data_5WV
#
_chem_comp.id 5WV
_chem_comp.name 2-methyl-3~{H}-isoindol-1-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H9 N O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-12-17
_chem_comp.pdbx_modified_date 2016-01-08
_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 147.174
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 5WV
_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 5FE2
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
5WV OAB O1 O 0 1 N N N N N N -9.081 36.798 -39.153 -1.660 -1.830 0.002 OAB 5WV 1
5WV CAH C1 C 0 1 N N N N N N -9.260 37.413 -40.199 -1.135 -0.734 0.002 CAH 5WV 2
5WV CAJ C2 C 0 1 Y N N N N N -10.078 38.466 -40.330 0.321 -0.496 0.001 CAJ 5WV 3
5WV CAF C3 C 0 1 Y N N N N N -10.861 39.095 -39.424 1.415 -1.363 -0.001 CAF 5WV 4
5WV CAD C4 C 0 1 Y N N N N N -11.655 40.185 -39.807 2.696 -0.851 -0.002 CAD 5WV 5
5WV CAC C5 C 0 1 Y N N N N N -11.627 40.612 -41.141 2.902 0.517 -0.001 CAC 5WV 6
5WV CAE C6 C 0 1 Y N N N N N -10.803 39.926 -42.045 1.821 1.384 0.001 CAE 5WV 7
5WV CAI C7 C 0 1 Y N N N N N -10.057 38.878 -41.629 0.540 0.884 0.001 CAI 5WV 8
5WV CAG C8 C 0 1 N N N N N N -9.183 38.053 -42.343 -0.822 1.531 0.003 CAG 5WV 9
5WV NAK N1 N 0 1 N N N N N N -8.704 37.075 -41.346 -1.798 0.435 -0.002 NAK 5WV 10
5WV CAA C9 C 0 1 N N N N N N -7.768 35.978 -41.609 -3.255 0.590 -0.003 CAA 5WV 11
5WV H1 H1 H 0 1 N N N N N N -10.875 38.755 -38.399 1.259 -2.432 -0.001 H1 5WV 12
5WV H2 H2 H 0 1 N N N N N N -12.279 40.688 -39.084 3.543 -1.521 -0.004 H2 5WV 13
5WV H3 H3 H 0 1 N N N N N N -12.226 41.450 -41.466 3.907 0.911 -0.002 H3 5WV 14
5WV H4 H4 H 0 1 N N N N N N -10.764 40.236 -43.079 1.984 2.451 0.002 H4 5WV 15
5WV H5 H5 H 0 1 N N N N N N -9.710 37.545 -43.164 -0.946 2.142 0.897 H5 5WV 16
5WV H6 H6 H 0 1 N N N N N N -8.344 38.636 -42.751 -0.947 2.144 -0.890 H6 5WV 17
5WV H7 H7 H 0 1 N N N N N N -7.593 35.414 -40.681 -3.615 0.633 -1.031 H7 5WV 18
5WV H8 H8 H 0 1 N N N N N N -8.193 35.308 -42.371 -3.711 -0.258 0.507 H8 5WV 19
5WV H9 H9 H 0 1 N N N N N N -6.815 36.389 -41.973 -3.523 1.512 0.514 H9 5WV 20
#
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
5WV CAG CAI SING N N 1
5WV CAG NAK SING N N 2
5WV CAE CAI DOUB Y N 3
5WV CAE CAC SING Y N 4
5WV CAI CAJ SING Y N 5
5WV CAA NAK SING N N 6
5WV NAK CAH SING N N 7
5WV CAC CAD DOUB Y N 8
5WV CAJ CAH SING N N 9
5WV CAJ CAF DOUB Y N 10
5WV CAH OAB DOUB N N 11
5WV CAD CAF SING Y N 12
5WV CAF H1 SING N N 13
5WV CAD H2 SING N N 14
5WV CAC H3 SING N N 15
5WV CAE H4 SING N N 16
5WV CAG H5 SING N N 17
5WV CAG H6 SING N N 18
5WV CAA H7 SING N N 19
5WV CAA H8 SING N N 20
5WV CAA H9 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
5WV InChI InChI 1.03 InChI=1S/C9H9NO/c1-10-6-7-4-2-3-5-8(7)9(10)11/h2-5H,6H2,1H3
5WV InChIKey InChI 1.03 JHMBTUMIVBSJFS-UHFFFAOYSA-N
5WV SMILES_CANONICAL CACTVS 3.385 CN1Cc2ccccc2C1=O
5WV SMILES CACTVS 3.385 CN1Cc2ccccc2C1=O
5WV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 CN1Cc2ccccc2C1=O
5WV SMILES "OpenEye OEToolkits" 2.0.4 CN1Cc2ccccc2C1=O
#
_pdbx_chem_comp_identifier.comp_id 5WV
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.4
_pdbx_chem_comp_identifier.identifier 2-methyl-3~{H}-isoindol-1-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
5WV 'Create component' 2015-12-17 EBI
5WV 'Initial release' 2016-01-13 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
5WV OAB O 7.483 2.066 1
5WV CAH C 7.018 0.641 2
5WV CAJ C 5.598 0.184 3
5WV CAF C 4.299 0.934 4
