data_O1J
#
_chem_comp.id O1J
_chem_comp.name "(benzyloxy)acetic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H10 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-06-04
_chem_comp.pdbx_modified_date 2019-08-16
_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 166.174
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code O1J
_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 5QSK
_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
O1J C4 C1 C 0 1 Y N N N N N 5.911 -13.512 -4.707 2.071 0.501 1.113 C4 O1J 1
O1J C5 C2 C 0 1 Y N N N N N 6.886 -14.453 -4.989 3.299 -0.117 1.254 C5 O1J 2
O1J C6 C3 C 0 1 Y N N N N N 8.151 -14.043 -5.322 3.911 -0.699 0.159 C6 O1J 3
O1J C7 C4 C 0 1 Y N N N N N 8.441 -12.698 -5.374 3.294 -0.661 -1.077 C7 O1J 4
O1J C8 C5 C 0 1 Y N N N N N 7.492 -11.770 -5.096 2.066 -0.043 -1.219 C8 O1J 5
O1J C C6 C 0 1 N N N N N N 6.303 -9.917 -1.635 -3.260 -0.294 0.068 C O1J 6
O1J O O1 O 0 1 N N N N N N 6.344 -8.900 -0.887 -4.571 -0.016 0.004 O O1J 7
O1J C1 C7 C 0 1 N N N N N N 5.824 -9.640 -3.083 -2.246 0.793 -0.181 C1 O1J 8
O1J C2 C8 C 0 1 N N N N N N 5.135 -11.140 -4.672 0.113 1.207 -0.276 C2 O1J 9
O1J C3 C9 C 0 1 Y N N N N N 6.213 -12.170 -4.781 1.452 0.533 -0.122 C3 O1J 10
O1J O1 O2 O 0 1 N N N N N N 6.571 -11.103 -1.370 -2.891 -1.416 0.324 O1 O1J 11
O1J O2 O3 O 0 1 N N N N N N 5.037 -10.742 -3.377 -0.929 0.254 -0.058 O2 O1J 12
O1J H1 H1 H 0 1 N N N N N N 4.916 -13.829 -4.430 1.594 0.956 1.969 H1 O1J 13
O1J H2 H2 H 0 1 N N N N N N 6.651 -15.506 -4.947 3.781 -0.147 2.220 H2 O1J 14
O1J H3 H3 H 0 1 N N N N N N 8.917 -14.772 -5.543 4.870 -1.182 0.270 H3 O1J 15
O1J H4 H4 H 0 1 N N N N N N 9.438 -12.378 -5.640 3.772 -1.115 -1.933 H4 O1J 16
O1J H5 H5 H 0 1 N N N N N N 7.739 -10.719 -5.122 1.584 -0.013 -2.185 H5 O1J 17
O1J H6 H6 H 0 1 N N N N N N 6.628 -9.157 -0.018 -5.183 -0.746 0.171 H6 O1J 18
O1J H7 H7 H 0 1 N N N N N N 6.677 -9.570 -3.773 -2.382 1.194 -1.186 H7 O1J 19
O1J H8 H8 H 0 1 N N N N N N 5.236 -8.712 -3.132 -2.382 1.590 0.549 H8 O1J 20
O1J H9 H9 H 0 1 N N N N N N 5.384 -10.276 -5.306 0.026 2.013 0.452 H9 O1J 21
O1J H10 H10 H 0 1 N N N N N N 4.178 -11.571 -4.999 0.026 1.617 -1.283 H10 O1J 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
O1J C7 C6 DOUB Y N 1
O1J C7 C8 SING Y N 2
O1J C6 C5 SING Y N 3
O1J C8 C3 DOUB Y N 4
O1J C5 C4 DOUB Y N 5
O1J C3 C4 SING Y N 6
O1J C3 C2 SING N N 7
O1J C2 O2 SING N N 8
O1J O2 C1 SING N N 9
O1J C1 C SING N N 10
O1J C O1 DOUB N N 11
O1J C O SING N N 12
O1J C4 H1 SING N N 13
O1J C5 H2 SING N N 14
O1J C6 H3 SING N N 15
O1J C7 H4 SING N N 16
O1J C8 H5 SING N N 17
O1J O H6 SING N N 18
O1J C1 H7 SING N N 19
O1J C1 H8 SING N N 20
O1J C2 H9 SING N N 21
O1J C2 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
O1J SMILES ACDLabs 12.01 c1ccccc1COCC(=O)O
O1J InChI InChI 1.03 InChI=1S/C9H10O3/c10-9(11)7-12-6-8-4-2-1-3-5-8/h1-5H,6-7H2,(H,10,11)
O1J InChIKey InChI 1.03 GRZHHTYDZVRPIC-UHFFFAOYSA-N
O1J SMILES_CANONICAL CACTVS 3.385 OC(=O)COCc1ccccc1
O1J SMILES CACTVS 3.385 OC(=O)COCc1ccccc1
O1J SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1ccc(cc1)COCC(=O)O
O1J SMILES "OpenEye OEToolkits" 2.0.6 c1ccc(cc1)COCC(=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
O1J "SYSTEMATIC NAME" ACDLabs 12.01 "(benzyloxy)acetic acid"
O1J "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "2-phenylmethoxyethanoic 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
O1J 'Create component' 2019-06-04 RCSB
O1J 'Initial release' 2019-08-21 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
O1J C4 C 5.598 -2.482 1
O1J C5 C 5.598 -3.982 2
O1J C6 C 4.299 -4.732 3
O1J C7 C 3.000 -3.982 4
O1J C8 C 3.000 -2.482 5
O1J C C 6.897 2.768 6
O1J O O 8.196 2.018 7
O1J C1 C 5.598 2.018 8
O1J C2 C 4.299 -0.233 9
O1J C3 C 4.299 -1.732 10
O1J O1 O 6.897 4.268 11
O1J O2 O 5.598 0.517 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
O1J C7 C6 DOUBLE NONE 1
O1J C7 C8 SINGLE NONE 2
O1J C6 C5 SINGLE NONE 3
O1J C8 C3 DOUBLE NONE 4
O1J C5 C4 DOUBLE NONE 5
O1J C3 C4 SINGLE NONE 6
O1J C3 C2 SINGLE NONE 7
O1J C2 O2 SINGLE NONE 8
O1J O2 C1 SINGLE NONE 9
O1J C1 C SINGLE NONE 10
O1J C O1 DOUBLE NONE 11
O1J C O 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
O1J MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
O1J 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
O1J C4 S1 1
O1J C5 S1 1
O1J C6 S1 1
O1J C7 S1 1
O1J C8 S1 1
O1J C3 S1 1
O1J C4 F1 1
O1J C5 F1 1
O1J C6 F1 1
O1J C7 F1 1
O1J C8 F1 1
O1J C3 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id O1J
_pdbe_chem_comp_rdkit_properties.exactmw 166.063
_pdbe_chem_comp_rdkit_properties.amw 166.176
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.222
_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 84.732
_pdbe_chem_comp_rdkit_properties.tpsa 46.530
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.233
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.468
_pdbe_chem_comp_rdkit_properties.chi0v 5.725
_pdbe_chem_comp_rdkit_properties.chi1v 2.816
_pdbe_chem_comp_rdkit_properties.chi2v 0.787
_pdbe_chem_comp_rdkit_properties.chi3v 0.787
_pdbe_chem_comp_rdkit_properties.chi4v 0.419
_pdbe_chem_comp_rdkit_properties.chi0n 15.725
_pdbe_chem_comp_rdkit_properties.chi1n 7.725
_pdbe_chem_comp_rdkit_properties.chi2n 0.787
_pdbe_chem_comp_rdkit_properties.chi3n 0.787
_pdbe_chem_comp_rdkit_properties.chi4n 0.419
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.350
_pdbe_chem_comp_rdkit_properties.kappa1 2.326
_pdbe_chem_comp_rdkit_properties.kappa2 4.512
_pdbe_chem_comp_rdkit_properties.kappa3 3.163
_pdbe_chem_comp_rdkit_properties.Phi 0.875
#
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
O1J UniChem ChEMBL CHEMBL3247413
O1J UniChem ChEBI 180539
O1J UniChem ZINC ZINC000000396091
O1J UniChem eMolecules 507563
O1J UniChem SureChEMBL SCHEMBL231282
O1J UniChem 'PubChem TPHARMA' 15437617
O1J UniChem NMRShiftDB 20032779
O1J UniChem ACTor 30379-55-6
O1J UniChem Nikkaji J783.827A
O1J UniChem ChemicalBook CB9346105
O1J UniChem PubChem 290301
O1J UniChem Mcule MCULE-7716016814
#
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
O1J C4 -0.351 0.893 -1.312 ETKDGv3 1
O1J C5 -0.933 2.034 -0.921 ETKDGv3 2
O1J C6 -1.919 2.023 0.178 ETKDGv3 3
O1J C7 -2.232 0.872 0.786 ETKDGv3 4
O1J C8 -1.589 -0.389 0.361 ETKDGv3 5
O1J C 1.944 -0.542 1.314 ETKDGv3 6
O1J O 1.829 0.839 1.181 ETKDGv3 7
O1J C1 2.017 -1.406 0.097 ETKDGv3 8
O1J C2 -0.008 -1.663 -1.057 ETKDGv3 9
O1J C3 -0.693 -0.387 -0.642 ETKDGv3 10
O1J O1 1.959 -1.065 2.460 ETKDGv3 11
O1J O2 0.823 -2.161 -0.024 ETKDGv3 12
O1J H1 0.375 0.910 -2.115 ETKDGv3 13
O1J H2 -0.680 2.967 -1.408 ETKDGv3 14
O1J H3 -2.387 2.948 0.491 ETKDGv3 15
O1J H4 -2.953 0.863 1.593 ETKDGv3 16
O1J H5 -1.844 -1.309 0.871 ETKDGv3 17
O1J H6 1.760 1.435 1.996 ETKDGv3 18
O1J H7 2.261 -0.781 -0.794 ETKDGv3 19
O1J H8 2.863 -2.114 0.222 ETKDGv3 20
O1J H9 -0.790 -2.425 -1.265 ETKDGv3 21
O1J H10 0.548 -1.541 -2.014 ETKDGv3 22
#