data_8DMD # _model_server_result.job_id J4ZFYhQYP3MJ03Lst53uHQ _model_server_result.datetime_utc '2024-11-16 16:49:52' _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 8dmd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8DMD # _exptl.entry_id 8DMD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.846 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[(3R)-4-[(3-chlorophenyl)methyl]-3-(2-methylpropyl)piperazin-1-yl]ethan-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 101.38 _cell.angle_gamma 90 _cell.entry_id 8DMD _cell.length_a 45.475 _cell.length_b 54.671 _cell.length_c 114.645 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DMD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 1 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,C _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' 2_555 -x,y,-z -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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 145 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 145 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C9 _struct_conn.ptnr2_label_comp_id SVL _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id SVL _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.831 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C17 H25 Cl N2 O' _chem_comp.formula_weight 308.846 _chem_comp.id SVL _chem_comp.mon_nstd_flag . _chem_comp.name 1-[(3R)-4-[(3-chlorophenyl)methyl]-3-(2-methylpropyl)piperazin-1-yl]ethan-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 O10 C7 SVL doub 290 n n C22 C21 SVL sing 291 n n C7 N6 SVL sing 292 n n C7 C9 SVL sing 293 n n C1 N6 SVL sing 294 n n C1 C2 SVL sing 295 n n N6 C5 SVL sing 296 n n C21 C20 SVL sing 297 n n C21 C23 SVL sing 298 n n C2 C20 SVL sing 299 n n C2 N3 SVL sing 300 n n C5 C4 SVL sing 301 n n C4 N3 SVL sing 302 n n N3 C8 SVL sing 303 n n C8 C11 SVL sing 304 n n C11 C16 SVL doub 305 n y C11 C12 SVL sing 306 n y C16 C15 SVL sing 307 n y C12 C13 SVL doub 308 n y C15 C14 SVL doub 309 n y C13 C14 SVL sing 310 n y C13 CL24 SVL sing 311 n n C1 H1 SVL sing 312 n n C1 H2 SVL sing 313 n n C4 H3 SVL sing 314 n n C4 H4 SVL sing 315 n n C5 H5 SVL sing 316 n n C5 H6 SVL sing 317 n n C8 H7 SVL sing 318 n n C8 H8 SVL sing 319 n n C14 H9 SVL sing 320 n n C16 H10 SVL sing 321 n n C20 H11 SVL sing 322 n n C20 H12 SVL sing 323 n n C21 H13 SVL sing 324 n n C22 H14 SVL sing 325 n n C22 H15 SVL sing 326 n n C22 H16 SVL sing 327 n n C12 H17 SVL sing 328 n n C15 H18 SVL sing 329 n n C2 H19 SVL sing 330 n n C23 H20 SVL sing 331 n n C23 H21 SVL sing 332 n n C23 H22 SVL sing 333 n n C9 H23 SVL sing 334 n n C9 H24 SVL sing 335 n n C9 H25 SVL sing 336 n n # _atom_sites.entry_id 8DMD _atom_sites.fract_transf_matrix[1][1] 0.02199 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004425 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018291 _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] 0.008897 _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 SVL A 1 401 401 SVL Z91 . C 3 HOH A 1 501 38 HOH HOH . C 3 HOH A 2 502 33 HOH HOH . C 3 HOH A 3 503 56 HOH HOH . C 3 HOH A 4 504 31 HOH HOH . C 3 HOH A 5 505 23 HOH HOH . C 3 HOH A 6 506 24 HOH HOH . C 3 HOH A 7 507 62 HOH HOH . C 3 HOH A 8 508 54 HOH HOH . C 3 HOH A 9 509 39 HOH HOH . C 3 HOH A 10 510 15 HOH HOH . C 3 HOH A 11 511 29 HOH HOH . C 3 HOH A 12 512 68 HOH HOH . C 3 HOH A 13 513 44 HOH HOH . C 3 HOH A 14 514 18 HOH HOH . C 3 HOH A 15 515 74 HOH HOH . C 