data_LV4
#
_chem_comp.id LV4
_chem_comp.name 1-[2-(trifluoromethyloxy)phenyl]thiourea
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H7 F3 N2 O S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-03-15
_chem_comp.pdbx_modified_date 2019-07-05
_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 236.214
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LV4
_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 5QPP
_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
LV4 N1 N1 N 0 1 N N N N N N -7.046 -7.501 -18.825 3.338 2.245 0.501 N1 LV4 1
LV4 C4 C1 C 0 1 Y N N N N N -5.152 -9.943 -16.780 0.821 -0.350 0.506 C4 LV4 2
LV4 C5 C2 C 0 1 Y N N N N N -5.536 -11.276 -16.540 1.537 -1.537 0.547 C5 LV4 3
LV4 C6 C3 C 0 1 N N N N N N -6.542 -8.065 -17.670 2.665 1.121 0.183 C6 LV4 4
LV4 C7 C4 C 0 1 N N N N N N -2.566 -7.778 -16.624 -2.643 0.689 -0.127 C7 LV4 5
LV4 N N2 N 0 1 N N N N N N -5.725 -9.187 -17.844 1.467 0.869 0.748 N LV4 6
LV4 C C5 C 0 1 Y N N N N N -4.941 -12.014 -15.516 0.898 -2.738 0.302 C LV4 7
LV4 O O1 O 0 1 N N N N N N -3.757 -8.058 -16.078 -1.250 0.788 0.175 O LV4 8
LV4 C1 C6 C 0 1 Y N N N N N -3.972 -11.423 -14.724 -0.454 -2.760 0.016 C1 LV4 9
LV4 C2 C7 C 0 1 Y N N N N N -3.576 -10.085 -14.923 -1.175 -1.580 -0.027 C2 LV4 10
LV4 C3 C8 C 0 1 Y N N N N N -4.140 -9.361 -15.936 -0.542 -0.372 0.217 C3 LV4 11
LV4 F F1 F 0 1 N N N N N N -2.408 -6.442 -16.568 -3.274 -0.101 0.840 F LV4 12
LV4 F1 F2 F 0 1 N N N N N N -1.586 -8.261 -15.957 -3.212 1.967 -0.129 F1 LV4 13
LV4 F2 F3 F 0 1 N N N N N N -2.480 -8.145 -17.875 -2.806 0.103 -1.387 F2 LV4 14
LV4 S S1 S 0 1 N N N N N N -6.849 -7.406 -16.157 3.331 0.014 -0.940 S LV4 15
LV4 H1 H1 H 0 1 N N N N N N -7.611 -6.677 -18.774 4.199 2.426 0.094 H1 LV4 16
LV4 H2 H2 H 0 1 N N N N N N -6.846 -7.916 -19.713 2.958 2.874 1.134 H2 LV4 17
LV4 H3 H3 H 0 1 N N N N N N -6.298 -11.732 -17.154 2.593 -1.523 0.770 H3 LV4 18
LV4 H4 H4 H 0 1 N N N N N N -5.529 -9.479 -18.780 1.053 1.533 1.322 H4 LV4 19
LV4 H5 H5 H 0 1 N N N N N N -5.234 -13.039 -15.343 1.456 -3.662 0.335 H5 LV4 20
LV4 H6 H6 H 0 1 N N N N N N -3.509 -11.999 -13.937 -0.949 -3.700 -0.176 H6 LV4 21
LV4 H7 H7 H 0 1 N N N N N N -2.833 -9.636 -14.281 -2.231 -1.600 -0.252 H7 LV4 22
#
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
LV4 N1 C6 SING N N 1
LV4 F2 C7 SING N N 2
LV4 N C6 SING N N 3
LV4 N C4 SING N N 4
LV4 C6 S DOUB N N 5
LV4 C4 C5 DOUB Y N 6
LV4 C4 C3 SING Y N 7
LV4 C7 F SING N N 8
LV4 C7 O SING N N 9
LV4 C7 F1 SING N N 10
LV4 C5 C SING Y N 11
LV4 O C3 SING N N 12
LV4 C3 C2 DOUB Y N 13
LV4 C C1 DOUB Y N 14
LV4 C2 C1 SING Y N 15
LV4 N1 H1 SING N N 16
LV4 N1 H2 SING N N 17
LV4 C5 H3 SING N N 18
LV4 N H4 SING N N 19
LV4 C H5 SING N N 20
LV4 C1 H6 SING N N 21
LV4 C2 H7 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
LV4 InChI InChI 1.03 InChI=1S/C8H7F3N2OS/c9-8(10,11)14-6-4-2-1-3-5(6)13-7(12)15/h1-4H,(H3,12,13,15)
LV4 InChIKey InChI 1.03 HYKOSRYWIURWQI-UHFFFAOYSA-N
LV4 SMILES_CANONICAL CACTVS 3.385 NC(=S)Nc1ccccc1OC(F)(F)F
LV4 SMILES CACTVS 3.385 NC(=S)Nc1ccccc1OC(F)(F)F
LV4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1ccc(c(c1)NC(=S)N)OC(F)(F)F
LV4 SMILES "OpenEye OEToolkits" 2.0.6 c1ccc(c(c1)NC(=S)N)OC(F)(F)F
#
_pdbx_chem_comp_identifier.comp_id LV4
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier 1-[2-(trifluoromethyloxy)phenyl]thiourea
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LV4 'Create component' 2019-03-15 RCSB
LV4 'Initial release' 2019-07-10 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
LV4 N1 N 10.794 0.892 1
LV4 C4 C 8.196 -0.608 2
LV4 C5 C 9.495 -1.357 3
LV4 C6 C 9.495 1.643 4
LV4 C7 C 4.299 -1.357 5
LV4 N N 8.196 0.892 6
LV4 C C 9.495 -2.857 7
LV4 O O 5.598 -0.608 8
LV4 C1 C 8.196 -3.607 9
LV4 C2 C 6.897 -2.857 10
LV4 C3 C 6.897 -1.357 11
LV4 F F 3.549 -0.059 12
LV4 F1 F 5.049 -2.656 13
LV4 F2 F 3.000 -2.107 14
LV4 S S 9.495 3.143 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
LV4 N1 C6 SINGLE NONE 1
LV4 F2 C7 SINGLE NONE 2
LV4 N C6 SINGLE NONE 3
LV4 N C4 SINGLE NONE 4
LV4 C6 S DOUBLE NONE 5
LV4 C4 C5 DOUBLE NONE 6
LV4 C4 C3 SINGLE NONE 7
LV4 C7 F SINGLE NONE 8
LV4 C7 O SINGLE NONE 9
LV4 C7 F1 SINGLE NONE 10
LV4 C5 C SINGLE NONE 11
LV4 O C3 SINGLE NONE 12
LV4 C3 C2 DOUBLE NONE 13
LV4 C C1 DOUBLE NONE 14
LV4 C2 C1 SINGLE NONE 15
#
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
LV4 MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
LV4 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
LV4 Z56822813 F2 fragment Nc1ccccc1OC(F)F InChI=1S/C7H7F2NO/c8-7(9)11-6-4-2-1-3-5(6)10/h1-4,7H,10H2 CGNAIUUCOVWLLL-UHFFFAOYSA-N
LV4 Z291279160 F3 fragment NC(=S)Nc1ccccc1OC(F)(F)F InChI=1S/C8H7F3N2OS/c9-8(10,11)14-6-4-2-1-3-5(6)13-7(12)15/h1-4H,(H3,12,13,15) HYKOSRYWIURWQI-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
LV4 C4 S1 1
LV4 C5 S1 1
LV4 C S1 1
LV4 C1 S1 1
LV4 C2 S1 1
LV4 C3 S1 1
LV4 C4 F1 1
LV4 C5 F1 1
LV4 C F1 1
LV4 C1 F1 1
LV4 C2 F1 1
LV4 C3 F1 1
LV4 N F2 1
LV4 C4 F2 1
LV4 C5 F2 1
LV4 C F2 1
LV4 C1 F2 1
LV4 C2 F2 1
LV4 C3 F2 1
LV4 O F2 1
LV4 C7 F2 1
LV4 F2 F2 1
LV4 F F2 1
LV4 N F2 2
LV4 C4 F2 2
LV4 C5 F2 2
LV4 C F2 2
LV4 C1 F2 2
LV4 C2 F2 2
LV4 C3 F2 2
LV4 O F2 2
LV4 C7 F2 2
LV4 F2 F2 2
LV4 F1 F2 2
LV4 N F2 3
LV4 C4 F2 3
LV4 C5 F2 3
LV4 C F2 3
LV4 C1 F2 3
LV4 C2 F2 3
LV4 C3 F2 3
LV4 O F2 3
LV4 C7 F2 3
LV4 F F2 3
LV4 F1 F2 3
LV4 N1 F3 1
LV4 C6 F3 1
LV4 S F3 1
LV4 N F3 1
LV4 C4 F3 1
LV4 C5 F3 1
LV4 C F3 1
LV4 C1 F3 1
LV4 C2 F3 1
LV4 C3 F3 1
LV4 O F3 1
LV4 C7 F3 1
LV4 F2 F3 1
LV4 F F3 1
LV4 F1 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LV4
_pdbe_chem_comp_rdkit_properties.exactmw 236.023
_pdbe_chem_comp_rdkit_properties.amw 236.218
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_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 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.125
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 99.029
_pdbe_chem_comp_rdkit_properties.tpsa 47.280
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.398
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.099
_pdbe_chem_comp_rdkit_properties.chi0v 7.661
_pdbe_chem_comp_rdkit_properties.chi1v 3.758
_pdbe_chem_comp_rdkit_properties.chi2v 1.151
_pdbe_chem_comp_rdkit_properties.chi3v 1.151
_pdbe_chem_comp_rdkit_properties.chi4v 0.750
_pdbe_chem_comp_rdkit_properties.chi0n 13.845
_pdbe_chem_comp_rdkit_properties.chi1n 6.692
_pdbe_chem_comp_rdkit_properties.chi2n 1.060
_pdbe_chem_comp_rdkit_properties.chi3n 1.060
_pdbe_chem_comp_rdkit_properties.chi4n 0.658
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.500
_pdbe_chem_comp_rdkit_properties.kappa1 5.019
_pdbe_chem_comp_rdkit_properties.kappa2 4.347
_pdbe_chem_comp_rdkit_properties.kappa3 4.027
_pdbe_chem_comp_rdkit_properties.Phi 1.455
#
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
LV4 UniChem PDBe LV4
LV4 UniChem ZINC ZINC000000102765
LV4 UniChem SureChEMBL SCHEMBL5521725
LV4 UniChem 'PubChem TPHARMA' 15839137
LV4 UniChem 'EPA CompTox Dashboard' DTXSID60369741
LV4 UniChem ChemicalBook CB4271680
LV4 UniChem PubChem 2732749
#
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
LV4 N1 3.694 -0.962 -1.185 ETKDGv3 1
LV4 C4 0.385 0.417 0.099 ETKDGv3 2
LV4 C5 0.684 1.649 0.553 ETKDGv3 3
LV4 C6 2.751 -0.466 -0.235 ETKDGv3 4
LV4 C7 -2.548 -2.045 -0.201 ETKDGv3 5
LV4 N 1.365 -0.369 -0.602 ETKDGv3 6
LV4 C -0.340 2.464 1.234 ETKDGv3 7
LV4 O -1.284 -1.387 -0.258 ETKDGv3 8
LV4 C1 -1.580 1.990 1.383 ETKDGv3 9
LV4 C2 -1.930 0.653 0.867 ETKDGv3 10
LV4 C3 -1.000 -0.106 0.249 ETKDGv3 11
LV4 F -3.502 -1.306 -0.877 ETKDGv3 12
LV4 F1 -2.436 -3.283 -0.804 ETKDGv3 13
LV4 F2 -2.934 -2.224 1.115 ETKDGv3 14
LV4 S 3.238 -0.216 1.314 ETKDGv3 15
LV4 H1 3.394 -1.181 -2.161 ETKDGv3 16
LV4 H2 4.695 -1.101 -0.923 ETKDGv3 17
LV4 H3 1.670 2.070 0.406 ETKDGv3 18
LV4 H4 1.040 -0.941 -1.414 ETKDGv3 19
LV4 H5 -0.085 3.448 1.606 ETKDGv3 20
LV4 H6 -2.333 2.589 1.880 ETKDGv3 21
LV4 H7 -2.945 0.308 1.000 ETKDGv3 22
#