data_WHM
#
_chem_comp.id WHM
_chem_comp.name 2-[(3-fluorophenyl)methyl]-1lambda~6~,2-thiazolidine-1,1-dione
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H12 F N O2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-10-30
_chem_comp.pdbx_modified_date 2020-11-06
_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 229.271
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code WHM
_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 5RZA
_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
WHM C4 C1 C 0 1 Y N N N N N -11.940 2.315 -23.140 1.177 0.390 0.742 C4 WHM 1
WHM C5 C2 C 0 1 N N N N N N -11.495 3.126 -24.371 -0.080 0.192 1.549 C5 WHM 2
WHM C6 C3 C 0 1 N N N N N N -11.455 2.909 -26.857 -1.319 -1.809 0.401 C6 WHM 3
WHM C7 C4 C 0 1 N N N N N N -10.163 3.297 -27.594 -1.961 -1.980 -0.990 C7 WHM 4
WHM C8 C5 C 0 1 N N N N N N -9.127 2.225 -27.220 -3.104 -0.925 -1.018 C8 WHM 5
WHM N N1 N 0 1 N N N N N N -10.890 2.494 -25.584 -1.123 -0.382 0.695 N WHM 6
WHM C C6 C 0 1 Y N N N N N -13.021 2.465 -20.991 3.274 -0.437 -0.069 C WHM 7
WHM O O1 O 0 1 N N N N N N -8.705 1.803 -24.702 -3.163 0.979 0.892 O WHM 8
WHM C1 C7 C 0 1 Y N N N N N -12.860 1.071 -20.768 3.484 0.756 -0.741 C1 WHM 9
WHM C2 C8 C 0 1 Y N N N N N -12.222 0.313 -21.765 2.543 1.765 -0.666 C2 WHM 10
WHM C3 C9 C 0 1 Y N N N N N -11.760 0.924 -22.954 1.390 1.582 0.075 C3 WHM 11
WHM C9 C10 C 0 1 Y N N N N N -12.567 3.074 -22.154 2.119 -0.619 0.673 C9 WHM 12
WHM F F1 F 0 1 N N N N N N -13.624 3.245 -20.082 4.193 -1.424 -0.142 F WHM 13
WHM O1 O2 O 0 1 N N N N N N -9.867 0.095 -25.951 -1.608 1.319 -1.013 O1 WHM 14
WHM S S1 S 0 1 N N N N N N -9.579 1.488 -25.756 -2.309 0.464 -0.121 S WHM 15
WHM H3 H1 H 0 1 N N N N N N -12.390 3.661 -24.722 0.124 -0.484 2.379 H3 WHM 16
WHM H4 H2 H 0 1 N N N N N N -10.754 3.852 -24.005 -0.417 1.153 1.938 H4 WHM 17
WHM H5 H3 H 0 1 N N N N N N -11.983 2.085 -27.360 -1.972 -2.248 1.156 H5 WHM 18
WHM H6 H4 H 0 1 N N N N N N -12.136 3.766 -26.744 -0.355 -2.316 0.418 H6 WHM 19
WHM H7 H5 H 0 1 N N N N N N -10.330 3.305 -28.681 -1.232 -1.772 -1.774 H7 WHM 20
WHM H8 H6 H 0 1 N N N N N N -9.820 4.290 -27.269 -2.366 -2.985 -1.102 H8 WHM 21
WHM H9 H7 H 0 1 N N N N N N -9.082 1.466 -28.014 -3.354 -0.642 -2.040 H9 WHM 22
WHM H10 H8 H 0 1 N N N N N N -8.139 2.694 -27.105 -3.985 -1.285 -0.485 H10 WHM 23
WHM H H9 H 0 1 N N N N N N -13.217 0.608 -19.860 4.384 0.899 -1.320 H WHM 24
WHM H1 H10 H 0 1 N N N N N N -12.083 -0.748 -21.621 2.706 2.695 -1.190 H1 WHM 25
WHM H2 H11 H 0 1 N N N N N N -11.273 0.333 -23.715 0.655 2.371 0.133 H2 WHM 26
WHM H11 H12 H 0 1 N N N N N N -12.700 4.137 -22.294 1.955 -1.548 1.197 H11 WHM 27
#
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
WHM F C SING N N 1
WHM C C1 SING Y N 2
WHM C1 C2 DOUB Y N 3
WHM C2 C3 SING Y N 4
