data_R8V
#
_chem_comp.id R8V
_chem_comp.name (3S)-3-hydroxy-2-methyl-2,3-dihydro-1H-isoindol-1-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H9 N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-02-10
_chem_comp.pdbx_modified_date 2020-05-29
_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 163.173
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code R8V
_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 5RBS
_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
R8V C4 C1 C 0 1 Y N N N N N 31.469 -10.371 82.502 2.952 0.626 -0.096 C4 R8V 1
R8V C5 C2 C 0 1 Y N N N N N 32.788 -10.574 82.105 2.908 -0.741 0.111 C5 R8V 2
R8V C6 C3 C 0 1 Y N N N N N 33.820 -9.937 82.768 1.696 -1.399 0.163 C6 R8V 3
R8V C7 C4 C 0 1 Y N N N N N 33.520 -9.134 83.869 0.510 -0.682 0.006 C7 R8V 4
R8V C8 C5 C 0 1 N N N N N N 34.426 -8.381 84.760 -0.908 -1.091 0.012 C8 R8V 5
R8V O O1 O 0 1 N N N N N N 35.616 -8.214 84.647 -1.301 -2.230 0.170 O R8V 6
R8V N N1 N 0 1 N N N N N N 33.611 -7.827 85.757 -1.702 -0.024 -0.183 N R8V 7
R8V C C6 C 0 1 N N N N N N 34.084 -6.947 86.823 -3.166 -0.049 -0.238 C R8V 8
R8V C2 C7 C 0 1 Y N N N N N 32.222 -8.971 84.299 0.566 0.699 -0.202 C2 R8V 9
R8V C1 C8 C 0 1 N N S N N N 32.222 -8.145 85.590 -0.862 1.169 -0.331 C1 R8V 10
R8V O1 O2 O 0 1 N N N N N N 31.417 -7.066 85.619 -1.163 2.113 0.699 O1 R8V 11
R8V C3 C9 C 0 1 Y N N N N N 31.179 -9.569 83.600 1.779 1.345 -0.252 C3 R8V 12
R8V H1 H1 H 0 1 N N N N N N 30.666 -10.840 81.953 3.904 1.135 -0.131 H1 R8V 13
R8V H2 H2 H 0 1 N N N N N N 33.005 -11.231 81.276 3.827 -1.297 0.231 H2 R8V 14
R8V H3 H3 H 0 1 N N N N N N 34.842 -10.059 82.439 1.666 -2.467 0.324 H3 R8V 15
R8V H4 H4 H 0 1 N N N N N N 33.238 -6.659 87.464 -3.518 -1.071 -0.097 H4 R8V 16
R8V H5 H5 H 0 1 N N N N N N 34.838 -7.474 87.426 -3.570 0.586 0.550 H5 R8V 17
R8V H6 H6 H 0 1 N N N N N N 34.532 -6.045 86.382 -3.499 0.319 -1.209 H6 R8V 18
R8V H7 H7 H 0 1 N N N N N N 31.934 -8.829 86.402 -1.020 1.621 -1.311 H7 R8V 19
R8V H8 H8 H 0 1 N N N N N N 31.497 -6.633 86.461 -2.068 2.452 0.669 H8 R8V 20
R8V H9 H9 H 0 1 N N N N N N 30.155 -9.412 83.907 1.816 2.413 -0.409 H9 R8V 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
R8V C5 C4 DOUB Y N 1
R8V C5 C6 SING Y N 2
R8V C4 C3 SING Y N 3
R8V C6 C7 DOUB Y N 4
R8V C3 C2 DOUB Y N 5
R8V C7 C2 SING Y N 6
R8V C7 C8 SING N N 7
R8V C2 C1 SING N N 8
R8V O C8 DOUB N N 9
R8V C8 N SING N N 10
R8V C1 O1 SING N N 11
R8V C1 N SING N N 12
R8V N C SING N N 13
R8V C4 H1 SING N N 14
R8V C5 H2 SING N N 15
R8V C6 H3 SING N N 16
R8V C H4 SING N N 17
R8V C H5 SING N N 18
R8V C H6 SING N N 19
R8V C1 H7 SING N N 20
R8V O1 H8 SING N N 21
R8V C3 H9 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
R8V SMILES ACDLabs 12.01 c1cc2c(cc1)C(N(C)C2O)=O
R8V InChI InChI 1.03 InChI=1S/C9H9NO2/c1-10-8(11)6-4-2-3-5-7(6)9(10)12/h2-5,8,11H,1H3/t8-/m0/s1
R8V InChIKey InChI 1.03 UCEXMNLISKKYAE-QMMMGPOBSA-N
R8V SMILES_CANONICAL CACTVS 3.385 CN1[C@@H](O)c2ccccc2C1=O
R8V SMILES CACTVS 3.385 CN1[CH](O)c2ccccc2C1=O
R8V SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CN1[C@H](c2ccccc2C1=O)O
R8V SMILES "OpenEye OEToolkits" 2.0.6 CN1C(c2ccccc2C1=O)O
#
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
R8V "SYSTEMATIC NAME" ACDLabs 12.01 (3S)-3-hydroxy-2-methyl-2,3-dihydro-1H-isoindol-1-one
R8V "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 (3~{S})-2-methyl-3-oxidanyl-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
R8V 'Create component' 2020-02-10 RCSB
R8V 'Modify model coordinates code' 2020-03-19 RCSB
R8V 'Initial release' 2020-06-03 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
R8V C4 C 3.000 -0.846 1
R8V C5 C 3.000 0.654 2
R8V C6 C 4.299 1.404 3
R8V C7 C 5.598 0.654 4
R8V C8 C 7.018 1.111 5
R8V O O 7.483 2.537 6
R8V N N 7.893 -0.096 7
R8V C C 9.393 -0.096 8
R8V C2 C 5.598 -0.846 9
R8V C1 C 7.018 -1.303 10
R8V O1 O 7.483 -2.729 11
R8V C3 C 4.299 -1.596 12
#
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
R8V C5 C4 DOUBLE NONE 1
R8V C5 C6 SINGLE NONE 2
R8V C4 C3 SINGLE NONE 3
R8V C6 C7 DOUBLE NONE 4
R8V C3 C2 DOUBLE NONE 5
R8V C7 C2 SINGLE NONE 6
R8V C7 C8 SINGLE NONE 7
R8V C2 C1 SINGLE NONE 8
R8V O C8 DOUBLE NONE 9
R8V C8 N SINGLE NONE 10
R8V C1 O1 SINGLE BEGINWEDGE 11
R8V C1 N SINGLE NONE 12
R8V N C SINGLE NONE 13
#
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
R8V 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
R8V amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
R8V 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
R8V C4 S1 1
R8V C5 S1 1
R8V C6 S1 1
R8V C7 S1 1
R8V C8 S1 1
R8V O S1 1
R8V N S1 1
R8V C2 S1 1
R8V C1 S1 1
R8V C3 S1 1
R8V N F1 1
R8V C8 F1 1
R8V O F1 1
R8V C7 F1 1
R8V C4 F2 1
R8V C5 F2 1
R8V C6 F2 1
R8V C7 F2 1
R8V C2 F2 1
R8V C3 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id R8V
_pdbe_chem_comp_rdkit_properties.exactmw 163.063
_pdbe_chem_comp_rdkit_properties.amw 163.176
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_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 0.222
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 82.967
_pdbe_chem_comp_rdkit_properties.tpsa 40.540
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.654
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.963
_pdbe_chem_comp_rdkit_properties.chi0v 5.764
_pdbe_chem_comp_rdkit_properties.chi1v 3.079
_pdbe_chem_comp_rdkit_properties.chi2v 1.521
_pdbe_chem_comp_rdkit_properties.chi3v 1.521
_pdbe_chem_comp_rdkit_properties.chi4v 0.949
_pdbe_chem_comp_rdkit_properties.chi0n 14.764
_pdbe_chem_comp_rdkit_properties.chi1n 7.487
_pdbe_chem_comp_rdkit_properties.chi2n 1.521
_pdbe_chem_comp_rdkit_properties.chi3n 1.521
_pdbe_chem_comp_rdkit_properties.chi4n 0.949
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.350
_pdbe_chem_comp_rdkit_properties.kappa1 2.326
_pdbe_chem_comp_rdkit_properties.kappa2 2.318
_pdbe_chem_comp_rdkit_properties.kappa3 0.769
_pdbe_chem_comp_rdkit_properties.Phi 0.449
#
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
R8V UniChem PDBe R8V
R8V UniChem ZINC ZINC000000335289
R8V UniChem PubChem 819572
R8V UniChem SureChEMBL SCHEMBL22623757
#
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
R8V C4 2.977 -0.646 0.053 ETKDGv3 1
R8V C5 3.042 0.635 -0.368 ETKDGv3 2
R8V C6 1.799 1.430 -0.546 ETKDGv3 3
R8V C7 0.637 0.829 -0.278 ETKDGv3 4
R8V C8 -0.718 1.315 -0.336 ETKDGv3 5
R8V O -1.070 2.476 -0.675 ETKDGv3 6
R8V N -1.622 0.285 0.062 ETKDGv3 7
R8V C -3.063 0.457 0.204 ETKDGv3 8
R8V C2 0.557 -0.546 0.172 ETKDGv3 9
R8V C1 -0.876 -0.940 0.396 ETKDGv3 10
R8V O1 -1.226 -1.977 -0.479 ETKDGv3 11
R8V C3 1.662 -1.279 0.344 ETKDGv3 12
R8V H1 3.886 -1.219 0.182 ETKDGv3 13
R8V H2 4.002 1.089 -0.577 ETKDGv3 14
R8V H3 1.837 2.460 -0.877 ETKDGv3 15
R8V H4 -3.528 -0.471 0.598 ETKDGv3 16
R8V H5 -3.272 1.289 0.909 ETKDGv3 17
R8V H6 -3.508 0.692 -0.785 ETKDGv3 18
R8V H7 -1.037 -1.223 1.461 ETKDGv3 19
R8V H8 -2.083 -2.349 -0.145 ETKDGv3 20
R8V H9 1.604 -2.305 0.684 ETKDGv3 21
#