data_T1B
#
_chem_comp.id T1B
_chem_comp.name 5-ethyl-2-(3-methyl-1,2,3-triazol-4-yl)-1~{H}-benzimidazole
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H13 N5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-12-10
_chem_comp.pdbx_modified_date 2021-10-15
_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 227.265
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code T1B
_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 7B7B
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
T1B C12 C1 C 0 1 Y N N N N N 7.925 7.369 -10.060 -2.493 -0.417 0.016 C12 T1B 1
T1B C13 C2 C 0 1 Y N N N N N 6.566 7.575 -9.896 -3.104 -1.642 0.020 C13 T1B 2
T1B C01 C3 C 0 1 N N N N N N 10.212 3.123 -3.740 5.437 -0.936 0.958 C01 T1B 3
T1B C02 C4 C 0 1 N N N N N N 10.616 2.529 -5.092 4.880 -0.591 -0.425 C02 T1B 4
T1B C03 C5 C 0 1 Y N N N N N 10.562 3.518 -6.265 3.474 -0.067 -0.283 C03 T1B 5
T1B C04 C6 C 0 1 Y N N N N N 11.695 3.850 -7.006 3.260 1.293 -0.111 C04 T1B 6
T1B C05 C7 C 0 1 Y N N N N N 11.612 4.742 -8.065 1.980 1.788 0.020 C05 T1B 7
T1B C06 C8 C 0 1 Y N N N N N 10.367 5.319 -8.370 0.896 0.923 -0.020 C06 T1B 8
T1B C08 C9 C 0 1 Y N N N N N 8.739 6.427 -9.217 -1.045 -0.144 -0.035 C08 T1B 9
T1B C10 C10 C 0 1 Y N N N N N 9.263 5.000 -7.660 1.107 -0.457 -0.194 C10 T1B 10
T1B C11 C11 C 0 1 Y N N N N N 9.344 4.097 -6.578 2.412 -0.942 -0.331 C11 T1B 11
T1B C17 C12 C 0 1 N N N N N N 9.655 8.358 -11.565 -3.348 1.959 0.078 C17 T1B 12
T1B N07 N1 N 0 1 Y N N N N N 10.041 6.200 -9.334 -0.471 1.095 0.078 N07 T1B 13
T1B N09 N2 N 0 1 Y N N N N N 8.251 5.709 -8.190 -0.111 -1.052 -0.194 N09 T1B 14
T1B N14 N3 N 0 1 Y N N N N N 6.194 8.473 -10.783 -4.416 -1.406 0.074 N14 T1B 15
T1B N15 N4 N 0 1 Y N N N N N 7.287 8.872 -11.458 -4.622 -0.138 0.102 N15 T1B 16
T1B N16 N5 N 0 1 Y N N N N N 8.336 8.177 -11.009 -3.506 0.502 0.063 N16 T1B 17
T1B H1 H1 H 0 1 N N N N N N 5.928 7.088 -9.173 -2.620 -2.607 -0.013 H1 T1B 18
T1B H2 H2 H 0 1 N N N N N N 10.280 2.347 -2.963 5.443 -0.042 1.581 H2 T1B 19
T1B H3 H3 H 0 1 N N N N N N 10.887 3.954 -3.488 4.811 -1.698 1.422 H3 T1B 20
T1B H4 H4 H 0 1 N N N N N N 9.178 3.495 -3.797 6.454 -1.315 0.855 H4 T1B 21
T1B H5 H5 H 0 1 N N N N N N 9.937 1.693 -5.316 5.506 0.170 -0.889 H5 T1B 22
T1B H6 H6 H 0 1 N N N N N N 11.646 2.152 -5.008 4.873 -1.486 -1.047 H6 T1B 23
T1B H7 H7 H 0 1 N N N N N N 12.647 3.408 -6.753 4.102 1.968 -0.080 H7 T1B 24
T1B H8 H8 H 0 1 N N N N N N 12.489 4.989 -8.645 1.821 2.848 0.154 H8 T1B 25
T1B H9 H9 H 0 1 N N N N N N 8.463 3.860 -5.999 2.586 -1.999 -0.465 H9 T1B 26
T1B H10 H10 H 0 1 N N N N N N 9.617 9.117 -12.361 -3.160 2.294 1.098 H10 T1B 27
T1B H11 H11 H 0 1 N N N N N N 10.344 8.690 -10.774 -2.508 2.240 -0.557 H11 T1B 28
T1B H12 H12 H 0 1 N N N N N N 10.010 7.405 -11.984 -4.258 2.427 -0.296 H12 T1B 29
T1B H13 H13 H 0 1 N N N N N N 10.660 6.605 -10.007 -0.938 1.936 0.203 H13 T1B 30
#
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
T1B C17 N16 SING N N 1
T1B N15 N16 SING Y N 2
T1B N15 N14 DOUB Y N 3
T1B N16 C12 SING Y N 4
T1B N14 C13 SING Y N 5
T1B C12 C13 DOUB Y N 6
T1B C12 C08 SING N N 7
T1B N07 C08 SING Y N 8
T1B N07 C06 SING Y N 9
T1B C08 N09 DOUB Y N 10
T1B C06 C05 DOUB Y N 11
T1B C06 C10 SING Y N 12
T1B N09 C10 SING Y N 13
T1B C05 C04 SING Y N 14
T1B C10 C11 DOUB Y N 15
T1B C04 C03 DOUB Y N 16
T1B C11 C03 SING Y N 17
T1B C03 C02 SING N N 18
T1B C02 C01 SING N N 19
T1B C13 H1 SING N N 20
T1B C01 H2 SING N N 21
T1B C01 H3 SING N N 22
T1B C01 H4 SING N N 23
T1B C02 H5 SING N N 24
T1B C02 H6 SING N N 25
T1B C04 H7 SING N N 26
T1B C05 H8 SING N N 27
T1B C11 H9 SING N N 28
T1B C17 H10 SING N N 29
T1B C17 H11 SING N N 30
T1B C17 H12 SING N N 31
T1B N07 H13 SING N N 32
#
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
T1B InChI InChI 1.03 InChI=1S/C12H13N5/c1-3-8-4-5-9-10(6-8)15-12(14-9)11-7-13-16-17(11)2/h4-7H,3H2,1-2H3,(H,14,15)
T1B InChIKey InChI 1.03 ODOFHRIEFOAOCH-UHFFFAOYSA-N
T1B SMILES_CANONICAL CACTVS 3.385 CCc1ccc2[nH]c(nc2c1)c3cnnn3C
T1B SMILES CACTVS 3.385 CCc1ccc2[nH]c(nc2c1)c3cnnn3C
T1B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CCc1ccc2c(c1)nc([nH]2)c3cnnn3C
T1B SMILES "OpenEye OEToolkits" 2.0.7 CCc1ccc2c(c1)nc([nH]2)c3cnnn3C
#
_pdbx_chem_comp_identifier.comp_id T1B
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier 5-ethyl-2-(3-methyl-1,2,3-triazol-4-yl)-1~{H}-benzimidazole
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
T1B 'Create component' 2020-12-10 PDBE
T1B 'Initial release' 2021-10-20 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
T1B C12 C 11.991 -0.570 1
T1B C13 C 12.873 -1.784 2
T1B C01 C 3.000 0.180 3
T1B C02 C 4.299 0.930 4
T1B C03 C 5.598 0.180 5
T1B C04 C 5.598 -1.320 6
T1B C05 C 6.897 -2.070 7
T1B C06 C 8.196 -1.320 8
T1B C08 C 10.491 -0.570 9
T1B C10 C 8.196 0.180 10
T1B C11 C 6.897 0.930 11
T1B C17 C 12.409 2.070 12
T1B N07 N 9.616 -1.777 13
T1B N09 N 9.616 0.637 14
T1B N14 N 14.299 -1.320 15
T1B N15 N 14.299 0.180 16
T1B N16 N 12.873 0.643 17
#
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
T1B C17 N16 SINGLE NONE 1
T1B N15 N16 SINGLE NONE 2
T1B N15 N14 DOUBLE NONE 3
T1B N16 C12 SINGLE NONE 4
T1B N14 C13 SINGLE NONE 5
T1B C12 C13 DOUBLE NONE 6
T1B C12 C08 SINGLE NONE 7
T1B N07 C08 SINGLE NONE 8
T1B N07 C06 SINGLE NONE 9
T1B C08 N09 DOUBLE NONE 10
T1B C06 C05 DOUBLE NONE 11
T1B C06 C10 SINGLE NONE 12
T1B N09 C10 SINGLE NONE 13
T1B C05 C04 SINGLE NONE 14
T1B C10 C11 DOUBLE NONE 15
T1B C04 C03 DOUBLE NONE 16
T1B C11 C03 SINGLE NONE 17
T1B C03 C02 SINGLE NONE 18
T1B C02 C01 SINGLE NONE 19
#
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
T1B MurckoScaffold S1 scaffold 'c1ccc2[nH]c(-c3cnn[nH]3)nc2c1' InChI=1S/C9H7N5/c1-2-4-7-6(3-1)11-9(12-7)8-5-10-14-13-8/h1-5H,(H,11,12)(H,10,13,14) NLOXYFLUIXGLPW-UHFFFAOYSA-N
T1B 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
T1B imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
