data_BNZ
#
_chem_comp.id BNZ
_chem_comp.name BENZENE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 78.112
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code BNZ
_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 1A7Z
_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
BNZ C1 C1 C 0 1 Y N N N N N 4.570 21.971 1.549 0.675 -1.206 -0.000 C1 BNZ 1
BNZ C2 C2 C 0 1 Y N N N N N 3.941 23.164 1.882 -0.707 -1.188 0.000 C2 BNZ 2
BNZ C3 C3 C 0 1 Y N N N N N 4.662 24.352 1.889 -1.382 0.019 -0.000 C3 BNZ 3
BNZ C4 C4 C 0 1 Y N N N N N 6.026 24.319 1.587 -0.675 1.206 -0.000 C4 BNZ 4
BNZ C5 C5 C 0 1 Y N N N N N 6.643 23.128 1.254 0.707 1.188 0.001 C5 BNZ 5
BNZ C6 C6 C 0 1 Y N N N N N 5.908 21.952 1.218 1.382 -0.019 -0.001 C6 BNZ 6
BNZ H1 H1 H 0 1 N N N N N N 4.006 21.050 1.549 1.202 -2.149 0.004 H1 BNZ 7
BNZ H2 H2 H 0 1 N N N N N N 2.891 23.168 2.136 -1.260 -2.115 0.000 H2 BNZ 8
BNZ H3 H3 H 0 1 N N N N N N 4.175 25.287 2.124 -2.462 0.034 -0.001 H3 BNZ 9
BNZ H4 H4 H 0 1 N N N N N N 6.603 25.232 1.614 -1.202 2.149 -0.001 H4 BNZ 10
BNZ H5 H5 H 0 1 N N N N N N 7.698 23.113 1.022 1.260 2.115 -0.000 H5 BNZ 11
BNZ H6 H6 H 0 1 N N N N N N 6.382 21.025 0.932 2.462 -0.034 -0.001 H6 BNZ 12
#
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
BNZ C1 C2 DOUB Y N 1
BNZ C1 C6 SING Y N 2
BNZ C1 H1 SING N N 3
BNZ C2 C3 SING Y N 4
BNZ C2 H2 SING N N 5
BNZ C3 C4 DOUB Y N 6
BNZ C3 H3 SING N N 7
BNZ C4 C5 SING Y N 8
BNZ C4 H4 SING N N 9
BNZ C5 C6 DOUB Y N 10
BNZ C5 H5 SING N N 11
BNZ C6 H6 SING N N 12
#
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
BNZ SMILES ACDLabs 11.02 c1ccccc1
BNZ SMILES_CANONICAL CACTVS 3.352 c1ccccc1
BNZ SMILES CACTVS 3.352 c1ccccc1
BNZ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 c1ccccc1
BNZ SMILES "OpenEye OEToolkits" 1.7.0 c1ccccc1
BNZ InChI InChI 1.03 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
BNZ InChIKey InChI 1.03 UHOVQNZJYSORNB-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
BNZ "SYSTEMATIC NAME" ACDLabs 11.02 benzene
BNZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 benzene
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
BNZ 'Create component' 1999-07-08 RCSB
BNZ 'Modify descriptor' 2011-06-04 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
BNZ C1 C 4.299 1.500 1
BNZ C2 C 3.000 0.750 2
BNZ C3 C 3.000 -0.750 3
BNZ C4 C 4.299 -1.500 4
BNZ C5 C 5.598 -0.750 5
BNZ C6 C 5.598 0.750 6
#
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
BNZ C1 C2 DOUBLE NONE 1
BNZ C1 C6 SINGLE NONE 2
BNZ C2 C3 SINGLE NONE 3
BNZ C3 C4 DOUBLE NONE 4
BNZ C4 C5 SINGLE NONE 5
BNZ C5 C6 DOUBLE NONE 6
#
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
BNZ MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
BNZ 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
BNZ C1 S1 1
BNZ C2 S1 1
BNZ C3 S1 1
BNZ C4 S1 1
BNZ C5 S1 1
BNZ C6 S1 1
BNZ C1 F1 1
BNZ C2 F1 1
BNZ C3 F1 1
BNZ C4 F1 1
BNZ C5 F1 1
BNZ C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id BNZ
_pdbe_chem_comp_rdkit_properties.exactmw 78.047
_pdbe_chem_comp_rdkit_properties.amw 78.114
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 0
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 0
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 6
_pdbe_chem_comp_rdkit_properties.NumAtoms 12
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 0
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_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 45.861
_pdbe_chem_comp_rdkit_properties.tpsa 0
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.687
_pdbe_chem_comp_rdkit_properties.CrippenMR 26.442
_pdbe_chem_comp_rdkit_properties.chi0v 3
_pdbe_chem_comp_rdkit_properties.chi1v 1.500
_pdbe_chem_comp_rdkit_properties.chi2v 0.375
_pdbe_chem_comp_rdkit_properties.chi3v 0.375
_pdbe_chem_comp_rdkit_properties.chi4v 0.188
_pdbe_chem_comp_rdkit_properties.chi0n 9
_pdbe_chem_comp_rdkit_properties.chi1n 4.500
_pdbe_chem_comp_rdkit_properties.chi2n 0.375
_pdbe_chem_comp_rdkit_properties.chi3n 0.375
_pdbe_chem_comp_rdkit_properties.chi4n 0.188
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.780
_pdbe_chem_comp_rdkit_properties.kappa1 0.738
_pdbe_chem_comp_rdkit_properties.kappa2 1.606
_pdbe_chem_comp_rdkit_properties.kappa3 0.582
_pdbe_chem_comp_rdkit_properties.Phi 0.198
#
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
BNZ UniChem 'KEGG LIGAND' C01407
BNZ UniChem ChEBI 16716
BNZ UniChem ZINC ZINC000000967532
BNZ UniChem atlas Benzene
BNZ UniChem fdasrs J64922108F
BNZ UniChem HMDB HMDB0001505
BNZ UniChem 'PubChem TPHARMA' 15321034
BNZ UniChem NMRShiftDB 7901
BNZ UniChem ACTor 26181-88-4
BNZ UniChem ACTor 27271-55-2
BNZ UniChem Nikkaji J2.375B
BNZ UniChem BRENDA 121990
BNZ UniChem BRENDA 1750
BNZ UniChem BRENDA 9107
BNZ UniChem Rhea 16716
BNZ UniChem ChemicalBook CB6854153
BNZ UniChem rxnorm BENZENE
BNZ UniChem 'EPA CompTox Dashboard' DTXSID3039242
BNZ UniChem eMolecules 479848
BNZ UniChem SureChEMBL SCHEMBL194
BNZ UniChem PubChem 241
BNZ UniChem Mcule MCULE-4899719484
BNZ UniChem ACTor 174973-66-1
BNZ UniChem ACTor 71-43-2
BNZ UniChem Nikkaji J1.749.610G
BNZ UniChem BindingDb 50167939
#
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
BNZ C1 -1.398 -0.169 -0.055 ETKDGv3 1
BNZ C2 -0.625 -1.263 -0.031 ETKDGv3 2
BNZ C3 0.846 -1.127 0.027 ETKDGv3 3
BNZ C4 1.406 0.089 0.055 ETKDGv3 4
BNZ C5 0.553 1.297 0.028 ETKDGv3 5
BNZ C6 -0.780 1.174 -0.024 ETKDGv3 6
BNZ H1 -2.476 -0.266 -0.097 ETKDGv3 7
BNZ H2 -1.075 -2.247 -0.054 ETKDGv3 8
BNZ H3 1.468 -2.013 0.046 ETKDGv3 9
BNZ H4 2.483 0.191 0.097 ETKDGv3 10
BNZ H5 1.008 2.278 0.051 ETKDGv3 11
BNZ H6 -1.407 2.056 -0.043 ETKDGv3 12
#