data_D6V # _chem_comp.id D6V _chem_comp.name "2-[(3S)-pyrrolidin-3-yl]-1H-benzimidazole" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H13 N3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-10-20 _chem_comp.pdbx_modified_date 2020-04-17 _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 187.241 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D6V _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 5QBA _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.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 D6V C4 C1 C 0 1 Y N N -2.100 8.982 7.339 1.479 0.639 0.080 C4 D6V 1 D6V C5 C2 C 0 1 Y N N -3.098 9.943 7.275 2.576 1.463 0.294 C5 D6V 2 D6V C6 C3 C 0 1 Y N N -0.333 7.731 7.720 -0.469 -0.356 -0.217 C6 D6V 3 D6V N1 N1 N 0 1 Y N N -1.013 7.050 6.814 0.441 -1.278 -0.338 N1 D6V 4 D6V C7 C4 C 0 1 N N S 0.986 7.277 8.257 -1.953 -0.585 -0.348 C7 D6V 5 D6V C8 C5 C 0 1 N N N 2.135 8.305 8.255 -2.619 -0.677 1.050 C8 D6V 6 D6V N2 N2 N 0 1 N N N 2.392 6.768 10.110 -3.924 0.835 -0.280 N2 D6V 7 D6V C9 C6 C 0 1 N N N 3.174 7.698 9.237 -4.069 -0.229 0.736 C9 D6V 8 D6V C10 C7 C 0 1 N N N 0.946 6.875 9.730 -2.641 0.643 -0.981 C10 D6V 9 D6V C3 C8 C 0 1 Y N N -2.135 7.829 6.556 1.671 -0.732 -0.162 C3 D6V 10 D6V C2 C9 C 0 1 Y N N -3.195 7.623 5.677 2.968 -1.252 -0.178 C2 D6V 11 D6V C1 C10 C 0 1 Y N N -4.197 8.580 5.608 4.035 -0.427 0.040 C1 D6V 12 D6V N N3 N 0 1 Y N N -0.929 8.897 8.085 0.115 0.846 0.034 N D6V 13 D6V C C11 C 0 1 Y N N -4.150 9.725 6.397 3.846 0.928 0.275 C D6V 14 D6V H1 H1 H 0 1 N N N -3.058 10.831 7.888 2.434 2.518 0.475 H1 D6V 15 D6V H3 H3 H 0 1 N N N 1.315 6.403 7.675 -2.153 -1.483 -0.933 H3 D6V 16 D6V H4 H4 H 0 1 N N N 2.564 8.412 7.248 -2.599 -1.700 1.426 H4 D6V 17 D6V H5 H5 H 0 1 N N N 1.785 9.285 8.611 -2.144 0.006 1.755 H5 D6V 18 D6V H6 H6 H 0 1 N N N 2.709 5.829 9.975 -4.696 0.822 -0.930 H6 D6V 19 D6V H8 H8 H 0 1 N N N 3.951 7.148 8.685 -4.644 -1.063 0.333 H8 D6V 20 D6V H9 H9 H 0 1 N N N 3.643 8.489 9.840 -4.547 0.165 1.632 H9 D6V 21 D6V H10 H10 H 0 1 N N N 0.438 7.643 10.332 -2.013 1.525 -0.854 H10 D6V 22 D6V H11 H11 H 0 1 N N N 0.434 5.910 9.859 -2.820 0.462 -2.041 H11 D6V 23 D6V H12 H12 H 0 1 N N N -3.236 6.736 5.062 3.127 -2.304 -0.363 H12 D6V 24 D6V H13 H13 H 0 1 N N N -5.026 8.434 4.932 5.036 -0.832 0.026 H13 D6V 25 D6V H14 H14 H 0 1 N N N -0.593 9.560 8.754 -0.343 1.693 0.159 H14 D6V 26 D6V H15 H15 H 0 1 N N N -4.943 10.454 6.325 4.700 1.567 0.445 H15 D6V 27 # # 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 D6V C1 C2 DOUB Y N 1 D6V C1 C SING Y N 2 D6V C2 C3 SING Y N 3 D6V C C5 DOUB Y N 4 D6V C3 N1 SING Y N 5 D6V C3 C4 DOUB Y N 6 D6V N1 C6 DOUB Y N 7 D6V C5 C4 SING Y N 8 D6V C4 N SING Y N 9 D6V C6 N SING Y N 10 D6V C6 C7 SING N N 11 D6V C8 C7 SING N N 12 D6V C8 C9 SING N N 13 D6V C7 C10 SING N N 14 D6V C9 N2 SING N N 15 D6V C10 N2 SING N N 16 D6V C5 H1 SING N N 17 D6V C7 H3 SING N N 18 D6V C8 H4 SING N N 19 D6V C8 H5 SING N N 20 D6V N2 H6 SING N N 21 D6V C9 H8 SING N N 22 D6V C9 H9 SING N N 23 D6V C10 H10 SING N N 24 D6V C10 H11 SING N N 25 D6V C2 H12 SING N N 26 D6V C1 H13 SING N N 27 D6V N H14 SING N N 28 D6V C H15 SING N N 29 # # 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 D6V SMILES ACDLabs 12.01 "c32nc(C1CNCC1)nc2cccc3" D6V InChI InChI 1.03 "InChI=1S/C11H13N3/c1-2-4-10-9(3-1)13-11(14-10)8-5-6-12-7-8/h1-4,8,12H,5-7H2,(H,13,14)/t8-/m0/s1" D6V InChIKey InChI 1.03 OFQGVINTJUCLFL-QMMMGPOBSA-N D6V SMILES_CANONICAL CACTVS 3.385 "C1C[C@@H](CN1)c2[nH]c3ccccc3n2" D6V SMILES CACTVS 3.385 "C1C[CH](CN1)c2[nH]c3ccccc3n2" D6V SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc2c(c1)[nH]c(n2)[C@H]3CCNC3" D6V SMILES "OpenEye OEToolkits" 2.0.6 "c1ccc2c(c1)[nH]c(n2)C3CCNC3" # # 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 D6V "SYSTEMATIC NAME" ACDLabs 12.01 "2-[(3S)-pyrrolidin-3-yl]-1H-benzimidazole" D6V "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "2-[(3~{S})-pyrrolidin-3-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 D6V "Create component" 2017-10-20 RCSB D6V "Initial release" 2020-04-22 RCSB ##