data_5R0B # _model_server_result.job_id 7Un5eTQzNlhHakmeqHjvSw _model_server_result.datetime_utc '2024-11-27 17:10:11' _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 5r0b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2501}' # _entry.id 5R0B # _exptl.entry_id 5R0B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 514.576 _entity.id 3 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 2-methoxy-4-[[(4~{S},5~{S})-2,4,5-tris(2-methoxypyridin-4-yl)imidazolidin-1-yl]methyl]pyridine _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 108.52 _cell.angle_gamma 90 _cell.entry_id 5R0B _cell.length_a 87.832 _cell.length_b 82.009 _cell.length_c 93.331 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5R0B _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C28 H30 N6 O4' _chem_comp.formula_weight 514.576 _chem_comp.id SY7 _chem_comp.mon_nstd_flag . _chem_comp.name 2-methoxy-4-[[(4~{S},5~{S})-2,4,5-tris(2-methoxypyridin-4-yl)imidazolidin-1-yl]methyl]pyridine _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 C O SY7 sing 290 n n O C1 SY7 sing 291 n n C17 O2 SY7 sing 292 n n O2 C16 SY7 sing 293 n n C1 N5 SY7 doub 294 n y C1 C2 SY7 sing 295 n y N5 C27 SY7 sing 296 n y C2 C3 SY7 doub 297 n y C16 N3 SY7 doub 298 n y C16 C18 SY7 sing 299 n y N3 C15 SY7 sing 300 n y N2 C5 SY7 sing 301 n n N2 C12 SY7 sing 302 n n C18 C13 SY7 doub 303 n y C27 C26 SY7 doub 304 n y C15 C14 SY7 doub 305 n y C3 C26 SY7 sing 306 n y C3 C4 SY7 sing 307 n n C5 C6 SY7 sing 308 n n C5 N SY7 sing 309 n n C6 C11 SY7 doub 310 n y C6 C7 SY7 sing 311 n y C11 C9 SY7 sing 312 n y C13 C14 SY7 sing 313 n y C13 C12 SY7 sing 314 n n C7 C8 SY7 doub 315 n y C9 O1 SY7 sing 316 n n C9 N1 SY7 doub 317 n y O1 C10 SY7 sing 318 n n N C4 SY7 sing 319 n n N C19 SY7 sing 320 n n C12 C19 SY7 sing 321 n n C8 N1 SY7 sing 322 n y C19 C20 SY7 sing 323 n n C20 C21 SY7 doub 324 n y C20 C25 SY7 sing 325 n y C21 C22 SY7 sing 326 n y C25 C23 SY7 doub 327 n y C22 N4 SY7 doub 328 n y C23 N4 SY7 sing 329 n y C23 O3 SY7 sing 330 n n O3 C24 SY7 sing 331 n n C4 H4 SY7 sing 332 n n C4 H5 SY7 sing 333 n n C5 H6 SY7 sing 334 n n C7 H7 SY7 sing 335 n n C8 H8 SY7 sing 336 n n N2 H30 SY7 sing 337 n n C10 H11 SY7 sing 338 n n C10 H9 SY7 sing 339 n n C10 H10 SY7 sing 340 n n C11 H12 SY7 sing 341 n n C12 H14 SY7 sing 342 n n C14 H15 SY7 sing 343 n n C15 H16 SY7 sing 344 n n C24 H25 SY7 sing 345 n n C24 H24 SY7 sing 346 n n C24 H26 SY7 sing 347 n n C22 H23 SY7 sing 348 n n C21 H22 SY7 sing 349 n n C25 H27 SY7 sing 350 n n C19 H21 SY7 sing 351 n n C18 H20 SY7 sing 352 n n C17 H18 SY7 sing 353 n n C17 H19 SY7 sing 354 n n C17 H17 SY7 sing 355 n n C2 H3 SY7 sing 356 n n C26 H28 SY7 sing 357 n n C27 H29 SY7 sing 358 n n C H1 SY7 sing 359 n n C H2 SY7 sing 360 n n C H SY7 sing 361 n n # _atom_sites.entry_id 5R0B _atom_sites.fract_transf_matrix[1][1] 0.011385 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003814 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012194 _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] 0.0113 _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 C 3 SY7 A 1 2501 2501 SY7 XXX . D 4 HOH A 1 2601 53 HOH HOH . D 4 HOH A 2 2602 72 HOH HOH . D 4 HOH A 3 2603 68 HOH HOH . D 4 HOH A 4 2604 6 HOH HOH . D 4 HOH A 5 2605 37 HOH HOH . D 4 HOH A 6 2606 58 HOH HOH . D 4 HOH A 7 2607 39 HOH HOH . D 4 HOH A 8 2608 79 HOH HOH . D 4 HOH A 9 2609 74 HOH HOH . D 4 HOH A 10 2610 9 HOH HOH . D 4 HOH A 11 2611 83 HOH HOH . D 4 HOH A 12 2612 19 HOH HOH . D 4 HOH A 13 2613 82 HOH HOH . D 4 HOH A 14 2614 3 HOH HOH . D 4 HOH A 15 2615 15 HOH HOH . D 4 HOH A 16 2616 40 HOH HOH . D 4 HOH A 17 2617 27 HOH HOH . D 4 HOH A 18 2618 11 HOH HOH . D 4 HOH A 19 2619 46 HOH HOH . D 4 HOH A 20 2620 35 HOH HOH . D 4 HOH A 21 2621 77 HOH HOH . D 4 HOH A 22 2622 16 HOH HOH . D 4 HOH A 23 2623 17 HOH HOH . D 4 HOH A 24 2624 12 HOH HOH . D 4 HOH A 25 2625 29 HOH HOH . D 4 HOH A 26 2626 55 HOH HOH . D 4 HOH A 27 2627 71 HOH HOH . D 4 HOH A 28 2628 24 HOH HOH . D 4 HOH A 29 2629 75 HOH HOH . D 4 HOH A 30 2630 5 HOH HOH . D 4 HOH A 31 2631 2 HOH HOH . D 4 HOH A 32 2632 41 HOH HOH . D 4 HOH A 33 2633 62 HOH HOH . D 4 HOH A 34 2634 14 HOH HOH . D 4 HOH A 35 2635 21 HOH HOH . D 4 HOH A 36 2636 57 HOH HOH . D 4 HOH A 37 2637 25 HOH HOH . D 4 HOH A 38 2638 26 HOH HOH . D 4 HOH A 39 2639 31 HOH HOH . D 4 HOH A 40 2640 49 HOH HOH . D 4 HOH A 41 2641 81 HOH HOH . D 4 HOH A 42 2642 80 HOH HOH . E 4 HOH B 1 401 4 HOH HOH . E 4 HOH B 2 402 23 HOH HOH . E 4 HOH B 3 403 22 HOH HOH . E 4 HOH B 4 404 45 HOH HOH . E 4 HOH B 5 405 61 HOH HOH . E 4 HOH B 6 406 20 HOH HOH . E 4 HOH B 7 407 8 HOH HOH . E 4 HOH B 8 408 76 HOH HOH . E 4 HOH B 9 409 56 HOH HOH . E 4 HOH B 10 410 43 HOH HOH . E 4 HOH B 11 411 47 HOH HOH . E 4 HOH B 12 412 30 HOH HOH . E 4 HOH B 13 413 67 HOH HOH . E 4 HOH B 14 414 70 HOH HOH . E 4 HOH B 15 415 73 HOH HOH . E 4 HOH B 16 416 34 HOH HOH . E 4 HOH B 17 417 66 HOH HOH . E 4 HOH B 18 418 48 HOH HOH . E 4 HOH B 19 419 42 HOH HOH . E 4 HOH B 20 420 18 HOH HOH . E 4 HOH B 21 421 28 HOH HOH . E 4 HOH B 22 422 51 HOH HOH . E 4 HOH B 23 423 33 HOH HOH . E 4 HOH B 24 424 69 HOH HOH . E 4 HOH B 25 425 52 HOH HOH . E 4 HOH B 26 426 64 HOH HOH . E 4 HOH B 27 427 32 HOH HOH . E 4 HOH B 28 428 7 HOH HOH . E 4 HOH B 29 429 36 HOH HOH . E 4 HOH B 30 430 10 HOH HOH . E 4 HOH B 31 431 78 HOH HOH . E 4 HOH B 32 432 50 HOH HOH . E 4 HOH B 33 433 44 HOH HOH . E 4 HOH B 34 434 13 HOH HOH . E 4 HOH B 35 435 59 HOH HOH . E 4 HOH B 36 436 65 HOH HOH . E 4 HOH B 37 437 38 HOH HOH . E 4 HOH B 38 438 60 HOH HOH . E 4 HOH B 39 439 63 HOH HOH . E 4 HOH B 40 440 54 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 O3 SY7 . . . C 3 32.704 