data_7HQ
#
_chem_comp.id 7HQ
_chem_comp.name benzimidazol-1-ylmethanol
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H8 N2 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-11-01
_chem_comp.pdbx_modified_date 2016-12-09
_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 148.162
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 7HQ
_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 5H4I
_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
7HQ CAI C1 C 0 1 Y N N N N N -5.715 4.954 -17.085 2.261 0.975 -0.001 CAI 7HQ 1
7HQ CAK C2 C 0 1 Y N N N N N -5.049 5.022 -18.302 2.982 -0.186 -0.000 CAK 7HQ 2
7HQ CAJ C3 C 0 1 Y N N N N N -5.743 4.679 -19.451 2.341 -1.417 0.001 CAJ 7HQ 3
7HQ CAF C4 C 0 1 Y N N N N N -7.063 4.282 -19.320 0.964 -1.488 0.000 CAF 7HQ 4
7HQ CAD C5 C 0 1 Y N N N N N -7.661 4.237 -18.131 0.215 -0.319 -0.001 CAD 7HQ 5
7HQ CAE C6 C 0 1 Y N N N N N -6.989 4.567 -17.027 0.865 0.927 -0.001 CAE 7HQ 6
7HQ NAC N1 N 0 1 Y N N N N N -7.812 4.428 -15.991 -0.104 1.878 0.002 NAC 7HQ 7
7HQ CAG C7 C 0 1 Y N N N N N -8.989 4.013 -16.447 -1.275 1.310 -0.001 CAG 7HQ 8
7HQ NAB N2 N 0 1 Y N N N N N -8.898 3.894 -17.767 -1.137 -0.043 -0.001 NAB 7HQ 9
7HQ CAH C8 C 0 1 N N N N N N -10.036 3.451 -18.609 -2.224 -1.026 0.000 CAH 7HQ 10
7HQ OAA O1 O 0 1 N N N N N N -9.615 3.031 -19.908 -3.481 -0.347 -0.000 OAA 7HQ 11
7HQ H1 H1 H 0 1 N N N N N N -5.195 5.218 -16.176 2.770 1.927 0.003 H1 7HQ 12
7HQ H2 H2 H 0 1 N N N N N N -4.016 5.334 -18.351 4.061 -0.146 -0.000 H2 7HQ 13
7HQ H3 H3 H 0 1 N N N N N N -5.268 4.720 -20.420 2.925 -2.326 0.001 H3 7HQ 14
7HQ H4 H4 H 0 1 N N N N N N -7.620 4.003 -20.202 0.470 -2.448 0.001 H4 7HQ 15
7HQ H5 H5 H 0 1 N N N N N N -9.865 3.808 -15.850 -2.218 1.836 0.001 H5 7HQ 16
7HQ H6 H6 H 0 1 N N N N N N -10.742 4.287 -18.719 -2.148 -1.652 -0.890 H6 7HQ 17
7HQ H7 H7 H 0 1 N N N N N N -10.539 2.609 -18.110 -2.148 -1.651 0.891 H7 7HQ 18
7HQ H8 H8 H 0 1 N N N N N N -10.371 2.756 -20.413 -4.247 -0.937 0.000 H8 7HQ 19
#
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
7HQ OAA CAH SING N N 1
7HQ CAJ CAF DOUB Y N 2
7HQ CAJ CAK SING Y N 3
7HQ CAF CAD SING Y N 4
7HQ CAH NAB SING N N 5
7HQ CAK CAI DOUB Y N 6
7HQ CAD NAB SING Y N 7
7HQ CAD CAE DOUB Y N 8
7HQ NAB CAG SING Y N 9
7HQ CAI CAE SING Y N 10
7HQ CAE NAC SING Y N 11
7HQ CAG NAC DOUB Y N 12
7HQ CAI H1 SING N N 13
7HQ CAK H2 SING N N 14
7HQ CAJ H3 SING N N 15
7HQ CAF H4 SING N N 16
7HQ CAG H5 SING N N 17
7HQ CAH H6 SING N N 18
7HQ CAH H7 SING N N 19
7HQ OAA H8 SING N N 20
#
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
7HQ InChI InChI 1.03 InChI=1S/C8H8N2O/c11-6-10-5-9-7-3-1-2-4-8(7)10/h1-5,11H,6H2
7HQ InChIKey InChI 1.03 IWCRZZKSGBFRSJ-UHFFFAOYSA-N
7HQ SMILES_CANONICAL CACTVS 3.385 OCn1cnc2ccccc12
7HQ SMILES CACTVS 3.385 OCn1cnc2ccccc12
7HQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1ccc2c(c1)ncn2CO
7HQ SMILES "OpenEye OEToolkits" 2.0.6 c1ccc2c(c1)ncn2CO
#
_pdbx_chem_comp_identifier.comp_id 7HQ
_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 benzimidazol-1-ylmethanol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
7HQ 'Create component' 2016-11-01 RCSB
7HQ 'Initial release' 2016-12-14 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
7HQ CAI C 4.299 -2.663 1
7HQ CAK C 3.000 -1.913 2
7HQ CAJ C 3.000 -0.413 3
7HQ CAF C 4.299 0.337 4
7HQ CAD C 5.598 -0.413 5
7HQ CAE C 5.598 -1.913 6
7HQ NAC N 7.018 -2.370 7
7HQ CAG C 7.893 -1.163 8
7HQ NAB N 7.018 0.044 9
7HQ CAH C 7.483 1.470 10
7HQ OAA O 8.951 1.779 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
7HQ OAA CAH SINGLE NONE 1
7HQ CAJ CAF DOUBLE NONE 2
7HQ CAJ CAK SINGLE NONE 3
7HQ CAF CAD SINGLE NONE 4
7HQ CAH NAB SINGLE NONE 5
7HQ CAK CAI DOUBLE NONE 6
7HQ CAD NAB SINGLE NONE 7
7HQ CAD CAE DOUBLE NONE 8
7HQ NAB CAG SINGLE NONE 9
7HQ CAI CAE SINGLE NONE 10
7HQ CAE NAC SINGLE NONE 11
7HQ CAG NAC DOUBLE 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
7HQ MurckoScaffold S1 scaffold 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
7HQ benzimidazole F1 fragment 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
7HQ imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
7HQ phenyl F3 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
7HQ CAI S1 1
7HQ CAK S1 1
7HQ CAJ S1 1
7HQ CAF S1 1
7HQ CAD S1 1
7HQ CAE S1 1
7HQ NAC S1 1
7HQ CAG S1 1
7HQ NAB S1 1
7HQ CAD F1 1
7HQ NAB F1 1
7HQ CAG F1 1
7HQ NAC F1 1
7HQ CAE F1 1
7HQ CAI F1 1
7HQ CAK F1 1
7HQ CAJ F1 1
7HQ CAF F1 1
7HQ CAD F2 1
7HQ CAE F2 1
7HQ NAC F2 1
7HQ CAG F2 1
7HQ NAB F2 1
7HQ CAI F3 1
7HQ CAK F3 1
7HQ CAJ F3 1
7HQ CAF F3 1
7HQ CAD F3 1
7HQ CAE F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 7HQ
_pdbe_chem_comp_rdkit_properties.exactmw 148.064
_pdbe_chem_comp_rdkit_properties.amw 148.165
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_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 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 19
_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 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 75.237
_pdbe_chem_comp_rdkit_properties.tpsa 38.050
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.558
_pdbe_chem_comp_rdkit_properties.CrippenMR 39.746
_pdbe_chem_comp_rdkit_properties.chi0v 5.303
_pdbe_chem_comp_rdkit_properties.chi1v 2.822
_pdbe_chem_comp_rdkit_properties.chi2v 1.225
_pdbe_chem_comp_rdkit_properties.chi3v 1.225
_pdbe_chem_comp_rdkit_properties.chi4v 0.758
_pdbe_chem_comp_rdkit_properties.chi0n 13.303
_pdbe_chem_comp_rdkit_properties.chi1n 6.730
_pdbe_chem_comp_rdkit_properties.chi2n 1.225
_pdbe_chem_comp_rdkit_properties.chi3n 1.225
_pdbe_chem_comp_rdkit_properties.chi4n 0.758
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.350
_pdbe_chem_comp_rdkit_properties.kappa1 2.076
_pdbe_chem_comp_rdkit_properties.kappa2 2.359
_pdbe_chem_comp_rdkit_properties.kappa3 0.897
_pdbe_chem_comp_rdkit_properties.Phi 0.445
#
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
7HQ UniChem PDBe 7HQ
7HQ UniChem ZINC ZINC000000043480
7HQ UniChem eMolecules 931610
7HQ UniChem ACTor 19541-99-2
7HQ UniChem 'EPA CompTox Dashboard' DTXSID10173214
7HQ UniChem ChemicalBook CB2780849
7HQ UniChem Nikkaji J1.379.503G
7HQ UniChem SureChEMBL SCHEMBL3862944
7HQ UniChem 'PubChem TPHARMA' 144201673
7HQ UniChem PubChem 146489
7HQ UniChem Mcule MCULE-9512294660
#
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
7HQ CAI -2.378 0.715 0.476 ETKDGv3 1
7HQ CAK -2.770 -0.572 0.524 ETKDGv3 2
7HQ CAJ -1.817 -1.666 0.167 ETKDGv3 3
7HQ CAF -0.557 -1.377 -0.208 ETKDGv3 4
7HQ CAD -0.161 0.042 -0.261 ETKDGv3 5
7HQ CAE -0.997 1.004 0.056 ETKDGv3 6
7HQ NAC -0.347 2.269 0.024 ETKDGv3 7
7HQ CAG 0.875 1.994 -0.328 ETKDGv3 8
7HQ NAB 1.105 0.601 -0.567 ETKDGv3 9
7HQ CAH 2.394 -0.074 -0.490 ETKDGv3 10
7HQ OAA 2.732 -0.285 0.852 ETKDGv3 11
7HQ H1 -3.056 1.515 0.744 ETKDGv3 12
7HQ H2 -3.778 -0.818 0.829 ETKDGv3 13
7HQ H3 -2.143 -2.697 0.216 ETKDGv3 14
7HQ H4 0.141 -2.163 -0.462 ETKDGv3 15
7HQ H5 1.644 2.751 -0.411 ETKDGv3 16
7HQ H6 2.335 -1.047 -1.026 ETKDGv3 17
7HQ H7 3.168 0.556 -0.981 ETKDGv3 18
7HQ H8 3.609 -0.749 0.844 ETKDGv3 19
#