data_4D9E
#
_model_server_result.job_id            hXxXxWhmVQgqsD-GXC4JWA 
_model_server_result.datetime_utc      '2025-06-20 12:46:33' 
_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          4d9e 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":401}' 
#
_entry.id    4D9E 
#
_exptl.entry_id    4D9E 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              120.152 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            BENZAMIDINE 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          119.03 
_cell.angle_gamma         90 
_cell.entry_id            4D9E 
_cell.length_a            66.42 
_cell.length_b            165.84 
_cell.length_c            68.06 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4D9E 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,L,M 1 1 
C,D,I,J,K,N,O 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 E N N 
? 2 G N N 
? 2 J N N 
#
_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                     4D9E 
_atom_sites.fract_transf_matrix[1][1]    0.015056 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.008356 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00603 
_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]    0.016804 
_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 BEN A 1 401 402 BEN BEN . 
F 3 LCS A 1 402 1 LCS LCS . 
G 2 BEN B 1 401 1 BEN BEN . 
H 3 LCS B 1 402 1 LCS LCS . 
I 3 LCS C 1 401 1 LCS LCS . 
J 2 BEN D 1 401 403 BEN BEN . 
K 3 LCS D 1 402 1 LCS LCS . 
L 4 HOH A 1 501 1 HOH HOH . 
L 4 HOH A 2 502 3 HOH HOH . 
L 4 HOH A 3 503 8 HOH HOH . 
L 4 HOH A 4 504 9 HOH HOH . 
L 4 HOH A 5 505 12 HOH HOH . 
L 4 HOH A 6 506 13 HOH HOH . 
L 4 HOH A 7 507 16 HOH HOH . 
L 4 HOH A 8 508 18 HOH HOH . 
L 4 HOH A 9 509 22 HOH HOH . 
L 4 HOH A 10 510 24 HOH HOH . 
L 4 HOH A 11 511 32 HOH HOH . 
L 4 HOH A 12 512 35 HOH HOH . 
L 4 HOH A 13 513 46 HOH HOH . 
L 4 HOH A 14 514 47 HOH HOH . 
L 4 HOH A 15 515 52 HOH HOH . 
L 4 HOH A 16 516 56 HOH HOH . 
L 4 HOH A 17 517 58 HOH HOH . 
L 4 HOH A 18 518 60 HOH HOH . 
L 4 HOH A 19 519 61 HOH HOH . 
L 4 HOH A 20 520 62 HOH HOH . 
L 4 HOH A 21 521 65 HOH HOH . 
L 4 HOH A 22 522 75 HOH HOH . 
L 4 HOH A 23 523 78 HOH HOH . 
L 4 HOH A 24 524 79 HOH HOH . 
L 4 HOH A 25 525 82 HOH HOH . 
L 4 HOH A 26 526 83 HOH HOH . 
L 4 HOH A 27 527 86 HOH HOH . 
L 4 HOH A 28 528 90 HOH HOH . 
L 4 HOH A 29 529 92 HOH HOH . 
L 4 HOH A 30 530 94 HOH HOH . 
L 4 HOH A 31 531 95 HOH HOH . 
L 4 HOH A 32 532 96 HOH HOH . 
L 4 HOH A 33 533 99 HOH HOH . 
L 4 HOH A 34 534 104 HOH HOH . 
L 4 HOH A 35 535 107 HOH HOH . 
L 4 HOH A 36 536 111 HOH HOH . 
L 4 HOH A 37 537 114 HOH HOH . 
L 4 HOH A 38 538 124 HOH HOH . 
L 4 HOH A 39 539 127 HOH HOH . 
L 4 HOH A 40 540 128 HOH HOH . 
L 4 HOH A 41 541 129 HOH HOH . 
L 4 HOH A 42 542 133 HOH HOH . 
L 4 HOH A 43 543 134 HOH HOH . 
L 4 HOH A 44 544 136 HOH HOH . 
L 4 HOH A 45 545 138 HOH HOH . 
L 4 HOH A 46 546 140 HOH HOH . 
L 4 HOH A 47 547 142 HOH HOH . 
L 4 HOH A 48 548 144 HOH HOH . 
L 4 HOH A 49 549 145 HOH HOH . 
L 4 HOH A 50 550 158 HOH HOH . 
L 4 HOH A 51 551 160 HOH HOH . 
L 4 HOH A 52 552 161 HOH HOH . 
L 4 HOH A 53 553 163 HOH HOH . 
L 4 HOH A 54 554 166 HOH HOH . 
L 4 HOH A 55 555 170 HOH HOH . 
L 4 HOH A 56 556 171 HOH HOH . 
L 4 HOH A 57 557 182 HOH HOH . 
L 4 HOH A 58 558 184 HOH HOH . 
L 4 HOH A 59 559 190 HOH HOH . 
L 4 HOH A 60 560 191 HOH HOH . 
L 4 HOH A 61 561 192 HOH HOH . 
L 4 HOH A 62 562 196 HOH HOH . 
L 4 HOH A 63 563 200 HOH HOH . 
L 4 HOH A 64 564 208 HOH HOH . 
L 4 HOH A 65 565 222 HOH HOH . 
L 4 HOH A 66 566 232 HOH HOH . 
L 4 HOH A 67 567 235 HOH HOH . 
L 4 HOH A 68 568 3 HOH HOH . 
M 4 HOH B 1 501 6 HOH HOH . 
M 4 HOH B 2 502 7 HOH HOH . 
M 4 HOH B 3 503 10 HOH HOH . 
M 4 HOH B 4 504 17 HOH HOH . 
M 4 HOH B 5 505 21 HOH HOH . 
M 4 HOH B 6 506 25 HOH HOH . 
M 4 HOH B 7 507 26 HOH HOH . 
M 4 HOH B 8 508 36 HOH HOH . 
M 4 HOH B 9 509 39 HOH HOH . 
M 4 HOH B 10 510 43 HOH HOH . 
M 4 HOH B 11 511 53 HOH HOH . 
M 4 HOH B 12 512 55 HOH HOH . 
M 4 HOH B 13 513 66 HOH HOH . 
M 4 HOH B 14 514 73 HOH HOH . 
M 4 HOH B 15 515 81 HOH HOH . 
M 4 HOH B 16 516 87 HOH HOH . 
M 4 HOH B 17 517 103 HOH HOH . 
M 4 HOH B 18 518 109 HOH HOH . 
M 4 HOH B 19 519 115 HOH HOH . 
M 4 HOH B 20 520 116 HOH HOH . 
M 4 HOH B 21 521 117 HOH HOH . 
M 4 HOH B 22 522 118 HOH HOH . 
M 4 HOH B 23 523 120 HOH HOH . 
M 4 HOH B 24 524 130 HOH HOH . 
M 4 HOH B 25 525 131 HOH HOH . 
M 4 HOH B 26 526 146 HOH HOH . 
M 4 HOH B 27 527 159 HOH HOH . 
M 4 HOH B 28 528 162 HOH HOH . 
M 4 HOH B 29 529 164 HOH HOH . 
M 4 HOH B 30 530 167 HOH HOH . 
M 4 HOH B 31 531 168 HOH HOH . 
M 4 HOH B 32 532 172 HOH HOH . 
M 4 HOH B 33 533 176 HOH HOH . 
M 4 HOH B 34 534 179 HOH HOH . 
M 4 HOH B 35 535 181 HOH HOH . 
M 4 HOH B 36 536 185 HOH HOH . 
M 4 HOH B 37 537 189 HOH HOH . 
M 4 HOH B 38 538 195 HOH HOH . 
M 4 HOH B 39 539 197 HOH HOH . 
M 4 HOH B 40 540 198 HOH HOH . 
M 4 HOH B 41 541 199 HOH HOH . 
M 4 HOH B 42 542 202 HOH HOH . 
M 4 HOH B 43 543 205 HOH HOH . 
M 4 HOH B 44 544 206 HOH HOH . 
M 4 HOH B 45 545 215 HOH HOH . 
M 4 HOH B 46 546 218 HOH HOH . 
M 4 HOH B 47 547 220 HOH HOH . 
M 4 HOH B 48 548 221 HOH HOH . 
M 4 HOH B 49 549 230 HOH HOH . 
M 4 HOH B 50 550 231 HOH HOH . 
M 4 HOH B 51 551 234 HOH HOH . 
M 4 HOH B 52 552 239 HOH HOH . 
M 4 HOH B 53 553 1 HOH HOH . 
N 4 HOH C 1 501 4 HOH HOH . 
N 4 HOH C 2 502 11 HOH HOH . 
N 4 HOH C 3 503 14 HOH HOH . 
N 4 HOH C 4 504 15 HOH HOH . 
N 4 HOH C 5 505 19 HOH HOH . 
N 4 HOH C 6 506 20 HOH HOH . 
N 4 HOH C 7 507 23 HOH HOH . 
N 4 HOH C 8 508 28 HOH HOH . 
N 4 HOH C 9 509 30 HOH HOH . 
N 4 HOH C 10 510 31 HOH HOH . 
N 4 HOH C 11 511 33 HOH HOH . 
N 4 HOH C 12 512 40 HOH HOH . 
N 4 HOH C 13 513 57 HOH HOH . 
N 4 HOH C 14 514 63 HOH HOH . 
N 4 HOH C 15 515 72 HOH HOH . 
N 4 HOH C 16 516 77 HOH HOH . 
N 4 HOH C 17 517 80 HOH HOH . 
N 4 HOH C 18 518 84 HOH HOH . 
N 4 HOH C 19 519 89 HOH HOH . 
N 4 HOH C 20 520 93 HOH HOH . 
N 4 HOH C 21 521 105 HOH HOH . 
N 4 HOH C 22 522 108 HOH HOH . 
N 4 HOH C 23 523 121 HOH HOH . 
N 4 HOH C 24 524 132 HOH HOH . 
N 4 HOH C 25 525 135 HOH HOH . 
N 4 HOH C 26 526 143 HOH HOH . 
N 4 HOH C 27 527 147 HOH HOH . 
N 4 HOH C 28 528 149 HOH HOH . 
N 4 HOH C 29 529 151 HOH HOH . 
N 4 HOH C 30 530 153 HOH HOH . 
N 4 HOH C 31 531 156 HOH HOH . 
N 4 HOH C 32 532 174 HOH HOH . 
N 4 HOH C 33 533 175 HOH HOH . 
N 4 HOH C 34 534 178 HOH HOH . 
N 4 HOH C 35 535 187 HOH HOH . 
N 4 HOH C 36 536 188 HOH HOH . 
N 4 HOH C 37 537 193 HOH HOH . 
N 4 HOH C 38 538 203 HOH HOH . 
N 4 HOH C 39 539 204 HOH HOH . 
N 4 HOH C 40 540 207 HOH HOH . 
N 4 HOH C 41 541 212 HOH HOH . 
N 4 HOH C 42 542 214 HOH HOH . 
N 4 HOH C 43 543 219 HOH HOH . 
N 4 HOH C 44 544 223 HOH HOH . 
N 4 HOH C 45 545 225 HOH HOH . 
N 4 HOH C 46 546 227 HOH HOH . 
N 4 HOH C 47 547 228 HOH HOH . 
N 4 HOH C 48 548 229 HOH HOH . 
N 4 HOH C 49 549 238 HOH HOH . 
N 4 HOH C 50 550 241 HOH HOH . 
N 4 HOH C 51 551 1 HOH HOH . 
N 4 HOH C 52 552 2 HOH HOH . 
N 4 HOH C 53 553 4 HOH HOH . 
N 4 HOH C 54 554 8 HOH HOH . 
O 4 HOH D 1 501 2 HOH HOH . 
O 4 HOH D 2 502 5 HOH HOH . 
O 4 HOH D 3 503 27 HOH HOH . 
O 4 HOH D 4 504 29 HOH HOH . 
O 4 HOH D 5 505 34 HOH HOH . 
O 4 HOH D 6 506 38 HOH HOH . 
O 4 HOH D 7 507 41 HOH HOH . 
O 4 HOH D 8 508 42 HOH HOH . 
O 4 HOH D 9 509 44 HOH HOH . 
O 4 HOH D 10 510 45 HOH HOH . 
O 4 HOH D 11 511 48 HOH HOH . 
O 4 HOH D 12 512 49 HOH HOH . 
O 4 HOH D 13 513 50 HOH HOH . 
O 4 HOH D 14 514 51 HOH HOH . 
O 4 HOH D 15 515 54 HOH HOH . 
O 4 HOH D 16 516 59 HOH HOH . 
O 4 HOH D 17 517 64 HOH HOH . 
O 4 HOH D 18 518 67 HOH HOH . 
O 4 HOH D 19 519 69 HOH HOH . 
O 4 HOH D 20 520 70 HOH HOH . 
O 4 HOH D 21 521 71 HOH HOH . 
