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fix PRO and all P-peptides (#38)
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fixed wrong PRO restraints: N atom was considered sp2
now all P-peptides have two hydrogen at N (charge +1)
DEL-HNP modification updated accordingly
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@keitaroyam
keitaroyam authored Feb 16, 2024
1 parent ec41608 commit 828e23c
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282 changes: 158 additions & 124 deletions 0/037.cif
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Expand Up @@ -7,76 +7,108 @@ _chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
037 037 "(1S,3aR,6aS)-octahydrocyclopenta[c]pyrrole-1-carboxylic acid" P-peptide 23 11 .
037 037 "(1S,3aR,6aS)-octahydrocyclopenta[c]pyrrole-1-carboxylic acid" P-peptide 24 11 .

data_comp_037
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
037 C C C 0 1.952 0.458 -0.691
037 N N NT1 0 0.529 -1.584 -0.523
037 O O O 0 2.659 0.145 0.251
037 CA C CH1 0 0.531 -0.125 -0.743
037 CB C CH1 0 -0.367 0.358 0.407
037 CG C CH1 0 -1.407 -0.777 0.587
037 CBE C CH2 0 -1.185 1.638 0.153
037 CBF C CH2 0 -2.644 1.241 0.352
037 CD C CH2 0 -0.829 -1.987 -0.143
037 CD2 C CH2 0 -2.695 -0.210 -0.029
037 OXT O OC -1 2.285 1.200 -1.598
037 H H H 0 0.746 -2.015 -1.271
037 HA H H 0 0.105 0.100 -1.606
037 HB2 H H 0 0.159 0.467 1.240
037 HG2 H H 0 -1.550 -0.970 1.544
037 HBE H H 0 -1.040 1.967 -0.759
037 HBEA H H 0 -0.931 2.340 0.788
037 HBF H H 0 -3.234 1.774 -0.221
037 HBFA H H 0 -2.916 1.367 1.286
037 HD2 H H 0 -0.798 -2.767 0.442
037 HD3 H H 0 -1.351 -2.208 -0.937
037 H1 H H 0 -3.487 -0.646 0.350
037 HD2A H H 0 -2.698 -0.315 -1.003
037 C C C C 0 1.962 0.497 -0.664
037 N N N NT2 1 0.585 -1.580 -0.548
037 O O O O 0 2.690 0.159 0.297
037 CA CA C CH1 0 0.553 -0.093 -0.728
037 CB CB C CH1 0 -0.389 0.385 0.402
037 CG CG C CH1 0 -1.394 -0.786 0.576
037 CBE CBE C CH2 0 -1.239 1.647 0.170
037 CBF CBF C CH2 0 -2.672 1.232 0.421
037 CD CD1 C CH2 0 -0.810 -1.987 -0.184
037 CD2 CD2 C CH2 0 -2.716 -0.221 0.032
037 OXT OXT O OC -1 2.304 1.283 -1.576
037 H H H H 0 0.848 -1.978 -1.320
037 H2 H2 H H 0 1.170 -1.812 0.108
037 HA HA H H 0 0.133 0.129 -1.593
037 HB2 HB2 H H 0 0.133 0.503 1.237
037 HG2 HG2 H H 0 -1.481 -1.017 1.529
037 HBE HBE H H 0 -1.135 1.971 -0.749
037 HBEA HBEA H H 0 -0.979 2.359 0.792
037 HBF HBF H H 0 -3.303 1.771 -0.138
037 HBFA HBFA H H 0 -2.916 1.352 1.383
037 HD2 HD2 H H 0 -0.790 -2.794 0.390
037 HD3 HD3 H H 0 -1.333 -2.181 -1.002
037 H1 H1 H H 0 -3.483 -0.669 0.442
037 HD2A HD2A H H 0 -2.764 -0.314 -0.942

loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
037 C C(C[5]C[5,5]N[5]H)(O)2
037 N N[5](C[5]C[5,5]CH)(C[5]C[5,5]HH)(H)2{2|C<4>,2|H<1>}
037 O O(CC[5]O)
037 CA C[5](C[5,5]C[5,5]C[5]H)(N[5]C[5]HH)(COO)(H){2|C<4>,5|H<1>}
037 CB C[5,5](C[5,5]C[5]2H)(C[5]C[5]HH)(C[5]N[5]CH)(H){8|H<1>}
037 CG C[5,5](C[5,5]C[5]2H)(C[5]C[5]HH)(C[5]N[5]HH)(H){1|C<3>,7|H<1>}
037 CBE C[5](C[5,5]C[5,5]C[5]H)(C[5]C[5]HH)(H)2{1|C<3>,1|C<4>,1|N<4>,4|H<1>}
037 CBF C[5](C[5]C[5,5]HH)2(H)2{2|C<4>,2|H<1>}
037 CD C[5](C[5,5]C[5,5]C[5]H)(N[5]C[5]HH)(H)2{1|C<3>,2|C<4>,4|H<1>}
037 CD2 C[5](C[5,5]C[5,5]C[5]H)(C[5]C[5]HH)(H)2{1|C<4>,1|N<4>,5|H<1>}
037 OXT O(CC[5]O)
037 H H(N[5]C[5]2H)
037 H2 H(N[5]C[5]2H)
037 HA H(C[5]C[5,5]N[5]C)
037 HB2 H(C[5,5]C[5,5]C[5]2)
037 HG2 H(C[5,5]C[5,5]C[5]2)
037 HBE H(C[5]C[5,5]C[5]H)
037 HBEA H(C[5]C[5,5]C[5]H)
037 HBF H(C[5]C[5]2H)
037 HBFA H(C[5]C[5]2H)
037 HD2 H(C[5]C[5,5]N[5]H)
037 HD3 H(C[5]C[5,5]N[5]H)
037 H1 H(C[5]C[5,5]C[5]H)
037 HD2A H(C[5]C[5,5]C[5]H)

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.aromatic
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.value_dist_nucleus
_chem_comp_bond.value_dist_nucleus_esd
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
037 C O DOUBLE n 1.218 0.0200 1.218 0.0200
037 C CA SINGLE n 1.536 0.0100 1.536 0.0100
037 N CD SINGLE n 1.466 0.0155 1.466 0.0155
037 N CA SINGLE n 1.478 0.0111 1.478 0.0111
037 CA CB SINGLE n 1.539 0.0139 1.539 0.0139
037 CB CG SINGLE n 1.546 0.0136 1.546 0.0136
037 CB CBE SINGLE n 1.536 0.0113 1.536 0.0113
037 CG CD SINGLE n 1.524 0.0101 1.524 0.0101
037 CG CD2 SINGLE n 1.538 0.0100 1.538 0.0100
037 CBE CBF SINGLE n 1.520 0.0200 1.520 0.0200
037 CBF CD2 SINGLE n 1.507 0.0183 1.507 0.0183
037 C OXT SINGLE n 1.218 0.0200 1.218 0.0200
037 N H SINGLE n 1.036 0.0160 0.890 0.0200
037 CA HA SINGLE n 1.089 0.0100 0.988 0.0200
037 CB HB2 SINGLE n 1.089 0.0100 0.992 0.0108
037 CG HG2 SINGLE n 1.089 0.0100 0.987 0.0121
037 CBE HBE SINGLE n 1.089 0.0100 0.980 0.0135
037 CBE HBEA SINGLE n 1.089 0.0100 0.980 0.0135
037 CBF HBF SINGLE n 1.089 0.0100 0.981 0.0129
037 CBF HBFA SINGLE n 1.089 0.0100 0.981 0.0129
037 CD HD2 SINGLE n 1.089 0.0100 0.975 0.0121
