data_3VAF
#
_model_server_result.job_id            Whgj-n_eVcYx3vXDNSKcsQ 
_model_server_result.datetime_utc      '2024-10-25 20:23:15' 
_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          3vaf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":402}' 
#
_entry.id    3VAF 
#
_exptl.entry_id    3VAF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              88.105 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '1,4-DIETHYLENE DIOXIDE' 
_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          125.67 
_cell.angle_gamma         90 
_cell.entry_id            3VAF 
_cell.length_a            164.296 
_cell.length_b            36.981 
_cell.length_c            99.431 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VAF 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_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,Q,R,S,T 
_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 E N N 
? 3 F N N 
? 3 K N N 
? 3 L 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
covale ? covale1 C O3' DU 2 P DU 3 1_555 C P BRU 3 P BRU 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? 
covale ? covale2 C O3' BRU 3 P BRU 4 1_555 C P BRU 4 P BRU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.583 ? 
covale ? covale3 C O3' BRU 4 P BRU 5 1_555 C P DU 5 P DU 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.59 ? 
covale ? covale4 D O3' DU 2 E DU 3 1_555 D P BRU 3 E BRU 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.587 ? 
covale ? covale5 D O3' BRU 3 E BRU 4 1_555 D P BRU 4 E BRU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.59 ? 
covale ? covale6 D O3' BRU 4 E BRU 5 1_555 D P DU 5 E DU 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? 
#
_chem_comp.formula           'C4 H8 O2' 
_chem_comp.formula_weight    88.105 
_chem_comp.id                DIO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '1,4-DIETHYLENE DIOXIDE' 
_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 C1' DIO sing 255 n n 
C1 O1 DIO sing 256 n n 
C1 H11 DIO sing 257 n n 
C1 H12 DIO sing 258 n n 
C2 C2' DIO sing 259 n n 
C2 O1 DIO sing 260 n n 
C2 H21 DIO sing 261 n n 
C2 H22 DIO sing 262 n n 
C1' O1' DIO sing 263 n n 
C1' "H1'1" DIO sing 264 n n 
C1' "H1'2" DIO sing 265 n n 
C2' O1' DIO sing 266 n n 
C2' "H2'1" DIO sing 267 n n 
C2' "H2'2" DIO sing 268 n n 
#
_atom_sites.entry_id                     3VAF 
_atom_sites.fract_transf_matrix[1][1]    0.006087 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004368 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.027041 
_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]    0.012379 
_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 3 DIO A 1 401 6 DIO DIO . 
F 3 DIO A 1 402 8 DIO DIO . 
G 4 SO4 A 1 403 5 SO4 SO4 . 
H 4 SO4 A 1 404 10 SO4 SO4 . 
I 5 GOL A 1 405 1 GOL GOL . 
J 6 CPQ B 1 401 101 CPQ CPQ . 
K 3 DIO B 1 402 1 DIO DIO . 
L 3 DIO B 1 403 4 DIO DIO . 
M 4 SO4 B 1 404 1 SO4 SO4 . 
N 4 SO4 B 1 405 6 SO4 SO4 . 
O 4 SO4 B 1 406 9 SO4 SO4 . 
P 4 SO4 P 1 101 8 SO4 SO4 . 
Q 7 HOH A 1 501 1 HOH HOH . 
Q 7 HOH A 2 502 2 HOH HOH . 
Q 7 HOH A 3 503 3 HOH HOH . 
Q 7 HOH A 4 504 10 HOH HOH . 
Q 7 HOH A 5 505 15 HOH HOH . 
Q 7 HOH A 6 506 22 HOH HOH . 
Q 7 HOH A 7 507 23 HOH HOH . 
Q 7 HOH A 8 508 27 HOH HOH . 
Q 7 HOH A 9 509 28 HOH HOH . 
Q 7 HOH A 10 510 33 HOH HOH . 
Q 7 HOH A 11 511 34 HOH HOH . 
Q 7 HOH A 12 512 36 HOH HOH . 
Q 7 HOH A 13 513 37 HOH HOH . 
Q 7 HOH A 14 514 38 HOH HOH . 
Q 7 HOH A 15 515 39 HOH HOH . 
Q 7 HOH A 16 516 42 HOH HOH . 
Q 7 HOH A 17 517 43 HOH HOH . 
Q 7 HOH A 18 518 44 HOH HOH . 
Q 7 HOH A 19 519 46 HOH HOH . 
Q 7 HOH A 20 520 48 HOH HOH . 
Q 7 HOH A 21 521 51 HOH HOH . 
Q 7 HOH A 22 522 54 HOH HOH . 
Q 7 HOH A 23 523 55 HOH HOH . 
Q 7 HOH A 24 524 56 HOH HOH . 
Q 7 HOH A 25 525 58 HOH HOH . 
Q 7 HOH A 26 526 64 HOH HOH . 
Q 7 HOH A 27 527 65 HOH HOH . 
Q 7 HOH A 28 528 67 HOH HOH . 
Q 7 HOH A 29 529 68 HOH HOH . 
Q 7 HOH A 30 530 69 HOH HOH . 
Q 7 HOH A 31 531 70 HOH HOH . 
Q 7 HOH A 32 532 74 HOH HOH . 
Q 7 HOH A 33 533 83 HOH HOH . 
Q 7 HOH A 34 534 84 HOH HOH . 
Q 7 HOH A 35 535 85 HOH HOH . 
Q 7 HOH A 36 536 90 HOH HOH . 
Q 7 HOH A 37 537 94 HOH HOH . 
Q 7 HOH A 38 538 97 HOH HOH . 
Q 7 HOH A 39 539 98 HOH HOH . 
Q 7 HOH A 40 540 99 HOH HOH . 
Q 7 HOH A 41 541 109 HOH HOH . 
Q 7 HOH A 42 542 111 HOH HOH . 
Q 7 HOH A 43 543 115 HOH HOH . 
Q 7 HOH A 44 544 117 HOH HOH . 
Q 7 HOH A 45 545 118 HOH HOH . 
R 7 HOH B 1 501 4 HOH HOH . 
R 7 HOH B 2 502 5 HOH HOH . 
R 7 HOH B 3 503 8 HOH HOH . 
R 7 HOH B 4 504 14 HOH HOH . 
R 7 HOH B 5 505 16 HOH HOH . 
R 7 HOH B 6 506 17 HOH HOH . 
R 7 HOH B 7 507 19 HOH HOH . 
R 7 HOH B 8 508 24 HOH HOH . 
R 7 HOH B 9 509 25 HOH HOH . 
R 7 HOH B 10 510 26 HOH HOH . 
R 7 HOH B 11 511 29 HOH HOH . 
R 7 HOH B 12 512 30 HOH HOH . 
R 7 HOH B 13 513 31 HOH HOH . 
R 7 HOH B 14 514 32 HOH HOH . 
R 7 HOH B 15 515 35 HOH HOH . 
R 7 HOH B 16 516 40 HOH HOH . 
R 7 HOH B 17 517 45 HOH HOH . 
R 7 HOH B 18 518 47 HOH HOH . 
R 7 HOH B 19 519 49 HOH HOH . 
R 7 HOH B 20 520 50 HOH HOH . 
R 7 HOH B 21 521 52 HOH HOH . 
R 7 HOH B 22 522 53 HOH HOH . 
R 7 HOH B 23 523 59 HOH HOH . 
R 7 HOH B 24 524 60 HOH HOH . 
R 7 HOH B 25 525 61 HOH HOH . 
R 7 HOH B 26 526 62 HOH HOH . 
R 7 HOH B 27 527 63 HOH HOH . 
R 7 HOH B 28 528 71 HOH HOH . 
R 7 HOH B 29 529 72 HOH HOH . 
R 7 HOH B 30 530 75 HOH HOH . 
R 7 HOH B 31 531 76 HOH HOH . 
R 7 HOH B 32 532 77 HOH HOH . 
R 7 HOH B 33 533 78 HOH HOH . 
R 7 HOH B 34 534 79 HOH HOH . 
R 7 HOH B 35 535 80 HOH HOH . 
R 7 HOH B 36 536 81 HOH HOH . 
R 7 HOH B 37 537 82 HOH HOH . 
R 7 HOH B 38 538 87 HOH HOH . 
R 7 HOH B 39 539 89 HOH HOH . 
R 7 HOH B 40 540 91 HOH HOH . 
R 7 HOH B 41 541 92 HOH HOH . 
R 7 HOH B 42 542 95 HOH HOH . 
R 7 HOH B 43 543 96 HOH HOH . 
R 7 HOH B 44 544 101 HOH HOH . 
R 7 HOH B 45 545 102 HOH HOH . 
R 7 HOH B 46 546 103 HOH HOH . 
R 7 HOH B 47 547 104 HOH HOH . 
R 7 HOH B 48 548 105 HOH HOH . 
R 7 HOH B 49 549 107 HOH HOH . 
R 7 HOH B 50 550 108 HOH HOH . 
R 7 HOH B 51 551 110 HOH HOH . 
R 7 HOH B 52 552 112 HOH HOH . 
R 7 HOH B 53 553 113 HOH HOH . 
R 7 HOH B 54 554 114 HOH HOH . 
R 7 HOH B 55 555 116 HOH HOH . 
R 7 HOH B 56 556 20 HOH HOH . 
S 7 HOH P 1 201 9 HOH HOH . 
S 7 HOH P 2 202 11 HOH HOH . 
S 7 HOH P 3 203 18 HOH HOH . 
S 7 HOH P 4 204 21 HOH HOH . 
S 7 HOH P 5 205 41 HOH HOH . 
S 7 HOH P 6 206 66 HOH HOH . 
S 7 HOH P 7 207 106 HOH HOH . 
S 7 HOH P 8 208 119 HOH HOH . 
T 7 HOH E 1 101 6 HOH HOH . 
T 7 HOH E 2 102 7 HOH HOH . 
T 7 HOH E 3 103 12 HOH HOH . 
T 7 HOH E 4 104 13 HOH HOH . 
T 7 HOH E 5 105 57 HOH HOH . 
T 7 HOH E 6 106 73 HOH HOH . 
T 7 HOH E 7 107 86 HOH HOH . 
T 7 HOH E 8 108 88 HOH HOH . 
T 7 HOH E 9 109 93 HOH HOH . 
T 7 HOH E 10 110 100 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 DIO . . . F 3 -2.89 92.379 107.8 1 42.41 ? C1 DIO 402 A 1 
HETATM 2 C C2 DIO . . . F 3 -1.774 90.796 106.461 1 41.99 ? C2 DIO 402 A 1 
HETATM 3 C C1' DIO . . . F 3 -3.323 91.286 108.781 1 42.8 ? C1' DIO 402 A 1 
HETATM 4 C C2' DIO . . . F 3 -2.197 89.67 107.405 1 42.44 ? C2' DIO 402 A 1 
HETATM 5 O O1 DIO . . . F 3 -2.76 91.833 106.486 1 42.03 ? O1 DIO 402 A 1 
HETATM 6 O O1' DIO . . . F 3 -2.449 90.146 108.737 1 42.23 ? O1' DIO 402 A 1 
#
_model_server_stats.io_time_ms              56 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           6 
#