data_3QO9
#
_model_server_result.job_id            X7-XKwPWJ8sEG7DgeO61mQ 
_model_server_result.datetime_utc      '2025-02-26 09:07:22' 
_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          3qo9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":556}' 
#
_entry.id    3QO9 
#
_exptl.entry_id    3QO9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              589.85 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-[(5R,6R,8R,9R)-4-amino-9-{[tert-butyl(dimethyl)silyl]oxy}-6-({[tert-butyl(dimethyl)silyl]oxy}methyl)-2,2-dioxido-1,7-dioxa-2-thiaspiro[4.4]non-3-en-8-yl]-5-methylpyrimidine-2,4(1H,3H)-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          98.75 
_cell.angle_gamma         90 
_cell.entry_id            3QO9 
_cell.length_a            162.76 
_cell.length_b            72.59 
_cell.length_c            108.97 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3QO9 
_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        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,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           'C24 H43 N3 O8 S Si2' 
_chem_comp.formula_weight    589.85 
_chem_comp.id                QO9 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-[(5R,6R,8R,9R)-4-amino-9-{[tert-butyl(dimethyl)silyl]oxy}-6-({[tert-butyl(dimethyl)silyl]oxy}methyl)-2,2-dioxido-1,7-dioxa-2-thiaspiro[4.4]non-3-en-8-yl]-5-methylpyrimidine-2,4(1H,3H)-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
C1 O1 QO9 doub 277 n n 
N1 C1 QO9 sing 278 n n 
N1 HN1 QO9 sing 279 n n 
S1 O7 QO9 doub 280 n n 
S1 O4 QO9 sing 281 n n 
C2 C1 QO9 sing 282 n n 
C2 C5 QO9 sing 283 n n 
N2 C3 QO9 sing 284 n n 
N2 C4 QO9 sing 285 n n 
O2 C4 QO9 doub 286 n n 
C3 C2 QO9 doub 287 n n 
C3 H3 QO9 sing 288 n n 
C4 N1 QO9 sing 289 n n 
C5 H5 QO9 sing 290 n n 
C5 H5A QO9 sing 291 n n 
C5 H5B QO9 sing 292 n n 
O5 C9 QO9 sing 293 n n 
C6 N2 QO9 sing 294 n n 
C6 O3 QO9 sing 295 n n 
C6 H6 QO9 sing 296 n n 
C7 O3 QO9 sing 297 n n 
C7 H7 QO9 sing 298 n n 
C8 O4 QO9 sing 299 n n 
C8 C7 QO9 sing 300 n n 
C8 C9 QO9 sing 301 n n 
O8 S1 QO9 doub 302 n n 
C9 C6 QO9 sing 303 n n 
C9 H9 QO9 sing 304 n n 
C10 O6 QO9 sing 305 n n 
C10 C7 QO9 sing 306 n n 
C10 H10 QO9 sing 307 n n 
C10 H10A QO9 sing 308 n n 
C11 C8 QO9 sing 309 n n 
C12 S1 QO9 sing 310 n n 
C12 C11 QO9 doub 311 n n 
C13 SI1 QO9 sing 312 n n 
C13 C18 QO9 sing 313 n n 
C14 H14 QO9 sing 314 n n 
C14 H14A QO9 sing 315 n n 
C14 H14B QO9 sing 316 n n 
C15 SI1 QO9 sing 317 n n 
C15 H15 QO9 sing 318 n n 
C15 H15A QO9 sing 319 n n 
C15 H15B QO9 sing 320 n n 
C16 C13 QO9 sing 321 n n 
C16 H16 QO9 sing 322 n n 
C16 H16A QO9 sing 323 n n 
C16 H16B QO9 sing 324 n n 
C17 C13 QO9 sing 325 n n 
C17 H17 QO9 sing 326 n n 
C17 H17A QO9 sing 327 n n 
C17 H17B QO9 sing 328 n n 
C18 H18 QO9 sing 329 n n 
C18 H18A QO9 sing 330 n n 
C18 H18B QO9 sing 331 n n 
C19 SI2 QO9 sing 332 n n 
C19 C22 QO9 sing 333 n n 
C19 C23 QO9 sing 334 n n 
C20 SI2 QO9 sing 335 n n 
C20 H20 QO9 sing 336 n n 
C20 H20A QO9 sing 337 n n 
C20 H20B QO9 sing 338 n n 
C21 H21 QO9 sing 339 n n 
C21 H21A QO9 sing 340 n n 
C21 H21B QO9 sing 341 n n 
C22 H22 QO9 sing 342 n n 
C22 H22A QO9 sing 343 n n 
C22 H22B QO9 sing 344 n n 
C23 H23 QO9 sing 345 n n 
C23 H23A QO9 sing 346 n n 
C23 H23B QO9 sing 347 n n 
C24 C19 QO9 sing 348 n n 
C24 H24 QO9 sing 349 n n 
C24 H24A QO9 sing 350 n n 
C24 H24B QO9 sing 351 n n 
SI1 O5 QO9 sing 352 n n 
SI1 C14 QO9 sing 353 n n 
SI2 O6 QO9 sing 354 n n 
SI2 C21 QO9 sing 355 n n 
C11 N3 QO9 sing 356 n n 
N3 HN3 QO9 sing 357 n n 
N3 H42 QO9 sing 358 n n 
C12 H12 QO9 sing 359 n n 
#
_atom_sites.entry_id                     3QO9 
_atom_sites.fract_transf_matrix[1][1]    0.006144 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000946 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013776 
_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]    0.009285 
_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 QO9 A 1 556 1 QO9 QO9 . 
D 4 HOH A 1 557 1 HOH HOH . 
D 4 HOH A 2 558 3 HOH HOH . 
D 4 HOH A 3 559 4 HOH HOH . 
D 4 HOH A 4 560 5 HOH HOH . 
D 4 HOH A 5 561 6 HOH HOH . 
D 4 HOH A 6 562 7 HOH HOH . 
D 4 HOH A 7 563 8 HOH HOH . 
D 4 HOH A 8 564 10 HOH HOH . 
D 4 HOH A 9 565 13 HOH HOH . 
D 4 HOH A 10 566 14 HOH HOH . 
D 4 HOH A 11 567 15 HOH HOH . 
D 4 HOH A 12 568 17 HOH HOH . 
D 4 HOH A 13 569 18 HOH HOH . 
D 4 HOH A 14 570 19 HOH HOH . 
D 4 HOH A 15 571 20 HOH HOH . 
D 4 HOH A 16 572 21 HOH HOH . 
D 4 HOH A 17 573 22 HOH HOH . 
D 4 HOH A 18 574 23 HOH HOH . 
D 4 HOH A 19 575 24 HOH HOH . 
D 4 HOH A 20 576 25 HOH HOH . 
D 4 HOH A 21 577 27 HOH HOH . 
D 4 HOH A 22 578 28 HOH HOH . 
D 4 HOH A 23 579 30 HOH HOH . 
D 4 HOH A 24 580 31 HOH HOH . 
D 4 HOH A 25 581 32 HOH HOH . 
E 4 HOH B 1 429 2 HOH HOH . 
E 4 HOH B 2 430 9 HOH HOH . 
E 4 HOH B 3 431 11 HOH HOH . 
E 4 HOH B 4 432 12 HOH HOH . 
E 4 HOH B 5 433 16 HOH HOH . 
E 4 HOH B 6 434 26 HOH HOH . 
E 4 HOH B 7 435 29 HOH HOH . 
E 4 HOH B 8 436 33 HOH HOH . 
E 4 HOH B 9 437 34 HOH HOH . 
E 4 HOH B 10 438 35 HOH HOH . 
E 4 HOH B 11 439 36 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 QO9 . . . C 3 46.895 -30.814 41.996 1 66.6 ? C1 QO9 556 A 1 
HETATM 2 N N1 QO9 . . . C 3 47.992 -31.633 41.807 1 61.73 ? N1 QO9 556 A 1 
HETATM 3 O O1 QO9 . . . C 3 45.905 -31.223 42.829 1 75.45 ? O1 QO9 556 A 1 
HETATM 4 S S1 QO9 . . . C 3 53.203 -29.209 36.386 1 82.08 ? S1 QO9 556 A 1 
HETATM 5 C C2 QO9 . . . C 3 46.803 -29.572 41.313 1 62.58 ? C2 QO9 556 A 1 
HETATM 6 N N2 QO9 . . . C 3 49.006 -30.053 40.305 1 75.45 ? N2 QO9 556 A 1 
HETATM 7 O O2 QO9 . . . C 3 50.089 -32.112 40.864 1 73.87 ? O2 QO9 556 A 1 
HETATM 8 C C3 QO9 . . . C 3 47.901 -29.221 40.478 1 71.21 ? C3 QO9 556 A 1 
HETATM 9 O O3 QO9 . . . C 3 50.771 -28.488 40.002 1 69.88 ? O3 QO9 556 A 1 
HETATM 10 C C4 QO9 . . . C 3 49.04 -31.271 40.992 1 69.93 ? C4 QO9 556 A 1 
HETATM 11 O O4 QO9 . . . C 3 52.328 -29.392 37.747 1 73.66 ? O4 QO9 556 A 1 
HETATM 12 C C5 QO9 . . . C 3 45.715 -28.737 41.482 1 50.43 ? C5 QO9 556 A 1 
HETATM 13 O O5 QO9 . . . C 3 50.025 -30.543 37.185 1 79.49 ? O5 QO9 556 A 1 
HETATM 14 C C6 QO9 . . . C 3 50.18 -29.653 39.448 1 74.58 ? C6 QO9 556 A 1 
HETATM 15 O O6 QO9 . . . C 3 49.504 -26.314 40.159 1 72.44 ? O6 QO9 556 A 1 
HETATM 16 C C7 QO9 . . . C 3 51.147 -27.623 38.95 1 71.53 ? C7 QO9 556 A 1 
HETATM 17 O O7 QO9 . . . C 3 54.581 -28.683 36.683 1 67.16 ? O7 QO9 556 A 1 
HETATM 18 C C8 QO9 . . . C 3 51.175 -28.504 37.695 1 72.02 ? C8 QO9 556 A 1 
HETATM 19 O O8 QO9 . . . C 3 53.337 -30.49 35.589 1 77.61 ? O8 QO9 556 A 1 
HETATM 20 C C9 QO9 . . . C 3 49.919 -29.349 37.939 1 74.89 ? C9 QO9 556 A 1 
HETATM 21 C C10 QO9 . . . C 3 50.136 -26.436 38.918 1 67.74 ? C10 QO9 556 A 1 
HETATM 22 C C11 QO9 . . . C 3 51.197 -27.711 36.375 1 71.36 ? C11 QO9 556 A 1 
HETATM 23 C C12 QO9 . . . C 3 52.341 -28.066 35.566 1 72.61 ? C12 QO9 556 A 1 
HETATM 24 C C13 QO9 . . . C 3 48.875 -32.767 35.817 1 78.69 ? C13 QO9 556 A 1 
HETATM 25 C C14 QO9 . . . C 3 47.082 -30.593 37.1 1 69.73 ? C14 QO9 556 A 1 
HETATM 26 C C15 QO9 . . . C 3 48.742 -29.914 34.644 1 72.89 ? C15 QO9 556 A 1 
HETATM 27 C C16 QO9 . . . C 3 47.643 -33.242 35.042 1 72.03 ? C16 QO9 556 A 1 
HETATM 28 C C17 QO9 . . . C 3 50.137 -32.984 34.957 1 79.56 ? C17 QO9 556 A 1 
HETATM 29 C C18 QO9 . . . C 3 49.007 -33.581 37.124 1 78.13 ? C18 QO9 556 A 1 
HETATM 30 C C19 QO9 . . . C 3 48.375 -23.599 39.871 1 71.88 ? C19 QO9 556 A 1 
HETATM 31 C C20 QO9 . . . C 3 46.82 -26.088 38.894 1 65.13 ? C20 QO9 556 A 1 
HETATM 32 C C21 QO9 . . . C 3 47.341 -25.718 41.836 1 75.07 ? C21 QO9 556 A 1 
HETATM 33 C C22 QO9 . . . C 3 47.098 -22.835 40.258 1 67.34 ? C22 QO9 556 A 1 
HETATM 34 C C23 QO9 . . . C 3 49.531 -23.117 40.782 1 67.24 ? C23 QO9 556 A 1 
HETATM 35 C C24 QO9 . . . C 3 48.72 -23.311 38.401 1 69.83 ? C24 QO9 556 A 1 
HETATM 36 SI SI1 QO9 . . . C 3 48.716 -30.908 36.228 1 84.23 ? SI1 QO9 556 A 1 
HETATM 37 SI SI2 QO9 . . . C 3 48.082 -25.465 40.141 1 74.86 ? SI2 QO9 556 A 1 
HETATM 38 N N3 QO9 . . . C 3 50.252 -26.749 35.96 1 72.03 ? N3 QO9 556 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           38 
#