67.6 0.000 +21 H4O HO E 20 18 9 0.958 109.2 -21.8 0.292 +22 EP+4 EP E 20 18 9 0.700 109.5 -141.8 -0.202 +23 EP-4 EP E 20 18 9 0.700 109.5 98.2 -0.202 +24 C3 CG M 18 9 6 1.519 110.1 -54.4 0.139 +25 H3 H1 E 24 18 9 1.101 108.4 -66.7 0.000 +26 O3 OH 3 24 18 9 1.421 108.7 173.5 0.000 +27 H30 HO E 26 24 18 0.976 108.5 51.3 0.281 +28 EP+3 EP E 26 24 18 0.700 109.5 171.3 -0.217 +29 EP-3 EP E 26 24 18 0.700 109.5 -68.7 -0.217 +30 C2 CG M 24 18 9 1.529 110.6 52.8 0.231 +31 H2 H1 E 30 24 18 1.105 104.4 63.4 0.000 +32 O2 OS M 30 24 18 1.415 109.5 -174.5 0.000 +33 EP+2 EP E 32 30 24 0.700 109.5 -29.4 -0.140 +34 EP-2 EP E 32 30 24 0.700 109.5 90.6 -0.140 + +LOOP +C2 C1 + +DONE +2-[B-D-MANNO] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +2mb.dat +2MB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.144 +12 H61 H1 E 11 9 6 1.092 108.3 179.3 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 62.9 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 -65.1 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -96.0 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 24.0 -0.209 +17 EP-6 EP E 14 11 9 0.700 109.5 144.0 -0.209 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.196 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 O4 OH 3 18 9 6 1.430 107.9 -174.0 0.000 +21 H4O HO E 20 18 9 0.958 109.2 -124.9 0.279 +22 EP+4 EP E 20 18 9 0.700 109.5 -4.9 -0.224 +23 EP-4 EP E 20 18 9 0.700 109.5 115.1 -0.224 +24 C3 CG M 18 9 6 1.519 110.1 -54.4 0.143 +25 H3 H1 E 24 18 9 1.101 108.4 -66.7 0.000 +26 O3 OH 3 24 18 9 1.421 108.7 173.5 0.000 +27 H30 HO E 26 24 18 0.976 108.5 168.7 0.278 +28 EP+3 EP E 26 24 18 0.700 109.5 48.7 -0.214 +29 EP-3 EP E 26 24 18 0.700 109.5 -71.3 -0.214 +30 C2 CG M 24 18 9 1.529 110.6 52.8 0.138 +31 H2 H1 E 30 24 18 1.105 106.2 -171.0 0.000 +32 O2 OS M 30 24 18 1.415 113.9 66.1 0.000 +33 EP+2 EP E 32 30 24 0.700 109.5 166.3 -0.114 +34 EP-2 EP E 32 30 24 0.700 109.5 -73.7 -0.114 + +LOOP +C2 C1 + +DONE +3,4-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +34gb.dat +WGB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.143 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.277 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.212 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.212 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.178 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 C3 CG 3 18 9 6 1.519 110.1 -54.4 0.113 +21 H3 H1 E 20 18 9 1.101 108.4 -66.7 0.000 +22 O3 OS B 20 18 9 1.421 108.7 173.5 0.000 +23 EP+3 EP E 22 20 18 0.700 109.5 171.3 -0.135 +24 EP-3 EP E 22 20 18 0.700 109.5 -68.7 -0.135 +25 C2 CG B 20 18 9 1.529 110.6 52.8 0.230 +26 H2 H1 E 25 20 18 1.105 104.4 63.4 0.000 +27 O2 OH 3 25 20 18 1.415 109.5 -174.5 0.000 +28 H2O HO E 27 25 20 0.957 110.0 -149.4 0.276 +29 EP+2 EP E 27 25 20 0.700 109.5 -29.4 -0.218 +30 EP-2 EP E 27 25 20 0.700 109.5 90.6 -0.218 +31 O4 OS M 18 9 6 1.430 107.9 -174.0 0.000 +32 EP+4 EP E 31 18 9 0.700 109.5 -19.6 -0.133 +33 EP-4 EP E 31 18 9 0.700 109.5 100.4 -0.133 + +LOOP +C2 C1 + +DONE +3,4-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +34lb.dat +WLB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.173 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.213 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.213 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.095 +19 H4 H1 E 18 9 6 1.100 107.5 -173.8 0.000 +20 C3 CG 3 18 9 6 1.519 110.1 -54.4 0.139 +21 H3 H1 E 20 18 9 1.101 108.4 -66.7 0.000 +22 O3 OS B 20 18 9 1.421 108.7 173.5 0.000 +23 EP+3 EP E 22 20 18 0.700 109.5 171.3 -0.133 +24 EP-3 EP E 22 20 18 0.700 109.5 -68.7 -0.133 +25 C2 CG B 20 18 9 1.529 110.6 52.8 0.230 +26 H2 H1 E 25 20 18 1.105 104.4 63.4 0.000 +27 O2 OH 3 25 20 18 1.415 109.5 -174.5 0.000 +28 H2O HO E 27 25 20 0.957 110.0 -149.4 0.272 +29 EP+2 EP E 27 25 20 0.700 109.5 -29.4 -0.219 +30 EP-2 EP E 27 25 20 0.700 109.5 90.6 -0.219 +31 O4 OS M 18 9 6 1.430 111.7 67.6 0.000 +32 EP+4 EP E 31 18 9 0.700 109.5 -141.8 -0.113 +33 EP-4 EP E 31 18 9 0.700 109.5 98.2 -0.113 + +LOOP +C2 C1 + +DONE +3,4-[B-D-MANNO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +34mb.dat +WMB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.144 +12 H61 H1 E 11 9 6 1.092 108.3 179.3 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 62.9 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 -65.1 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -96.0 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 24.0 -0.209 +17 EP-6 EP E 14 11 9 0.700 109.5 144.0 -0.209 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.196 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 C3 CG 3 18 9 6 1.519 110.1 -54.4 0.144 +21 H3 H1 E 20 18 9 1.101 108.4 -66.7 0.000 +22 O3 OS B 20 18 9 1.421 108.7 173.5 0.000 +23 EP+3 EP E 22 20 18 0.700 109.5 48.7 -0.132 +24 EP-3 EP E 22 20 18 0.700 109.5 -71.3 -0.132 +25 C2 CG B 20 18 9 1.529 110.6 52.8 0.138 +26 H2 H1 E 25 20 18 1.105 106.2 -171.0 0.000 +27 O2 OH 3 25 20 18 1.415 113.9 66.1 0.000 +28 H2O HO E 27 25 20 0.957 110.0 46.3 0.287 +29 EP+2 EP E 27 25 20 0.700 109.5 166.3 -0.201 +30 EP-2 EP E 27 25 20 0.700 109.5 -73.7 -0.201 +31 O4 OS M 18 9 6 1.430 107.9 -174.0 0.000 +32 EP+4 EP E 31 18 9 0.700 109.5 -4.9 -0.141 +33 EP-4 EP E 31 18 9 0.700 109.5 115.1 -0.141 + +LOOP +C2 C1 + +DONE +3,6-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +36gb.dat +VGB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS M 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.178 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OH 3 11 9 6 1.430 107.9 -174.0 0.000 +14 H4O HO E 16 11 9 0.958 109.2 -139.6 0.281 +15 EP+4 EP E 16 11 9 0.700 109.5 -19.6 -0.217 +16 EP-4 EP E 16 11 9 0.700 109.5 100.4 -0.217 +17 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.113 +18 H3 H1 E 17 11 9 1.101 108.4 -66.7 0.000 +19 O3 OS B 17 11 9 1.421 108.7 173.5 0.000 +20 EP+3 EP E 19 17 11 0.700 109.5 171.3 -0.135 +21 EP-3 EP E 19 17 11 0.700 109.5 -68.7 -0.135 +22 C2 CG B 17 11 9 1.529 110.6 52.8 0.230 +23 H2 H1 E 22 17 11 1.105 104.4 63.4 0.000 +24 O2 OH 3 22 17 11 1.415 109.5 -174.5 0.000 +25 H2O HO E 24 22 17 0.957 110.0 -149.4 0.276 +26 EP+2 EP E 24 22 17 0.700 109.5 -29.4 -0.218 +27 EP-2 EP E 24 22 17 0.700 109.5 90.6 -0.218 +28 C6 CG M 9 6 4 1.517 106.6 -177.2 0.143 +29 H61 H1 E 28 9 6 1.092 108.3 -178.0 0.000 +30 H62 H1 E 28 9 6 1.093 108.8 -59.0 0.000 +31 O6 OS M 28 9 6 1.413 112.7 65.2 0.000 +32 EP+6 EP E 31 28 9 0.700 109.5 178.1 -0.130 +33 EP-6 EP E 31 28 9 0.700 109.5 61.9 -0.130 + +LOOP +C2 C1 + +DONE +3,6-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +36lb.dat +VLB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.094 +12 H4 H1 E 11 9 6 1.100 107.5 -173.8 0.000 +13 O4 OH 3 11 9 6 1.430 111.7 67.6 0.000 +14 H4O HO E 13 11 9 0.958 109.2 -21.8 0.292 +15 EP+4 EP E 13 11 9 0.700 109.5 -141.8 -0.202 +16 EP-4 EP E 13 11 9 0.700 109.5 98.2 -0.202 +17 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.139 +18 H3 H1 E 17 11 9 1.101 108.4 -66.7 0.000 +19 O3 OS B 17 11 9 1.421 108.7 173.5 0.000 +20 EP+3 EP E 19 17 11 0.700 109.5 171.3 -0.133 +21 EP-3 EP E 19 17 11 0.700 109.5 -68.7 -0.133 +22 C2 CG B 17 11 9 1.529 110.6 52.8 0.230 +23 H2 H1 E 22 17 11 1.105 104.4 63.4 0.000 +24 O2 OH 3 22 17 11 1.415 109.5 -174.5 0.000 +25 H2O HO E 24 22 17 0.957 110.0 -149.4 0.272 +26 EP+2 EP E 24 22 17 0.700 109.5 -29.4 -0.219 +27 EP-2 EP E 24 22 17 0.700 109.5 90.6 -0.219 +28 C6 CG M 9 6 4 1.517 106.6 -177.2 0.173 +29 H61 H1 E 28 9 6 1.092 108.3 -178.0 0.000 +30 H62 H1 E 28 9 6 1.093 108.8 -59.0 0.000 +31 O6 OS M 28 9 6 1.413 112.7 65.2 0.000 +32 EP+6 EP E 31 28 9 0.700 109.5 178.1 -0.133 +33 EP-6 EP E 31 28 9 0.700 109.5 61.9 -0.133 + +LOOP +C2 C1 + +DONE +3,6-[B-D-MANNO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +36mb.dat +VMB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.196 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OH 3 11 9 6 1.430 107.9 -174.0 0.000 +14 H4O HO E 13 11 9 0.958 109.2 -124.9 0.279 +15 EP+4 EP E 13 11 9 0.700 109.5 -4.9 -0.224 +16 EP-4 EP E 13 11 9 0.700 109.5 115.1 -0.224 +17 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.144 +18 H3 H1 E 17 11 9 1.101 108.4 -66.7 0.000 +19 O3 OS B 17 11 9 1.421 108.7 173.5 0.000 +20 EP+3 EP E 19 17 11 0.700 109.5 48.7 -0.132 +21 EP-3 EP E 19 17 11 0.700 109.5 -71.3 -0.132 +22 C2 CG B 17 11 9 1.529 110.6 52.8 0.138 +23 H2 H1 E 22 17 11 1.105 106.2 -171.0 0.000 +24 O2 OH 3 22 17 11 1.415 113.9 66.1 0.000 +25 H2O HO E 24 22 17 0.957 110.0 46.3 0.287 +26 EP+2 EP E 24 22 17 0.700 109.5 166.3 -0.201 +27 EP-2 EP E 24 22 17 0.700 109.5 -73.7 -0.201 +28 C6 CG M 9 6 4 1.517 106.6 -177.2 0.144 +29 H61 H1 E 28 9 6 1.092 108.3 179.3 0.000 +30 H62 H1 E 28 9 6 1.093 108.8 62.9 0.000 +31 O6 OS M 28 9 6 1.413 112.7 -65.1 0.000 +32 EP+6 EP E 31 28 9 0.700 109.5 24.0 -0.129 +33 EP-6 EP E 31 28 9 0.700 109.5 144.0 -0.129 + +LOOP +C2 C1 + +DONE +3-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +3gb.dat +3GB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.143 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.277 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.212 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.212 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.178 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 O4 OH 3 18 9 6 1.430 107.9 -174.0 0.000 +21 H4O HO E 20 18 9 0.958 109.2 -139.6 0.281 +22 EP+4 EP E 20 18 9 0.700 109.5 -19.6 -0.217 +23 EP-4 EP E 20 18 9 0.700 109.5 100.4 -0.217 +24 C3 CG M 18 9 6 1.519 110.1 -54.4 0.113 +25 H3 H1 E 24 18 9 1.101 108.4 -66.7 0.000 +26 C2 CG B 24 18 9 1.529 110.6 52.8 0.230 +27 H2 H1 E 26 24 18 1.105 104.4 63.4 0.000 +28 O2 OH 3 26 24 18 1.415 109.5 -174.5 0.000 +29 H2O HO E 28 26 24 0.957 110.0 -149.4 0.276 +30 EP+2 EP E 28 26 24 0.700 109.5 -29.4 -0.218 +31 EP-2 EP E 28 26 24 0.700 109.5 90.6 -0.218 +32 O3 OS M 24 18 9 1.421 108.7 173.5 0.000 +33 EP+3 EP E 32 24 18 0.700 109.5 171.3 -0.135 +34 EP-3 EP E 32 24 18 0.700 109.5 -68.7 -0.135 + +LOOP +C2 C1 + +DONE +3-[B-D-GALACTO] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +3lb.dat +3LB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.173 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.213 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.213 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.094 +19 H4 H1 E 18 9 6 1.100 107.5 -173.8 0.000 +20 O4 OH 3 18 9 6 1.430 111.7 67.6 0.000 +21 H4O HO E 20 18 9 0.958 109.2 -21.8 0.292 +22 EP+4 EP E 20 18 9 0.700 109.5 -141.8 -0.202 +23 EP-4 EP E 20 18 9 0.700 109.5 98.2 -0.202 +24 C3 CG M 18 9 6 1.519 110.1 -54.4 0.139 +25 H3 H1 E 24 18 9 1.101 108.4 -66.7 0.000 +26 C2 CG B 24 18 9 1.529 110.6 52.8 0.230 +27 H2 H1 E 26 24 18 1.105 104.4 63.4 0.000 +28 O2 OH 3 26 24 18 1.415 109.5 -174.5 0.000 +29 H2O HO E 28 26 24 0.957 110.0 -149.4 0.272 +30 EP+2 EP E 28 26 24 0.700 109.5 -29.4 -0.219 +31 EP-2 EP E 28 26 24 0.700 109.5 90.6 -0.219 +32 O3 OS M 24 18 9 1.421 108.7 173.5 0.000 +33 EP+3 EP E 32 24 18 0.700 109.5 171.3 -0.133 +34 EP-3 EP E 32 24 18 0.700 109.5 -68.7 -0.133 + +LOOP +C2 C1 + +DONE +3-[B-D-MANNO] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +3mb.dat +3MB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.144 +12 H61 H1 E 11 9 6 1.092 108.3 179.3 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 62.9 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 -65.1 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -96.0 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 24.0 -0.209 +17 EP-6 EP E 14 11 9 0.700 109.5 144.0 -0.209 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.196 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 O4 OH 3 18 9 6 1.430 107.9 -174.0 0.000 +21 H4O HO E 20 18 9 0.958 109.2 -124.9 0.279 +22 EP+4 EP E 20 18 9 0.700 109.5 -4.9 -0.224 +23 EP-4 EP E 20 18 9 0.700 109.5 115.1 -0.224 +24 C3 CG M 18 9 6 1.519 110.1 -54.4 0.144 +25 H3 H1 E 24 18 9 1.101 108.4 -66.7 0.000 +26 C2 CG B 24 18 9 1.529 110.6 52.8 0.138 +27 H2 H1 E 26 24 18 1.105 106.2 -171.0 0.000 +28 O2 OH 3 26 24 18 1.415 113.9 66.1 0.000 +29 H2O HO E 28 26 24 0.957 110.0 46.3 0.287 +30 EP+2 EP E 28 26 24 0.700 109.5 166.3 -0.201 +31 EP-2 EP E 28 26 24 0.700 109.5 -73.7 -0.201 +32 O3 OS M 24 18 9 1.421 108.7 173.5 0.000 +33 EP+3 EP E 32 24 18 0.700 109.5 48.7 -0.132 +34 EP-3 EP E 32 24 18 0.700 109.5 -71.3 -0.132 + +LOOP +C2 C1 + +DONE +4,6-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +46gb.dat +UGB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS M 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.178 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OS B 11 9 6 1.430 107.9 -174.0 0.000 +14 EP+4 EP E 13 11 9 0.700 109.5 -19.6 -0.133 +15 EP-4 EP E 13 11 9 0.700 109.5 100.4 -0.133 +16 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.112 +17 H3 H1 E 16 11 9 1.101 108.4 -66.7 0.000 +18 O3 OH 3 16 11 9 1.421 108.7 173.5 0.000 +19 H30 HO E 18 16 11 0.976 108.5 51.3 0.282 +20 EP+3 EP E 18 16 11 0.700 109.5 171.3 -0.219 +21 EP-3 EP E 18 16 11 0.700 109.5 -68.7 -0.219 +22 C2 CG B 16 14 9 1.529 110.6 52.8 0.230 +23 H2 H1 E 22 16 11 1.105 104.4 63.4 0.000 +24 O2 OH 3 22 16 11 1.415 109.5 -174.5 0.000 +25 H2O HO E 24 22 16 0.957 110.0 -149.4 0.276 +26 EP+2 EP E 24 22 16 0.700 109.5 -29.4 -0.218 +27 EP-2 EP E 24 22 16 0.700 109.5 90.6 -0.218 +28 C6 CG M 9 6 4 1.517 106.6 -177.2 0.143 +29 H61 H1 E 28 9 6 1.092 108.3 -178.0 0.000 +30 H62 H1 E 28 9 6 1.093 108.8 -59.0 0.000 +31 O6 OS M 28 9 6 1.413 112.7 65.2 0.000 +32 EP+6 EP E 31 28 9 0.700 109.5 178.1 -0.130 +33 EP-6 EP E 31 28 9 0.700 109.5 61.9 -0.130 + +LOOP +C2 C1 + +DONE +4,6-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +46lb.dat +ULB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.095 +12 H4 H1 E 11 9 6 1.100 107.5 -173.8 0.000 +13 O4 OS B 11 9 6 1.430 111.7 67.6 0.000 +14 EP+4 EP E 13 11 9 0.700 109.5 -141.8 -0.113 +15 EP-4 EP E 13 11 9 0.700 109.5 98.2 -0.113 +16 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.139 +17 H3 H1 E 16 11 9 1.101 108.4 -66.7 0.000 +18 O3 OH 3 16 11 9 1.421 108.7 173.5 0.000 +19 H30 HO E 18 16 11 0.976 108.5 51.3 0.281 +20 EP+3 EP E 18 16 11 0.700 109.5 171.3 -0.217 +21 EP-3 EP E 18 16 11 0.700 109.5 -68.7 -0.217 +22 C2 CG B 16 11 9 1.529 110.6 52.8 0.230 +23 H2 H1 E 22 16 11 1.105 104.4 63.4 0.000 +24 O2 OH 3 22 16 11 1.415 109.5 -174.5 0.000 +25 H2O HO E 24 22 16 0.957 110.0 -149.4 0.272 +26 EP+2 EP E 24 22 16 0.700 109.5 -29.4 -0.219 +27 EP-2 EP E 24 22 16 0.700 109.5 90.6 -0.219 +28 C6 CG M 9 6 4 1.517 106.6 -177.2 0.173 +29 H61 H1 E 28 9 6 1.092 108.3 -178.0 0.000 +30 H62 H1 E 28 9 6 1.093 108.8 -59.0 0.000 +31 O6 OS M 28 9 6 1.413 112.7 65.2 0.000 +32 EP+6 EP E 31 28 9 0.700 109.5 178.1 -0.133 +33 EP-6 EP E 31 28 9 0.700 109.5 61.9 -0.133 + +LOOP +C2 C1 + +DONE +4,6-[B-D-MANNO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +46mb.dat +UMB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.196 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OS B 11 9 6 1.430 107.9 -174.0 0.000 +14 EP+4 EP E 13 11 9 0.700 109.5 -4.9 -0.141 +15 EP-4 EP E 13 11 9 0.700 109.5 115.1 -0.141 +16 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.143 +17 H3 H1 E 16 11 9 1.101 108.4 -66.7 0.000 +18 O3 OH 3 16 11 9 1.421 108.7 173.5 0.000 +19 H30 HO E 18 16 11 0.976 108.5 168.7 0.278 +20 EP+3 EP E 18 16 11 0.700 109.5 48.7 -0.214 +21 EP-3 EP E 18 16 11 0.700 109.5 -71.3 -0.214 +22 C2 CG B 16 11 9 1.529 110.6 52.8 0.138 +23 H2 H1 E 22 16 11 1.105 106.2 -171.0 0.000 +24 O2 OH 3 22 16 11 1.415 113.9 66.1 0.000 +25 H2O HO E 24 22 16 0.957 110.0 46.3 0.287 +26 EP+2 EP E 24 22 16 0.700 109.5 166.3 -0.201 +27 EP-2 EP E 24 22 16 0.700 109.5 -73.7 -0.201 +28 C6 CG M 9 6 4 1.517 106.6 -177.2 0.144 +29 H61 H1 E 28 9 6 1.092 108.3 179.3 0.000 +30 H62 H1 E 28 9 6 1.093 108.8 62.9 0.000 +31 O6 OS M 28 9 6 1.413 112.7 -65.1 0.000 +32 EP+6 EP E 31 28 9 0.700 109.5 24.0 -0.129 +33 EP-6 EP E 31 28 9 0.700 109.5 144.0 -0.129 + +LOOP +C2 C1 + +DONE +4-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +4gb.dat +4GB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.143 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.277 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.212 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.212 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.178 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 C3 CG 3 18 9 6 1.519 110.1 -54.4 0.112 +21 H3 H1 E 20 18 9 1.101 108.4 -66.7 0.000 +22 O3 OH 3 20 18 9 1.421 108.7 173.5 0.000 +23 H30 HO E 22 20 18 0.976 108.5 51.3 0.282 +24 EP+3 EP E 22 20 18 0.700 109.5 171.3 -0.219 +25 EP-3 EP E 22 20 18 0.700 109.5 -68.7 -0.219 +26 C2 CG B 20 18 9 1.529 110.6 52.8 0.230 +27 H2 H1 E 26 20 18 1.105 104.4 63.4 0.000 +28 O2 OH 3 26 20 18 1.415 109.5 -174.5 0.000 +29 H2O HO E 28 26 20 0.957 110.0 -149.4 0.276 +30 EP+2 EP E 28 26 20 0.700 109.5 -29.4 -0.218 +31 EP-2 EP E 28 26 20 0.700 109.5 90.6 -0.218 +32 O4 OS M 18 9 6 1.430 107.9 -174.0 0.000 +33 EP+4 EP E 32 18 9 0.700 109.5 -19.6 -0.133 +34 EP-4 EP E 32 18 9 0.700 109.5 100.4 -0.133 + +LOOP +C2 C1 + +DONE +4-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +4lb.dat +4LB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.173 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.213 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.213 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.095 +19 H4 H1 E 18 9 6 1.100 107.5 -173.8 0.000 +20 C3 CG 3 18 9 6 1.519 110.1 -54.4 0.139 +21 H3 H1 E 20 18 9 1.101 108.4 -66.7 0.000 +22 O3 OH 3 20 18 9 1.421 108.7 173.5 0.000 +23 H30 HO E 22 20 18 0.976 108.5 51.3 0.281 +24 EP+3 EP E 22 20 18 0.700 109.5 171.3 -0.217 +25 EP-3 EP E 22 20 18 0.700 109.5 -68.7 -0.217 +26 C2 CG B 20 18 9 1.529 110.6 52.8 0.230 +27 H2 H1 E 26 20 18 1.105 104.4 63.4 0.000 +28 O2 OH 3 26 20 18 1.415 109.5 -174.5 0.000 +29 H2O HO E 28 26 20 0.957 110.0 -149.4 0.272 +30 EP+2 EP E 28 26 20 0.700 109.5 -29.4 -0.219 +31 EP-2 EP E 28 26 20 0.700 109.5 90.6 -0.219 +32 O4 OS M 18 9 6 1.430 111.7 67.6 0.000 +33 EP+4 EP E 32 18 9 0.700 109.5 -141.8 -0.113 +34 EP-4 EP E 32 18 9 0.700 109.5 98.2 -0.113 + +LOOP +C2 C1 + +DONE +4-[B-D-MANNO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +4mb.dat +4MB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.144 +12 H61 H1 E 11 9 6 1.092 108.3 179.3 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 62.9 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 -65.1 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -96.0 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 24.0 -0.209 +17 EP-6 EP E 14 11 9 0.700 109.5 144.0 -0.209 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.196 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 C3 CG 3 18 9 6 1.519 110.1 -54.4 0.143 +21 H3 H1 E 20 18 9 1.101 108.4 -66.7 0.000 +22 O3 OH 3 20 18 9 1.421 108.7 173.5 0.000 +23 H30 HO E 22 20 18 0.976 108.5 168.7 0.278 +24 EP+3 EP E 22 20 18 0.700 109.5 48.7 -0.214 +25 EP-3 EP E 22 20 18 0.700 109.5 -71.3 -0.214 +26 C2 CG B 20 18 9 1.529 110.6 52.8 0.138 +27 H2 H1 E 26 20 18 1.105 106.2 -171.0 0.000 +28 O2 OH 3 26 20 18 1.415 113.9 66.1 0.000 +29 H2O HO E 28 26 20 0.957 110.0 46.3 0.287 +30 EP+2 EP E 28 26 20 0.700 109.5 166.3 -0.201 +31 EP-2 EP E 28 26 20 0.700 109.5 -73.7 -0.201 +32 O4 OS M 18 9 6 1.430 107.9 -174.0 0.000 +33 EP+4 EP E 32 18 9 0.700 109.5 -4.9 -0.141 +34 EP-4 EP E 32 18 9 0.700 109.5 115.1 -0.141 + +LOOP +C2 C1 + +DONE +6-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +6gb.dat +6GB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS M 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.178 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OH 3 11 9 6 1.430 107.9 -174.0 0.000 +14 H4O HO E 13 11 9 0.958 109.2 -139.6 0.281 +15 EP+4 EP E 13 11 9 0.700 109.5 -19.6 -0.217 +16 EP-4 EP E 13 11 9 0.700 109.5 100.4 -0.217 +17 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.112 +18 H3 H1 E 17 11 9 1.101 108.4 -66.7 0.000 +19 O3 OH 3 17 11 9 1.421 108.7 173.5 0.000 +20 H30 HO E 19 17 11 0.976 108.5 51.3 0.282 +21 EP+3 EP E 19 17 11 0.700 109.5 171.3 -0.219 +22 EP-3 EP E 19 17 11 0.700 109.5 -68.7 -0.219 +23 C2 CG B 17 11 9 1.529 110.6 52.8 0.230 +24 H2 H1 E 23 17 11 1.105 104.4 63.4 0.000 +25 O2 OH 3 23 17 11 1.415 109.5 -174.5 0.000 +26 H2O HO E 25 23 17 0.957 110.0 -149.4 0.276 +27 EP+2 EP E 25 23 17 0.700 109.5 -29.4 -0.218 +28 EP-2 EP E 25 23 17 0.700 109.5 90.6 -0.218 +29 C6 CG M 9 6 4 1.517 106.6 -177.2 0.143 +30 H61 H1 E 29 9 6 1.092 108.3 -178.0 0.000 +31 H62 H1 E 29 9 6 1.093 108.8 -59.0 0.000 +32 O6 OS M 29 9 6 1.413 112.7 65.2 0.000 +33 EP+6 EP E 32 29 9 0.700 109.5 178.1 -0.130 +34 EP-6 EP E 32 29 9 0.700 109.5 61.9 -0.130 + +LOOP +C2 C1 + +DONE +6-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +6lb.dat +6LB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.094 +12 H4 H1 E 11 9 6 1.100 107.5 -173.8 0.000 +13 O4 OH 3 11 9 6 1.430 111.7 67.6 0.000 +14 H4O HO E 13 11 9 0.958 109.2 -21.8 0.292 +15 EP+4 EP E 13 11 9 0.700 109.5 -141.8 -0.202 +16 EP-4 EP E 13 11 9 0.700 109.5 98.2 -0.202 +17 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.139 +18 H3 H1 E 17 11 9 1.101 108.4 -66.7 0.000 +19 O3 OH 3 17 11 9 1.421 108.7 173.5 0.000 +20 H30 HO E 19 17 11 0.976 108.5 51.3 0.281 +21 EP+3 EP E 19 17 11 0.700 109.5 171.3 -0.217 +22 EP-3 EP E 19 17 11 0.700 109.5 -68.7 -0.217 +23 C2 CG B 17 11 9 1.529 110.6 52.8 0.230 +24 H2 H1 E 23 17 11 1.105 104.4 63.4 0.000 +25 O2 OH 3 23 17 11 1.415 109.5 -174.5 0.000 +26 H2O HO E 25 23 17 0.957 110.0 -149.4 0.272 +27 EP+2 EP E 25 23 17 0.700 109.5 -29.4 -0.219 +28 EP-2 EP E 25 23 17 0.700 109.5 90.6 -0.219 +29 C6 CG M 9 6 4 1.517 106.6 -177.2 0.173 +30 H61 H1 E 29 9 6 1.092 108.3 -178.0 0.000 +31 H62 H1 E 29 9 6 1.093 108.8 -59.0 0.000 +32 O6 OS M 29 9 6 1.413 112.7 65.2 0.000 +33 EP+6 EP E 32 29 9 0.700 109.5 178.1 -0.133 +34 EP-6 EP E 32 29 9 0.700 109.5 61.9 -0.133 + +LOOP +C2 C1 + +DONE +6-[B-D-MANNO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +6mb.dat +6MB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.196 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OH 3 11 9 6 1.430 107.9 -174.0 0.000 +14 H4O HO E 13 11 9 0.958 109.2 -124.9 0.279 +15 EP+4 EP E 13 11 9 0.700 109.5 -4.9 -0.224 +16 EP-4 EP E 13 11 9 0.700 109.5 115.1 -0.224 +17 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.143 +18 H3 H1 E 17 11 9 1.101 108.4 -66.7 0.000 +19 O3 OH 3 17 11 9 1.421 108.7 173.5 0.000 +20 H30 HO E 19 17 11 0.976 108.5 168.7 0.278 +21 EP+3 EP E 19 17 11 0.700 109.5 48.7 -0.214 +22 EP-3 EP E 19 17 11 0.700 109.5 -71.3 -0.214 +23 C2 CG B 17 11 9 1.529 110.6 52.8 0.138 +24 H2 H1 E 23 17 11 1.105 106.2 -171.0 0.000 +25 O2 OH 3 23 17 11 1.415 113.9 66.1 0.000 +26 H2O HO E 25 23 17 0.957 110.0 46.3 0.287 +27 EP+2 EP E 25 23 17 0.700 109.5 166.3 -0.201 +28 EP-2 EP E 25 23 17 0.700 109.5 -73.7 -0.201 +29 C6 CG M 9 6 4 1.517 106.6 -177.2 0.144 +30 H61 H1 E 29 9 6 1.092 108.3 179.3 0.000 +31 H62 H1 E 29 9 6 1.093 108.8 62.9 0.000 +32 O6 OS M 29 9 6 1.413 112.7 -65.1 0.000 +33 EP+6 EP E 32 29 9 0.700 109.5 24.0 -0.129 +34 EP-6 EP E 32 29 9 0.700 109.5 144.0 -0.129 + +LOOP +C2 C1 + +DONE +B-D-GLUCOPYRANO terminal RESP010 ESP hf/6-31G* ENS AVG EPS +gb.dat +1GB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.143 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.277 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.212 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.212 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.178 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 O4 OH 3 18 9 6 1.430 107.9 -174.0 0.000 +21 H4O HO E 20 18 9 0.958 109.2 -139.6 0.281 +22 EP+4 EP E 20 18 9 0.700 109.5 -19.6 -0.217 +23 EP-4 EP E 20 18 9 0.700 109.5 100.4 -0.217 +24 C3 CG M 18 9 6 1.519 110.1 -54.4 0.112 +25 H3 H1 E 24 18 9 1.101 108.4 -66.7 0.000 +26 O3 OH 3 24 18 9 1.421 108.7 173.5 0.000 +27 H30 HO E 26 24 18 0.976 108.5 51.3 0.282 +28 EP+3 EP E 26 24 18 0.700 109.5 171.3 -0.219 +29 EP-3 EP E 26 24 18 0.700 109.5 -68.7 -0.219 +30 C2 CG M 24 18 9 1.529 110.6 52.8 0.230 +31 H2 H1 E 30 24 18 1.105 104.4 63.4 0.000 +32 O2 OH M 30 24 18 1.415 109.5 -174.5 0.000 +33 H2O HO E 32 30 24 0.957 110.0 -149.4 0.276 +34 EP+2 EP E 32 30 24 0.700 109.5 -29.4 -0.218 +35 EP-2 EP E 32 30 24 0.700 109.5 90.6 -0.218 + +LOOP +C2 C1 + +DONE +B-D-GALACTO terminal RESP010 ESP hf/6-31G* ENS AVG EPs +lb.dat +1LB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.173 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.213 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.213 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.094 +19 H4 H1 E 18 9 6 1.100 107.5 -173.8 0.000 +20 O4 OH 3 18 9 6 1.430 111.7 67.6 0.000 +21 H4O HO E 20 18 9 0.958 109.2 -21.8 0.292 +22 EP+4 EP E 20 18 9 0.700 109.5 -141.8 -0.202 +23 EP-4 EP E 20 18 9 0.700 109.5 98.2 -0.202 +24 C3 CG M 18 9 6 1.519 110.1 -54.4 0.139 +25 H3 H1 E 24 18 9 1.101 108.4 -66.7 0.000 +26 O3 OH 3 24 18 9 1.421 108.7 173.5 0.000 +27 H30 HO E 26 24 18 0.976 108.5 51.3 0.281 +28 EP+3 EP E 26 24 18 0.700 109.5 171.3 -0.217 +29 EP-3 EP E 26 24 18 0.700 109.5 -68.7 -0.217 +30 C2 CG M 24 18 9 1.529 110.6 52.8 0.230 +31 H2 H1 E 30 24 18 1.105 104.4 63.4 0.000 +32 O2 OH M 30 24 18 1.415 109.5 -174.5 0.000 +33 H2O HO E 32 30 24 0.957 110.0 -149.4 0.272 +34 EP+2 EP E 32 30 24 0.700 109.5 -29.4 -0.219 +35 EP-2 EP E 32 30 24 0.700 109.5 90.6 -0.219 + +LOOP +C2 C1 + +DONE +B-D-MANNO terminal RESP010 ESP hf/6-31G* ENS AVG EPs +mb.dat +1MB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.144 +12 H61 H1 E 11 9 6 1.092 108.3 179.3 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 62.9 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 -65.1 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -96.0 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 24.0 -0.209 +17 EP-6 EP E 14 11 9 0.700 109.5 144.0 -0.209 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.196 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 O4 OH 3 18 9 6 1.430 107.9 -174.0 0.000 +21 H4O HO E 20 18 9 0.958 109.2 -124.9 0.279 +22 EP+4 EP E 20 18 9 0.700 109.5 -4.9 -0.224 +23 EP-4 EP E 20 18 9 0.700 109.5 115.1 -0.224 +24 C3 CG M 18 9 6 1.519 110.1 -54.4 0.143 +25 H3 H1 E 24 18 9 1.101 108.4 -66.7 0.000 +26 O3 OH 3 24 18 9 1.421 108.7 173.5 0.000 +27 H30 HO E 26 24 18 0.976 108.5 168.7 0.278 +28 EP+3 EP E 26 24 18 0.700 109.5 48.7 -0.214 +29 EP-3 EP E 26 24 18 0.700 109.5 -71.3 -0.214 +30 C2 CG M 24 18 9 1.529 110.6 52.8 0.138 +31 H2 H1 E 30 24 18 1.105 106.2 -171.0 0.000 +32 O2 OH M 30 24 18 1.415 113.9 66.1 0.000 +33 H2O HO E 32 30 24 0.957 110.0 46.3 0.287 +34 EP+2 EP E 32 30 24 0.700 109.5 166.3 -0.201 +35 EP-2 EP E 32 30 24 0.700 109.5 -73.7 -0.201 + +LOOP +C2 C1 + +DONE +2,3,4-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +234gb.dat +TGB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.143 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.277 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.212 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.212 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.178 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 C3 CG 3 18 9 6 1.519 110.1 -54.4 0.113 +21 H3 H1 E 20 18 9 1.101 108.4 -66.7 0.000 +22 O3 OS B 20 18 9 1.421 108.7 173.5 0.000 +23 EP+3 EP E 22 20 18 0.700 109.5 171.3 -0.135 +24 EP-3 EP E 22 20 18 0.700 109.5 -68.7 -0.135 +25 C2 CG B 20 18 9 1.529 110.6 52.8 0.231 +26 H2 H1 E 25 20 18 1.105 104.4 63.4 0.000 +27 O2 OS B 25 20 18 1.415 109.5 -174.5 0.000 +28 EP+2 EP E 27 25 20 0.700 109.5 -29.4 -0.137 +29 EP-2 EP E 27 25 20 0.700 109.5 90.6 -0.137 +30 O4 OS M 18 9 6 1.430 107.9 -174.0 0.000 +31 EP+4 EP E 30 18 9 0.700 109.5 -19.6 -0.133 +32 EP-4 EP E 30 18 9 0.700 109.5 100.4 -0.133 + +LOOP +C2 C1 + +DONE +2,3,6-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +236gb.dat +SGB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS M 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.178 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OH 3 11 9 6 1.430 107.9 -174.0 0.000 +14 H4O HO E 16 11 9 0.958 109.2 -139.6 0.281 +15 EP+4 EP E 16 11 9 0.700 109.5 -19.6 -0.217 +16 EP-4 EP E 16 11 9 0.700 109.5 100.4 -0.217 +17 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.113 +18 H3 H1 E 17 11 9 1.101 108.4 -66.7 0.000 +19 O3 OS B 17 11 9 1.421 108.7 173.5 0.000 +20 EP+3 EP E 19 17 11 0.700 109.5 171.3 -0.135 +21 EP-3 EP E 19 17 11 0.700 109.5 -68.7 -0.135 +22 C2 CG B 17 11 9 1.529 110.6 52.8 0.231 +23 H2 H1 E 22 17 11 1.105 104.4 63.4 0.000 +24 O2 OS B 22 17 11 1.415 109.5 -174.5 0.000 +25 EP+2 EP E 24 22 17 0.700 109.5 -29.4 -0.137 +26 EP-2 EP E 24 22 17 0.700 109.5 90.6 -0.137 +27 C6 CG M 9 6 4 1.517 106.6 -177.2 0.143 +28 H61 H1 E 27 9 6 1.092 108.3 -178.0 0.000 +29 H62 H1 E 27 9 6 1.093 108.8 -59.0 0.000 +30 O6 OS M 27 9 6 1.413 112.7 65.2 0.000 +31 EP+6 EP E 30 27 9 0.700 109.5 178.1 -0.130 +32 EP-6 EP E 30 27 9 0.700 109.5 61.9 -0.130 + +LOOP +C2 C1 + +DONE +2,4,6-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +246gb.dat +RGB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS M 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.178 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OS B 11 9 6 1.430 107.9 -174.0 0.000 +14 EP+4 EP E 13 11 9 0.700 109.5 -19.6 -0.133 +15 EP-4 EP E 13 11 9 0.700 109.5 100.4 -0.133 +16 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.112 +17 H3 H1 E 16 11 9 1.101 108.4 -66.7 0.000 +18 O3 OH 3 16 11 9 1.421 108.7 173.5 0.000 +19 H30 HO E 18 16 11 0.976 108.5 51.3 0.282 +20 EP+3 EP E 18 16 11 0.700 109.5 171.3 -0.219 +21 EP-3 EP E 18 16 11 0.700 109.5 -68.7 -0.219 +22 C2 CG B 16 14 9 1.529 110.6 52.8 0.231 +23 H2 H1 E 22 16 11 1.105 104.4 63.4 0.000 +24 O2 OS B 22 16 11 1.415 109.5 -174.5 0.000 +25 EP+2 EP E 24 22 16 0.700 109.5 -29.4 -0.137 +26 EP-2 EP E 24 22 16 0.700 109.5 90.6 -0.137 +27 C6 CG M 9 6 4 1.517 106.6 -177.2 0.143 +28 H61 H1 E 27 9 6 1.092 108.3 -178.0 0.000 +29 H62 H1 E 27 9 6 1.093 108.8 -59.0 0.000 +30 O6 OS M 27 9 6 1.413 112.7 65.2 0.000 +31 EP+6 EP E 30 27 9 0.700 109.5 178.1 -0.130 +32 EP-6 EP E 30 27 9 0.700 109.5 61.9 -0.130 + +LOOP +C2 C1 + +DONE +3,4,6-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +346gb.dat +QGB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS M 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.178 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OS B 11 9 6 1.430 107.9 -174.0 0.000 +14 EP+4 EP E 13 11 9 0.700 109.5 -19.6 -0.133 +15 EP-4 EP E 13 11 9 0.700 109.5 100.4 -0.133 +16 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.113 +17 H3 H1 E 16 11 9 1.101 108.4 -66.7 0.000 +18 O3 OS B 16 11 9 1.421 108.7 173.5 0.000 +19 EP+3 EP E 18 16 11 0.700 109.5 171.3 -0.135 +20 EP-3 EP E 18 16 11 0.700 109.5 -68.7 -0.135 +21 C2 CG B 16 14 9 1.529 110.6 52.8 0.230 +22 H2 H1 E 21 16 11 1.105 104.4 63.4 0.000 +23 O2 OH 3 21 16 11 1.415 109.5 -174.5 0.000 +24 H2O HO E 23 21 16 0.957 110.0 -149.4 0.276 +25 EP+2 EP E 23 21 16 0.700 109.5 -29.4 -0.218 +26 EP-2 EP E 23 21 16 0.700 109.5 90.6 -0.218 +27 C6 CG M 9 6 4 1.517 106.6 -177.2 0.143 +28 H61 H1 E 27 9 6 1.092 108.3 -178.0 0.000 +29 H62 H1 E 27 9 6 1.093 108.8 -59.0 0.000 +30 O6 OS M 27 9 6 1.413 112.7 65.2 0.000 +31 EP+6 EP E 30 27 9 0.700 109.5 178.1 -0.130 +32 EP-6 EP E 30 27 9 0.700 109.5 61.9 -0.130 + +LOOP +C2 C1 + +DONE +2,3,4,6-[B-D-GLUCOPYRANO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPS +2346gb.dat +PGB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 60.0 0.182 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS M 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.151 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.151 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.186 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.178 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OS B 11 9 6 1.430 107.9 -174.0 0.000 +14 EP+4 EP E 13 11 9 0.700 109.5 -19.6 -0.133 +15 EP-4 EP E 13 11 9 0.700 109.5 100.4 -0.133 +16 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.113 +17 H3 H1 E 16 11 9 1.101 108.4 -66.7 0.000 +18 O3 OS B 16 11 9 1.421 108.7 173.5 0.000 +19 EP+3 EP E 18 16 11 0.700 109.5 171.3 -0.135 +20 EP-3 EP E 18 16 11 0.700 109.5 -68.7 -0.135 +21 C2 CG B 16 14 9 1.529 110.6 52.8 0.231 +22 H2 H1 E 21 16 11 1.105 104.4 63.4 0.000 +23 O2 OS B 21 16 11 1.415 109.5 -174.5 0.000 +24 EP+2 EP E 23 21 16 0.700 109.5 -29.4 -0.137 +25 EP-2 EP E 23 21 16 0.700 109.5 90.6 -0.137 +26 C6 CG M 9 6 4 1.517 106.6 -177.2 0.143 +27 H61 H1 E 26 9 6 1.092 108.3 -178.0 0.000 +28 H62 H1 E 26 9 6 1.093 108.8 -59.0 0.000 +29 O6 OS M 26 9 6 1.413 112.7 65.2 0.000 +30 EP+6 EP E 29 26 9 0.700 109.5 178.1 -0.130 +31 EP-6 EP E 29 26 9 0.700 109.5 61.9 -0.130 + +LOOP +C2 C1 + +DONE +2,3,6-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +236lb.dat +SLB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.094 +12 H4 H1 E 11 9 6 1.100 107.5 -173.8 0.000 +13 O4 OH 3 11 9 6 1.430 111.7 67.6 0.000 +14 H4O HO E 13 11 9 0.958 109.2 -21.8 0.292 +15 EP+4 EP E 13 11 9 0.700 109.5 -141.8 -0.202 +16 EP-4 EP E 13 11 9 0.700 109.5 98.2 -0.202 +17 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.139 +18 H3 H1 E 17 11 9 1.101 108.4 -66.7 0.000 +19 O3 OS B 17 11 9 1.421 108.7 173.5 0.000 +20 EP+3 EP E 19 17 11 0.700 109.5 171.3 -0.133 +21 EP-3 EP E 19 17 11 0.700 109.5 -68.7 -0.133 +22 C2 CG B 17 11 9 1.529 110.6 52.8 0.231 +23 H2 H1 E 22 17 11 1.105 104.4 63.4 0.000 +24 O2 OS B 22 17 11 1.415 109.5 -174.5 0.000 +25 EP+2 EP E 24 22 17 0.700 109.5 -29.4 -0.140 +26 EP-2 EP E 24 22 17 0.700 109.5 90.6 -0.140 +27 C6 CG M 9 6 4 1.517 106.6 -177.2 0.173 +28 H61 H1 E 27 9 6 1.092 108.3 -178.0 0.000 +29 H62 H1 E 27 9 6 1.093 108.8 -59.0 0.000 +30 O6 OS M 27 9 6 1.413 112.7 65.2 0.000 +31 EP+6 EP E 30 27 9 0.700 109.5 178.1 -0.133 +32 EP-6 EP E 30 27 9 0.700 109.5 61.9 -0.133 + +LOOP +C2 C1 + +DONE +2,4,6-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +246lb.dat +RLB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.095 +12 H4 H1 E 11 9 6 1.100 107.5 -173.8 0.000 +13 O4 OS B 11 9 6 1.430 111.7 67.6 0.000 +14 EP+4 EP E 13 11 9 0.700 109.5 -141.8 -0.113 +15 EP-4 EP E 13 11 9 0.700 109.5 98.2 -0.113 +16 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.139 +17 H3 H1 E 16 11 9 1.101 108.4 -66.7 0.000 +18 O3 OH 3 16 11 9 1.421 108.7 173.5 0.000 +19 H30 HO E 18 16 11 0.976 108.5 51.3 0.281 +20 EP+3 EP E 18 16 11 0.700 109.5 171.3 -0.217 +21 EP-3 EP E 18 16 11 0.700 109.5 -68.7 -0.217 +22 C2 CG B 16 11 9 1.529 110.6 52.8 0.231 +23 H2 H1 E 22 16 11 1.105 104.4 63.4 0.000 +24 O2 OS B 22 16 11 1.415 109.5 -174.5 0.000 +25 EP+2 EP E 24 22 16 0.700 109.5 -29.4 -0.140 +26 EP-2 EP E 24 22 16 0.700 109.5 90.6 -0.140 +27 C6 CG M 9 6 4 1.517 106.6 -177.2 0.173 +28 H61 H1 E 27 9 6 1.092 108.3 -178.0 0.000 +29 H62 H1 E 27 9 6 1.093 108.8 -59.0 0.000 +30 O6 OS M 27 9 6 1.413 112.7 65.2 0.000 +31 EP+6 EP E 30 27 9 0.700 109.5 178.1 -0.133 +32 EP-6 EP E 30 27 9 0.700 109.5 61.9 -0.133 + +LOOP +C2 C1 + +DONE +2,3,4,6-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +2346lb.dat +PLB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.095 +12 H4 H1 E 11 9 6 1.100 107.5 -173.8 0.000 +13 O4 OS B 11 9 6 1.430 111.7 67.6 0.000 +14 EP+4 EP E 13 11 9 0.700 109.5 -141.8 -0.113 +15 EP-4 EP E 13 11 9 0.700 109.5 98.2 -0.113 +16 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.139 +17 H3 H1 E 16 11 9 1.101 108.4 -66.7 0.000 +18 O3 OS B 16 11 9 1.421 108.7 173.5 0.000 +19 EP+3 EP E 18 16 11 0.700 109.5 171.3 -0.133 +20 EP-3 EP E 18 16 11 0.700 109.5 -68.7 -0.133 +21 C2 CG B 16 11 9 1.529 110.6 52.8 0.231 +22 H2 H1 E 21 16 11 1.105 104.4 63.4 0.000 +23 O2 OS B 21 16 11 1.415 109.5 -174.5 0.000 +24 EP+2 EP E 23 21 16 0.700 109.5 -29.4 -0.140 +25 EP-2 EP E 23 21 16 0.700 109.5 90.6 -0.140 +26 C6 CG M 9 6 4 1.517 106.6 -177.2 0.173 +27 H61 H1 E 26 9 6 1.092 108.3 -178.0 0.000 +28 H62 H1 E 26 9 6 1.093 108.8 -59.0 0.000 +29 O6 OS M 26 9 6 1.413 112.7 65.2 0.000 +30 EP+6 EP E 29 26 9 0.700 109.5 178.1 -0.133 +31 EP-6 EP E 29 26 9 0.700 109.5 61.9 -0.133 + +LOOP +C2 C1 + +DONE +2,3,4-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +234lb.dat +TLB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.173 +12 H61 H1 E 11 9 6 1.092 108.3 -178.0 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 -59.0 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 65.2 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -58.1 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 178.1 -0.213 +17 EP-6 EP E 14 11 9 0.700 109.5 61.9 -0.213 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.095 +19 H4 H1 E 18 9 6 1.100 107.5 -173.8 0.000 +20 C3 CG 3 18 9 6 1.519 110.1 -54.4 0.139 +21 H3 H1 E 20 18 9 1.101 108.4 -66.7 0.000 +22 O3 OS B 20 18 9 1.421 108.7 173.5 0.000 +23 EP+3 EP E 22 20 18 0.700 109.5 171.3 -0.133 +24 EP-3 EP E 22 20 18 0.700 109.5 -68.7 -0.133 +25 C2 CG B 20 18 9 1.529 110.6 52.8 0.231 +26 H2 H1 E 25 20 18 1.105 104.4 63.4 0.000 +27 O2 OS B 25 20 18 1.415 109.5 -174.5 0.000 +28 EP+2 EP E 27 25 20 0.700 109.5 -29.4 -0.140 +29 EP-2 EP E 27 25 20 0.700 109.5 90.6 -0.140 +30 O4 OS M 18 9 6 1.430 111.7 67.6 0.000 +31 EP+4 EP E 30 18 9 0.700 109.5 -141.8 -0.113 +32 EP-4 EP E 30 18 9 0.700 109.5 98.2 -0.113 + +LOOP +C2 C1 + +DONE +3,4,6-[B-D-GALACTO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +346lb.dat +QLB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.196 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.132 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.132 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.129 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.095 +12 H4 H1 E 11 9 6 1.100 107.5 -173.8 0.000 +13 O4 OS B 11 9 6 1.430 111.7 67.6 0.000 +14 EP+4 EP E 13 11 9 0.700 109.5 -141.8 -0.113 +15 EP-4 EP E 13 11 9 0.700 109.5 98.2 -0.113 +16 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.139 +17 H3 H1 E 16 11 9 1.101 108.4 -66.7 0.000 +18 O3 OS B 16 11 9 1.421 108.7 173.5 0.000 +19 EP+3 EP E 18 16 11 0.700 109.5 171.3 -0.133 +20 EP-3 EP E 18 16 11 0.700 109.5 -68.7 -0.133 +21 C2 CG B 16 11 9 1.529 110.6 52.8 0.230 +22 H2 H1 E 21 16 11 1.105 104.4 63.4 0.000 +23 O2 OH 3 21 16 11 1.415 109.5 -174.5 0.000 +24 H2O HO E 23 21 16 0.957 110.0 -149.4 0.272 +25 EP+2 EP E 23 21 16 0.700 109.5 -29.4 -0.219 +26 EP-2 EP E 23 21 16 0.700 109.5 90.6 -0.219 +27 C6 CG M 9 6 4 1.517 106.6 -177.2 0.173 +28 H61 H1 E 27 9 6 1.092 108.3 -178.0 0.000 +29 H62 H1 E 27 9 6 1.093 108.8 -59.0 