O 4 HOH D 22 522 74 HOH HOH . 
O 4 HOH D 23 523 76 HOH HOH . 
O 4 HOH D 24 524 85 HOH HOH . 
O 4 HOH D 25 525 88 HOH HOH . 
O 4 HOH D 26 526 91 HOH HOH . 
O 4 HOH D 27 527 97 HOH HOH . 
O 4 HOH D 28 528 98 HOH HOH . 
O 4 HOH D 29 529 100 HOH HOH . 
O 4 HOH D 30 530 101 HOH HOH . 
O 4 HOH D 31 531 102 HOH HOH . 
O 4 HOH D 32 532 106 HOH HOH . 
O 4 HOH D 33 533 110 HOH HOH . 
O 4 HOH D 34 534 112 HOH HOH . 
O 4 HOH D 35 535 113 HOH HOH . 
O 4 HOH D 36 536 119 HOH HOH . 
O 4 HOH D 37 537 122 HOH HOH . 
O 4 HOH D 38 538 123 HOH HOH . 
O 4 HOH D 39 539 125 HOH HOH . 
O 4 HOH D 40 540 126 HOH HOH . 
O 4 HOH D 41 541 137 HOH HOH . 
O 4 HOH D 42 542 139 HOH HOH . 
O 4 HOH D 43 543 141 HOH HOH . 
O 4 HOH D 44 544 148 HOH HOH . 
O 4 HOH D 45 545 150 HOH HOH . 
O 4 HOH D 46 546 152 HOH HOH . 
O 4 HOH D 47 547 154 HOH HOH . 
O 4 HOH D 48 548 155 HOH HOH . 
O 4 HOH D 49 549 157 HOH HOH . 
O 4 HOH D 50 550 165 HOH HOH . 
O 4 HOH D 51 551 169 HOH HOH . 
O 4 HOH D 52 552 173 HOH HOH . 
O 4 HOH D 53 553 177 HOH HOH . 
O 4 HOH D 54 554 180 HOH HOH . 
O 4 HOH D 55 555 183 HOH HOH . 
O 4 HOH D 56 556 194 HOH HOH . 
O 4 HOH D 57 557 201 HOH HOH . 
O 4 HOH D 58 558 209 HOH HOH . 
O 4 HOH D 59 559 211 HOH HOH . 
O 4 HOH D 60 560 213 HOH HOH . 
O 4 HOH D 61 561 216 HOH HOH . 
O 4 HOH D 62 562 217 HOH HOH . 
O 4 HOH D 63 563 224 HOH HOH . 
O 4 HOH D 64 564 226 HOH HOH . 
O 4 HOH D 65 565 233 HOH HOH . 
O 4 HOH D 66 566 236 HOH HOH . 
O 4 HOH D 67 567 240 HOH HOH . 
O 4 HOH D 68 568 242 HOH HOH . 
O 4 HOH D 69 569 243 HOH HOH . 
O 4 HOH D 70 570 244 HOH HOH . 
O 4 HOH D 71 571 5 HOH HOH . 
O 4 HOH D 72 572 6 HOH HOH . 
O 4 HOH D 73 573 7 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 . . . G 2 24.21 57.943 32.51 1 20.67 ? C1 BEN 401 B 1 
HETATM 2 C C2 BEN . . . G 2 23.054 58.432 33.112 1 20.91 ? C2 BEN 401 B 1 
HETATM 3 C C3 BEN . . . G 2 21.885 58.531 32.376 1 21.55 ? C3 BEN 401 B 1 
HETATM 4 C C4 BEN . . . G 2 21.852 58.161 31.032 1 21.61 ? C4 BEN 401 B 1 
HETATM 5 C C5 BEN . . . G 2 22.993 57.681 30.427 1 20.05 ? C5 BEN 401 B 1 
HETATM 6 C C6 BEN . . . G 2 24.168 57.584 31.161 1 20.38 ? C6 BEN 401 B 1 
HETATM 7 C C BEN . . . G 2 25.409 57.841 33.253 1 20.06 ? C BEN 401 B 1 
HETATM 8 N N1 BEN . . . G 2 25.601 58.596 34.309 1 19.7 ? N1 BEN 401 B 1 
HETATM 9 N N2 BEN . . . G 2 26.388 57.013 32.924 1 19.04 ? N2 BEN 401 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           259 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           9 
#