data_VSQ
#
_chem_comp.id VSQ
_chem_comp.name N~2~-phenylglycinamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H10 N2 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-09-02
_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 150.178
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VSQ
_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 7FMP
_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
VSQ N1 N1 N 0 1 N N N N N N -3.490 15.627 -36.689 3.925 -0.844 -0.000 N1 VSQ 1
VSQ C7 C1 C 0 1 N N N N N N -3.838 15.694 -35.389 2.862 -0.016 -0.000 C7 VSQ 2
VSQ C1 C2 C 0 1 Y N N N N N 0.791 13.173 -36.062 -2.669 -1.357 -0.000 C1 VSQ 3
VSQ C5 C3 C 0 1 Y N N N N N -0.697 11.628 -35.221 -3.150 0.992 0.000 C5 VSQ 4
VSQ C6 C4 C 0 1 N N N N N N -3.220 14.730 -34.442 1.466 -0.583 0.000 C6 VSQ 5
VSQ C4 C5 C 0 1 Y N N N N N -1.545 12.677 -34.938 -1.797 1.272 0.000 C4 VSQ 6
VSQ C3 C6 C 0 1 Y N N N N N -1.188 14.048 -35.242 -0.874 0.234 0.000 C3 VSQ 7
VSQ C2 C7 C 0 1 Y N N N N N -0.026 14.332 -35.840 -1.316 -1.083 0.000 C2 VSQ 8
VSQ O O1 O 0 1 N N N N N N -4.547 16.499 -34.990 3.029 1.185 -0.000 O VSQ 9
VSQ N N2 N 0 1 N N N N N N -1.879 14.995 -34.698 0.494 0.514 0.000 N VSQ 10
VSQ C C8 C 0 1 Y N N N N N 0.488 11.873 -35.776 -3.585 -0.321 -0.000 C VSQ 11
VSQ H1 H1 H 0 1 N N N N N N -3.854 16.294 -37.339 4.824 -0.479 -0.000 H1 VSQ 12
VSQ H2 H2 H 0 1 N N N N N N -2.868 14.910 -37.004 3.792 -1.805 0.004 H2 VSQ 13
VSQ H3 H3 H 0 1 N N N N N N 1.759 13.350 -36.507 -3.013 -2.380 -0.005 H3 VSQ 14
VSQ H4 H4 H 0 1 N N N N N N -0.992 10.614 -34.994 -3.868 1.799 -0.000 H4 VSQ 15
VSQ H5 H5 H 0 1 N N N N N N -3.491 14.948 -33.398 1.322 -1.196 -0.890 H5 VSQ 16
VSQ H6 H6 H 0 1 N N N N N N -3.487 13.690 -34.681 1.322 -1.195 0.890 H6 VSQ 17
VSQ H7 H7 H 0 1 N N N N N N -2.500 12.472 -34.478 -1.458 2.297 -0.000 H7 VSQ 18
VSQ H8 H8 H 0 1 N N N N N N 0.268 15.331 -36.127 -0.601 -1.893 0.001 H8 VSQ 19
VSQ H9 H9 H 0 1 N N N N N N -1.445 15.223 -33.827 0.801 1.434 -0.000 H9 VSQ 20
VSQ H10 H10 H 0 1 N N N N N N 1.182 11.074 -35.992 -4.643 -0.537 -0.000 H10 VSQ 21
#
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
VSQ N1 C7 SING N N 1
VSQ C1 C2 DOUB Y N 2
VSQ C1 C SING Y N 3
VSQ C2 C3 SING Y N 4
VSQ C C5 DOUB Y N 5
VSQ C7 O DOUB N N 6
VSQ C7 C6 SING N N 7
VSQ C3 C4 DOUB Y N 8
VSQ C3 N SING N N 9
VSQ C5 C4 SING Y N 10
VSQ N C6 SING N N 11
VSQ N1 H1 SING N N 12
VSQ N1 H2 SING N N 13
VSQ C1 H3 SING N N 14
VSQ C5 H4 SING N N 15
VSQ C6 H5 SING N N 16
VSQ C6 H6 SING N N 17
VSQ C4 H7 SING N N 18
VSQ C2 H8 SING N N 19
VSQ N H9 SING N N 20
VSQ C H10 SING N N 21
#
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
VSQ SMILES ACDLabs 12.01 NC(=O)CNc1ccccc1
VSQ InChI InChI 1.06 InChI=1S/C8H10N2O/c9-8(11)6-10-7-4-2-1-3-5-7/h1-5,10H,6H2,(H2,9,11)
VSQ InChIKey InChI 1.06 GXBRYTMUEZNYJT-UHFFFAOYSA-N
VSQ SMILES_CANONICAL CACTVS 3.385 NC(=O)CNc1ccccc1
VSQ SMILES CACTVS 3.385 NC(=O)CNc1ccccc1
VSQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)NCC(=O)N
VSQ SMILES "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)NCC(=O)N
#
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
VSQ "SYSTEMATIC NAME" ACDLabs 12.01 N~2~-phenylglycinamide
VSQ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 2-phenylazanylethanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VSQ 'Create component' 2022-09-02 RCSB
VSQ 'Initial release' 2022-11-02 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
VSQ N1 N 4.299 3.285 1
VSQ C7 C 5.598 2.535 2
VSQ C1 C 5.598 -3.465 3
VSQ C5 C 3.000 -3.465 4
VSQ C6 C 5.598 1.035 5
VSQ C4 C 3.000 -1.965 6
VSQ C3 C 4.299 -1.215 7
VSQ C2 C 5.598 -1.965 8
VSQ O O 6.897 3.285 9
VSQ N N 4.299 0.285 10
VSQ C C 4.299 -4.215 11
#
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
VSQ N1 C7 SINGLE NONE 1
VSQ C1 C2 DOUBLE NONE 2
VSQ C1 C SINGLE NONE 3
VSQ C2 C3 SINGLE NONE 4
VSQ C C5 DOUBLE NONE 5
VSQ C7 O DOUBLE NONE 6
VSQ C7 C6 SINGLE NONE 7
VSQ C3 C4 DOUBLE NONE 8
VSQ C3 N SINGLE NONE 9
VSQ C5 C4 SINGLE NONE 10
VSQ N C6 SINGLE NONE 11
#
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
VSQ MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
VSQ amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
VSQ peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
VSQ phenyl F3 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
VSQ C1 S1 1
VSQ C5 S1 1
VSQ C4 S1 1
VSQ C3 S1 1
VSQ C2 S1 1
VSQ C S1 1
VSQ N1 F1 1
VSQ C7 F1 1
VSQ O F1 1
VSQ C6 F1 1
VSQ O F2 1
VSQ C7 F2 1
VSQ C6 F2 1
VSQ N F2 1
VSQ C1 F3 1
VSQ C2 F3 1
VSQ C3 F3 1
VSQ C4 F3 1
VSQ C5 F3 1
VSQ C F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VSQ
_pdbe_chem_comp_rdkit_properties.exactmw 150.079
_pdbe_chem_comp_rdkit_properties.amw 150.181
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.125
_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 79.436
_pdbe_chem_comp_rdkit_properties.tpsa 55.120
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.203
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.302
_pdbe_chem_comp_rdkit_properties.chi0v 5.303
_pdbe_chem_comp_rdkit_properties.chi1v 2.625
_pdbe_chem_comp_rdkit_properties.chi2v 0.750
_pdbe_chem_comp_rdkit_properties.chi3v 0.750
_pdbe_chem_comp_rdkit_properties.chi4v 0.403
_pdbe_chem_comp_rdkit_properties.chi0n 15.303
_pdbe_chem_comp_rdkit_properties.chi1n 7.467
_pdbe_chem_comp_rdkit_properties.chi2n 0.750
_pdbe_chem_comp_rdkit_properties.chi3n 0.750
_pdbe_chem_comp_rdkit_properties.chi4n 0.403
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.510
_pdbe_chem_comp_rdkit_properties.kappa1 1.801
_pdbe_chem_comp_rdkit_properties.kappa2 3.608
_pdbe_chem_comp_rdkit_properties.kappa3 2.709
_pdbe_chem_comp_rdkit_properties.Phi 0.591
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
VSQ UniChem ZINC ZINC000009322539
VSQ UniChem 'EPA CompTox Dashboard' DTXSID30572083
VSQ UniChem eMolecules 2871571
VSQ UniChem SureChEMBL SCHEMBL353358
VSQ UniChem PubChem 15370319
VSQ UniChem Mcule MCULE-7476540506
VSQ UniChem Nikkaji J410.714D
#
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
VSQ N1 2.913 -0.590 1.094 ETKDGv3 1
VSQ C7 2.523 0.181 -0.042 ETKDGv3 2
VSQ C1 -1.770 1.780 0.018 ETKDGv3 3
VSQ C5 -2.863 -0.300 0.663 ETKDGv3 4
VSQ C6 1.798 -0.465 -1.183 ETKDGv3 5
VSQ C4 -1.658 -1.027 0.214 ETKDGv3 6
VSQ C3 -0.603 -0.359 -0.288 ETKDGv3 7
VSQ C2 -0.675 1.126 -0.390 ETKDGv3 8
VSQ O 2.804 1.408 -0.090 ETKDGv3 9
VSQ N 0.562 -1.092 -0.716 ETKDGv3 10
VSQ C -2.916 1.033 0.571 ETKDGv3 11
VSQ H1 3.419 -0.139 1.889 ETKDGv3 12
VSQ H2 2.699 -1.611 1.144 ETKDGv3 13
VSQ H3 -1.819 2.858 -0.059 ETKDGv3 14
VSQ H4 -3.704 -0.850 1.067 ETKDGv3 15
VSQ H5 1.575 0.267 -1.988 ETKDGv3 16
VSQ H6 2.461 -1.243 -1.619 ETKDGv3 17
VSQ H7 -1.636 -2.106 0.300 ETKDGv3 18
VSQ H8 0.148 1.696 -0.797 ETKDGv3 19
VSQ H9 0.539 -2.137 -0.688 ETKDGv3 20
VSQ H10 -3.799 1.567 0.899 ETKDGv3 21
#