0.000 +30 O6 OS M 27 9 6 1.413 112.7 65.2 0.000 +31 EP+6 EP E 30 27 9 0.700 109.5 178.1 -0.133 +32 EP-6 EP E 30 27 9 0.700 109.5 61.9 -0.133 + +LOOP +C2 C1 + +DONE +2,3,6-[B-D-MANNO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +236mb.dat +SMB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.196 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OH 3 11 9 6 1.430 107.9 -174.0 0.000 +14 H4O HO E 13 11 9 0.958 109.2 -124.9 0.279 +15 EP+4 EP E 13 11 9 0.700 109.5 -4.9 -0.224 +16 EP-4 EP E 13 11 9 0.700 109.5 115.1 -0.224 +17 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.144 +18 H3 H1 E 17 11 9 1.101 108.4 -66.7 0.000 +19 O3 OS B 17 11 9 1.421 108.7 173.5 0.000 +20 EP+3 EP E 19 17 11 0.700 109.5 48.7 -0.132 +21 EP-3 EP E 19 17 11 0.700 109.5 -71.3 -0.132 +22 C2 CG B 17 11 9 1.529 110.6 52.8 0.138 +23 H2 H1 E 22 17 11 1.105 106.2 -171.0 0.000 +24 O2 OS B 22 17 11 1.415 113.9 66.1 0.000 +25 EP+2 EP E 24 22 17 0.700 109.5 166.3 -0.114 +26 EP-2 EP E 24 22 17 0.700 109.5 -73.7 -0.114 +27 C6 CG M 9 6 4 1.517 106.6 -177.2 0.144 +28 H61 H1 E 27 9 6 1.092 108.3 179.3 0.000 +29 H62 H1 E 27 9 6 1.093 108.8 62.9 0.000 +30 O6 OS M 27 9 6 1.413 112.7 -65.1 0.000 +31 EP+6 EP E 30 27 9 0.700 109.5 24.0 -0.129 +32 EP-6 EP E 30 27 9 0.700 109.5 144.0 -0.129 + +LOOP +C2 C1 + +DONE +2,3,4-[B-D-MANNO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +234mb.dat +TMB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C6 CG 3 9 6 4 1.517 106.6 -177.2 0.144 +12 H61 H1 E 11 9 6 1.092 108.3 179.3 0.000 +13 H62 H1 E 11 9 6 1.093 108.8 62.9 0.000 +14 O6 OH 3 11 9 6 1.413 112.7 -65.1 0.000 +15 H6O HO E 14 11 9 0.955 108.1 -96.0 0.273 +16 EP+6 EP E 14 11 9 0.700 109.5 24.0 -0.209 +17 EP-6 EP E 14 11 9 0.700 109.5 144.0 -0.209 +18 C4 CG M 9 6 4 1.528 110.8 59.1 0.196 +19 H4 H1 E 18 9 6 1.100 109.8 66.4 0.000 +20 C3 CG 3 18 9 6 1.519 110.1 -54.4 0.144 +21 H3 H1 E 20 18 9 1.101 108.4 -66.7 0.000 +22 O3 OS B 20 18 9 1.421 108.7 173.5 0.000 +23 EP+3 EP E 22 20 18 0.700 109.5 48.7 -0.132 +24 EP-3 EP E 22 20 18 0.700 109.5 -71.3 -0.132 +25 C2 CG B 20 18 9 1.529 110.6 52.8 0.138 +26 H2 H1 E 25 20 18 1.105 106.2 -171.0 0.000 +27 O2 OS B 25 20 18 1.415 113.9 66.1 0.000 +28 EP+2 EP E 27 25 20 0.700 109.5 166.3 -0.114 +29 EP-2 EP E 27 25 20 0.700 109.5 -73.7 -0.114 +30 O4 OS M 18 9 6 1.430 107.9 -174.0 0.000 +31 EP+4 EP E 30 18 9 0.700 109.5 -4.9 -0.141 +32 EP-4 EP E 30 18 9 0.700 109.5 115.1 -0.141 + +LOOP +C2 C1 + +DONE +2,3,4,6-[B-D-MANNO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +2346mb.dat +PMB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.196 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OS B 11 9 6 1.430 107.9 -174.0 0.000 +14 EP+4 EP E 13 11 9 0.700 109.5 -4.9 -0.141 +15 EP-4 EP E 13 11 9 0.700 109.5 115.1 -0.141 +16 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.144 +17 H3 H1 E 16 11 9 1.101 108.4 -66.7 0.000 +18 O3 OS B 16 11 9 1.421 108.7 173.5 0.000 +19 EP+3 EP E 18 16 11 0.700 109.5 48.7 -0.132 +20 EP-3 EP E 18 16 11 0.700 109.5 -71.3 -0.132 +21 C2 CG B 16 11 9 1.529 110.6 52.8 0.138 +22 H2 H1 E 22 16 11 1.105 106.2 -171.0 0.000 +23 O2 OS B 22 16 11 1.415 113.9 66.1 0.000 +24 EP+2 EP E 24 22 16 0.700 109.5 166.3 -0.114 +25 EP-2 EP E 24 22 16 0.700 109.5 -73.7 -0.114 +26 C6 CG M 9 6 4 1.517 106.6 -177.2 0.144 +27 H61 H1 E 26 9 6 1.092 108.3 179.3 0.000 +28 H62 H1 E 26 9 6 1.093 108.8 62.9 0.000 +29 O6 OS M 26 9 6 1.413 112.7 -65.1 0.000 +30 EP+6 EP E 29 26 9 0.700 109.5 24.0 -0.129 +31 EP-6 EP E 29 26 9 0.700 109.5 144.0 -0.129 + +LOOP +C2 C1 + +DONE +3,4,6-[B-D-MANNO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +346mb.dat +QMB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.196 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OS B 11 9 6 1.430 107.9 -174.0 0.000 +14 EP+4 EP E 13 11 9 0.700 109.5 -4.9 -0.141 +15 EP-4 EP E 13 11 9 0.700 109.5 115.1 -0.141 +16 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.144 +17 H3 H1 E 16 11 9 1.101 108.4 -66.7 0.000 +18 O3 OS B 16 11 9 1.421 108.7 173.5 0.000 +19 EP+3 EP E 18 16 11 0.700 109.5 48.7 -0.132 +20 EP-3 EP E 18 16 11 0.700 109.5 -71.3 -0.132 +21 C2 CG B 16 11 9 1.529 110.6 52.8 0.138 +22 H2 H1 E 22 16 11 1.105 106.2 -171.0 0.000 +23 O2 OH 3 22 16 11 1.415 113.9 66.1 0.000 +24 H2O HO E 24 22 16 0.957 110.0 46.3 0.287 +25 EP+2 EP E 24 22 16 0.700 109.5 166.3 -0.201 +26 EP-2 EP E 24 22 16 0.700 109.5 -73.7 -0.201 +27 C6 CG M 9 6 4 1.517 106.6 -177.2 0.144 +28 H61 H1 E 27 9 6 1.092 108.3 179.3 0.000 +29 H62 H1 E 27 9 6 1.093 108.8 62.9 0.000 +30 O6 OS M 27 9 6 1.413 112.7 -65.1 0.000 +31 EP+6 EP E 30 27 9 0.700 109.5 24.0 -0.129 +32 EP-6 EP E 30 27 9 0.700 109.5 144.0 -0.129 + +LOOP +C2 C1 + +DONE +2,4,6-[B-D-MANNO-] non-terminal RESP010 ESP hf/6-31G* ENS AVG EPs +246mb.dat +RMB INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0 + 4 C1 CG M 3 2 1 1.400 113.3 180.0 0.163 + 5 H1 H2 E 4 3 2 1.102 111.6 56.2 0.000 + 6 O5 OS 3 4 3 2 1.412 112.9 -68.7 0.000 + 7 EP+5 EP E 6 4 3 0.700 109.5 -59.7 -0.136 + 8 EP-5 EP E 6 4 3 0.700 109.5 60.3 -0.136 + 9 C5 CG M 6 4 3 1.435 114.3 -179.7 0.180 +10 H5 H1 E 9 6 4 1.105 109.1 -60.7 0.000 +11 C4 CG 3 9 6 4 1.528 110.8 59.1 0.196 +12 H4 H1 E 11 9 6 1.100 109.8 66.4 0.000 +13 O4 OS B 11 9 6 1.430 107.9 -174.0 0.000 +14 EP+4 EP E 13 11 9 0.700 109.5 -4.9 -0.141 +15 EP-4 EP E 13 11 9 0.700 109.5 115.1 -0.141 +16 C3 CG 3 11 9 6 1.519 110.1 -54.4 0.143 +17 H3 H1 E 16 11 9 1.101 108.4 -66.7 0.000 +18 O3 OH 3 16 11 9 1.421 108.7 173.5 0.000 +19 H30 HO E 18 16 11 0.976 108.5 168.7 0.278 +20 EP+3 EP E 18 16 11 0.700 109.5 48.7 -0.214 +21 EP-3 EP E 18 16 11 0.700 109.5 -71.3 -0.214 +22 C2 CG B 16 11 9 1.529 110.6 52.8 0.138 +23 H2 H1 E 22 16 11 1.105 106.2 -171.0 0.000 +24 O2 OS B 22 16 11 1.415 113.9 66.1 0.000 +25 EP+2 EP E 24 22 16 0.700 109.5 166.3 -0.114 +26 EP-2 EP E 24 22 16 0.700 109.5 -73.7 -0.114 +27 C6 CG M 9 6 4 1.517 106.6 -177.2 0.144 +28 H61 H1 E 27 9 6 1.092 108.3 179.3 0.000 +29 H62 H1 E 27 9 6 1.093 108.8 62.9 0.000 +30 O6 OS M 27 9 6 1.413 112.7 -65.1 0.000 +31 EP+6 EP E 30 27 9 0.700 109.5 24.0 -0.129 +32 EP-6 EP E 30 27 9 0.700 109.5 144.0 -0.129 + +LOOP +C2 C1 + +DONE +o-methyl for glycon RESP 0.010 (avg. from ens avg a/b-glcgalman w/ EPs) +ome.dat +OME INT 0 +CORRECT OMIT DU BEG +0.0 + 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0 + 2 DUMM DU M 1 0 -1 1.000 0.0 0.0 0.0 + 3 DUMM DU M 2 1 0 1.000 90.0 0.0 0.0 + 4 H1 H1 M 3 2 1 1.000 90.0 180.0 0.000 + 5 CH3 CG M 4 3 2 1.085 109.5 180.0 0.197 + 6 H2 H1 E 5 4 3 1.085 111.4 60.0 0.000 + 7 H3 H1 E 5 4 3 1.085 111.4 -60.0 0.000 + 8 O OS M 5 4 3 1.399 107.0 180.0 0.000 + 9 EP+1 EP E 8 5 4 0.700 109.5 60.0 -0.155 +10 EP-1 EP E 8 5 4 0.700 109.5 -60.0 -0.155 + +DONE +STOP + diff --git a/cad/tests/AMBER_test_structures/dot_in/meoh/meoh.in b/cad/tests/AMBER_test_structures/dot_in/meoh/meoh.in new file mode 100644 index 000000000..523d5034c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/meoh/meoh.in @@ -0,0 +1,20 @@ + 0 0 2 + + methanol +meoh.res +MOH INT 0 +CORRECT OMIT DU BEG +0.0 +1 DUMM DU M 0 0 0 0. +2 DUMM DU M 0 0 0 1.000 +3 DUMM DU M 0 0 0 1.000 90. +4 HC1 H1 M 0 0 0 1.0 90. 180. 0.0372 +5 C1 CT M 0 0 0 1.0 109.5 180. 0.1166 +6 HC2 H1 E 0 0 0 1.0 109.5 60. 0.0372 +7 HC3 H1 E 0 0 0 1.0 109.5 -60. 0.0372 +8 O1 OH M 0 0 0 1.410 109.5 180. -.6497 +9 HO1 HO E 0 0 0 0.960 108. 180. 0.4215 + + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_nacl/CL_Chloride_Ion.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_nacl/CL_Chloride_Ion.in_frag new file mode 100644 index 000000000..0ea6e9685 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_nacl/CL_Chloride_Ion.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 CL CL M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_nacl/NA_Sodium_Ion.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_nacl/NA_Sodium_Ion.in_frag new file mode 100644 index 000000000..b23bcd6bc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_nacl/NA_Sodium_Ion.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 NA SO M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_nacl/opls_nacl.in b/cad/tests/AMBER_test_structures/dot_in/opls_nacl/opls_nacl.in new file mode 100644 index 000000000..ff7f3ba28 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_nacl/opls_nacl.in @@ -0,0 +1,25 @@ + 1 1 3 +db4.dat +Sodium Ion +NA +NA INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 NA SO M 3 2 1 1.0000 90.0000 180.0000 1.000 + +DONE +Chloride Ion +CL +CL INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 CL CL M 3 2 1 1.0000 90.0000 180.0000 -1.000 + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/ACE_ACE_BEGINNING_GROUP.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/ACE_ACE_BEGINNING_GROUP.in_frag new file mode 100644 index 000000000..1dacd6a47 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/ACE_ACE_BEGINNING_GROUP.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 CH3 C3 M 3 2 1 1.000 90.000 180.000 + 5 C C M 4 3 2 1.530 111.100 180.000 + 6 O O E 5 4 3 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/ALA_ALANINE.in_frag new file mode 100644 index 000000000..e881477c8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/ALA_ALANINE.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C3 E 6 4 3 1.525 111.100 60.000 + 8 C C M 6 4 3 1.522 111.100 180.000 + 9 O O E 8 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/AME_TERMINAL_METHYL_AMIDE,_OPLS_MODEL.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/AME_TERMINAL_METHYL_AMIDE,_OPLS_MODEL.in_frag new file mode 100644 index 000000000..8c5b987f7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/AME_TERMINAL_METHYL_AMIDE,_OPLS_MODEL.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 NT N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CT CW E 4 3 2 1.449 121.900 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/ARG_ARGININE.in_frag new file mode 100644 index 000000000..3353b5756 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/ARG_ARGININE.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 + 10 NE N2 B 9 8 7 1.480 111.000 180.000 + 11 HNE H3 E 10 9 8 1.010 118.500 0.000 + 12 CZ C4 B 10 9 8 1.330 123.000 180.000 + 13 NH1 N2 B 12 10 9 1.330 122.000 0.000 + 14 HN11 H3 E 13 12 10 1.010 119.800 0.000 + 15 HN12 H3 E 13 12 10 1.010 119.800 180.000 + 16 NH2 N2 B 12 10 9 1.330 118.000 180.000 + 17 HN21 H3 E 16 12 10 1.010 119.800 0.000 + 18 HN22 H3 E 16 12 10 1.010 119.800 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..3b3cf000b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/ASN_ASPARAGINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C B 7 6 4 1.522 111.100 180.000 + 9 OD1 O E 8 7 6 1.229 120.500 0.000 + 10 ND2 N B 8 7 6 1.335 116.600 180.000 + 11 HND1 H E 10 8 7 1.010 119.800 0.000 + 12 HND2 H E 10 8 7 1.010 119.800 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..89680f395 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C B 7 6 4 1.527 109.470 180.000 + 9 OD1 O2 E 8 7 6 1.260 117.200 90.000 + 10 OD2 O2 E 8 7 6 1.260 117.200 270.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..07fd3c61c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/CYS_CYSTEINE.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 SG SH S 7 6 4 1.810 116.000 180.000 + 9 HG HS E 8 7 6 1.330 96.000 180.000 + 10 C C M 6 4 3 1.522 111.100 180.000 + 11 O O E 10 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..31f22b701 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CQ S 6 4 3 1.525 111.100 60.000 + 8 SG S E 7 6 4 1.810 116.000 180.000 + 9 C C M 6 4 3 1.522 111.100 180.000 + 10 O O E 9 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/DAL_D-ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/DAL_D-ALANINE.in_frag new file mode 100644 index 000000000..c26ac0ab7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/DAL_D-ALANINE.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C3 E 6 4 3 1.525 111.100 -60.000 + 8 C C M 6 4 3 1.522 111.100 180.000 + 9 O O E 8 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..bcbd74bb8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/GLN_GLUTAMINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C B 8 7 6 1.522 111.100 180.000 + 10 OE1 O E 9 8 7 1.229 120.500 0.000 + 11 NE2 N B 9 8 7 1.335 116.600 180.000 + 12 HNE1 H E 11 9 8 1.010 119.800 0.000 + 13 HNE2 H E 11 9 8 1.010 119.800 180.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..92be049d5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.510 109.470 180.000 + 9 CD C B 8 7 6 1.527 109.470 180.000 + 10 OE1 O2 E 9 8 7 1.260 117.200 90.000 + 11 OE2 O2 E 9 8 7 1.260 117.200 270.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..5e2eadd01 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/GLY_GLYCINE.in_frag @@ -0,0 +1,8 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CQ M 4 3 2 1.449 121.900 180.000 + 7 C C M 6 4 3 1.522 110.400 180.000 + 8 O O E 7 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/HDU_HISTIDINE_DELTAH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/HDU_HISTIDINE_DELTAH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..695b4c564 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/HDU_HISTIDINE_DELTAH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 + 12 NE2 NB S 11 9 8 1.310 109.000 0.000 + 13 CD2 CF E 12 11 9 1.360 110.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/HEU_HISTIDINE_EPSILONH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/HEU_HISTIDINE_EPSILONH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..b26af0398 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/HEU_HISTIDINE_EPSILONH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NB S 8 7 6 1.390 122.000 180.000 + 10 CE1 CP S 9 8 7 1.320 108.000 180.000 + 11 NE2 NA B 10 9 8 1.310 109.000 0.000 + 12 HNE H E 11 10 9 1.010 125.000 180.000 + 13 CD2 CG E 11 10 9 1.360 110.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/HID_HISTIDINE_DELTAH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/HID_HISTIDINE_DELTAH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..16b791356 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/HID_HISTIDINE_DELTAH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CK S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CK B 9 8 7 1.320 108.000 180.000 + 12 HE HK E 11 9 8 1.090 120.000 180.000 + 13 NE2 NB S 11 9 8 1.310 109.000 0.000 + 14 CD2 CK S 13 11 9 1.360 110.000 0.000 + 15 HD HK E 14 13 11 1.090 120.000 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/HIE_HISTIDINE_EPSILONH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/HIE_HISTIDINE_EPSILONH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..7330dce19 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/HIE_HISTIDINE_EPSILONH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CK S 7 6 4 1.510 115.000 180.000 + 9 ND1 NB S 8 7 6 1.390 122.000 180.000 + 10 CE1 CK B 9 8 7 1.320 108.000 180.000 + 11 HE HK E 10 9 8 1.090 120.000 180.000 + 12 NE2 NA B 10 9 8 1.310 109.000 0.000 + 13 HNE H E 12 10 9 1.010 125.000 180.000 + 14 CD2 CK S 12 10 9 1.360 110.000 0.000 + 15 HD HK E 14 12 10 1.090 120.000 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/HIP_HISTIDINE_PLUS,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/HIP_HISTIDINE_PLUS,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..728eef3c4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/HIP_HISTIDINE_PLUS,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CK S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CK B 9 8 7 1.320 108.000 180.000 + 12 HE HK E 11 9 8 1.090 120.000 180.000 + 13 NE2 NA B 11 9 8 1.310 109.000 0.000 + 14 HNE H E 13 11 9 1.010 125.000 180.000 + 15 CD2 CK S 13 11 9 1.360 110.000 0.000 + 16 HD HK E 15 13 11 1.090 120.000 180.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O E 17 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/HPU_HISTIDINE_PLUS,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/HPU_HISTIDINE_PLUS,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..722338062 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/HPU_HISTIDINE_PLUS,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 + 12 NE2 NA B 11 9 8 1.310 109.000 0.000 + 13 HNE H E 12 11 9 1.010 125.000 180.000 + 14 CD2 CG E 12 11 9 1.360 110.000 0.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..0b66545e1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CZ B 6 4 3 1.525 109.470 60.000 + 8 CG2 C3 E 7 6 4 1.525 109.470 60.000 + 9 CG1 C2 S 7 6 4 1.525 109.470 180.000 + 10 CD1 CV E 9 7 6 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..987b74778 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/LEU_LEUCINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CZ B 7 6 4 1.525 109.470 180.000 + 9 CD1 C3 E 8 7 6 1.525 109.470 60.000 + 10 CD2 C3 E 8 7 6 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/LYS_LYSINE.in_frag new file mode 100644 index 000000000..a290c069e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/LYS_LYSINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 + 10 CE C2 S 9 8 7 1.525 109.470 180.000 + 11 NZ N3 3 10 9 8 1.470 109.470 180.000 + 12 HNZ1 H3 E 11 10 9 1.010 109.470 60.000 + 13 HNZ2 H3 E 11 10 9 1.010 109.470 180.000 + 14 HNZ3 H3 E 11 10 9 1.010 109.470 300.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/MET_METHIONINE.in_frag new file mode 100644 index 000000000..7802a30a0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/MET_METHIONINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CQ S 7 6 4 1.525 109.470 180.000 + 9 SD S S 8 7 6 1.810 110.000 180.000 + 10 CE CW E 9 8 7 1.780 100.000 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/OME_O_MINUS_END_ATOM.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/OME_O_MINUS_END_ATOM.in_frag new file mode 100644 index 000000000..42d0572bf --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/OME_O_MINUS_END_ATOM.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 OXT O2 E 3 2 1 1.260 117.200 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/PHE_PHENYLALANINE,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/PHE_PHENYLALANINE,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..2a83dbff4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/PHE_PHENYLALANINE,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CK S 7 6 4 1.510 115.000 180.000 + 9 CD1 CK B 8 7 6 1.400 120.000 180.000 + 10 HD1 HK E 9 8 7 1.090 120.000 0.000 + 11 CE1 CK B 9 8 7 1.400 120.000 180.000 + 12 HE1 HK E 11 9 8 1.090 120.000 180.000 + 13 CZ CK B 11 9 8 1.400 120.000 0.000 + 14 HZ HK E 13 11 9 1.090 120.000 180.000 + 15 CE2 CK B 13 11 9 1.400 120.000 0.000 + 16 HE2 HK E 15 13 11 1.090 120.000 180.000 + 17 CD2 CK S 15 13 11 1.400 120.000 0.000 + 18 HD2 HK E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/PHU_PHENYLALANINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/PHU_PHENYLALANINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..65bb9b9ae --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/PHU_PHENYLALANINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CA S 7 6 4 1.510 115.000 180.000 + 9 CD1 CD S 8 7 6 1.400 120.000 180.000 + 10 CE1 CD S 9 8 7 1.400 120.000 180.000 + 11 CZ CD S 10 9 8 1.400 120.000 0.000 + 12 CE2 CD S 11 10 9 1.400 120.000 0.000 + 13 CD2 CD E 12 11 10 1.400 120.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/PRO_PROLINE.in_frag new file mode 100644 index 000000000..f5f82728d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/PRO_PROLINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CQ S 4 3 2 1.458 126.100 356.100 + 6 CG C2 S 5 4 3 1.500 103.200 200.100 + 7 CB C2 E 6 5 4 1.510 106.000 338.300 + 8 CA CH M 4 3 2 1.451 120.600 175.200 + 9 C C M 8 4 3 1.522 111.100 0.000 + 10 O O E 9 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/SER_SERINE.in_frag new file mode 100644 index 000000000..06c1c4c80 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/SER_SERINE.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 OG OH S 7 6 4 1.430 109.470 180.000 + 9 HOG HO E 8 7 6 0.960 109.470 180.000 + 10 C C M 6 4 3 1.522 111.100 180.000 + 11 O O E 10 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_uni/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/THR_THREONINE.in_frag new file mode 100644 index 000000000..9e7c47beb --- /dev/null +++ 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a/cad/tests/AMBER_test_structures/dot_in/opls_uni/TRU_TRYPTOPHAN,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_uni/TRU_TRYPTOPHAN,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..54fd52d96 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_uni/TRU_TRYPTOPHAN,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C* S 7 6 4 1.510 115.000 180.000 + 9 CD1 CG S 8 7 6 1.340 127.000 180.000 + 10 NE1 NA B 9 8 7 1.430 107.000 180.000 + 11 HNE H E 10 9 8 1.010 125.500 180.000 + 12 CE2 CN S 10 9 8 1.310 109.000 0.000 + 13 CZ2 CD S 12 10 9 1.400 128.000 180.000 + 14 CH2 CD S 13 12 10 1.390 116.000 180.000 + 15 CZ3 CD S 14 13 12 1.350 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180.000 -0.57000 + 10 HND H E 9 8 7 1.010 126.000 0.000 0.42000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 0.41000 + 12 NE2 NB S 11 9 8 1.310 109.000 0.000 -0.49000 + 13 CD2 CF E 12 11 9 1.360 110.000 0.000 0.10000 + 14 C C M 6 4 3 1.522 111.100 180.000 0.50000 + 15 O O E 14 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + +LOOP + CG CD2 + +DONE + HISTIDINE EPSILONH, UNITED ATOM AROMATIC PARAMETERS +HEU + HEU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.57000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.37000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.20000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.00000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 0.10000 + 9 ND1 NB S 8 7 6 1.390 122.000 180.000 -0.49000 + 10 CE1 CP S 9 8 7 1.320 108.000 180.000 0.41000 + 11 NE2 NA B 10 9 8 1.310 109.000 0.000 -0.57000 + 12 HNE H E 11 10 9 1.010 125.000 180.000 0.42000 + 13 CD2 CG E 11 10 9 1.360 110.000 0.000 0.13000 + 14 C C M 6 4 3 1.522 111.100 180.000 0.50000 + 15 O O E 14 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + +LOOP + CG CD2 + +DONE + HISTIDINE PLUS, UNITED ATOM AROMATIC PARAMETERS +HPU + HPU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.57000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.37000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.20000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.00000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 0.33000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 -0.54000 + 10 HND H E 9 8 7 1.010 126.000 0.000 0.46000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 0.50000 + 12 NE2 NA B 11 9 8 1.310 109.000 0.000 -0.54000 + 13 HNE H E 12 11 9 1.010 125.000 180.000 0.46000 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CD S 14 13 12 1.350 121.000 0.000 0.00000 + 16 CE3 CD S 15 14 13 1.410 122.000 0.000 0.00000 + 17 CD2 CB E 16 15 14 1.400 117.000 0.000 -0.05500 + 18 C C M 6 4 3 1.522 111.100 180.000 0.50000 + 19 O O E 18 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + +LOOP + CG CD2 + CE2 CD2 + +DONE + D-ALANINE +DAL + DAL INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.57000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.37000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.20000 + 7 CB C3 E 6 4 3 1.525 111.100 -60.000 0.00000 + 8 C C M 6 4 3 1.522 111.100 180.000 0.50000 + 9 O O E 8 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/ALA_ALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/ALA_ALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..90561b527 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/ALA_ALANINE_COO-_ANION.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C3 E 6 4 3 1.525 111.100 60.000 + 8 C C M 6 4 3 1.522 111.100 180.000 + 9 O O2 E 8 6 4 1.229 120.500 0.000 + 10 OXT O2 E 8 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/AME_TERMINAL_METHYL_AMIDE,_OPLS_MODEL.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/AME_TERMINAL_METHYL_AMIDE,_OPLS_MODEL.in_frag new file mode 100644 index 000000000..8c5b987f7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/AME_TERMINAL_METHYL_AMIDE,_OPLS_MODEL.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 NT N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CT CW E 4 3 2 1.449 121.900 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/ARG_ARGININE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/ARG_ARGININE_COO-_ANION.in_frag new file mode 100644 index 000000000..fa5654026 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/ARG_ARGININE_COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 + 10 NE N2 B 9 8 7 1.480 111.000 180.000 + 11 HNE H3 E 10 9 8 1.010 118.500 0.000 + 12 CZ C B 10 9 8 1.330 123.000 180.000 + 13 NH1 N2 B 12 10 9 1.330 122.000 0.000 + 14 HN11 H3 E 13 12 10 1.010 119.800 0.000 + 15 HN12 H3 E 13 12 10 1.010 119.800 180.000 + 16 NH2 N2 B 12 10 9 1.330 118.000 180.000 + 17 HN21 H3 E 16 12 10 1.010 119.800 0.000 + 18 HN22 H3 E 16 12 10 1.010 119.800 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/ASN_ASPARAGINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/ASN_ASPARAGINE_COO-_ANION.in_frag new file mode 100644 index 000000000..b8a598e3f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/ASN_ASPARAGINE_COO-_ANION.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU 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1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C B 7 6 4 1.527 109.470 180.000 + 9 OD1 O2 E 8 7 6 1.260 117.200 90.000 + 10 OD2 O2 E 8 7 6 1.260 117.200 270.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/CYS_CYSTEINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/CYS_CYSTEINE_COO-_ANION.in_frag new file mode 100644 index 000000000..c079a5f5f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/CYS_CYSTEINE_COO-_ANION.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 SG SH S 7 6 4 1.810 116.000 180.000 + 9 HG HS E 8 7 6 1.330 96.000 180.000 + 10 C C M 6 4 3 1.522 111.100 180.000 + 11 O O2 E 10 6 4 1.229 120.500 0.000 + 12 OXT O2 E 10 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/CYX_CYSTINE_op_S-S_BRIDGE_cp__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/CYX_CYSTINE_op_S-S_BRIDGE_cp__COO-_ANION.in_frag new file mode 100644 index 000000000..3d5e524d7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/CYX_CYSTINE_op_S-S_BRIDGE_cp__COO-_ANION.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CQ S 6 4 3 1.525 111.100 60.000 + 8 SG S E 7 6 4 1.810 116.000 180.000 + 9 C C M 6 4 3 1.522 111.100 180.000 + 10 O O2 E 9 6 4 1.229 120.500 0.000 + 11 OXT O2 E 9 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/GLN_GLUTAMINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/GLN_GLUTAMINE_COO-_ANION.in_frag new file mode 100644 index 000000000..235b27d6a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/GLN_GLUTAMINE_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C B 8 7 6 1.522 111.100 180.000 + 10 OE1 O E 9 8 7 1.229 120.500 0.000 + 11 NE2 N B 9 8 7 1.335 116.600 180.000 + 12 HNE1 H E 11 9 8 1.010 119.800 0.000 + 13 HNE2 H E 11 9 8 1.010 119.800 180.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..a5bc9d735 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.510 109.470 180.000 + 9 CD C B 8 7 6 1.527 109.470 180.000 + 10 OE1 O2 E 9 8 7 1.260 117.200 90.000 + 11 OE2 O2 E 9 8 7 1.260 117.200 270.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/GLY_GLYCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/GLY_GLYCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..a7a71acc1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/GLY_GLYCINE_COO-_ANION.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CQ M 4 3 2 1.449 121.900 180.000 + 7 C C M 6 4 3 1.522 110.400 180.000 + 8 O O2 E 7 6 4 1.229 120.500 0.000 + 9 OXT O2 E 7 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/HDU_HISTIDINE_DELTAH_COO-_ANION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/HDU_HISTIDINE_DELTAH_COO-_ANION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..28511c954 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/HDU_HISTIDINE_DELTAH_COO-_ANION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 + 12 NE2 NB S 11 9 8 1.310 109.000 0.000 + 13 CD2 CF E 12 11 9 1.360 110.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/HEU_HISTIDINE_EPSILONH_COO-_ANION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/HEU_HISTIDINE_EPSILONH_COO-_ANION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..b83dcd5a7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/HEU_HISTIDINE_EPSILONH_COO-_ANION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NB S 8 7 6 1.390 122.000 180.000 + 10 CE1 CP S 9 8 7 1.320 108.000 180.000 + 11 NE2 NA B 10 9 8 1.310 109.000 0.000 + 12 HNE H E 11 10 9 1.010 125.000 180.000 + 13 CD2 CG E 11 10 9 1.360 110.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/HID_HISTIDINE_DELTAH_COO-_ANION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/HID_HISTIDINE_DELTAH_COO-_ANION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..3a735268f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/HID_HISTIDINE_DELTAH_COO-_ANION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CK S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CK B 9 8 7 1.320 108.000 180.000 + 12 HE HK E 11 9 8 1.090 120.000 180.000 + 13 NE2 NB S 11 9 8 1.310 109.000 0.000 + 14 CD2 CK S 13 11 9 1.360 110.000 0.000 + 15 HD HK E 14 13 11 1.090 120.000 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/HIE_HISTIDINE_EPSILONH_COO-_ANION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/HIE_HISTIDINE_EPSILONH_COO-_ANION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..92506a16b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/HIE_HISTIDINE_EPSILONH_COO-_ANION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CK S 7 6 4 1.510 115.000 180.000 + 9 ND1 NB S 8 7 6 1.390 122.000 180.000 + 10 CE1 CK B 9 8 7 1.320 108.000 180.000 + 11 HE HK E 10 9 8 1.090 120.000 180.000 + 12 NE2 NA B 10 9 8 1.310 109.000 0.000 + 13 HNE H E 12 10 9 1.010 125.000 180.000 + 14 CD2 CK S 12 10 9 1.360 110.000 0.000 + 15 HD HK E 14 12 10 1.090 120.000 180.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/HIP_HISTIDINE_PLUS_ZWITTERION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/HIP_HISTIDINE_PLUS_ZWITTERION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..33c6d17b3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/HIP_HISTIDINE_PLUS_ZWITTERION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CK S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CK B 9 8 7 1.320 108.000 180.000 + 12 HE HK E 11 9 8 1.090 120.000 180.000 + 13 NE2 NA B 11 9 8 1.310 109.000 0.000 + 14 HNE H E 13 11 9 1.010 125.000 180.000 + 15 CD2 CK S 13 11 9 1.360 110.000 0.000 + 16 HD HK E 15 13 11 1.090 120.000 180.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O E 17 6 4 1.229 120.500 0.000 + 19 OXT O E 17 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/HPU_HISTIDINE_PLUS_ZWITTERION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/HPU_HISTIDINE_PLUS_ZWITTERION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..6e56049d7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/HPU_HISTIDINE_PLUS_ZWITTERION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 + 12 NE2 NA B 11 9 8 1.310 109.000 0.000 + 13 HNE H E 12 11 9 1.010 125.000 180.000 + 14 CD2 CG E 12 11 9 1.360 110.000 0.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 + 17 OXT O E 15 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/ILE_ISOLEUCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/ILE_ISOLEUCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..b91e41fa4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/ILE_ISOLEUCINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CZ B 6 4 3 1.525 109.470 60.000 + 8 CG2 C3 E 7 6 4 1.525 109.470 60.000 + 9 CG1 C2 S 7 6 4 1.525 109.470 180.000 + 10 CD1 CV E 9 7 6 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/LEU_LEUCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/LEU_LEUCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..938fa3d04 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/LEU_LEUCINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CZ B 7 6 4 1.525 109.470 180.000 + 9 CD1 C3 E 8 7 6 1.525 109.470 60.000 + 10 CD2 C3 E 8 7 6 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/LYS_LYSINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/LYS_LYSINE_COO-_ANION.in_frag new file mode 100644 index 000000000..2992cec4d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/LYS_LYSINE_COO-_ANION.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 + 10 CE C2 S 9 8 7 1.525 109.470 180.000 + 11 NZ N3 3 10 9 8 1.470 109.470 180.000 + 12 HNZ1 H3 E 11 10 9 1.010 109.470 60.000 + 13 HNZ2 H3 E 11 10 9 1.010 109.470 180.000 + 14 HNZ3 H3 E 11 10 9 1.010 109.470 300.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O2 E 15 6 4 1.229 120.500 0.000 + 17 OXT O2 E 15 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/MET_METHIONINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/MET_METHIONINE_COO-_ANION.in_frag new file mode 100644 index 000000000..2f6d72203 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/MET_METHIONINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CQ S 7 6 4 1.525 109.470 180.000 + 9 SD S S 8 7 6 1.810 110.000 180.000 + 10 CE CW E 9 8 7 1.780 100.000 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/PHE_PHENYLALANINE,_ALL_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/PHE_PHENYLALANINE,_ALL_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag new file mode 100644 index 000000000..f7accd9e9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/PHE_PHENYLALANINE,_ALL_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CK S 7 6 4 1.510 115.000 180.000 + 9 CD1 CK B 8 7 6 1.400 120.000 180.000 + 10 HD1 HK E 9 8 7 1.090 120.000 0.000 + 11 CE1 CK B 9 8 7 1.400 120.000 180.000 + 12 HE1 HK E 11 9 8 1.090 120.000 180.000 + 13 CZ CK B 11 9 8 1.400 120.000 0.000 + 14 HZ HK E 13 11 9 1.090 120.000 180.000 + 15 CE2 CK B 13 11 9 1.400 120.000 0.000 + 16 HE2 HK E 15 13 11 1.090 120.000 180.000 + 17 CD2 CK S 15 13 11 1.400 120.000 0.000 + 18 HD2 HK E 17 15 13 1.090 120.000 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 14 6 4 1.229 120.500 0.000 + 21 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/PHU_PHENYLALANINE,_UNITED_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/PHU_PHENYLALANINE,_UNITED_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag new file mode 100644 index 000000000..213b626fe --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/PHU_PHENYLALANINE,_UNITED_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CA S 7 6 4 1.510 115.000 180.000 + 9 CD1 CD S 8 7 6 1.400 120.000 180.000 + 10 CE1 CD S 9 8 7 1.400 120.000 180.000 + 11 CZ CD S 10 9 8 1.400 120.000 0.000 + 12 CE2 CD S 11 10 9 1.400 120.000 0.000 + 13 CD2 CD E 12 11 10 1.400 120.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/PRO_PROLINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/PRO_PROLINE_COO-_ANION.in_frag new file mode 100644 index 000000000..3d70e1e04 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/PRO_PROLINE_COO-_ANION.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD CQ S 4 3 2 1.458 126.100 356.100 + 6 CG C2 S 5 4 3 1.500 103.200 200.100 + 7 CB C2 E 6 5 4 1.510 106.000 338.300 + 8 CA CH M 4 3 2 1.451 120.600 175.200 + 9 C C M 8 4 3 1.522 111.100 0.000 + 10 O O2 E 9 8 4 1.229 120.500 0.000 + 11 OXT O2 E 9 8 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/SER_SERINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/SER_SERINE_COO-_ANION.in_frag new file mode 100644 index 000000000..14ac4cdeb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/SER_SERINE_COO-_ANION.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 OG OH S 7 6 4 1.430 109.470 180.000 + 9 HOG HO E 8 7 6 0.960 109.470 180.000 + 10 C C M 6 4 3 1.522 111.100 180.000 + 11 O O2 E 10 6 4 1.229 120.500 0.000 + 12 OXT O2 E 10 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/THR_THREONINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/THR_THREONINE_COO-_ANION.in_frag new file mode 100644 index 000000000..f418dffd4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/THR_THREONINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CZ B 6 4 3 1.525 111.100 60.000 + 8 CG2 C3 E 7 6 4 1.525 109.470 300.000 + 9 OG1 OH S 7 6 4 1.430 109.470 60.000 + 10 HOG HO E 9 7 6 0.960 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/TRP_TRYPTOPHAN_COO-_ANION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/TRP_TRYPTOPHAN_COO-_ANION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..149d0089f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/TRP_TRYPTOPHAN_COO-_ANION,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CK S 7 6 4 1.510 115.000 180.000 + 9 CD1 CK B 8 7 6 1.340 127.000 180.000 + 10 HD HK E 9 8 7 1.090 120.000 0.000 + 11 NE1 NA B 9 8 7 1.430 107.000 180.000 + 12 HNE H E 11 9 8 1.010 125.500 180.000 + 13 CE2 CN S 11 9 8 1.310 109.000 0.000 + 14 CZ2 CK B 13 11 9 1.400 128.000 180.000 + 15 HZ1 HK E 14 13 11 1.090 120.000 0.000 + 16 CH2 CK B 14 13 11 1.390 116.000 180.000 + 17 HH HK E 16 14 13 1.090 120.000 180.000 + 18 CZ3 CK B 16 14 13 1.350 121.000 0.000 + 19 HZ2 HK E 18 16 14 1.090 120.000 180.000 + 20 CE3 CK B 18 16 14 1.410 122.000 0.000 + 21 HE HK E 20 18 16 1.090 120.000 180.000 + 22 CD2 CB E 20 18 16 1.400 117.000 0.000 + 23 C C M 6 4 3 1.522 111.100 180.000 + 24 O O2 E 23 6 4 1.229 120.500 0.000 + 25 OXT O2 E 23 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/TRU_TRYPTOPHAN_COO-_ANION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/TRU_TRYPTOPHAN_COO-_ANION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..fca2ea91f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/TRU_TRYPTOPHAN_COO-_ANION,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C* S 7 6 4 1.510 115.000 180.000 + 9 CD1 CG S 8 7 6 1.340 127.000 180.000 + 10 NE1 NA B 9 8 7 1.430 107.000 180.000 + 11 HNE H E 10 9 8 1.010 125.500 180.000 + 12 CE2 CN S 10 9 8 1.310 109.000 0.000 + 13 CZ2 CD S 12 10 9 1.400 128.000 180.000 + 14 CH2 CD S 13 12 10 1.390 116.000 180.000 + 15 CZ3 CD S 14 13 12 1.350 121.000 0.000 + 16 CE3 CD S 15 14 13 1.410 122.000 0.000 + 17 CD2 CB E 16 15 14 1.400 117.000 0.