037 CD HD3 SINGLE n 1.089 0.0100 0.975 0.0121
037 CD2 H1 SINGLE n 1.089 0.0100 0.980 0.0105
037 CD2 HD2A SINGLE n 1.089 0.0100 0.980 0.0105
037 C O DOUBLE n 1.252 0.0117 1.252 0.0117
037 C CA SINGLE n 1.527 0.0122 1.527 0.0122
037 N CD SINGLE n 1.499 0.0125 1.499 0.0125
037 N CA SINGLE n 1.498 0.0129 1.498 0.0129
037 CA CB SINGLE n 1.546 0.0150 1.546 0.0150
037 CB CG SINGLE n 1.551 0.0129 1.551 0.0129
037 CB CBE SINGLE n 1.535 0.0145 1.535 0.0145
037 CG CD SINGLE n 1.535 0.0107 1.535 0.0107
037 CG CD2 SINGLE n 1.539 0.0102 1.539 0.0102
037 CBE CBF SINGLE n 1.510 0.0200 1.510 0.0200
037 CBF CD2 SINGLE n 1.510 0.0200 1.510 0.0200
037 C OXT SINGLE n 1.252 0.0117 1.252 0.0117
037 N H SINGLE n 1.018 0.0520 0.908 0.0200
037 N H2 SINGLE n 1.018 0.0520 0.908 0.0200
037 CA HA SINGLE n 1.092 0.0100 0.987 0.0188
037 CB HB2 SINGLE n 1.092 0.0100 0.991 0.0100
037 CG HG2 SINGLE n 1.092 0.0100 0.984 0.0100
037 CBE HBE SINGLE n 1.092 0.0100 0.980 0.0150
037 CBE HBEA SINGLE n 1.092 0.0100 0.980 0.0150
037 CBF HBF SINGLE n 1.092 0.0100 1.000 0.0200
037 CBF HBFA SINGLE n 1.092 0.0100 1.000 0.0200
037 CD HD2 SINGLE n 1.092 0.0100 0.990 0.0100
037 CD HD3 SINGLE n 1.092 0.0100 0.990 0.0100
037 CD2 H1 SINGLE n 1.092 0.0100 0.979 0.0106
037 CD2 HD2A SINGLE n 1.092 0.0100 0.979 0.0106

loop_
_chem_comp_angle.comp_id
Expand All @@ -85,54 +117,57 @@ _chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
037 O C CA 117.484 3.00
037 O C OXT 125.032 1.50
037 CA C OXT 117.484 3.00
037 CD N CA 109.056 3.00
037 CD N H 107.991 2.32
037 CA N H 110.603 3.00
037 C CA N 111.420 2.45
037 C CA CB 112.773 2.71
037 C CA HA 110.011 1.50
037 N CA CB 103.016 1.95
037 N CA HA 111.303 3.00
037 CB CA HA 109.110 1.50
037 CA CB CG 104.802 1.87
037 CA CB CBE 116.412 3.00
037 CA CB HB2 110.785 1.50
037 CG CB CBE 104.606 1.50
037 CG CB HB2 110.523 2.79
037 CBE CB HB2 109.658 2.16
037 CB CG CD 104.314 1.50
037 CB CG CD2 104.606 1.50
037 CB CG HG2 110.523 2.79
037 CD CG CD2 114.013 1.50
037 CD CG HG2 111.202 1.50
037 CD2 CG HG2 109.658 2.16
037 CB CBE CBF 104.282 1.50
037 CB CBE HBE 110.793 1.50
037 CB CBE HBEA 110.793 1.50
037 CBF CBE HBE 110.933 1.77
037 CBF CBE HBEA 110.933 1.77
037 HBE CBE HBEA 109.306 1.50
037 CBE CBF CD2 104.636 2.09
037 CBE CBF HBF 110.938 1.53
037 CBE CBF HBFA 110.938 1.53
037 CD2 CBF HBF 110.938 1.53
037 CD2 CBF HBFA 110.938 1.53
037 HBF CBF HBFA 108.664 1.50
037 N CD CG 103.016 1.95
037 N CD HD2 110.320 1.50
037 N CD HD3 110.320 1.50
037 CG CD HD2 111.084 1.50
037 CG CD HD3 111.084 1.50
037 HD2 CD HD3 108.987 1.50
037 CG CD2 CBF 104.282 1.50
037 CG CD2 H1 110.855 1.50
037 CG CD2 HD2A 110.855 1.50
037 CBF CD2 H1 110.933 1.77
037 CBF CD2 HD2A 110.933 1.77
037 H1 CD2 HD2A 109.306 1.50
037 O C CA 117.661 3.00
037 O C OXT 124.677 2.17
037 CA C OXT 117.661 3.00
037 CD N CA 107.534 2.54
037 CD N H 110.919 1.50
037 CD N H2 110.919 1.50
037 CA N H 109.756 3.00
037 CA N H2 109.756 3.00
037 H N H2 108.287 3.00
037 C CA N 110.160 1.67
037 C CA CB 112.760 3.00
037 C CA HA 108.696 3.00
037 N CA CB 103.888 3.00
037 N CA HA 109.430 1.50
037 CB CA HA 107.735 1.69
037 CA CB CG 104.797 3.00
037 CA CB CBE 119.030 1.50
037 CA CB HB2 110.134 2.27
037 CG CB CBE 105.009 2.26
037 CG CB HB2 110.949 3.00
037 CBE CB HB2 110.134 3.00
037 CB CG CD 105.306 3.00
037 CB CG CD2 105.009 2.26
037 CB CG HG2 110.949 3.00
037 CD CG CD2 115.616 2.74
037 CD CG HG2 110.256 3.00
037 CD2 CG HG2 110.897 1.50
037 CB CBE CBF 104.590 1.83
037 CB CBE HBE 110.853 1.69
037 CB CBE HBEA 110.853 1.69
037 CBF CBE HBE 110.664 3.00
037 CBF CBE HBEA 110.664 3.00
037 HBE CBE HBEA 109.370 2.57
037 CBE CBF CD2 104.574 3.00
037 CBE CBF HBF 110.973 2.86
037 CBE CBF HBFA 110.973 2.86
037 CD2 CBF HBF 110.973 2.86
037 CD2 CBF HBFA 110.973 2.86
037 HBF CBF HBFA 108.686 2.00
037 N CD CG 103.888 3.00
037 N CD HD2 109.644 2.45
037 N CD HD3 109.644 2.45
037 CG CD HD2 110.802 1.50
037 CG CD HD3 110.802 1.50
037 HD2 CD HD3 109.110 1.50
037 CG CD2 CBF 104.625 1.50
037 CG CD2 H1 110.837 1.50
037 CG CD2 HD2A 110.837 1.50
037 CBF CD2 H1 110.664 3.00
037 CBF CD2 HD2A 110.664 3.00
037 H1 CD2 HD2A 109.370 2.57

loop_
_chem_comp_tor.comp_id
Expand All @@ -144,16 +179,16 @@ _chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
037 sp2_sp3_1 O C CA N 0.000 10.0 6
037 sp3_sp3_63 C CA N CD 60.000 10.0 3
037 sp3_sp3_1 CG CD N CA 60.000 10.0 3
037 sp3_sp3_28 C CA CB CG 180.000 10.0 3
037 sp3_sp3_16 CA CB CG CD 60.000 10.0 3
037 sp3_sp3_70 CA CB CBE CBF 60.000 10.0 3
037 sp3_sp3_7 N CD CG CB -60.000 10.0 3
037 sp3_sp3_34 CBF CD2 CG CB -60.000 10.0 3
037 sp3_sp3_52 CB CBE CBF CD2 -60.000 10.0 3
037 sp3_sp3_43 CBE CBF CD2 CG 60.000 10.0 3
037 sp2_sp3_1 O C CA N 0.000 10.0 6
037 sp3_sp3_67 C CA N CD 60.000 10.0 3
037 sp3_sp3_1 CG CD N CA 60.000 10.0 3
037 sp3_sp3_31 C CA CB CG 180.000 10.0 3
037 sp3_sp3_19 CA CB CG CD 60.000 10.0 3
037 sp3_sp3_76 CA CB CBE CBF 60.000 10.0 3
037 sp3_sp3_10 N CD CG CB -60.000 10.0 3
037 sp3_sp3_37 CBF CD2 CG CB -60.000 10.0 3
037 sp3_sp3_55 CB CBE CBF CD2 -60.000 10.0 3
037 sp3_sp3_46 CBE CBF CD2 CG 60.000 10.0 3

loop_
_chem_comp_chir.comp_id
Expand All @@ -163,19 +198,18 @@ _chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
037 chir_1 CA N C CB positive
037 chir_1 CA N C CB positive
037 chir_2 CB CA CG CBE positive
037 chir_3 CG CD CB CD2 negative
037 chir_4 N CA CD H both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
037 plan-1 C 0.020
037 plan-1 CA 0.020
037 plan-1 O 0.020
037 plan-1 C 0.020
037 plan-1 CA 0.020
037 plan-1 O 0.020
037 plan-1 OXT 0.020

loop_
Expand All @@ -184,20 +218,20 @@ _pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
037 SMILES ACDLabs 12.01 O=C(O)C1NCC2CCCC12
037 InChI InChI 1.03 InChI=1S/C8H13NO2/c10-8(11)7-6-3-1-2-5(6)4-9-7/h5-7,9H,1-4H2,(H,10,11)/t5-,6-,7-/m0/s1
037 InChIKey InChI 1.03 KWRNCAUXSJOYQO-ACZMJKKPSA-N
037 SMILES_CANONICAL CACTVS 3.370 OC(=O)[C@H]1NC[C@@H]2CCC[C@H]12
037 SMILES CACTVS 3.370 OC(=O)[CH]1NC[CH]2CCC[CH]12
037 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 C1C[C@H]2CN[C@@H]([C@H]2C1)C(=O)O
037 SMILES "OpenEye OEToolkits" 1.7.2 C1CC2CNC(C2C1)C(=O)O
037 SMILES ACDLabs 12.01 "O=C(O)C1NCC2CCCC12"
037 InChI InChI 1.03 "InChI=1S/C8H13NO2/c10-8(11)7-6-3-1-2-5(6)4-9-7/h5-7,9H,1-4H2,(H,10,11)/t5-,6-,7-/m0/s1"
037 InChIKey InChI 1.03 KWRNCAUXSJOYQO-ACZMJKKPSA-N
037 SMILES_CANONICAL CACTVS 3.370 "OC(=O)[C@H]1NC[C@@H]2CCC[C@H]12"
037 SMILES CACTVS 3.370 "OC(=O)[CH]1NC[CH]2CCC[CH]12"
037 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C1C[C@H]2CN[C@@H]([C@H]2C1)C(=O)O"
037 SMILES "OpenEye OEToolkits" 1.7.2 "C1CC2CNC(C2C1)C(=O)O"

loop_
_pdbx_chem_comp_description_generator.comp_id
_pdbx_chem_comp_description_generator.program_name
_pdbx_chem_comp_description_generator.program_version
_pdbx_chem_comp_description_generator.descriptor
037 acedrg 243 "dictionary generator"
037 acedrg_database 11 "data source"
037 rdkit 2017.03.2 "Chemoinformatics tool"
037 refmac5 5.8.0238 "optimization tool"
037 acedrg 281 "dictionary generator"
037 acedrg_database 12 "data source"
037 rdkit 2019.09.1 "Chemoinformatics tool"
037 refmac5 5.8.0419 "optimization tool"
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