data_6DZF
#
_model_server_result.job_id            dmfn_QnjaCMLqTZutIz6rA 
_model_server_result.datetime_utc      '2024-10-20 00:45:02' 
_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          6dzf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    6DZF 
#
_exptl.entry_id    6DZF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              120.152 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            BENZAMIDINE 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            6DZF 
_cell.length_a            54.122 
_cell.length_b            56.841 
_cell.length_c            65.478 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DZF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
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 7 A CYS 22 1_555 A SG CYS 137 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf4 A SG CYS 116 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
metalc ? metalc1 A OE1 GLU 52 A GLU 70 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc2 A O ASN 54 A ASN 72 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc3 A O VAL 57 A VAL 75 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? 
metalc ? metalc4 A OE2 GLU 62 A GLU 80 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? 
metalc ? metalc5 B CA CA . A CA 301 1_555 F O HOH . A HOH 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? 
metalc ? metalc6 B CA CA . A CA 301 1_555 F O HOH . A HOH 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
#
_chem_comp.formula           'C7 H8 N2' 
_chem_comp.formula_weight    120.152 
_chem_comp.id                BEN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              BENZAMIDINE 
_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 BEN doub 70 n y 
C1 C6 BEN sing 71 n y 
C1 C BEN sing 72 n n 
C2 C3 BEN sing 73 n y 
C2 H2 BEN sing 74 n n 
C3 C4 BEN doub 75 n y 
C3 H3 BEN sing 76 n n 
C4 C5 BEN sing 77 n y 
C4 H4 BEN sing 78 n n 
C5 C6 BEN doub 79 n y 
C5 H5 BEN sing 80 n n 
C6 H6 BEN sing 81 n n 
C N1 BEN doub 82 e n 
C N2 BEN sing 83 n n 
N1 HN1 BEN sing 84 n n 
N2 HN21 BEN sing 85 n n 
N2 HN22 BEN sing 86 n n 
#
_atom_sites.entry_id                     6DZF 
_atom_sites.fract_transf_matrix[1][1]    0.018477 
_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]    0.017593 
_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]    0.015272 
_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
B 2 CA A 1 301 301 CA CA . 
C 3 BEN A 1 302 302 BEN BEN . 
D 4 SO4 A 1 303 303 SO4 SO4 . 
E 5 XYS A 1 304 304 XYS XYS . 
F 6 HOH A 1 401 401 HOH HOH . 
F 6 HOH A 2 402 402 HOH HOH . 
F 6 HOH A 3 403 403 HOH HOH . 
F 6 HOH A 4 404 404 HOH HOH . 
F 6 HOH A 5 405 405 HOH HOH . 
F 6 HOH A 6 406 406 HOH HOH . 
F 6 HOH A 7 407 407 HOH HOH . 
F 6 HOH A 8 408 409 HOH HOH . 
F 6 HOH A 9 409 412 HOH HOH . 
F 6 HOH A 10 410 414 HOH HOH . 
F 6 HOH A 11 411 411 HOH HOH . 
F 6 HOH A 12 412 408 HOH HOH . 
F 6 HOH A 13 413 410 HOH HOH . 
F 6 HOH A 14 414 413 HOH HOH . 
F 6 HOH A 15 415 415 HOH HOH . 
F 6 HOH A 16 416 416 HOH HOH . 
F 6 HOH A 17 417 417 HOH HOH . 
F 6 HOH A 18 418 418 HOH HOH . 
F 6 HOH A 19 419 419 HOH HOH . 
F 6 HOH A 20 420 420 HOH HOH . 
F 6 HOH A 21 421 421 HOH HOH . 
F 6 HOH A 22 422 422 HOH HOH . 
F 6 HOH A 23 423 423 HOH HOH . 
F 6 HOH A 24 424 424 HOH HOH . 
F 6 HOH A 25 425 426 HOH HOH . 
F 6 HOH A 26 426 427 HOH HOH . 
F 6 HOH A 27 427 428 HOH HOH . 
F 6 HOH A 28 428 425 HOH HOH . 
F 6 HOH A 29 429 429 HOH HOH . 
F 6 HOH A 30 430 430 HOH HOH . 
F 6 HOH A 31 431 431 HOH HOH . 
F 6 HOH A 32 432 432 HOH HOH . 
F 6 HOH A 33 433 435 HOH HOH . 
F 6 HOH A 34 434 433 HOH HOH . 
F 6 HOH A 35 435 434 HOH HOH . 
F 6 HOH A 36 436 436 HOH HOH . 
F 6 HOH A 37 437 437 HOH HOH . 
F 6 HOH A 38 438 438 HOH HOH . 
F 6 HOH A 39 439 439 HOH HOH . 
F 6 HOH A 40 440 442 HOH HOH . 
F 6 HOH A 41 441 443 HOH HOH . 
F 6 HOH A 42 442 440 HOH HOH . 
F 6 HOH A 43 443 441 HOH HOH . 
F 6 HOH A 44 444 444 HOH HOH . 
F 6 HOH A 45 445 445 HOH HOH . 
F 6 HOH A 46 446 446 HOH HOH . 
F 6 HOH A 47 447 447 HOH HOH . 
F 6 HOH A 48 448 448 HOH HOH . 
F 6 HOH A 49 449 452 HOH HOH . 
F 6 HOH A 50 450 449 HOH HOH . 
F 6 HOH A 51 451 451 HOH HOH . 
F 6 HOH A 52 452 455 HOH HOH . 
F 6 HOH A 53 453 450 HOH HOH . 
F 6 HOH A 54 454 453 HOH HOH . 
F 6 HOH A 55 455 454 HOH HOH . 
F 6 HOH A 56 456 457 HOH HOH . 
F 6 HOH A 57 457 456 HOH HOH . 
F 6 HOH A 58 458 459 HOH HOH . 
F 6 HOH A 59 459 458 HOH HOH . 
F 6 HOH A 60 460 460 HOH HOH . 
F 6 HOH A 61 461 461 HOH HOH . 
F 6 HOH A 62 462 462 HOH HOH . 
F 6 HOH A 63 463 464 HOH HOH . 
F 6 HOH A 64 464 463 HOH HOH . 
F 6 HOH A 65 465 465 HOH HOH . 
F 6 HOH A 66 466 466 HOH HOH . 
F 6 HOH A 67 467 467 HOH HOH . 
F 6 HOH A 68 468 468 HOH HOH . 
F 6 HOH A 69 469 469 HOH HOH . 
F 6 HOH A 70 470 471 HOH HOH . 
F 6 HOH A 71 471 470 HOH HOH . 
F 6 HOH A 72 472 472 HOH HOH . 
F 6 HOH A 73 473 473 HOH HOH . 
F 6 HOH A 74 474 474 HOH HOH . 
F 6 HOH A 75 475 475 HOH HOH . 
F 6 HOH A 76 476 476 HOH HOH . 
F 6 HOH A 77 477 477 HOH HOH . 
F 6 HOH A 78 478 478 HOH HOH . 
F 6 HOH A 79 479 479 HOH HOH . 
F 6 HOH A 80 480 480 HOH HOH . 
F 6 HOH A 81 481 481 HOH HOH . 
F 6 HOH A 82 482 482 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 BEN . . . C 3 -1.88 -15.089 -16.949 1 10.95 ? C1 BEN 302 A 1 
HETATM 2 C C2 BEN . . . C 3 -1.73 -15.69 -15.705 1 15.75 ? C2 BEN 302 A 1 
HETATM 3 C C3 BEN . . . C 3 -1.329 -14.934 -14.61 1 15.08 ? C3 BEN 302 A 1 
HETATM 4 C C4 BEN . . . C 3 -1.077 -13.575 -14.762 1 33.65 ? C4 BEN 302 A 1 
HETATM 5 C C5 BEN . . . C 3 -1.226 -12.974 -16.006 1 24.15 ? C5 BEN 302 A 1 
HETATM 6 C C6 BEN . . . C 3 -1.63 -13.731 -17.099 1 24.93 ? C6 BEN 302 A 1 
HETATM 7 C C BEN . . . C 3 -2.285 -15.849 -18.053 1 16.98 ? C BEN 302 A 1 
HETATM 8 N N1 BEN . . . C 3 -2.125 -17.159 -18.076 1 14.61 ? N1 BEN 302 A 1 
HETATM 9 N N2 BEN . . . C 3 -2.831 -15.274 -19.109 1 16.1 ? N2 BEN 302 A 1 
HETATM 10 H H2 BEN . . . C 3 -1.927 -16.756 -15.588 1 18.9 ? H2 BEN 302 A 1 
HETATM 11 H H3 BEN . . . C 3 -1.272 -15.391 -13.623 1 18.09 ? H3 BEN 302 A 1 
HETATM 12 H H4 BEN . . . C 3 -0.762 -12.98 -13.905 1 40.38 ? H4 BEN 302 A 1 
HETATM 13 H H5 BEN . . . C 3 -0.997 -11.915 -16.131 1 28.98 ? H5 BEN 302 A 1 
HETATM 14 H H6 BEN . . . C 3 -1.749 -13.259 -18.075 1 29.91 ? H6 BEN 302 A 1 
HETATM 15 H HN21 BEN . . . C 3 -3.735 -14.821 -19.029 1 19.32 ? HN21 BEN 302 A 1 
HETATM 16 H HN22 BEN . . . C 3 -2.348 -15.288 -20.001 1 19.32 ? HN22 BEN 302 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           577 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           16 
#