T1B 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
T1B C12 S1 1
T1B C13 S1 1
T1B C03 S1 1
T1B C04 S1 1
T1B C05 S1 1
T1B C06 S1 1
T1B C08 S1 1
T1B C10 S1 1
T1B C11 S1 1
T1B N07 S1 1
T1B N09 S1 1
T1B N14 S1 1
T1B N15 S1 1
T1B N16 S1 1
T1B C06 F1 1
T1B N07 F1 1
T1B C08 F1 1
T1B N09 F1 1
T1B C10 F1 1
T1B C11 F1 1
T1B C03 F1 1
T1B C04 F1 1
T1B C05 F1 1
T1B C06 F2 1
T1B C10 F2 1
T1B N09 F2 1
T1B C08 F2 1
T1B N07 F2 1
T1B C03 F3 1
T1B C04 F3 1
T1B C05 F3 1
T1B C06 F3 1
T1B C10 F3 1
T1B C11 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id T1B
_pdbe_chem_comp_rdkit_properties.exactmw 227.117
_pdbe_chem_comp_rdkit_properties.amw 227.271
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.250
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 116.812
_pdbe_chem_comp_rdkit_properties.tpsa 59.390
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.058
_pdbe_chem_comp_rdkit_properties.CrippenMR 61.675
_pdbe_chem_comp_rdkit_properties.chi0v 8.236
_pdbe_chem_comp_rdkit_properties.chi1v 4.465
_pdbe_chem_comp_rdkit_properties.chi2v 2.048
_pdbe_chem_comp_rdkit_properties.chi3v 2.048
_pdbe_chem_comp_rdkit_properties.chi4v 1.308
_pdbe_chem_comp_rdkit_properties.chi0n 21.236
_pdbe_chem_comp_rdkit_properties.chi1n 10.912
_pdbe_chem_comp_rdkit_properties.chi2n 2.048
_pdbe_chem_comp_rdkit_properties.chi3n 2.048
_pdbe_chem_comp_rdkit_properties.chi4n 1.308
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.170
_pdbe_chem_comp_rdkit_properties.kappa1 3.188
_pdbe_chem_comp_rdkit_properties.kappa2 3.693
_pdbe_chem_comp_rdkit_properties.kappa3 1.595
_pdbe_chem_comp_rdkit_properties.Phi 0.692
#
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
T1B UniChem PDBe T1B
T1B UniChem PubChem 136518179
#
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
T1B C12 -3.044 0.652 -0.868 ETKDGv3 1
T1B C13 -3.380 1.392 -1.915 ETKDGv3 2
T1B C01 4.771 0.793 0.856 ETKDGv3 3
T1B C02 4.251 -0.236 -0.142 ETKDGv3 4
T1B C03 2.777 -0.465 0.049 ETKDGv3 5
T1B C04 2.330 -1.410 0.918 ETKDGv3 6
T1B C05 0.870 -1.613 1.131 ETKDGv3 7
T1B C06 0.042 -0.817 0.456 ETKDGv3 8
T1B C08 -1.671 0.258 -0.494 ETKDGv3 9
T1B C10 0.500 0.183 -0.450 ETKDGv3 10
T1B C11 1.795 0.394 -0.683 ETKDGv3 11
T1B C17 -4.419 -0.202 1.163 ETKDGv3 12
T1B N07 -1.370 -0.790 0.450 ETKDGv3 13
T1B N09 -0.623 0.830 -1.029 ETKDGv3 14
T1B N14 -4.797 1.571 -1.913 ETKDGv3 15
T1B N15 -5.270 0.965 -0.900 ETKDGv3 16
T1B N16 -4.249 0.343 -0.177 ETKDGv3 17
T1B H1 -2.706 1.806 -2.654 ETKDGv3 18
T1B H2 4.245 1.763 0.719 ETKDGv3 19
T1B H3 4.614 0.435 1.896 ETKDGv3 20
T1B H4 5.857 0.953 0.695 ETKDGv3 21
T1B H5 4.811 -1.188 -0.014 ETKDGv3 22
T1B H6 4.445 0.127 -1.174 ETKDGv3 23
T1B H7 3.030 -2.027 1.469 ETKDGv3 24
T1B H8 0.497 -2.370 1.809 ETKDGv3 25
T1B H9 2.118 1.157 -1.380 ETKDGv3 26
T1B H10 -5.427 0.057 1.551 ETKDGv3 27
T1B H11 -3.656 0.224 1.848 ETKDGv3 28
T1B H12 -4.330 -1.307 1.130 ETKDGv3 29
T1B H13 -2.013 -1.477 0.897 ETKDGv3 30
#