3 HOH A 16 516 36 HOH HOH . C 3 HOH A 17 517 72 HOH HOH . C 3 HOH A 18 518 71 HOH HOH . C 3 HOH A 19 519 42 HOH HOH . C 3 HOH A 20 520 17 HOH HOH . C 3 HOH A 21 521 49 HOH HOH . C 3 HOH A 22 522 53 HOH HOH . C 3 HOH A 23 523 16 HOH HOH . C 3 HOH A 24 524 1 HOH HOH . C 3 HOH A 25 525 43 HOH HOH . C 3 HOH A 26 526 27 HOH HOH . C 3 HOH A 27 527 9 HOH HOH . C 3 HOH A 28 528 6 HOH HOH . C 3 HOH A 29 529 70 HOH HOH . C 3 HOH A 30 530 35 HOH HOH . C 3 HOH A 31 531 2 HOH HOH . C 3 HOH A 32 532 8 HOH HOH . C 3 HOH A 33 533 14 HOH HOH . C 3 HOH A 34 534 45 HOH HOH . C 3 HOH A 35 535 63 HOH HOH . C 3 HOH A 36 536 51 HOH HOH . C 3 HOH A 37 537 25 HOH HOH . C 3 HOH A 38 538 11 HOH HOH . C 3 HOH A 39 539 10 HOH HOH . C 3 HOH A 40 540 13 HOH HOH . C 3 HOH A 41 541 66 HOH HOH . C 3 HOH A 42 542 30 HOH HOH . C 3 HOH A 43 543 7 HOH HOH . C 3 HOH A 44 544 73 HOH HOH . C 3 HOH A 45 545 64 HOH HOH . C 3 HOH A 46 546 20 HOH HOH . C 3 HOH A 47 547 37 HOH HOH . C 3 HOH A 48 548 41 HOH HOH . C 3 HOH A 49 549 3 HOH HOH . C 3 HOH A 50 550 28 HOH HOH . C 3 HOH A 51 551 60 HOH HOH . C 3 HOH A 52 552 5 HOH HOH . C 3 HOH A 53 553 21 HOH HOH . C 3 HOH A 54 554 46 HOH HOH . C 3 HOH A 55 555 57 HOH HOH . C 3 HOH A 56 556 26 HOH HOH . C 3 HOH A 57 557 19 HOH HOH . C 3 HOH A 58 558 48 HOH HOH . C 3 HOH A 59 559 47 HOH HOH . C 3 HOH A 60 560 55 HOH HOH . C 3 HOH A 61 561 22 HOH HOH . C 3 HOH A 62 562 50 HOH HOH . C 3 HOH A 63 563 32 HOH HOH . C 3 HOH A 64 564 67 HOH HOH . C 3 HOH A 65 565 40 HOH HOH . C 3 HOH A 66 566 4 HOH HOH . C 3 HOH A 67 567 69 HOH HOH . C 3 HOH A 68 568 61 HOH HOH . C 3 HOH A 69 569 12 HOH HOH . C 3 HOH A 70 570 65 HOH HOH . C 3 HOH A 71 571 58 HOH HOH . C 3 HOH A 72 572 52 HOH HOH . C 3 HOH A 73 573 59 HOH HOH . C 3 HOH A 74 574 34 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 SVL . . . B 2 -20.315 -2.473 10.922 1 48.45 ? C1 SVL 401 A 1 HETATM 2 C C4 SVL . . . B 2 -20.051 -0.84 13.05 1 56.75 ? C4 SVL 401 A 1 HETATM 3 C C5 SVL . . . B 2 -18.816 -0.986 12.171 1 46.28 ? C5 SVL 401 A 1 HETATM 4 C C7 SVL . . . B 2 -17.913 -2.922 10.857 1 43.1 ? C7 SVL 401 A 1 HETATM 5 C C8 SVL . . . B 2 -21.648 -1.985 14.445 1 53.45 ? C8 SVL 401 A 1 HETATM 6 C C11 SVL . . . B 2 -21.355 -0.971 15.54 1 56.51 ? C11 SVL 401 A 1 HETATM 7 C C14 SVL . . . B 2 -20.789 0.891 17.593 1 54.57 ? C14 SVL 401 A 1 HETATM 8 C C16 SVL . . . B 2 -22.084 0.222 15.651 1 61.51 ? C16 SVL 401 A 1 HETATM 9 C C20 SVL . . . B 2 -21.488 -4.263 12.22 1 53.76 ? C20 SVL 401 A 1 HETATM 10 C C21 SVL . . . B 2 -22.918 -4.751 11.9 1 64.03 ? C21 SVL 401 A 1 HETATM 11 C C22 SVL . . . B 2 -23.48 -4.144 10.605 1 60.81 ? C22 SVL 401 A 1 HETATM 12 C C12 SVL . . . B 2 -20.339 -1.227 16.471 1 57.48 ? C12 SVL 401 A 1 HETATM 13 C C13 SVL . . . B 2 -20.072 -0.296 17.475 1 60.88 ? C13 SVL 401 A 1 HETATM 14 C C15 SVL . . . B 2 -21.802 1.139 16.663 1 56.81 ? C15 SVL 401 A 1 HETATM 15 C C2 SVL . . . B 2 -21.236 -2.736 12.128 1 55.04 ? C2 SVL 401 A 1 HETATM 16 C C23 SVL . . . B 2 -23.863 -4.472 13.076 1 72.61 ? C23 SVL 401 A 1 HETATM 17 C C9 SVL . . . B 2 -16.515 -2.521 11.304 1 29.85 ? C9 SVL 401 A 1 HETATM 18 N N3 SVL . . . B 2 -20.65 -2.152 13.367 1 50.26 ? N3 SVL 401 A 1 HETATM 19 N N6 SVL . . . B 2 -18.938 -2.158 11.303 1 47.84 ? N6 SVL 401 A 1 HETATM 20 O O10 SVL . . . B 2 -18.085 -3.908 10.119 1 42.08 ? O10 SVL 401 A 1 HETATM 21 CL CL24 SVL . . . B 2 -18.785 -0.639 18.641 1 69.5 ? CL24 SVL 401 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #