data_RYM # _chem_comp.id RYM _chem_comp.name "4-(benzimidazol-1-ylmethyl)benzenecarbonitrile" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H11 N3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-03-02 _chem_comp.pdbx_modified_date 2020-06-26 _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 233.268 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RYM _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 5R54 _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 RYM N1 N1 N 0 1 Y N N 14.063 23.250 -1.470 2.661 -1.587 -1.136 N1 RYM 1 RYM N3 N2 N 0 1 N N N 8.197 27.358 2.794 -5.622 1.250 -1.151 N3 RYM 2 RYM C4 C1 C 0 1 Y N N 12.214 22.107 -0.809 2.043 -0.013 0.303 C4 RYM 3 RYM C5 C2 C 0 1 Y N N 12.918 22.593 -1.911 2.939 -0.319 -0.735 C5 RYM 4 RYM C6 C3 C 0 1 Y N N 12.429 22.378 -3.196 3.874 0.636 -1.141 C6 RYM 5 RYM C7 C4 C 0 1 Y N N 14.030 23.166 -0.163 1.679 -2.064 -0.429 C7 RYM 6 RYM C8 C5 C 0 1 N N N 12.600 22.246 1.692 0.175 -1.299 1.446 C8 RYM 7 RYM C10 C6 C 0 1 Y N N 10.262 23.113 1.940 -1.946 -1.554 0.142 C10 RYM 8 RYM C13 C7 C 0 1 Y N N 11.197 25.626 2.619 -2.591 1.112 0.563 C13 RYM 9 RYM C15 C8 C 0 1 N N N 8.906 26.460 2.774 -4.660 0.827 -0.720 C15 RYM 10 RYM C1 C9 C 0 1 Y N N 11.244 21.687 -3.332 3.910 1.857 -0.527 C1 RYM 11 RYM C11 C10 C 0 1 Y N N 9.363 24.129 2.204 -3.116 -1.047 -0.384 C11 RYM 12 RYM C12 C11 C 0 1 Y N N 9.833 25.387 2.550 -3.447 0.294 -0.176 C12 RYM 13 RYM C14 C12 C 0 1 Y N N 12.083 24.597 2.364 -1.424 0.591 1.084 C14 RYM 14 RYM C2 C13 C 0 1 Y N N 10.551 21.203 -2.220 3.025 2.160 0.498 C2 RYM 15 RYM C3 C14 C 0 1 Y N N 11.023 21.404 -0.944 2.094 1.232 0.914 C3 RYM 16 RYM C9 C15 C 0 1 Y N N 11.622 23.328 2.065 -1.102 -0.738 0.874 C9 RYM 17 RYM N2 N3 N 0 1 Y N N 12.967 22.461 0.296 1.258 -1.136 0.473 N2 RYM 18 RYM H1 H1 H 0 1 N N N 12.962 22.742 -4.062 4.568 0.411 -1.937 H1 RYM 19 RYM H2 H2 H 0 1 N N N 14.773 23.612 0.482 1.258 -3.052 -0.542 H2 RYM 20 RYM H3 H3 H 0 1 N N N 12.132 21.257 1.811 0.427 -0.767 2.363 H3 RYM 21 RYM H4 H4 H 0 1 N N N 13.493 22.308 2.331 0.040 -2.358 1.665 H4 RYM 22 RYM H5 H5 H 0 1 N N N 9.899 22.143 1.634 -1.690 -2.592 -0.014 H5 RYM 23 RYM H6 H6 H 0 1 N N N 11.564 26.610 2.870 -2.841 2.149 0.728 H6 RYM 24 RYM H7 H7 H 0 1 N N N 10.843 21.516 -4.320 4.635 2.592 -0.844 H7 RYM 25 RYM H8 H8 H 0 1 N N N 8.301 23.944 2.141 -3.774 -1.685 -0.955 H8 RYM 26 RYM H9 H9 H 0 1 N N N 13.146 24.786 2.399 -0.761 1.223 1.656 H9 RYM 27 RYM H10 H10 H 0 1 N N N 9.628 20.661 -2.365 3.066 3.129 0.972 H10 RYM 28 RYM H11 H11 H 0 1 N N N 10.490 21.031 -0.082 1.408 1.474 1.713 H11 RYM 29 # # 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 RYM C1 C6 DOUB Y N 1 RYM C1 C2 SING Y N 2 RYM C6 C5 SING Y N 3 RYM C2 C3 DOUB Y N 4 RYM C5 N1 SING Y N 5 RYM C5 C4 DOUB Y N 6 RYM N1 C7 DOUB Y N 7 RYM C3 C4 SING Y N 8 RYM C4 N2 SING Y N 9 RYM C7 N2 SING Y N 10 RYM N2 C8 SING N N 11 RYM C8 C9 SING N N 12 RYM C10 C9 DOUB Y N 13 RYM C10 C11 SING Y N 14 RYM C9 C14 SING Y N 15 RYM C11 C12 DOUB Y N 16 RYM C14 C13 DOUB Y N 17 RYM C12 C13 SING Y N 18 RYM C12 C15 SING N N 19 RYM C15 N3 TRIP N N 20 RYM C6 H1 SING N N 21 RYM C7 H2 SING N N 22 RYM C8 H3 SING N N 23 RYM C8 H4 SING N N 24 RYM C10 H5 SING N N 25 RYM C13 H6 SING N N 26 RYM C1 H7 SING N N 27 RYM C11 H8 SING N N 28 RYM C14 H9 SING N N 29 RYM C2 H10 SING N N 30 RYM C3 H11 SING N N 31 # # 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 RYM InChI InChI 1.03 "InChI=1S/C15H11N3/c16-9-12-5-7-13(8-6-12)10-18-11-17-14-3-1-2-4-15(14)18/h1-8,11H,10H2" RYM InChIKey InChI 1.03 KZMYEQMVROHICO-UHFFFAOYSA-N RYM SMILES_CANONICAL CACTVS 3.385 "N#Cc1ccc(Cn2cnc3ccccc23)cc1" RYM SMILES CACTVS 3.385 "N#Cc1ccc(Cn2cnc3ccccc23)cc1" RYM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc2c(c1)ncn2Cc3ccc(cc3)C#N" RYM SMILES "OpenEye OEToolkits" 2.0.6 "c1ccc2c(c1)ncn2Cc3ccc(cc3)C#N" # _pdbx_chem_comp_identifier.comp_id RYM _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "4-(benzimidazol-1-ylmethyl)benzenecarbonitrile" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site RYM "Create component" 2020-03-02 RCSB RYM "Initial release" 2020-07-01 RCSB ##