data_8WDD
#
_model_server_result.job_id            jEo0hU3Jp52XcuXAwETN7Q 
_model_server_result.datetime_utc      '2024-12-09 23:26:39' 
_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          8wdd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":601}' 
#
_entry.id    8WDD 
#
_exptl.entry_id    8WDD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              289.394 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ~{N},~{N}-dimethyl-6-[(~{E})-2-(1-methylpyridin-1-ium-4-yl)ethenyl]naphthalen-2-amine 
_entity.pdbx_number_of_molecules    9 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          104.5 
_cell.angle_gamma         90 
_cell.entry_id            8WDD 
_cell.length_a            145.822 
_cell.length_b            45.133 
_cell.length_c            209.207 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8WDD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E 1 1 
B,F,G,H,I,J,K 2 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
? 2 C N N 
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 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
disulf ? disulf1 A SG CYS 53 A CYS 53 1_555 A SG CYS 62 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 A SG CYS 75 A CYS 75 1_555 A SG CYS 91 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf3 A SG CYS 90 A CYS 90 1_555 A SG CYS 101 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf4 A SG CYS 123 A CYS 123 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf5 A SG CYS 167 A CYS 167 1_555 A SG CYS 176 A CYS 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf6 A SG CYS 199 A CYS 199 1_555 A SG CYS 245 A CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf7 A SG CYS 244 A CYS 244 1_555 A SG CYS 252 A CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf8 A SG CYS 264 A CYS 264 1_555 A SG CYS 278 A CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf9 A SG CYS 277 A CYS 277 1_555 A SG CYS 288 A CYS 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf10 A SG CYS 315 A CYS 315 1_555 A SG CYS 360 A CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf11 A SG CYS 359 A CYS 359 1_555 A SG CYS 368 A CYS 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf12 A SG CYS 391 A CYS 391 1_555 A SG CYS 437 A CYS 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf13 A SG CYS 436 A CYS 436 1_555 A SG CYS 447 A CYS 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf14 A SG CYS 460 A CYS 460 1_555 A SG CYS 476 A CYS 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf15 A SG CYS 475 A CYS 475 1_555 A SG CYS 486 A CYS 486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf16 A SG CYS 513 A CYS 513 1_555 A SG CYS 558 A CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf17 A SG CYS 557 A CYS 557 1_555 A SG CYS 566 A CYS 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf18 B SG CYS 53 B CYS 53 1_555 B SG CYS 62 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf19 B SG CYS 75 B CYS 75 1_555 B SG CYS 91 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf20 B SG CYS 90 B CYS 90 1_555 B SG CYS 101 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf21 B SG CYS 123 B CYS 123 1_555 B SG CYS 168 B CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf22 B SG CYS 167 B CYS 167 1_555 B SG CYS 176 B CYS 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf23 B SG CYS 199 B CYS 199 1_555 B SG CYS 245 B CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf24 B SG CYS 244 B CYS 244 1_555 B SG CYS 252 B CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf25 B SG CYS 264 B CYS 264 1_555 B SG CYS 278 B CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf26 B SG CYS 277 B CYS 277 1_555 B SG CYS 288 B CYS 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf27 B SG CYS 315 B CYS 315 1_555 B SG CYS 360 B CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf28 B SG CYS 359 B CYS 359 1_555 B SG CYS 368 B CYS 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf29 B SG CYS 391 B CYS 391 1_555 B SG CYS 437 B CYS 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf30 B SG CYS 436 B CYS 436 1_555 B SG CYS 447 B CYS 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf31 B SG CYS 460 B CYS 460 1_555 B SG CYS 476 B CYS 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf32 B SG CYS 475 B CYS 475 1_555 B SG CYS 486 B CYS 486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf33 B SG CYS 513 B CYS 513 1_555 B SG CYS 558 B CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf34 B SG CYS 557 B CYS 557 1_555 B SG CYS 566 B CYS 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
#
_chem_comp.formula           'C20 H21 N2 1' 
_chem_comp.formula_weight    289.394 
_chem_comp.id                VZK 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              ~{N},~{N}-dimethyl-6-[(~{E})-2-(1-methylpyridin-1-ium-4-yl)ethenyl]naphthalen-2-amine 
_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
C07 C08 VZK doub 374 n y 
C07 N06 VZK sing 375 n y 
C09 N06 VZK sing 376 n n 
C08 C03 VZK sing 377 n y 
N06 C05 VZK doub 378 n y 
C01 C18 VZK sing 379 n n 
C01 C02 VZK doub 380 e n 
C17 C18 VZK doub 381 n y 
C17 C16 VZK sing 382 n y 
C03 C02 VZK sing 383 n n 
C03 C04 VZK doub 384 n y 
C05 C04 VZK sing 385 n y 
C18 C19 VZK sing 386 n y 
C16 C13 VZK doub 387 n y 
C19 C14 VZK doub 388 n y 
C13 C14 VZK sing 389 n y 
C13 C12 VZK sing 390 n y 
C14 C15 VZK sing 391 n y 
C12 C11 VZK doub 392 n y 
C15 C10 VZK doub 393 n y 
C21 N20 VZK sing 394 n n 
C11 C10 VZK sing 395 n y 
C11 N20 VZK sing 396 n n 
N20 C22 VZK sing 397 n n 
C02 H1 VZK sing 398 n n 
C04 H2 VZK sing 399 n n 
C05 H3 VZK sing 400 n n 
C07 H4 VZK sing 401 n n 
C08 H5 VZK sing 402 n n 
C09 H6 VZK sing 403 n n 
C09 H7 VZK sing 404 n n 
C09 H8 VZK sing 405 n n 
C15 H9 VZK sing 406 n n 
C16 H10 VZK sing 407 n n 
C17 H11 VZK sing 408 n n 
C22 H12 VZK sing 409 n n 
C22 H13 VZK sing 410 n n 
C22 H14 VZK sing 411 n n 
C01 H15 VZK sing 412 n n 
C10 H16 VZK sing 413 n n 
C12 H17 VZK sing 414 n n 
C19 H18 VZK sing 415 n n 
C21 H19 VZK sing 416 n n 
C21 H20 VZK sing 417 n n 
C21 H21 VZK sing 418 n n 
#
_atom_sites.entry_id                     8WDD 
_atom_sites.fract_transf_matrix[1][1]    0.006858 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001774 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022157 
_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]    0.004937 
_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 VZK A 1 601 2 VZK YHB . 
