data_L3C
#
_chem_comp.id L3C
_chem_comp.name "4-(chloromethyl)benzoic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H7 Cl O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-02-25
_chem_comp.pdbx_modified_date 2023-03-10
_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 170.593
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code L3C
_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 7TZX
_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
L3C C01 C1 C 0 1 Y N N N N N 3.317 1.535 17.564 0.553 1.216 -0.432 C01 L3C 1
L3C C02 C2 C 0 1 Y N N N N N 3.481 2.830 17.097 -0.803 1.237 -0.183 C02 L3C 2
L3C C03 C3 C 0 1 Y N N N N N 4.447 3.642 17.667 -1.509 0.037 -0.074 C03 L3C 3
L3C C04 C4 C 0 1 Y N N N N N 5.253 3.146 18.693 -0.834 -1.177 -0.218 C04 L3C 4
L3C C05 C5 C 0 1 Y N N N N N 5.084 1.850 19.147 0.522 -1.184 -0.467 C05 L3C 5
L3C C06 C6 C 0 1 Y N N N N N 4.121 1.028 18.573 1.215 0.009 -0.574 C06 L3C 6
L3C C07 C7 C 0 1 N N N N N N 3.903 -0.417 19.047 2.696 -0.005 -0.851 C07 L3C 7
L3C C09 C8 C 0 1 N N N N N N 4.588 5.074 17.172 -2.961 0.052 0.194 C09 L3C 8
L3C O10 O1 O 0 1 N N N N N N 3.681 5.565 16.444 -3.545 1.109 0.319 O10 L3C 9
L3C O11 O2 O 0 1 N N N N N N 5.578 5.756 17.542 -3.639 -1.108 0.298 O11 L3C 10
L3C CL08 CL1 CL 0 0 N N N N N N 4.656 -1.679 18.015 3.600 -0.036 0.708 CL08 L3C 11
L3C H011 H1 H 0 0 N N N N N N 2.549 0.910 17.134 1.099 2.144 -0.521 H011 L3C 12
L3C H021 H2 H 0 0 N N N N N N 2.861 3.202 16.295 -1.319 2.180 -0.072 H021 L3C 13
L3C H041 H3 H 0 0 N N N N N N 6.011 3.776 19.134 -1.374 -2.109 -0.134 H041 L3C 14
L3C H051 H4 H 0 0 N N N N N N 5.702 1.476 19.950 1.045 -2.122 -0.578 H051 L3C 15
L3C H071 H5 H 0 0 N N N N N N 2.820 -0.605 19.080 2.948 -0.891 -1.434 H071 L3C 16
L3C H072 H6 H 0 0 N N N N N N 4.322 -0.510 20.060 2.970 0.888 -1.412 H072 L3C 17
L3C H1 H7 H 0 1 N N N N N N 5.506 6.636 17.191 -4.588 -1.048 0.474 H1 L3C 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
L3C O10 C09 DOUB N N 1
L3C C02 C01 DOUB Y N 2
L3C C02 C03 SING Y N 3
L3C C09 O11 SING N N 4
L3C C09 C03 SING N N 5
L3C C01 C06 SING Y N 6
L3C C03 C04 DOUB Y N 7
L3C CL08 C07 SING N N 8
L3C C06 C07 SING N N 9
L3C C06 C05 DOUB Y N 10
L3C C04 C05 SING Y N 11
L3C C01 H011 SING N N 12
L3C C02 H021 SING N N 13
L3C C04 H041 SING N N 14
L3C C05 H051 SING N N 15
L3C C07 H071 SING N N 16
L3C C07 H072 SING N N 17
L3C O11 H1 SING N N 18
#
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
L3C SMILES ACDLabs 12.01 ClCc1ccc(cc1)C(=O)O
L3C InChI InChI 1.03 InChI=1S/C8H7ClO2/c9-5-6-1-3-7(4-2-6)8(10)11/h1-4H,5H2,(H,10,11)
L3C InChIKey InChI 1.03 OITNBJHJJGMFBN-UHFFFAOYSA-N
L3C SMILES_CANONICAL CACTVS 3.385 OC(=O)c1ccc(CCl)cc1
L3C SMILES CACTVS 3.385 OC(=O)c1ccc(CCl)cc1
L3C SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cc(ccc1CCl)C(=O)O
L3C SMILES "OpenEye OEToolkits" 2.0.7 c1cc(ccc1CCl)C(=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
L3C "SYSTEMATIC NAME" ACDLabs 12.01 "4-(chloromethyl)benzoic acid"
L3C "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "4-(chloromethyl)benzoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
L3C 'Create component' 2022-02-25 RCSB
L3C 'Initial release' 2023-03-15 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
L3C C01 C 5.598 -1.215 1
L3C C02 C 5.598 0.285 2
L3C C03 C 4.299 1.035 3
L3C C04 C 3.000 0.285 4
L3C C05 C 3.000 -1.215 5
L3C C06 C 4.299 -1.965 6
L3C C07 C 4.299 -3.465 7
L3C C09 C 4.299 2.535 8
L3C O10 O 5.598 3.285 9
L3C O11 O 3.000 3.285 10
L3C CL08 Cl 3.000 -4.215 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
L3C O10 C09 DOUBLE NONE 1
L3C C02 C01 DOUBLE NONE 2
L3C C02 C03 SINGLE NONE 3
L3C C09 O11 SINGLE NONE 4
L3C C09 C03 SINGLE NONE 5
L3C C01 C06 SINGLE NONE 6
L3C C03 C04 DOUBLE NONE 7
L3C CL08 C07 SINGLE NONE 8
L3C C06 C07 SINGLE NONE 9
L3C C06 C05 DOUBLE NONE 10
L3C C04 C05 SINGLE NONE 11
#
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
L3C MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
L3C 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
L3C C01 S1 1
L3C C02 S1 1
L3C C03 S1 1
L3C C04 S1 1
L3C C05 S1 1
L3C C06 S1 1
L3C C01 F1 1
L3C C02 F1 1
L3C C03 F1 1
L3C C04 F1 1
L3C C05 F1 1
L3C C06 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id L3C
_pdbe_chem_comp_rdkit_properties.exactmw 170.013
_pdbe_chem_comp_rdkit_properties.amw 170.595
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_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 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_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 79.342
_pdbe_chem_comp_rdkit_properties.tpsa 37.300
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.014
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.426
_pdbe_chem_comp_rdkit_properties.chi0v 5.950
_pdbe_chem_comp_rdkit_properties.chi1v 2.975
_pdbe_chem_comp_rdkit_properties.chi2v 1.113
_pdbe_chem_comp_rdkit_properties.chi3v 1.113
_pdbe_chem_comp_rdkit_properties.chi4v 0.556
_pdbe_chem_comp_rdkit_properties.chi0n 12.194
_pdbe_chem_comp_rdkit_properties.chi1n 6.005
_pdbe_chem_comp_rdkit_properties.chi2n 0.924
_pdbe_chem_comp_rdkit_properties.chi3n 0.924
_pdbe_chem_comp_rdkit_properties.chi4n 0.462
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.020
_pdbe_chem_comp_rdkit_properties.kappa1 2.791
_pdbe_chem_comp_rdkit_properties.kappa2 3.394
_pdbe_chem_comp_rdkit_properties.kappa3 1.950
_pdbe_chem_comp_rdkit_properties.Phi 0.861
#
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
L3C UniChem ChEMBL CHEMBL101844
L3C UniChem PDBe L3C
L3C UniChem ZINC ZINC000001713271
L3C UniChem eMolecules 493239
L3C UniChem Mcule MCULE-3762893562
L3C UniChem NMRShiftDB 20040437
L3C UniChem Nikkaji J26.889E
L3C UniChem 'EPA CompTox Dashboard' DTXSID80167726
L3C UniChem ChemicalBook CB5739282
L3C UniChem SureChEMBL SCHEMBL40281
L3C UniChem 'PubChem TPHARMA' 15141035
L3C UniChem PubChem 74234
L3C UniChem ACTor 1642-81-5
#
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
L3C C01 -0.766 1.022 0.816 ETKDGv3 1
L3C C02 0.570 0.976 0.883 ETKDGv3 2
L3C C03 1.327 -0.045 0.112 ETKDGv3 3
L3C C04 0.649 -0.917 -0.658 ETKDGv3 4
L3C C05 -0.825 -0.860 -0.734 ETKDGv3 5
L3C C06 -1.508 0.052 -0.023 ETKDGv3 6
L3C C07 -3.003 0.140 -0.123 ETKDGv3 7
L3C C09 2.803 -0.094 0.194 ETKDGv3 8
L3C O10 3.426 0.729 0.918 ETKDGv3 9
L3C O11 3.519 -1.047 -0.527 ETKDGv3 10
L3C CL08 -3.454 1.220 -1.465 ETKDGv3 11
L3C H011 -1.305 1.775 1.378 ETKDGv3 12
L3C H021 1.093 1.693 1.502 ETKDGv3 13
L3C H041 1.167 -1.672 -1.236 ETKDGv3 14
L3C H051 -1.345 -1.564 -1.374 ETKDGv3 15
L3C H071 -3.447 -0.864 -0.298 ETKDGv3 16
L3C H072 -3.428 0.541 0.821 ETKDGv3 17
L3C H1 4.530 -1.086 -0.476 ETKDGv3 18
#