data_8Q5L # _model_server_result.job_id dBcribNIxCuq4fChz-kMgQ _model_server_result.datetime_utc '2024-11-16 06:39:06' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 8q5l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8Q5L # _exptl.entry_id 8Q5L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.886 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[4-[(2~{S})-3-[(6-chloranyl-1-propan-2-yl-benzimidazol-2-yl)amino]-2-oxidanyl-propoxy]phenyl]ethanenitrile _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 8Q5L _cell.length_a 121.121 _cell.length_b 121.121 _cell.length_c 115.534 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Q5L _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 1 A,B,C 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C21 H23 Cl N4 O2' _chem_comp.formula_weight 398.886 _chem_comp.id JVO _chem_comp.mon_nstd_flag . _chem_comp.name 2-[4-[(2~{S})-3-[(6-chloranyl-1-propan-2-yl-benzimidazol-2-yl)amino]-2-oxidanyl-propoxy]phenyl]ethanenitrile _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 JVO sing 173 n n C2 C3 JVO sing 174 n n C2 N1 JVO sing 175 n n C14 C15 JVO doub 176 n y C14 C11 JVO sing 177 n y C15 C8 JVO sing 178 n y C20 C21 JVO doub 179 n y C20 C19 JVO sing 180 n y C5 C6 JVO sing 181 n n C5 N2 JVO sing 182 n n N1 C21 JVO sing 183 n y N1 C4 JVO sing 184 n y CL1 C19 JVO sing 185 n n C12 C11 JVO sing 186 n n C12 C13 JVO sing 187 n n C21 C16 JVO sing 188 n y C11 C10 JVO doub 189 n y C6 C7 JVO sing 190 n n C6 O1 JVO sing 191 n n C19 C18 JVO doub 192 n y C4 N2 JVO sing 193 n n C4 N4 JVO doub 194 n y C8 O2 JVO sing 195 n n C8 C9 JVO doub 196 n y C7 O2 JVO sing 197 n n C13 N3 JVO trip 198 n n C16 N4 JVO sing 199 n y C16 C17 JVO doub 200 n y C10 C9 JVO sing 201 n y C18 C17 JVO sing 202 n y C1 H1 JVO sing 203 n n C1 H2 JVO sing 204 n n C1 H3 JVO sing 205 n n C2 H4 JVO sing 206 n n C3 H5 JVO sing 207 n n C3 H6 JVO sing 208 n n C3 H7 JVO sing 209 n n N2 H8 JVO sing 210 n n C5 H9 JVO sing 211 n n C5 H10 JVO sing 212 n n C6 H11 JVO sing 213 n n O1 H12 JVO sing 214 n n C7 H13 JVO sing 215 n n C7 H14 JVO sing 216 n n C9 H15 JVO sing 217 n n C10 H16 JVO sing 218 n n C12 H17 JVO sing 219 n n C12 H18 JVO sing 220 n n C14 H19 JVO sing 221 n n C15 H20 JVO sing 222 n n C17 H21 JVO sing 223 n n C18 H22 JVO sing 224 n n C20 H23 JVO sing 225 n n # _atom_sites.entry_id 8Q5L _atom_sites.fract_transf_matrix[1][1] 0.008256 _atom_sites.fract_transf_matrix[1][2] 0.004767 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009533 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008655 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 JVO A 1 401 301 JVO SEN . C 3 HOH A 1 501 1 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O2 JVO . . . B 2 -56.201 -2.846 11.36 1 88.38 ? O2 JVO 401 A 1 HETATM 2 N N1 JVO . . . B 2 -53.729 2.019 10.028 1 71.62 ? N1 JVO 401 A 1 HETATM 3 C C1 JVO . . . B 2 -53.411 2.383 7.599 1 77.06 ? C1 JVO 401 A 1 HETATM 4 C C2 JVO . . . B 2 -53.592 1.37 8.72 1 75.65 ? C2 JVO 401 A 1 HETATM 5 C C3 JVO . . . B 2 -52.483 0.33 8.73 1 73.5 ? C3 JVO 401 A 1 HETATM 6 C C4 JVO . . . B 2 -54.717 1.979 11.018 1 75.3 ? C4 JVO 401 A 1 HETATM 7 N N2 JVO . . . B 2 -55.888 1.307 11.052 1 76.6 ? N2 JVO 401 A 1 HETATM 8 C C5 JVO . . . B 2 -56.504 0.503 10.016 1 77.19 ? C5 JVO 401 A 1 HETATM 9 C C6 JVO . . . B 2 -57.011 -0.792 10.623 1 78.97 ? C6 JVO 401 A 1 HETATM 10 O O1 JVO . . . B 2 -57.961 -0.583 11.662 1 62.76 ? O1 JVO 401 A 1 HETATM 11 C C7 JVO . . . B 2 -55.774 -1.507 11.112 1 81.17 ? C7 JVO 401 A 1 HETATM 12 C C8 JVO . . . B 2 -55.351 -3.877 11.075 1 86.92 ? C8 JVO 401 A 1 HETATM 13 C C9 JVO . . . B 2 -55.086 -4.783 12.089 1 88.98 ? C9 JVO 401 A 1 HETATM 14 C C10 JVO . . . B 2 -54.256 -5.862 11.848 1 88.91 ? C10 JVO 401 A 1 HETATM 15 C C11 JVO . . . B 2 -53.686 -6.066 10.603 1 88.12 ? C11 JVO 401 A 1 HETATM 16 C C12 JVO . . . B 2 -52.789 -7.258 10.348 1 91.22 ? C12 JVO 401 A 1 HETATM 17 C C13 JVO . . . B 2 -51.807 -7.503 11.398 1 90.28 ? C13 JVO 401 A 1 HETATM 18 N N3 JVO . . . B 2 -50.967 -7.673 12.155 1 87.8 ? N3 JVO 401 A 1 HETATM 19 C C14 JVO . . . B 2 -53.975 -5.154 9.598 1 87.58 ? C14 JVO 401 A 1 HETATM 20 C C15 JVO . . . B 2 -54.804 -4.067 9.819 1 84.73 ? C15 JVO 401 A 1 HETATM 21 N N4 JVO . . . B 2 -54.439 2.725 12.065 1 80.49 ? N4 JVO 401 A 1 HETATM 22 C C16 JVO . . . B 2 -53.204 3.29 11.775 1 77.07 ? C16 JVO 401 A 1 HETATM 23 C C17 JVO . . . B 2 -52.435 4.16 12.543 1 77.27 ? C17 JVO 401 A 1 HETATM 24 C C18 JVO . . . B 2 -51.232 4.586 12.039 1 73.54 ? C18 JVO 401 A 1 HETATM 25 C C19 JVO . . . B 2 -50.807 4.155 10.795 1 70.45 ? C19 JVO 401 A 1 HETATM 26 CL CL1 JVO . . . B 2 -49.267 4.727 10.206 1 94.02 ? CL1 JVO 401 A 1 HETATM 27 C C20 JVO . . . B 2 -51.546 3.291 10.009 1 70.39 ? C20 JVO 401 A 1 HETATM 28 C C21 JVO . . . B 2 -52.759 2.862 10.525 1 69.92 ? C21 JVO 401 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 28 #