D 2 VZK A 1 602 5 VZK YHB . 
E 2 VZK A 1 603 6 VZK YHB . 
F 2 VZK B 1 601 601 VZK YHB . 
G 2 VZK B 1 602 701 VZK YHB . 
H 2 VZK B 1 603 901 VZK YHB . 
I 2 VZK B 1 604 1 VZK YHB . 
J 2 VZK B 1 605 3 VZK YHB . 
K 2 VZK B 1 606 7 VZK YHB . 
#
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 C02 VZK . . . F 2 -54.297 -29.708 -50.96 1 131.81 ? C02 VZK 601 B 1 
HETATM 2 C C04 VZK . . . F 2 -56.305 -28.25 -50.894 1 125.99 ? C04 VZK 601 B 1 
HETATM 3 C C05 VZK . . . F 2 -57.614 -27.948 -51.225 1 124.67 ? C05 VZK 601 B 1 
HETATM 4 C C07 VZK . . . F 2 -57.763 -29.943 -52.449 1 122.78 ? C07 VZK 601 B 1 
HETATM 5 C C08 VZK . . . F 2 -56.452 -30.249 -52.117 1 125.97 ? C08 VZK 601 B 1 
HETATM 6 C C09 VZK . . . F 2 -59.697 -28.472 -52.339 1 123.27 ? C09 VZK 601 B 1 
HETATM 7 C C11 VZK . . . F 2 -47.907 -32.33 -49.13 1 146.4 ? C11 VZK 601 B 1 
HETATM 8 C C13 VZK . . . F 2 -49.49 -31.019 -50.356 1 139.31 ? C13 VZK 601 B 1 
HETATM 9 C C14 VZK . . . F 2 -50.491 -31.92 -50.032 1 137.93 ? C14 VZK 601 B 1 
HETATM 10 C C15 VZK . . . F 2 -50.199 -33.03 -49.254 1 135.71 ? C15 VZK 601 B 1 
HETATM 11 C C16 VZK . . . F 2 -49.775 -29.908 -51.132 1 131.44 ? C16 VZK 601 B 1 
HETATM 12 C C17 VZK . . . F 2 -51.064 -29.698 -51.586 1 129.56 ? C17 VZK 601 B 1 
HETATM 13 C C18 VZK . . . F 2 -52.064 -30.6 -51.267 1 131.66 ? C18 VZK 601 B 1 
HETATM 14 C C22 VZK . . . F 2 -46.312 -33.392 -47.516 1 148.06 ? C22 VZK 601 B 1 
HETATM 15 C C01 VZK . . . F 2 -53.484 -30.353 -51.766 1 132.82 ? C01 VZK 601 B 1 
HETATM 16 C C03 VZK . . . F 2 -55.74 -29.396 -51.342 1 126.98 ? C03 VZK 601 B 1 
HETATM 17 C C10 VZK . . . F 2 -48.905 -33.234 -48.802 1 138.96 ? C10 VZK 601 B 1 
HETATM 18 C C12 VZK . . . F 2 -48.199 -31.223 -49.905 1 144.48 ? C12 VZK 601 B 1 
HETATM 19 C C19 VZK . . . F 2 -51.782 -31.71 -50.486 1 134.23 ? C19 VZK 601 B 1 
HETATM 20 C C21 VZK . . . F 2 -45.44 -31.881 -49.323 1 153.21 ? C21 VZK 601 B 1 
HETATM 21 N N06 VZK . . . F 2 -58.325 -28.797 -51.998 1 122.07 ? N06 VZK 601 B 1 
HETATM 22 N N20 VZK . . . F 2 -46.552 -32.535 -48.66 1 150.68 ? N20 VZK 601 B 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           22 
#