data_D4Y
#
_chem_comp.id D4Y
_chem_comp.name (3S)-5-fluoro-3-hydroxy-1,3-dihydro-2H-indol-2-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H6 F N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-10-18
_chem_comp.pdbx_modified_date 2018-09-07
_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 167.137
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code D4Y
_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 6AXA
_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
D4Y C7 C1 C 0 1 Y N N N N N -1.285 27.149 54.405 -0.008 -0.382 0.187 C7 D4Y 1
D4Y C4 C2 C 0 1 Y N N N N N -3.963 26.897 53.862 2.254 1.155 -0.182 C4 D4Y 2
D4Y C5 C3 C 0 1 Y N N N N N -3.089 25.898 53.513 2.373 -0.205 0.051 C5 D4Y 3
D4Y C6 C4 C 0 1 Y N N N N N -1.738 26.009 53.762 1.234 -0.973 0.236 C6 D4Y 4
D4Y C3 C5 C 0 1 Y N N N N N -3.505 28.060 54.474 1.010 1.747 -0.238 C3 D4Y 5
D4Y C2 C6 C 0 1 Y N N N N N -2.157 28.160 54.729 -0.139 0.980 -0.052 C2 D4Y 6
D4Y C1 C7 C 0 1 N N N N N N -0.164 28.923 55.432 -2.297 0.291 0.162 C1 D4Y 7
D4Y F F1 F 0 1 N N N N N N -3.552 24.785 52.912 3.594 -0.781 0.097 F D4Y 8
D4Y C C8 C 0 1 N N S N N N 0.104 27.643 54.639 -1.411 -0.923 0.343 C D4Y 9
D4Y O O1 O 0 1 N N N N N N 1.025 26.713 55.168 -1.686 -1.898 -0.664 O D4Y 10
D4Y N N1 N 0 1 N N N N N N -1.476 29.188 55.296 -1.488 1.341 -0.060 N D4Y 11
D4Y O1 O2 O 0 1 N N N N N N 0.692 29.665 55.943 -3.508 0.312 0.209 O1 D4Y 12
D4Y H4 H1 H 0 1 N N N N N N -5.017 26.779 53.660 3.141 1.754 -0.327 H4 D4Y 13
D4Y H5 H2 H 0 1 N N N N N N -1.052 25.229 53.464 1.321 -2.034 0.418 H5 D4Y 14
D4Y H3 H3 H 0 1 N N N N N N -4.184 28.856 54.740 0.925 2.808 -0.420 H3 D4Y 15
D4Y H1 H4 H 0 1 N N N N N N 0.488 27.967 53.660 -1.546 -1.352 1.336 H1 D4Y 16
D4Y H H5 H 0 1 N N N N N N 1.871 27.131 55.276 -2.573 -2.279 -0.611 H D4Y 17
D4Y H2 H6 H 0 1 N N N N N N -1.902 30.047 55.581 -1.805 2.246 -0.209 H2 D4Y 18
#
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
D4Y F C5 SING N N 1
D4Y C5 C6 DOUB Y N 2
D4Y C5 C4 SING Y N 3
D4Y C6 C7 SING Y N 4
D4Y C4 C3 DOUB Y N 5
D4Y C7 C SING N N 6
D4Y C7 C2 DOUB Y N 7
D4Y C3 C2 SING Y N 8
D4Y C O SING N N 9
D4Y C C1 SING N N 10
D4Y C2 N SING N N 11
D4Y N C1 SING N N 12
D4Y C1 O1 DOUB N N 13
D4Y C4 H4 SING N N 14
D4Y C6 H5 SING N N 15
D4Y C3 H3 SING N N 16
D4Y C H1 SING N N 17
D4Y O H SING N N 18
D4Y N H2 SING N N 19
#
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
D4Y SMILES ACDLabs 12.01 c12C(C(=O)Nc1ccc(c2)F)O
D4Y InChI InChI 1.03 InChI=1S/C8H6FNO2/c9-4-1-2-6-5(3-4)7(11)8(12)10-6/h1-3,7,11H,(H,10,12)/t7-/m0/s1
D4Y InChIKey InChI 1.03 XYDTZHMQTYEJQN-ZETCQYMHSA-N
D4Y SMILES_CANONICAL CACTVS 3.385 O[C@@H]1C(=O)Nc2ccc(F)cc12
D4Y SMILES CACTVS 3.385 O[CH]1C(=O)Nc2ccc(F)cc12
D4Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1cc2c(cc1F)[C@@H](C(=O)N2)O
D4Y SMILES "OpenEye OEToolkits" 2.0.6 c1cc2c(cc1F)C(C(=O)N2)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
D4Y "SYSTEMATIC NAME" ACDLabs 12.01 (3S)-5-fluoro-3-hydroxy-1,3-dihydro-2H-indol-2-one
D4Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 (3~{S})-5-fluoranyl-3-oxidanyl-1,3-dihydroindol-2-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
D4Y 'Create component' 2017-10-18 RCSB
D4Y 'Initial release' 2018-09-12 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
D4Y C7 C 6.897 0.383 1
D4Y C4 C 4.299 -1.117 2
D4Y C5 C 4.299 0.383 3
D4Y C6 C 5.598 1.133 4
D4Y C3 C 5.598 -1.867 5
D4Y C2 C 6.897 -1.117 6
D4Y C1 C 9.192 -0.367 7
D4Y F F 3.000 1.133 8
D4Y C C 8.316 0.840 9
D4Y O O 8.783 2.266 10
D4Y N N 8.316 -1.574 11
D4Y O1 O 10.692 -0.367 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
D4Y F C5 SINGLE NONE 1
D4Y C5 C6 SINGLE NONE 2
D4Y C5 C4 DOUBLE NONE 3
D4Y C6 C7 DOUBLE NONE 4
D4Y C4 C3 SINGLE NONE 5
D4Y C7 C SINGLE NONE 6
D4Y C7 C2 SINGLE NONE 7
D4Y C3 C2 DOUBLE NONE 8
D4Y C O SINGLE BEGINDASH 9
D4Y C C1 SINGLE NONE 10
D4Y C2 N SINGLE NONE 11
D4Y N C1 SINGLE NONE 12
D4Y C1 O1 DOUBLE 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
D4Y MurckoScaffold S1 scaffold O=C1Cc2ccccc2N1 InChI=1S/C8H7NO/c10-8-5-6-3-1-2-4-7(6)9-8/h1-4H,5H2,(H,9,10) JYGFTBXVXVMTGB-UHFFFAOYSA-N
D4Y amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
D4Y 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
D4Y C7 S1 1
D4Y C4 S1 1
D4Y C5 S1 1
D4Y C6 S1 1
D4Y C3 S1 1
D4Y C2 S1 1
D4Y C1 S1 1
D4Y C S1 1
D4Y N S1 1
D4Y O1 S1 1
D4Y N F1 1
D4Y C1 F1 1
D4Y O1 F1 1
D4Y C F1 1
D4Y C7 F2 1
D4Y C6 F2 1
D4Y C5 F2 1
D4Y C4 F2 1
D4Y C3 F2 1
D4Y C2 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id D4Y
_pdbe_chem_comp_rdkit_properties.exactmw 167.038
_pdbe_chem_comp_rdkit_properties.amw 167.139
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.125
_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 76.401
_pdbe_chem_comp_rdkit_properties.tpsa 49.330
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.376
_pdbe_chem_comp_rdkit_properties.CrippenMR 38.900
_pdbe_chem_comp_rdkit_properties.chi0v 5.642
_pdbe_chem_comp_rdkit_properties.chi1v 3.044
_pdbe_chem_comp_rdkit_properties.chi2v 1.397
_pdbe_chem_comp_rdkit_properties.chi3v 1.397
_pdbe_chem_comp_rdkit_properties.chi4v 0.884
_pdbe_chem_comp_rdkit_properties.chi0n 11.642
_pdbe_chem_comp_rdkit_properties.chi1n 5.900
_pdbe_chem_comp_rdkit_properties.chi2n 1.397
_pdbe_chem_comp_rdkit_properties.chi3n 1.397
_pdbe_chem_comp_rdkit_properties.chi4n 0.884
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.420
_pdbe_chem_comp_rdkit_properties.kappa1 3.142
_pdbe_chem_comp_rdkit_properties.kappa2 2.282
_pdbe_chem_comp_rdkit_properties.kappa3 0.887
_pdbe_chem_comp_rdkit_properties.Phi 0.597
#
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
D4Y UniChem PDBe D4Y
D4Y UniChem ZINC ZINC000000111128
D4Y UniChem PubChem 6926190
#
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
D4Y C7 -0.157 -0.505 0.258 ETKDGv3 1
D4Y C4 2.427 0.499 -0.124 ETKDGv3 2
D4Y C5 2.248 -0.793 0.227 ETKDGv3 3
D4Y C6 0.878 -1.332 0.433 ETKDGv3 4
D4Y C3 1.257 1.397 -0.307 ETKDGv3 5
D4Y C2 0.040 0.882 -0.116 ETKDGv3 6
D4Y C1 -2.191 0.584 0.079 ETKDGv3 7
D4Y F 3.321 -1.604 0.393 ETKDGv3 8
D4Y C -1.624 -0.778 0.403 ETKDGv3 9
D4Y O -2.066 -1.755 -0.506 ETKDGv3 10
D4Y N -1.197 1.560 -0.231 ETKDGv3 11
D4Y O1 -3.422 0.849 0.085 ETKDGv3 12
D4Y H4 3.426 0.888 -0.272 ETKDGv3 13
D4Y H5 0.724 -2.365 0.717 ETKDGv3 14
D4Y H3 1.389 2.435 -0.584 ETKDGv3 15
D4Y H1 -1.872 -1.073 1.445 ETKDGv3 16
D4Y H -1.829 -1.451 -1.422 ETKDGv3 17
D4Y H2 -1.351 2.563 -0.479 ETKDGv3 18
#