data_3OMK # _model_server_result.job_id 4XYRl2VUinf9WfbH-gLaTA _model_server_result.datetime_utc '2025-07-13 03:24:08' _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 3omk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1}' # _entry.id 3OMK # _exptl.entry_id 3OMK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 493.975 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2S)-2-[2-(4-chlorophenyl)-5,6-difluoro-1H-benzimidazol-1-yl]-2-cyclohexyl-N-(2-methylphenyl)ethanamide _entity.pdbx_number_of_molecules 2 _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 90 _cell.entry_id 3OMK _cell.length_a 72.32 _cell.length_b 84.71 _cell.length_c 190.01 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OMK _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,G,H 1 1 C,D,F,I,J 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N # _chem_comp.formula 'C28 H26 Cl F2 N3 O' _chem_comp.formula_weight 493.975 _chem_comp.id OMK _chem_comp.mon_nstd_flag . _chem_comp.name (2S)-2-[2-(4-chlorophenyl)-5,6-difluoro-1H-benzimidazol-1-yl]-2-cyclohexyl-N-(2-methylphenyl)ethanamide _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 N1 C2 OMK sing 237 n y N1 C4 OMK sing 238 n y N1 C7 OMK sing 239 n n C2 N3 OMK doub 240 n y C2 C12 OMK sing 241 n y N3 C5 OMK sing 242 n y C4 C5 OMK doub 243 n y C4 C8 OMK sing 244 n y C5 C10 OMK sing 245 n y C6 C7 OMK sing 246 n n C6 N9 OMK sing 247 n n C6 O15 OMK doub 248 n n C7 C17 OMK sing 249 n n C8 C11 OMK doub 250 n y N9 C14 OMK sing 251 n n C10 C13 OMK doub 252 n y C11 C13 OMK sing 253 n y C11 F20 OMK sing 254 n n C12 C18 OMK doub 255 n y C12 C19 OMK sing 256 n y C13 F21 OMK sing 257 n n C14 C16 OMK doub 258 n y C14 C26 OMK sing 259 n y C16 C27 OMK sing 260 n n C16 C28 OMK sing 261 n y C17 C29 OMK sing 262 n n C17 C30 OMK sing 263 n n C18 C24 OMK sing 264 n y C19 C23 OMK doub 265 n y C22 C23 OMK sing 266 n y C22 C24 OMK doub 267 n y C22 CL25 OMK sing 268 n n C26 C31 OMK doub 269 n y C28 C32 OMK doub 270 n y C29 C34 OMK sing 271 n n C30 C33 OMK sing 272 n n C31 C32 OMK sing 273 n y C33 C35 OMK sing 274 n n C34 C35 OMK sing 275 n n C7 H7 OMK sing 276 n n C8 H8 OMK sing 277 n n N9 HN9 OMK sing 278 n n C10 H10 OMK sing 279 n n C17 H17 OMK sing 280 n n C18 H18 OMK sing 281 n n C19 H19 OMK sing 282 n n C23 H23 OMK sing 283 n n C24 H24 OMK sing 284 n n C26 H26 OMK sing 285 n n C27 H27 OMK sing 286 n n C27 H27A OMK sing 287 n n C27 H27B OMK sing 288 n n C28 H28 OMK sing 289 n n C29 H29 OMK sing 290 n n C29 H29A OMK sing 291 n n C30 H30 OMK sing 292 n n C30 H30A OMK sing 293 n n C31 H31 OMK sing 294 n n C32 H32 OMK sing 295 n n C33 H33 OMK sing 296 n n C33 H33A OMK sing 297 n n C34 H34 OMK sing 298 n n C34 H34A OMK sing 299 n n C35 H35 OMK sing 300 n n C35 H35A OMK sing 301 n n # _atom_sites.entry_id 3OMK _atom_sites.fract_transf_matrix[1][1] 0.013827 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011805 _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] 0.005263 _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 E 3 OMK A 1 1 1 OMK UNL . F 3 OMK C 1 2 2 OMK UNL . G 4 HOH A 1 3 3 HOH HOH . G 4 HOH A 2 4 4 HOH HOH . G 4 HOH A 3 5 5 HOH HOH . G 4 HOH A 4 7 7 HOH HOH . G 4 HOH A 5 8 8 HOH HOH . G 4 HOH A 6 14 14 HOH HOH . G 4 HOH A 7 15 15 HOH HOH . G 4 HOH A 8 20 20 HOH HOH . G 4 HOH A 9 21 21 HOH HOH . G 4 HOH A 10 23 23 HOH HOH . G 4 HOH A 11 24 24 HOH HOH . G 4 HOH A 12 25 25 HOH HOH . G 4 HOH A 13 26 26 HOH HOH . G 4 HOH A 14 27 27 HOH HOH . G 4 HOH A 15 28 28 HOH HOH . G 4 HOH A 16 29 29 HOH HOH . G 4 HOH A 17 30 30 HOH HOH . G 4 HOH A 18 31 31 HOH HOH . G 4 HOH A 19 32 32 HOH HOH . G 4 HOH A 20 34 34 HOH HOH . G 4 HOH A 21 35 35 HOH HOH . G 4 HOH A 22 37 37 HOH HOH . G 4 HOH A 23 39 39 HOH HOH . G 4 HOH A 24 40 40 HOH HOH . G 4 HOH A 25 41 41 HOH HOH . G 4 HOH A 26 44 44 HOH HOH . G 4 HOH A 27 46 46 HOH HOH . G 4 HOH A 28 47 47 HOH HOH . G 4 HOH A 29 49 49 HOH HOH . G 4 HOH A 30 52 52 HOH HOH . G 4 HOH A 31 53 53 HOH HOH . G 4 HOH A 32 54 54 HOH HOH . G 4 HOH A 33 56 56 HOH HOH . G 4 HOH A 34 58 58 HOH HOH . G 4 HOH A 35 59 59 HOH HOH . G 4 HOH A 36 60 60 HOH HOH . G 4 HOH A 37 61 61 HOH HOH . G 4 HOH A 38 62 62 HOH HOH . G 4 HOH A 39 64 64 HOH HOH . G 4 HOH A 40 67 67 HOH HOH . G 4 HOH A 41 68 68 HOH HOH . G 4 HOH A 42 69 69 HOH HOH . G 4 HOH A 43 70 70 HOH HOH . G 4 HOH A 44 73 73 HOH HOH . G 4 HOH A 45 74 74 HOH HOH . G 4 HOH A 46 75 75 HOH HOH . G 4 HOH A 47 80 80 HOH HOH . G 4 HOH A 48 81 81 HOH HOH . G 4 HOH A 49 83 83 HOH HOH . G 4 HOH A 50 85 85 HOH HOH . G 4 HOH A 51 86 86 HOH HOH . G 4 HOH A 52 89 89 HOH HOH . G 4 HOH A 53 90 90 HOH HOH . G 4 HOH A 54 95 95 HOH HOH . G 4 HOH A 55 97 97 HOH HOH . G 4 HOH A 56 98 98 HOH HOH . G 4 HOH A 57 100 100 HOH HOH . G 4 HOH A 58 101 101 HOH HOH . G 4 HOH A 59 103 103 