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O2 E 18 6 4 1.229 120.500 0.000 + 20 OXT O2 E 18 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unict/TYR_TYROSINE,_ALL_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unict/TYR_TYROSINE,_ALL_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag new file mode 100644 index 000000000..daf1548c8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unict/TYR_TYROSINE,_ALL_ATOM_AROMATIC_PARAMETERS,_COO-_ANION.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CK S 7 6 4 1.510 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a/cad/tests/AMBER_test_structures/dot_in/opls_unint/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/ALA_ALANINE.in_frag new file mode 100644 index 000000000..f5467e388 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/ALA_ALANINE.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C3 E 8 5 4 1.525 111.100 60.000 + 10 C C M 8 5 4 1.522 111.100 180.000 + 11 O O E 10 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/ARG_ARGININE.in_frag new file mode 100644 index 000000000..5098771ed --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/ARG_ARGININE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.525 109.470 180.000 + 11 CD C2 S 10 9 8 1.525 109.470 180.000 + 12 NE N2 B 11 10 9 1.480 111.000 180.000 + 13 HNE H3 E 12 11 10 1.010 118.500 0.000 + 14 CZ C B 12 11 10 1.330 123.000 180.000 + 15 NH1 N2 B 14 12 11 1.330 122.000 0.000 + 16 HN11 H3 E 15 14 12 1.010 119.800 0.000 + 17 HN12 H3 E 15 14 12 1.010 119.800 180.000 + 18 NH2 N2 B 14 12 11 1.330 118.000 180.000 + 19 HN21 H3 E 18 14 12 1.010 119.800 0.000 + 20 HN22 H3 E 18 14 12 1.010 119.800 180.000 + 21 C C M 8 5 4 1.522 111.100 180.000 + 22 O O E 21 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..e19ac12a5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/ASN_ASPARAGINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C B 9 8 5 1.522 111.100 180.000 + 11 OD1 O E 10 9 8 1.229 120.500 0.000 + 12 ND2 N B 10 9 8 1.335 116.600 180.000 + 13 HND1 H E 12 10 9 1.010 119.800 0.000 + 14 HND2 H E 12 10 9 1.010 119.800 180.000 + 15 C C M 8 5 4 1.522 111.100 180.000 + 16 O O E 15 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..6a5ee54dd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C B 9 8 5 1.527 109.470 180.000 + 11 OD1 O2 E 10 9 8 1.260 117.200 90.000 + 12 OD2 O2 E 10 9 8 1.260 117.200 270.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..c4a5f2a40 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/CYS_CYSTEINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 SG SH S 9 8 5 1.810 116.000 180.000 + 11 HG HS E 10 9 8 1.330 96.000 180.000 + 12 C C M 8 5 4 1.522 111.100 180.000 + 13 O O E 12 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..53f5cf430 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB CQ S 8 5 4 1.525 111.100 60.000 + 10 SG S E 9 8 5 1.810 116.000 180.000 + 11 C C M 8 5 4 1.522 111.100 180.000 + 12 O O E 11 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..ae5f4ff02 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/GLN_GLUTAMINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.525 109.470 180.000 + 11 CD C B 10 9 8 1.522 111.100 180.000 + 12 OE1 O E 11 10 9 1.229 120.500 0.000 + 13 NE2 N B 11 10 9 1.335 116.600 180.000 + 14 HNE1 H E 13 11 10 1.010 119.800 0.000 + 15 HNE2 H E 13 11 10 1.010 119.800 180.000 + 16 C C M 8 5 4 1.522 111.100 180.000 + 17 O O E 16 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..337434304 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.510 109.470 180.000 + 11 CD C B 10 9 8 1.527 109.470 180.000 + 12 OE1 O2 E 11 10 9 1.260 117.200 90.000 + 13 OE2 O2 E 11 10 9 1.260 117.200 270.000 + 14 C C M 8 5 4 1.522 111.100 180.000 + 15 O O E 14 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..c17f0507e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/GLY_GLYCINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CQ M 5 4 3 1.449 121.900 180.000 + 9 C C M 8 5 4 1.522 110.400 180.000 + 10 O O E 9 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/HDU_HISTIDINE_DELTAH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/HDU_HISTIDINE_DELTAH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..83070a54a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/HDU_HISTIDINE_DELTAH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CC S 9 8 5 1.510 115.000 180.000 + 11 ND1 NA B 10 9 8 1.390 122.000 180.000 + 12 HND H E 11 10 9 1.010 126.000 0.000 + 13 CE1 CP S 11 10 9 1.320 108.000 180.000 + 14 NE2 NB S 13 11 10 1.310 109.000 0.000 + 15 CD2 CF E 14 13 11 1.360 110.000 0.000 + 16 C C M 8 5 4 1.522 111.100 180.000 + 17 O O E 16 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/HEU_HISTIDINE_EPSILONH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/HEU_HISTIDINE_EPSILONH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..36c9aee64 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/HEU_HISTIDINE_EPSILONH,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CC S 9 8 5 1.510 115.000 180.000 + 11 ND1 NB S 10 9 8 1.390 122.000 180.000 + 12 CE1 CP S 11 10 9 1.320 108.000 180.000 + 13 NE2 NA B 12 11 10 1.310 109.000 0.000 + 14 HNE H E 13 12 11 1.010 125.000 180.000 + 15 CD2 CG E 13 12 11 1.360 110.000 0.000 + 16 C C M 8 5 4 1.522 111.100 180.000 + 17 O O E 16 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/HID_HISTIDINE_DELTAH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/HID_HISTIDINE_DELTAH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..78eaec77a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/HID_HISTIDINE_DELTAH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CK S 9 8 5 1.510 115.000 180.000 + 11 ND1 NA B 10 9 8 1.390 122.000 180.000 + 12 HND H E 11 10 9 1.010 126.000 0.000 + 13 CE1 CK B 11 10 9 1.320 108.000 180.000 + 14 HE HK E 13 11 10 1.090 120.000 180.000 + 15 NE2 NB S 13 11 10 1.310 109.000 0.000 + 16 CD2 CK S 15 13 11 1.360 110.000 0.000 + 17 HD HK E 16 15 13 1.090 120.000 180.000 + 18 C C M 8 5 4 1.522 111.100 180.000 + 19 O O E 18 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/HIE_HISTIDINE_EPSILONH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/HIE_HISTIDINE_EPSILONH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..cf55122b3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/HIE_HISTIDINE_EPSILONH,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CK S 9 8 5 1.510 115.000 180.000 + 11 ND1 NB S 10 9 8 1.390 122.000 180.000 + 12 CE1 CK B 11 10 9 1.320 108.000 180.000 + 13 HE HK E 12 11 10 1.090 120.000 180.000 + 14 NE2 NA B 12 11 10 1.310 109.000 0.000 + 15 HNE H E 14 12 11 1.010 125.000 180.000 + 16 CD2 CK S 14 12 11 1.360 110.000 0.000 + 17 HD HK E 16 14 12 1.090 120.000 180.000 + 18 C C M 8 5 4 1.522 111.100 180.000 + 19 O O E 18 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/HIP_HISTIDINE_PLUS,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/HIP_HISTIDINE_PLUS,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..41db4ac1d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/HIP_HISTIDINE_PLUS,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CK S 9 8 5 1.510 115.000 180.000 + 11 ND1 NA B 10 9 8 1.390 122.000 180.000 + 12 HND H E 11 10 9 1.010 126.000 0.000 + 13 CE1 CK B 11 10 9 1.320 108.000 180.000 + 14 HE HK E 13 11 10 1.090 120.000 180.000 + 15 NE2 NA B 13 11 10 1.310 109.000 0.000 + 16 HNE H E 15 13 11 1.010 125.000 180.000 + 17 CD2 CK S 15 13 11 1.360 110.000 0.000 + 18 HD HK E 17 15 13 1.090 120.000 180.000 + 19 C C M 8 5 4 1.522 111.100 180.000 + 20 O O E 19 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/HPU_HISTIDINE_PLUS,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/HPU_HISTIDINE_PLUS,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..1911ffaa6 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/HPU_HISTIDINE_PLUS,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CC S 9 8 5 1.510 115.000 180.000 + 11 ND1 NA B 10 9 8 1.390 122.000 180.000 + 12 HND H E 11 10 9 1.010 126.000 0.000 + 13 CE1 CP S 11 10 9 1.320 108.000 180.000 + 14 NE2 NA B 13 11 10 1.310 109.000 0.000 + 15 HNE H E 14 13 11 1.010 125.000 180.000 + 16 CD2 CG E 14 13 11 1.360 110.000 0.000 + 17 C C M 8 5 4 1.522 111.100 180.000 + 18 O O E 17 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..86c383213 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB CZ B 8 5 4 1.525 109.470 60.000 + 10 CG2 C3 E 9 8 5 1.525 109.470 60.000 + 11 CG1 C2 S 9 8 5 1.525 109.470 180.000 + 12 CD1 CV E 11 9 8 1.525 109.470 180.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..cbabe6c68 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/LEU_LEUCINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CZ B 9 8 5 1.525 109.470 180.000 + 11 CD1 C3 E 10 9 8 1.525 109.470 60.000 + 12 CD2 C3 E 10 9 8 1.525 109.470 180.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/LYS_LYSINE.in_frag new file mode 100644 index 000000000..036907951 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/LYS_LYSINE.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.525 109.470 180.000 + 11 CD C2 S 10 9 8 1.525 109.470 180.000 + 12 CE C2 S 11 10 9 1.525 109.470 180.000 + 13 NZ N3 3 12 11 10 1.470 109.470 180.000 + 14 HNZ1 H3 E 13 12 11 1.010 109.470 60.000 + 15 HNZ2 H3 E 13 12 11 1.010 109.470 180.000 + 16 HNZ3 H3 E 13 12 11 1.010 109.470 300.000 + 17 C C M 8 5 4 1.522 111.100 180.000 + 18 O O E 17 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/MET_METHIONINE.in_frag new file mode 100644 index 000000000..68349c7db --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/MET_METHIONINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CQ S 9 8 5 1.525 109.470 180.000 + 11 SD S S 10 9 8 1.810 110.000 180.000 + 12 CE CW E 11 10 9 1.780 100.000 180.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/PHE_PHENYLALANINE,_ALL_ATOM_AROMATIC_PARAMETERS,_N-TERMINAL.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/PHE_PHENYLALANINE,_ALL_ATOM_AROMATIC_PARAMETERS,_N-TERMINAL.in_frag new file mode 100644 index 000000000..692f57aac --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/PHE_PHENYLALANINE,_ALL_ATOM_AROMATIC_PARAMETERS,_N-TERMINAL.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 4 3 2 1.010 111.800 60.000 + 7 HN3 H3 E 4 3 2 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CK S 9 8 5 1.510 115.000 180.000 + 11 CD1 CK B 10 9 8 1.400 120.000 180.000 + 12 HD1 HK E 11 10 9 1.090 120.000 0.000 + 13 CE1 CK B 11 10 9 1.400 120.000 180.000 + 14 HE1 HK E 13 11 10 1.090 120.000 180.000 + 15 CZ CK B 13 11 10 1.400 120.000 0.000 + 16 HZ HK E 15 13 11 1.090 120.000 180.000 + 17 CE2 CK B 15 13 11 1.400 120.000 0.000 + 18 HE2 HK E 17 15 13 1.090 120.000 180.000 + 19 CD2 CK S 17 15 13 1.400 120.000 0.000 + 20 HD2 HK E 19 17 15 1.090 120.000 180.000 + 21 C C M 8 5 4 1.522 111.100 180.000 + 22 O O E 21 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/PHU_PHENYLALANINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/PHU_PHENYLALANINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..c0363ce33 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/PHU_PHENYLALANINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CA S 9 8 5 1.510 115.000 180.000 + 11 CD1 CD S 10 9 8 1.400 120.000 180.000 + 12 CE1 CD S 11 10 9 1.400 120.000 180.000 + 13 CZ CD S 12 11 10 1.400 120.000 0.000 + 14 CE2 CD S 13 12 11 1.400 120.000 0.000 + 15 CD2 CD E 14 13 12 1.400 120.000 0.000 + 16 C C M 8 5 4 1.522 111.100 180.000 + 17 O O E 16 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/PRO_PROLINE.in_frag new file mode 100644 index 000000000..49a0370bd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/PRO_PROLINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 N N3 M 3 2 1 1.010 90.000 180.000 + 5 HN2 H3 E 4 3 2 1.010 58.800 90.000 + 6 HN3 H3 E 4 3 2 1.010 58.800 -90.000 + 7 CD CQ S 4 3 2 1.458 126.100 356.100 + 8 CG C2 S 7 4 3 1.500 103.200 200.100 + 9 CB C2 E 8 7 4 1.510 106.000 338.300 + 10 CA CH M 4 3 2 1.451 120.600 175.200 + 11 C C M 10 4 3 1.522 111.100 0.000 + 12 O O E 11 10 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/SER_SERINE.in_frag new file mode 100644 index 000000000..96291ef68 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/SER_SERINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 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14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/TRP_TRYPTOPHAN,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/TRP_TRYPTOPHAN,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..7aeffb9ca --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/TRP_TRYPTOPHAN,_ALL_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,26 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CK S 9 8 5 1.510 115.000 180.000 + 11 CD1 CK B 10 9 8 1.340 127.000 180.000 + 12 HD HK E 11 10 9 1.090 120.000 0.000 + 13 NE1 NA B 11 10 9 1.430 107.000 180.000 + 14 HNE H E 13 11 10 1.010 125.500 180.000 + 15 CE2 CN S 13 11 10 1.310 109.000 0.000 + 16 CZ2 CK B 15 13 11 1.400 128.000 180.000 + 17 HZ1 HK E 16 15 13 1.090 120.000 0.000 + 18 CH2 CK B 16 15 13 1.390 116.000 180.000 + 19 HH HK E 18 16 15 1.090 120.000 180.000 + 20 CZ3 CK B 18 16 15 1.350 121.000 0.000 + 21 HZ2 HK E 20 18 16 1.090 120.000 180.000 + 22 CE3 CK B 20 18 16 1.410 122.000 0.000 + 23 HE HK E 22 20 18 1.090 120.000 180.000 + 24 CD2 CB E 22 20 18 1.400 117.000 0.000 + 25 C C M 8 5 4 1.522 111.100 180.000 + 26 O O E 25 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/TRU_TRYPTOPHAN,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/TRU_TRYPTOPHAN,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..fe815dcf8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/TRU_TRYPTOPHAN,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C* S 9 8 5 1.510 115.000 180.000 + 11 CD1 CG S 10 9 8 1.340 127.000 180.000 + 12 NE1 NA B 11 10 9 1.430 107.000 180.000 + 13 HNE H E 12 11 10 1.010 125.500 180.000 + 14 CE2 CN S 12 11 10 1.310 109.000 0.000 + 15 CZ2 CD S 14 12 11 1.400 128.000 180.000 + 16 CH2 CD S 15 14 12 1.390 116.000 180.000 + 17 CZ3 CD S 16 15 14 1.350 121.000 0.000 + 18 CE3 CD S 17 16 15 1.410 122.000 0.000 + 19 CD2 CB E 18 17 16 1.400 117.000 0.000 + 20 C C M 8 5 4 1.522 111.100 180.000 + 21 O O E 20 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/TYR_TYROSINE,_ALL_ATOM_AROMATIC_PARAMETERS,_N-TERMINUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/TYR_TYROSINE,_ALL_ATOM_AROMATIC_PARAMETERS,_N-TERMINUS.in_frag new file mode 100644 index 000000000..92c21e394 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/TYR_TYROSINE,_ALL_ATOM_AROMATIC_PARAMETERS,_N-TERMINUS.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 4 3 2 1.010 111.800 60.000 + 7 HN3 H3 E 4 3 2 1.010 111.800 -60.000 + 8 CA CH M 4 3 2 1.449 121.900 180.000 + 9 CB C2 S 6 4 3 1.525 111.100 60.000 + 10 CG CK S 7 6 4 1.510 109.470 180.000 + 11 CD1 CK B 8 7 6 1.400 120.000 180.000 + 12 HD1 HK E 9 8 7 1.090 120.000 0.000 + 13 CE1 CK B 9 8 7 1.400 120.000 180.000 + 14 HE1 HK E 11 9 8 1.090 120.000 180.000 + 15 CZ CK B 11 9 8 1.400 120.000 0.000 + 16 OH OH S 13 11 9 1.360 120.000 180.000 + 17 HOH HO E 14 13 11 0.960 113.000 0.000 + 18 CE2 CK B 13 11 9 1.400 120.000 0.000 + 19 HE2 HK E 16 13 11 1.090 120.000 180.000 + 20 CD2 CK S 16 13 11 1.400 120.000 0.000 + 21 HD2 HK E 18 16 13 1.090 120.000 180.000 + 22 C C M 6 4 3 1.522 111.100 180.000 + 23 O O E 20 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/TYU_TYROSINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag b/cad/tests/AMBER_test_structures/dot_in/opls_unint/TYU_TYROSINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag new file mode 100644 index 000000000..69b4c9b0a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/TYU_TYROSINE,_UNITED_ATOM_AROMATIC_PARAMETERS.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 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5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB CZ B 8 5 4 1.525 111.100 60.000 + 10 CG1 C3 E 9 8 5 1.525 109.470 60.000 + 11 CG2 C3 E 9 8 5 1.525 109.470 180.000 + 12 C C M 8 5 4 1.522 111.100 180.000 + 13 O O E 12 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/opls_unint/opls_unint.in b/cad/tests/AMBER_test_structures/dot_in/opls_unint/opls_unint.in new file mode 100644 index 000000000..2257b3eb2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/opls_unint/opls_unint.in @@ -0,0 +1,863 @@ + 1 1 300 +db4.dat + ALANINE +ALA + ALA INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 0.33000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 -0.30000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 0.33000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 0.33000 + 8 CA CH M 5 4 3 1.449 121.900 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0.000 -0.05500 + 20 C C M 8 5 4 1.522 111.100 180.000 0.50000 + 21 O O E 20 8 5 1.229 120.500 0.000 -0.50000 + +IMPROPER + CA +M C O + CB CA N C + +LOOP + CG CD2 + CE2 CD2 + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ALA_ALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ALA_ALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..90561b527 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ALA_ALANINE_COO-_ANION.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C3 E 6 4 3 1.525 111.100 60.000 + 8 C C M 6 4 3 1.522 111.100 180.000 + 9 O O2 E 8 6 4 1.229 120.500 0.000 + 10 OXT O2 E 8 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ARG_ARGININE.in_frag new file mode 100644 index 000000000..985684f73 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ARG_ARGININE.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 + 10 NE N2 B 9 8 7 1.480 111.000 180.000 + 11 HNE H3 E 10 9 8 1.010 118.500 0.000 + 12 CZ CA B 10 9 8 1.330 123.000 180.000 + 13 NH1 N2 B 12 10 9 1.330 122.000 0.000 + 14 HN11 H3 E 13 12 10 1.010 119.800 0.000 + 15 HN12 H3 E 13 12 10 1.010 119.800 180.000 + 16 NH2 N2 B 12 10 9 1.330 118.000 180.000 + 17 HN21 H3 E 16 12 10 1.010 119.800 0.000 + 18 HN22 H3 E 16 12 10 1.010 119.800 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O2 E 19 6 4 1.229 120.500 0.000 + 21 OXT O2 E 19 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ASN_ASPARAGINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ASN_ASPARAGINE_COO-_ANION.in_frag new file mode 100644 index 000000000..b8a598e3f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ASN_ASPARAGINE_COO-_ANION.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C B 7 6 4 1.522 111.100 180.000 + 9 OD1 O E 8 7 6 1.229 120.500 0.000 + 10 ND2 N B 8 7 6 1.335 116.600 180.000 + 11 HND1 H E 10 8 7 1.010 119.800 0.000 + 12 HND2 H E 10 8 7 1.010 119.800 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ASP_ASPARTIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ASP_ASPARTIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..7173d3159 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ASP_ASPARTIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C B 7 6 4 1.527 109.470 180.000 + 9 OD1 O2 E 8 7 6 1.260 117.200 90.000 + 10 OD2 O2 E 8 7 6 1.260 117.200 270.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/CYS_CYSTEINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/CYS_CYSTEINE_COO-_ANION.in_frag new file mode 100644 index 000000000..c14e0ece3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/CYS_CYSTEINE_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 SG SH 3 7 6 4 1.810 116.000 180.000 + 9 HSG HS E 8 7 6 1.330 96.000 180.000 + 10 LP1 LP E 8 7 6 0.679 96.700 80.000 + 11 LP2 LP E 8 7 6 0.679 96.700 280.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/CYX_CYSTINE_op_S-S_BRIDGE_cp__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/CYX_CYSTINE_op_S-S_BRIDGE_cp__COO-_ANION.in_frag new file mode 100644 index 000000000..ca1a6b548 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/CYX_CYSTINE_op_S-S_BRIDGE_cp__COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 SG S B 7 6 4 1.810 116.000 180.000 + 9 LP1 LP E 8 7 6 0.679 96.700 80.000 + 10 LP2 LP E 8 7 6 0.679 96.700 280.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/GLN_GLUTAMINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/GLN_GLUTAMINE_COO-_ANION.in_frag new file mode 100644 index 000000000..235b27d6a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/GLN_GLUTAMINE_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C B 8 7 6 1.522 111.100 180.000 + 10 OE1 O E 9 8 7 1.229 120.500 0.000 + 11 NE2 N B 9 8 7 1.335 116.600 180.000 + 12 HNE1 H E 11 9 8 1.010 119.800 0.000 + 13 HNE2 H E 11 9 8 1.010 119.800 180.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..a5bc9d735 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.510 109.470 180.000 + 9 CD C B 8 7 6 1.527 109.470 180.000 + 10 OE1 O2 E 9 8 7 1.260 117.200 90.000 + 11 OE2 O2 E 9 8 7 1.260 117.200 270.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/GLY_GLYCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/GLY_GLYCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..eb200653b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/GLY_GLYCINE_COO-_ANION.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA C2 M 4 3 2 1.449 121.900 180.000 + 7 C C M 6 4 3 1.522 110.400 180.000 + 8 O O2 E 7 6 4 1.229 120.500 0.000 + 9 OXT O2 E 7 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag new file mode 100644 index 000000000..28511c954 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 + 12 NE2 NB S 11 9 8 1.310 109.000 0.000 + 13 CD2 CF E 12 11 9 1.360 110.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/HIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/HIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag new file mode 100644 index 000000000..b83dcd5a7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/HIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NB S 8 7 6 1.390 122.000 180.000 + 10 CE1 CP S 9 8 7 1.320 108.000 180.000 + 11 NE2 NA B 10 9 8 1.310 109.000 0.000 + 12 HNE H E 11 10 9 1.010 125.000 180.000 + 13 CD2 CG E 11 10 9 1.360 110.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/HIP_HISTIDINE_PLUS_ZWITTERION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/HIP_HISTIDINE_PLUS_ZWITTERION.in_frag new file mode 100644 index 000000000..b121790e8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/HIP_HISTIDINE_PLUS_ZWITTERION.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 + 12 NE2 NA B 11 9 8 1.310 109.000 0.000 + 13 HNE H E 12 11 9 1.010 125.000 180.000 + 14 CD2 CG E 12 11 9 1.360 110.000 0.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O2 E 15 6 4 1.229 120.500 0.000 + 17 OXT O2 E 15 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ILE_ISOLEUCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ILE_ISOLEUCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..d9e21d0f8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/ILE_ISOLEUCINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CH B 6 4 3 1.525 109.470 60.000 + 8 CG2 C3 E 7 6 4 1.525 109.470 60.000 + 9 CG1 C2 S 7 6 4 1.525 109.470 180.000 + 10 CD1 C3 E 9 7 6 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/LEU_LEUCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/LEU_LEUCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..dec659475 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/LEU_LEUCINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CH B 7 6 4 1.525 109.470 180.000 + 9 CD1 C3 E 8 7 6 1.525 109.470 60.000 + 10 CD2 C3 E 8 7 6 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/LYS_LYSINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/LYS_LYSINE_COO-_ANION.in_frag new file mode 100644 index 000000000..2992cec4d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/LYS_LYSINE_COO-_ANION.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 + 10 CE C2 S 9 8 7 1.525 109.470 180.000 + 11 NZ N3 3 10 9 8 1.470 109.470 180.000 + 12 HNZ1 H3 E 11 10 9 1.010 109.470 60.000 + 13 HNZ2 H3 E 11 10 9 1.010 109.470 180.000 + 14 HNZ3 H3 E 11 10 9 1.010 109.470 300.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O2 E 15 6 4 1.229 120.500 0.000 + 17 OXT O2 E 15 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/MET_METHIONINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/MET_METHIONINE_COO-_ANION.in_frag new file mode 100644 index 000000000..cb610771d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/MET_METHIONINE_COO-_ANION.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 SD S 3 8 7 6 1.810 110.000 180.000 + 10 CE C3 E 9 8 7 1.780 100.000 180.000 + 11 LP1 LP E 9 8 7 0.679 96.700 80.000 + 12 LP2 LP E 9 8 7 0.679 96.700 280.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/PHE_PHENYLALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/PHE_PHENYLALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..213b626fe --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/PHE_PHENYLALANINE_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CA S 7 6 4 1.510 115.000 180.000 + 9 CD1 CD S 8 7 6 1.400 120.000 180.000 + 10 CE1 CD S 9 8 7 1.400 120.000 180.000 + 11 CZ CD S 10 9 8 1.400 120.000 0.000 + 12 CE2 CD S 11 10 9 1.400 120.000 0.000 + 13 CD2 CD E 12 11 10 1.400 120.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/PRO_PROLINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/PRO_PROLINE_COO-_ANION.in_frag new file mode 100644 index 000000000..1a43d2f1f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/PRO_PROLINE_COO-_ANION.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD C2 S 4 3 2 1.458 126.100 356.100 + 6 CG C2 S 5 4 3 1.500 103.200 200.100 + 7 CB C2 E 6 5 4 1.510 106.000 338.300 + 8 CA CH M 4 3 2 1.451 120.600 175.200 + 9 C C M 8 4 3 1.522 111.100 0.000 + 10 O O2 E 9 8 4 1.229 120.500 0.000 + 11 OXT O2 E 9 8 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/SER_SERINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/SER_SERINE_COO-_ANION.in_frag new file mode 100644 index 000000000..14ac4cdeb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/SER_SERINE_COO-_ANION.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 OG OH S 7 6 4 1.430 109.470 180.000 + 9 HOG HO E 8 7 6 0.960 109.470 180.000 + 10 C C M 6 4 3 1.522 111.100 180.000 + 11 O O2 E 10 6 4 1.229 120.500 0.000 + 12 OXT O2 E 10 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/THR_THREONINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/THR_THREONINE_COO-_ANION.in_frag new file mode 100644 index 000000000..201b0554e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/THR_THREONINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CH B 6 4 3 1.525 111.100 60.000 + 8 CG2 C3 E 7 6 4 1.525 109.470 300.000 + 9 OG1 OH S 7 6 4 1.430 109.470 60.000 + 10 HOG HO E 9 7 6 0.960 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/TRP_TRYPTOPHAN_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/TRP_TRYPTOPHAN_COO-_ANION.in_frag new file mode 100644 index 000000000..fca2ea91f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/TRP_TRYPTOPHAN_COO-_ANION.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C* S 7 6 4 1.510 115.000 180.000 + 9 CD1 CG S 8 7 6 1.340 127.000 180.000 + 10 NE1 NA B 9 8 7 1.430 107.000 180.000 + 11 HNE H E 10 9 8 1.010 125.500 180.000 + 12 CE2 CN S 10 9 8 1.310 109.000 0.000 + 13 CZ2 CD S 12 10 9 1.400 128.000 180.000 + 14 CH2 CD S 13 12 10 1.390 116.000 180.000 + 15 CZ3 CD S 14 13 12 1.350 121.000 0.000 + 16 CE3 CD S 15 14 13 1.410 122.000 0.000 + 17 CD2 CB E 16 15 14 1.400 117.000 0.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O2 E 18 6 4 1.229 120.500 0.000 + 20 OXT O2 E 18 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/TYR_TYROSINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/TYR_TYROSINE_COO-_ANION.in_frag new file mode 100644 index 000000000..d6bff81ee --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/TYR_TYROSINE_COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CA S 7 6 4 1.510 109.470 180.000 + 9 CD1 CD S 8 7 6 1.400 120.000 180.000 + 10 CE1 CD S 9 8 7 1.400 120.000 180.000 + 11 CZ C B 10 9 8 1.400 120.000 0.000 + 12 OH OH S 11 10 9 1.360 120.000 180.000 + 13 HOH HO E 12 11 10 0.960 113.000 0.000 + 14 CE2 CD S 11 10 9 1.400 120.000 0.000 + 15 CD2 CD E 14 11 10 1.400 120.000 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/VAL_VALINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/VAL_VALINE.in_frag new file mode 100644 index 000000000..5fef9f7bc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/VAL_VALINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CH B 6 4 3 1.525 111.100 60.000 + 8 CG1 C3 E 7 6 4 1.525 109.470 60.000 + 9 CG2 C3 E 7 6 4 1.525 109.470 180.000 + 10 C C M 6 4 3 1.522 111.100 180.000 + 11 O O2 E 10 6 4 1.229 120.500 0.000 + 12 OXT O2 E 10 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/protein.amberua.C.in b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/protein.amberua.C.in new file mode 100644 index 000000000..9f4364f6a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.C/protein.amberua.C.in @@ -0,0 +1,645 @@ + 1 1 101 +protein.amberua.db4 + ALANINE COO- ANION +ALA + ALA INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.20900 + 7 CB C3 E 6 4 3 1.525 111.100 60.000 0.03100 + 8 C C M 6 4 3 1.522 111.100 180.000 0.44400 + 9 O O2 E 8 6 4 1.229 120.500 0.000 -0.70600 + 10 OXT O2 E 8 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N HN + CA OXT C O + CB CA N C + +DONE + GLYCINE COO- ANION +GLY + GLY INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 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0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.24000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 -0.20800 + 8 CG C B 7 6 4 1.527 109.470 180.000 0.62000 + 9 OD1 O2 E 8 7 6 1.260 117.200 90.000 -0.70600 + 10 OD2 O2 E 8 7 6 1.260 117.200 270.000 -0.70600 + 11 C C M 6 4 3 1.522 111.100 180.000 0.44400 + 12 O O2 E 11 6 4 1.229 120.500 0.000 -0.70600 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N HN + CB CA N C + CB OD1 CG OD2 + CA OXT C O + +DONE + LYSINE COO- ANION +LYS + LYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.22100 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.03900 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 0.05300 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 0.04800 + 10 CE C2 S 9 8 7 1.525 109.470 180.000 0.21800 + 11 NZ N3 3 10 9 8 1.470 109.470 180.000 -0.27200 + 12 HNZ1 H3 E 11 10 9 1.010 109.470 60.000 0.31100 + 13 HNZ2 H3 E 11 10 9 1.010 109.470 180.000 0.31100 + 14 HNZ3 H3 E 11 10 9 1.010 109.470 300.000 0.31100 + 15 C C M 6 4 3 1.522 111.100 180.000 0.44400 + 16 O O2 E 15 6 4 1.229 120.500 0.000 -0.70600 + 17 OXT O2 E 15 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N HN + CB CA N C + CA OXT C O + +DONE + PROLINE COO- ANION +PRO + PRO INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.337 117.000 180.000 -0.25700 + 5 CD C2 S 4 3 2 1.458 126.100 356.100 0.08400 + 6 CG C2 S 5 4 3 1.500 103.200 200.100 0.03000 + 7 CB C2 E 6 5 4 1.510 106.000 338.300 -0.00100 + 8 CA CH M 4 3 2 1.451 120.600 175.200 0.11200 + 9 C C M 8 4 3 1.522 111.100 0.000 0.44400 + 10 O O2 E 9 8 4 1.229 120.500 0.000 -0.70600 + 11 OXT O2 E 9 8 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + CB CA N C + -M CA N CD + CA OXT C O + +LOOP + CB CA + +DONE + CYSTEINE COO- ANION +CYS + CYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.14000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.10000 + 8 SG SH 3 7 6 4 1.810 116.000 180.000 0.82700 + 9 HSG HS E 8 7 6 1.330 96.000 180.000 0.13500 + 10 LP1 LP E 8 7 6 0.679 96.700 80.000 -0.48100 + 11 LP2 LP E 8 7 6 0.679 96.700 280.000 -0.48100 + 12 C C M 6 4 3 1.522 111.100 180.000 0.44400 + 13 O O2 E 12 6 4 1.229 120.500 0.000 -0.70600 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N HN + CB CA N C + CA OXT C O + +DONE + CYSTINE(S-S BRIDGE) COO- ANION +CYX + CYX INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.08200 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.14300 + 8 SG S B 7 6 4 1.810 116.000 180.000 0.82400 + 9 LP1 LP E 8 7 6 0.679 96.700 80.000 -0.40450 + 10 LP2 LP E 8 7 6 0.679 96.700 280.000 -0.40450 + 11 C C M 6 4 3 1.522 111.100 180.000 0.44400 + 12 O O2 E 11 6 4 1.229 120.500 0.000 -0.70600 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N HN + CB CA N C + CA OXT C O + +DONE + METHIONINE COO- ANION +MET + MET INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.13100 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.03700 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 0.09000 + 9 SD S 3 8 7 6 1.810 110.000 180.000 0.73700 + 10 CE C3 E 9 8 7 1.780 100.000 180.000 0.00700 + 11 LP1 LP E 9 8 7 0.679 96.700 80.000 -0.38100 + 12 LP2 LP E 9 8 7 0.679 96.700 280.000 -0.38100 + 13 C C M 6 4 3 1.522 111.100 180.000 0.44400 + 14 O O2 E 13 6 4 1.229 120.500 0.000 -0.70600 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N HN + CB CA N C + CA OXT C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ALA_ALANINE.in_frag new file mode 100644 index 000000000..f5467e388 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ALA_ALANINE.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C3 E 8 5 4 1.525 111.100 60.000 + 10 C C M 8 5 4 1.522 111.100 180.000 + 11 O O E 10 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ARG_ARGININE.in_frag new file mode 100644 index 000000000..32783c7fc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ARG_ARGININE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.525 109.470 180.000 + 11 CD C2 S 10 9 8 1.525 109.470 180.000 + 12 NE N2 B 11 10 9 1.480 111.000 180.000 + 13 HNE H3 E 12 11 10 1.010 118.500 0.000 + 14 CZ CA B 12 11 10 1.330 123.000 180.000 + 15 NH1 N2 B 14 12 11 1.330 122.000 0.000 + 16 HN11 H3 E 15 14 12 1.010 119.800 0.000 + 17 HN12 H3 E 15 14 12 1.010 119.800 180.000 + 18 NH2 N2 B 14 12 11 1.330 118.000 180.000 + 19 HN21 H3 E 18 14 12 1.010 119.800 0.000 + 20 HN22 H3 E 18 14 12 1.010 119.800 180.000 + 21 C C M 8 5 4 1.522 111.100 180.000 + 22 O O E 21 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..e19ac12a5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ASN_ASPARAGINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C B 9 8 5 1.522 111.100 180.000 + 11 OD1 O E 10 9 8 1.229 120.500 0.000 + 12 ND2 N B 10 9 8 1.335 116.600 180.000 + 13 HND1 H E 12 10 9 1.010 119.800 0.000 + 14 HND2 H E 12 10 9 1.010 119.800 180.000 + 15 C C M 8 5 4 1.522 111.100 180.000 + 16 O O E 15 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..6a5ee54dd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C B 9 8 5 1.527 109.470 180.000 + 11 OD1 O2 E 10 9 8 1.260 117.200 90.000 + 12 OD2 O2 E 10 9 8 1.260 117.200 270.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..76fc4c5cd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/CYS_CYSTEINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 SG SH 3 9 8 5 1.810 116.000 180.000 + 11 HSG HS E 10 9 8 1.330 96.000 180.000 + 12 LP1 LP E 10 9 8 0.679 96.700 80.000 + 13 LP2 LP E 10 9 8 0.679 96.700 280.000 + 14 C C M 8 5 4 1.522 111.100 180.000 + 15 O O E 14 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..15c9d5a4a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 SG S B 9 8 5 1.810 116.000 180.000 + 11 LP1 LP E 10 9 8 0.679 96.700 80.000 + 12 LP2 LP E 10 9 8 0.679 96.700 280.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..ae5f4ff02 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/GLN_GLUTAMINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.525 109.470 180.000 + 11 CD C B 10 9 8 1.522 111.100 180.000 + 12 OE1 O E 11 10 9 1.229 120.500 0.000 + 13 NE2 N B 11 10 9 1.335 116.600 180.000 + 14 HNE1 H E 13 11 10 1.010 119.800 0.000 + 15 HNE2 H E 13 11 10 1.010 119.800 180.000 + 16 C C M 8 5 4 1.522 111.100 180.000 + 17 O O E 16 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..337434304 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.510 109.470 180.000 + 11 CD C B 10 9 8 1.527 109.470 180.000 + 12 OE1 O2 E 11 10 9 1.260 117.200 90.000 + 13 OE2 O2 E 11 10 9 1.260 117.200 270.000 + 14 C C M 8 5 4 1.522 111.100 180.000 + 15 O O E 14 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..626b84473 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/GLY_GLYCINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA C2 M 5 4 3 1.449 121.900 180.000 + 9 C C M 8 5 4 1.522 110.400 180.000 + 10 O O E 9 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..83070a54a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CC S 9 8 5 1.510 115.000 180.000 + 11 ND1 NA B 10 9 8 1.390 122.000 180.000 + 12 HND H E 11 10 9 1.010 126.000 0.000 + 13 CE1 CP S 11 10 9 1.320 108.000 180.000 + 14 NE2 NB S 13 11 10 1.310 109.000 0.000 + 15 CD2 CF E 14 13 11 1.360 110.000 0.000 + 16 C C M 8 5 4 1.522 111.100 180.000 + 17 O O E 16 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..36c9aee64 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CC S 9 8 5 1.510 115.000 180.000 + 11 ND1 NB S 10 9 8 1.390 122.000 180.000 + 12 CE1 CP S 11 10 9 1.320 108.000 180.000 + 13 NE2 NA B 12 11 10 1.310 109.000 0.000 + 14 HNE H E 13 12 11 1.010 125.000 180.000 + 15 CD2 CG E 13 12 11 1.360 110.000 0.000 + 16 C C M 8 5 4 1.522 111.100 180.000 + 17 O O E 16 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..1911ffaa6 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CC S 9 8 5 1.510 115.000 180.000 + 11 ND1 NA B 10 9 8 1.390 122.000 180.000 + 12 HND H E 11 10 9 1.010 126.000 0.000 + 13 CE1 CP S 11 10 9 1.320 108.000 180.000 + 14 NE2 NA B 13 11 10 1.310 109.000 0.000 + 15 HNE H E 14 13 11 1.010 125.000 180.000 + 16 CD2 CG E 14 13 11 1.360 110.000 0.000 + 17 C C M 8 5 4 1.522 111.100 180.000 + 18 O O E 17 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..d03671a52 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB CH B 8 5 4 1.525 109.470 60.000 + 10 CG2 C3 E 9 8 5 1.525 109.470 60.000 + 11 CG1 C2 S 9 8 5 1.525 109.470 180.000 + 12 CD1 C3 E 11 9 8 1.525 109.470 180.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..57860b2c3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/LEU_LEUCINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CH B 9 8 5 1.525 109.470 180.000 + 11 CD1 C3 E 10 9 8 1.525 109.470 60.000 + 12 CD2 C3 E 10 9 8 1.525 109.470 180.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/LYS_LYSINE.in_frag new file mode 100644 index 000000000..036907951 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/LYS_LYSINE.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.525 109.470 180.000 + 11 CD C2 S 10 9 8 1.525 109.470 180.000 + 12 CE C2 S 11 10 9 1.525 109.470 180.000 + 13 NZ N3 3 12 11 10 1.470 109.470 180.000 + 14 HNZ1 H3 E 13 12 11 1.010 109.470 60.000 + 15 HNZ2 H3 E 13 12 11 1.010 109.470 180.000 + 16 HNZ3 H3 E 13 12 11 1.010 109.470 300.000 + 17 C C M 8 5 4 1.522 111.100 180.000 + 18 O O E 17 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/MET_METHIONINE.in_frag new file mode 100644 index 000000000..3153776e0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/MET_METHIONINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.525 109.470 180.000 + 11 SD S 3 10 9 8 1.810 110.000 180.000 + 12 CE C3 E 11 10 9 1.780 100.000 180.000 + 13 LP1 LP E 11 10 9 0.679 96.700 80.000 + 14 LP2 LP E 11 10 9 0.679 96.700 280.000 + 15 C C M 8 5 4 1.522 111.100 180.000 + 16 O O E 15 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..c0363ce33 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CA S 9 8 5 1.510 115.000 180.000 + 11 CD1 CD S 10 9 8 1.400 120.000 180.000 + 12 CE1 CD S 11 10 9 1.400 120.000 180.000 + 13 CZ CD S 12 11 10 1.400 120.000 0.000 + 14 CE2 CD S 13 12 11 1.400 120.000 0.000 + 15 CD2 CD E 14 13 12 1.400 120.000 0.000 + 16 C C M 8 5 4 1.522 111.100 180.000 + 17 O O E 16 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/PRO_PROLINE.in_frag new file mode 100644 index 000000000..818f36d0f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/PRO_PROLINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 N N3 M 3 2 1 1.010 90.000 180.000 + 5 HN2 H3 E 4 3 2 1.010 58.800 90.000 + 6 HN3 H3 E 4 3 2 1.010 58.800 -90.000 + 7 CD C2 S 4 3 2 1.458 126.100 356.100 + 8 CG C2 S 7 4 3 1.500 103.200 200.100 + 9 CB C2 E 8 7 4 1.510 106.000 338.300 + 10 CA CH M 4 3 2 1.451 120.600 175.200 + 11 C C M 10 4 3 1.522 111.100 0.000 + 12 O O E 11 10 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/SER_SERINE.in_frag new file mode 100644 index 000000000..96291ef68 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/SER_SERINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 OG OH S 9 8 5 1.430 109.470 180.000 + 11 HOG HO E 10 9 8 0.960 109.470 180.000 + 12 C C M 8 5 4 1.522 111.100 180.000 + 13 O O E 12 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/THR_THREONINE.in_frag new file mode 100644 index 000000000..fa189b4f0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/THR_THREONINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB CH B 8 5 4 1.525 111.100 60.000 + 10 CG2 C3 E 9 8 5 1.525 109.470 300.000 + 11 OG1 OH S 9 8 5 1.430 109.470 60.000 + 12 HOG HO E 11 9 8 0.960 109.470 180.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/TRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/TRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..fe815dcf8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/TRP_TRYPTOPHAN.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C* S 9 8 5 1.510 115.000 180.000 + 11 CD1 CG S 10 9 8 1.340 127.000 180.000 + 12 NE1 NA B 11 10 9 1.430 107.000 180.000 + 13 HNE H E 12 11 10 1.010 125.500 180.000 + 14 CE2 CN S 12 11 10 1.310 109.000 0.000 + 15 CZ2 CD S 14 12 11 1.400 128.000 180.000 + 16 CH2 CD S 15 14 12 1.390 116.000 180.000 + 17 CZ3 CD S 16 15 14 1.350 121.000 0.000 + 18 CE3 CD S 17 16 15 1.410 122.000 0.000 + 19 CD2 CB E 18 17 16 1.400 117.000 0.000 + 20 C C M 8 5 4 1.522 111.100 180.000 + 21 O O E 20 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/TYR_TYROSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/TYR_TYROSINE.in_frag new file mode 100644 index 000000000..bfe9514c3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/TYR_TYROSINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CA S 9 8 5 1.510 109.470 180.000 + 11 CD1 CD S 10 9 8 1.400 120.000 180.000 + 12 CE1 CD S 11 10 9 1.400 120.000 180.000 + 13 CZ C B 12 11 10 1.400 120.000 0.000 + 14 OH OH S 13 12 11 1.360 120.000 180.000 + 15 HOH HO E 14 13 12 0.960 113.000 0.000 + 16 CE2 CD S 13 12 11 1.400 120.000 0.000 + 17 CD2 CD E 16 13 12 1.400 120.000 0.000 + 18 C C M 8 5 4 1.522 111.100 180.000 + 19 O O E 18 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/VAL_VALINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/VAL_VALINE.in_frag new file mode 100644 index 000000000..a05dde2df --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/VAL_VALINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB CH B 8 5 4 1.525 111.100 60.000 + 10 CG1 C3 E 9 8 5 1.525 109.470 60.000 + 11 CG2 C3 E 9 8 5 1.525 109.470 180.000 + 12 C C M 8 5 4 1.522 111.100 180.000 + 13 O O E 12 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/protein.amberua.N.in b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/protein.amberua.N.in new file mode 100644 index 000000000..64ee36e2e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua.N/protein.amberua.N.in @@ -0,0 +1,646 @@ + 1 1 100 +protein.amberua.db4 + ALANINE +ALA + ALA INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 0.31200 + 5 N N3 M 4 3 2 1.010 90.000 180.000 -0.26300 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 0.31200 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 0.31200 + 8 CA CH M 5 4 3 1.449 121.900 180.000 0.27000 + 9 CB C3 E 8 5 4 1.525 111.100 60.000 0.03100 + 10 C C M 8 5 4 1.522 111.100 180.000 0.52600 + 11 O O E 10 8 5 1.229 120.500 0.000 -0.50000 + +IMPROPER + CA +M C O + CB CA N C + +DONE + GLYCINE +GLY + GLY INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 0.31200 + 5 N N3 M 4 3 2 1.010 90.000 180.000 -0.26300 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 0.31200 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 0.31200 + 8 CA C2 M 5 4 3 1.449 121.900 180.000 0.30100 + 9 C C M 8 5 4 1.522 110.400 180.000 0.52600 + 10 O O E 9 8 5 1.229 120.500 0.000 -0.50000 + +IMPROPER + CA +M C O + +DONE + SERINE +SER + SER INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 0.31200 + 5 N N3 M 4 3 2 1.010 90.000 180.000 -0.26300 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 0.31200 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 0.31200 + 8 CA CH M 5 4 3 1.449 121.900 180.000 0.34700 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 0.19400 + 10 OG OH S 9 8 5 1.430 109.470 180.000 -0.55000 + 11 HOG HO E 10 9 8 0.960 109.470 180.000 0.31000 + 12 C C M 8 5 4 1.522 111.100 180.000 0.52600 + 13 O O E 12 8 5 1.229 120.500 0.000 -0.50000 + +IMPROPER + CA +M C O + CB CA N C + +DONE + THREONINE +THR + THR INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 0.31200 + 5 N N3 M 4 3 2 1.010 90.000 180.000 -0.26300 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 0.31200 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 0.31200 + 8 CA CH M 5 4 3 1.449 121.900 180.000 0.32300 + 9 CB CH B 8 5 4 1.525 111.100 60.000 0.21100 + 10 CG2 C3 E 9 8 5 1.525 109.470 300.000 0.00700 + 11 OG1 OH S 9 8 5 1.430 109.470 60.000 -0.55000 + 12 HOG HO E 11 9 8 0.960 109.470 180.000 0.31000 + 13 C C M 8 5 4 1.522 111.100 180.000 0.52600 + 14 O O E 13 8 5 1.229 120.500 0.000 -0.50000 + +IMPROPER + CA +M C O + CB CA N C + CG2 CB CA OG1 + +DONE + LEUCINE +LEU + 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8 1.810 110.000 180.000 0.73700 + 12 CE C3 E 11 10 9 1.780 100.000 180.000 0.00700 + 13 LP1 LP E 11 10 9 0.679 96.700 80.000 -0.38100 + 14 LP2 LP E 11 10 9 0.679 96.700 280.000 -0.38100 + 15 C C M 8 5 4 1.522 111.100 180.000 0.52600 + 16 O O E 15 8 5 1.229 120.500 0.000 -0.50000 + +IMPROPER + CA +M C O + CB CA N C + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ACE_ACE_BEGINNING_GROUP.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ACE_ACE_BEGINNING_GROUP.in_frag new file mode 100644 index 000000000..1dacd6a47 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ACE_ACE_BEGINNING_GROUP.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 CH3 C3 M 3 2 1 1.000 90.000 180.000 + 5 C C M 4 3 2 1.530 111.100 180.000 + 6 O O E 5 4 3 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ALA_ALANINE.in_frag new file mode 100644 index 000000000..e881477c8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ALA_ALANINE.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C3 E 6 4 3 1.525 111.100 60.000 + 8 C C M 6 4 3 1.522 111.100 180.000 + 9 O O E 8 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ARG_ARGININE.in_frag new file mode 100644 index 000000000..5cce86313 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ARG_ARGININE.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 + 10 NE N2 B 9 8 7 1.480 111.000 180.000 + 11 HNE H3 E 10 9 8 1.010 118.500 0.000 + 12 CZ CA B 10 9 8 1.330 123.000 180.000 + 13 NH1 N2 B 12 10 9 1.330 122.000 0.000 + 14 HN11 H3 E 13 12 10 1.010 119.800 0.000 + 15 HN12 H3 E 13 12 10 1.010 119.800 180.000 + 16 NH2 N2 B 12 10 9 1.330 118.000 180.000 + 17 HN21 H3 E 16 12 10 1.010 119.800 0.000 + 18 HN22 H3 E 16 12 10 1.010 119.800 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..3b3cf000b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ASN_ASPARAGINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C B 7 6 4 1.522 111.100 180.000 + 9 OD1 O E 8 7 6 1.229 120.500 0.000 + 10 ND2 N B 8 7 6 1.335 116.600 180.000 + 11 HND1 H E 10 8 7 1.010 119.800 0.000 + 12 HND2 H E 10 8 7 1.010 119.800 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..89680f395 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C B 7 6 4 1.527 109.470 180.000 + 9 OD1 O2 E 8 7 6 1.260 117.200 90.000 + 10 OD2 O2 E 8 7 6 1.260 117.200 270.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/CL_CL__PREP.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/CL_CL__PREP.in_frag new file mode 100644 index 000000000..0ea6e9685 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/CL_CL__PREP.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 CL CL M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..a442843fb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/CYS_CYSTEINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 SG SH 3 7 6 4 1.810 116.000 180.000 + 9 HSG HS E 8 7 6 1.330 96.000 180.000 + 10 LP1 LP E 8 7 6 0.679 96.700 80.000 + 11 LP2 LP E 8 7 6 0.679 96.700 280.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..9525449d3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 SG S B 7 6 4 1.810 116.000 180.000 + 9 LP1 LP E 8 7 6 0.679 96.700 80.000 + 10 LP2 LP E 8 7 6 0.679 96.700 280.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..bcbd74bb8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/GLN_GLUTAMINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C B 8 7 6 1.522 111.100 180.000 + 10 OE1 O E 9 8 7 1.229 120.500 0.000 + 11 NE2 N B 9 8 7 1.335 116.600 180.000 + 12 HNE1 H E 11 9 8 1.010 119.800 0.000 + 13 HNE2 H E 11 9 8 1.010 119.800 180.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..92be049d5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.510 109.470 180.000 + 9 CD C B 8 7 6 1.527 109.470 180.000 + 10 OE1 O2 E 9 8 7 1.260 117.200 90.000 + 11 OE2 O2 E 9 8 7 1.260 117.200 270.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..d7659076b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/GLY_GLYCINE.in_frag @@ -0,0 +1,8 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA C2 M 4 3 2 1.449 121.900 180.000 + 7 C C M 6 4 3 1.522 110.400 180.000 + 8 O O E 7 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..695b4c564 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 + 12 NE2 NB S 11 9 8 1.310 109.000 0.000 + 13 CD2 CF E 12 11 9 1.360 110.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..b26af0398 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NB S 8 7 6 1.390 122.000 180.000 + 10 CE1 CP S 9 8 7 1.320 108.000 180.000 + 11 NE2 NA B 10 9 8 1.310 109.000 0.000 + 12 HNE H E 11 10 9 1.010 125.000 180.000 + 13 CD2 CG E 11 10 9 1.360 110.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..722338062 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 + 12 NE2 NA B 11 9 8 1.310 109.000 0.000 + 13 HNE H E 12 11 9 1.010 125.000 180.000 + 14 CD2 CG E 12 11 9 1.360 110.000 0.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..342207b5f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CH B 6 4 3 1.525 109.470 60.000 + 8 CG2 C3 E 7 6 4 1.525 109.470 60.000 + 9 CG1 C2 S 7 6 4 1.525 109.470 180.000 + 10 CD1 C3 E 9 7 6 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/K_K___PREP.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/K_K___PREP.in_frag new file mode 100644 index 000000000..d32904a32 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/K_K___PREP.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 K SO M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..e05afa2b0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/LEU_LEUCINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CH B 7 6 4 1.525 109.470 180.000 + 9 CD1 C3 E 8 7 6 1.525 109.470 60.000 + 10 CD2 C3 E 8 7 6 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/LYS_LYSINE.in_frag new file mode 100644 index 000000000..a290c069e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/LYS_LYSINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 + 10 CE C2 S 9 8 7 1.525 109.470 180.000 + 11 NZ N3 3 10 9 8 1.470 109.470 180.000 + 12 HNZ1 H3 E 11 10 9 1.010 109.470 60.000 + 13 HNZ2 H3 E 11 10 9 1.010 109.470 180.000 + 14 HNZ3 H3 E 11 10 9 1.010 109.470 300.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/MET_METHIONINE.in_frag new file mode 100644 index 000000000..4054d970e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/MET_METHIONINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 SD S 3 8 7 6 1.810 110.000 180.000 + 10 CE C3 E 9 8 7 1.780 100.000 180.000 + 11 LP1 LP E 9 8 7 0.679 96.700 80.000 + 12 LP2 LP E 9 8 7 0.679 96.700 280.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/MG_MG__PREP.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/MG_MG__PREP.in_frag new file mode 100644 index 000000000..a51eeeba2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/MG_MG__PREP.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 MG MG M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/NA_NA__PREP.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/NA_NA__PREP.in_frag new file mode 100644 index 000000000..b23bcd6bc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/NA_NA__PREP.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 NA SO M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/NME_N-Methyl_end_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/NME_N-Methyl_end_group.in_frag new file mode 100644 index 000000000..900206056 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/NME_N-Methyl_end_group.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CM C3 E 4 3 2 1.449 121.900 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..65bb9b9ae --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CA S 7 6 4 1.510 115.000 180.000 + 9 CD1 CD S 8 7 6 1.400 120.000 180.000 + 10 CE1 CD S 9 8 7 1.400 120.000 180.000 + 11 CZ CD S 10 9 8 1.400 120.000 0.000 + 12 CE2 CD S 11 10 9 1.400 120.000 0.000 + 13 CD2 CD E 12 11 10 1.400 120.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/PRO_PROLINE.in_frag new file mode 100644 index 000000000..5f078dd35 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/PRO_PROLINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD C2 S 4 3 2 1.458 126.100 356.100 + 6 CG C2 S 5 4 3 1.500 103.200 200.100 + 7 CB C2 E 6 5 4 1.510 106.000 338.300 + 8 CA CH M 4 3 2 1.451 120.600 175.200 + 9 C C M 8 4 3 1.522 111.100 0.000 + 10 O O E 9 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/SER_SERINE.in_frag new file mode 100644 index 000000000..06c1c4c80 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/SER_SERINE.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 OG OH S 7 6 4 1.430 109.470 180.000 + 9 HOG HO E 8 7 6 0.960 109.470 180.000 + 10 C C M 6 4 3 1.522 111.100 180.000 + 11 O O E 10 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/THR_THREONINE.in_frag new file mode 100644 index 000000000..55931b7b3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/THR_THREONINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CH B 6 4 3 1.525 111.100 60.000 + 8 CG2 C3 E 7 6 4 1.525 109.470 300.000 + 9 OG1 OH S 7 6 4 1.430 109.470 60.000 + 10 HOG HO E 9 7 6 0.960 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/TRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/TRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..54fd52d96 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/TRP_TRYPTOPHAN.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C* S 7 6 4 1.510 115.000 180.000 + 9 CD1 CG S 8 7 6 1.340 127.000 180.000 + 10 NE1 NA B 9 8 7 1.430 107.000 180.000 + 11 HNE H E 10 9 8 1.010 125.500 180.000 + 12 CE2 CN S 10 9 8 1.310 109.000 0.000 + 13 CZ2 CD S 12 10 9 1.400 128.000 180.000 + 14 CH2 CD S 13 12 10 1.390 116.000 180.000 + 15 CZ3 CD S 14 13 12 1.350 121.000 0.000 + 16 CE3 CD S 15 14 13 1.410 122.000 0.000 + 17 CD2 CB E 16 15 14 1.400 117.000 0.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/TYR_TYROSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/TYR_TYROSINE.in_frag new file mode 100644 index 000000000..80819bb07 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/TYR_TYROSINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CA S 7 6 4 1.510 109.470 180.000 + 9 CD1 CD S 8 7 6 1.400 120.000 180.000 + 10 CE1 CD S 9 8 7 1.400 120.000 180.000 + 11 CZ C B 10 9 8 1.400 120.000 0.000 + 12 OH OH S 11 10 9 1.360 120.000 180.000 + 13 HOH HO E 12 11 10 0.960 113.000 0.000 + 14 CE2 CD S 11 10 9 1.400 120.000 0.000 + 15 CD2 CD E 14 11 10 1.400 120.000 0.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/VAL_VALINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/VAL_VALINE.in_frag new file mode 100644 index 000000000..61d2e5ddc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/VAL_VALINE.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CH B 6 4 3 1.525 111.100 60.000 + 8 CG1 C3 E 7 6 4 1.525 109.470 60.000 + 9 CG2 C3 E 7 6 4 1.525 109.470 180.000 + 10 C C M 6 4 3 1.522 111.100 180.000 + 11 O O E 10 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/protein.amberua/protein.amberua.in b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/protein.amberua.in new file mode 100644 index 000000000..22fc46ac4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/protein.amberua/protein.amberua.in @@ -0,0 +1,698 @@ + 1 0 1 +protein.amberua.db4 + ALANINE +ALA + ALA INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.21500 + 7 CB C3 E 6 4 3 1.525 111.100 60.000 0.03100 + 8 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 9 O O E 8 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + +DONE + GLYCINE +GLY + GLY INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA C2 M 4 3 2 1.449 121.900 180.000 0.24600 + 7 C C M 6 4 3 1.522 110.400 180.000 0.52600 + 8 O O E 7 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + +DONE + SERINE +SER + SER INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.29200 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.19400 + 8 OG OH S 7 6 4 1.430 109.470 180.000 -0.55000 + 9 HOG HO E 8 7 6 0.960 109.470 180.000 0.31000 + 10 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 11 O O E 10 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + +DONE + THREONINE +THR + THR INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.26800 + 7 CB CH B 6 4 3 1.525 111.100 60.000 0.21100 + 8 CG2 C3 E 7 6 4 1.525 109.470 300.000 0.00700 + 9 OG1 OH S 7 6 4 1.430 109.470 60.000 -0.55000 + 10 HOG HO E 9 7 6 0.960 109.470 180.000 0.31000 + 11 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 12 O O E 11 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + CG2 CB CA OG1 + +DONE + LEUCINE +LEU + LEU INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.20400 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.01600 + 8 CG CH B 7 6 4 1.525 109.470 180.000 0.05400 + 9 CD1 C3 E 8 7 6 1.525 109.470 60.000 -0.01400 + 10 CD2 C3 E 8 7 6 1.525 109.470 180.000 -0.01400 + 11 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 12 O O E 11 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + CD1 CG CB CD2 + +DONE + ISOLEUCINE +ILE + ILE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.19900 + 7 CB CH B 6 4 3 1.525 109.470 60.000 0.03000 + 8 CG2 C3 E 7 6 4 1.525 109.470 60.000 0.00100 + 9 CG1 C2 S 7 6 4 1.525 109.470 180.000 0.01700 + 10 CD1 C3 E 9 7 6 1.525 109.470 180.000 -0.00100 + 11 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 12 O O E 11 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + CG2 CB CA CG1 + +DONE + VALINE +VAL + VAL INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.20100 + 7 CB CH B 6 4 3 1.525 111.100 60.000 0.03300 + 8 CG1 C3 E 7 6 4 1.525 109.470 60.000 0.00600 + 9 CG2 C3 E 7 6 4 1.525 109.470 180.000 0.00600 + 10 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 11 O O E 10 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + CG1 CB CA CG2 + +DONE + ASPARAGINE +ASN + ASN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.21700 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.00300 + 8 CG C B 7 6 4 1.522 111.100 180.000 0.67500 + 9 OD1 O E 8 7 6 1.229 120.500 0.000 -0.47000 + 10 ND2 N B 8 7 6 1.335 116.600 180.000 -0.86700 + 11 HND1 H E 10 8 7 1.010 119.800 0.000 0.34400 + 12 HND2 H E 10 8 7 1.010 119.800 180.000 0.34400 + 13 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 14 O O E 13 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + CB ND2 CG OD1 + CG HND1 ND2 HND2 + +DONE + GLUTAMINE +GLN + GLN INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.21000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.05300 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 -0.04300 + 9 CD C B 8 7 6 1.522 111.100 180.000 0.67500 + 10 OE1 O E 9 8 7 1.229 120.500 0.000 -0.47000 + 11 NE2 N B 9 8 7 1.335 116.600 180.000 -0.86700 + 12 HNE1 H E 11 9 8 1.010 119.800 0.000 0.34400 + 13 HNE2 H E 11 9 8 1.010 119.800 180.000 0.34400 + 14 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 15 O O E 14 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + CG NE2 CD OE1 + CD HNE1 NE2 HNE2 + +DONE + ARGININE +ARG + ARG INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.23700 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.04900 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 0.05800 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 0.11100 + 10 NE N2 B 9 8 7 1.480 111.000 180.000 -0.49300 + 11 HNE H3 E 10 9 8 1.010 118.500 0.000 0.29400 + 12 CZ CA B 10 9 8 1.330 123.000 180.000 0.81300 + 13 NH1 N2 B 12 10 9 1.330 122.000 0.000 -0.63450 + 14 HN11 H3 E 13 12 10 1.010 119.800 0.000 0.36150 + 15 HN12 H3 E 13 12 10 1.010 119.800 180.000 0.36150 + 16 NH2 N2 B 12 10 9 1.330 118.000 180.000 -0.63450 + 17 HN21 H3 E 16 12 10 1.010 119.800 0.000 0.36150 + 18 HN22 H3 E 16 12 10 1.010 119.800 180.000 0.36150 + 19 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 20 O O E 19 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + NE NH1 CZ NH2 + +DONE + HISTIDINE DELTAH +HID + HID INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.21900 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.06000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 0.08900 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 -0.44400 + 10 HND H E 9 8 7 1.010 126.000 0.000 0.32000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 0.38400 + 12 NE2 NB S 11 9 8 1.310 109.000 0.000 -0.52700 + 13 CD2 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mode 100644 index 000000000..1dacd6a47 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/ACE_ACE_BEGINNING_GROUP.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 CH3 C3 M 3 2 1 1.000 90.000 180.000 + 5 C C M 4 3 2 1.530 111.100 180.000 + 6 O O E 5 4 3 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/ALA_ALANINE.in_frag new file mode 100644 index 000000000..e881477c8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/ALA_ALANINE.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C3 E 6 4 3 1.525 111.100 60.000 + 8 C C M 6 4 3 1.522 111.100 180.000 + 9 O O E 8 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/ARG_ARGININE.in_frag new file mode 100644 index 000000000..5cce86313 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/ARG_ARGININE.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 + 10 NE N2 B 9 8 7 1.480 111.000 180.000 + 11 HNE H3 E 10 9 8 1.010 118.500 0.000 + 12 CZ CA B 10 9 8 1.330 123.000 180.000 + 13 NH1 N2 B 12 10 9 1.330 122.000 0.000 + 14 HN11 H3 E 13 12 10 1.010 119.800 0.000 + 15 HN12 H3 E 13 12 10 1.010 119.800 180.000 + 16 NH2 N2 B 12 10 9 1.330 118.000 180.000 + 17 HN21 H3 E 16 12 10 1.010 119.800 0.000 + 18 HN22 H3 E 16 12 10 1.010 119.800 180.000 + 19 C C M 6 4 3 1.522 111.100 180.000 + 20 O O E 19 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..3b3cf000b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/ASN_ASPARAGINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C B 7 6 4 1.522 111.100 180.000 + 9 OD1 O E 8 7 6 1.229 120.500 0.000 + 10 ND2 N B 8 7 6 1.335 116.600 180.000 + 11 HND1 H E 10 8 7 1.010 119.800 0.000 + 12 HND2 H E 10 8 7 1.010 119.800 180.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..89680f395 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C B 7 6 4 1.527 109.470 180.000 + 9 OD1 O2 E 8 7 6 1.260 117.200 90.000 + 10 OD2 O2 E 8 7 6 1.260 117.200 270.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/CL_CL__PREP.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/CL_CL__PREP.in_frag new file mode 100644 index 000000000..0ea6e9685 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/CL_CL__PREP.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 CL CL M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..0124a0251 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/CYS_CYSTEINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 SG SH 3 7 6 4 1.810 116.000 180.000 + 9 HG HS E 8 7 6 1.330 96.000 180.000 + 10 LP1 LP E 8 7 6 0.679 96.700 80.000 + 11 LP2 LP E 8 7 6 0.679 96.700 280.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..9525449d3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 SG S B 7 6 4 1.810 116.000 180.000 + 9 LP1 LP E 8 7 6 0.679 96.700 80.000 + 10 LP2 LP E 8 7 6 0.679 96.700 280.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/DADE_D-ADENOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/DADE_D-ADENOSINE.in_frag new file mode 100644 index 000000000..5bcbc2ca7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/DADE_D-ADENOSINE.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' C2 M 4 3 2 1.440 119.000 -39.220 + 6 C4' CH M 5 4 3 1.520 110.000 -151.000 + 7 O1' OS S 6 5 4 1.460 108.860 -86.310 + 8 C1' CH S 7 6 5 1.420 110.040 105.600 + 9 N9 N* S 8 7 6 1.520 109.590 -127.700 + 10 C8 CE S 9 8 7 1.370 131.200 81.590 + 11 N7 NB S 10 9 8 1.300 113.930 177.000 + 12 C5 CB S 11 10 9 1.390 104.000 0.000 + 13 C6 CA B 12 11 10 1.400 132.420 180.000 + 14 N6 N2 B 13 12 11 1.340 123.500 0.000 + 15 H61 H2 E 14 13 12 1.010 120.000 0.000 + 16 H62 H2 E 14 13 12 1.010 120.000 180.000 + 17 N1 NC S 13 12 11 1.340 117.430 180.000 + 18 C2 CI S 17 13 12 1.330 118.800 0.000 + 19 N3 NC S 18 17 13 1.320 129.170 0.000 + 20 C4 CB E 19 18 17 1.350 110.800 0.000 + 21 C3' CH M 6 5 4 1.530 115.780 -329.110 + 22 C2' C2 E 21 6 5 1.530 102.800 -86.300 + 23 O3' OS M 21 6 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/DCYT_D-CYTOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/DCYT_D-CYTOSINE.in_frag new file mode 100644 index 000000000..33fc25fc8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/DCYT_D-CYTOSINE.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' C2 M 4 3 2 1.440 119.000 -39.220 + 6 C4' CH M 5 4 3 1.520 110.000 -151.000 + 7 O1' OS S 6 5 4 1.460 108.860 -86.310 + 8 C1' CH S 7 6 5 1.420 110.040 105.600 + 9 N1 N* S 8 7 6 1.490 108.100 -127.700 + 10 C6 CJ S 9 8 7 1.360 121.100 81.590 + 11 C5 CJ S 10 9 8 1.360 121.000 180.000 + 12 C4 CA B 11 10 9 1.430 116.900 0.000 + 13 N4 N2 B 12 11 10 1.320 120.100 180.000 + 14 H41 H2 E 13 12 11 1.010 117.700 0.000 + 15 H42 H2 E 13 12 11 1.010 120.270 180.000 + 16 N3 NC S 12 11 10 1.330 121.700 0.000 + 17 C2 C S 16 12 11 1.360 120.500 0.000 + 18 O2 O E 17 16 12 1.240 122.400 180.000 + 19 C3' CH M 6 5 4 1.530 115.780 -329.110 + 20 C2' C2 E 19 6 5 1.530 102.800 -86.300 + 21 O3' OS M 19 6 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/DGUA_D-GUANOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/DGUA_D-GUANOSINE.in_frag new file mode 100644 index 000000000..ef8da74c2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/DGUA_D-GUANOSINE.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' C2 M 4 3 2 1.440 119.000 -39.220 + 6 C4' CH M 5 4 3 1.520 110.000 -151.000 + 7 O1' OS S 6 5 4 1.460 108.860 -86.310 + 8 C1' CH S 7 6 5 1.420 110.040 105.600 + 9 N9 N* S 8 7 6 1.490 108.060 -127.700 + 10 C8 CE S 9 8 7 1.380 129.200 81.590 + 11 N7 NB S 10 9 8 1.310 114.000 -179.900 + 12 C5 CB S 11 10 9 1.390 103.900 0.000 + 13 C6 C B 12 11 10 1.420 130.400 180.000 + 14 O6 O E 13 12 11 1.230 128.800 0.000 + 15 N1 NA B 13 12 11 1.400 111.380 180.000 + 16 H1 H E 15 13 12 1.000 117.360 179.900 + 17 C2 CA B 15 13 12 1.380 125.240 -0.100 + 18 N2 N2 B 17 15 13 1.340 116.020 180.000 + 19 H21 H2 E 18 17 15 1.010 127.000 -0.820 + 20 H22 H2 E 18 17 15 1.010 116.530 -179.440 + 21 N3 NC S 17 15 13 1.330 123.300 0.000 + 22 C4 CB E 21 17 15 1.360 112.200 0.000 + 23 C3' CH M 6 5 4 1.530 115.780 -329.110 + 24 C2' C2 E 23 6 5 1.530 102.800 -86.300 + 25 O3' OS M 23 6 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/DOHE_D-OH_END.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/DOHE_D-OH_END.in_frag new file mode 100644 index 000000000..a45d14691 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/DOHE_D-OH_END.in_frag @@ -0,0 +1,5 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O OH M 3 2 1 1.600 101.430 -98.890 + 5 H HO M 4 3 2 0.960 119.000 -39.220 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/DPOM_D_-_PHOSPATE_MINUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/DPOM_D_-_PHOSPATE_MINUS.in_frag new file mode 100644 index 000000000..65776e120 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/DPOM_D_-_PHOSPATE_MINUS.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 -200.850 + 5 OA O2 E 4 3 2 1.480 109.610 -214.890 + 6 OB O2 E 4 3 2 1.480 109.580 -342.910 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/DTHY_D-THYMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/DTHY_D-THYMINE.in_frag new file mode 100644 index 000000000..3dcfd0838 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/DTHY_D-THYMINE.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.430 -98.890 + 5 C5' C2 M 4 3 2 1.440 119.000 -39.220 + 6 C4' CH M 5 4 3 1.520 110.000 -151.000 + 7 O1' OS S 6 5 4 1.460 108.860 -86.310 + 8 C1' CH S 7 6 5 1.420 110.040 105.600 + 9 N1 N* S 8 7 6 1.530 109.590 -127.700 + 10 C6 CJ S 9 8 7 1.370 123.040 81.590 + 11 C5 CM B 10 9 8 1.340 121.220 177.300 + 12 C7 C3 E 11 10 9 1.500 121.630 180.000 + 13 C4 C B 11 10 9 1.440 120.780 0.000 + 14 O4 O E 13 11 10 1.230 125.350 180.000 + 15 N3 NA B 13 11 10 1.380 114.070 0.000 + 16 H3 H E 15 13 11 1.090 116.770 180.000 + 17 C2 C S 15 13 11 1.380 126.460 0.000 + 18 O2 O E 17 15 13 1.220 121.700 180.000 + 19 C3' CH M 6 5 4 1.530 115.780 -329.110 + 20 C2' C2 E 19 6 5 1.530 102.800 -86.300 + 21 O3' OS M 19 6 5 1.420 116.520 -203.470 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..bcbd74bb8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/GLN_GLUTAMINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C B 8 7 6 1.522 111.100 180.000 + 10 OE1 O E 9 8 7 1.229 120.500 0.000 + 11 NE2 N B 9 8 7 1.335 116.600 180.000 + 12 HNE1 H E 11 9 8 1.010 119.800 0.000 + 13 HNE2 H E 11 9 8 1.010 119.800 180.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..92be049d5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.510 109.470 180.000 + 9 CD C B 8 7 6 1.527 109.470 180.000 + 10 OE1 O2 E 9 8 7 1.260 117.200 90.000 + 11 OE2 O2 E 9 8 7 1.260 117.200 270.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..d7659076b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/GLY_GLYCINE.in_frag @@ -0,0 +1,8 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA C2 M 4 3 2 1.449 121.900 180.000 + 7 C C M 6 4 3 1.522 110.400 180.000 + 8 O O E 7 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/HB_H_BEGINNING.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/HB_H_BEGINNING.in_frag new file mode 100644 index 000000000..ea2ea360e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/HB_H_BEGINNING.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H HO M 3 2 1 1.000 120.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/HE_H_END.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/HE_H_END.in_frag new file mode 100644 index 000000000..b57452ff1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/HE_H_END.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H HO M 3 2 1 0.960 114.970 -211.370 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..695b4c564 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 + 12 NE2 NB S 11 9 8 1.310 109.000 0.000 + 13 CD2 CF E 12 11 9 1.360 110.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..b26af0398 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NB S 8 7 6 1.390 122.000 180.000 + 10 CE1 CP S 9 8 7 1.320 108.000 180.000 + 11 NE2 NA B 10 9 8 1.310 109.000 0.000 + 12 HNE H E 11 10 9 1.010 125.000 180.000 + 13 CD2 CG E 11 10 9 1.360 110.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..722338062 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 + 12 NE2 NA B 11 9 8 1.310 109.000 0.000 + 13 HNE H E 12 11 9 1.010 125.000 180.000 + 14 CD2 CG E 12 11 9 1.360 110.000 0.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..342207b5f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CH B 6 4 3 1.525 109.470 60.000 + 8 CG2 C3 E 7 6 4 1.525 109.470 60.000 + 9 CG1 C2 S 7 6 4 1.525 109.470 180.000 + 10 CD1 C3 E 9 7 6 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/K_K___PREP.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/K_K___PREP.in_frag new file mode 100644 index 000000000..d32904a32 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/K_K___PREP.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 K SO M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..e05afa2b0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/LEU_LEUCINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CH B 7 6 4 1.525 109.470 180.000 + 9 CD1 C3 E 8 7 6 1.525 109.470 60.000 + 10 CD2 C3 E 8 7 6 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/LYS_LYSINE.in_frag new file mode 100644 index 000000000..a290c069e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/LYS_LYSINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 + 10 CE C2 S 9 8 7 1.525 109.470 180.000 + 11 NZ N3 3 10 9 8 1.470 109.470 180.000 + 12 HNZ1 H3 E 11 10 9 1.010 109.470 60.000 + 13 HNZ2 H3 E 11 10 9 1.010 109.470 180.000 + 14 HNZ3 H3 E 11 10 9 1.010 109.470 300.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/MET_METHIONINE.in_frag new file mode 100644 index 000000000..4054d970e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/MET_METHIONINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 SD S 3 8 7 6 1.810 110.000 180.000 + 10 CE C3 E 9 8 7 1.780 100.000 180.000 + 11 LP1 LP E 9 8 7 0.679 96.700 80.000 + 12 LP2 LP E 9 8 7 0.679 96.700 280.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/MG_MG__PREP.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/MG_MG__PREP.in_frag new file mode 100644 index 000000000..a51eeeba2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/MG_MG__PREP.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 MG MG M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/NA_NA__PREP.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/NA_NA__PREP.in_frag new file mode 100644 index 000000000..b23bcd6bc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/NA_NA__PREP.in_frag @@ -0,0 +1,4 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 NA SO M 3 2 1 1.000 90.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/NME_N-Methyl_end_group.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/NME_N-Methyl_end_group.in_frag new file mode 100644 index 000000000..900206056 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/NME_N-Methyl_end_group.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CM C3 E 4 3 2 1.449 121.900 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/OHB_OH_BEGINNING.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/OHB_OH_BEGINNING.in_frag new file mode 100644 index 000000000..1b92cda5c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/OHB_OH_BEGINNING.in_frag @@ -0,0 +1,5 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 H HO M 3 2 1 1.000 120.000 180.000 + 5 O OH M 4 3 2 0.960 120.000 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..65bb9b9ae --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CA S 7 6 4 1.510 115.000 180.000 + 9 CD1 CD S 8 7 6 1.400 120.000 180.000 + 10 CE1 CD S 9 8 7 1.400 120.000 180.000 + 11 CZ CD S 10 9 8 1.400 120.000 0.000 + 12 CE2 CD S 11 10 9 1.400 120.000 0.000 + 13 CD2 CD E 12 11 10 1.400 120.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/POHE_PROTEIN-OH_END.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/POHE_PROTEIN-OH_END.in_frag new file mode 100644 index 000000000..35c38e0ca --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/POHE_PROTEIN-OH_END.in_frag @@ -0,0 +1,5 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O OH M 3 2 1 1.360 113.000 180.890 + 5 H HO M 4 3 2 0.960 107.000 -39.220 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/PRO_PROLINE.in_frag new file mode 100644 index 000000000..5f078dd35 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/PRO_PROLINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD C2 S 4 3 2 1.458 126.100 356.100 + 6 CG C2 S 5 4 3 1.500 103.200 200.100 + 7 CB C2 E 6 5 4 1.510 106.000 338.300 + 8 CA CH M 4 3 2 1.451 120.600 175.200 + 9 C C M 8 4 3 1.522 111.100 0.000 + 10 O O E 9 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/RADE_R-ADENOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/RADE_R-ADENOSINE.in_frag new file mode 100644 index 000000000..4f9de4109 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/RADE_R-ADENOSINE.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.340 -78.600 + 5 C5' C2 M 4 3 2 1.440 119.020 -60.180 + 6 C4' CH M 5 4 3 1.520 110.020 174.900 + 7 O1' OS S 6 5 4 1.460 108.870 -67.740 + 8 C1' CH S 7 6 5 1.420 109.840 144.700 + 9 N9 N* S 8 7 6 1.520 109.590 -119.920 + 10 C8 CE S 9 8 7 1.370 131.200 13.450 + 11 N7 NB S 10 9 8 1.300 113.930 177.000 + 12 C5 CB S 11 10 9 1.390 104.000 0.000 + 13 C6 CA B 12 11 10 1.400 132.420 180.000 + 14 N6 N2 B 13 12 11 1.340 123.500 0.000 + 15 H61 H2 E 14 13 12 1.010 120.000 0.000 + 16 H62 H2 E 14 13 12 1.010 120.000 180.000 + 17 N1 NC S 13 12 11 1.340 117.430 180.000 + 18 C2 CI S 17 13 12 1.330 118.800 0.000 + 19 N3 NC S 18 17 13 1.320 129.170 0.000 + 20 C4 CB E 19 18 17 1.350 110.800 0.000 + 21 C3' CH M 6 5 4 1.530 115.820 48.860 + 22 C2' CH S 21 6 5 1.530 102.080 -155.280 + 23 O2' OH S 22 21 6 1.420 110.780 -76.400 + 24 HO2' HO E 23 22 21 0.960 109.470 180.000 + 25 O3' OS M 21 6 5 1.420 111.950 83.180 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/RCYT_R-CYTOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/RCYT_R-CYTOSINE.in_frag new file mode 100644 index 000000000..fb5ec84cc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/RCYT_R-CYTOSINE.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.340 -78.600 + 5 C5' C2 M 4 3 2 1.440 119.020 -60.180 + 6 C4' CH M 5 4 3 1.520 110.020 174.900 + 7 O1' OS S 6 5 4 1.460 108.870 -67.740 + 8 C1' CH S 7 6 5 1.420 109.840 144.700 + 9 N1 N* S 8 7 6 1.490 108.100 -119.920 + 10 C6 CJ S 9 8 7 1.360 121.100 13.450 + 11 C5 CJ S 10 9 8 1.360 121.000 180.000 + 12 C4 CA B 11 10 9 1.430 116.900 0.000 + 13 N4 N2 B 12 11 10 1.320 120.100 180.000 + 14 H41 H2 E 13 12 11 1.010 117.700 0.000 + 15 H42 H2 E 13 12 11 1.010 120.270 180.000 + 16 N3 NC S 12 11 10 1.330 121.700 0.000 + 17 C2 C S 16 12 11 1.360 120.500 0.000 + 18 O2 O E 17 16 12 1.240 122.400 180.000 + 19 C3' CH M 6 5 4 1.530 115.820 48.860 + 20 C2' CH S 19 6 5 1.530 102.080 -155.280 + 21 O2' OH S 20 19 6 1.420 110.780 -76.400 + 22 HO2' HO E 21 20 19 0.960 109.470 180.000 + 23 O3' OS M 19 6 5 1.420 111.950 83.180 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/RGUA_R-GUANOSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/RGUA_R-GUANOSINE.in_frag new file mode 100644 index 000000000..8f32452b2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/RGUA_R-GUANOSINE.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.340 -78.600 + 5 C5' C2 M 4 3 2 1.440 119.020 -60.180 + 6 C4' CH M 5 4 3 1.520 110.020 174.900 + 7 O1' OS S 6 5 4 1.460 108.870 -67.740 + 8 C1' CH S 7 6 5 1.420 109.840 144.700 + 9 N9 N* S 8 7 6 1.490 108.060 -119.920 + 10 C8 CE S 9 8 7 1.380 129.200 13.450 + 11 N7 NB S 10 9 8 1.310 114.000 -179.900 + 12 C5 CB S 11 10 9 1.390 103.900 0.000 + 13 C6 C B 12 11 10 1.420 130.400 180.000 + 14 O6 O E 13 12 11 1.230 128.800 0.000 + 15 N1 NA B 13 12 11 1.400 111.380 180.000 + 16 H1 H E 15 13 12 1.000 117.360 179.900 + 17 C2 CA B 15 13 12 1.380 125.240 -0.100 + 18 N2 N2 B 17 15 13 1.340 116.020 180.000 + 19 H21 H2 E 18 17 15 1.010 127.000 -0.820 + 20 H22 H2 E 18 17 15 1.010 116.530 -179.440 + 21 N3 NC S 17 15 13 1.330 123.300 0.000 + 22 C4 CB E 21 17 15 1.360 112.200 0.000 + 23 C3' CH M 6 5 4 1.530 115.820 48.860 + 24 C2' CH S 23 6 5 1.530 102.080 -155.280 + 25 O2' OH S 24 23 6 1.420 110.780 -76.400 + 26 HO2' HO E 25 24 23 0.960 109.470 180.000 + 27 O3' OS M 23 6 5 1.420 111.950 83.180 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/ROHE_R-OH_END.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/ROHE_R-OH_END.in_frag new file mode 100644 index 000000000..378496e5f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/ROHE_R-OH_END.in_frag @@ -0,0 +1,5 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O OH M 3 2 1 1.600 101.430 -78.600 + 5 H HO M 4 3 2 0.960 119.000 -39.220 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/RPOM_R_-_PHOSPHATE_MINUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/RPOM_R_-_PHOSPHATE_MINUS.in_frag new file mode 100644 index 000000000..319ce47eb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/RPOM_R_-_PHOSPHATE_MINUS.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 P P M 3 2 1 1.600 119.040 -213.190 + 5 OA O2 E 4 3 2 1.480 109.580 -194.890 + 6 OB O2 E 4 3 2 1.480 109.650 -332.610 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/RURA_R-URACIL.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/RURA_R-URACIL.in_frag new file mode 100644 index 000000000..5b7d8b70c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/RURA_R-URACIL.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 O5' OS M 3 2 1 1.600 101.340 -78.600 + 5 C5' C2 M 4 3 2 1.440 119.020 -60.180 + 6 C4' CH M 5 4 3 1.520 110.020 174.900 + 7 O1' OS S 6 5 4 1.460 108.870 -67.740 + 8 C1' CH S 7 6 5 1.420 109.840 144.700 + 9 N1 N* S 8 7 6 1.530 109.590 -119.920 + 10 C6 CJ S 9 8 7 1.370 123.040 13.450 + 11 C5 CJ S 10 9 8 1.340 121.220 177.300 + 12 C4 C B 11 10 9 1.440 120.780 0.000 + 13 O4 O E 12 11 10 1.230 125.350 180.000 + 14 N3 NA B 12 11 10 1.380 114.070 0.000 + 15 H3 H E 14 12 11 1.090 116.770 180.000 + 16 C2 C S 14 12 11 1.380 126.460 0.000 + 17 O2 O E 16 14 12 1.220 121.700 180.000 + 18 C3' CH M 6 5 4 1.530 115.820 48.860 + 19 C2' CH S 18 6 5 1.530 102.080 -155.280 + 20 O2' OH S 19 18 6 1.420 110.780 -76.400 + 21 HO2' HO E 20 19 18 0.960 109.470 180.000 + 22 O3' OS M 18 6 5 1.420 111.950 83.180 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/SER_SERINE.in_frag new file mode 100644 index 000000000..06c1c4c80 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/SER_SERINE.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 OG OH S 7 6 4 1.430 109.470 180.000 + 9 HOG HO E 8 7 6 0.960 109.470 180.000 + 10 C C M 6 4 3 1.522 111.100 180.000 + 11 O O E 10 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/THR_THREONINE.in_frag new file mode 100644 index 000000000..55931b7b3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/THR_THREONINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CH B 6 4 3 1.525 111.100 60.000 + 8 CG2 C3 E 7 6 4 1.525 109.470 300.000 + 9 OG1 OH S 7 6 4 1.430 109.470 60.000 + 10 HOG HO E 9 7 6 0.960 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/TRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni/TRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..54fd52d96 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni/TRP_TRYPTOPHAN.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C* S 7 6 4 1.510 115.000 180.000 + 9 CD1 CG S 8 7 6 1.340 127.000 180.000 + 10 NE1 NA B 9 8 7 1.430 107.000 180.000 + 11 HNE H E 10 9 8 1.010 125.500 180.000 + 12 CE2 CN S 10 9 8 1.310 109.000 0.000 + 13 CZ2 CD S 12 10 9 1.400 128.000 180.000 + 14 CH2 CD S 13 12 10 1.390 116.000 180.000 + 15 CZ3 CD S 14 13 12 1.350 121.000 0.000 + 16 CE3 CD S 15 14 13 1.410 122.000 0.000 + 17 CD2 CB E 16 15 14 1.400 117.000 0.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni/TYR_TYROSINE.in_frag 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180.000 0.04800 + 10 CE C2 S 9 8 7 1.525 109.470 180.000 0.21800 + 11 NZ N3 3 10 9 8 1.470 109.470 180.000 -0.27200 + 12 HNZ1 H3 E 11 10 9 1.010 109.470 60.000 0.31100 + 13 HNZ2 H3 E 11 10 9 1.010 109.470 180.000 0.31100 + 14 HNZ3 H3 E 11 10 9 1.010 109.470 300.000 0.31100 + 15 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 16 O O E 15 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + +DONE + PROLINE +PRO + PRO INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.337 117.000 180.000 -0.25700 + 5 CD C2 S 4 3 2 1.458 126.100 356.100 0.08400 + 6 CG C2 S 5 4 3 1.500 103.200 200.100 0.03600 + 7 CB C2 E 6 5 4 1.510 106.000 338.300 -0.00100 + 8 CA CH M 4 3 2 1.451 120.600 175.200 0.11200 + 9 C C M 8 4 3 1.522 111.100 0.000 0.52600 + 10 O O E 9 8 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + CA +M C O + CB CA N C + -M CA N CD + +LOOP + CB CA + +DONE + CYSTEINE +CYS + CYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.14600 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.10000 + 8 SG SH 3 7 6 4 1.810 116.000 180.000 0.82700 + 9 HG HS E 8 7 6 1.330 96.000 180.000 0.13500 + 10 LP1 LP E 8 7 6 0.679 96.700 80.000 -0.48100 + 11 LP2 LP E 8 7 6 0.679 96.700 280.000 -0.48100 + 12 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 13 O O E 12 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + +DONE + CYSTINE(S-S BRIDGE) +CYX + CYX INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.08800 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.14300 + 8 SG S B 7 6 4 1.810 116.000 180.000 0.82400 + 9 LP1 LP E 8 7 6 0.679 96.700 80.000 -0.40450 + 10 LP2 LP E 8 7 6 0.679 96.700 280.000 -0.40450 + 11 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 12 O O E 11 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + +DONE + METHIONINE +MET + MET INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.13700 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.03700 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 0.09000 + 9 SD S 3 8 7 6 1.810 110.000 180.000 0.73700 + 10 CE C3 E 9 8 7 1.780 100.000 180.000 0.00700 + 11 LP1 LP E 9 8 7 0.679 96.700 80.000 -0.38100 + 12 LP2 LP E 9 8 7 0.679 96.700 280.000 -0.38100 + 13 C C M 6 4 3 1.522 111.100 180.000 0.52600 + 14 O O E 13 6 4 1.229 120.500 0.000 -0.50000 + +IMPROPER + -M CA N HN + CA +M C O + CB CA N C + +DONE + ACE BEGINNING GROUP +ACE + ACE INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 CH3 C3 M 3 2 1 1.000 90.000 180.000 -0.02600 + 5 C C M 4 3 2 1.530 111.100 180.000 0.52600 + 6 O O E 5 4 3 1.229 120.500 0.000 -0.50000 + +IMPROPER + CH3 +M C O + +DONE + N-Methyl end group +NME + NME INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.52000 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CM C3 E 4 3 2 1.449 121.900 180.000 0.27200 + +IMPROPER + -M CM N HN + +DONE +MG PREP +MG +MG INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 MG MG M 3 2 1 1.0000 90.0000 180.0000 2.000 + +DONE +K PREP +K +K INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 K SO M 3 2 1 1.0000 90.0000 180.0000 1.000 + +DONE +NA PREP +NA +NA INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 NA SO M 3 2 1 1.0000 90.0000 180.0000 1.000 + +DONE +CL PREP +CL +CL INT 1 +CORR OMIT DU BEG + 0.000000 + 1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000 + 2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000 + 3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000 + 4 CL CL M 3 2 1 1.0000 90.0000 180.0000 -1.000 + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ACE_ACE_BEGINNING_GROUP.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ACE_ACE_BEGINNING_GROUP.in_frag new file mode 100644 index 000000000..887cc6573 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ACE_ACE_BEGINNING_GROUP.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 CH3 C3 M 3 2 1 1.090 90.000 180.000 + 5 C C M 4 3 2 1.530 111.100 180.000 + 6 O O E 5 4 3 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ALA_ALANINE.in_frag new file mode 100644 index 000000000..932105de5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ALA_ALANINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C3 E 6 4 3 1.525 111.100 60.000 + 9 C C M 6 4 3 1.522 111.100 180.000 + 10 O O E 9 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ARG_ARGININE.in_frag new file mode 100644 index 000000000..16f858402 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ARG_ARGININE.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C2 S 8 6 4 1.525 109.470 180.000 + 10 CD C2 S 9 8 6 1.525 109.470 180.000 + 11 NE N2 B 10 9 8 1.480 111.000 180.000 + 12 HE H E 11 10 9 1.010 118.500 0.000 + 13 CZ CA B 11 10 9 1.330 123.000 180.000 + 14 NH1 N2 B 13 11 10 1.330 122.000 0.000 + 15 HH11 H E 14 13 11 1.010 119.800 0.000 + 16 HH12 H E 14 13 11 1.010 119.800 180.000 + 17 NH2 N2 B 13 11 10 1.330 118.000 180.000 + 18 HH21 H E 17 13 11 1.010 119.800 0.000 + 19 HH22 H E 17 13 11 1.010 119.800 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O E 20 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..7b3d4c900 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ASN_ASPARAGINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C B 8 6 4 1.522 111.100 180.000 + 10 OD1 O E 9 8 6 1.229 120.500 0.000 + 11 ND2 N B 9 8 6 1.335 116.600 180.000 + 12 HD21 H E 11 9 8 1.010 119.800 180.000 + 13 HD22 H E 11 9 8 1.010 119.800 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O E 14 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..fd1d28ee1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C B 8 6 4 1.527 109.470 180.000 + 10 OD1 O2 E 9 8 6 1.260 117.200 90.000 + 11 OD2 O2 E 9 8 6 1.260 117.200 270.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..aa99fca44 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/CYS_CYSTEINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 SG SH S 8 6 4 1.810 116.000 180.000 + 10 HG HS E 9 8 6 1.330 96.000 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..b8b6396b6 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 SG S E 7 6 4 1.810 116.000 180.000 + 10 C C M 6 4 3 1.522 111.100 180.000 + 11 O O E 10 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..48f33064c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/GLN_GLUTAMINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C2 S 8 6 4 1.525 109.470 180.000 + 10 CD C B 9 8 6 1.522 111.100 180.000 + 11 OE1 O E 10 9 8 1.229 120.500 0.000 + 12 NE2 N B 10 9 8 1.335 116.600 180.000 + 13 HE21 H E 12 10 9 1.010 119.800 180.000 + 14 HE22 H E 12 10 9 1.010 119.800 0.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O E 15 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..cbdb48fdc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C2 S 8 6 4 1.510 109.470 180.000 + 10 CD C B 9 8 6 1.527 109.470 180.000 + 11 OE1 O2 E 10 9 8 1.260 117.200 90.000 + 12 OE2 O2 E 10 9 8 1.260 117.200 270.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O E 13 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..8ac9c1995 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/GLY_GLYCINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H0 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H0 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O E 9 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..c2a789c7e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG CC S 8 6 4 1.510 115.000 180.000 + 10 ND1 NA B 9 8 6 1.390 122.000 180.000 + 11 HD1 H E 10 9 8 1.010 126.000 0.000 + 12 CE1 CR B 10 9 8 1.320 108.000 180.000 + 13 HE1 H5 E 12 10 9 1.090 120.000 180.000 + 14 NE2 NB S 12 10 9 1.310 109.000 0.000 + 15 CD2 CV S 14 12 10 1.360 110.000 0.000 + 16 HD2 H4 E 15 14 12 1.090 120.000 180.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O E 17 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..937fd0f8e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG CC S 8 6 4 1.510 115.000 180.000 + 10 ND1 NB S 9 8 6 1.390 122.000 180.000 + 11 CE1 CR B 10 9 8 1.320 108.000 180.000 + 12 HE1 H5 E 11 10 9 1.090 120.000 180.000 + 13 NE2 NA B 11 10 9 1.310 109.000 0.000 + 14 HE2 H E 13 11 10 1.010 125.000 180.000 + 15 CD2 CW S 13 11 10 1.360 110.000 0.000 + 16 HD2 H4 E 15 13 11 1.090 120.000 180.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O E 17 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..cf8622b4b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG CC S 8 6 4 1.510 115.000 180.000 + 10 ND1 NA B 9 8 6 1.390 122.000 180.000 + 11 HD1 H E 10 9 8 1.010 126.000 0.000 + 12 CE1 CR B 10 9 8 1.320 108.000 180.000 + 13 HE1 H5 E 12 10 9 1.090 120.000 180.000 + 14 NE2 NA B 12 10 9 1.310 109.000 0.000 + 15 HE2 H E 14 12 10 1.010 125.000 180.000 + 16 CD2 CW S 14 12 10 1.360 110.000 0.000 + 17 HD2 H4 E 16 14 12 1.090 120.000 180.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O E 18 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..0780bb2ea --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C1 B 6 4 3 1.525 109.470 60.000 + 9 CG2 C3 E 8 6 4 1.525 109.470 60.000 + 10 CG1 C2 S 8 6 4 1.525 109.470 180.000 + 11 CD1 C3 E 10 8 6 1.525 109.470 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..48693cc0e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/LEU_LEUCINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C1 B 8 6 4 1.525 109.470 180.000 + 10 CD1 C3 E 9 8 6 1.525 109.470 60.000 + 11 CD2 C3 E 9 8 6 1.525 109.470 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/LYS_LYSINE.in_frag new file mode 100644 index 000000000..d59902c6f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/LYS_LYSINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C2 S 8 6 4 1.525 109.470 180.000 + 10 CD C2 S 9 8 6 1.525 109.470 180.000 + 11 CE C2 S 10 9 8 1.525 109.470 180.000 + 12 NZ N3 3 11 10 9 1.470 109.470 180.000 + 13 HZ1 H E 12 11 10 1.010 109.470 60.000 + 14 HZ2 H E 12 11 10 1.010 109.470 180.000 + 15 HZ3 H E 12 11 10 1.010 109.470 300.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O E 16 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/MET_METHIONINE.in_frag new file mode 100644 index 000000000..96bdb5c3c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/MET_METHIONINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C2 S 8 6 4 1.525 109.470 180.000 + 10 SD S S 9 8 6 1.810 110.000 180.000 + 11 CE C3 E 10 9 8 1.780 100.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/NME_N-methyl_all_atom.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/NME_N-methyl_all_atom.in_frag new file mode 100644 index 000000000..870b56ca7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/NME_N-methyl_all_atom.in_frag @@ -0,0 +1,6 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CH3 C3 E 4 3 2 1.449 121.900 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..ac7a7a975 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG CA S 8 6 4 1.510 115.000 180.000 + 10 CD1 CA B 9 8 6 1.400 120.000 180.000 + 11 HD1 HA E 10 9 8 1.090 120.000 0.000 + 12 CE1 CA B 10 9 8 1.400 120.000 180.000 + 13 HE1 HA E 12 10 9 1.090 120.000 180.000 + 14 CZ CA B 12 10 9 1.400 120.000 0.000 + 15 HZ HA E 14 12 10 1.090 120.000 180.000 + 16 CE2 CA B 14 12 10 1.400 120.000 0.000 + 17 HE2 HA E 16 14 12 1.090 120.000 180.000 + 18 CD2 CA S 16 14 12 1.400 120.000 0.000 + 19 HD2 HA E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O E 20 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/PRO_PROLINE.in_frag new file mode 100644 index 000000000..9bf91e5eb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/PRO_PROLINE.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD C2 S 4 3 2 1.458 126.100 356.100 + 6 CG C2 S 5 4 3 1.500 103.200 200.100 + 7 CB C2 E 6 5 4 1.510 106.000 338.300 + 8 CA CT M 4 3 2 1.451 120.600 175.200 + 9 HA H1 E 8 4 3 1.090 109.500 60.000 + 10 C C M 8 4 3 1.522 109.500 300.000 + 11 O O E 10 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/SER_SERINE.in_frag new file mode 100644 index 000000000..2704d8408 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/SER_SERINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 OG OH S 8 6 4 1.430 109.470 180.000 + 10 HG HO E 9 8 6 0.960 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/THR_THREONINE.in_frag new file mode 100644 index 000000000..4995d71cb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/THR_THREONINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C1 B 6 4 3 1.525 111.100 60.000 + 9 CG2 C3 E 8 6 4 1.525 109.470 300.000 + 10 OG1 OH S 8 6 4 1.430 109.470 60.000 + 11 HG1 HO E 10 8 6 0.960 109.470 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O E 12 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/TRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/TRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..3fa7d3c9b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/TRP_TRYPTOPHAN.in_frag @@ -0,0 +1,25 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C* S 8 6 4 1.510 115.000 180.000 + 10 CD1 CW B 9 8 6 1.340 127.000 180.000 + 11 HD1 H4 E 10 9 8 1.090 120.000 0.000 + 12 NE1 NA B 10 9 8 1.430 107.000 180.000 + 13 HE1 H E 12 10 9 1.010 125.500 180.000 + 14 CE2 CN S 12 10 9 1.310 109.000 0.000 + 15 CZ2 CA B 14 12 10 1.400 128.000 180.000 + 16 HZ2 HA E 15 14 12 1.090 120.000 0.000 + 17 CH2 CA B 15 14 12 1.390 116.000 180.000 + 18 HH2 HA E 17 15 14 1.090 120.000 180.000 + 19 CZ3 CA B 17 15 14 1.350 121.000 0.000 + 20 HZ3 HA E 19 17 15 1.090 120.000 180.000 + 21 CE3 CA B 19 17 15 1.410 122.000 0.000 + 22 HE3 HA E 21 19 17 1.090 120.000 180.000 + 23 CD2 CB E 21 19 17 1.400 117.000 0.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O E 24 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/TYR_TYROSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/TYR_TYROSINE.in_frag new file mode 100644 index 000000000..8e473916c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/TYR_TYROSINE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG CA S 8 6 4 1.510 109.470 180.000 + 10 CD1 CA B 9 8 6 1.400 120.000 180.000 + 11 HD1 HA E 10 9 8 1.090 120.000 0.000 + 12 CE1 CA B 10 9 8 1.400 120.000 180.000 + 13 HE1 HA E 12 10 9 1.090 120.000 180.000 + 14 CZ C B 12 10 9 1.400 120.000 0.000 + 15 OH OH S 14 12 10 1.360 120.000 180.000 + 16 HH HO E 15 14 12 0.960 113.000 0.000 + 17 CE2 CA B 14 12 10 1.400 120.000 0.000 + 18 HE2 HA E 17 14 12 1.090 120.000 180.000 + 19 CD2 CA S 17 14 12 1.400 120.000 0.000 + 20 HD2 HA E 19 17 14 1.090 120.000 180.000 + 21 C C M 6 4 3 1.522 111.100 180.000 + 22 O O E 21 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/VAL_VALINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/VAL_VALINE.in_frag new file mode 100644 index 000000000..3536fecad --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/VAL_VALINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C1 B 6 4 3 1.525 111.100 60.000 + 9 CG1 C3 E 8 6 4 1.525 109.470 60.000 + 10 CG2 C3 E 8 6 4 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O E 11 6 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_amino03/uni_amino03.in b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/uni_amino03.in new file mode 100644 index 000000000..e6b4d7827 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_amino03/uni_amino03.in @@ -0,0 +1,701 @@ + 1 1 2 +db94.dat +ALANINE + +ALA INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.404773 + 5 H H E 4 3 2 1.010 119.800 0.000 0.294276 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.008639 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.105187 + 8 CB C3 E 6 4 3 1.525 111.100 60.000 -0.001146 + 9 C C M 6 4 3 1.522 111.100 180.000 0.570224 + 10 O O E 9 6 4 1.229 120.500 0.000 -0.555129 + +IMPROPER + -M CA N H + CA +M C O + +DONE +GLYCINE + +GLY INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.372157 + 5 H H E 4 3 2 1.010 119.800 0.000 0.289253 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.131460 + 7 HA2 H0 E 6 4 3 1.090 109.500 300.000 0.102138 + 8 HA3 H0 E 6 4 3 1.090 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CG C1 B 8 6 4 1.525 109.470 180.000 0.106149 + 10 CD1 C3 E 9 8 6 1.525 109.470 60.000 -0.032069 + 11 CD2 C3 E 9 8 6 1.525 109.470 180.000 -0.032069 + 12 C C M 6 4 3 1.522 111.100 180.000 0.573471 + 13 O O E 12 6 4 1.229 120.500 0.000 -0.557847 + +IMPROPER + -M CA N H + CA +M C O + +DONE +ISOLEUCINE + +ILE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.382433 + 5 H H E 4 3 2 1.010 119.800 0.000 0.267891 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.161079 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.114397 + 8 CB C1 B 6 4 3 1.525 109.470 60.000 0.088803 + 9 CG2 C3 E 8 6 4 1.525 109.470 60.000 -0.022775 + 10 CG1 C2 S 8 6 4 1.525 109.470 180.000 0.043975 + 11 CD1 C3 E 10 8 6 1.525 109.470 180.000 -0.022775 + 12 C C M 6 4 3 1.522 111.100 180.000 0.670457 + 13 O O E 12 6 4 1.229 120.500 0.000 -0.596460 + +IMPROPER + -M CA N H + 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0.046248 + 8 CA CT M 4 3 2 1.451 120.600 175.200 -0.005001 + 9 HA H1 E 8 4 3 1.090 109.500 60.000 0.064367 + 10 C C M 8 4 3 1.522 109.500 300.000 0.332443 + 11 O O E 10 8 4 1.229 120.500 0.000 -0.482635 + +LOOP + CB CA + +IMPROPER + CA +M C O + -M CD N CA + +DONE +CYSTEINE + +CYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.396165 + 5 H H E 4 3 2 1.010 119.800 0.000 0.295187 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.059919 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.126669 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 0.140485 + 9 SG SH S 8 6 4 1.810 116.000 180.000 -0.318857 + 10 HG HS E 9 8 6 1.330 96.000 180.000 0.154428 + 11 C C M 6 4 3 1.522 111.100 180.000 0.643035 + 12 O O E 11 6 4 1.229 120.500 0.000 -0.584861 + +IMPROPER + -M CA N H + CA +M C O + +DONE +METHIONINE + +MET INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.394918 + 5 H H E 4 3 2 1.010 119.800 0.000 0.280537 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.080979 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.113428 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 0.064107 + 9 CG C2 S 8 6 4 1.525 109.470 180.000 0.154042 + 10 SD S S 9 8 6 1.810 110.000 180.000 -0.346102 + 11 CE C3 E 10 9 8 1.780 100.000 180.000 0.176624 + 12 C C M 6 4 3 1.522 111.100 180.000 0.599684 + 13 O O E 12 6 4 1.229 120.500 0.000 -0.566424 + +IMPROPER + -M CA N H + CA +M C O + +DONE + ACE BEGINNING GROUP + +ACE INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 CH3 C3 M 3 2 1 1.090 90.000 180.000 0.057379 + 5 C C M 4 3 2 1.530 111.100 180.000 0.453097 + 6 O O E 5 4 3 1.229 120.500 0.000 -0.540735 + +IMPROPER + CH3 +M C O + +DONE +N-methyl all atom + +NME INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.481458 + 5 H H E 4 3 2 1.010 119.800 0.000 0.286377 + 6 CH3 C3 E 4 3 2 1.449 121.900 180.000 0.225339 + +IMPROPER + -M CH3 N H + +DONE +CYSTINE(S-S BRIDGE) + + CYX INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.435921 + 5 H H E 4 3 2 1.010 119.800 0.000 0.290077 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.016965 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.118305 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 -0.193674 + 9 SG S E 7 6 4 1.810 116.000 180.000 -0.200793 + 10 C C M 6 4 3 1.522 111.100 180.000 0.624788 + 11 O O E 10 6 4 1.229 120.500 0.000 -0.573167 + +IMPROPER + -M CA N H + CA +M C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CALA_ALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CALA_ALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..de510b780 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CALA_ALANINE_COO-_ANION.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C3 E 6 4 3 1.525 111.100 60.000 + 9 C C M 6 4 3 1.522 111.100 180.000 + 10 O O2 E 9 6 4 1.229 120.500 0.000 + 11 OXT O2 E 9 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CARG_ARGININE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CARG_ARGININE_COO-_ANION.in_frag new file mode 100644 index 000000000..8c6c97fe0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CARG_ARGININE_COO-_ANION.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C2 S 8 6 4 1.525 109.470 180.000 + 10 CD C2 S 9 8 6 1.525 109.470 180.000 + 11 NE N2 B 10 9 8 1.480 111.000 180.000 + 12 HE H E 11 10 9 1.010 118.500 0.000 + 13 CZ CA B 11 10 9 1.330 123.000 180.000 + 14 NH1 N2 B 13 11 10 1.330 122.000 0.000 + 15 HH11 H E 14 13 11 1.010 119.800 0.000 + 16 HH12 H E 14 13 11 1.010 119.800 180.000 + 17 NH2 N2 B 13 11 10 1.330 118.000 180.000 + 18 HH21 H E 17 13 11 1.010 119.800 0.000 + 19 HH22 H E 17 13 11 1.010 119.800 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O2 E 20 6 4 1.229 120.500 0.000 + 22 OXT O2 E 20 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CASN_ASPARAGINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CASN_ASPARAGINE_COO-_ANION.in_frag new file mode 100644 index 000000000..48f8add83 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CASN_ASPARAGINE_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C B 8 6 4 1.522 111.100 180.000 + 10 OD1 O E 9 8 6 1.229 120.500 0.000 + 11 ND2 N B 9 8 6 1.335 116.600 180.000 + 12 HD21 H E 11 9 8 1.010 119.800 180.000 + 13 HD22 H E 11 9 8 1.010 119.800 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CASP_ASPARTIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CASP_ASPARTIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..20a0c7e94 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CASP_ASPARTIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C B 8 6 4 1.527 109.470 180.000 + 10 OD1 O2 E 9 8 6 1.260 117.200 90.000 + 11 OD2 O2 E 9 8 6 1.260 117.200 270.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CCYS_CYSTEINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CCYS_CYSTEINE_COO-_ANION.in_frag new file mode 100644 index 000000000..5ace055c9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CCYS_CYSTEINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 SG SH S 8 6 4 1.810 116.000 180.000 + 10 HG HS E 9 8 6 1.330 96.000 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CGLN_GLUTAMINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CGLN_GLUTAMINE_COO-_ANION.in_frag new file mode 100644 index 000000000..66c8a553f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CGLN_GLUTAMINE_COO-_ANION.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C2 S 8 6 4 1.525 109.470 180.000 + 10 CD C B 9 8 6 1.522 111.100 180.000 + 11 OE1 O E 10 9 8 1.229 120.500 0.000 + 12 NE2 N B 10 9 8 1.335 116.600 180.000 + 13 HE21 H E 12 10 9 1.010 119.800 180.000 + 14 HE22 H E 12 10 9 1.010 119.800 0.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O2 E 15 6 4 1.229 120.500 0.000 + 17 OXT O2 E 15 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CGLU_GLUTAMIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CGLU_GLUTAMIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..4768134d2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CGLU_GLUTAMIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C2 S 8 6 4 1.510 109.470 180.000 + 10 CD C B 9 8 6 1.527 109.470 180.000 + 11 OE1 O2 E 10 9 8 1.260 117.200 90.000 + 12 OE2 O2 E 10 9 8 1.260 117.200 270.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CGLY_GLYCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CGLY_GLYCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..3bd07e87c --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CGLY_GLYCINE_COO-_ANION.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA2 H0 E 6 4 3 1.090 109.500 300.000 + 8 HA3 H0 E 6 4 3 1.090 109.500 60.000 + 9 C C M 6 4 3 1.522 110.400 180.000 + 10 O O2 E 9 6 4 1.229 120.500 0.000 + 11 OXT O2 E 9 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CHID_HISTIDINE_DELTAH_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CHID_HISTIDINE_DELTAH_COO-_ANION.in_frag new file mode 100644 index 000000000..cd2d35068 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CHID_HISTIDINE_DELTAH_COO-_ANION.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG CC S 8 6 4 1.510 115.000 180.000 + 10 ND1 NA B 9 8 6 1.390 122.000 180.000 + 11 HD1 H E 10 9 8 1.010 126.000 0.000 + 12 CE1 CR B 10 9 8 1.320 108.000 180.000 + 13 HE1 H5 E 12 10 9 1.090 120.000 180.000 + 14 NE2 NB S 12 10 9 1.310 109.000 0.000 + 15 CD2 CV S 14 12 10 1.360 110.000 0.000 + 16 HD2 H4 E 15 14 12 1.090 120.000 180.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O2 E 17 6 4 1.229 120.500 0.000 + 19 OXT O2 E 17 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CHIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CHIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag new file mode 100644 index 000000000..f581d51e2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CHIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG CC S 8 6 4 1.510 115.000 180.000 + 10 ND1 NB S 9 8 6 1.390 122.000 180.000 + 11 CE1 CR B 10 9 8 1.320 108.000 180.000 + 12 HE1 H5 E 11 10 9 1.090 120.000 180.000 + 13 NE2 NA B 11 10 9 1.310 109.000 0.000 + 14 HE2 H E 13 11 10 1.010 125.000 180.000 + 15 CD2 CW S 13 11 10 1.360 110.000 0.000 + 16 HD2 H4 E 15 13 11 1.090 120.000 180.000 + 17 C C M 6 4 3 1.522 111.100 180.000 + 18 O O2 E 17 6 4 1.229 120.500 0.000 + 19 OXT O2 E 17 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CHIP_HISTIDINE_PLUS_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CHIP_HISTIDINE_PLUS_COO-_ANION.in_frag new file mode 100644 index 000000000..cb0dfbd8f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CHIP_HISTIDINE_PLUS_COO-_ANION.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG CC S 8 6 4 1.510 115.000 180.000 + 10 ND1 NA B 9 8 6 1.390 122.000 180.000 + 11 HD1 H E 10 9 8 1.010 126.000 0.000 + 12 CE1 CR B 10 9 8 1.320 108.000 180.000 + 13 HE1 H5 E 12 10 9 1.090 120.000 180.000 + 14 NE2 NA B 12 10 9 1.310 109.000 0.000 + 15 HE2 H E 14 12 10 1.010 125.000 180.000 + 16 CD2 CW S 14 12 10 1.360 110.000 0.000 + 17 HD2 H4 E 16 14 12 1.090 120.000 180.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O2 E 18 6 4 1.229 120.500 0.000 + 20 OXT O2 E 18 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CILE_ISOLEUCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CILE_ISOLEUCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..8b4165060 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CILE_ISOLEUCINE_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C1 B 6 4 3 1.525 109.470 60.000 + 9 CG2 C3 E 8 6 4 1.525 109.470 60.000 + 10 CG1 C2 S 8 6 4 1.525 109.470 180.000 + 11 CD1 C3 E 10 8 6 1.525 109.470 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CLEU_LEUCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CLEU_LEUCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..dd39d42eb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CLEU_LEUCINE_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C1 B 8 6 4 1.525 109.470 180.000 + 10 CD1 C3 E 9 8 6 1.525 109.470 60.000 + 11 CD2 C3 E 9 8 6 1.525 109.470 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CLYS_LYSINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CLYS_LYSINE_COO-_ANION.in_frag new file mode 100644 index 000000000..93f41309b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CLYS_LYSINE_COO-_ANION.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C2 S 8 6 4 1.525 109.470 180.000 + 10 CD C2 S 9 8 6 1.525 109.470 180.000 + 11 CE C2 S 10 9 8 1.525 109.470 180.000 + 12 NZ N3 3 11 10 9 1.470 109.470 180.000 + 13 HZ1 H E 12 11 10 1.010 109.470 60.000 + 14 HZ2 H E 12 11 10 1.010 109.470 180.000 + 15 HZ3 H E 12 11 10 1.010 109.470 300.000 + 16 C C M 6 4 3 1.522 111.100 180.000 + 17 O O2 E 16 6 4 1.229 120.500 0.000 + 18 OXT O2 E 16 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CMET_METHIONINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CMET_METHIONINE_COO-_ANION.in_frag new file mode 100644 index 000000000..9ca142f96 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CMET_METHIONINE_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C2 S 8 6 4 1.525 109.470 180.000 + 10 SD S S 9 8 6 1.810 110.000 180.000 + 11 CE C3 E 10 9 8 1.780 100.000 180.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CPHE_PHENYLALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CPHE_PHENYLALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..c67f69201 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CPHE_PHENYLALANINE_COO-_ANION.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG CA S 8 6 4 1.510 115.000 180.000 + 10 CD1 CA B 9 8 6 1.400 120.000 180.000 + 11 HD1 HA E 10 9 8 1.090 120.000 0.000 + 12 CE1 CA B 10 9 8 1.400 120.000 180.000 + 13 HE1 HA E 12 10 9 1.090 120.000 180.000 + 14 CZ CA B 12 10 9 1.400 120.000 0.000 + 15 HZ HA E 14 12 10 1.090 120.000 180.000 + 16 CE2 CA B 14 12 10 1.400 120.000 0.000 + 17 HE2 HA E 16 14 12 1.090 120.000 180.000 + 18 CD2 CA S 16 14 12 1.400 120.000 0.000 + 19 HD2 HA E 18 16 14 1.090 120.000 180.000 + 20 C C M 6 4 3 1.522 111.100 180.000 + 21 O O2 E 20 6 4 1.229 120.500 0.000 + 22 OXT O2 E 20 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CPRO_PROLINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CPRO_PROLINE_COO-_ANION.in_frag new file mode 100644 index 000000000..68a8c6c63 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CPRO_PROLINE_COO-_ANION.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD C2 S 4 3 2 1.458 126.100 356.100 + 6 CG C2 S 5 4 3 1.500 103.200 200.100 + 7 CB C2 E 6 5 4 1.510 106.000 338.300 + 8 CA CT M 4 3 2 1.451 120.600 175.200 + 9 HA H1 E 8 4 3 1.090 109.500 60.000 + 10 C C M 8 4 3 1.522 109.500 300.000 + 11 O O2 E 10 8 4 1.229 120.500 0.000 + 12 OXT O2 E 10 8 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CSER_SERINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CSER_SERINE_COO-_ANION.in_frag new file mode 100644 index 000000000..ac0984074 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CSER_SERINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 OG OH S 8 6 4 1.430 109.470 180.000 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13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CTRP_TRYPTOPHAN_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CTRP_TRYPTOPHAN_COO-_ANION.in_frag new file mode 100644 index 000000000..0f39d50ff --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CTRP_TRYPTOPHAN_COO-_ANION.in_frag @@ -0,0 +1,26 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 + 9 CG C* S 8 6 4 1.510 115.000 180.000 + 10 CD1 CW B 9 8 6 1.340 127.000 180.000 + 11 HD1 H4 E 10 9 8 1.090 120.000 0.000 + 12 NE1 NA B 10 9 8 1.430 107.000 180.000 + 13 HE1 H E 12 10 9 1.010 125.500 180.000 + 14 CE2 CN S 12 10 9 1.310 109.000 0.000 + 15 CZ2 CA B 14 12 10 1.400 128.000 180.000 + 16 HZ2 HA E 15 14 12 1.090 120.000 0.000 + 17 CH2 CA B 15 14 12 1.390 116.000 180.000 + 18 HH2 HA E 17 15 14 1.090 120.000 180.000 + 19 CZ3 CA B 17 15 14 1.350 121.000 0.000 + 20 HZ3 HA E 19 17 15 1.090 120.000 180.000 + 21 CE3 CA B 19 17 15 1.410 122.000 0.000 + 22 HE3 HA E 21 19 17 1.090 120.000 180.000 + 23 CD2 CB E 21 19 17 1.400 117.000 0.000 + 24 C C M 6 4 3 1.522 111.100 180.000 + 25 O O2 E 24 6 4 1.229 120.500 0.000 + 26 OXT O2 E 24 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CTYR_TYROSINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CTYR_TYROSINE_COO-_ANION.in_frag new file mode 100644 index 000000000..11fafa7ce --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CTYR_TYROSINE_COO-_ANION.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 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b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CVAL_VALINE_COO-_ANION.in_frag new file mode 100644 index 000000000..af7bcc648 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/CVAL_VALINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H H E 4 3 2 1.010 119.800 0.000 + 6 CA CT M 4 3 2 1.449 121.900 180.000 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 + 8 CB C1 B 6 4 3 1.525 111.100 60.000 + 9 CG1 C3 E 8 6 4 1.525 109.470 60.000 + 10 CG2 C3 E 8 6 4 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/uni_aminoct03.in b/cad/tests/AMBER_test_structures/dot_in/uni_aminoct03/uni_aminoct03.in new file mode 100644 index 000000000..70d4727cf --- /dev/null +++ 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0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.629974 + 5 H H E 4 3 2 1.010 119.800 0.000 0.341228 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.119932 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.145924 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 0.214496 + 9 CG C* S 8 6 4 1.510 115.000 180.000 -0.240323 + 10 CD1 CW B 9 8 6 1.340 127.000 180.000 -0.170800 + 11 HD1 H4 E 10 9 8 1.090 120.000 0.000 0.178645 + 12 NE1 NA B 10 9 8 1.430 107.000 180.000 -0.282385 + 13 HE1 H E 12 10 9 1.010 125.500 180.000 0.338407 + 14 CE2 CN S 12 10 9 1.310 109.000 0.000 0.143186 + 15 CZ2 CA B 14 12 10 1.400 128.000 180.000 -0.228458 + 16 HZ2 HA E 15 14 12 1.090 120.000 0.000 0.137621 + 17 CH2 CA B 15 14 12 1.390 116.000 180.000 -0.133210 + 18 HH2 HA E 17 15 14 1.090 120.000 180.000 0.121962 + 19 CZ3 CA B 17 15 14 1.350 121.000 0.000 -0.175254 + 20 HZ3 HA E 19 17 15 1.090 120.000 180.000 0.123020 + 21 CE3 CA B 19 17 15 1.410 122.000 0.000 -0.195086 + 22 HE3 HA E 21 19 17 1.090 120.000 180.000 0.144439 + 23 CD2 CB E 21 19 17 1.400 117.000 0.000 0.116493 + 24 C C M 6 4 3 1.522 111.100 180.000 0.615569 + 25 O O2 E 24 6 4 1.229 120.500 0.000 -0.722785 + 26 OXT O2 E 24 6 4 1.229 120.500 180.000 -0.722785 + +LOOP + CG CD2 + CE2 CD2 + +IMPROPER + -M CA N H + CA OXT C O + CD1 CE2 NE1 HE1 + CE2 CH2 CZ2 HZ2 + CZ2 CZ3 CH2 HH2 + CH2 CE3 CZ3 HZ3 + CZ3 CD2 CE3 HE3 + +DONE +PHENYLALANINE COO- ANION + +CPHE INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.625562 + 5 H H E 4 3 2 1.010 119.800 0.000 0.349898 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.126475 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.130502 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 0.161994 + 9 CG CA S 8 6 4 1.510 115.000 180.000 -0.019907 + 10 CD1 CA B 9 8 6 1.400 120.000 180.000 -0.124825 + 11 HD1 HA E 10 9 8 1.090 120.000 0.000 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HA H1 E 6 4 3 1.090 109.500 300.000 0.166499 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 -0.001548 + 9 CG CA S 8 6 4 1.510 109.470 180.000 0.140060 + 10 CD1 CA B 9 8 6 1.400 120.000 180.000 -0.209254 + 11 HD1 HA E 10 9 8 1.090 120.000 0.000 0.151973 + 12 CE1 CA B 10 9 8 1.400 120.000 180.000 -0.208909 + 13 HE1 HA E 12 10 9 1.090 120.000 180.000 0.147409 + 14 CZ C B 12 10 9 1.400 120.000 0.000 0.241077 + 15 OH OH S 14 12 10 1.360 120.000 180.000 -0.476143 + 16 HH HO E 15 14 12 0.960 113.000 0.000 0.371386 + 17 CE2 CA B 14 12 10 1.400 120.000 0.000 -0.208909 + 18 HE2 HA E 17 14 12 1.090 120.000 180.000 0.147409 + 19 CD2 CA S 17 14 12 1.400 120.000 0.000 -0.209254 + 20 HD2 HA E 19 17 14 1.090 120.000 180.000 0.151973 + 21 C C M 6 4 3 1.522 111.100 180.000 0.665555 + 22 O O2 E 21 6 4 1.229 120.500 0.000 -0.747778 + 23 OXT O2 E 21 6 4 1.229 120.500 180.000 -0.747778 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +GLUTAMIC ACID COO- ANION + +CGLU INT 1 + CORR OMIT DU BEG + 0.00000 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106.000 338.300 0.130355 + 8 CA CT M 4 3 2 1.451 120.600 175.200 -0.435355 + 9 HA H1 E 8 4 3 1.090 109.500 60.000 0.196885 + 10 C C M 8 4 3 1.522 109.500 300.000 0.643321 + 11 O O2 E 10 8 4 1.229 120.500 0.000 -0.736661 + 12 OXT O2 E 10 8 4 1.229 120.500 180.000 -0.736661 + +LOOP + CA CB + +IMPROPER + CA OXT C O + -M CA N CD + +DONE +CYSTEINE COO- ANION + +CCYS INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.555037 + 5 H H E 4 3 2 1.010 119.800 0.000 0.345483 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.192867 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.137305 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 0.270487 + 9 SG SH S 8 6 4 1.810 116.000 180.000 -0.358543 + 10 HG HS E 9 8 6 1.330 96.000 180.000 0.183171 + 11 C C M 6 4 3 1.522 111.100 180.000 0.671942 + 12 O O2 E 11 6 4 1.229 120.500 0.000 -0.750971 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 -0.750971 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +METHIONINE COO- ANION + +CMET INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.564246 + 5 H H E 4 3 2 1.010 119.800 0.000 0.334412 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.177392 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.143077 + 8 CB C2 S 6 4 3 1.525 111.100 60.000 0.127752 + 9 CG C2 S 8 6 4 1.525 109.470 180.000 0.141107 + 10 SD S S 9 8 6 1.810 110.000 180.000 -0.354512 + 11 CE C3 E 10 9 8 1.780 100.000 180.000 0.179804 + 12 C C M 6 4 3 1.522 111.100 180.000 0.664918 + 13 O O2 E 12 6 4 1.229 120.500 0.000 -0.747459 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 -0.747459 + +IMPROPER + -M CA N H + CA OXT C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NALA_ALANINE.in_frag new file mode 100644 index 000000000..b4560bc22 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NALA_ALANINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 119.800 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C3 E 8 4 3 1.525 111.100 60.000 + 11 C C M 8 4 3 1.522 111.100 180.000 + 12 O O E 11 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NARG_ARGININE.in_frag new file mode 100644 index 000000000..c25acbdc2 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NARG_ARGININE.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG C2 S 10 8 4 1.525 109.470 180.000 + 12 CD C2 S 11 10 8 1.525 109.470 180.000 + 13 NE N2 B 12 11 10 1.480 111.000 180.000 + 14 HE H E 13 12 11 1.010 118.500 0.000 + 15 CZ CA B 13 12 11 1.330 123.000 180.000 + 16 NH1 N2 B 15 13 12 1.330 122.000 0.000 + 17 HH11 H E 16 15 13 1.010 119.800 0.000 + 18 HH12 H E 16 15 13 1.010 119.800 180.000 + 19 NH2 N2 B 15 13 12 1.330 118.000 180.000 + 20 HH21 H E 19 15 13 1.010 119.800 0.000 + 21 HH22 H E 19 15 13 1.010 119.800 180.000 + 22 C C M 8 4 3 1.522 111.100 180.000 + 23 O O E 22 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..56a9a199a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NASN_ASPARAGINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG C B 10 8 4 1.522 111.100 180.000 + 12 OD1 O E 11 10 8 1.229 120.500 0.000 + 13 ND2 N B 11 10 8 1.335 116.600 180.000 + 14 HD21 H E 13 11 10 1.010 119.800 180.000 + 15 HD22 H E 13 11 10 1.010 119.800 0.000 + 16 C C M 8 4 3 1.522 111.100 180.000 + 17 O O E 16 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..08017f8ee --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG C B 10 8 4 1.527 109.470 180.000 + 12 OD1 O2 E 11 10 8 1.260 117.200 90.000 + 13 OD2 O2 E 11 10 8 1.260 117.200 270.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NCYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NCYS_CYSTEINE.in_frag new file mode 100644 index 000000000..73a5f7ba1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NCYS_CYSTEINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 SG SH S 10 8 4 1.810 116.000 180.000 + 12 HG HS E 11 10 8 1.330 96.000 180.000 + 13 C C M 8 4 3 1.522 111.100 180.000 + 14 O O E 13 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NGLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NGLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..14108f90d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NGLN_GLUTAMINE.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG C2 S 10 8 4 1.525 109.470 180.000 + 12 CD C B 11 10 8 1.522 111.100 180.000 + 13 OE1 O E 12 11 10 1.229 120.500 0.000 + 14 NE2 N B 12 11 10 1.335 116.600 180.000 + 15 HE21 H E 14 12 11 1.010 119.800 180.000 + 16 HE22 H E 14 12 11 1.010 119.800 0.000 + 17 C C M 8 4 3 1.522 111.100 180.000 + 18 O O E 17 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NGLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NGLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..54af094d6 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NGLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG C2 S 10 8 4 1.510 109.470 180.000 + 12 CD C B 11 10 8 1.527 109.470 180.000 + 13 OE1 O2 E 12 11 10 1.260 117.200 90.000 + 14 OE2 O2 E 12 11 10 1.260 117.200 270.000 + 15 C C M 8 4 3 1.522 111.100 180.000 + 16 O O E 15 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NGLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NGLY_GLYCINE.in_frag new file mode 100644 index 000000000..f5332ed36 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NGLY_GLYCINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA2 H0 E 8 4 3 1.090 109.500 300.000 + 10 HA3 H0 E 8 4 3 1.090 109.500 60.000 + 11 C C M 8 4 3 1.522 110.400 180.000 + 12 O O E 11 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NHID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NHID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..15e1e5620 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NHID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG CC S 10 8 4 1.510 115.000 180.000 + 12 ND1 NA B 11 10 8 1.390 122.000 180.000 + 13 HD1 H E 12 11 10 1.010 126.000 0.000 + 14 CE1 CR B 12 11 10 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NB S 14 12 11 1.310 109.000 0.000 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 + 19 C C M 8 4 3 1.522 111.100 180.000 + 20 O O E 19 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NHIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NHIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..769bb6e80 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NHIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG CC S 10 8 4 1.510 115.000 180.000 + 12 ND1 NB S 11 10 8 1.390 122.000 180.000 + 13 CE1 CR B 12 11 10 1.320 108.000 180.000 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 + 17 CD2 CW S 12 13 12 1.360 110.000 0.000 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 + 19 C C M 8 4 3 1.522 111.100 180.000 + 20 O O E 19 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NHIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NHIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..d55fbc0a9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NHIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG CC S 10 8 4 1.510 115.000 180.000 + 12 ND1 NA B 11 10 8 1.390 122.000 180.000 + 13 HD1 H E 12 11 10 1.010 126.000 0.000 + 14 CE1 CR B 12 11 10 1.320 108.000 180.000 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 + 16 NE2 NA B 14 12 11 1.310 109.000 0.000 + 17 HE2 H E 16 14 12 1.010 125.000 180.000 + 18 CD2 CW S 16 14 12 1.360 110.000 0.000 + 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 + 20 C C M 8 4 3 1.522 111.100 180.000 + 21 O O E 20 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..59b3e0b54 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NILE_ISOLEUCINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C1 B 8 4 3 1.525 109.470 60.000 + 11 CG2 C3 E 10 8 4 1.525 109.470 60.000 + 12 CG1 C2 S 10 8 4 1.525 109.470 180.000 + 13 CD1 C3 E 12 10 8 1.525 109.470 180.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NLEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NLEU_LEUCINE.in_frag new file mode 100644 index 000000000..0092dbff9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NLEU_LEUCINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG C1 B 10 8 4 1.525 109.470 180.000 + 12 CD1 C3 E 11 10 8 1.525 109.470 60.000 + 13 CD2 C3 E 11 10 8 1.525 109.470 180.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NLYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NLYS_LYSINE.in_frag new file mode 100644 index 000000000..b370d8b34 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NLYS_LYSINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG C2 S 10 8 4 1.525 109.470 180.000 + 12 CD C2 S 11 10 8 1.525 109.470 180.000 + 13 CE C2 S 12 11 10 1.525 109.470 180.000 + 14 NZ N3 3 13 12 11 1.470 109.470 180.000 + 15 HZ1 H E 14 13 12 1.010 109.470 60.000 + 16 HZ2 H E 14 13 12 1.010 109.470 180.000 + 17 HZ3 H E 14 13 12 1.010 109.470 300.000 + 18 C C M 8 4 3 1.522 111.100 180.000 + 19 O O E 18 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NMET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NMET_METHIONINE.in_frag new file mode 100644 index 000000000..2b934d7a3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NMET_METHIONINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG C2 S 10 8 4 1.525 109.470 180.000 + 12 SD S S 11 10 8 1.810 110.000 180.000 + 13 CE C3 E 12 11 10 1.780 100.000 180.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NPHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NPHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..2c38982a0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NPHE_PHENYLALANINE.in_frag @@ -0,0 +1,23 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG CA S 10 8 4 1.510 115.000 180.000 + 12 CD1 CA B 11 10 8 1.400 120.000 180.000 + 13 HD1 HA E 12 11 10 1.090 120.000 0.000 + 14 CE1 CA B 12 11 10 1.400 120.000 180.000 + 15 HE1 HA E 14 12 11 1.090 120.000 180.000 + 16 CZ CA B 14 12 11 1.400 120.000 0.000 + 17 HZ HA E 16 14 12 1.090 120.000 180.000 + 18 CE2 CA B 16 14 12 1.400 120.000 0.000 + 19 HE2 HA E 18 16 14 1.090 120.000 180.000 + 20 CD2 CA S 18 16 14 1.400 120.000 0.000 + 21 HD2 HA E 20 18 16 1.090 120.000 180.000 + 22 C C M 8 4 3 1.522 111.100 180.000 + 23 O O E 22 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NPRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NPRO_PROLINE.in_frag new file mode 100644 index 000000000..84f820e9e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NPRO_PROLINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 H2 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1.430 109.470 60.000 + 13 HG1 HO E 12 10 8 0.960 109.470 180.000 + 14 C C M 8 4 3 1.522 111.100 180.000 + 15 O O E 14 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NTRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NTRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..2bd47269b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NTRP_TRYPTOPHAN.in_frag @@ -0,0 +1,27 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C2 S 8 4 3 1.525 111.100 60.000 + 11 CG C* S 10 8 4 1.510 115.000 180.000 + 12 CD1 CW B 11 10 8 1.340 127.000 180.000 + 13 HD1 H4 E 12 11 10 1.090 120.000 0.000 + 14 NE1 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b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NVAL_VALINE.in_frag new file mode 100644 index 000000000..289854bb3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/NVAL_VALINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 H1 H E 4 3 2 1.010 130.000 0.000 + 6 H2 H E 4 3 2 1.010 60.000 90.000 + 7 H3 H E 4 3 2 1.010 60.000 -90.000 + 8 CA CT M 4 3 2 1.449 121.900 180.000 + 9 HA H1 E 8 4 3 1.090 109.500 300.000 + 10 CB C1 B 8 4 3 1.525 111.100 60.000 + 11 CG1 C3 E 10 8 4 1.525 109.470 60.000 + 12 CG2 C3 E 10 8 4 1.525 109.470 180.000 + 13 C C M 8 4 3 1.522 111.100 180.000 + 14 O O E 13 8 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/uni_aminont03.in b/cad/tests/AMBER_test_structures/dot_in/uni_aminont03/uni_aminont03.in new file mode 100644 index 000000000..8c268fabf --- /dev/null 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0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C B 7 6 4 1.527 109.470 180.000 + 9 OD1 O2 E 8 7 6 1.260 117.200 90.000 + 10 OD2 O2 E 8 7 6 1.260 117.200 270.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/CYS_CYSTEINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/CYS_CYSTEINE_COO-_ANION.in_frag new file mode 100644 index 000000000..76ea5d170 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/CYS_CYSTEINE_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 SG SH 3 7 6 4 1.810 116.000 180.000 + 9 HG HS E 8 7 6 1.330 96.000 180.000 + 10 LP1 LP E 8 7 6 0.679 96.700 80.000 + 11 LP2 LP E 8 7 6 0.679 96.700 280.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/CYX_CYSTINE_op_S-S_BRIDGE_cp__COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/CYX_CYSTINE_op_S-S_BRIDGE_cp__COO-_ANION.in_frag new file mode 100644 index 000000000..ca1a6b548 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/CYX_CYSTINE_op_S-S_BRIDGE_cp__COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 SG S B 7 6 4 1.810 116.000 180.000 + 9 LP1 LP E 8 7 6 0.679 96.700 80.000 + 10 LP2 LP E 8 7 6 0.679 96.700 280.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/GLN_GLUTAMINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/GLN_GLUTAMINE_COO-_ANION.in_frag new file mode 100644 index 000000000..235b27d6a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/GLN_GLUTAMINE_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C B 8 7 6 1.522 111.100 180.000 + 10 OE1 O E 9 8 7 1.229 120.500 0.000 + 11 NE2 N B 9 8 7 1.335 116.600 180.000 + 12 HNE1 H E 11 9 8 1.010 119.800 0.000 + 13 HNE2 H E 11 9 8 1.010 119.800 180.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag new file mode 100644 index 000000000..a5bc9d735 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/GLU_GLUTAMIC_ACID_COO-_ANION.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.510 109.470 180.000 + 9 CD C B 8 7 6 1.527 109.470 180.000 + 10 OE1 O2 E 9 8 7 1.260 117.200 90.000 + 11 OE2 O2 E 9 8 7 1.260 117.200 270.000 + 12 C C M 6 4 3 1.522 111.100 180.000 + 13 O O2 E 12 6 4 1.229 120.500 0.000 + 14 OXT O2 E 12 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/GLY_GLYCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/GLY_GLYCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..eb200653b --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/GLY_GLYCINE_COO-_ANION.in_frag @@ -0,0 +1,9 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA C2 M 4 3 2 1.449 121.900 180.000 + 7 C C M 6 4 3 1.522 110.400 180.000 + 8 O O2 E 7 6 4 1.229 120.500 0.000 + 9 OXT O2 E 7 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag new file mode 100644 index 000000000..28511c954 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/HID_HISTIDINE_DELTAH_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 + 12 NE2 NB S 11 9 8 1.310 109.000 0.000 + 13 CD2 CF E 12 11 9 1.360 110.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/HIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/HIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag new file mode 100644 index 000000000..b83dcd5a7 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/HIE_HISTIDINE_EPSILONH_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NB S 8 7 6 1.390 122.000 180.000 + 10 CE1 CP S 9 8 7 1.320 108.000 180.000 + 11 NE2 NA B 10 9 8 1.310 109.000 0.000 + 12 HNE H E 11 10 9 1.010 125.000 180.000 + 13 CD2 CG E 11 10 9 1.360 110.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/HIP_HISTIDINE_PLUS_ZWITTERION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/HIP_HISTIDINE_PLUS_ZWITTERION.in_frag new file mode 100644 index 000000000..b121790e8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/HIP_HISTIDINE_PLUS_ZWITTERION.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CC S 7 6 4 1.510 115.000 180.000 + 9 ND1 NA B 8 7 6 1.390 122.000 180.000 + 10 HND H E 9 8 7 1.010 126.000 0.000 + 11 CE1 CP S 9 8 7 1.320 108.000 180.000 + 12 NE2 NA B 11 9 8 1.310 109.000 0.000 + 13 HNE H E 12 11 9 1.010 125.000 180.000 + 14 CD2 CG E 12 11 9 1.360 110.000 0.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O2 E 15 6 4 1.229 120.500 0.000 + 17 OXT O2 E 15 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/ILE_ISOLEUCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/ILE_ISOLEUCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..d9e21d0f8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/ILE_ISOLEUCINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CH B 6 4 3 1.525 109.470 60.000 + 8 CG2 C3 E 7 6 4 1.525 109.470 60.000 + 9 CG1 C2 S 7 6 4 1.525 109.470 180.000 + 10 CD1 C3 E 9 7 6 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/LEU_LEUCINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/LEU_LEUCINE_COO-_ANION.in_frag new file mode 100644 index 000000000..dec659475 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/LEU_LEUCINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CH B 7 6 4 1.525 109.470 180.000 + 9 CD1 C3 E 8 7 6 1.525 109.470 60.000 + 10 CD2 C3 E 8 7 6 1.525 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/LYS_LYSINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/LYS_LYSINE_COO-_ANION.in_frag new file mode 100644 index 000000000..2992cec4d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/LYS_LYSINE_COO-_ANION.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 CD C2 S 8 7 6 1.525 109.470 180.000 + 10 CE C2 S 9 8 7 1.525 109.470 180.000 + 11 NZ N3 3 10 9 8 1.470 109.470 180.000 + 12 HNZ1 H3 E 11 10 9 1.010 109.470 60.000 + 13 HNZ2 H3 E 11 10 9 1.010 109.470 180.000 + 14 HNZ3 H3 E 11 10 9 1.010 109.470 300.000 + 15 C C M 6 4 3 1.522 111.100 180.000 + 16 O O2 E 15 6 4 1.229 120.500 0.000 + 17 OXT O2 E 15 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/MET_METHIONINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/MET_METHIONINE_COO-_ANION.in_frag new file mode 100644 index 000000000..cb610771d --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/MET_METHIONINE_COO-_ANION.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 + 9 SD S 3 8 7 6 1.810 110.000 180.000 + 10 CE C3 E 9 8 7 1.780 100.000 180.000 + 11 LP1 LP E 9 8 7 0.679 96.700 80.000 + 12 LP2 LP E 9 8 7 0.679 96.700 280.000 + 13 C C M 6 4 3 1.522 111.100 180.000 + 14 O O2 E 13 6 4 1.229 120.500 0.000 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/PHE_PHENYLALANINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/PHE_PHENYLALANINE_COO-_ANION.in_frag new file mode 100644 index 000000000..213b626fe --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/PHE_PHENYLALANINE_COO-_ANION.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG CA S 7 6 4 1.510 115.000 180.000 + 9 CD1 CD S 8 7 6 1.400 120.000 180.000 + 10 CE1 CD S 9 8 7 1.400 120.000 180.000 + 11 CZ CD S 10 9 8 1.400 120.000 0.000 + 12 CE2 CD S 11 10 9 1.400 120.000 0.000 + 13 CD2 CD E 12 11 10 1.400 120.000 0.000 + 14 C C M 6 4 3 1.522 111.100 180.000 + 15 O O2 E 14 6 4 1.229 120.500 0.000 + 16 OXT O2 E 14 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/PRO_PROLINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/PRO_PROLINE_COO-_ANION.in_frag new file mode 100644 index 000000000..1a43d2f1f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/PRO_PROLINE_COO-_ANION.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.337 117.000 180.000 + 5 CD C2 S 4 3 2 1.458 126.100 356.100 + 6 CG C2 S 5 4 3 1.500 103.200 200.100 + 7 CB C2 E 6 5 4 1.510 106.000 338.300 + 8 CA CH M 4 3 2 1.451 120.600 175.200 + 9 C C M 8 4 3 1.522 111.100 0.000 + 10 O O2 E 9 8 4 1.229 120.500 0.000 + 11 OXT O2 E 9 8 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/SER_SERINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/SER_SERINE_COO-_ANION.in_frag new file mode 100644 index 000000000..14ac4cdeb --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/SER_SERINE_COO-_ANION.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 OG OH S 7 6 4 1.430 109.470 180.000 + 9 HOG HO E 8 7 6 0.960 109.470 180.000 + 10 C C M 6 4 3 1.522 111.100 180.000 + 11 O O2 E 10 6 4 1.229 120.500 0.000 + 12 OXT O2 E 10 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/THR_THREONINE_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/THR_THREONINE_COO-_ANION.in_frag new file mode 100644 index 000000000..201b0554e --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/THR_THREONINE_COO-_ANION.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB CH B 6 4 3 1.525 111.100 60.000 + 8 CG2 C3 E 7 6 4 1.525 109.470 300.000 + 9 OG1 OH S 7 6 4 1.430 109.470 60.000 + 10 HOG HO E 9 7 6 0.960 109.470 180.000 + 11 C C M 6 4 3 1.522 111.100 180.000 + 12 O O2 E 11 6 4 1.229 120.500 0.000 + 13 OXT O2 E 11 6 4 1.229 120.500 180.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unict/TRP_TRYPTOPHAN_COO-_ANION.in_frag b/cad/tests/AMBER_test_structures/dot_in/unict/TRP_TRYPTOPHAN_COO-_ANION.in_frag new file mode 100644 index 000000000..fca2ea91f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unict/TRP_TRYPTOPHAN_COO-_ANION.in_frag @@ -0,0 +1,20 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 + 4 N N M 3 2 1 1.335 116.600 180.000 + 5 HN H E 4 3 2 1.010 119.800 0.000 + 6 CA CH M 4 3 2 1.449 121.900 180.000 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 + 8 CG C* S 7 6 4 1.510 115.000 180.000 + 9 CD1 CG S 8 7 6 1.340 127.000 180.000 + 10 NE1 NA B 9 8 7 1.430 107.000 180.000 + 11 HNE H E 10 9 8 1.010 125.500 180.000 + 12 CE2 CN S 10 9 8 1.310 109.000 0.000 + 13 CZ2 CD S 12 10 9 1.400 128.000 180.000 + 14 CH2 CD S 13 12 10 1.390 116.000 180.000 + 15 CZ3 CD S 14 13 12 1.350 121.000 0.000 + 16 CE3 CD S 15 14 13 1.410 122.000 0.000 + 17 CD2 CB E 16 15 14 1.400 117.000 0.000 + 18 C C M 6 4 3 1.522 111.100 180.000 + 19 O O2 E 18 6 4 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HN H E 4 3 2 1.010 119.800 0.000 0.24800 + 6 CA CH M 4 3 2 1.449 121.900 180.000 0.13100 + 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.03700 + 8 CG C2 S 7 6 4 1.525 109.470 180.000 0.09000 + 9 SD S 3 8 7 6 1.810 110.000 180.000 0.73700 + 10 CE C3 E 9 8 7 1.780 100.000 180.000 0.00700 + 11 LP1 LP E 9 8 7 0.679 96.700 80.000 -0.38100 + 12 LP2 LP E 9 8 7 0.679 96.700 280.000 -0.38100 + 13 C C M 6 4 3 1.522 111.100 180.000 0.44400 + 14 O O2 E 13 6 4 1.229 120.500 0.000 -0.70600 + 15 OXT O2 E 13 6 4 1.229 120.500 180.000 -0.70600 + +IMPROPER + -M CA N HN + CB CA N C + CA OXT C O + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/ALA_ALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/ALA_ALANINE.in_frag new file mode 100644 index 000000000..f5467e388 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/ALA_ALANINE.in_frag @@ -0,0 +1,11 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C3 E 8 5 4 1.525 111.100 60.000 + 10 C C M 8 5 4 1.522 111.100 180.000 + 11 O O E 10 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/ARG_ARGININE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/ARG_ARGININE.in_frag new file mode 100644 index 000000000..32783c7fc --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/ARG_ARGININE.in_frag @@ -0,0 +1,22 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.525 109.470 180.000 + 11 CD C2 S 10 9 8 1.525 109.470 180.000 + 12 NE N2 B 11 10 9 1.480 111.000 180.000 + 13 HNE H3 E 12 11 10 1.010 118.500 0.000 + 14 CZ CA B 12 11 10 1.330 123.000 180.000 + 15 NH1 N2 B 14 12 11 1.330 122.000 0.000 + 16 HN11 H3 E 15 14 12 1.010 119.800 0.000 + 17 HN12 H3 E 15 14 12 1.010 119.800 180.000 + 18 NH2 N2 B 14 12 11 1.330 118.000 180.000 + 19 HN21 H3 E 18 14 12 1.010 119.800 0.000 + 20 HN22 H3 E 18 14 12 1.010 119.800 180.000 + 21 C C M 8 5 4 1.522 111.100 180.000 + 22 O O E 21 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/ASN_ASPARAGINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/ASN_ASPARAGINE.in_frag new file mode 100644 index 000000000..e19ac12a5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/ASN_ASPARAGINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C B 9 8 5 1.522 111.100 180.000 + 11 OD1 O E 10 9 8 1.229 120.500 0.000 + 12 ND2 N B 10 9 8 1.335 116.600 180.000 + 13 HND1 H E 12 10 9 1.010 119.800 0.000 + 14 HND2 H E 12 10 9 1.010 119.800 180.000 + 15 C C M 8 5 4 1.522 111.100 180.000 + 16 O O E 15 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/ASP_ASPARTIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/ASP_ASPARTIC_ACID.in_frag new file mode 100644 index 000000000..6a5ee54dd --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/ASP_ASPARTIC_ACID.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C B 9 8 5 1.527 109.470 180.000 + 11 OD1 O2 E 10 9 8 1.260 117.200 90.000 + 12 OD2 O2 E 10 9 8 1.260 117.200 270.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/CYS_CYSTEINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/CYS_CYSTEINE.in_frag new file mode 100644 index 000000000..9a2b19010 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/CYS_CYSTEINE.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 SG SH 3 9 8 5 1.810 116.000 180.000 + 11 HG HS E 10 9 8 1.330 96.000 180.000 + 12 LP1 LP E 10 9 8 0.679 96.700 80.000 + 13 LP2 LP E 10 9 8 0.679 96.700 280.000 + 14 C C M 8 5 4 1.522 111.100 180.000 + 15 O O E 14 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag new file mode 100644 index 000000000..15c9d5a4a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/CYX_CYSTINE_op_S-S_BRIDGE_cp_.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 SG S B 9 8 5 1.810 116.000 180.000 + 11 LP1 LP E 10 9 8 0.679 96.700 80.000 + 12 LP2 LP E 10 9 8 0.679 96.700 280.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/GLN_GLUTAMINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/GLN_GLUTAMINE.in_frag new file mode 100644 index 000000000..ae5f4ff02 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/GLN_GLUTAMINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.525 109.470 180.000 + 11 CD C B 10 9 8 1.522 111.100 180.000 + 12 OE1 O E 11 10 9 1.229 120.500 0.000 + 13 NE2 N B 11 10 9 1.335 116.600 180.000 + 14 HNE1 H E 13 11 10 1.010 119.800 0.000 + 15 HNE2 H E 13 11 10 1.010 119.800 180.000 + 16 C C M 8 5 4 1.522 111.100 180.000 + 17 O O E 16 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/GLU_GLUTAMIC_ACID.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/GLU_GLUTAMIC_ACID.in_frag new file mode 100644 index 000000000..337434304 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/GLU_GLUTAMIC_ACID.in_frag @@ -0,0 +1,15 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.510 109.470 180.000 + 11 CD C B 10 9 8 1.527 109.470 180.000 + 12 OE1 O2 E 11 10 9 1.260 117.200 90.000 + 13 OE2 O2 E 11 10 9 1.260 117.200 270.000 + 14 C C M 8 5 4 1.522 111.100 180.000 + 15 O O E 14 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/GLY_GLYCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/GLY_GLYCINE.in_frag new file mode 100644 index 000000000..626b84473 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/GLY_GLYCINE.in_frag @@ -0,0 +1,10 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA C2 M 5 4 3 1.449 121.900 180.000 + 9 C C M 8 5 4 1.522 110.400 180.000 + 10 O O E 9 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/HID_HISTIDINE_DELTAH.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/HID_HISTIDINE_DELTAH.in_frag new file mode 100644 index 000000000..83070a54a --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/HID_HISTIDINE_DELTAH.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CC S 9 8 5 1.510 115.000 180.000 + 11 ND1 NA B 10 9 8 1.390 122.000 180.000 + 12 HND H E 11 10 9 1.010 126.000 0.000 + 13 CE1 CP S 11 10 9 1.320 108.000 180.000 + 14 NE2 NB S 13 11 10 1.310 109.000 0.000 + 15 CD2 CF E 14 13 11 1.360 110.000 0.000 + 16 C C M 8 5 4 1.522 111.100 180.000 + 17 O O E 16 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/HIE_HISTIDINE_EPSILONH.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/HIE_HISTIDINE_EPSILONH.in_frag new file mode 100644 index 000000000..36c9aee64 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/HIE_HISTIDINE_EPSILONH.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CC S 9 8 5 1.510 115.000 180.000 + 11 ND1 NB S 10 9 8 1.390 122.000 180.000 + 12 CE1 CP S 11 10 9 1.320 108.000 180.000 + 13 NE2 NA B 12 11 10 1.310 109.000 0.000 + 14 HNE H E 13 12 11 1.010 125.000 180.000 + 15 CD2 CG E 13 12 11 1.360 110.000 0.000 + 16 C C M 8 5 4 1.522 111.100 180.000 + 17 O O E 16 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/HIP_HISTIDINE_PLUS.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/HIP_HISTIDINE_PLUS.in_frag new file mode 100644 index 000000000..1911ffaa6 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/HIP_HISTIDINE_PLUS.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CC S 9 8 5 1.510 115.000 180.000 + 11 ND1 NA B 10 9 8 1.390 122.000 180.000 + 12 HND H E 11 10 9 1.010 126.000 0.000 + 13 CE1 CP S 11 10 9 1.320 108.000 180.000 + 14 NE2 NA B 13 11 10 1.310 109.000 0.000 + 15 HNE H E 14 13 11 1.010 125.000 180.000 + 16 CD2 CG E 14 13 11 1.360 110.000 0.000 + 17 C C M 8 5 4 1.522 111.100 180.000 + 18 O O E 17 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/ILE_ISOLEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/ILE_ISOLEUCINE.in_frag new file mode 100644 index 000000000..d03671a52 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/ILE_ISOLEUCINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB CH B 8 5 4 1.525 109.470 60.000 + 10 CG2 C3 E 9 8 5 1.525 109.470 60.000 + 11 CG1 C2 S 9 8 5 1.525 109.470 180.000 + 12 CD1 C3 E 11 9 8 1.525 109.470 180.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/LEU_LEUCINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/LEU_LEUCINE.in_frag new file mode 100644 index 000000000..57860b2c3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/LEU_LEUCINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CH B 9 8 5 1.525 109.470 180.000 + 11 CD1 C3 E 10 9 8 1.525 109.470 60.000 + 12 CD2 C3 E 10 9 8 1.525 109.470 180.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/LYS_LYSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/LYS_LYSINE.in_frag new file mode 100644 index 000000000..036907951 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/LYS_LYSINE.in_frag @@ -0,0 +1,18 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.525 109.470 180.000 + 11 CD C2 S 10 9 8 1.525 109.470 180.000 + 12 CE C2 S 11 10 9 1.525 109.470 180.000 + 13 NZ N3 3 12 11 10 1.470 109.470 180.000 + 14 HNZ1 H3 E 13 12 11 1.010 109.470 60.000 + 15 HNZ2 H3 E 13 12 11 1.010 109.470 180.000 + 16 HNZ3 H3 E 13 12 11 1.010 109.470 300.000 + 17 C C M 8 5 4 1.522 111.100 180.000 + 18 O O E 17 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/MET_METHIONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/MET_METHIONINE.in_frag new file mode 100644 index 000000000..3153776e0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/MET_METHIONINE.in_frag @@ -0,0 +1,16 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C2 S 9 8 5 1.525 109.470 180.000 + 11 SD S 3 10 9 8 1.810 110.000 180.000 + 12 CE C3 E 11 10 9 1.780 100.000 180.000 + 13 LP1 LP E 11 10 9 0.679 96.700 80.000 + 14 LP2 LP E 11 10 9 0.679 96.700 280.000 + 15 C C M 8 5 4 1.522 111.100 180.000 + 16 O O E 15 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/PHE_PHENYLALANINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/PHE_PHENYLALANINE.in_frag new file mode 100644 index 000000000..c0363ce33 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/PHE_PHENYLALANINE.in_frag @@ -0,0 +1,17 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CA S 9 8 5 1.510 115.000 180.000 + 11 CD1 CD S 10 9 8 1.400 120.000 180.000 + 12 CE1 CD S 11 10 9 1.400 120.000 180.000 + 13 CZ CD S 12 11 10 1.400 120.000 0.000 + 14 CE2 CD S 13 12 11 1.400 120.000 0.000 + 15 CD2 CD E 14 13 12 1.400 120.000 0.000 + 16 C C M 8 5 4 1.522 111.100 180.000 + 17 O O E 16 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/PRO_PROLINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/PRO_PROLINE.in_frag new file mode 100644 index 000000000..818f36d0f --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/PRO_PROLINE.in_frag @@ -0,0 +1,12 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 N N3 M 3 2 1 1.010 90.000 180.000 + 5 HN2 H3 E 4 3 2 1.010 58.800 90.000 + 6 HN3 H3 E 4 3 2 1.010 58.800 -90.000 + 7 CD C2 S 4 3 2 1.458 126.100 356.100 + 8 CG C2 S 7 4 3 1.500 103.200 200.100 + 9 CB C2 E 8 7 4 1.510 106.000 338.300 + 10 CA CH M 4 3 2 1.451 120.600 175.200 + 11 C C M 10 4 3 1.522 111.100 0.000 + 12 O O E 11 10 4 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/SER_SERINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/SER_SERINE.in_frag new file mode 100644 index 000000000..96291ef68 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/SER_SERINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 OG OH S 9 8 5 1.430 109.470 180.000 + 11 HOG HO E 10 9 8 0.960 109.470 180.000 + 12 C C M 8 5 4 1.522 111.100 180.000 + 13 O O E 12 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/THR_THREONINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/THR_THREONINE.in_frag new file mode 100644 index 000000000..fa189b4f0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/THR_THREONINE.in_frag @@ -0,0 +1,14 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB CH B 8 5 4 1.525 111.100 60.000 + 10 CG2 C3 E 9 8 5 1.525 109.470 300.000 + 11 OG1 OH S 9 8 5 1.430 109.470 60.000 + 12 HOG HO E 11 9 8 0.960 109.470 180.000 + 13 C C M 8 5 4 1.522 111.100 180.000 + 14 O O E 13 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/TRP_TRYPTOPHAN.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/TRP_TRYPTOPHAN.in_frag new file mode 100644 index 000000000..fe815dcf8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/TRP_TRYPTOPHAN.in_frag @@ -0,0 +1,21 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG C* S 9 8 5 1.510 115.000 180.000 + 11 CD1 CG S 10 9 8 1.340 127.000 180.000 + 12 NE1 NA B 11 10 9 1.430 107.000 180.000 + 13 HNE H E 12 11 10 1.010 125.500 180.000 + 14 CE2 CN S 12 11 10 1.310 109.000 0.000 + 15 CZ2 CD S 14 12 11 1.400 128.000 180.000 + 16 CH2 CD S 15 14 12 1.390 116.000 180.000 + 17 CZ3 CD S 16 15 14 1.350 121.000 0.000 + 18 CE3 CD S 17 16 15 1.410 122.000 0.000 + 19 CD2 CB E 18 17 16 1.400 117.000 0.000 + 20 C C M 8 5 4 1.522 111.100 180.000 + 21 O O E 20 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/TYR_TYROSINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/TYR_TYROSINE.in_frag new file mode 100644 index 000000000..bfe9514c3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/TYR_TYROSINE.in_frag @@ -0,0 +1,19 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 + 10 CG CA S 9 8 5 1.510 109.470 180.000 + 11 CD1 CD S 10 9 8 1.400 120.000 180.000 + 12 CE1 CD S 11 10 9 1.400 120.000 180.000 + 13 CZ C B 12 11 10 1.400 120.000 0.000 + 14 OH OH S 13 12 11 1.360 120.000 180.000 + 15 HOH HO E 14 13 12 0.960 113.000 0.000 + 16 CE2 CD S 13 12 11 1.400 120.000 0.000 + 17 CD2 CD E 16 13 12 1.400 120.000 0.000 + 18 C C M 8 5 4 1.522 111.100 180.000 + 19 O O E 18 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/VAL_VALINE.in_frag b/cad/tests/AMBER_test_structures/dot_in/unint/VAL_VALINE.in_frag new file mode 100644 index 000000000..a05dde2df --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/VAL_VALINE.in_frag @@ -0,0 +1,13 @@ + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 + 5 N N3 M 4 3 2 1.010 90.000 180.000 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 + 8 CA CH M 5 4 3 1.449 121.900 180.000 + 9 CB CH B 8 5 4 1.525 111.100 60.000 + 10 CG1 C3 E 9 8 5 1.525 109.470 60.000 + 11 CG2 C3 E 9 8 5 1.525 109.470 180.000 + 12 C C M 8 5 4 1.522 111.100 180.000 + 13 O O E 12 8 5 1.229 120.500 0.000 diff --git a/cad/tests/AMBER_test_structures/dot_in/unint/unint.in b/cad/tests/AMBER_test_structures/dot_in/unint/unint.in new file mode 100644 index 000000000..28d5269c0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/dot_in/unint/unint.in @@ -0,0 +1,646 @@ + 1 1 100 +db4.dat + ALANINE +ALA + ALA INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 0.31200 + 5 N N3 M 4 3 2 1.010 90.000 180.000 -0.26300 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 0.31200 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 0.31200 + 8 CA CH M 5 4 3 1.449 121.900 180.000 0.27000 + 9 CB C3 E 8 5 4 1.525 111.100 60.000 0.03100 + 10 C C M 8 5 4 1.522 111.100 180.000 0.52600 + 11 O O E 10 8 5 1.229 120.500 0.000 -0.50000 + +IMPROPER + 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0.31100 + 15 HNZ2 H3 E 13 12 11 1.010 109.470 180.000 0.31100 + 16 HNZ3 H3 E 13 12 11 1.010 109.470 300.000 0.31100 + 17 C C M 8 5 4 1.522 111.100 180.000 0.52600 + 18 O O E 17 8 5 1.229 120.500 0.000 -0.50000 + +IMPROPER + CA +M C O + CB CA N C + +DONE + PROLINE +PRO + PRO INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 N N3 M 3 2 1 1.010 90.000 180.000 -0.16100 + 5 HN2 H3 E 4 3 2 1.010 58.800 90.000 0.31200 + 6 HN3 H3 E 4 3 2 1.010 58.800 -90.000 0.31200 + 7 CD C2 S 4 3 2 1.458 126.100 356.100 0.19100 + 8 CG C2 S 7 4 3 1.500 103.200 200.100 -0.01100 + 9 CB C2 E 8 7 4 1.510 106.000 338.300 0.00000 + 10 CA CH M 4 3 2 1.451 120.600 175.200 0.21200 + 11 C C M 10 4 3 1.522 111.100 0.000 0.59600 + 12 O O E 11 10 4 1.229 120.500 0.000 -0.45100 + +IMPROPER + CA +M C O + CB CA N C + -M CA N CD + +LOOP + CB CA + +DONE + CYSTEINE +CYS + CYS INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 0.31200 + 5 N N3 M 4 3 2 1.010 90.000 180.000 -0.26300 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 0.31200 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 0.31200 + 8 CA CH M 5 4 3 1.449 121.900 180.000 0.20100 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 0.10000 + 10 SG SH 3 9 8 5 1.810 116.000 180.000 0.82700 + 11 HG HS E 10 9 8 1.330 96.000 180.000 0.13500 + 12 LP1 LP E 10 9 8 0.679 96.700 80.000 -0.48100 + 13 LP2 LP E 10 9 8 0.679 96.700 280.000 -0.48100 + 14 C C M 8 5 4 1.522 111.100 180.000 0.52600 + 15 O O E 14 8 5 1.229 120.500 0.000 -0.50000 + +IMPROPER + CA +M C O + CB CA N C + +DONE + CYSTINE(S-S BRIDGE) +CYX + CYX INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 0.31200 + 5 N N3 M 4 3 2 1.010 90.000 180.000 -0.26300 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 0.31200 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 0.31200 + 8 CA CH M 5 4 3 1.449 121.900 180.000 0.14300 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 0.14300 + 10 SG S B 9 8 5 1.810 116.000 180.000 0.82400 + 11 LP1 LP E 10 9 8 0.679 96.700 80.000 -0.40450 + 12 LP2 LP E 10 9 8 0.679 96.700 280.000 -0.40450 + 13 C C M 8 5 4 1.522 111.100 180.000 0.52600 + 14 O O E 13 8 5 1.229 120.500 0.000 -0.50000 + +IMPROPER + CA +M C O + CB CA N C + +DONE + METHIONINE +MET + MET INT 1 + CORR NOMI DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 + 4 HN1 H3 M 3 2 1 1.000 90.000 180.000 0.31200 + 5 N N3 M 4 3 2 1.010 90.000 180.000 -0.26300 + 6 HN2 H3 E 5 4 3 1.010 111.800 60.000 0.31200 + 7 HN3 H3 E 5 4 3 1.010 111.800 -60.000 0.31200 + 8 CA CH M 5 4 3 1.449 121.900 180.000 0.19200 + 9 CB C2 S 8 5 4 1.525 111.100 60.000 0.03700 + 10 CG C2 S 9 8 5 1.525 109.470 180.000 0.09000 + 11 SD S 3 10 9 8 1.810 110.000 180.000 0.73700 + 12 CE C3 E 11 10 9 1.780 100.000 180.000 0.00700 + 13 LP1 LP E 11 10 9 0.679 96.700 80.000 -0.38100 + 14 LP2 LP E 11 10 9 0.679 96.700 280.000 -0.38100 + 15 C C M 8 5 4 1.522 111.100 180.000 0.52600 + 16 O O E 15 8 5 1.229 120.500 0.000 -0.50000 + +IMPROPER + CA +M C O + CB CA N C + +DONE +STOP diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/ALA_ALANINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/ALA_ALANINE.mmp new file mode 100644 index 000000000..0995f3f12 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/ALA_ALANINE.mmp @@ -0,0 +1,44 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (9.554274) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (ALA_ALANINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-6469, -1679, 111) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-6893, -1391, 887) def +bond1 1 +atom 3 (1) (-6955, -2127, -544) def +bond1 1 +atom 4 (6) (-4994, -1415, -86) def +bond1 1 +atom 5 (1) (-4448, -1699, 804) def +bond1 4 +atom 6 (6) (-4693, 95, -306) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-5386, 829, -1358) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3718, 784, 532) def +bond1 6 +atom 9 (1) (-4192, 1188, 1315) def +bond1 8 +atom 10 (6) (-4373, -2243, -1250) def +bond1 4 +atom 11 (1) (-4504, -3303, -1078) def +bond1 10 +atom 12 (1) (-3313, -2047, -1342) def +bond1 10 +atom 13 (1) (-4843, -1995, -2193) def +bond1 10 +egroup (ALA_ALANINE) +end1 +group (Clipboard) +info opengroup open = False +egroup (Clipboard) +end molecular machine part ALA_ALANINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/ARG_ARGININE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/ARG_ARGININE.mmp new file mode 100644 index 000000000..daa86c0de --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/ARG_ARGININE.mmp @@ -0,0 +1,76 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (7.909874) (-0.031137, 0.287926, 0.000000) (1.000000) +egroup (View Data) +group (ARG_ARGININE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-6582, -1092, 18) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-7030, -298, 203) def +bond1 1 +atom 3 (1) (-7065, -1866, -163) def +bond1 1 +atom 4 (6) (-5071, -1120, 10) def +bond1 1 +atom 5 (1) (-4689, -636, 899) def +bond1 4 +atom 6 (6) (-4476, -333, -1192) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4901, -649, -2550) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3492, 721, -970) def +bond1 6 +atom 9 (1) (-3969, 1596, -879) def +bond1 8 +atom 10 (6) (-4489, -2552, 26) def +bond1 4 +atom 11 (1) (-4821, -3067, 918) def +bond1 10 +atom 12 (1) (-4831, -3090, -849) def +bond1 10 +atom 13 (6) (-2945, -2481, 16) def +bond1 10 +atom 14 (1) (-2612, -1967, -876) def +bond1 13 +atom 15 (1) (-2603, -1944, 891) def +bond1 13 +atom 16 (6) (-2363, -3914, 32) def +bond1 13 +atom 17 (1) (-2695, -4429, 924) def +bond1 16 +atom 18 (1) (-2704, -4452, -843) def +bond1 16 +atom 19 (7) (-970, -3850, 23) def +info atom atomtype = sp2(graphitic) +bond1 16 +atom 20 (1) (-528, -3436, -682) def +bond1 19 +atom 21 (6) (-248, -4402, 1061) def +info atom atomtype = sp2 +bond1 19 +atom 22 (7) (-924, -5036, 2140) def +info atom atomtype = sp2(graphitic) +bond1 21 +atom 23 (1) (-1853, -5079, 2146) def +bond1 22 +atom 24 (1) (-438, -5408, 2840) def +bond1 22 +atom 25 (7) (1173, -4337, 1053) def +info atom atomtype = sp2(graphitic) +bond1 21 +atom 26 (1) (1616, -3923, 348) def +bond1 25 +atom 27 (1) (1660, -4709, 1753) def +bond1 25 +egroup (ARG_ARGININE) +end1 +group (Clipboard) +info opengroup open = False +egroup (Clipboard) +end molecular machine part ARG_ARGININE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/ASH_ASPARTIC_ACID_neutral.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/ASH_ASPARTIC_ACID_neutral.mmp new file mode 100644 index 000000000..bba27b7d3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/ASH_ASPARTIC_ACID_neutral.mmp @@ -0,0 +1,52 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.452692) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (ASH_ASPARTIC_ACID_neutral) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-6582, -1092, 18) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-7030, -298, 203) def +bond1 1 +atom 3 (1) (-7065, -1866, -163) def +bond1 1 +atom 4 (6) (-5071, -1120, 10) def +bond1 1 +atom 5 (1) (-4689, -636, 899) def +bond1 4 +atom 6 (6) (-4476, -333, -1192) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4901, -649, -2550) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3492, 721, -970) def +bond1 6 +atom 9 (1) (-3969, 1596, -879) def +bond1 8 +atom 10 (6) (-4489, -2552, 26) def +bond1 4 +atom 11 (1) (-4821, -3067, 918) def +bond1 10 +atom 12 (1) (-4831, -3090, -849) def +bond1 10 +atom 13 (6) (-3006, -2484, 17) def +info atom atomtype = sp2 +bond1 10 +atom 14 (8) (-2368, -1886, -1001) def +info atom atomtype = sp2 +bond2 13 +atom 15 (8) (-2272, -3045, 1072) def +bond1 13 +atom 16 (1) (-2579, -2557, 1889) def +bond1 15 +egroup (ASH_ASPARTIC_ACID_neutral) +end1 +group (Clipboard) +info opengroup open = False +egroup (Clipboard) +end molecular machine part ASH_ASPARTIC_ACID_neutral diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/ASN_ASPARAGINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/ASN_ASPARAGINE.mmp new file mode 100644 index 000000000..925e599f3 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/ASN_ASPARAGINE.mmp @@ -0,0 +1,55 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.624049) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (ASN_ASPARAGINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-6601, -1899, -95) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-7276, -1473, 383) def +bond1 1 +atom 3 (1) (-6814, -2583, -688) def +bond1 1 +atom 4 (6) (-5163, -1476, 92) def +bond1 1 +atom 5 (1) (-4933, -1409, 1147) def +bond1 4 +atom 6 (6) (-4886, -62, -494) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-5224, 229, -1882) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-4289, 978, 337) def +bond1 6 +atom 9 (1) (-5020, 1508, 769) def +bond1 8 +atom 10 (6) (-4150, -2484, -498) def +bond1 4 +atom 11 (1) (-4274, -3444, -15) def +bond1 10 +atom 12 (1) (-4325, -2589, -1561) def +bond1 10 +atom 13 (6) (-2769, -1989, -270) def +info atom atomtype = sp2 +bond1 10 +atom 14 (7) (-1892, -2735, 457) def +info atom atomtype = sp2(graphitic) +bond1 13 +atom 15 (1) (-2157, -3554, 810) def +bond1 14 +atom 16 (1) (-1026, -2425, 600) def +bond1 14 +atom 17 (8) (-2386, -809, -780) def +info atom atomtype = sp2 +bond2 13 +egroup (ASN_ASPARAGINE) +end1 +group (Clipboard) +info opengroup open = False +egroup (Clipboard) +end molecular machine part ASN_ASPARAGINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/ASP_ASPARTIC_ACID.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/ASP_ASPARTIC_ACID.mmp new file mode 100644 index 000000000..355055f8c --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/ASP_ASPARTIC_ACID.mmp @@ -0,0 +1,51 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (9.998639) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (ASP_ASPARTIC_ACID) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-6593, -1506, -30) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-7157, -906, 403) def +bond1 1 +atom 3 (1) (-6953, -2222, -503) def +bond1 1 +atom 4 (6) (-5096, -1314, 35) def +bond1 1 +atom 5 (1) (-4792, -1137, 1058) def +bond1 4 +atom 6 (6) (-4629, -67, -769) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-5002, 75, -2171) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3817, 962, -129) def +bond1 6 +atom 9 (1) (-4422, 1667, 244) def +bond1 8 +atom 10 (6) (-4302, -2555, -433) def +bond1 4 +atom 11 (1) (-4551, -3401, 195) def +bond1 10 +atom 12 (1) (-4558, -2781, -1460) def +bond1 10 +atom 13 (6) (-2847, -2278, -335) def +info atom atomtype = sp2 +bond1 10 +atom 14 (8) (-2308, -1266, -1033) def +info atom atomtype = sp2 +bond2 13 +atom 15 (8) (-2035, -3073, 486) def +info atom atomtype = sp2(-) +bond1 13 +egroup (ASP_ASPARTIC_ACID) +end1 +group (Clipboard) +info opengroup open = False +egroup (Clipboard) +end molecular machine part ASP_ASPARTIC_ACID diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/CYM_CYSTEINE_negative.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/CYM_CYSTEINE_negative.mmp new file mode 100644 index 000000000..912db327b --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/CYM_CYSTEINE_negative.mmp @@ -0,0 +1,45 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (9.547120) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (CYM_CYSTEINE_negative) +info opengroup open = True +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 1 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-6647, -648, 393) def +bond1 1 +atom 3 (1) (-6234, -2264, -166) def +bond1 1 +atom 4 (6) (-4521, -878, -132) def +bond1 1 +atom 5 (1) (-4223, -240, 701) def +bond1 4 +atom 6 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3544, 1199, -1313) def +bond1 6 +atom 9 (1) (-4100, 1908, -964) def +bond1 8 +atom 10 (6) (-3527, -2085, -141) def +bond1 4 +atom 11 (1) (-3647, -2708, 744) def +bond1 10 +atom 12 (1) (-3647, -2700, -1031) def +bond1 10 +atom 13 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 10 +egroup (CYM_CYSTEINE_negative) +end1 +group (Clipboard) +info opengroup open = False +egroup (Clipboard) +end molecular machine part CYM_CYSTEINE_negative diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/CYS_CYSTEINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/CYS_CYSTEINE.mmp new file mode 100644 index 000000000..fd02fb5cc --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/CYS_CYSTEINE.mmp @@ -0,0 +1,46 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.042905) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (CYS_CYSTEINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-6582, -1092, 18) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-7030, -298, 203) def +bond1 1 +atom 3 (1) (-7065, -1866, -163) def +bond1 1 +atom 4 (6) (-5071, -1120, 10) def +bond1 1 +atom 5 (1) (-4689, -636, 899) def +bond1 4 +atom 6 (6) (-4476, -333, -1192) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4901, -649, -2550) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3492, 721, -970) def +bond1 6 +atom 9 (1) (-3969, 1596, -879) def +bond1 8 +atom 10 (6) (-4489, -2552, 26) def +bond1 4 +atom 11 (1) (-4821, -3067, 918) def +bond1 10 +atom 12 (1) (-4831, -3090, -849) def +bond1 10 +atom 13 (16) (-2614, -2466, 14) def +bond1 10 +atom 14 (1) (-2179, -1812, -1119) def +bond1 13 +egroup (CYS_CYSTEINE) +end1 +group (Clipboard) +info opengroup open = False +egroup (Clipboard) +end molecular machine part CYS_CYSTEINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/CYX_CYSTEINE-S-S-CYSTEINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/CYX_CYSTEINE-S-S-CYSTEINE.mmp new file mode 100644 index 000000000..7be7cb02a --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/CYX_CYSTEINE-S-S-CYSTEINE.mmp @@ -0,0 +1,108 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (CYX_CYSTEINE-S-S-CYSTEINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-4876, -1615, 96) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-5409, -1336, 916) def +bond1 1 +atom 3 (1) (-5219, -2365, -499) def +bond1 1 +atom 4 (6) (-3581, -916, -239) def +bond1 1 +atom 5 (1) (-3230, -355, 627) def +bond1 4 +atom 6 (6) (-3764, 126, -1384) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4219, -177, -2467) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3364, 1502, -1113) def +bond1 6 +atom 9 (1) (-4106, 1974, -713) def +bond1 8 +atom 10 (6) (-2441, -1920, -606) def +bond1 4 +atom 11 (1) (-2312, -2671, 171) def +bond1 10 +atom 12 (1) (-2649, -2424, -1548) def +bond1 10 +atom 13 (7) (3919, -2625, -2687) def +info atom atomtype = sp2(graphitic) +atom 14 (1) (4421, -2422, -3548) def +bond1 13 +atom 15 (1) (4241, -3372, -2078) def +bond1 13 +atom 16 (6) (2696, -1820, -2316) def +bond1 13 +atom 17 (1) (2468, -1119, -3118) def +bond1 16 +atom 18 (6) (2933, -947, -1048) def +info atom atomtype = sp2 +bond1 16 +atom 19 (8) (3491, -1377, -62) def +info atom atomtype = sp2 +bond2 18 +atom 20 (8) (2452, 430, -1080) def +bond1 18 +atom 21 (1) (3151, 1002, -1422) def +bond1 20 +atom 22 (6) (1430, -2722, -2113) def +bond1 16 +atom 23 (1) (1491, -3623, -2720) def +bond1 22 +atom 24 (1) (1302, -3020, -1074) def +bond1 22 +atom 25 (16) (-793, -1064, -753) def +bond1 10 +atom 26 (16) (-135, -1875, -2658) def +bond1 25 22 +egroup (CYX_CYSTEINE-S-S-CYSTEINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 27 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 28 (1) (-6647, -648, 393) def +bond1 27 +atom 29 (1) (-6234, -2264, -166) def +bond1 27 +atom 30 (6) (-4521, -878, -132) def +bond1 27 +atom 31 (1) (-4223, -240, 701) def +bond1 30 +atom 32 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 30 +atom 33 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 32 +atom 34 (8) (-3544, 1199, -1313) def +bond1 32 +atom 35 (1) (-4100, 1908, -964) def +bond1 34 +atom 36 (6) (-3527, -2085, -141) def +bond1 30 +atom 37 (1) (-3647, -2708, 744) def +bond1 36 +atom 38 (1) (-3647, -2700, -1031) def +bond1 36 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 39 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 36 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part CYX_CYSTEINE-S-S-CYSTEINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/GLH_GLUTAMIC_ACID_neutral.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/GLH_GLUTAMIC_ACID_neutral.mmp new file mode 100644 index 000000000..8bdbf0988 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/GLH_GLUTAMIC_ACID_neutral.mmp @@ -0,0 +1,94 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.090780) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (GLU_GLUTAMIC_ACID) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-5575, -1434, 165) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-6123, -1061, 936) def +bond1 1 +atom 3 (1) (-5919, -2234, -360) def +bond1 1 +atom 4 (6) (-4257, -796, -204) def +bond1 1 +atom 5 (1) (-3880, -215, 637) def +bond1 4 +atom 6 (6) (-4404, 207, -1386) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4977, -85, -2414) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3819, 1534, -1220) def +bond1 6 +atom 9 (1) (-4458, 2109, -781) def +bond1 8 +atom 10 (6) (-3147, -1849, -532) def +bond1 4 +atom 11 (1) (-3155, -2622, 235) def +bond1 10 +atom 12 (1) (-3387, -2347, -1471) def +bond1 10 +atom 13 (6) (-1715, -1232, -625) def +bond1 10 +atom 14 (1) (-1698, -450, -1382) def +bond1 13 +atom 15 (1) (-1452, -761, 320) def +bond1 13 +atom 16 (6) (-635, -2295, -975) def +info atom atomtype = sp2 +bond1 13 +atom 17 (8) (95, -2199, -2234) def +info atom atomtype = sp2 +bond2 16 +atom 18 (8) (-351, -3346, -90) def +bond1 16 +atom 19 (1) (-48, -2901, 752) def +bond1 18 +egroup (GLU_GLUTAMIC_ACID) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 20 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 21 (1) (-6647, -648, 393) def +bond1 20 +atom 22 (1) (-6234, -2264, -166) def +bond1 20 +atom 23 (6) (-4521, -878, -132) def +bond1 20 +atom 24 (1) (-4223, -240, 701) def +bond1 23 +atom 25 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 23 +atom 26 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 25 +atom 27 (8) (-3544, 1199, -1313) def +bond1 25 +atom 28 (1) (-4100, 1908, -964) def +bond1 27 +atom 29 (6) (-3527, -2085, -141) def +bond1 23 +atom 30 (1) (-3647, -2708, 744) def +bond1 29 +atom 31 (1) (-3647, -2700, -1031) def +bond1 29 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 32 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 29 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part GLU_GLUTAMIC_ACID diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/GLN_GLUTAMINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/GLN_GLUTAMINE.mmp new file mode 100644 index 000000000..acfe3c2c1 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/GLN_GLUTAMINE.mmp @@ -0,0 +1,97 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.739564) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (GLN_GLUTAMINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-5575, -1434, 165) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-6123, -1061, 936) def +bond1 1 +atom 3 (1) (-5919, -2234, -360) def +bond1 1 +atom 4 (6) (-4257, -796, -204) def +bond1 1 +atom 5 (1) (-3880, -215, 637) def +bond1 4 +atom 6 (6) (-4404, 207, -1386) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4977, -85, -2414) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3819, 1534, -1220) def +bond1 6 +atom 9 (1) (-4458, 2109, -781) def +bond1 8 +atom 10 (6) (-3147, -1849, -532) def +bond1 4 +atom 11 (1) (-3155, -2622, 235) def +bond1 10 +atom 12 (1) (-3387, -2347, -1471) def +bond1 10 +atom 13 (6) (-1715, -1232, -625) def +bond1 10 +atom 14 (1) (-1698, -450, -1382) def +bond1 13 +atom 15 (1) (-1452, -761, 320) def +bond1 13 +atom 16 (6) (-635, -2295, -975) def +info atom atomtype = sp2 +bond1 13 +atom 17 (8) (95, -2199, -2234) def +info atom atomtype = sp2 +bond2 16 +atom 18 (7) (-330, -3424, -25) def +info atom atomtype = sp2(graphitic) +bond1 16 +atom 19 (1) (-716, -3418, 916) def +bond1 18 +atom 20 (1) (263, -4194, -324) def +bond1 18 +egroup (GLN_GLUTAMINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 21 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 22 (1) (-6647, -648, 393) def +bond1 21 +atom 23 (1) (-6234, -2264, -166) def +bond1 21 +atom 24 (6) (-4521, -878, -132) def +bond1 21 +atom 25 (1) (-4223, -240, 701) def +bond1 24 +atom 26 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 24 +atom 27 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 26 +atom 28 (8) (-3544, 1199, -1313) def +bond1 26 +atom 29 (1) (-4100, 1908, -964) def +bond1 28 +atom 30 (6) (-3527, -2085, -141) def +bond1 24 +atom 31 (1) (-3647, -2708, 744) def +bond1 30 +atom 32 (1) (-3647, -2700, -1031) def +bond1 30 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 33 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 30 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part GLN_GLUTAMINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/GLU_GLUTAMIC_ACID.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/GLU_GLUTAMIC_ACID.mmp new file mode 100644 index 000000000..a5bfb0b35 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/GLU_GLUTAMIC_ACID.mmp @@ -0,0 +1,93 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.184217) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (GLU_GLUTAMIC_ACID) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-5575, -1434, 165) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-6123, -1061, 936) def +bond1 1 +atom 3 (1) (-5919, -2234, -360) def +bond1 1 +atom 4 (6) (-4257, -796, -204) def +bond1 1 +atom 5 (1) (-3880, -215, 637) def +bond1 4 +atom 6 (6) (-4404, 207, -1386) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4977, -85, -2414) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3819, 1534, -1220) def +bond1 6 +atom 9 (1) (-4458, 2109, -781) def +bond1 8 +atom 10 (6) (-3147, -1849, -532) def +bond1 4 +atom 11 (1) (-3155, -2622, 235) def +bond1 10 +atom 12 (1) (-3387, -2347, -1471) def +bond1 10 +atom 13 (6) (-1715, -1232, -625) def +bond1 10 +atom 14 (1) (-1698, -450, -1382) def +bond1 13 +atom 15 (1) (-1452, -761, 320) def +bond1 13 +atom 16 (6) (-635, -2295, -975) def +info atom atomtype = sp2 +bond1 13 +atom 17 (8) (95, -2199, -2234) def +info atom atomtype = sp2 +bond2 16 +atom 18 (8) (-351, -3346, -90) def +info atom atomtype = sp2(-) +bond1 16 +egroup (GLU_GLUTAMIC_ACID) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 19 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 20 (1) (-6647, -648, 393) def +bond1 19 +atom 21 (1) (-6234, -2264, -166) def +bond1 19 +atom 22 (6) (-4521, -878, -132) def +bond1 19 +atom 23 (1) (-4223, -240, 701) def +bond1 22 +atom 24 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 22 +atom 25 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 24 +atom 26 (8) (-3544, 1199, -1313) def +bond1 24 +atom 27 (1) (-4100, 1908, -964) def +bond1 26 +atom 28 (6) (-3527, -2085, -141) def +bond1 22 +atom 29 (1) (-3647, -2708, 744) def +bond1 28 +atom 30 (1) (-3647, -2700, -1031) def +bond1 28 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 31 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 28 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part GLU_GLUTAMIC_ACID diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/GLY_GLYCINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/GLY_GLYCINE.mmp new file mode 100644 index 000000000..16c212c63 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/GLY_GLYCINE.mmp @@ -0,0 +1,74 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (0.999942, 0.009645, -0.003794, 0.002956) (8.793595) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (GLY_GLYCINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-5575, -1434, 165) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-6123, -1061, 936) def +bond1 1 +atom 3 (1) (-5919, -2234, -360) def +bond1 1 +atom 4 (6) (-4257, -796, -204) def +bond1 1 +atom 5 (1) (-3880, -215, 637) def +bond1 4 +atom 6 (6) (-4404, 207, -1386) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4977, -85, -2414) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3819, 1534, -1220) def +bond1 6 +atom 9 (1) (-4458, 2109, -781) def +bond1 8 +atom 10 (1) (-3490, -1524, -431) def +bond1 4 +egroup (GLY_GLYCINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 11 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 12 (1) (-6647, -648, 393) def +bond1 11 +atom 13 (1) (-6234, -2264, -166) def +bond1 11 +atom 14 (6) (-4521, -878, -132) def +bond1 11 +atom 15 (1) (-4223, -240, 701) def +bond1 14 +atom 16 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 14 +atom 17 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 16 +atom 18 (8) (-3544, 1199, -1313) def +bond1 16 +atom 19 (1) (-4100, 1908, -964) def +bond1 18 +atom 20 (6) (-3527, -2085, -141) def +bond1 14 +atom 21 (1) (-3647, -2708, 744) def +bond1 20 +atom 22 (1) (-3647, -2700, -1031) def +bond1 20 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 23 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 20 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part GLY_GLYCINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/HID_HISTIDINE_DELTAH.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/HID_HISTIDINE_DELTAH.mmp new file mode 100644 index 000000000..9e4fd403f --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/HID_HISTIDINE_DELTAH.mmp @@ -0,0 +1,99 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.317516) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (HID_HISTIDINE_DELTAH) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-5610, -1361, 99) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-6148, -1022, 892) def +bond1 1 +atom 3 (1) (-5948, -2156, -438) def +bond1 1 +atom 4 (6) (-4314, -687, -281) def +bond1 1 +atom 5 (1) (-3945, -89, 552) def +bond1 4 +atom 6 (6) (-4490, 307, -1468) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-5099, 12, -2473) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3885, 1628, -1333) def +bond1 6 +atom 9 (1) (-4479, 2199, -830) def +bond1 8 +atom 10 (6) (-3177, -1702, -612) def +bond1 4 +atom 11 (1) (-2254, -1170, -833) def +bond1 10 +atom 12 (1) (-3438, -2267, -1505) def +bond1 10 +atom 13 (6) (-2923, -2689, 560) def +info atom atomtype = sp2 +bond1 10 +atom 14 (6) (-2427, -2344, 1985) def +info atom atomtype = sp2 +bond1 13 +atom 15 (1) (-2177, -1344, 2334) def +bond1 14 +atom 16 (7) (-2337, -3591, 2827) def +info atom atomtype = sp2 +bond1 14 +atom 17 (7) (-3119, -4174, 551) def +info atom atomtype = sp2(graphitic) +bond1 13 +atom 18 (1) (-3431, -4728, -242) def +bond1 17 +atom 19 (6) (-2774, -4707, 1912) def +info atom atomtype = sp2 +bond1 17 16 +atom 20 (1) (-2832, -5755, 2199) def +bond1 19 +egroup (HID_HISTIDINE_DELTAH) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 21 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 22 (1) (-6647, -648, 393) def +bond1 21 +atom 23 (1) (-6234, -2264, -166) def +bond1 21 +atom 24 (6) (-4521, -878, -132) def +bond1 21 +atom 25 (1) (-4223, -240, 701) def +bond1 24 +atom 26 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 24 +atom 27 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 26 +atom 28 (8) (-3544, 1199, -1313) def +bond1 26 +atom 29 (1) (-4100, 1908, -964) def +bond1 28 +atom 30 (6) (-3527, -2085, -141) def +bond1 24 +atom 31 (1) (-3647, -2708, 744) def +bond1 30 +atom 32 (1) (-3647, -2700, -1031) def +bond1 30 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 33 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 30 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part HID_HISTIDINE_DELTAH diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/HIE_HISTIDINE_EPSILONH.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/HIE_HISTIDINE_EPSILONH.mmp new file mode 100644 index 000000000..813799841 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/HIE_HISTIDINE_EPSILONH.mmp @@ -0,0 +1,99 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (11.654935) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (HIE_HISTIDINE_EPSILONH) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-5610, -1361, 99) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-6148, -1022, 892) def +bond1 1 +atom 3 (1) (-5948, -2156, -438) def +bond1 1 +atom 4 (6) (-4314, -687, -281) def +bond1 1 +atom 5 (1) (-3945, -89, 552) def +bond1 4 +atom 6 (6) (-4490, 307, -1468) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-5099, 12, -2473) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3885, 1628, -1333) def +bond1 6 +atom 9 (1) (-4479, 2199, -830) def +bond1 8 +atom 10 (6) (-3177, -1702, -612) def +bond1 4 +atom 11 (1) (-2254, -1170, -833) def +bond1 10 +atom 12 (1) (-3438, -2267, -1505) def +bond1 10 +atom 13 (6) (-2923, -2689, 560) def +info atom atomtype = sp2 +bond1 10 +atom 14 (6) (-2427, -2344, 1985) def +info atom atomtype = sp2 +bond1 13 +atom 15 (1) (-2177, -1344, 2334) def +bond1 14 +atom 16 (7) (-2337, -3591, 2827) def +info atom atomtype = sp2(graphitic) +bond1 14 +atom 17 (7) (-3119, -4174, 551) def +info atom atomtype = sp2 +bond1 13 +atom 18 (6) (-2774, -4707, 1912) def +info atom atomtype = sp2 +bond1 17 16 +atom 19 (1) (-2832, -5755, 2199) def +bond1 18 +atom 20 (1) (-2056, -3536, 3712) def +bond1 16 +egroup (HIE_HISTIDINE_EPSILONH) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 21 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 22 (1) (-6647, -648, 393) def +bond1 21 +atom 23 (1) (-6234, -2264, -166) def +bond1 21 +atom 24 (6) (-4521, -878, -132) def +bond1 21 +atom 25 (1) (-4223, -240, 701) def +bond1 24 +atom 26 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 24 +atom 27 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 26 +atom 28 (8) (-3544, 1199, -1313) def +bond1 26 +atom 29 (1) (-4100, 1908, -964) def +bond1 28 +atom 30 (6) (-3527, -2085, -141) def +bond1 24 +atom 31 (1) (-3647, -2708, 744) def +bond1 30 +atom 32 (1) (-3647, -2700, -1031) def +bond1 30 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 33 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 30 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part HIE_HISTIDINE_EPSILONH diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/HIP_HISTIDINE_plus.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/HIP_HISTIDINE_plus.mmp new file mode 100644 index 000000000..0fb7b4037 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/HIP_HISTIDINE_plus.mmp @@ -0,0 +1,101 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (11.896795) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (HIP_HISTIDINE_plus) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-5610, -1361, 99) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-6148, -1022, 892) def +bond1 1 +atom 3 (1) (-5948, -2156, -438) def +bond1 1 +atom 4 (6) (-4314, -687, -281) def +bond1 1 +atom 5 (1) (-3945, -89, 552) def +bond1 4 +atom 6 (6) (-4490, 307, -1468) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-5099, 12, -2473) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3885, 1628, -1333) def +bond1 6 +atom 9 (1) (-4479, 2199, -830) def +bond1 8 +atom 10 (6) (-3177, -1702, -612) def +bond1 4 +atom 11 (1) (-2254, -1170, -833) def +bond1 10 +atom 12 (1) (-3438, -2267, -1505) def +bond1 10 +atom 13 (6) (-2923, -2689, 560) def +info atom atomtype = sp2 +bond1 10 +atom 14 (6) (-2427, -2344, 1985) def +info atom atomtype = sp2 +bond1 13 +atom 15 (1) (-2177, -1344, 2334) def +bond1 14 +atom 16 (7) (-2337, -3591, 2827) def +info atom atomtype = sp2(graphitic) +bond1 14 +atom 17 (7) (-3119, -4174, 551) def +info atom atomtype = sp2(graphitic) +bond1 13 +atom 18 (6) (-2774, -4707, 1912) def +info atom atomtype = sp2 +bond1 17 16 +atom 19 (1) (-2832, -5755, 2199) def +bond1 18 +atom 20 (1) (-2056, -3536, 3712) def +bond1 16 +atom 21 (1) (-3410, -4600, -223) def +bond1 17 +egroup (HIP_HISTIDINE_plus) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 22 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 23 (1) (-6647, -648, 393) def +bond1 22 +atom 24 (1) (-6234, -2264, -166) def +bond1 22 +atom 25 (6) (-4521, -878, -132) def +bond1 22 +atom 26 (1) (-4223, -240, 701) def +bond1 25 +atom 27 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 25 +atom 28 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 27 +atom 29 (8) (-3544, 1199, -1313) def +bond1 27 +atom 30 (1) (-4100, 1908, -964) def +bond1 29 +atom 31 (6) (-3527, -2085, -141) def +bond1 25 +atom 32 (1) (-3647, -2708, 744) def +bond1 31 +atom 33 (1) (-3647, -2700, -1031) def +bond1 31 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 34 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 31 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part HIP_HISTIDINE_plus diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/ILE_ISOLEUCINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/ILE_ISOLEUCINE.mmp new file mode 100644 index 000000000..9ede83cb0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/ILE_ISOLEUCINE.mmp @@ -0,0 +1,98 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (11.463560) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (ILE_ISOLEUCINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-5610, -1361, 99) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-6148, -1022, 892) def +bond1 1 +atom 3 (1) (-5948, -2156, -438) def +bond1 1 +atom 4 (6) (-4314, -687, -281) def +bond1 1 +atom 5 (1) (-3945, -89, 552) def +bond1 4 +atom 6 (6) (-4490, 307, -1468) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-5099, 12, -2473) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3885, 1628, -1333) def +bond1 6 +atom 9 (1) (-4479, 2199, -830) def +bond1 8 +atom 10 (6) (-3177, -1702, -612) def +bond1 4 +atom 11 (1) (-3000, -2390, 205) def +bond1 10 +atom 12 (6) (-3548, -2506, -1882) def +bond1 10 +atom 13 (1) (-4471, -3044, -1712) def +bond1 12 +atom 14 (1) (-2757, -3209, -2108) def +bond1 12 +atom 15 (1) (-3674, -1826, -2714) def +bond1 12 +atom 16 (6) (-1864, -945, -927) def +bond1 10 +atom 17 (1) (-2018, -295, -1777) def +bond1 16 +atom 18 (1) (-1574, -354, -68) def +bond1 16 +atom 19 (6) (-747, -1964, -1252) def +bond1 16 +atom 20 (1) (-593, -2614, -402) def +bond1 19 +atom 21 (1) (170, -1434, -1472) def +bond1 19 +atom 22 (1) (-1037, -2555, -2111) def +bond1 19 +egroup (ILE_ISOLEUCINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 23 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 24 (1) (-6647, -648, 393) def +bond1 23 +atom 25 (1) (-6234, -2264, -166) def +bond1 23 +atom 26 (6) (-4521, -878, -132) def +bond1 23 +atom 27 (1) (-4223, -240, 701) def +bond1 26 +atom 28 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 26 +atom 29 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 28 +atom 30 (8) (-3544, 1199, -1313) def +bond1 28 +atom 31 (1) (-4100, 1908, -964) def +bond1 30 +atom 32 (6) (-3527, -2085, -141) def +bond1 26 +atom 33 (1) (-3647, -2708, 744) def +bond1 32 +atom 34 (1) (-3647, -2700, -1031) def +bond1 32 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 35 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 32 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part ILE_ISOLEUCINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/LEU_LEUCINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/LEU_LEUCINE.mmp new file mode 100644 index 000000000..a439e78e5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/LEU_LEUCINE.mmp @@ -0,0 +1,98 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.194312) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (LEU_LEUCINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-5610, -1361, 99) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-6148, -1022, 892) def +bond1 1 +atom 3 (1) (-5948, -2156, -438) def +bond1 1 +atom 4 (6) (-4314, -687, -281) def +bond1 1 +atom 5 (1) (-3945, -89, 552) def +bond1 4 +atom 6 (6) (-4490, 307, -1468) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-5099, 12, -2473) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3885, 1628, -1333) def +bond1 6 +atom 9 (1) (-4479, 2199, -830) def +bond1 8 +atom 10 (6) (-3177, -1702, -612) def +bond1 4 +atom 11 (1) (-3000, -2390, 205) def +bond1 10 +atom 12 (6) (-1864, -945, -927) def +bond1 10 +atom 13 (1) (-2018, -295, -1777) def +bond1 12 +atom 14 (6) (-747, -1964, -1252) def +bond1 12 +atom 15 (1) (-593, -2614, -402) def +bond1 14 +atom 16 (1) (170, -1434, -1472) def +bond1 14 +atom 17 (1) (-1037, -2555, -2111) def +bond1 14 +atom 18 (1) (-3436, -2264, -1500) def +bond1 10 +atom 19 (6) (-1449, -99, 301) def +bond1 12 +atom 20 (1) (-2231, 614, 529) def +bond1 19 +atom 21 (1) (-532, 430, 81) def +bond1 19 +atom 22 (1) (-1295, -750, 1152) def +bond1 19 +egroup (LEU_LEUCINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 23 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 24 (1) (-6647, -648, 393) def +bond1 23 +atom 25 (1) (-6234, -2264, -166) def +bond1 23 +atom 26 (6) (-4521, -878, -132) def +bond1 23 +atom 27 (1) (-4223, -240, 701) def +bond1 26 +atom 28 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 26 +atom 29 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 28 +atom 30 (8) (-3544, 1199, -1313) def +bond1 28 +atom 31 (1) (-4100, 1908, -964) def +bond1 30 +atom 32 (6) (-3527, -2085, -141) def +bond1 26 +atom 33 (1) (-3647, -2708, 744) def +bond1 32 +atom 34 (1) (-3647, -2700, -1031) def +bond1 32 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 35 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 32 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part LEU_LEUCINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/LYN_LYSINE_neutral.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/LYN_LYSINE_neutral.mmp new file mode 100644 index 000000000..977c22450 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/LYN_LYSINE_neutral.mmp @@ -0,0 +1,101 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.252237) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (LYN_LYSINE_neutral) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-4655, -1651, -66) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-5155, -1475, 801) def +bond1 1 +atom 3 (1) (-4912, -2447, -646) def +bond1 1 +atom 4 (6) (-3537, -732, -496) def +bond1 1 +atom 5 (1) (-3219, -118, 346) def +bond1 4 +atom 6 (6) (-3993, 264, -1603) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4561, -103, -2609) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3707, 1680, -1393) def +bond1 6 +atom 9 (1) (-4428, 2077, -889) def +bond1 8 +atom 10 (6) (-2265, -1510, -968) def +bond1 4 +atom 11 (1) (-2009, -2256, -217) def +bond1 10 +atom 12 (6) (-1027, -587, -1220) def +bond1 10 +atom 13 (1) (-1261, 127, -2009) def +bond1 12 +atom 14 (6) (251, -1393, -1621) def +bond1 12 +atom 15 (1) (446, -2158, -871) def +bond1 14 +atom 16 (1) (68, -1916, -2559) def +bond1 14 +atom 17 (1) (-2498, -2060, -1880) def +bond1 10 +atom 18 (7) (2741, -1219, -2289) def +atom 19 (1) (2647, -1419, -3283) def +bond1 18 +atom 20 (1) (2871, -2100, -1797) def +bond1 18 +atom 21 (1) (-822, -10, -329) def +bond1 12 +atom 22 (6) (1518, -490, -1774) def +bond1 14 18 +atom 23 (1) (1253, 340, -2415) def +bond1 22 +atom 24 (1) (1705, -32, -812) def +bond1 22 +egroup (LYN_LYSINE_neutral) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 25 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 26 (1) (-6647, -648, 393) def +bond1 25 +atom 27 (1) (-6234, -2264, -166) def +bond1 25 +atom 28 (6) (-4521, -878, -132) def +bond1 25 +atom 29 (1) (-4223, -240, 701) def +bond1 28 +atom 30 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 28 +atom 31 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 30 +atom 32 (8) (-3544, 1199, -1313) def +bond1 30 +atom 33 (1) (-4100, 1908, -964) def +bond1 32 +atom 34 (6) (-3527, -2085, -141) def +bond1 28 +atom 35 (1) (-3647, -2708, 744) def +bond1 34 +atom 36 (1) (-3647, -2700, -1031) def +bond1 34 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 37 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 34 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part LYN_LYSINE_neutral diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/LYS_LYSINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/LYS_LYSINE.mmp new file mode 100644 index 000000000..b72ed3ad8 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/LYS_LYSINE.mmp @@ -0,0 +1,103 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.617534) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (LYS_LYSINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-4655, -1651, -66) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-5155, -1475, 801) def +bond1 1 +atom 3 (1) (-4912, -2447, -646) def +bond1 1 +atom 4 (6) (-3537, -732, -496) def +bond1 1 +atom 5 (1) (-3219, -118, 346) def +bond1 4 +atom 6 (6) (-3993, 264, -1603) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4561, -103, -2609) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3707, 1680, -1393) def +bond1 6 +atom 9 (1) (-4428, 2077, -889) def +bond1 8 +atom 10 (6) (-2265, -1510, -968) def +bond1 4 +atom 11 (1) (-2009, -2256, -217) def +bond1 10 +atom 12 (6) (-1027, -587, -1220) def +bond1 10 +atom 13 (1) (-1261, 127, -2009) def +bond1 12 +atom 14 (6) (251, -1393, -1621) def +bond1 12 +atom 15 (1) (446, -2158, -871) def +bond1 14 +atom 16 (1) (68, -1916, -2559) def +bond1 14 +atom 17 (1) (-2498, -2060, -1880) def +bond1 10 +atom 18 (7) (2741, -1219, -2289) def +atom 19 (1) (2647, -1419, -3283) def +bond1 18 +atom 20 (1) (3577, -655, -2156) def +bond1 18 +atom 21 (1) (2871, -2100, -1797) def +bond1 18 +atom 22 (1) (-822, -10, -329) def +bond1 12 +atom 23 (6) (1518, -490, -1774) def +bond1 14 18 +atom 24 (1) (1253, 340, -2415) def +bond1 23 +atom 25 (1) (1705, -32, -812) def +bond1 23 +egroup (LYS_LYSINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 26 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 27 (1) (-6647, -648, 393) def +bond1 26 +atom 28 (1) (-6234, -2264, -166) def +bond1 26 +atom 29 (6) (-4521, -878, -132) def +bond1 26 +atom 30 (1) (-4223, -240, 701) def +bond1 29 +atom 31 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 29 +atom 32 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 31 +atom 33 (8) (-3544, 1199, -1313) def +bond1 31 +atom 34 (1) (-4100, 1908, -964) def +bond1 33 +atom 35 (6) (-3527, -2085, -141) def +bond1 29 +atom 36 (1) (-3647, -2708, 744) def +bond1 35 +atom 37 (1) (-3647, -2700, -1031) def +bond1 35 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 38 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 35 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part LYS_LYSINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/MET_METHIONINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/MET_METHIONINE.mmp new file mode 100644 index 000000000..6816822f9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/MET_METHIONINE.mmp @@ -0,0 +1,94 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.108515) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (MET_METHIONINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-4585, -1744, -132) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-5107, -1642, 735) def +bond1 1 +atom 3 (1) (-4777, -2530, -748) def +bond1 1 +atom 4 (6) (-3532, -729, -506) def +bond1 1 +atom 5 (1) (-3288, -113, 359) def +bond1 4 +atom 6 (6) (-4029, 256, -1605) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4617, -123, -2595) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3757, 1677, -1408) def +bond1 6 +atom 9 (1) (-4467, 2064, -880) def +bond1 8 +atom 10 (6) (-2190, -1393, -955) def +bond1 4 +atom 11 (1) (-1893, -2123, -202) def +bond1 10 +atom 12 (6) (-1036, -359, -1166) def +bond1 10 +atom 13 (1) (-1206, 264, -2041) def +bond1 12 +atom 14 (1) (-2355, -1948, -1878) def +bond1 10 +atom 15 (1) (-899, 273, -291) def +bond1 12 +atom 16 (16) (579, -1223, -1467) def +bond1 12 +atom 17 (6) (1777, -35, -711) def +bond1 16 +atom 18 (1) (1521, 961, -1046) def +bond1 17 +atom 19 (1) (2767, -314, -1046) def +bond1 17 +atom 20 (1) (1693, -121, 364) def +bond1 17 +egroup (MET_METHIONINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 21 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 22 (1) (-6647, -648, 393) def +bond1 21 +atom 23 (1) (-6234, -2264, -166) def +bond1 21 +atom 24 (6) (-4521, -878, -132) def +bond1 21 +atom 25 (1) (-4223, -240, 701) def +bond1 24 +atom 26 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 24 +atom 27 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 26 +atom 28 (8) (-3544, 1199, -1313) def +bond1 26 +atom 29 (1) (-4100, 1908, -964) def +bond1 28 +atom 30 (6) (-3527, -2085, -141) def +bond1 24 +atom 31 (1) (-3647, -2708, 744) def +bond1 30 +atom 32 (1) (-3647, -2700, -1031) def +bond1 30 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 33 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 30 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part MET_METHIONINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/PHE_PHENYLALANINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/PHE_PHENYLALANINE.mmp new file mode 100644 index 000000000..e8b9a35e9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/PHE_PHENYLALANINE.mmp @@ -0,0 +1,106 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.462033) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (PHE_PHENYLALANINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-4585, -1744, -132) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-5107, -1642, 735) def +bond1 1 +atom 3 (1) (-4777, -2530, -748) def +bond1 1 +atom 4 (6) (-3532, -729, -506) def +bond1 1 +atom 5 (1) (-3288, -113, 359) def +bond1 4 +atom 6 (6) (-4029, 256, -1605) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4617, -123, -2595) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3757, 1677, -1408) def +bond1 6 +atom 9 (1) (-4467, 2064, -880) def +bond1 8 +atom 10 (6) (-2190, -1393, -955) def +bond1 4 +atom 11 (1) (-1893, -2123, -202) def +bond1 10 +atom 12 (1) (-1391, -678, -1101) def +bond1 10 +atom 13 (6) (-2416, -2150, -2213) def +info atom atomtype = sp2 +bond1 10 +atom 14 (6) (-3377, -3238, -2243) def +info atom atomtype = sp2 +bond1 13 +atom 15 (1) (-3898, -3482, -1400) def +bond1 14 +atom 16 (6) (-1675, -1803, -3413) def +info atom atomtype = sp2 +bond1 13 +atom 17 (1) (-1000, -1039, -3391) def +bond1 16 +atom 18 (6) (-1901, -2559, -4670) def +info atom atomtype = sp2 +bond1 16 +atom 19 (1) (-1381, -2315, -5512) def +bond1 18 +atom 20 (6) (-3603, -3994, -3500) def +info atom atomtype = sp2 +bond1 14 +atom 21 (1) (-4279, -4758, -3521) def +bond1 20 +atom 22 (6) (-2865, -3655, -4713) def +info atom atomtype = sp2 +bond1 20 18 +atom 23 (1) (-3027, -4180, -5573) def +bond1 22 +egroup (PHE_PHENYLALANINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 24 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 25 (1) (-6647, -648, 393) def +bond1 24 +atom 26 (1) (-6234, -2264, -166) def +bond1 24 +atom 27 (6) (-4521, -878, -132) def +bond1 24 +atom 28 (1) (-4223, -240, 701) def +bond1 27 +atom 29 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 27 +atom 30 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 29 +atom 31 (8) (-3544, 1199, -1313) def +bond1 29 +atom 32 (1) (-4100, 1908, -964) def +bond1 31 +atom 33 (6) (-3527, -2085, -141) def +bond1 27 +atom 34 (1) (-3647, -2708, 744) def +bond1 33 +atom 35 (1) (-3647, -2700, -1031) def +bond1 33 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 36 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 33 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part PHE_PHENYLALANINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/PRO_PROLINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/PRO_PROLINE.mmp new file mode 100644 index 000000000..18194687c --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/PRO_PROLINE.mmp @@ -0,0 +1,88 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (9.252082) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (PRO_PROLINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-4985, -1491, -402) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-5759, -1209, 195) def +bond1 1 +atom 3 (6) (-3808, -618, -721) def +bond1 1 +atom 4 (1) (-3278, -325, 185) def +bond1 3 +atom 5 (6) (-4204, 693, -1462) def +info atom atomtype = sp2 +bond1 3 +atom 6 (8) (-4962, 697, -2408) def +info atom atomtype = sp2 +bond2 5 +atom 7 (8) (-3623, 1941, -977) def +bond1 5 +atom 8 (1) (-4257, 2380, -396) def +bond1 7 +atom 9 (6) (-2835, -1479, -1591) def +bond1 3 +atom 10 (1) (-1899, -1635, -1072) def +bond1 9 +atom 11 (1) (-2603, -982, -2524) def +bond1 9 +atom 12 (6) (-4883, -2831, -1064) def +bond1 1 +atom 13 (1) (-4892, -3647, -355) def +bond1 12 +atom 14 (1) (-5705, -3023, -1742) def +bond1 12 +atom 15 (6) (-3542, -2849, -1859) def +bond1 12 9 +atom 16 (1) (-3728, -2979, -2917) def +bond1 15 +atom 17 (1) (-2917, -3671, -1537) def +bond1 15 +egroup (PRO_PROLINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 18 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 19 (1) (-6647, -648, 393) def +bond1 18 +atom 20 (1) (-6234, -2264, -166) def +bond1 18 +atom 21 (6) (-4521, -878, -132) def +bond1 18 +atom 22 (1) (-4223, -240, 701) def +bond1 21 +atom 23 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 21 +atom 24 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 23 +atom 25 (8) (-3544, 1199, -1313) def +bond1 23 +atom 26 (1) (-4100, 1908, -964) def +bond1 25 +atom 27 (6) (-3527, -2085, -141) def +bond1 21 +atom 28 (1) (-3647, -2708, 744) def +bond1 27 +atom 29 (1) (-3647, -2700, -1031) def +bond1 27 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 30 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 27 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part PRO_PROLINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/SER_SERINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/SER_SERINE.mmp new file mode 100644 index 000000000..8a6a0234e --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/SER_SERINE.mmp @@ -0,0 +1,82 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.241352) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (SER_SERINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-4585, -1744, -132) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-5107, -1642, 735) def +bond1 1 +atom 3 (1) (-4777, -2530, -748) def +bond1 1 +atom 4 (6) (-3532, -729, -506) def +bond1 1 +atom 5 (1) (-3288, -113, 359) def +bond1 4 +atom 6 (6) (-4029, 256, -1605) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4617, -123, -2595) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3757, 1677, -1408) def +bond1 6 +atom 9 (1) (-4467, 2064, -880) def +bond1 8 +atom 10 (6) (-2190, -1393, -955) def +bond1 4 +atom 11 (1) (-1893, -2123, -202) def +bond1 10 +atom 12 (1) (-1391, -678, -1101) def +bond1 10 +atom 13 (8) (-2417, -2156, -2222) def +bond1 10 +atom 14 (1) (-3111, -2839, -1992) def +bond1 13 +egroup (SER_SERINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 15 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 16 (1) (-6647, -648, 393) def +bond1 15 +atom 17 (1) (-6234, -2264, -166) def +bond1 15 +atom 18 (6) (-4521, -878, -132) def +bond1 15 +atom 19 (1) (-4223, -240, 701) def +bond1 18 +atom 20 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 18 +atom 21 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 20 +atom 22 (8) (-3544, 1199, -1313) def +bond1 20 +atom 23 (1) (-4100, 1908, -964) def +bond1 22 +atom 24 (6) (-3527, -2085, -141) def +bond1 18 +atom 25 (1) (-3647, -2708, 744) def +bond1 24 +atom 26 (1) (-3647, -2700, -1031) def +bond1 24 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 27 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 24 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part SER_SERINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/THR_THREONINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/THR_THREONINE.mmp new file mode 100644 index 000000000..b5d92bdc0 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/THR_THREONINE.mmp @@ -0,0 +1,88 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (8.890516) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (THR_THREONINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-4585, -1744, -132) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-5107, -1642, 735) def +bond1 1 +atom 3 (1) (-4777, -2530, -748) def +bond1 1 +atom 4 (6) (-3532, -729, -506) def +bond1 1 +atom 5 (1) (-3288, -113, 359) def +bond1 4 +atom 6 (6) (-4029, 256, -1605) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4617, -123, -2595) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3757, 1677, -1408) def +bond1 6 +atom 9 (1) (-4467, 2064, -880) def +bond1 8 +atom 10 (6) (-2190, -1393, -955) def +bond1 4 +atom 11 (1) (-1391, -678, -1101) def +bond1 10 +atom 12 (8) (-2417, -2156, -2222) def +bond1 10 +atom 13 (1) (-3111, -2839, -1992) def +bond1 12 +atom 14 (6) (-1768, -2430, 115) def +bond1 10 +atom 15 (1) (-1633, -1933, 1066) def +bond1 14 +atom 16 (1) (-839, -2898, -183) def +bond1 14 +atom 17 (1) (-2538, -3184, 208) def +bond1 14 +egroup (THR_THREONINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 18 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 19 (1) (-6647, -648, 393) def +bond1 18 +atom 20 (1) (-6234, -2264, -166) def +bond1 18 +atom 21 (6) (-4521, -878, -132) def +bond1 18 +atom 22 (1) (-4223, -240, 701) def +bond1 21 +atom 23 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 21 +atom 24 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 23 +atom 25 (8) (-3544, 1199, -1313) def +bond1 23 +atom 26 (1) (-4100, 1908, -964) def +bond1 25 +atom 27 (6) (-3527, -2085, -141) def +bond1 21 +atom 28 (1) (-3647, -2708, 744) def +bond1 27 +atom 29 (1) (-3647, -2700, -1031) def +bond1 27 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 30 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 27 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part THR_THREONINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/TRP_TRYPTOPHAN.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/TRP_TRYPTOPHAN.mmp new file mode 100644 index 000000000..0705cb2ed --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/TRP_TRYPTOPHAN.mmp @@ -0,0 +1,117 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (11.027374) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (TRP_TRYPTOPHAN) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-4678, -1653, -216) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-5182, -1570, 663) def +bond1 1 +atom 3 (1) (-4881, -2428, -843) def +bond1 1 +atom 4 (6) (-3632, -632, -590) def +bond1 1 +atom 5 (1) (-3394, -8, 272) def +bond1 4 +atom 6 (6) (-4125, 347, -1695) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4731, -37, -2676) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3830, 1764, -1520) def +bond1 6 +atom 9 (1) (-4508, 2162, -958) def +bond1 8 +atom 10 (6) (-2283, -1282, -1029) def +bond1 4 +atom 11 (1) (-1522, -514, -1157) def +bond1 10 +atom 12 (1) (-2407, -1766, -1989) def +bond1 10 +atom 13 (6) (-1782, -2326, 6) def +info atom atomtype = sp2 +bond1 10 +atom 14 (6) (-1414, -2051, 1489) def +info atom atomtype = sp2 +bond1 13 +atom 15 (1) (-1432, -1139, 1946) def +bond1 14 +atom 16 (6) (-1570, -3844, -235) def +info atom atomtype = sp2 +bond1 13 +atom 17 (6) (-1110, -4499, 1090) def +info atom atomtype = sp2 +bond1 16 +atom 18 (7) (-1015, -3387, 2159) def +info atom atomtype = sp2(graphitic) +bond1 14 17 +atom 19 (6) (-828, -5876, 1288) def +info atom atomtype = sp2 +bond1 17 +atom 20 (1) (-529, -6209, 2205) def +bond1 19 +atom 21 (6) (-1765, -4521, -1468) def +info atom atomtype = sp2 +bond1 16 +atom 22 (1) (-2070, -4003, -2292) def +bond1 21 +atom 23 (6) (-1525, -5984, -1558) def +info atom atomtype = sp2 +bond1 21 +atom 24 (1) (-1665, -6470, -2443) def +bond1 23 +atom 25 (6) (-1024, -6785, -99) def +info atom atomtype = sp2 +bond1 19 23 +atom 26 (1) (-850, -7790, -79) def +bond1 25 +atom 27 (1) (-777, -3404, 3058) def +bond1 18 +egroup (TRP_TRYPTOPHAN) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 28 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 29 (1) (-6647, -648, 393) def +bond1 28 +atom 30 (1) (-6234, -2264, -166) def +bond1 28 +atom 31 (6) (-4521, -878, -132) def +bond1 28 +atom 32 (1) (-4223, -240, 701) def +bond1 31 +atom 33 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 31 +atom 34 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 33 +atom 35 (8) (-3544, 1199, -1313) def +bond1 33 +atom 36 (1) (-4100, 1908, -964) def +bond1 35 +atom 37 (6) (-3527, -2085, -141) def +bond1 31 +atom 38 (1) (-3647, -2708, 744) def +bond1 37 +atom 39 (1) (-3647, -2700, -1031) def +bond1 37 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 40 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 37 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part TRP_TRYPTOPHAN diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/TYR_TYROSINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/TYR_TYROSINE.mmp new file mode 100644 index 000000000..80a83a030 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/TYR_TYROSINE.mmp @@ -0,0 +1,108 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (12.530908) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (TYR_TYROSINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-4678, -1653, -216) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-5182, -1570, 663) def +bond1 1 +atom 3 (1) (-4881, -2428, -843) def +bond1 1 +atom 4 (6) (-3632, -632, -590) def +bond1 1 +atom 5 (1) (-3394, -8, 272) def +bond1 4 +atom 6 (6) (-4125, 347, -1695) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4731, -37, -2676) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3830, 1764, -1520) def +bond1 6 +atom 9 (1) (-4508, 2162, -958) def +bond1 8 +atom 10 (6) (-2283, -1282, -1029) def +bond1 4 +atom 11 (1) (-1522, -514, -1157) def +bond1 10 +atom 12 (1) (-2407, -1766, -1989) def +bond1 10 +atom 13 (6) (-1793, -2302, -18) def +info atom atomtype = sp2 +bond1 10 +atom 14 (6) (-1603, -3685, -415) def +info atom atomtype = sp2 +bond1 13 +atom 15 (1) (-1798, -3971, -1374) def +bond1 14 +atom 16 (6) (-1515, -1894, 1348) def +info atom atomtype = sp2 +bond1 13 +atom 17 (1) (-1649, -922, 1627) def +bond1 16 +atom 18 (6) (-1123, -4682, 574) def +info atom atomtype = sp2 +bond1 14 +atom 19 (1) (-989, -5654, 295) def +bond1 18 +atom 20 (6) (-1036, -2891, 2337) def +info atom atomtype = sp2 +bond1 16 +atom 21 (1) (-840, -2604, 3297) def +bond1 20 +atom 22 (6) (-840, -4285, 1950) def +info atom atomtype = sp2 +bond1 20 18 +atom 23 (8) (-366, -5259, 2936) def +bond1 22 +atom 24 (1) (524, -4914, 3234) def +bond1 23 +egroup (TYR_TYROSINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 25 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 26 (1) (-6647, -648, 393) def +bond1 25 +atom 27 (1) (-6234, -2264, -166) def +bond1 25 +atom 28 (6) (-4521, -878, -132) def +bond1 25 +atom 29 (1) (-4223, -240, 701) def +bond1 28 +atom 30 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 28 +atom 31 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 30 +atom 32 (8) (-3544, 1199, -1313) def +bond1 30 +atom 33 (1) (-4100, 1908, -964) def +bond1 32 +atom 34 (6) (-3527, -2085, -141) def +bond1 28 +atom 35 (1) (-3647, -2708, 744) def +bond1 34 +atom 36 (1) (-3647, -2700, -1031) def +bond1 34 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 37 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 34 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part TYR_TYROSINE diff --git a/cad/tests/AMBER_test_structures/mmp/AminoAcids/VAL_VALINE.mmp b/cad/tests/AMBER_test_structures/mmp/AminoAcids/VAL_VALINE.mmp new file mode 100644 index 000000000..01206dc6f --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/AminoAcids/VAL_VALINE.mmp @@ -0,0 +1,92 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (10.629864) (0.000000, 0.000000, 0.000000) (1.000000) +csys (HomeView1) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView1) (0.965474, 0.127192, -0.200452, 0.107242) (9.547311) (0.000000, 0.000000, 0.000000) (1.000000) +egroup (View Data) +group (VAL_VALINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (7) (-4678, -1653, -216) def +info atom atomtype = sp2(graphitic) +atom 2 (1) (-5182, -1570, 663) def +bond1 1 +atom 3 (1) (-4881, -2428, -843) def +bond1 1 +atom 4 (6) (-3632, -632, -590) def +bond1 1 +atom 5 (1) (-3394, -8, 272) def +bond1 4 +atom 6 (6) (-4125, 347, -1695) def +info atom atomtype = sp2 +bond1 4 +atom 7 (8) (-4731, -37, -2676) def +info atom atomtype = sp2 +bond2 6 +atom 8 (8) (-3830, 1764, -1520) def +bond1 6 +atom 9 (1) (-4508, 2162, -958) def +bond1 8 +atom 10 (6) (-2283, -1282, -1029) def +bond1 4 +atom 11 (1) (-1522, -514, -1157) def +bond1 10 +atom 12 (6) (-1773, -2343, 24) def +bond1 10 +atom 13 (1) (-1621, -1859, 979) def +bond1 12 +atom 14 (1) (-839, -2769, -317) def +bond1 12 +atom 15 (1) (-2510, -3128, 130) def +bond1 12 +atom 16 (6) (-2460, -1974, -2402) def +bond1 10 +atom 17 (1) (-3220, -2740, -2325) def +bond1 16 +atom 18 (1) (-1523, -2424, -2703) def +bond1 16 +atom 19 (1) (-2761, -1240, -3139) def +bond1 16 +egroup (VAL_VALINE) +end1 +group (Clipboard) +info opengroup open = False +group (Clipboard item 1) +info opengroup open = True +mol (Chunk1) def +atom 20 (7) (-5956, -1311, 53) def +info atom atomtype = sp2(graphitic) +atom 21 (1) (-6647, -648, 393) def +bond1 20 +atom 22 (1) (-6234, -2264, -166) def +bond1 20 +atom 23 (6) (-4521, -878, -132) def +bond1 20 +atom 24 (1) (-4223, -240, 701) def +bond1 23 +atom 25 (6) (-4335, -23, -1421) def +info atom atomtype = sp2 +bond1 23 +atom 26 (8) (-4820, -345, -2485) def +info atom atomtype = sp2 +bond2 25 +atom 27 (8) (-3544, 1199, -1313) def +bond1 25 +atom 28 (1) (-4100, 1908, -964) def +bond1 27 +atom 29 (6) (-3527, -2085, -141) def +bond1 23 +atom 30 (1) (-3647, -2708, 744) def +bond1 29 +atom 31 (1) (-3647, -2700, -1031) def +bond1 29 +mol (CYM_CYSTEINE_with_negative_charge.in_frag) def +atom 32 (16) (-1759, -1529, -132) def +info atom atomtype = sp2 +bond1 29 +egroup (Clipboard item 1) +egroup (Clipboard) +end molecular machine part VAL_VALINE diff --git a/cad/tests/AMBER_test_structures/mmp/Nucleotides/DA_D-ADENOSINE.mmp b/cad/tests/AMBER_test_structures/mmp/Nucleotides/DA_D-ADENOSINE.mmp new file mode 100644 index 000000000..a76e26fb5 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/Nucleotides/DA_D-ADENOSINE.mmp @@ -0,0 +1,97 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (8.306284) (-0.165303, 0.622569, 0.396058) (1.000000) +egroup (View Data) +group (DA_D-ADENOSINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (15) (72, -3515, 8066) def +info atom atomtype = sp3(p) +atom 2 (8) (-25, -3413, 6395) def +bond1 1 +atom 3 (8) (-710, -4900, 8578) def +bond1 1 +atom 4 (1) (-635, -5673, 8005) def +bond1 3 +atom 5 (8) (-689, -2188, 8735) def +info atom atomtype = sp2(-) +bond1 1 +atom 6 (8) (1421, -3545, 8466) def +info atom atomtype = sp2 +bond2 1 +atom 7 (6) (-1208, -2402, 4499) def +atom 8 (1) (-500, -2718, 3734) def +bond1 7 +atom 9 (6) (-931, -947, 4972) def +bond1 7 +atom 10 (1) (-898, -857, 6058) def +bond1 9 +atom 11 (8) (-2516, -2361, 3837) def +bond1 7 +atom 12 (6) (-3081, -1011, 3719) def +bond1 11 +atom 13 (1) (-3117, -830, 2645) def +bond1 12 +atom 14 (8) (370, -511, 4458) def +bond1 9 +atom 15 (1) (1087, -946, 4939) def +bond1 14 +atom 16 (6) (-2035, -56, 4364) def +bond1 9 12 +atom 17 (1) (-1623, 621, 3616) def +bond1 16 +atom 18 (1) (-2500, 557, 5134) def +bond1 16 +atom 19 (7) (-4446, -977, 4360) def +info atom atomtype = sp2(graphitic) +bond1 12 +atom 20 (6) (-5732, -552, 3719) def +info atom atomtype = sp2 +bond1 19 +atom 21 (6) (-6845, -709, 4758) def +info atom atomtype = sp2 +bond1 20 +atom 22 (6) (-4791, -1361, 5777) def +info atom atomtype = sp2 +bond1 19 +atom 23 (1) (-4065, -1692, 6514) def +bond1 22 +atom 24 (7) (-6270, -1218, 6052) def +info atom atomtype = sp2 +bond1 22 21 +atom 25 (7) (-6004, -45, 2333) def +info atom atomtype = sp2 +bond1 20 +atom 26 (6) (-8303, -357, 4391) def +info atom atomtype = sp2 +bond1 21 +atom 27 (6) (-7418, 389, 2017) def +info atom atomtype = sp2 +bond1 25 +atom 28 (1) (-7622, 896, 1077) def +bond1 27 +atom 29 (7) (-8556, 131, 2985) def +info atom atomtype = sp2 +bond1 27 26 +atom 30 (7) (-9421, -493, 5386) def +info atom atomtype = sp2(graphitic) +bond1 26 +atom 31 (1) (-9509, -1342, 5941) def +bond1 30 +atom 32 (1) (-10092, 262, 5507) def +bond1 30 +atom 33 (6) (-1286, -3450, 5649) def +bond1 2 7 +atom 34 (1) (-1391, -4457, 5267) def +bond1 33 +atom 35 (1) (-2098, -3237, 6332) def +bond1 33 +egroup (DA_D-ADENOSINE) +end1 +group (Clipboard) +info opengroup open = False +egroup (Clipboard) +end molecular machine part DA_D-ADENOSINE diff --git a/cad/tests/AMBER_test_structures/mmp/Nucleotides/DC_D-CYTOSINE.mmp b/cad/tests/AMBER_test_structures/mmp/Nucleotides/DC_D-CYTOSINE.mmp new file mode 100644 index 000000000..a9c1c7e8c --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/Nucleotides/DC_D-CYTOSINE.mmp @@ -0,0 +1,91 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (11.446953) (0.314756, -0.570569, -1.063136) (1.000000) +egroup (View Data) +group (DC_D-CYTOSINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (15) (110, -3534, 8075) def +info atom atomtype = sp3(p) +atom 2 (8) (-14, -3416, 6407) def +bond1 1 +atom 3 (8) (-673, -4917, 8589) def +bond1 1 +atom 4 (1) (-618, -5685, 8006) def +bond1 3 +atom 5 (8) (-629, -2207, 8768) def +info atom atomtype = sp2(-) +bond1 1 +atom 6 (8) (1466, -3577, 8453) def +info atom atomtype = sp2 +bond2 1 +atom 7 (6) (-1227, -2404, 4531) def +atom 8 (1) (-526, -2716, 3758) def +bond1 7 +atom 9 (6) (-950, -949, 5003) def +bond1 7 +atom 10 (1) (-914, -858, 6089) def +bond1 9 +atom 11 (8) (-2542, -2366, 3885) def +bond1 7 +atom 12 (6) (-3069, -1009, 3692) def +bond1 11 +atom 13 (1) (-3004, -854, 2616) def +bond1 12 +atom 14 (8) (348, -511, 4485) def +bond1 9 +atom 15 (1) (1067, -953, 4956) def +bond1 14 +atom 16 (6) (-2058, -58, 4396) def +bond1 9 12 +atom 17 (1) (-1640, 652, 3684) def +bond1 16 +atom 18 (1) (-2552, 521, 5175) def +bond1 16 +atom 19 (7) (-4488, -936, 4216) def +info atom atomtype = sp2(graphitic) +bond1 12 +atom 20 (6) (-1286, -3454, 5681) def +bond1 2 7 +atom 21 (1) (-1395, -4467, 5296) def +bond1 20 +atom 22 (1) (-2092, -3243, 6381) def +bond1 20 +atom 23 (6) (-4774, -1301, 5653) def +info atom atomtype = sp2 +bond1 19 +atom 24 (1) (-3967, -1608, 6313) def +bond1 23 +atom 25 (6) (-6224, -1228, 6192) def +info atom atomtype = sp2 +bond1 23 +atom 26 (1) (-6469, -1612, 7179) def +bond1 25 +atom 27 (6) (-5622, -500, 3313) def +info atom atomtype = sp2 +bond1 19 +atom 28 (7) (-7056, -328, 3822) def +info atom atomtype = sp2 +bond1 27 +atom 29 (6) (-7314, -594, 5295) def +info atom atomtype = sp2 +bond1 25 28 +atom 30 (7) (-8752, -538, 5739) def +info atom atomtype = sp2(graphitic) +bond1 29 +atom 31 (1) (-9006, -823, 6681) def +bond1 30 +atom 32 (1) (-9470, -215, 5097) def +bond1 30 +atom 33 (8) (-5393, -284, 2173) def +info atom atomtype = sp2 +bond2 27 +egroup (DC_D-CYTOSINE) +end1 +group (Clipboard) +info opengroup open = False +egroup (Clipboard) +end molecular machine part DC_D-CYTOSINE diff --git a/cad/tests/AMBER_test_structures/mmp/Nucleotides/DG_G-GUANOSINE.mmp b/cad/tests/AMBER_test_structures/mmp/Nucleotides/DG_G-GUANOSINE.mmp new file mode 100644 index 000000000..baa0e46e9 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/Nucleotides/DG_G-GUANOSINE.mmp @@ -0,0 +1,100 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (6.718170) (1.114212, -0.349788, -1.247040) (1.000000) +egroup (View Data) +group (DG_G-GUANOSINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (15) (72, -3515, 8066) def +info atom atomtype = sp3(p) +atom 2 (8) (-25, -3413, 6395) def +bond1 1 +atom 3 (8) (-710, -4900, 8578) def +bond1 1 +atom 4 (1) (-635, -5673, 8005) def +bond1 3 +atom 5 (8) (-689, -2188, 8735) def +info atom atomtype = sp2(-) +bond1 1 +atom 6 (8) (1421, -3545, 8466) def +info atom atomtype = sp2 +bond2 1 +atom 7 (6) (-1208, -2402, 4499) def +atom 8 (1) (-500, -2718, 3734) def +bond1 7 +atom 9 (6) (-931, -947, 4972) def +bond1 7 +atom 10 (1) (-898, -857, 6058) def +bond1 9 +atom 11 (8) (-2516, -2361, 3837) def +bond1 7 +atom 12 (6) (-3081, -1011, 3719) def +bond1 11 +atom 13 (1) (-3117, -830, 2645) def +bond1 12 +atom 14 (8) (370, -511, 4458) def +bond1 9 +atom 15 (1) (1087, -946, 4939) def +bond1 14 +atom 16 (6) (-2035, -56, 4364) def +bond1 9 12 +atom 17 (1) (-1623, 621, 3616) def +bond1 16 +atom 18 (1) (-2500, 557, 5134) def +bond1 16 +atom 19 (7) (-4446, -977, 4360) def +info atom atomtype = sp2(graphitic) +bond1 12 +atom 20 (6) (-5732, -552, 3719) def +info atom atomtype = sp2 +bond1 19 +atom 21 (6) (-6845, -709, 4758) def +info atom atomtype = sp2 +bond1 20 +atom 22 (6) (-4791, -1361, 5777) def +info atom atomtype = sp2 +bond1 19 +atom 23 (1) (-4065, -1692, 6514) def +bond1 22 +atom 24 (7) (-6270, -1218, 6052) def +info atom atomtype = sp2 +bond1 22 21 +atom 25 (7) (-6004, -45, 2333) def +info atom atomtype = sp2 +bond1 20 +atom 26 (6) (-8303, -357, 4391) def +info atom atomtype = sp2 +bond1 21 +atom 27 (6) (-7418, 389, 2017) def +info atom atomtype = sp2 +bond1 25 +atom 28 (7) (-8556, 131, 2985) def +info atom atomtype = sp2(graphitic) +bond1 27 26 +atom 29 (6) (-1286, -3450, 5649) def +bond1 2 7 +atom 30 (1) (-1391, -4457, 5267) def +bond1 29 +atom 31 (1) (-2098, -3237, 6332) def +bond1 29 +atom 32 (8) (-9346, -484, 5320) def +info atom atomtype = sp2 +bond2 26 +atom 33 (7) (-7676, 1032, 826) def +info atom atomtype = sp2(graphitic) +bond1 27 +atom 34 (1) (-6985, 1195, 227) def +bond1 33 +atom 35 (1) (-8543, 1302, 622) def +bond1 33 +atom 36 (1) (-9435, 274, 2717) def +bond1 28 +egroup (DG_G-GUANOSINE) +end1 +group (Clipboard) +info opengroup open = False +egroup (Clipboard) +end molecular machine part DG_G-GUANOSINE diff --git a/cad/tests/AMBER_test_structures/mmp/Nucleotides/DT_D-THYMINE.mmp b/cad/tests/AMBER_test_structures/mmp/Nucleotides/DT_D-THYMINE.mmp new file mode 100644 index 000000000..8fd324709 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/Nucleotides/DT_D-THYMINE.mmp @@ -0,0 +1,95 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (13.775312) (0.216567, -0.301530, -1.662551) (1.000000) +egroup (View Data) +group (DT_D-THYMINE) +info opengroup open = True +mol (Chunk1) def +atom 1 (15) (110, -3534, 8075) def +info atom atomtype = sp3(p) +atom 2 (8) (-14, -3416, 6407) def +bond1 1 +atom 3 (8) (-673, -4917, 8589) def +bond1 1 +atom 4 (1) (-618, -5685, 8006) def +bond1 3 +atom 5 (8) (-629, -2207, 8768) def +info atom atomtype = sp2(-) +bond1 1 +atom 6 (8) (1466, -3577, 8453) def +info atom atomtype = sp2 +bond2 1 +atom 7 (6) (-1227, -2404, 4531) def +atom 8 (1) (-526, -2716, 3758) def +bond1 7 +atom 9 (6) (-950, -949, 5003) def +bond1 7 +atom 10 (1) (-914, -858, 6089) def +bond1 9 +atom 11 (8) (-2542, -2366, 3885) def +bond1 7 +atom 12 (6) (-3069, -1009, 3692) def +bond1 11 +atom 13 (1) (-3004, -854, 2616) def +bond1 12 +atom 14 (8) (348, -511, 4485) def +bond1 9 +atom 15 (1) (1067, -953, 4956) def +bond1 14 +atom 16 (6) (-2058, -58, 4396) def +bond1 9 12 +atom 17 (1) (-1640, 652, 3684) def +bond1 16 +atom 18 (1) (-2552, 521, 5175) def +bond1 16 +atom 19 (7) (-4488, -936, 4216) def +info atom atomtype = sp2(graphitic) +bond1 12 +atom 20 (6) (-1286, -3454, 5681) def +bond1 2 7 +atom 21 (1) (-1395, -4467, 5296) def +bond1 20 +atom 22 (1) (-2092, -3243, 6381) def +bond1 20 +atom 23 (6) (-4774, -1301, 5653) def +info atom atomtype = sp2 +bond1 19 +atom 24 (1) (-3967, -1608, 6313) def +bond1 23 +atom 25 (6) (-6224, -1228, 6192) def +info atom atomtype = sp2 +bond1 23 +atom 26 (6) (-5622, -500, 3313) def +info atom atomtype = sp2 +bond1 19 +atom 27 (7) (-7056, -328, 3822) def +info atom atomtype = sp2(graphitic) +bond1 26 +atom 28 (6) (-7314, -594, 5295) def +info atom atomtype = sp2 +bond1 25 27 +atom 29 (8) (-5393, -284, 2173) def +info atom atomtype = sp2 +bond2 26 +atom 30 (8) (-8653, -542, 5709) def +info atom atomtype = sp2 +bond2 28 +atom 31 (6) (-6568, -1768, 7580) def +bond1 25 +atom 32 (1) (-6333, -2823, 7625) def +bond1 31 +atom 33 (1) (-7623, -1625, 7771) def +bond1 31 +atom 34 (1) (-5991, -1238, 8327) def +bond1 31 +atom 35 (1) (-7730, -70, 3236) def +bond1 27 +egroup (DT_D-THYMINE) +end1 +group (Clipboard) +info opengroup open = False +egroup (Clipboard) +end molecular machine part DT_D-THYMINE diff --git a/cad/tests/AMBER_test_structures/mmp/Nucleotides/RU_R-URACIL.mmp b/cad/tests/AMBER_test_structures/mmp/Nucleotides/RU_R-URACIL.mmp new file mode 100644 index 000000000..3721d8db4 --- /dev/null +++ b/cad/tests/AMBER_test_structures/mmp/Nucleotides/RU_R-URACIL.mmp @@ -0,0 +1,91 @@ +mmpformat 080327 required; 080529 preferred +kelvin 300 +group (View Data) +info opengroup open = True +csys (HomeView) (1.000000, 0.000000, 0.000000, 0.000000) (10.000000) (0.000000, 0.000000, 0.000000) (1.000000) +csys (LastView) (1.000000, 0.000000, 0.000000, 0.000000) (9.364035) (-2.007325, -0.140143, -0.191514) (1.000000) +egroup (View Data) +group (RU_R-URACIL) +info opengroup open = True +mol (Chunk1) def +atom 1 (15) (110, -3534, 8075) def +info atom atomtype = sp3(p) +atom 2 (8) (-14, -3416, 6407) def +bond1 1 +atom 3 (8) (-673, -4917, 8589) def +bond1 1 +atom 4 (1) (-618, -5685, 8006) def +bond1 3 +atom 5 (8) (-629, -2207, 8768) def +info atom atomtype = sp2(-) +bond1 1 +atom 6 (8) (1466, -3577, 8453) def +info atom atomtype = sp2 +bond2 1 +atom 7 (6) (-1227, -2404, 4531) def +atom 8 (1) (-526, -2716, 3758) def +bond1 7 +atom 9 (6) (-950, -949, 5003) def +bond1 7 +atom 10 (1) (-914, -858, 6089) def +bond1 9 +atom 11 (8) (-2542, -2366, 3885) def +bond1 7 +atom 12 (6) (-3069, -1009, 3692) def +bond1 11 +atom 13 (1) (-3004, -854, 2616) def +bond1 12 +atom 14 (8) (348, -511, 4485) def +bond1 9 +atom 15 (1) (1067, -953, 4956) def +bond1 14 +atom 16 (6) (-2058, -58, 4396) def +bond1 9 12 +atom 17 (1) (-2552, 521, 5175) def +bond1 16 +atom 18 (7) (-4488, -936, 4216) def +info atom atomtype = sp2(graphitic) +bond1 12 +atom 19 (6) (-1286, -3454, 5681) def +bond1 2 7 +atom 20 (1) (-1395, -4467, 5296) def +bond1 19 +atom 21 (1) (-2092, -3243, 6381) def +bond1 19 +atom 22 (6) (-4774, -1301, 5653) def +info atom atomtype = sp2 +bond1 18 +atom 23 (1) (-3967, -1608, 6313) def +bond1 22 +atom 24 (6) (-6224, -1228, 6192) def +info atom atomtype = sp2 +bond1 22 +atom 25 (6) (-5622, -500, 3313) def +info atom atomtype = sp2 +bond1 18 +atom 26 (7) (-7056, -328, 3822) def +info atom atomtype = sp2(graphitic) +bond1 25 +atom 27 (6) (-7314, -594, 5295) def +info atom atomtype = sp2 +bond1 24 26 +atom 28 (8) (-5393, -284, 2173) def +info atom atomtype = sp2 +bond2 25 +atom 29 (8) (-8653, -542, 5709) def +info atom atomtype = sp2 +bond2 27 +atom 30 (1) (-7730, -70, 3236) def +bond1 26 +atom 31 (8) (-1496, 898, 3438) def +bond1 16 +atom 32 (0) (-1049, 1273, 3802) def +bond1 31 +atom 33 (1) (-6453, -1588, 7118) def +bond1 24 +egroup (RU_R-URACIL) +end1 +group (Clipboard) +info opengroup open = False +egroup (Clipboard) +end molecular machine part RU_R-URACIL -- cgit v1.2.3