5WV CAD C 3.000 0.184 5
5WV CAC C 3.000 -1.316 6
5WV CAE C 4.299 -2.066 7
5WV CAI C 5.598 -1.316 8
5WV CAG C 7.018 -1.774 9
5WV NAK N 7.893 -0.566 10
5WV CAA C 9.393 -0.566 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
5WV CAG CAI SINGLE NONE 1
5WV CAG NAK SINGLE NONE 2
5WV CAE CAI DOUBLE NONE 3
5WV CAE CAC SINGLE NONE 4
5WV CAI CAJ SINGLE NONE 5
5WV CAA NAK SINGLE NONE 6
5WV NAK CAH SINGLE NONE 7
5WV CAC CAD DOUBLE NONE 8
5WV CAJ CAH SINGLE NONE 9
5WV CAJ CAF DOUBLE NONE 10
5WV CAH OAB DOUBLE NONE 11
5WV CAD CAF SINGLE NONE 12
#
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
5WV MurckoScaffold S1 scaffold O=C1NCc2ccccc21 InChI=1S/C8H7NO/c10-8-7-4-2-1-3-6(7)5-9-8/h1-4H,5H2,(H,9,10) PXZQEOJJUGGUIB-UHFFFAOYSA-N
5WV amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
5WV 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
5WV OAB S1 1
5WV CAH S1 1
5WV CAJ S1 1
5WV CAF S1 1
5WV CAD S1 1
5WV CAC S1 1
5WV CAE S1 1
5WV CAI S1 1
5WV CAG S1 1
5WV NAK S1 1
5WV NAK F1 1
5WV CAH F1 1
5WV OAB F1 1
5WV CAJ F1 1
5WV CAJ F2 1
5WV CAI F2 1
5WV CAE F2 1
5WV CAC F2 1
5WV CAD F2 1
5WV CAF F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 5WV
_pdbe_chem_comp_rdkit_properties.exactmw 147.068
_pdbe_chem_comp_rdkit_properties.amw 147.177
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 20
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.222
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 78.086
_pdbe_chem_comp_rdkit_properties.tpsa 20.310
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.163
_pdbe_chem_comp_rdkit_properties.CrippenMR 41.708
_pdbe_chem_comp_rdkit_properties.chi0v 5.355
_pdbe_chem_comp_rdkit_properties.chi1v 2.875
_pdbe_chem_comp_rdkit_properties.chi2v 1.328
_pdbe_chem_comp_rdkit_properties.chi3v 1.328
_pdbe_chem_comp_rdkit_properties.chi4v 0.831
_pdbe_chem_comp_rdkit_properties.chi0n 14.355
_pdbe_chem_comp_rdkit_properties.chi1n 7.375
_pdbe_chem_comp_rdkit_properties.chi2n 1.328
_pdbe_chem_comp_rdkit_properties.chi3n 1.328
_pdbe_chem_comp_rdkit_properties.chi4n 0.831
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.310
_pdbe_chem_comp_rdkit_properties.kappa1 1.887
_pdbe_chem_comp_rdkit_properties.kappa2 2.088
_pdbe_chem_comp_rdkit_properties.kappa3 0.827
_pdbe_chem_comp_rdkit_properties.Phi 0.358
#
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
5WV UniChem ZINC ZINC000000397856
5WV UniChem 'PubChem TPHARMA' 15922543
5WV UniChem Mcule MCULE-4831369773
5WV UniChem ACTor 5342-91-6
5WV UniChem Nikkaji J418.390H
5WV UniChem CCDC QENYEO
5WV UniChem eMolecules 1960147
5WV UniChem SureChEMBL SCHEMBL470341
5WV UniChem PubChem 220657
#
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
5WV OAB 1.182 -2.428 -0.311 ETKDGv3 1
5WV CAH 0.826 -1.229 -0.157 ETKDGv3 2
5WV CAJ -0.533 -0.755 -0.100 ETKDGv3 3
5WV CAF -1.696 -1.404 -0.188 ETKDGv3 4
5WV CAD -2.942 -0.599 -0.087 ETKDGv3 5
5WV CAC -2.878 0.739 0.086 ETKDGv3 6
5WV CAE -1.560 1.424 0.180 ETKDGv3 7
5WV CAI -0.454 0.680 0.087 ETKDGv3 8
5WV CAG 0.981 1.120 0.148 ETKDGv3 9
5WV NAK 1.729 -0.134 -0.012 ETKDGv3 10
5WV CAA 3.182 -0.243 -0.021 ETKDGv3 11
5WV H1 -1.734 -2.476 -0.327 ETKDGv3 12
5WV H2 -3.904 -1.090 -0.154 ETKDGv3 13
5WV H3 -3.788 1.319 0.159 ETKDGv3 14
5WV H4 -1.502 2.496 0.319 ETKDGv3 15
5WV H5 1.212 1.817 -0.685 ETKDGv3 16
5WV H6 1.206 1.581 1.133 ETKDGv3 17
5WV H7 3.517 -0.671 -0.989 ETKDGv3 18
5WV H8 3.644 0.758 0.110 ETKDGv3 19
5WV H9 3.512 -0.904 0.808 ETKDGv3 20
#