HOH HOH . G 4 HOH A 60 109 109 HOH HOH . G 4 HOH A 61 110 110 HOH HOH . G 4 HOH A 62 111 111 HOH HOH . G 4 HOH A 63 112 112 HOH HOH . G 4 HOH A 64 118 118 HOH HOH . G 4 HOH A 65 119 119 HOH HOH . G 4 HOH A 66 120 120 HOH HOH . G 4 HOH A 67 121 121 HOH HOH . G 4 HOH A 68 122 122 HOH HOH . G 4 HOH A 69 123 123 HOH HOH . G 4 HOH A 70 129 129 HOH HOH . G 4 HOH A 71 131 131 HOH HOH . G 4 HOH A 72 132 132 HOH HOH . G 4 HOH A 73 133 133 HOH HOH . G 4 HOH A 74 134 134 HOH HOH . G 4 HOH A 75 136 136 HOH HOH . G 4 HOH A 76 137 137 HOH HOH . G 4 HOH A 77 139 139 HOH HOH . G 4 HOH A 78 140 140 HOH HOH . G 4 HOH A 79 141 141 HOH HOH . G 4 HOH A 80 142 142 HOH HOH . G 4 HOH A 81 143 143 HOH HOH . G 4 HOH A 82 144 144 HOH HOH . G 4 HOH A 83 145 145 HOH HOH . G 4 HOH A 84 146 146 HOH HOH . G 4 HOH A 85 147 147 HOH HOH . G 4 HOH A 86 148 148 HOH HOH . G 4 HOH A 87 149 149 HOH HOH . G 4 HOH A 88 150 150 HOH HOH . G 4 HOH A 89 152 152 HOH HOH . G 4 HOH A 90 153 153 HOH HOH . G 4 HOH A 91 154 154 HOH HOH . G 4 HOH A 92 155 155 HOH HOH . G 4 HOH A 93 158 158 HOH HOH . G 4 HOH A 94 159 159 HOH HOH . G 4 HOH A 95 160 160 HOH HOH . G 4 HOH A 96 161 161 HOH HOH . G 4 HOH A 97 163 163 HOH HOH . G 4 HOH A 98 164 164 HOH HOH . G 4 HOH A 99 170 170 HOH HOH . G 4 HOH A 100 171 171 HOH HOH . G 4 HOH A 101 172 172 HOH HOH . G 4 HOH A 102 173 173 HOH HOH . G 4 HOH A 103 174 174 HOH HOH . G 4 HOH A 104 175 175 HOH HOH . G 4 HOH A 105 176 176 HOH HOH . G 4 HOH A 106 177 177 HOH HOH . G 4 HOH A 107 178 178 HOH HOH . G 4 HOH A 108 179 179 HOH HOH . G 4 HOH A 109 180 180 HOH HOH . G 4 HOH A 110 182 182 HOH HOH . G 4 HOH A 111 185 185 HOH HOH . G 4 HOH A 112 186 186 HOH HOH . G 4 HOH A 113 188 188 HOH HOH . G 4 HOH A 114 190 190 HOH HOH . G 4 HOH A 115 191 191 HOH HOH . G 4 HOH A 116 192 192 HOH HOH . G 4 HOH A 117 195 195 HOH HOH . G 4 HOH A 118 198 198 HOH HOH . G 4 HOH A 119 200 200 HOH HOH . G 4 HOH A 120 203 203 HOH HOH . G 4 HOH A 121 204 204 HOH HOH . G 4 HOH A 122 477 1 HOH HOH . H 4 HOH B 1 22 22 HOH HOH . H 4 HOH B 2 50 50 HOH HOH . H 4 HOH B 3 92 92 HOH HOH . H 4 HOH B 4 197 197 HOH HOH . I 4 HOH C 1 6 6 HOH HOH . I 4 HOH C 2 9 9 HOH HOH . I 4 HOH C 3 10 10 HOH HOH . I 4 HOH C 4 11 11 HOH HOH . I 4 HOH C 5 12 12 HOH HOH . I 4 HOH C 6 13 13 HOH HOH . I 4 HOH C 7 16 16 HOH HOH . I 4 HOH C 8 17 17 HOH HOH . I 4 HOH C 9 18 18 HOH HOH . I 4 HOH C 10 19 19 HOH HOH . I 4 HOH C 11 33 33 HOH HOH . I 4 HOH C 12 36 36 HOH HOH . I 4 HOH C 13 38 38 HOH HOH . I 4 HOH C 14 42 42 HOH HOH . I 4 HOH C 15 43 43 HOH HOH . I 4 HOH C 16 45 45 HOH HOH . I 4 HOH C 17 48 48 HOH HOH . I 4 HOH C 18 51 51 HOH HOH . I 4 HOH C 19 55 55 HOH HOH . I 4 HOH C 20 57 57 HOH HOH . I 4 HOH C 21 63 63 HOH HOH . I 4 HOH C 22 65 65 HOH HOH . I 4 HOH C 23 66 66 HOH HOH . I 4 HOH C 24 71 71 HOH HOH . I 4 HOH C 25 72 72 HOH HOH . I 4 HOH C 26 76 76 HOH HOH . I 4 HOH C 27 77 77 HOH HOH . I 4 HOH C 28 78 78 HOH HOH . I 4 HOH C 29 79 79 HOH HOH . I 4 HOH C 30 82 82 HOH HOH . I 4 HOH C 31 84 84 HOH HOH . I 4 HOH C 32 87 87 HOH HOH . I 4 HOH C 33 88 88 HOH HOH . I 4 HOH C 34 91 91 HOH HOH . I 4 HOH C 35 93 93 HOH HOH . I 4 HOH C 36 94 94 HOH HOH . I 4 HOH C 37 96 96 HOH HOH . I 4 HOH C 38 99 99 HOH HOH . I 4 HOH C 39 102 102 HOH HOH . I 4 HOH C 40 104 104 HOH HOH . I 4 HOH C 41 106 106 HOH HOH . I 4 HOH C 42 107 107 HOH HOH . I 4 HOH C 43 108 108 HOH HOH . I 4 HOH C 44 113 113 HOH HOH . I 4 HOH C 45 114 114 HOH HOH . I 4 HOH C 46 115 115 HOH HOH . I 4 HOH C 47 116 116 HOH HOH . I 4 HOH C 48 117 117 HOH HOH . I 4 HOH C 49 124 124 HOH HOH . I 4 HOH C 50 126 126 HOH HOH . I 4 HOH C 51 127 127 HOH HOH . I 4 HOH C 52 128 128 HOH HOH . I 4 HOH C 53 130 130 HOH HOH . I 4 HOH C 54 135 135 HOH HOH . I 4 HOH C 55 138 138 HOH HOH . I 4 HOH C 56 151 151 HOH HOH . I 4 HOH C 57 156 156 HOH HOH . I 4 HOH C 58 157 157 HOH HOH . I 4 HOH C 59 162 162 HOH HOH . I 4 HOH C 60 165 165 HOH HOH . I 4 HOH C 61 166 166 HOH HOH . I 4 HOH C 62 167 167 HOH HOH . I 4 HOH C 63 168 168 HOH HOH . I 4 HOH C 64 169 169 HOH HOH . I 4 HOH C 65 181 181 HOH HOH . I 4 HOH C 66 183 183 HOH HOH . I 4 HOH C 67 184 184 HOH HOH . I 4 HOH C 68 187 187 HOH HOH . I 4 HOH C 69 189 189 HOH HOH . I 4 HOH C 70 193 193 HOH HOH . I 4 HOH C 71 194 194 HOH HOH . I 4 HOH C 72 196 196 HOH HOH . I 4 HOH C 73 199 199 HOH HOH . I 4 HOH C 74 201 201 HOH HOH . I 4 HOH C 75 202 202 HOH HOH . I 4 HOH C 76 477 2 HOH HOH . J 4 HOH D 1 105 105 HOH HOH . J 4 HOH D 2 125 125 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 N N1 OMK . . . E 3 23.056 17.93 3.701 1 24.59 ? N1 OMK 1 A 1 HETATM 2 C C2 OMK . . . E 3 22.216 17.175 2.839 1 22.5 ? C2 OMK 1 A 1 HETATM 3 N N3 OMK . . . E 3 22.889 16.209 2.195 1 23.08 ? N3 OMK 1 A 1 HETATM 4 C C4 OMK . . . E 3 24.307 17.32 3.606 1 22.4 ? C4 OMK 1 A 1 HETATM 5 