data_5F04 # _model_server_result.job_id Jgul-Mlv6yyrUl5viCRKYA _model_server_result.datetime_utc '2025-01-25 07:19:04' _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 5f04 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5F04 # _exptl.entry_id 5F04 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 329.48 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-cyclopentyl-1-[3-[4-(methylaminomethyl)phenyl]-1,3-diazinan-1-yl]propan-1-one _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 90 _cell.entry_id 5F04 _cell.length_a 121.79 _cell.length_b 121.79 _cell.length_c 33.84 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F04 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 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 'C20 H31 N3 O' _chem_comp.formula_weight 329.48 _chem_comp.id 5TB _chem_comp.mon_nstd_flag . _chem_comp.name 3-cyclopentyl-1-[3-[4-(methylaminomethyl)phenyl]-1,3-diazinan-1-yl]propan-1-one _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 C3 C2 5TB sing 1 n n C3 C4 5TB sing 2 n n C2 C1 5TB sing 3 n n C4 C 5TB sing 4 n n C9 C8 5TB sing 5 n n C9 C10 5TB sing 6 n n C8 N 5TB sing 7 n n C6 C5 5TB sing 8 n n C6 C7 5TB sing 9 n n C1 C 5TB sing 10 n n C1 C5 5TB sing 11 n n C10 N1 5TB sing 12 n n N C7 5TB sing 13 n n N C11 5TB sing 14 n n C7 O 5TB doub 15 n n N1 C11 5TB sing 16 n n N1 C12 5TB sing 17 n n C17 C12 5TB doub 18 n y C17 C16 5TB sing 19 n y C12 C13 5TB sing 20 n y C16 C15 5TB doub 21 n y C13 C14 5TB doub 22 n y C15 C14 5TB sing 23 n y C15 C18 5TB sing 24 n n C19 N2 5TB sing 25 n n C18 N2 5TB sing 26 n n C1 H1 5TB sing 27 n n C2 H2 5TB sing 28 n n C2 H3 5TB sing 29 n n C3 H4 5TB sing 30 n n C3 H5 5TB sing 31 n n C6 H6 5TB sing 32 n n C6 H7 5TB sing 33 n n C5 H8 5TB sing 34 n n C5 H9 5TB sing 35 n n C4 H10 5TB sing 36 n n C4 H11 5TB sing 37 n n C H12 5TB sing 38 n n C H13 5TB sing 39 n n C11 H14 5TB sing 40 n n C11 H15 5TB sing 41 n n C10 H16 5TB sing 42 n n C10 H17 5TB sing 43 n n C9 H18 5TB sing 44 n n C9 H19 5TB sing 45 n n C8 H20 5TB sing 46 n n C8 H21 5TB sing 47 n n C17 H22 5TB sing 48 n n C16 H23 5TB sing 49 n n C14 H24 5TB sing 50 n n C13 H25 5TB sing 51 n n C18 H26 5TB sing 52 n n C18 H27 5TB sing 53 n n N2 H28 5TB sing 54 n n C19 H30 5TB sing 55 n n C19 H31 5TB sing 56 n n C19 H32 5TB sing 57 n n # _atom_sites.entry_id 5F04 _atom_sites.fract_transf_matrix[1][1] 0.008211 _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] 0.008211 _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] 0.029551 _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 5TB A 1 301 1 5TB 173 . C 3 SO4 A 1 302 1 SO4 SO4 . D 3 SO4 A 1 303 3 SO4 SO4 . E 4 GOL A 1 304 1 GOL GOL . F 5 EDO A 1 305 1 EDO EDO . G 6 HOH A 1 401 73 HOH HOH . G 6 HOH A 2 402 51 HOH HOH . G 6 HOH A 3 403 23 HOH HOH . G 6 HOH A 4 404 19 HOH HOH . G 6 HOH A 5 405 22 HOH HOH . G 6 HOH A 6 406 18 HOH HOH . G 6 HOH A 7 407 14 HOH HOH . G 6 HOH A 8 408 32 HOH HOH . G 6 HOH A 9 409 12 HOH HOH . G 6 HOH A 10 410 33 HOH HOH . G 6 HOH A 11 411 13 HOH HOH . G 6 HOH A 12 412 10 HOH HOH . G 6 HOH A 13 413 31 HOH HOH . G 6 HOH A 14 414 7 HOH HOH . G 6 HOH A 15 415 1 HOH HOH . G 6 HOH A 16 416 36 HOH HOH . G 6 HOH A 17 417 24 HOH HOH . G 6 HOH A 18 418 3 HOH HOH . G 6 HOH A 19 419 69 HOH HOH . G 6 HOH A 20 420 25 HOH HOH . G 6 HOH A 21 421 20 HOH HOH . G 6 HOH A 22 422 28 HOH HOH . G 6 HOH A 23 423 8 HOH HOH . G 6 HOH A 24 424 49 HOH HOH . G 6 HOH A 25 425 4 HOH HOH . G 6 HOH A 26 426 35 HOH HOH . G 6 HOH A 27 427 2 HOH HOH . G 6 HOH A 28 428 21 HOH HOH . G 6 HOH A 29 429 37 HOH HOH . G 6 HOH A 30 430 34 HOH HOH . G 6 HOH A 31 431 40 HOH HOH . G 6 HOH A 32 432 57 HOH HOH . G 6 HOH A 33 433 17 HOH HOH . G 6 HOH A 34 434 15 HOH HOH . G 6 HOH A 35 435 5 HOH HOH . G 6 HOH A 36 436 9 HOH HOH . G 6 HOH A 37 437 43 HOH HOH . G 6 HOH A 38 438 39 HOH HOH . G 6 HOH A 39 439 11 HOH HOH . G 6 HOH A 40 440 67 HOH HOH . G 6 HOH A 41 441 60 HOH HOH . G 6 HOH A 42 442 44 HOH HOH . G 6 HOH A 43 443 6 HOH HOH . G 6 HOH A 44 444 42 HOH HOH . G 6 HOH A 45 445 16 HOH HOH . G 6 HOH A 46 446 38 HOH HOH . G 6 HOH A 47 447 26 HOH HOH . G 6 HOH A 48 448 58 HOH HOH . G 6 HOH A 49 449 41 HOH HOH . G 6 HOH A 50 450 30 HOH HOH . G 6 HOH A 51 451 61 HOH HOH . G 6 HOH A 52 452 72 HOH HOH . G 6 HOH A 53 453 62 HOH HOH . G 6 HOH A 54 454 66 HOH HOH . G 6 HOH A 55 455 63 HOH HOH . G 6 HOH A 56 456 70 HOH HOH . G 6 HOH A 57 457 56 HOH HOH . G 6 HOH A 58 458 64 HOH HOH . G 6 HOH A 59 459 52 HOH HOH . G 6 HOH A 60 460 48 HOH HOH . G 6 HOH A 61 461 54 HOH HOH . G 6 HOH A 62 462 47 HOH HOH . G 6 HOH A 63 463 50 HOH HOH . G 6 HOH A 64 464 59 HOH HOH . G 6 HOH A 65 465 71 HOH HOH . G 6 HOH A 66 466 46 HOH HOH . G 6 HOH A 67 467 53 HOH HOH . G 6 HOH A 68 468 29 HOH HOH . G 6 HOH A 69 469 45 HOH HOH . G 6 HOH A 70 470 65 HOH HOH . G 6 HOH A 71 471 27 HOH HOH . G 6 HOH A 72 472 68 HOH HOH . G 6 HOH A 73 473 55 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 C C1 5TB . . . B 2 27.773 9.706 -2.985 1 39.97 ? C1 5TB 301 A 1 HETATM 2 C C2 5TB . . . B 2 27.899 9.783 -4.5 1 39.12 ? C2 5TB 301 A 1 HETATM 3 C C3 5TB . . . B 2 27.394 8.459 -5.068 1 41.05 ? C3 5TB 301 A 1 HETATM 4 O O 5TB . . . B 2 26.922 13.665 -1.505 1 53.65 ? O 5TB 301 A 1 HETATM 5 C C7 5TB . . . B 2 27.886 13.478 -2.212 1 46.21 ? C7 5TB 301 A 1 HETATM 6 C C6 5TB . . . B 2 28.051 12.212 -3.033 1 41.71 ? C6 5TB 301 A 1 HETATM 7 C C5 5TB . . . B 2 27.306 11.037 -2.405 1 39.05 ? C5 5TB 301 A 1 HETATM 8 C C4 5TB . . . B 2 26.707 7.705 -3.939 1 41.96 ? C4 5TB 301 A 1 HETATM 9 C C 5TB . . . B 2 26.764 8.593 -2.705 1 38.21 ? C 5TB 301 A 1 HETATM 10 N N 5TB . . . B 2 28.844 14.376 -2.292 1 44.31 ? N 5TB 301 A 1 HETATM 11 C C11 5TB . . . B 2 29.271 15.077 -1.087 1 51.48 ? C11 5TB 301 A 1 HETATM 12 N N1 5TB . . . B 2 29.708 16.409 -1.43 1 48.76 ? N1 5TB 301 A 1 HETATM 13 C C10 5TB . . . B 2 29.242 16.966 -2.672 1 40.39 ? C10 5TB 301 A 1 HETATM 14 C C9 5TB . . . B 2 29.943 16.062 -3.652 1 46.81 ? C9 5TB 301 A 1 HETATM 15 C C8 5TB . . . B 2 29.526 14.608 -3.562 1 42.37 ? C8 5TB 301 A 1 HETATM 16 C C12 5TB . . . B 2 30.55 17.136 -0.603 1 46.3 ? C12 5TB 301 A 1 HETATM 17 C C17 5TB . . . B 2 31.432 18.084 -1.124 1 50.53 ? C17 5TB 301 A 1 HETATM 18 C C16 5TB . . . B 2 32.241 18.793 -0.242 1 45.14 ? C16 5TB 301 A 1 HETATM 19 C C15 5TB . . . B 2 32.154 18.552 1.123 1 46.9 ? C15 5TB 301 A 1 HETATM 20 C C14 5TB . . . B 2 31.273 17.618 1.628 1 49.46 ? C14 5TB 301 A 1 HETATM 21 C C13 5TB . . . B 2 30.471 16.912 0.755 1 42.95 ? C13 5TB 301 A 1 HETATM 22 C C18 5TB . . . B 2 33.004 19.304 2.102 1 43.25 ? C18 5TB 301 A 1 HETATM 23 N N2 5TB . . . B 2 32.237 20.435 2.57 1 47.11 ? N2 5TB 301 A 1 HETATM 24 C C19 5TB . . . B 2 32.005 21.545 1.666 1 39.92 ? C19 5TB 301 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 364 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #