data_3QO
#
_chem_comp.id 3QO
_chem_comp.name 4-benzylpyridine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H11 N"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2011-02-16
_chem_comp.pdbx_modified_date 2011-09-09
_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 169.222
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 3QO
_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 3QOA
_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
3QO CAA CAA C 0 1 Y N N N N N -41.293 17.139 -25.238 3.507 0.002 -0.924 CAA 3QO 1
3QO CAB CAB C 0 1 Y N N N N N -41.298 15.952 -25.922 2.941 1.198 -0.524 CAB 3QO 2
3QO CAC CAC C 0 1 Y N N N N N -41.461 17.149 -23.865 2.943 -1.196 -0.526 CAC 3QO 3
3QO CAD CAD C 0 1 Y N N N N N -45.218 13.560 -21.807 -2.920 -1.152 -0.537 CAD 3QO 4
3QO CAE CAE C 0 1 Y N N N N N -43.773 13.209 -20.092 -2.924 1.152 -0.530 CAE 3QO 5
3QO CAF CAF C 0 1 Y N N N N N -41.488 14.761 -25.225 1.812 1.197 0.273 CAF 3QO 6
3QO CAG CAG C 0 1 Y N N N N N -41.618 15.959 -23.188 1.817 -1.197 0.277 CAG 3QO 7
3QO CAH CAH C 0 1 Y N N N N N -44.203 13.600 -22.709 -1.792 -1.192 0.260 CAH 3QO 8
3QO CAI CAI C 0 1 Y N N N N N -42.712 13.272 -20.941 -1.793 1.191 0.263 CAI 3QO 9
3QO CAJ CAJ C 0 1 N N N N N N -41.797 13.491 -23.165 0.018 -0.002 1.541 CAJ 3QO 10
3QO NAK NAK N 0 1 Y N N N N N -44.968 13.363 -20.564 -3.445 0.000 -0.906 NAK 3QO 11
3QO CAL CAL C 0 1 Y N N N N N -41.649 14.784 -23.861 1.248 -0.001 0.671 CAL 3QO 12
3QO CAM CAM C 0 1 Y N N N N N -42.944 13.461 -22.243 -1.213 -0.001 0.671 CAM 3QO 13
3QO HAA HAA H 0 1 N N N N N N -41.158 18.068 -25.771 4.386 0.002 -1.551 HAA 3QO 14
3QO HAB HAB H 0 1 N N N N N N -41.156 15.940 -26.993 3.382 2.134 -0.835 HAB 3QO 15
3QO HAC HAC H 0 1 N N N N N N -41.469 18.085 -23.326 3.381 -2.131 -0.842 HAC 3QO 16
3QO HAD HAD H 0 1 N N N N N N -46.238 13.694 -22.137 -3.375 -2.075 -0.865 HAD 3QO 17
3QO HAE HAE H 0 1 N N N N N N -43.620 13.033 -19.038 -3.382 2.076 -0.852 HAE 3QO 18
3QO HAF HAF H 0 1 N N N N N N -41.509 13.821 -25.756 1.371 2.132 0.586 HAF 3QO 19
3QO HAG HAG H 0 1 N N N N N N -41.717 15.963 -22.113 1.376 -2.133 0.587 HAG 3QO 20
3QO HAH HAH H 0 1 N N N N N N -44.397 13.738 -23.762 -1.367 -2.138 0.559 HAH 3QO 21
3QO HAI HAI H 0 1 N N N N N N -41.703 13.171 -20.570 -1.366 2.137 0.561 HAI 3QO 22
3QO HAJ HAJ H 0 1 N N N N N N -41.942 12.706 -23.922 0.018 -0.892 2.170 HAJ 3QO 23
3QO HAJA HAJA H 0 0 N N N N N N -40.882 13.305 -22.584 0.018 0.888 2.171 HAJA 3QO 24
#
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
3QO CAB CAA DOUB Y N 1
3QO CAA CAC SING Y N 2
3QO CAA HAA SING N N 3
3QO CAB CAF SING Y N 4
3QO CAB HAB SING N N 5
3QO CAC CAG DOUB Y N 6
3QO CAC HAC SING N N 7
3QO CAH CAD DOUB Y N 8
3QO CAD NAK SING Y N 9
3QO CAD HAD SING N N 10
3QO CAI CAE SING Y N 11
3QO NAK CAE DOUB Y N 12
3QO CAE HAE SING N N 13
3QO CAF CAL DOUB Y N 14
3QO CAF HAF SING N N 15
3QO CAL CAG SING Y N 16
3QO CAG HAG SING N N 17
3QO CAH CAM SING Y N 18
3QO CAH HAH SING N N 19
3QO CAM CAI DOUB Y N 20
3QO CAI HAI SING N N 21
3QO CAL CAJ SING N N 22
3QO CAJ CAM SING N N 23
3QO CAJ HAJ SING N N 24
3QO CAJ HAJA SING N N 25
#
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
3QO SMILES ACDLabs 12.01 n1ccc(cc1)Cc2ccccc2
3QO SMILES_CANONICAL CACTVS 3.370 C(c1ccccc1)c2ccncc2
3QO SMILES CACTVS 3.370 C(c1ccccc1)c2ccncc2
3QO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 c1ccc(cc1)Cc2ccncc2
3QO SMILES "OpenEye OEToolkits" 1.7.0 c1ccc(cc1)Cc2ccncc2
3QO InChI InChI 1.03 InChI=1S/C12H11N/c1-2-4-11(5-3-1)10-12-6-8-13-9-7-12/h1-9H,10H2
3QO InChIKey InChI 1.03 DBOLXXRVIFGDTI-UHFFFAOYSA-N
#
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
3QO "SYSTEMATIC NAME" ACDLabs 12.01 4-benzylpyridine
3QO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 4-(phenylmethyl)pyridine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
3QO 'Create component' 2011-02-16 RCSB
3QO 'Modify aromatic_flag' 2011-06-04 RCSB
3QO 'Modify descriptor' 2011-06-04 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
3QO CAA C 4.299 -3.750 1
3QO CAB C 5.598 -3.000 2
3QO CAC C 3.000 -3.000 3
3QO CAD C 8.196 1.500 4
3QO CAE C 6.897 3.750 5
3QO CAF C 5.598 -1.500 6
3QO CAG C 3.000 -1.500 7
3QO CAH C 6.897 0.750 8
3QO CAI C 5.598 3.000 9
3QO CAJ C 4.299 0.750 10
3QO NAK N 8.196 3.000 11
3QO CAL C 4.299 -0.750 12
3QO CAM C 5.598 1.500 13
#
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
3QO CAB CAA DOUBLE NONE 1
3QO CAA CAC SINGLE NONE 2
3QO CAB CAF SINGLE NONE 3
3QO CAC CAG DOUBLE NONE 4
3QO CAH CAD DOUBLE NONE 5
3QO CAD NAK SINGLE NONE 6
3QO CAI CAE SINGLE NONE 7
3QO NAK CAE DOUBLE NONE 8
3QO CAF CAL DOUBLE NONE 9
3QO CAL CAG SINGLE NONE 10
3QO CAH CAM SINGLE NONE 11
3QO CAM CAI DOUBLE NONE 12
3QO CAL CAJ SINGLE NONE 13
3QO CAJ CAM SINGLE NONE 14
#
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
3QO MurckoScaffold S1 scaffold c1ccc(Cc2ccncc2)cc1 InChI=1S/C12H11N/c1-2-4-11(5-3-1)10-12-6-8-13-9-7-12/h1-9H,10H2 DBOLXXRVIFGDTI-UHFFFAOYSA-N
3QO phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
3QO pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
3QO CAA S1 1
3QO CAB S1 1
3QO CAC S1 1
3QO CAD S1 1
3QO CAE S1 1
3QO CAF S1 1
3QO CAG S1 1
3QO CAH S1 1
3QO CAI S1 1
3QO CAJ S1 1
3QO NAK S1 1
3QO CAL S1 1
3QO CAM S1 1
3QO CAA F1 1
3QO CAB F1 1
3QO CAF F1 1
3QO CAL F1 1
3QO CAG F1 1
3QO CAC F1 1
3QO CAD F2 1
3QO CAH F2 1
3QO CAM F2 1
3QO CAI F2 1
3QO CAE F2 1
3QO NAK F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 3QO
_pdbe_chem_comp_rdkit_properties.exactmw 169.089
_pdbe_chem_comp_rdkit_properties.amw 169.227
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 1
_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 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 1
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.083
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 93.528
_pdbe_chem_comp_rdkit_properties.tpsa 12.890
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.563
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.953
_pdbe_chem_comp_rdkit_properties.chi0v 6.447
_pdbe_chem_comp_rdkit_properties.chi1v 3.447
_pdbe_chem_comp_rdkit_properties.chi2v 1.224
_pdbe_chem_comp_rdkit_properties.chi3v 1.224
_pdbe_chem_comp_rdkit_properties.chi4v 0.727
_pdbe_chem_comp_rdkit_properties.chi0n 17.447
_pdbe_chem_comp_rdkit_properties.chi1n 8.947
_pdbe_chem_comp_rdkit_properties.chi2n 1.224
_pdbe_chem_comp_rdkit_properties.chi3n 1.224
_pdbe_chem_comp_rdkit_properties.chi4n 0.727
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.630
_pdbe_chem_comp_rdkit_properties.kappa1 2.239
_pdbe_chem_comp_rdkit_properties.kappa2 3.854
_pdbe_chem_comp_rdkit_properties.kappa3 2.153
_pdbe_chem_comp_rdkit_properties.Phi 0.664
#
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
3QO UniChem ChEMBL CHEMBL357322
3QO UniChem PDBe 3QO
3QO UniChem ZINC ZINC000000967336
3QO UniChem eMolecules 535082
3QO UniChem fdasrs 1P29GQM0OH
3QO UniChem NMRShiftDB 20027614
3QO UniChem ACTor 2116-65-6
3QO UniChem BindingDb 50123254
3QO UniChem 'EPA CompTox Dashboard' DTXSID5062188
3QO UniChem ChemicalBook CB5682416
3QO UniChem Nikkaji J51.286I
3QO UniChem SureChEMBL SCHEMBL432308
3QO UniChem 'PubChem TPHARMA' 15147141
3QO UniChem PubChem 16458
3QO UniChem Mcule MCULE-7757409305
#
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
3QO CAA -3.208 0.659 1.170 ETKDGv3 1
3QO CAB -2.956 0.950 -0.111 ETKDGv3 2
3QO CAC -2.362 -0.317 1.887 ETKDGv3 3
3QO CAD 3.276 0.123 0.731 ETKDGv3 4
3QO CAE 2.873 1.378 -1.265 ETKDGv3 5
3QO CAF -1.832 0.296 -0.813 ETKDGv3 6
3QO CAG -1.345 -0.915 1.254 ETKDGv3 7
3QO CAH 2.196 -0.643 0.538 ETKDGv3 8
3QO CAI 1.670 0.560 -1.516 ETKDGv3 9
3QO CAJ 0.107 -1.248 -0.861 ETKDGv3 10
3QO NAK 3.606 1.157 -0.212 ETKDGv3 11
3QO CAL -1.065 -0.605 -0.171 ETKDGv3 12
3QO CAM 1.347 -0.422 -0.657 ETKDGv3 13
3QO HAA -4.031 1.139 1.685 ETKDGv3 14
3QO HAB -3.573 1.668 -0.637 ETKDGv3 15
3QO HAC -2.565 -0.545 2.925 ETKDGv3 16
3QO HAD 3.903 -0.031 1.600 ETKDGv3 17
3QO HAE 3.146 2.164 -1.955 ETKDGv3 18
3QO HAF -1.633 0.556 -1.845 ETKDGv3 19
3QO HAG -0.726 -1.626 1.787 ETKDGv3 20
3QO HAH 1.947 -1.418 1.252 ETKDGv3 21
3QO HAI 1.059 0.763 -2.387 ETKDGv3 22
3QO HAJ 0.267 -2.269 -0.453 ETKDGv3 23
3QO HAJA -0.102 -1.375 -1.947 ETKDGv3 24
#