C C5 OMK . . . E 3 24.189 16.247 2.663 1 21.2 ? C5 OMK 1 A 1 HETATM 6 C C6 OMK . . . E 3 23.515 20.303 4.163 1 27.56 ? C6 OMK 1 A 1 HETATM 7 C C7 OMK . . . E 3 22.662 19.038 4.535 1 27.61 ? C7 OMK 1 A 1 HETATM 8 C C8 OMK . . . E 3 25.512 17.586 4.238 1 26.77 ? C8 OMK 1 A 1 HETATM 9 N N9 OMK . . . E 3 23.827 20.433 2.836 1 24.37 ? N9 OMK 1 A 1 HETATM 10 C C10 OMK . . . E 3 25.305 15.421 2.355 1 22.86 ? C10 OMK 1 A 1 HETATM 11 C C11 OMK . . . E 3 26.61 16.799 3.914 1 27.11 ? C11 OMK 1 A 1 HETATM 12 C C12 OMK . . . E 3 20.833 17.553 2.631 1 26.1 ? C12 OMK 1 A 1 HETATM 13 C C13 OMK . . . E 3 26.514 15.761 2.969 1 25.21 ? C13 OMK 1 A 1 HETATM 14 C C14 OMK . . . E 3 24.489 21.496 2.218 1 24.55 ? C14 OMK 1 A 1 HETATM 15 O O15 OMK . . . E 3 23.889 21.122 4.997 1 29.6 ? O15 OMK 1 A 1 HETATM 16 C C16 OMK . . . E 3 23.782 22.709 2.045 1 24.7 ? C16 OMK 1 A 1 HETATM 17 C C17 OMK . . . E 3 22.786 18.697 6.044 1 27.46 ? C17 OMK 1 A 1 HETATM 18 C C18 OMK . . . E 3 20.561 18.722 1.909 1 26.61 ? C18 OMK 1 A 1 HETATM 19 C C19 OMK . . . E 3 19.795 16.827 3.225 1 29.11 ? C19 OMK 1 A 1 HETATM 20 F F20 OMK . . . E 3 27.818 17.03 4.478 1 32.64 ? F20 OMK 1 A 1 HETATM 21 F F21 OMK . . . E 3 27.643 15.053 2.804 1 29.35 ? F21 OMK 1 A 1 HETATM 22 C C22 OMK . . . E 3 18.208 18.41 2.352 1 32.95 ? C22 OMK 1 A 1 HETATM 23 C C23 OMK . . . E 3 18.484 17.269 3.095 1 31.49 ? C23 OMK 1 A 1 HETATM 24 C C24 OMK . . . E 3 19.235 19.157 1.769 1 29.38 ? C24 OMK 1 A 1 HETATM 25 CL CL25 OMK . . . E 3 16.592 18.916 2.211 1 36.19 ? CL25 OMK 1 A 1 HETATM 26 C C26 OMK . . . E 3 25.84 21.389 1.791 1 24.37 ? C26 OMK 1 A 1 HETATM 27 C C27 OMK . . . E 3 22.373 22.82 2.451 1 25.02 ? C27 OMK 1 A 1 HETATM 28 C C28 OMK . . . E 3 24.385 23.757 1.35 1 22.65 ? C28 OMK 1 A 1 HETATM 29 C C29 OMK . . . E 3 22.092 19.714 6.945 1 25.07 ? C29 OMK 1 A 1 HETATM 30 C C30 OMK . . . E 3 22.297 17.281 6.336 1 32.15 ? C30 OMK 1 A 1 HETATM 31 C C31 OMK . . . E 3 26.43 22.475 1.145 1 21.55 ? C31 OMK 1 A 1 HETATM 32 C C32 OMK . . . E 3 25.708 23.649 0.935 1 23.13 ? C32 OMK 1 A 1 HETATM 33 C C33 OMK . . . E 3 22.413 16.908 7.817 1 29.27 ? C33 OMK 1 A 1 HETATM 34 C C34 OMK . . . E 3 22.173 19.312 8.417 1 24.58 ? C34 OMK 1 A 1 HETATM 35 C C35 OMK . . . E 3 21.643 17.909 8.652 1 25.79 ? C35 OMK 1 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 538 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 35 #