WHM C3 C4 DOUB Y N 5
WHM C4 C5 SING N N 6
WHM C5 N SING N N 7
WHM N C6 SING N N 8
WHM C6 C7 SING N N 9
WHM C7 C8 SING N N 10
WHM C8 S SING N N 11
WHM N S SING N N 12
WHM O S DOUB N N 13
WHM S O1 DOUB N N 14
WHM C9 C4 SING Y N 15
WHM C C9 DOUB Y N 16
WHM C5 H3 SING N N 17
WHM C5 H4 SING N N 18
WHM C6 H5 SING N N 19
WHM C6 H6 SING N N 20
WHM C7 H7 SING N N 21
WHM C7 H8 SING N N 22
WHM C8 H9 SING N N 23
WHM C8 H10 SING N N 24
WHM C1 H SING N N 25
WHM C2 H1 SING N N 26
WHM C3 H2 SING N N 27
WHM C9 H11 SING N N 28
#
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
WHM SMILES ACDLabs 12.01 c2(CN1CCCS1(=O)=O)cccc(c2)F
WHM InChI InChI 1.03 InChI=1S/C10H12FNO2S/c11-10-4-1-3-9(7-10)8-12-5-2-6-15(12,13)14/h1,3-4,7H,2,5-6,8H2
WHM InChIKey InChI 1.03 RVDJKNWVTKGWCE-UHFFFAOYSA-N
WHM SMILES_CANONICAL CACTVS 3.385 Fc1cccc(CN2CCC[S]2(=O)=O)c1
WHM SMILES CACTVS 3.385 Fc1cccc(CN2CCC[S]2(=O)=O)c1
WHM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cc(cc(c1)F)CN2CCCS2(=O)=O
WHM SMILES "OpenEye OEToolkits" 2.0.7 c1cc(cc(c1)F)CN2CCCS2(=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
WHM "SYSTEMATIC NAME" ACDLabs 12.01 2-[(3-fluorophenyl)methyl]-1lambda~6~,2-thiazolidine-1,1-dione
WHM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[(3-fluorophenyl)methyl]-1,2-thiazolidine 1,1-dioxide"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
WHM 'Create component' 2020-10-30 RCSB
WHM 'Initial release' 2020-11-11 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
WHM C4 C 5.598 -1.104 1
WHM C5 C 5.598 0.396 2
WHM C6 C 8.267 0.535 3
WHM C7 C 9.271 1.650 4
WHM C8 C 8.521 2.949 5
WHM N N 6.897 1.146 6
WHM C C 4.299 -3.354 7
WHM O O 6.742 4.104 8
WHM C1 C 5.598 -4.104 9
WHM C2 C 6.897 -3.354 10
WHM C3 C 6.897 -1.854 11
WHM C9 C 4.299 -1.854 12
WHM F F 3.000 -4.104 13
WHM O1 O 5.562 2.794 14
WHM S S 7.054 2.637 15
#
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
WHM F C SINGLE NONE 1
WHM C C1 DOUBLE NONE 2
WHM C1 C2 SINGLE NONE 3
WHM C2 C3 DOUBLE NONE 4
WHM C3 C4 SINGLE NONE 5
WHM C4 C5 SINGLE NONE 6
WHM C5 N SINGLE NONE 7
WHM N C6 SINGLE NONE 8
WHM C6 C7 SINGLE NONE 9
WHM C7 C8 SINGLE NONE 10
WHM C8 S SINGLE NONE 11
WHM N S SINGLE NONE 12
WHM O S DOUBLE NONE 13
WHM S O1 DOUBLE NONE 14
WHM C9 C4 DOUBLE NONE 15
WHM C C9 SINGLE NONE 16
#
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
WHM MurckoScaffold S1 scaffold O=S1(=O)CCCN1Cc1ccccc1 InChI=1S/C10H13NO2S/c12-14(13)8-4-7-11(14)9-10-5-2-1-3-6-10/h1-3,5-6H,4,7-9H2 TZKMAPDWYRGEOB-UHFFFAOYSA-N
WHM phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
WHM Z729352906 F2 fragment O=S1(=O)CCCN1Cc1cccc(F)c1 InChI=1S/C10H12FNO2S/c11-10-4-1-3-9(7-10)8-12-5-2-6-15(12,13)14/h1,3-4,7H,2,5-6,8H2 RVDJKNWVTKGWCE-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
WHM C4 S1 1
WHM C5 S1 1
WHM C6 S1 1
WHM C7 S1 1
WHM C8 S1 1
WHM N S1 1
WHM C S1 1
WHM O S1 1
WHM C1 S1 1
WHM C2 S1 1
WHM C3 S1 1
WHM C9 S1 1
WHM O1 S1 1
WHM S S1 1
WHM C4 F1 1
WHM C3 F1 1
WHM C2 F1 1
WHM C1 F1 1
WHM C F1 1
WHM C9 F1 1
WHM F F2 1
WHM C F2 1
WHM C1 F2 1
WHM C2 F2 1
WHM C3 F2 1
WHM C4 F2 1
WHM C5 F2 1
WHM N F2 1
WHM C6 F2 1
WHM C7 F2 1
WHM C8 F2 1
WHM S F2 1
WHM O F2 1
WHM O1 F2 1
WHM C9 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id WHM
_pdbe_chem_comp_rdkit_properties.exactmw 229.057
_pdbe_chem_comp_rdkit_properties.amw 229.276
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.400
_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 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_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 105.431
_pdbe_chem_comp_rdkit_properties.tpsa 37.380
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.306
_pdbe_chem_comp_rdkit_properties.CrippenMR 54.948
_pdbe_chem_comp_rdkit_properties.chi0v 7.866
_pdbe_chem_comp_rdkit_properties.chi1v 5.046
_pdbe_chem_comp_rdkit_properties.chi2v 2.409
_pdbe_chem_comp_rdkit_properties.chi3v 2.409
_pdbe_chem_comp_rdkit_properties.chi4v 1.453
_pdbe_chem_comp_rdkit_properties.chi0n 19.050
_pdbe_chem_comp_rdkit_properties.chi1n 9.606
_pdbe_chem_comp_rdkit_properties.chi2n 1.386
_pdbe_chem_comp_rdkit_properties.chi3n 1.386
_pdbe_chem_comp_rdkit_properties.chi4n 0.810
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.940
_pdbe_chem_comp_rdkit_properties.kappa1 3.275
_pdbe_chem_comp_rdkit_properties.kappa2 3.903
_pdbe_chem_comp_rdkit_properties.kappa3 2.352
_pdbe_chem_comp_rdkit_properties.Phi 0.852
#
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
WHM UniChem ZINC ZINC000071965017
WHM UniChem PubChem 60523291
WHM UniChem Mcule MCULE-3313761937
#
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
WHM C4 1.222 -0.033 -0.763 ETKDGv3 1
WHM C5 0.147 0.706 -1.537 ETKDGv3 2
WHM C6 -1.046 1.374 0.576 ETKDGv3 3
WHM C7 -2.430 1.192 1.219 ETKDGv3 4
WHM C8 -2.990 -0.154 0.761 ETKDGv3 5
WHM N -1.129 0.917 -0.818 ETKDGv3 6
WHM C 2.540 -2.035 -0.247 ETKDGv3 7
WHM O -3.158 -0.401 -1.927 ETKDGv3 8
WHM C1 3.303 -1.362 0.621 ETKDGv3 9
WHM C2 3.077 0.080 0.838 ETKDGv3 10
WHM C3 2.099 0.713 0.178 ETKDGv3 11
WHM C9 1.464 -1.339 -0.984 ETKDGv3 12
WHM F 2.755 -3.357 -0.459 ETKDGv3 13
WHM O1 -1.455 -1.760 -0.759 ETKDGv3 14
WHM S -2.187 -0.449 -0.781 ETKDGv3 15
WHM H3 0.549 1.702 -1.821 ETKDGv3 16
WHM H4 -0.057 0.190 -2.501 ETKDGv3 17
WHM H5 -0.332 0.760 1.163 ETKDGv3 18
WHM H6 -0.738 2.440 0.612 ETKDGv3 19
WHM H7 -2.361 1.237 2.327 ETKDGv3 20
WHM H8 -3.101 2.007 0.869 ETKDGv3 21
WHM H9 -2.716 -0.953 1.483 ETKDGv3 22
WHM H10 -4.093 -0.111 0.637 ETKDGv3 23
WHM H 4.094 -1.869 1.160 ETKDGv3 24
WHM H1 3.708 0.626 1.528 ETKDGv3 25
WHM H2 1.947 1.773 0.336 ETKDGv3 26
WHM H11 0.890 -1.894 -1.714 ETKDGv3 27
#