data_VGU
#
_chem_comp.id VGU
_chem_comp.name N-[(1E)-2-(hydroxyamino)-2-oxoethylidene]benzamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H8 N2 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-08-29
_chem_comp.pdbx_modified_date 2022-10-28
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 192.171
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VGU
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 7FO8
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
VGU N1 N1 N 0 1 N N N N N N 26.158 21.485 42.336 4.135 -0.361 0.001 N1 VGU 1
VGU C7 C1 C 0 1 N N N N N N 27.809 19.731 41.816 1.697 -0.641 0.001 C7 VGU 2
VGU C8 C2 C 0 1 N N N N N N 26.627 20.176 42.641 2.914 0.210 -0.001 C8 VGU 3
VGU O1 O1 O 0 1 N N N N N N 26.115 19.497 43.530 2.809 1.420 -0.004 O1 VGU 4
VGU C1 C3 C 0 1 Y N N N N N 29.714 15.486 37.997 -3.302 1.732 0.003 C1 VGU 5
VGU C5 C4 C 0 1 Y N N N N N 27.394 15.570 37.958 -4.319 -0.443 -0.003 C5 VGU 6
VGU C6 C5 C 0 1 N N N N N N 28.713 18.076 40.321 -0.586 -0.862 -0.000 C6 VGU 7
VGU C4 C6 C 0 1 Y N N N N N 27.429 16.517 38.933 -3.072 -1.033 -0.001 C4 VGU 8
VGU C3 C7 C 0 1 Y N N N N N 28.594 16.926 39.400 -1.925 -0.236 -0.002 C3 VGU 9
VGU C2 C8 C 0 1 Y N N N N N 29.759 16.404 38.959 -2.050 1.155 0.005 C2 VGU 10
VGU O2 O2 O 0 1 N N N N N N 26.912 22.491 42.779 5.295 0.451 0.000 O2 VGU 11
VGU N N2 N 0 1 N N N N N N 27.593 18.594 40.926 0.518 -0.090 -0.001 N VGU 12
VGU O O3 O 0 1 N N N N N N 29.781 18.599 40.485 -0.481 -2.073 0.003 O VGU 13
VGU C C9 C 0 1 Y N N N N N 28.528 15.048 37.477 -4.434 0.936 -0.001 C VGU 14
VGU H1 H1 H 0 1 N N N N N N 25.315 21.640 41.821 4.219 -1.327 0.008 H1 VGU 15
VGU H2 H2 H 0 1 N N N N N N 28.766 20.228 41.880 1.790 -1.717 0.003 H2 VGU 16
VGU H3 H3 H 0 1 N N N N N N 30.638 15.076 37.617 -3.400 2.808 0.009 H3 VGU 17
VGU H4 H4 H 0 1 N N N N N N 26.443 15.237 37.569 -5.206 -1.058 -0.002 H4 VGU 18
VGU H5 H5 H 0 1 N N N N N N 26.511 16.931 39.322 -2.983 -2.110 0.002 H5 VGU 19
VGU H6 H6 H 0 1 N N N N N N 30.702 16.723 39.376 -1.167 1.777 0.012 H6 VGU 20
VGU H7 H7 H 0 1 N N N N N N 26.518 23.318 42.527 6.124 -0.048 0.002 H7 VGU 21
VGU H8 H8 H 0 1 N N N N N N 28.507 14.300 36.698 -5.413 1.393 -0.003 H8 VGU 22
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
VGU C C5 DOUB Y N 1
VGU C C1 SING Y N 2
VGU C5 C4 SING Y N 3
VGU C1 C2 DOUB Y N 4
VGU C4 C3 DOUB Y N 5
VGU C2 C3 SING Y N 6
VGU C3 C6 SING N N 7
VGU C6 O DOUB N N 8
VGU C6 N SING N N 9
VGU N C7 DOUB N N 10
VGU C7 C8 SING N N 11
VGU N1 C8 SING N N 12
VGU N1 O2 SING N N 13
VGU C8 O1 DOUB N N 14
VGU N1 H1 SING N N 15
VGU C7 H2 SING N N 16
VGU C1 H3 SING N N 17
VGU C5 H4 SING N N 18
VGU C4 H5 SING N N 19
VGU C2 H6 SING N N 20
VGU O2 H7 SING N N 21
VGU C H8 SING N N 22
#
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
VGU SMILES ACDLabs 12.01 O=C(/N=C/C(=O)NO)c1ccccc1
VGU InChI InChI 1.06 InChI=1S/C9H8N2O3/c12-8(11-14)6-10-9(13)7-4-2-1-3-5-7/h1-6,14H,(H,11,12)/b10-6+
VGU InChIKey InChI 1.06 FOKIIJXZYLWKMI-UXBLZVDNSA-N
VGU SMILES_CANONICAL CACTVS 3.385 ONC(=O)C=NC(=O)c1ccccc1
VGU SMILES CACTVS 3.385 ONC(=O)C=NC(=O)c1ccccc1
VGU SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)C(=O)/N=C/C(=O)NO
VGU SMILES "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)C(=O)N=CC(=O)NO
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
VGU "SYSTEMATIC NAME" ACDLabs 12.01 N-[(1E)-2-(hydroxyamino)-2-oxoethylidene]benzamide
VGU "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 (~{N}~{E})-~{N}-[2-(oxidanylamino)-2-oxidanylidene-ethylidene]benzamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VGU 'Create component' 2022-08-29 RCSB
VGU 'Initial release' 2022-11-02 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
VGU N1 N 4.636 0.874 1
VGU C7 C 2.038 0.864 2
VGU C8 C 3.340 0.119 3
VGU O1 O 3.345 -1.381 4
VGU C1 C -3.147 -2.154 5
VGU C5 C -4.454 0.091 6
VGU C6 C -0.560 0.855 7
VGU C4 C -3.158 0.846 8
VGU C3 C -1.856 0.101 9
VGU C2 C -1.851 -1.399 10
VGU O2 O 5.938 0.129 11
VGU N N 0.742 0.110 12
VGU O O -0.565 2.355 13
VGU C C -4.449 -1.409 14
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
VGU C C5 SINGLE NONE 1
VGU C C1 DOUBLE NONE 2
VGU C5 C4 DOUBLE NONE 3
VGU C1 C2 SINGLE NONE 4
VGU C4 C3 SINGLE NONE 5
VGU C2 C3 DOUBLE NONE 6
VGU C3 C6 SINGLE NONE 7
VGU C6 O DOUBLE NONE 8
VGU C6 N SINGLE ENDUPRIGHT 9
VGU N C7 DOUBLE NONE 10
VGU C7 C8 SINGLE ENDUPRIGHT 11
VGU N1 C8 SINGLE NONE 12
VGU N1 O2 SINGLE NONE 13
VGU C8 O1 DOUBLE NONE 14
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
VGU MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
VGU amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
VGU phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
VGU C1 S1 1
VGU C5 S1 1
VGU C4 S1 1
VGU C3 S1 1
VGU C2 S1 1
VGU C S1 1
VGU N1 F1 1
VGU C8 F1 1
VGU O1 F1 1
VGU C7 F1 1
VGU C1 F2 1
VGU C F2 1
VGU C5 F2 1
VGU C4 F2 1
VGU C3 F2 1
VGU C2 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VGU
_pdbe_chem_comp_rdkit_properties.exactmw 192.053
_pdbe_chem_comp_rdkit_properties.amw 192.174
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 91.427
_pdbe_chem_comp_rdkit_properties.tpsa 78.760
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.348
_pdbe_chem_comp_rdkit_properties.CrippenMR 48.928
_pdbe_chem_comp_rdkit_properties.chi0v 6.619
_pdbe_chem_comp_rdkit_properties.chi1v 3.262
_pdbe_chem_comp_rdkit_properties.chi2v 1.050
_pdbe_chem_comp_rdkit_properties.chi3v 1.050
_pdbe_chem_comp_rdkit_properties.chi4v 0.532
_pdbe_chem_comp_rdkit_properties.chi0n 14.619
_pdbe_chem_comp_rdkit_properties.chi1n 7.117
_pdbe_chem_comp_rdkit_properties.chi2n 1.050
_pdbe_chem_comp_rdkit_properties.chi3n 1.050
_pdbe_chem_comp_rdkit_properties.chi4n 0.532
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.010
_pdbe_chem_comp_rdkit_properties.kappa1 3.624
_pdbe_chem_comp_rdkit_properties.kappa2 4.881
_pdbe_chem_comp_rdkit_properties.kappa3 2.797
_pdbe_chem_comp_rdkit_properties.Phi 1.264
#
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
VGU N1 3.730 0.301 1.135 ETKDGv3 1
VGU C7 1.718 0.388 -0.363 ETKDGv3 2
VGU C8 3.060 0.858 0.002 ETKDGv3 3
VGU O1 3.623 1.754 -0.683 ETKDGv3 4
VGU C1 -2.412 -0.063 1.247 ETKDGv3 5
VGU C5 -3.161 -1.504 -0.572 ETKDGv3 6
VGU C6 -0.207 0.504 -1.832 ETKDGv3 7
VGU C4 -2.203 -1.041 -1.386 ETKDGv3 8
VGU C3 -1.237 -0.020 -0.905 ETKDGv3 9
VGU C2 -1.357 0.454 0.350 ETKDGv3 10
VGU O2 4.973 0.719 1.475 ETKDGv3 11
VGU N 1.109 0.881 -1.398 ETKDGv3 12
VGU O -0.499 0.642 -3.049 ETKDGv3 13
VGU C -3.268 -0.993 0.810 ETKDGv3 14
VGU H1 3.274 -0.450 1.700 ETKDGv3 15
VGU H2 1.258 -0.392 0.231 ETKDGv3 16
VGU H3 -2.493 0.317 2.257 ETKDGv3 17
VGU H4 -3.859 -2.251 -0.924 ETKDGv3 18
VGU H5 -2.133 -1.424 -2.396 ETKDGv3 19
VGU H6 -0.700 1.233 0.717 ETKDGv3 20
VGU H7 4.825 1.459 2.118 ETKDGv3 21
VGU H8 -4.042 -1.371 1.465 ETKDGv3 22
#