data_6VBN
#
_model_server_result.job_id            ESXCnRWcw4c4LKZNpz2AVA 
_model_server_result.datetime_utc      '2025-01-02 23:42:10' 
_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          6vbn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":402}' 
#
_entry.id    6VBN 
#
_exptl.entry_id    6VBN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              256.3 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,5-anhydro-2,3-dideoxy-3-[(5S)-5H-imidazo[5,1-a]isoindol-5-yl]-D-threo-pentitol 
_entity.pdbx_number_of_molecules    4 
_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            6VBN 
_cell.length_a            78.475 
_cell.length_b            143.044 
_cell.length_c            147.236 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VBN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,F,G,H,I,J,K,L,M,N,O,P 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 K N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_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
_struct_conn.pdbx_value_order
metalc ? metalc1 A NE2 HIS 314 A HIS 328 1_555 E FE HEM . A HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc2 E FE HEM . A HEM 401 1_555 F N9 QVY . A QVY 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc3 B NE2 HIS 314 B HIS 328 1_555 G FE HEM . B HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
metalc ? metalc4 G FE HEM . B HEM 401 1_555 H N9 QVY . B QVY 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc5 C NE2 HIS 314 C HIS 328 1_555 I FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? 
metalc ? metalc6 I FE HEM . C HEM 401 1_555 K N9 QVY . C QVY 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? 
metalc ? metalc7 J N9 QVY . C QVY 402 1_555 L FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? 
metalc ? metalc8 D NE2 HIS 314 D HIS 328 1_555 L FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
#
_chem_comp.formula           'C15 H16 N2 O2' 
_chem_comp.formula_weight    256.3 
_chem_comp.id                QVY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,5-anhydro-2,3-dideoxy-3-[(5S)-5H-imidazo[5,1-a]isoindol-5-yl]-D-threo-pentitol 
_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 C2 QVY doub 359 n y 
C1 C6 QVY sing 360 n y 
C2 C3 QVY sing 361 n y 
C6 C5 QVY doub 362 n y 
C3 C4 QVY doub 363 n y 
C5 C4 QVY sing 364 n y 
C5 C7 QVY sing 365 n n 
C4 C12 QVY sing 366 n n 
C7 C8 QVY doub 367 n y 
C7 N11 QVY sing 368 n y 
C8 N9 QVY sing 369 n y 
C12 N11 QVY sing 370 n n 
C12 C14 QVY sing 371 n n 
N11 C10 QVY sing 372 n y 
N9 C10 QVY doub 373 n y 
O22 C20 QVY sing 374 n n 
C14 C20 QVY sing 375 n n 
C14 C16 QVY sing 376 n n 
C20 C19 QVY sing 377 n n 
C16 C17 QVY sing 378 n n 
C19 O18 QVY sing 379 n n 
C17 O18 QVY sing 380 n n 
C14 H15 QVY sing 381 n n 
C6 H1 QVY sing 382 n n 
C8 H2 QVY sing 383 n n 
C10 H3 QVY sing 384 n n 
C12 H13 QVY sing 385 n n 
C3 H4 QVY sing 386 n n 
C1 H5 QVY sing 387 n n 
C2 H6 QVY sing 388 n n 
C16 H7 QVY sing 389 n n 
C16 H8 QVY sing 390 n n 
C17 H9 QVY sing 391 n n 
C17 H10 QVY sing 392 n n 
C19 H11 QVY sing 393 n n 
C19 H12 QVY sing 394 n n 
C20 H21 QVY sing 395 n n 
O22 H14 QVY sing 396 n n 
#
_atom_sites.entry_id                     6VBN 
_atom_sites.fract_transf_matrix[1][1]    0.012743 
_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]    0.006991 
_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]    0.006792 
_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
E 2 HEM A 1 401 401 HEM HEM . 
F 3 QVY A 1 402 1 QVY DRG . 
G 2 HEM B 1 401 401 HEM HEM . 
H 3 QVY B 1 402 1 QVY DRG . 
I 2 HEM C 1 401 401 HEM HEM . 
J 3 QVY C 1 402 1 QVY DRG . 
K 3 QVY C 1 403 1 QVY DRG . 
L 2 HEM D 1 401 401 HEM HEM . 
M 4 HOH A 1 501 49 HOH HOH . 
M 4 HOH A 2 502 48 HOH HOH . 
M 4 HOH A 3 503 50 HOH HOH . 
M 4 HOH A 4 504 1 HOH HOH . 
M 4 HOH A 5 505 55 HOH HOH . 
M 4 HOH A 6 506 54 HOH HOH . 
M 4 HOH A 7 507 3 HOH HOH . 
M 4 HOH A 8 508 16 HOH HOH . 
M 4 HOH A 9 509 21 HOH HOH . 
M 4 HOH A 10 510 40 HOH HOH . 
M 4 HOH A 11 511 43 HOH HOH . 
M 4 HOH A 12 512 38 HOH HOH . 
M 4 HOH A 13 513 58 HOH HOH . 
N 4 HOH B 1 501 33 HOH HOH . 
N 4 HOH B 2 502 28 HOH HOH . 
N 4 HOH B 3 503 25 HOH HOH . 
N 4 HOH B 4 504 51 HOH HOH . 
N 4 HOH B 5 505 47 HOH HOH . 
N 4 HOH B 6 506 7 HOH HOH . 
N 4 HOH B 7 507 45 HOH HOH . 
N 4 HOH B 8 508 57 HOH HOH . 
N 4 HOH B 9 509 24 HOH HOH . 
N 4 HOH B 10 510 56 HOH HOH . 
N 4 HOH B 11 511 60 HOH HOH . 
N 4 HOH B 12 512 59 HOH HOH . 
O 4 HOH C 1 501 5 HOH HOH . 
O 4 HOH C 2 502 22 HOH HOH . 
O 4 HOH C 3 503 27 HOH HOH . 
O 4 HOH C 4 504 46 HOH HOH . 
P 4 HOH D 1 501 6 HOH HOH . 
P 4 HOH D 2 502 44 HOH HOH . 
P 4 HOH D 3 503 53 HOH HOH . 
P 4 HOH D 4 504 52 HOH HOH . 
P 4 HOH D 5 505 4 HOH HOH . 
P 4 HOH D 6 506 20 HOH HOH . 
P 4 HOH D 7 507 12 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 C4 QVY . . . H 3 6.527 18.334 -6.608 1 86.84 ? C4 QVY 402 B 1 
HETATM 2 C C14 QVY . . . H 3 6.449 19.839 -8.695 1 90.23 ? C14 QVY 402 B 1 
HETATM 3 C C5 QVY . . . H 3 7.361 17.22 -6.538 1 85.78 ? C5 QVY 402 B 1 
HETATM 4 C C6 QVY . . . H 3 6.973 16.095 -5.808 1 85.86 ? C6 QVY 402 B 1 
HETATM 5 C C7 QVY . . . H 3 8.609 17.501 -7.229 1 85.06 ? C7 QVY 402 B 1 
HETATM 6 C C8 QVY . . . H 3 9.85 17.076 -7.637 1 83.85 ? C8 QVY 402 B 1 
HETATM 7 C C10 QVY . . . H 3 9.713 19.119 -8.212 1 84.17 ? C10 QVY 402 B 1 
HETATM 8 C C12 QVY . . . H 3 7.2 19.431 -7.402 1 87.3 ? C12 QVY 402 B 1 
HETATM 9 C C3 QVY . . . H 3 5.306 18.335 -5.941 1 87.32 ? C3 QVY 402 B 1 
HETATM 10 C C1 QVY . . . H 3 5.761 16.114 -5.135 1 87.3 ? C1 QVY 402 B 1 
HETATM 11 C C2 QVY . . . H 3 4.932 17.226 -5.199 1 88.01 ? C2 QVY 402 B 1 
HETATM 12 N N9 QVY . . . H 3 10.536 18.096 -8.251 1 83.48 ? N9 QVY 402 B 1 
HETATM 13 N N11 QVY . . . H 3 8.526 18.836 -7.607 1 85.52 ? N11 QVY 402 B 1 
HETATM 14 C C16 QVY . . . H 3 6.418 18.694 -9.718 1 88.66 ? C16 QVY 402 B 1 
HETATM 15 C C17 QVY . . . H 3 5.825 19.158 -11.024 1 88.17 ? C17 QVY 402 B 1 
HETATM 16 O O18 QVY . . . H 3 6.533 20.284 -11.536 1 88.81 ? O18 QVY 402 B 1 
HETATM 17 C C19 QVY . . . H 3 6.347 21.403 -10.664 1 90.87 ? C19 QVY 402 B 1 
HETATM 18 C C20 QVY . . . H 3 6.997 21.132 -9.317 1 92.74 ? C20 QVY 402 B 1 
HETATM 19 O O22 QVY . . . H 3 6.756 22.248 -8.453 1 94.32 ? O22 QVY 402 B 1 
HETATM 20 H H15 QVY . . . H 3 5.423 20.04 -8.39 1 90.48 ? H15 QVY 402 B 1 
HETATM 21 H H13 QVY . . . H 3 7.325 20.314 -6.779 1 87.07 ? H13 QVY 402 B 1 
HETATM 22 H H21 QVY . . . H 3 8.069 21.038 -9.476 1 93.02 ? H21 QVY 402 B 1 
#
_model_server_stats.io_time_ms              43 
_model_server_stats.parse_time_ms           40 
_model_server_stats.create_model_time_ms    91 
_model_server_stats.query_time_ms           761 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           22 
#