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reflecting changes in CCD #62

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Merged
keitaroyam merged 2 commits into from
Apr 18, 2025
Merged

reflecting changes in CCD #62

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5518466
reflecting changes in CCD
keitaroyam Mar 2, 2025
b9eba0f
7YO and others corrected using Acedrg 317
keitaroyam Apr 9, 2025
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504 changes: 288 additions & 216 deletions 0/0TJ.cif
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470 changes: 266 additions & 204 deletions 2/2MA.cif
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794 changes: 448 additions & 346 deletions 2/2N2.cif
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384 changes: 217 additions & 167 deletions 2/2UC.cif
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544 changes: 310 additions & 234 deletions 4/4M9.cif
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443 changes: 254 additions & 189 deletions 5/56J.cif
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204 changes: 114 additions & 90 deletions 5/5VV.cif
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ _chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
5VV 5VV N-carbamoyl-L-Asparagine NON-POLYMER 19 11 .
5VV 5VV N-carbamoyl-L-Asparagine NON-POLYMER 19 12 .

data_comp_5VV
loop_
Expand All @@ -20,54 +20,78 @@ _chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
5VV N N N NH1 0 -13.297 -15.836 37.778
5VV C9 C9 C C 0 -12.095 -16.357 38.115
5VV O10 O10 O OH1 0 -11.602 -15.838 39.250
5VV O11 O11 O O 0 -11.518 -17.205 37.472
5VV CA CA C CH1 0 -13.987 -14.812 38.549
5VV CB CB C CH2 0 -15.090 -14.115 37.747
5VV CG CG C C 0 -14.549 -13.394 36.526
5VV ND2 ND2 N NH2 0 -15.425 -12.713 35.803
5VV OD1 OD1 O O 0 -13.357 -13.452 36.227
5VV C C C C1 0 -14.594 -15.401 39.835
5VV O O O O 0 -14.296 -14.958 40.900
5VV H H1 H H 0 -13.686 -16.138 37.054
5VV H10 H2 H H 0 -11.108 -15.133 39.221
5VV HA H3 H H 0 -13.334 -14.118 38.807
5VV H4 H4 H H 0 -15.545 -13.469 38.325
5VV H5 H5 H H 0 -15.746 -14.783 37.461
5VV H6 H6 H H 0 -16.277 -12.690 36.041
5VV H7 H7 H H 0 -15.160 -12.280 35.079
5VV H8 H8 H H 0 -15.207 -16.120 39.774
5VV N N N NH1 0 0.712 0.416 -0.589
5VV C9 C9 C C 0 1.956 0.956 -0.490
5VV O10 O10 O OH1 0 2.120 2.070 -1.189
5VV O11 O11 O O 0 2.862 0.488 0.174
5VV CA CA C CH1 0 0.299 -0.780 0.126
5VV CB CB C CH2 0 -1.225 -0.886 0.284
5VV CG CG C C 0 -1.794 0.198 1.179
5VV ND2 ND2 N NH2 0 -2.149 1.349 0.618
5VV OD1 OD1 O O 0 -1.916 -0.009 2.391
5VV C C C C 0 0.838 -2.049 -0.564
5VV O O O O 0 0.738 -2.134 -1.812
5VV OXT OXT O OC -1 1.344 -2.922 0.179
5VV H H H H 0 0.134 0.799 -1.125
5VV H10 H10 H H 0 1.464 2.347 -1.626
5VV HA HA H H 0 0.699 -0.733 1.029
5VV H4 H4 H H 0 -1.642 -0.826 -0.599
5VV H5 H5 H H 0 -1.446 -1.761 0.664
5VV H6 H6 H H 0 -2.486 1.993 1.127
5VV H7 H7 H H 0 -2.056 1.495 -0.255

loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
5VV N N(CCCH)(COO)(H)
5VV C9 C(NCH)(OH)(O)
5VV O10 O(CNO)(H)
5VV O11 O(CNO)
5VV CA C(CCHH)(COO)(NCH)(H)
5VV CB C(CCHN)(CNO)(H)2
5VV CG C(CCHH)(NHH)(O)
5VV ND2 N(CCO)(H)2
5VV OD1 O(CCN)
5VV C C(CCHN)(O)2
5VV O O(CCO)
5VV OXT O(CCO)
5VV H H(NCC)
5VV H10 H(OC)
5VV HA H(CCCN)
5VV H4 H(CCCH)
5VV H5 H(CCCH)
5VV H6 H(NCH)
5VV H7 H(NCH)

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
5VV CG ND2 SINGLE n 1.323 0.0100 1.323 0.0100
5VV CG OD1 DOUBLE n 1.229 0.0102 1.229 0.0102
5VV CB CG SINGLE n 1.514 0.0100 1.514 0.0100
5VV C9 O11 DOUBLE n 1.210 0.0102 1.210 0.0102
5VV CA CB SINGLE n 1.529 0.0100 1.529 0.0100
5VV N C9 SINGLE n 1.345 0.0108 1.345 0.0108
5VV N CA SINGLE n 1.451 0.0103 1.451 0.0103
5VV C9 O10 SINGLE n 1.338 0.0153 1.338 0.0153
5VV CA C SINGLE n 1.539 0.0100 1.539 0.0100
5VV C O DOUBLE n 1.191 0.0200 1.191 0.0200
5VV N H SINGLE n 1.016 0.0100 0.875 0.0200
5VV O10 H10 SINGLE n 0.966 0.0059 0.861 0.0200
5VV CA HA SINGLE n 1.089 0.0100 0.987 0.0159
5VV CB H4 SINGLE n 1.089 0.0100 0.979 0.0159
5VV CB H5 SINGLE n 1.089 0.0100 0.979 0.0159
5VV ND2 H6 SINGLE n 1.016 0.0100 0.884 0.0200
5VV ND2 H7 SINGLE n 1.016 0.0100 0.884 0.0200
5VV C H8 SINGLE n 1.082 0.0130 0.947 0.0200
5VV CG ND2 SINGLE n 1.325 0.0100 1.325 0.0100
5VV CG OD1 DOUBLE n 1.236 0.0100 1.236 0.0100
5VV CB CG SINGLE n 1.514 0.0110 1.514 0.0110
5VV C9 O11 DOUBLE n 1.211 0.0167 1.211 0.0167
5VV CA CB SINGLE n 1.532 0.0109 1.532 0.0109
5VV N C9 SINGLE n 1.346 0.0115 1.346 0.0115
5VV N CA SINGLE n 1.447 0.0100 1.447 0.0100
5VV C9 O10 SINGLE n 1.307 0.0186 1.307 0.0186
5VV CA C SINGLE n 1.541 0.0100 1.541 0.0100
5VV C O DOUBLE n 1.252 0.0173 1.252 0.0173
5VV C OXT SINGLE n 1.252 0.0173 1.252 0.0173
5VV N H SINGLE n 1.013 0.0120 0.874 0.0200
5VV O10 H10 SINGLE n 0.966 0.0059 0.836 0.0100
5VV CA HA SINGLE n 1.092 0.0100 0.988 0.0200
5VV CB H4 SINGLE n 1.092 0.0100 0.979 0.0125
5VV CB H5 SINGLE n 1.092 0.0100 0.979 0.0125
5VV ND2 H6 SINGLE n 1.013 0.0120 0.887 0.0200
5VV ND2 H7 SINGLE n 1.013 0.0120 0.887 0.0200

loop_
_chem_comp_angle.comp_id
Expand All @@ -76,34 +100,34 @@ _chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
5VV C9 N CA 120.998 1.63
5VV C9 N H 119.619 1.99
5VV CA N H 119.383 1.92
5VV O11 C9 N 125.209 1.50
5VV O11 C9 O10 124.389 1.64
5VV N C9 O10 110.402 1.61
5VV C9 O10 H10 120.000 3.00
5VV CB CA N 112.687 1.50
5VV CB CA C 111.511 2.91
5VV CB CA HA 107.587 1.50
5VV N CA C 110.921 1.74
5VV N CA HA 108.161 1.50
5VV C CA HA 108.186 1.50
5VV CG CB CA 110.660 1.50
5VV CG CB H4 109.076 1.50
5VV CG CB H5 109.076 1.50
5VV CA CB H4 108.988 1.50
5VV CA CB H5 108.988 1.50
5VV H4 CB H5 108.069 1.50
5VV ND2 CG OD1 122.566 1.50
5VV ND2 CG CB 116.821 1.50
5VV OD1 CG CB 120.613 1.50
5VV CG ND2 H6 120.022 1.65
5VV CG ND2 H7 120.022 1.65
5VV H6 ND2 H7 119.956 2.38
5VV CA C O 120.289 1.60
5VV CA C H8 119.547 2.53
5VV O C H8 120.163 1.50
5VV C9 N CA 120.878 2.68
5VV C9 N H 119.329 3.00
5VV CA N H 119.793 2.04
5VV O11 C9 N 125.248 1.50
5VV O11 C9 O10 123.724 1.50
5VV N C9 O10 111.028 3.00
5VV C9 O10 H10 110.328 3.00
5VV CB CA N 111.753 2.29
5VV CB CA C 110.119 3.00
5VV CB CA HA 109.051 1.59
5VV N CA C 111.439 3.00
5VV N CA HA 107.447 1.50
5VV C CA HA 108.335 1.67
5VV CG CB CA 112.473 3.00
5VV CG CB H4 109.132 1.50
5VV CG CB H5 109.132 1.50
5VV CA CB H4 109.043 1.50
5VV CA CB H5 109.043 1.50
5VV H4 CB H5 108.039 1.50
5VV ND2 CG OD1 122.581 1.50
5VV ND2 CG CB 117.180 1.62
5VV OD1 CG CB 120.239 1.50
5VV CG ND2 H6 119.917 2.87
5VV CG ND2 H7 119.917 2.87
5VV H6 ND2 H7 120.165 3.00
5VV CA C O 117.283 2.93
5VV CA C OXT 117.283 2.93
5VV O C OXT 125.433 1.50

