data_5V4
#
_chem_comp.id 5V4
_chem_comp.name (1~{R},2~{R})-2,3-dihydro-1~{H}-indene-1,2-diol
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H10 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-12-04
_chem_comp.pdbx_modified_date 2016-02-12
_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 150.174
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 5V4
_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 5F4Z
_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
5V4 O01 O1 O 0 1 N N N N N N 9.652 7.890 13.583 3.076 0.665 0.377 O01 5V4 1
5V4 O O2 O 0 1 N N N N N N 10.744 8.285 16.392 1.417 -1.979 -0.478 O 5V4 2
5V4 C01 C1 C 0 1 N N R N N N 10.436 8.895 14.156 1.854 0.417 -0.320 C01 5V4 3
5V4 C02 C2 C 0 1 N N R N N N 11.350 8.321 15.119 1.120 -0.803 0.277 C02 5V4 4
5V4 C03 C3 C 0 1 N N N N N N 11.267 9.579 13.121 0.845 1.560 -0.081 C03 5V4 5
5V4 C04 C4 C 0 1 Y N N N N N 12.530 9.197 15.169 -0.353 -0.470 0.172 C04 5V4 6
5V4 C05 C5 C 0 1 Y N N N N N 12.528 9.979 13.996 -0.511 0.888 -0.034 C05 5V4 7
5V4 C06 C6 C 0 1 Y N N N N N 13.595 9.352 16.187 -1.466 -1.289 0.251 C06 5V4 8
5V4 C07 C7 C 0 1 Y N N N N N 13.604 10.967 13.780 -1.782 1.423 -0.161 C07 5V4 9
5V4 C08 C8 C 0 1 Y N N N N N 14.602 10.268 15.991 -2.734 -0.754 0.124 C08 5V4 10
5V4 C C9 C 0 1 Y N N N N N 14.638 11.128 14.743 -2.892 0.604 -0.083 C 5V4 11
5V4 H1 H1 H 0 1 N N N N N N 9.133 7.469 14.258 3.575 1.421 0.039 H1 5V4 12
5V4 H2 H2 H 0 1 N N N N N N 11.348 7.907 17.020 0.983 -2.778 -0.149 H2 5V4 13
5V4 H3 H3 H 0 1 N N N N N N 9.798 9.641 14.652 2.038 0.275 -1.385 H3 5V4 14
5V4 H4 H4 H 0 1 N N N N N N 11.649 7.311 14.802 1.403 -0.941 1.321 H4 5V4 15
5V4 H5 H5 H 0 1 N N N N N N 10.759 10.464 12.710 1.054 2.057 0.866 H5 5V4 16
5V4 H6 H6 H 0 1 N N N N N N 11.539 8.898 12.301 0.883 2.276 -0.902 H6 5V4 17
5V4 H7 H7 H 0 1 N N N N N N 13.581 8.747 17.081 -1.344 -2.350 0.412 H7 5V4 18
5V4 H8 H8 H 0 1 N N N N N N 13.606 11.571 12.885 -1.906 2.484 -0.322 H8 5V4 19
5V4 H9 H9 H 0 1 N N N N N N 15.377 10.376 16.736 -3.600 -1.395 0.186 H9 5V4 20
5V4 H10 H10 H 0 1 N N N N N N 15.430 11.846 14.589 -3.882 1.024 -0.182 H10 5V4 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
5V4 C03 C05 SING N N 1
5V4 C03 C01 SING N N 2
5V4 O01 C01 SING N N 3
5V4 C07 C05 DOUB Y N 4
5V4 C07 C SING Y N 5
5V4 C05 C04 SING Y N 6
5V4 C01 C02 SING N N 7
5V4 C C08 DOUB Y N 8
5V4 C02 C04 SING N N 9
5V4 C02 O SING N N 10
5V4 C04 C06 DOUB Y N 11
5V4 C08 C06 SING Y N 12
5V4 O01 H1 SING N N 13
5V4 O H2 SING N N 14
5V4 C01 H3 SING N N 15
5V4 C02 H4 SING N N 16
5V4 C03 H5 SING N N 17
5V4 C03 H6 SING N N 18
5V4 C06 H7 SING N N 19
5V4 C07 H8 SING N N 20
5V4 C08 H9 SING N N 21
5V4 C H10 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
5V4 InChI InChI 1.03 InChI=1S/C9H10O2/c10-8-5-6-3-1-2-4-7(6)9(8)11/h1-4,8-11H,5H2/t8-,9-/m1/s1
5V4 InChIKey InChI 1.03 YKXXBEOXRPZVCC-RKDXNWHRSA-N
5V4 SMILES_CANONICAL CACTVS 3.385 O[C@@H]1Cc2ccccc2[C@H]1O
5V4 SMILES CACTVS 3.385 O[CH]1Cc2ccccc2[CH]1O
5V4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 c1ccc2c(c1)C[C@H]([C@@H]2O)O
5V4 SMILES "OpenEye OEToolkits" 2.0.4 c1ccc2c(c1)CC(C2O)O
#
_pdbx_chem_comp_identifier.comp_id 5V4
_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 (1~{R},2~{R})-2,3-dihydro-1~{H}-indene-1,2-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
5V4 'Create component' 2015-12-04 RCSB
5V4 'Initial release' 2016-02-17 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
5V4 O01 O 9.393 -0.662 1
5V4 O O 7.483 1.971 2
5V4 C01 C 7.893 -0.662 3
5V4 C02 C 7.018 0.545 4
5V4 C03 C 7.018 -1.869 5
5V4 C04 C 5.598 0.088 6
5V4 C05 C 5.598 -1.412 7
5V4 C06 C 4.299 0.838 8
5V4 C07 C 4.299 -2.162 9
5V4 C08 C 3.000 0.088 10
5V4 C C 3.000 -1.412 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
5V4 C03 C05 SINGLE NONE 1
5V4 C03 C01 SINGLE NONE 2
5V4 C01 O01 SINGLE BEGINDASH 3
5V4 C07 C05 DOUBLE NONE 4
5V4 C07 C SINGLE NONE 5
5V4 C05 C04 SINGLE NONE 6
5V4 C01 C02 SINGLE NONE 7
5V4 C C08 DOUBLE NONE 8
5V4 C02 C04 SINGLE NONE 9
5V4 C02 O SINGLE BEGINWEDGE 10
5V4 C04 C06 DOUBLE NONE 11
5V4 C08 C06 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
5V4 MurckoScaffold S1 scaffold c1ccc2c(c1)CCC2 InChI=1S/C9H10/c1-2-5-9-7-3-6-8(9)4-1/h1-2,4-5H,3,6-7H2 PQNFLJBBNBOBRQ-UHFFFAOYSA-N
5V4 phenyl F1 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
5V4 C01 S1 1
5V4 C02 S1 1
5V4 C03 S1 1
5V4 C04 S1 1
5V4 C05 S1 1
5V4 C06 S1 1
5V4 C07 S1 1
5V4 C08 S1 1
5V4 C S1 1
5V4 C04 F1 1
5V4 C05 F1 1
5V4 C07 F1 1
5V4 C F1 1
5V4 C08 F1 1
5V4 C06 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 5V4
_pdbe_chem_comp_rdkit_properties.exactmw 150.068
_pdbe_chem_comp_rdkit_properties.amw 150.177
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_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 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_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 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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 79.332
_pdbe_chem_comp_rdkit_properties.tpsa 40.460
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.528
_pdbe_chem_comp_rdkit_properties.CrippenMR 40.581
_pdbe_chem_comp_rdkit_properties.chi0v 5.316
_pdbe_chem_comp_rdkit_properties.chi1v 2.908
_pdbe_chem_comp_rdkit_properties.chi2v 1.359
_pdbe_chem_comp_rdkit_properties.chi3v 1.359
_pdbe_chem_comp_rdkit_properties.chi4v 0.860
_pdbe_chem_comp_rdkit_properties.chi0n 15.316
_pdbe_chem_comp_rdkit_properties.chi1n 7.725
_pdbe_chem_comp_rdkit_properties.chi2n 1.359
_pdbe_chem_comp_rdkit_properties.chi3n 1.359
_pdbe_chem_comp_rdkit_properties.chi4n 0.860
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.860
_pdbe_chem_comp_rdkit_properties.kappa1 1.895
_pdbe_chem_comp_rdkit_properties.kappa2 2.325
_pdbe_chem_comp_rdkit_properties.kappa3 0.951
_pdbe_chem_comp_rdkit_properties.Phi 0.401
#
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
5V4 UniChem PDBe 5V4
5V4 UniChem ZINC ZINC000002037698
5V4 UniChem eMolecules 29260595
5V4 UniChem SureChEMBL SCHEMBL8049751
5V4 UniChem 'PubChem TPHARMA' 16901961
5V4 UniChem PubChem 247603
5V4 UniChem ACTor 4647-43-2
5V4 UniChem Nikkaji J513.007G
5V4 UniChem BRENDA 107676
5V4 UniChem BRENDA 32461
#
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
5V4 O01 -2.656 -0.360 1.212 ETKDGv3 1
5V4 O -1.300 1.852 -1.128 ETKDGv3 2
5V4 C01 -1.996 -0.187 -0.016 ETKDGv3 3
5V4 C02 -1.104 1.086 0.032 ETKDGv3 4
5V4 C03 -1.078 -1.406 -0.280 ETKDGv3 5
5V4 C04 0.281 0.554 0.062 ETKDGv3 6
5V4 C05 0.294 -0.876 -0.118 ETKDGv3 7
5V4 C06 1.417 1.246 0.220 ETKDGv3 8
5V4 C07 1.439 -1.567 -0.145 ETKDGv3 9
5V4 C08 2.704 0.507 0.204 ETKDGv3 10
5V4 C 2.715 -0.828 0.030 ETKDGv3 11
5V4 H1 -3.393 0.305 1.233 ETKDGv3 12
5V4 H2 -0.914 2.748 -0.947 ETKDGv3 13
5V4 H3 -2.749 -0.115 -0.836 ETKDGv3 14
5V4 H4 -1.311 1.690 0.946 ETKDGv3 15
5V4 H5 -1.211 -1.776 -1.320 ETKDGv3 16
5V4 H6 -1.266 -2.233 0.439 ETKDGv3 17
5V4 H7 1.401 2.320 0.353 ETKDGv3 18
5V4 H8 1.440 -2.640 -0.289 ETKDGv3 19
5V4 H9 3.634 1.046 0.330 ETKDGv3 20
5V4 H10 3.654 -1.366 0.016 ETKDGv3 21
#