data_BVG
#
_chem_comp.id BVG
_chem_comp.name 1H-IMIDAZOL-2-YLMETHANOL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C4 H6 N2 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-11-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 98.103
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code BVG
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 2EUU
_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
BVG O7 O7 O 0 1 N N N N N N -6.669 71.112 13.589 2.413 0.478 -0.001 O7 BVG 1
BVG C6 C6 C 0 1 N N N N N N -7.434 70.204 14.338 1.595 -0.695 0.001 C6 BVG 2
BVG C4 C4 C 0 1 Y N N N N N -8.283 70.933 15.349 0.143 -0.294 0.001 C4 BVG 3
BVG N5 N5 N 0 1 Y N N N N N -8.568 70.449 16.583 -0.872 -1.115 -0.003 N5 BVG 4
BVG N3 N3 N 0 1 Y N N N N N -8.831 72.152 15.218 -0.325 0.973 0.000 N3 BVG 5
BVG C2 C2 C 0 1 Y N N N N N -9.507 72.416 16.361 -1.692 0.900 0.000 C2 BVG 6
BVG C1 C1 C 0 1 Y N N N N N -9.352 71.359 17.215 -2.012 -0.408 0.001 C1 BVG 7
BVG HO7 HO7 H 0 1 N N N N N N -6.496 71.887 14.111 3.332 0.178 -0.001 HO7 BVG 8
BVG H61 1H6 H 0 1 N N N N N N -6.755 69.522 14.870 1.809 -1.288 -0.888 H61 BVG 9
BVG H62 2H6 H 0 1 N N N N N N -8.089 69.639 13.659 1.810 -1.285 0.892 H62 BVG 10
BVG HN3 HN3 H 0 1 N N N N N N -8.754 72.754 14.423 0.209 1.783 -0.001 HN3 BVG 11
BVG H2 H2 H 0 1 N N N N N N -10.074 73.312 16.565 -2.380 1.732 -0.001 H2 BVG 12
BVG H1 H1 H 0 1 N N N N N N -9.774 71.266 18.205 -3.012 -0.816 0.002 H1 BVG 13
#
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
BVG O7 C6 SING N N 1
BVG O7 HO7 SING N N 2
BVG C6 C4 SING N N 3
BVG C6 H61 SING N N 4
BVG C6 H62 SING N N 5
BVG C4 N5 DOUB Y N 6
BVG C4 N3 SING Y N 7
BVG N5 C1 SING Y N 8
BVG N3 C2 SING Y N 9
BVG N3 HN3 SING N N 10
BVG C2 C1 DOUB Y N 11
BVG C2 H2 SING N N 12
BVG C1 H1 SING N N 13
#
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
BVG SMILES ACDLabs 10.04 OCc1nccn1
BVG SMILES_CANONICAL CACTVS 3.341 OCc1[nH]ccn1
BVG SMILES CACTVS 3.341 OCc1[nH]ccn1
BVG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cnc([nH]1)CO
BVG SMILES "OpenEye OEToolkits" 1.5.0 c1cnc([nH]1)CO
BVG InChI InChI 1.03 InChI=1S/C4H6N2O/c7-3-4-5-1-2-6-4/h1-2,7H,3H2,(H,5,6)
BVG InChIKey InChI 1.03 ZOMATQMEHRJKLO-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
BVG "SYSTEMATIC NAME" ACDLabs 10.04 1H-imidazol-2-ylmethanol
BVG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 1H-imidazol-2-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
BVG 'Create component' 2005-11-08 RCSB
BVG '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
BVG O7 O 7.968 0.733 1
BVG C6 C 6.854 -0.271 2
BVG C4 C 5.427 0.193 3
BVG N5 N 4.213 -0.689 4
BVG N3 N 4.963 1.619 5
BVG C2 C 3.463 1.619 6
BVG C1 C 3.000 0.193 7
#
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
BVG O7 C6 SINGLE NONE 1
BVG C6 C4 SINGLE NONE 2
BVG C4 N5 DOUBLE NONE 3
BVG C4 N3 SINGLE NONE 4
BVG N5 C1 SINGLE NONE 5
BVG N3 C2 SINGLE NONE 6
BVG C2 C1 DOUBLE NONE 7
#
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
BVG MurckoScaffold S1 scaffold 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
BVG imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-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
BVG C4 S1 1
BVG N5 S1 1
BVG N3 S1 1
BVG C2 S1 1
BVG C1 S1 1
BVG C2 F1 1
BVG C1 F1 1
BVG N5 F1 1
BVG C4 F1 1
BVG N3 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id BVG
_pdbe_chem_comp_rdkit_properties.exactmw 98.048
_pdbe_chem_comp_rdkit_properties.amw 98.105
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_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 7
_pdbe_chem_comp_rdkit_properties.NumAtoms 13
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.250
_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 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 49.594
_pdbe_chem_comp_rdkit_properties.tpsa 48.910
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.153
_pdbe_chem_comp_rdkit_properties.CrippenMR 24.244
_pdbe_chem_comp_rdkit_properties.chi0v 3.303
_pdbe_chem_comp_rdkit_properties.chi1v 1.599
_pdbe_chem_comp_rdkit_properties.chi2v 0.465
_pdbe_chem_comp_rdkit_properties.chi3v 0.465
_pdbe_chem_comp_rdkit_properties.chi4v 0.227
_pdbe_chem_comp_rdkit_properties.chi0n 9.303
_pdbe_chem_comp_rdkit_properties.chi1n 4.454
_pdbe_chem_comp_rdkit_properties.chi2n 0.465
_pdbe_chem_comp_rdkit_properties.chi3n 0.465
_pdbe_chem_comp_rdkit_properties.chi4n 0.227
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.830
_pdbe_chem_comp_rdkit_properties.kappa1 1.113
_pdbe_chem_comp_rdkit_properties.kappa2 1.749
_pdbe_chem_comp_rdkit_properties.kappa3 0.778
_pdbe_chem_comp_rdkit_properties.Phi 0.278
#
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
BVG UniChem PDBe BVG
BVG UniChem ZINC ZINC000002509361
BVG UniChem SureChEMBL SCHEMBL381
BVG UniChem Nikkaji J100.708D
BVG UniChem ChemicalBook CB5122549
BVG UniChem 'EPA CompTox Dashboard' DTXSID30340729
BVG UniChem eMolecules 1014153
BVG UniChem 'PubChem TPHARMA' 49852339
BVG UniChem PubChem 566830
BVG UniChem Mcule MCULE-2118723726
#
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
BVG O7 2.357 -0.135 0.724 ETKDGv3 1
BVG C6 1.661 -0.172 -0.490 ETKDGv3 2
BVG C4 0.188 -0.121 -0.238 ETKDGv3 3
BVG N5 -0.546 -1.181 -0.118 ETKDGv3 4
BVG N3 -0.530 1.087 -0.018 ETKDGv3 5
BVG C2 -1.845 0.628 0.240 ETKDGv3 6
BVG C1 -1.854 -0.693 0.178 ETKDGv3 7
BVG HO7 2.281 -1.041 1.124 ETKDGv3 8
BVG H61 1.955 0.707 -1.100 ETKDGv3 9
BVG H62 1.923 -1.089 -1.065 ETKDGv3 10
BVG HN3 -0.175 2.068 -0.027 ETKDGv3 11
BVG H2 -2.695 1.262 0.455 ETKDGv3 12
BVG H1 -2.720 -1.321 0.336 ETKDGv3 13
#