15.016 49.38 1 30 ? O3 SY7 2501 A 1 HETATM 2 C C4 SY7 . . . C 3 32.018 10.588 44.517 1 30 ? C4 SY7 2501 A 1 HETATM 3 C C5 SY7 . . . C 3 33.351 12.316 43.584 1 30 ? C5 SY7 2501 A 1 HETATM 4 C C6 SY7 . . . C 3 34.81 11.887 43.686 1 30 ? C6 SY7 2501 A 1 HETATM 5 N N1 SY7 . . . C 3 37.397 11.155 44.304 1 30 ? N1 SY7 2501 A 1 HETATM 6 C C7 SY7 . . . C 3 35.797 12.818 43.916 1 30 ? C7 SY7 2501 A 1 HETATM 7 C C8 SY7 . . . C 3 37.037 12.406 44.216 1 30 ? C8 SY7 2501 A 1 HETATM 8 N N2 SY7 . . . C 3 33.053 13.361 43.051 1 30 ? N2 SY7 2501 A 1 HETATM 9 C C9 SY7 . . . C 3 36.492 10.272 44.022 1 30 ? C9 SY7 2501 A 1 HETATM 10 C C10 SY7 . . . C 3 36.135 7.915 44.138 1 30 ? C10 SY7 2501 A 1 HETATM 11 C C11 SY7 . . . C 3 35.181 10.575 43.708 1 30 ? C11 SY7 2501 A 1 HETATM 12 C C12 SY7 . . . C 3 32.393 13.998 44.185 1 30 ? C12 SY7 2501 A 1 HETATM 13 N N3 SY7 . . . C 3 30.429 17.495 42.846 1 30 ? N3 SY7 2501 A 1 HETATM 14 C C13 SY7 . . . C 3 31.691 15.21 43.73 1 30 ? C13 SY7 2501 A 1 HETATM 15 C C14 SY7 . . . C 3 32.311 16.425 43.821 1 30 ? C14 SY7 2501 A 1 HETATM 16 C C15 SY7 . . . C 3 31.629 17.535 43.41 1 30 ? C15 SY7 2501 A 1 HETATM 17 N N4 SY7 . . . C 3 32.916 13.01 49.001 1 30 ? N4 SY7 2501 A 1 HETATM 18 C C24 SY7 . . . C 3 31.805 16.101 49.638 1 30 ? C24 SY7 2501 A 1 HETATM 19 C C23 SY7 . . . C 3 32.343 14.073 48.502 1 30 ? C23 SY7 2501 A 1 HETATM 20 C C22 SY7 . . . C 3 32.718 11.887 48.345 1 30 ? C22 SY7 2501 A 1 HETATM 21 C C21 SY7 . . . C 3 32.02 11.798 47.185 1 30 ? C21 SY7 2501 A 1 HETATM 22 C C25 SY7 . . . C 3 31.594 14.086 47.312 1 30 ? C25 SY7 2501 A 1 HETATM 23 C C20 SY7 . . . C 3 31.575 12.931 46.543 1 30 ? C20 SY7 2501 A 1 HETATM 24 C C19 SY7 . . . C 3 31.497 13.019 44.983 1 30 ? C19 SY7 2501 A 1 HETATM 25 C C18 SY7 . . . C 3 30.454 15.147 43.152 1 30 ? C18 SY7 2501 A 1 HETATM 26 C C16 SY7 . . . C 3 29.9 16.31 42.706 1 30 ? C16 SY7 2501 A 1 HETATM 27 O O2 SY7 . . . C 3 28.834 16.126 41.962 1 30 ? O2 SY7 2501 A 1 HETATM 28 C C17 SY7 . . . C 3 28.225 17.259 41.423 1 30 ? C17 SY7 2501 A 1 HETATM 29 O O1 SY7 . . . C 3 37.012 9.041 44.118 1 30 ? O1 SY7 2501 A 1 HETATM 30 N N SY7 . . . C 3 32.09 11.944 44.181 1 30 ? N SY7 2501 A 1 HETATM 31 C C3 SY7 . . . C 3 31.431 9.743 43.491 1 30 ? C3 SY7 2501 A 1 HETATM 32 C C2 SY7 . . . C 3 30.535 10.166 42.541 1 30 ? C2 SY7 2501 A 1 HETATM 33 C C26 SY7 . . . C 3 31.47 8.444 43.799 1 30 ? C26 SY7 2501 A 1 HETATM 34 C C27 SY7 . . . C 3 30.543 7.626 43.298 1 30 ? C27 SY7 2501 A 1 HETATM 35 N N5 SY7 . . . C 3 29.607 7.994 42.457 1 30 ? N5 SY7 2501 A 1 HETATM 36 C C1 SY7 . . . C 3 29.652 9.238 42.042 1 30 ? C1 SY7 2501 A 1 HETATM 37 O O SY7 . . . C 3 28.881 9.561 40.996 1 30 ? O SY7 2501 A 1 HETATM 38 C C SY7 . . . C 3 28.055 8.58 40.483 1 30 ? C SY7 2501 A 1 # _model_server_stats.io_time_ms 110 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #