data_6VQM
#
_model_server_result.job_id            jaIyPLtoJrMc6GT5BThmlQ 
_model_server_result.datetime_utc      '2024-11-04 20:08:50' 
_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          6vqm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    6VQM 
#
_exptl.entry_id    6VQM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              459.543 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-({4-[(3R,5S)-3,5-dimethylpiperazin-1-yl]-2-methoxyphenyl}amino)-9-methyl-5,7-dihydro-6H-pyrimido[5,4-d][1,3]benzodiazepin-6-one 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          99.13 
_cell.angle_gamma         90 
_cell.entry_id            6VQM 
_cell.length_a            70.638 
_cell.length_b            42.453 
_cell.length_c            92.014 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VQM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
B,D,E 1 1 
A,C 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+1/2,-z -1 0 0 0 1 0 0 0 -1 0 21.2265 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C25 H29 N7 O2' 
_chem_comp.formula_weight    459.543 
_chem_comp.id                R7P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-({4-[(3R,5S)-3,5-dimethylpiperazin-1-yl]-2-methoxyphenyl}amino)-9-methyl-5,7-dihydro-6H-pyrimido[5,4-d][1,3]benzodiazepin-6-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
C31 C29 R7P sing 275 n n 
C29 N32 R7P sing 276 n n 
C29 C28 R7P sing 277 n n 
N32 C33 R7P sing 278 n n 
C33 C35 R7P sing 279 n n 
C33 C36 R7P sing 280 n n 
C28 N27 R7P sing 281 n n 
N27 C36 R7P sing 282 n n 
N27 C5 R7P sing 283 n n 
C6 C5 R7P doub 284 n y 
C6 C7 R7P sing 285 n y 
C5 C4 R7P sing 286 n y 
C7 C8 R7P doub 287 n y 
C4 C3 R7P doub 288 n y 
C8 C3 R7P sing 289 n y 
C8 N9 R7P sing 290 n n 
C3 O2 R7P sing 291 n n 
C21 C20 R7P sing 292 n n 
C22 C20 R7P doub 293 n y 
C22 C23 R7P sing 294 n y 
C20 C19 R7P sing 295 n y 
C23 C24 R7P doub 296 n y 
N9 C10 R7P sing 297 n n 
O2 C1 R7P sing 298 n n 
C19 C18 R7P doub 299 n y 
N26 C10 R7P doub 300 n y 
N26 C25 R7P sing 301 n y 
C10 N11 R7P sing 302 n y 
C24 C18 R7P sing 303 n y 
C24 C25 R7P sing 304 n n 
C18 N17 R7P sing 305 n n 
C25 C13 R7P doub 306 n y 
N11 C12 R7P doub 307 n y 
N17 C15 R7P sing 308 n n 
C13 C12 R7P sing 309 n y 
C13 N14 R7P sing 310 n n 
C15 N14 R7P sing 311 n n 
C15 O16 R7P doub 312 n n 
C1 H1 R7P sing 313 n n 
C1 H2 R7P sing 314 n n 
C1 H3 R7P sing 315 n n 
C4 H4 R7P sing 316 n n 
C6 H5 R7P sing 317 n n 
C7 H6 R7P sing 318 n n 
C12 H7 R7P sing 319 n n 
C19 H8 R7P sing 320 n n 
C21 H9 R7P sing 321 n n 
C21 H10 R7P sing 322 n n 
C21 H11 R7P sing 323 n n 
C23 H12 R7P sing 324 n n 
C31 H13 R7P sing 325 n n 
C31 H14 R7P sing 326 n n 
C31 H15 R7P sing 327 n n 
C33 H16 R7P sing 328 n n 
C35 H17 R7P sing 329 n n 
C35 H18 R7P sing 330 n n 
C35 H19 R7P sing 331 n n 
C36 H20 R7P sing 332 n n 
C36 H21 R7P sing 333 n n 
N9 H22 R7P sing 334 n n 
N14 H23 R7P sing 335 n n 
N17 H24 R7P sing 336 n n 
C22 H25 R7P sing 337 n n 
C28 H26 R7P sing 338 n n 
C28 H27 R7P sing 339 n n 
C29 H28 R7P sing 340 n n 
N32 H29 R7P sing 341 n n 
#
_atom_sites.entry_id                     6VQM 
_atom_sites.fract_transf_matrix[1][1]    0.014157 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002274 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023555 
_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]    0.011007 
_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 2 R7P A 1 401 1 R7P INX . 
D 2 R7P B 1 401 2 R7P INX . 
E 3 SO4 B 1 402 1 SO4 SO4 . 
#
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 R7P . . . C 2 11.92 12.722 -10.637 0 44.97 ? C1 R7P 401 A 1 
HETATM 2 C C3 R7P . . . C 2 11.333 10.448 -11.421 1 48.67 ? C3 R7P 401 A 1 
HETATM 3 C C4 R7P . . . C 2 10.222 10.947 -12.094 1 46.79 ? C4 R7P 401 A 1 
HETATM 4 C C5 R7P . . . C 2 9.389 10.103 -12.872 1 47.88 ? C5 R7P 401 A 1 
HETATM 5 C C6 R7P . . . C 2 9.738 8.748 -12.955 1 47.09 ? C6 R7P 401 A 1 
HETATM 6 C C7 R7P . . . C 2 10.844 8.25 -12.285 1 47.44 ? C7 R7P 401 A 1 
HETATM 7 C C8 R7P . . . C 2 11.67 9.082 -11.497 1 46.35 ? C8 R7P 401 A 1 
HETATM 8 C C12 R7P . . . C 2 14.786 5.916 -9.643 1 37.81 ? C12 R7P 401 A 1 
HETATM 9 C C15 R7P . . . C 2 14.007 2.357 -9.388 1 37.96 ? C15 R7P 401 A 1 
HETATM 10 C C18 R7P . . . C 2 11.667 2.616 -10.259 1 36.14 ? C18 R7P 401 A 1 
HETATM 11 C C19 R7P . . . C 2 10.567 1.766 -10.522 1 33.59 ? C19 R7P 401 A 1 
HETATM 12 C C21 R7P . . . C 2 8.206 1.329 -11.248 1 37.69 ? C21 R7P 401 A 1 
HETATM 13 C C23 R7P . . . C 2 10.256 4.508 -10.891 1 34.31 ? C23 R7P 401 A 1 
HETATM 14 C C24 R7P . . . C 2 11.513 4.03 -10.421 1 35.24 ? C24 R7P 401 A 1 
HETATM 15 C C31 R7P . . . C 2 6.784 13.871 -14.764 1 51.68 ? C31 R7P 401 A 1 
HETATM 16 C C33 R7P . . . C 2 5.782 10.204 -13.924 1 52.6 ? C33 R7P 401 A 1 
HETATM 17 C C35 R7P . . . C 2 4.489 9.646 -13.291 1 48.61 ? C35 R7P 401 A 1 
HETATM 18 C C36 R7P . . . C 2 6.978 9.979 -12.981 1 51.4 ? C36 R7P 401 A 1 
HETATM 19 O O2 R7P . . . C 2 12.084 11.314 -10.684 1 51.77 ? O2 R7P 401 A 1 
HETATM 20 N N9 R7P . . . C 2 12.822 8.662 -10.776 1 42.47 ? N9 R7P 401 A 1 
HETATM 21 C C10 R7P . . . C 2 13.156 7.351 -10.425 1 37.31 ? C10 R7P 401 A 1 
HETATM 22 N N11 R7P . . . C 2 14.388 7.14 -9.987 1 36.46 ? N11 R7P 401 A 1 
HETATM 23 C C13 R7P . . . C 2 13.916 4.813 -9.731 1 36.13 ? C13 R7P 401 A 1 
HETATM 24 N N14 R7P . . . C 2 14.504 3.603 -9.344 1 36.71 ? N14 R7P 401 A 1 
HETATM 25 O O16 R7P . . . C 2 14.779 1.491 -9 1 39.82 ? O16 R7P 401 A 1 
HETATM 26 N N17 R7P . . . C 2 12.802 1.912 -9.793 1 38.9 ? N17 R7P 401 A 1 
HETATM 27 C C20 R7P . . . C 2 9.349 2.273 -10.959 1 35.01 ? C20 R7P 401 A 1 
HETATM 28 C C22 R7P . . . C 2 9.2 3.64 -11.146 1 35.11 ? C22 R7P 401 A 1 
HETATM 29 C C25 R7P . . . C 2 12.599 5.049 -10.2 1 35.39 ? C25 R7P 401 A 1 
HETATM 30 N N26 R7P . . . C 2 12.309 6.318 -10.518 1 34.35 ? N26 R7P 401 A 1 
HETATM 31 N N27 R7P . . . C 2 8.229 10.52 -13.58 1 49.95 ? N27 R7P 401 A 1 
HETATM 32 C C28 R7P . . . C 2 8.096 11.98 -13.792 1 50.05 ? C28 R7P 401 A 1 
HETATM 33 C C29 R7P . . . C 2 6.925 12.334 -14.717 1 51.9 ? C29 R7P 401 A 1 
HETATM 34 N N32 R7P . . . C 2 5.699 11.65 -14.242 1 54.95 ? N32 R7P 401 A 1 
#
_model_server_stats.io_time_ms              65 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           34 
#