loop_
_chem_comp_tor.comp_id
Expand All @@ -115,13 +139,13 @@ _chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
5VV sp2_sp2_7 O11 C9 N CA 0.000 5.0 2
5VV sp2_sp3_7 C9 N CA CB 0.000 10.0 6
5VV sp2_sp2_9 O11 C9 O10 H10 180.000 5.0 2
5VV sp3_sp3_1 N CA CB CG 180.000 10.0 3
5VV sp2_sp3_13 O C CA CB 0.000 10.0 6
5VV sp2_sp3_2 ND2 CG CB CA 120.000 10.0 6
5VV sp2_sp2_3 OD1 CG ND2 H6 0.000 5.0 2
5VV sp2_sp2_1 O11 C9 N CA 0.000 5.0 2
5VV sp2_sp3_1 C9 N CA CB 0.000 20.0 6
5VV sp2_sp2_2 O11 C9 O10 H10 180.000 5.0 2
5VV sp3_sp3_1 N CA CB CG 180.000 10.0 3
5VV sp2_sp3_2 O C CA CB 0.000 20.0 6
5VV sp2_sp3_3 ND2 CG CB CA 120.000 20.0 6
5VV sp2_sp2_3 OD1 CG ND2 H6 0.000 5.0 2

loop_
_chem_comp_chir.comp_id
Expand Down Expand Up @@ -156,28 +180,28 @@ _chem_comp_plane_atom.dist_esd
5VV plan-4 ND2 0.020
5VV plan-5 C 0.020
5VV plan-5 CA 0.020
5VV plan-5 H8 0.020
5VV plan-5 O 0.020
5VV plan-5 OXT 0.020

loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
5VV InChI InChI 1.03 InChI=1S/C5H8N2O4/c6-4(9)1-3(2-8)7-5(10)11/h2-3,7H,1H2,(H2,6,9)(H,10,11)/t3-/m0/s1
5VV InChIKey InChI 1.03 AKNQOGQFPGWUDZ-VKHMYHEASA-N
5VV SMILES_CANONICAL CACTVS 3.385 NC(=O)C[C@H](NC(O)=O)C=O
5VV SMILES CACTVS 3.385 NC(=O)C[CH](NC(O)=O)C=O
5VV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 C([C@@H](C=O)NC(=O)O)C(=O)N
5VV SMILES "OpenEye OEToolkits" 2.0.4 C(C(C=O)NC(=O)O)C(=O)N
5VV InChI InChI 1.06 "InChI=1S/C5H8N2O5/c6-3(8)1-2(4(9)10)7-5(11)12/h2,7H,1H2,(H2,6,8)(H,9,10)(H,11,12)/t2-/m0/s1"
5VV InChIKey InChI 1.06 ZDDDMWAFNPCPER-REOHCLBHSA-N
5VV SMILES_CANONICAL CACTVS 3.385 "NC(=O)C[C@H](NC(O)=O)C(O)=O"
5VV SMILES CACTVS 3.385 "NC(=O)C[CH](NC(O)=O)C(O)=O"
5VV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C([C@@H](C(=O)O)NC(=O)O)C(=O)N"
5VV SMILES "OpenEye OEToolkits" 2.0.7 "C(C(C(=O)O)NC(=O)O)C(=O)N"

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
5VV acedrg 243 "dictionary generator"
5VV acedrg_database 11 "data source"
5VV rdkit 2017.03.2 "Chemoinformatics tool"
5VV refmac5 5.8.0238 "optimization tool"
_acedrg_chem_comp_descriptor.comp_id
_acedrg_chem_comp_descriptor.program_name
_acedrg_chem_comp_descriptor.program_version
_acedrg_chem_comp_descriptor.type
5VV acedrg 314 "dictionary generator"
5VV acedrg_database 12 "data source"
5VV rdkit 2023.03.3 "Chemoinformatics tool"
5VV servalcat 0.4.102 'optimization tool'
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