data_5NQ5 # _model_server_result.job_id gl1ZoAyMzCXQEENIFoP2cg _model_server_result.datetime_utc '2024-11-14 18:26:10' _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 5nq5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5NQ5 # _exptl.entry_id 5NQ5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 391.463 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-methyl-1-[(3~{S})-1-[(3-phenoxyphenyl)methyl]piperidin-3-yl]pyrimidine-2,4-dione _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 5NQ5 _cell.length_a 71.39 _cell.length_b 71.39 _cell.length_c 133.75 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NQ5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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' 6_554 -x,-x+y,-z-1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -44.583333 # _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 'C23 H25 N3 O3' _chem_comp.formula_weight 391.463 _chem_comp.id 952 _chem_comp.mon_nstd_flag . _chem_comp.name 5-methyl-1-[(3~{S})-1-[(3-phenoxyphenyl)methyl]piperidin-3-yl]pyrimidine-2,4-dione _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 C18 C19 952 doub 1 n y C18 C17 952 sing 2 n y C19 C20 952 sing 3 n y C17 C16 952 doub 4 n y C20 C15 952 doub 5 n y O2 C22 952 doub 6 n n C16 C15 952 sing 7 n y C15 O 952 sing 8 n n N2 C22 952 sing 9 n n N2 C21 952 sing 10 n n C22 C1 952 sing 11 n n C12 C13 952 doub 12 n y C12 C11 952 sing 13 n y O1 C21 952 doub 14 n n O C11 952 sing 15 n n C21 N 952 sing 16 n n C13 C14 952 sing 17 n y C11 C10 952 doub 18 n y C1 C 952 sing 19 n n C1 C2 952 doub 20 n n N C2 952 sing 21 n n N C3 952 sing 22 n n C14 C9 952 doub 23 n y C10 C9 952 sing 24 n y C9 C8 952 sing 25 n n C3 C7 952 sing 26 n n C3 C4 952 sing 27 n n C7 N1 952 sing 28 n n N1 C8 952 sing 29 n n N1 C6 952 sing 30 n n C4 C5 952 sing 31 n n C6 C5 952 sing 32 n n C H2 952 sing 33 n n C H1 952 sing 34 n n C H3 952 sing 35 n n N2 H24 952 sing 36 n n C2 H4 952 sing 37 n n C3 H 952 sing 38 n n C7 H12 952 sing 39 n n C7 H11 952 sing 40 n n C6 H9 952 sing 41 n n C6 H10 952 sing 42 n n C5 H8 952 sing 43 n n C5 H7 952 sing 44 n n C4 H6 952 sing 45 n n C4 H5 952 sing 46 n n C8 H14 952 sing 47 n n C8 H13 952 sing 48 n n C14 H18 952 sing 49 n n C13 H17 952 sing 50 n n C12 H16 952 sing 51 n n C10 H15 952 sing 52 n n C20 H23 952 sing 53 n n C19 H22 952 sing 54 n n C18 H21 952 sing 55 n n C17 H20 952 sing 56 n n C16 H19 952 sing 57 n n # _atom_sites.entry_id 5NQ5 _atom_sites.fract_transf_matrix[1][1] 0.014008 _atom_sites.fract_transf_matrix[1][2] 0.008087 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016175 _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] 0.007477 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id 952 _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 301 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id 952 _pdbx_nonpoly_scheme.auth_mon_id WUI _pdbx_nonpoly_scheme.pdb_ins_code . # 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 952 . . . B 2 -24.771 28.549 -12.063 1 86.77 ? O2 952 301 A 1 HETATM 2 C C22 952 . . . B 2 -24.734 29.389 -11.165 1 87.01 ? C22 952 301 A 1 HETATM 3 C C1 952 . . . B 2 -24.04 29.227 -9.906 1 87.59 ? C1 952 301 A 1 HETATM 4 C C 952 . . . B 2 -23.3 27.945 -9.646 1 87.91 ? C 952 301 A 1 HETATM 5 N N2 952 . . . B 2 -25.394 30.594 -11.322 1 86.84 ? N2 952 301 A 1 HETATM 6 C C21 952 . . . B 2 -25.455 31.629 -10.423 1 87.23 ? C21 952 301 A 1 HETATM 7 O O1 952 . . . B 2 -26.065 32.662 -10.658 1 87.01 ? O1 952 301 A 1 HETATM 8 N N 952 . . . B 2 -24.771 31.41 -9.247 1 88.17 ? N 952 301 A 1 HETATM 9 C C2 952 . . . B 2 -24.093 30.234 -9.02 1 87.96 ? C2 952 301 A 1 HETATM 10 C C3 952 . . . B 2 -24.764 32.484 -8.23 1 88.88 ? C3 952 301 A 1 HETATM 11 C C7 952 . . . B 2 -23.369 33.06 -8.181 1 89.69 ? C7 952 301 A 1 HETATM 12 N N1 952 . . . B 2 -23.264 34.141 -7.198 1 89.93 ? N1 952 301 A 1 HETATM 13 C C6 952 . . . B 2 -23.609 33.641 -5.861 1 88.85 ? C6 952 301 A 1 HETATM 14 C C5 952 . . . B 2 -25.001 33.052 -5.818 1 88.23 ? C5 952 301 A 1 HETATM 15 C C4 952 . . . B 2 -25.146 31.95 -6.859 1 88.28 ? C4 952 301 A 1 HETATM 16 C C8 952 . . . B 2 -21.927 34.751 -7.197 1 91.05 ? C8 952 301 A 1 HETATM 17 C C9 952 . . . B 2 -21.591 35.48 -8.477 1 92.67 ? C9 952 301 A 1 HETATM 18 C C14 952 . . . B 2 -20.494 35.103 -9.237 1 92.98 ? C14 952 301 A 1 HETATM 19 C C13 952 . . . B 2 -20.177 35.776 -10.404 1 93.28 ? C13 952 301 A 1 HETATM 20 C C12 952 . . . B 2 -20.949 36.84 -10.832 1 93.73 ? C12 952 301 A 1 HETATM 21 C C11 952 . . . B 2 -22.042 37.222 -10.074 1 94.2 ? C11 952 301 A 1 HETATM 22 C C10 952 . . . B 2 -22.369 36.548 -8.907 1 93.55 ? C10 952 301 A 1 HETATM 23 O O 952 . . . B 2 -22.813 38.318 -10.46 1 95.29 ? O 952 301 A 1 HETATM 24 C C15 952 . . . B 2 -23.622 38.229 -11.592 1 95.9 ? C15 952 301 A 1 HETATM 25 C C20 952 . . . B 2 -23.95 39.388 -12.276 1 95.87 ? C20 952 301 A 1 HETATM 26 C C19 952 . . . B 2 -24.776 39.312 -13.384 1 95.92 ? C19 952 301 A 1 HETATM 27 C C18 952 . . . B 2 -25.266 38.095 -13.807 1 95.94 ? C18 952 301 A 1 HETATM 28 C C17 952 . . . B 2 -24.931 36.944 -13.126 1 96 ? C17 952 301 A 1 HETATM 29 C C16 952 . . . B 2 -24.106 37.001 -12.015 1 95.97 ? C16 952 301 A 1 HETATM 30 H H2 952 . . . B 2 -22.641 27.666 -10.468 0 105.49 ? H2 952 301 A 1 HETATM 31 H H1 952 . . . B 2 -23.991 27.119 -9.481 0 105.49 ? H1 952 301 A 1 HETATM 32 H H3 952 . . . B 2 -22.674 28.021 -8.758 0 105.49 ? H3 952 301 A 1 HETATM 33 H H24 952 . . . B 2 -25.893 30.742 -12.193 0 104.21 ? H24 952 301 A 1 HETATM 34 H H4 952 . . . B 2 -23.585 30.153 -8.06 0 105.55 ? H4 952 301 A 1 HETATM 35 H H 952 . . . B 2 -25.508 33.223 -8.524 0 106.66 ? H 952 301 A 1 HETATM 36 H H12 952 . . . B 2 -23.033 33.41 -9.156 0 107.62 ? H12 952 301 A 1 HETATM 37 H H11 952 . . . B 2 -22.631 32.317 -7.883 0 107.62 ? H11 952 301 A 1 HETATM 38 H H9 952 . . . B 2 -23.49 34.429 -5.119 0 106.62 ? H9 952 301 A 1 HETATM 39 H H10 952 . . . B 2 -22.862 32.902 -5.576 0 106.62 ? H10 952 301 A 1 HETATM 40 H H8 952 . . . B 2 -25.236 32.689 -4.818 0 105.88 ? H8 952 301 A 1 HETATM 41 H H7 952 . . . B 2 -25.753 33.819 -5.996 0 105.88 ? H7 952 301 A 1 HETATM 42 H H6 952 . . . B 2 -24.542 31.093 -6.567 0 105.94 ? H6 952 301 A 1 HETATM 43 H H5 952 . . . B 2 -26.169 31.577 -6.871 0 105.94 ? H5 952 301 A 1 HETATM 44 H H14 952 . . . B 2 -21.905 35.447 -6.36 0 109.26 ? H14 952 301 A 1 HETATM 45 H H13 952 . . . B 2 -21.145 34.031 -6.961 0 109.26 ? H13 952 301 A 1 HETATM 46 H H18 952 . . . B 2 -19.866 34.27 -8.923 0 111.58 ? H18 952 301 A 1 HETATM 47 H H17 952 . . . B 2 -19.313 35.462 -10.988 0 111.93 ? H17 952 301 A 1 HETATM 48 H H16 952 . . . B 2 -20.698 37.367 -11.752 0 112.48 ? H16 952 301 A 1 HETATM 49 H H15 952 . . . B 2 -23.24 36.865 -8.335 0 112.26 ? H15 952 301 A 1 HETATM 50 H H23 952 . . . B 2 -23.559 40.347 -11.939 0 115.04 ? H23 952 301 A 1 HETATM 51 H H22 952 . . . B 2 -25.034 40.224 -13.92 0 115.1 ? H22 952 301 A 1 HETATM 52 H H21 952 . . . B 2 -25.916 38.055 -14.68 0 115.13 ? H21 952 301 A 1 HETATM 53 H H20 952 . . . B 2 -25.318 35.984 -13.463 0 115.19 ? H20 952 301 A 1 HETATM 54 H H19 952 . . . B 2 -23.843 36.089 -11.482 0 115.16 ? H19 952 301 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 225 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 54 #