data_BEN
#
_chem_comp.id BEN
_chem_comp.name BENZAMIDINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H8 N2"
_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 BDN
_chem_comp.formula_weight 120.152
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code BEN
_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 1CC7
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
BEN C1 C1 C 0 1 Y N N N N N 6.724 10.069 20.638 -0.023 -0.000 0.207 C1 BEN 1
BEN C2 C2 C 0 1 Y N N N N N 5.992 9.273 19.790 -1.211 0.000 -0.524 C2 BEN 2
BEN C3 C3 C 0 1 Y N N N N N 6.536 8.622 18.685 -1.168 0.000 -1.903 C3 BEN 3
BEN C4 C4 C 0 1 Y N N N N N 7.912 8.859 18.402 0.048 -0.000 -2.560 C4 BEN 4
BEN C5 C5 C 0 1 Y N N N N N 8.666 9.739 19.180 1.230 -0.002 -1.840 C5 BEN 5
BEN C6 C6 C 0 1 Y N N N N N 8.078 10.313 20.307 1.200 0.004 -0.461 C6 BEN 6
BEN C C C 0 1 N N N N N N 6.165 10.646 21.844 -0.062 -0.000 1.687 C BEN 7
BEN N1 N1 N 0 1 N N N N N N 6.905 10.765 22.901 -1.206 0.000 2.309 N1 BEN 8
BEN N2 N2 N 0 1 N N N N N N 4.866 11.058 21.813 1.112 -0.001 2.407 N2 BEN 9
BEN H2 H2 H 0 1 N N N N N N 4.917 9.150 20.006 -2.161 0.000 -0.012 H2 BEN 10
BEN H3 H3 H 0 1 N N N N N N 5.911 7.955 18.067 -2.087 0.000 -2.470 H3 BEN 11
BEN H4 H4 H 0 1 N N N N N N 8.406 8.348 17.558 0.076 -0.001 -3.640 H4 BEN 12
BEN H5 H5 H 0 1 N N N N N N 9.708 9.976 18.908 2.177 -0.003 -2.359 H5 BEN 13
BEN H6 H6 H 0 1 N N N N N N 8.692 10.969 20.945 2.123 0.004 0.099 H6 BEN 14
BEN HN1 HN1 H 0 1 N N N N N N 7.277 10.307 22.069 -2.033 0.000 1.802 HN1 BEN 15
BEN HN21 1HN2 H 0 0 N N N N N N 4.472 11.464 22.661 1.087 -0.001 3.377 HN21 BEN 16
BEN HN22 2HN2 H 0 0 N N N N N N 4.276 10.283 21.508 1.965 -0.005 1.944 HN22 BEN 17
#
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
BEN C1 C2 DOUB Y N 1
BEN C1 C6 SING Y N 2
BEN C1 C SING N N 3
BEN C2 C3 SING Y N 4
BEN C2 H2 SING N N 5
BEN C3 C4 DOUB Y N 6
BEN C3 H3 SING N N 7
BEN C4 C5 SING Y N 8
BEN C4 H4 SING N N 9
BEN C5 C6 DOUB Y N 10
BEN C5 H5 SING N N 11
BEN C6 H6 SING N N 12
BEN C N1 DOUB N E 13
BEN C N2 SING N N 14
BEN N1 HN1 SING N N 15
BEN N2 HN21 SING N N 16
BEN N2 HN22 SING N N 17
#
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
BEN SMILES ACDLabs 10.04 "[N@H]=C(N)c1ccccc1"
BEN SMILES_CANONICAL CACTVS 3.341 NC(=N)c1ccccc1
BEN SMILES CACTVS 3.341 NC(=N)c1ccccc1
BEN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[H]/N=C(\c1ccccc1)/N"
BEN SMILES "OpenEye OEToolkits" 1.5.0 "[H]N=C(c1ccccc1)N"
BEN InChI InChI 1.03 InChI=1S/C7H8N2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H3,8,9)
BEN InChIKey InChI 1.03 PXXJHWLDUBFPOL-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
BEN "SYSTEMATIC NAME" ACDLabs 10.04 benzenecarboximidamide
BEN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 benzenecarboximidamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
BEN 'Create component' 1999-07-08 PDBJ
BEN '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
BEN C1 C 4.299 -0.090 1
BEN C2 C 3.000 -0.840 2
BEN C3 C 3.000 -2.340 3
BEN C4 C 4.299 -3.090 4
BEN C5 C 5.598 -2.340 5
BEN C6 C 5.598 -0.840 6
BEN C C 4.299 1.410 7
BEN N1 N 5.598 2.160 8
BEN N2 N 3.000 2.160 9
BEN HN1 H 5.598 3.660 10
#
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
BEN C1 C2 DOUBLE NONE 1
BEN C1 C6 SINGLE NONE 2
BEN C1 C SINGLE ENDUPRIGHT 3
BEN C2 C3 SINGLE NONE 4
BEN C3 C4 DOUBLE NONE 5
BEN C4 C5 SINGLE NONE 6
BEN C5 C6 DOUBLE NONE 7
BEN C N1 DOUBLE NONE 8
BEN C N2 SINGLE ENDUPRIGHT 9
#
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
BEN MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
BEN 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
BEN C1 S1 1
BEN C2 S1 1
BEN C3 S1 1
BEN C4 S1 1
BEN C5 S1 1
BEN C6 S1 1
BEN C1 F1 1
BEN C2 F1 1
BEN C3 F1 1
BEN C4 F1 1
BEN C5 F1 1
BEN C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id BEN
_pdbe_chem_comp_rdkit_properties.exactmw 120.069
_pdbe_chem_comp_rdkit_properties.amw 120.155
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 17
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_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 65.236
_pdbe_chem_comp_rdkit_properties.tpsa 49.870
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.916
_pdbe_chem_comp_rdkit_properties.CrippenMR 37.192
_pdbe_chem_comp_rdkit_properties.chi0v 4.394
_pdbe_chem_comp_rdkit_properties.chi1v 2.197
_pdbe_chem_comp_rdkit_properties.chi2v 0.724
_pdbe_chem_comp_rdkit_properties.chi3v 0.724
_pdbe_chem_comp_rdkit_properties.chi4v 0.362
_pdbe_chem_comp_rdkit_properties.chi0n 12.394
_pdbe_chem_comp_rdkit_properties.chi1n 6.039
_pdbe_chem_comp_rdkit_properties.chi2n 0.724
_pdbe_chem_comp_rdkit_properties.chi3n 0.724
_pdbe_chem_comp_rdkit_properties.chi4n 0.362
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.310
_pdbe_chem_comp_rdkit_properties.kappa1 1.398
_pdbe_chem_comp_rdkit_properties.kappa2 2.307
_pdbe_chem_comp_rdkit_properties.kappa3 1.288
_pdbe_chem_comp_rdkit_properties.Phi 0.358
#
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
BEN UniChem ChEMBL CHEMBL20936
BEN UniChem PDBe BEN
BEN UniChem 'Guide to Pharmacology' 7566
BEN UniChem 'KEGG LIGAND' C01784
BEN UniChem ChEBI 41033
BEN UniChem ZINC ZINC000000036634
BEN UniChem fdasrs KUE3ZY3J1F
BEN UniChem HMDB HMDB0248970
BEN UniChem 'PubChem TPHARMA' 15218879
BEN UniChem Nikkaji J95.743G
BEN UniChem BindingDb 50038002
BEN UniChem BRENDA 29765
BEN UniChem BRENDA 579
BEN UniChem ChemicalBook CB8718710
BEN UniChem 'Probes And Drugs' PD051080
BEN UniChem 'EPA CompTox Dashboard' DTXSID8045012
BEN UniChem eMolecules 479296
BEN UniChem SureChEMBL SCHEMBL9207
BEN UniChem PubChem 2332
BEN UniChem Mcule MCULE-3828251614
BEN UniChem ACTor 618-39-3
#
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
BEN C1 0.330 -0.141 0.002 ETKDGv3 1
BEN C2 -0.412 -1.116 0.564 ETKDGv3 2
BEN C3 -1.888 -1.033 0.557 ETKDGv3 3
BEN C4 -2.498 0.016 -0.006 ETKDGv3 4
BEN C5 -1.698 1.091 -0.624 ETKDGv3 5
BEN C6 -0.361 1.019 -0.621 ETKDGv3 6
BEN C 1.813 -0.199 0.011 ETKDGv3 7
BEN N1 2.441 -1.325 -0.132 ETKDGv3 8
BEN N2 2.576 1.001 0.161 ETKDGv3 9
BEN H2 0.054 -1.962 1.053 ETKDGv3 10
BEN H3 -2.473 -1.821 1.012 ETKDGv3 11
BEN H4 -3.579 0.078 -0.010 ETKDGv3 12
BEN H5 -2.196 1.934 -1.085 ETKDGv3 13
BEN H6 0.211 1.807 -1.094 ETKDGv3 14
BEN HN1 1.950 -2.236 -0.271 ETKDGv3 15
BEN HN21 2.112 1.915 0.361 ETKDGv3 16
BEN HN22 3.619 0.971 0.124 ETKDGv3 17
#