data_2B0Q
#
_model_server_result.job_id            Hq15NBGPoIUo9ZRQ9IAcjg 
_model_server_result.datetime_utc      '2025-01-24 23:17:23' 
_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          2b0q 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":305}' 
#
_entry.id    2B0Q 
#
_exptl.entry_id    2B0Q 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              614.644 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            NEOMYCIN 
_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            2B0Q 
_cell.length_a            46.357 
_cell.length_b            46.357 
_cell.length_c            301.613 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2B0Q 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        95 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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                      2 
_struct_asym.id                             B 
_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
metalc ? metalc1 A OG SER 193 A SER 194 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.777 ? 
metalc ? metalc2 A OD1 ASN 194 A ASN 195 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc3 A OD2 ASP 207 A ASP 208 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? 
metalc ? metalc4 A OD1 ASP 207 A ASP 208 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? 
metalc ? metalc5 E O3B ADP . A ADP 300 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? 
metalc ? metalc6 E O2A ADP . A ADP 300 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? 
metalc ? metalc7 E O1B ADP . A ADP 300 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc8 C MG MG . A MG 301 1_555 F O HOH . A HOH 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc9 D MG MG . A MG 302 1_555 F O HOH . A HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
#
_chem_comp.formula           'C23 H46 N6 O13' 
_chem_comp.formula_weight    614.644 
_chem_comp.id                NMY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              NEOMYCIN 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     MYCIFRADIN;NEOMAS;PIMAVECORT;VONAMYCIN 
#
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 O5 NMY sing 281 n n 
C1 O1 NMY sing 282 n n 
C1 C2 NMY sing 283 n n 
C1 H1 NMY sing 284 n n 
O1 C10 NMY sing 285 n n 
C2 N2 NMY sing 286 n n 
C2 C3 NMY sing 287 n n 
C2 H2 NMY sing 288 n n 
N2 HN21 NMY sing 289 n n 
N2 HN22 NMY sing 290 n n 
C3 C4 NMY sing 291 n n 
C3 O3 NMY sing 292 n n 
C3 H3 NMY sing 293 n n 
O3 HO3 NMY sing 294 n n 
C4 C5 NMY sing 295 n n 
C4 O4 NMY sing 296 n n 
C4 H4 NMY sing 297 n n 
O4 HO4 NMY sing 298 n n 
C5 O5 NMY sing 299 n n 
C5 C6 NMY sing 300 n n 
C5 H5 NMY sing 301 n n 
C6 N6 NMY sing 302 n n 
C6 H61 NMY sing 303 n n 
C6 H62 NMY sing 304 n n 
C7 N7 NMY sing 305 n n 
C7 C12 NMY sing 306 n n 
C7 C8 NMY sing 307 n n 
C7 H7 NMY sing 308 n n 
N7 H71 NMY sing 309 n n 
N7 H72 NMY sing 310 n n 
C12 O12 NMY sing 311 n n 
C12 C11 NMY sing 312 n n 
C12 H12 NMY sing 313 n n 
C11 O11 NMY sing 314 n n 
C11 C10 NMY sing 315 n n 
C11 H11 NMY sing 316 n n 
O11 C13 NMY sing 317 n n 
C10 C9 NMY sing 318 n n 
C10 H10 NMY sing 319 n n 
C9 C8 NMY sing 320 n n 
C9 N9 NMY sing 321 n n 
C9 H9 NMY sing 322 n n 
N9 H91 NMY sing 323 n n 
N9 H92 NMY sing 324 n n 
C8 H81 NMY sing 325 n n 
C8 H82 NMY sing 326 n n 
C13 C14 NMY sing 327 n n 
C13 O16 NMY sing 328 n n 
C13 H13 NMY sing 329 n n 
C14 O14 NMY sing 330 n n 
C14 C15 NMY sing 331 n n 
C14 H14 NMY sing 332 n n 
C15 O18 NMY sing 333 n n 
C15 C16 NMY sing 334 n n 
C15 H15 NMY sing 335 n n 
C16 O16 NMY sing 336 n n 
C16 C17 NMY sing 337 n n 
C16 H16 NMY sing 338 n n 
C17 O17 NMY sing 339 n n 
C17 H171 NMY sing 340 n n 
C17 H172 NMY sing 341 n n 
C21 C20 NMY sing 342 n n 
C21 C22 NMY sing 343 n n 
C21 O21 NMY sing 344 n n 
C21 H21 NMY sing 345 n n 
C20 C19 NMY sing 346 n n 
C20 O20 NMY sing 347 n n 
C20 H20 NMY sing 348 n n 
C19 N23 NMY sing 349 n n 
C19 C18 NMY sing 350 n n 
C19 H19 NMY sing 351 n n 
C18 O22 NMY sing 352 n n 
C18 O18 NMY sing 353 n n 
C18 H18 NMY sing 354 n n 
C22 O22 NMY sing 355 n n 
C22 C23 NMY sing 356 n n 
C22 H22 NMY sing 357 n n 
C23 N19 NMY sing 358 n n 
C23 H231 NMY sing 359 n n 
C23 H232 NMY sing 360 n n 
N6 HN61 NMY sing 361 n n 
N6 HN62 NMY sing 362 n n 
O14 HO41 NMY sing 363 n n 
O20 HO22 NMY sing 364 n n 
O21 HO21 NMY sing 365 n n 
O17 H17 NMY sing 366 n n 
O12 HO12 NMY sing 367 n n 
N19 H191 NMY sing 368 n n 
N19 H192 NMY sing 369 n n 
N23 HN31 NMY sing 370 n n 
N23 HN32 NMY sing 371 n n 
#
_atom_sites.entry_id                     2B0Q 
_atom_sites.fract_transf_matrix[1][1]    0.021572 
_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]    0.021572 
_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]    0.003316 
_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 NMY A 1 305 305 NMY NMY . 
C 3 MG A 1 301 301 MG MG . 
D 3 MG A 1 302 302 MG MG . 
E 4 ADP A 1 300 300 ADP ADP . 
F 5 HOH A 1 501 501 HOH WAT . 
F 5 HOH A 2 502 502 HOH WAT . 
F 5 HOH A 3 503 503 HOH WAT . 
F 5 HOH A 4 504 504 HOH WAT . 
F 5 HOH A 5 505 505 HOH WAT . 
F 5 HOH A 6 506 506 HOH WAT . 
F 5 HOH A 7 507 507 HOH WAT . 
F 5 HOH A 8 508 508 HOH WAT . 
F 5 HOH A 9 509 509 HOH WAT . 
F 5 HOH A 10 510 510 HOH WAT . 
F 5 HOH A 11 511 511 HOH WAT . 
F 5 HOH A 12 512 512 HOH WAT . 
F 5 HOH A 13 513 513 HOH WAT . 
F 5 HOH A 14 514 514 HOH WAT . 
F 5 HOH A 15 515 515 HOH WAT . 
F 5 HOH A 16 516 516 HOH WAT . 
F 5 HOH A 17 517 517 HOH WAT . 
F 5 HOH A 18 518 518 HOH WAT . 
F 5 HOH A 19 519 519 HOH WAT . 
F 5 HOH A 20 520 520 HOH WAT . 
F 5 HOH A 21 521 521 HOH WAT . 
F 5 HOH A 22 522 522 HOH WAT . 
F 5 HOH A 23 523 523 HOH WAT . 
F 5 HOH A 24 524 524 HOH WAT . 
F 5 HOH A 25 525 525 HOH WAT . 
F 5 HOH A 26 526 526 HOH WAT . 
F 5 HOH A 27 527 527 HOH WAT . 
F 5 HOH A 28 528 528 HOH WAT . 
F 5 HOH A 29 529 529 HOH WAT . 
F 5 HOH A 30 530 530 HOH WAT . 
F 5 HOH A 31 531 531 HOH WAT . 
F 5 HOH A 32 532 532 HOH WAT . 
F 5 HOH A 33 533 533 HOH WAT . 
F 5 HOH A 34 534 534 HOH WAT . 
F 5 HOH A 35 535 535 HOH WAT . 
F 5 HOH A 36 536 536 HOH WAT . 
F 5 HOH A 37 537 537 HOH WAT . 
F 5 HOH A 38 538 538 HOH WAT . 
F 5 HOH A 39 539 539 HOH WAT . 
F 5 HOH A 40 540 540 HOH WAT . 
F 5 HOH A 41 541 541 HOH WAT . 
F 5 HOH A 42 542 542 HOH WAT . 
F 5 HOH A 43 543 543 HOH WAT . 
F 5 HOH A 44 544 544 HOH WAT . 
F 5 HOH A 45 545 545 HOH WAT . 
#
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 NMY . . . B 2 58.627 14.889 -276.215 1 52.19 ? C1 NMY 305 A 1 
HETATM 2 O O1 NMY . . . B 2 58.037 15.079 -277.51 1 52.51 ? O1 NMY 305 A 1 
HETATM 3 C C2 NMY . . . B 2 59.902 14.023 -276.312 1 52.28 ? C2 NMY 305 A 1 
HETATM 4 N N2 NMY . . . B 2 60.668 14.478 -277.511 1 53.29 ? N2 NMY 305 A 1 
HETATM 5 C C3 NMY . . . B 2 59.637 12.536 -276.544 1 51.55 ? C3 NMY 305 A 1 
HETATM 6 O O3 NMY . . . B 2 60.81 11.844 -276.16 1 53.88 ? O3 NMY 305 A 1 
HETATM 7 C C4 NMY . . . B 2 58.481 12.029 -275.699 1 51.18 ? C4 NMY 305 A 1 
HETATM 8 O O4 NMY . . . B 2 58.151 10.714 -276.145 1 48.34 ? O4 NMY 305 A 1 
HETATM 9 C C5 NMY . . . B 2 57.273 12.932 -275.9 1 51.05 ? C5 NMY 305 A 1 
HETATM 10 O O5 NMY . . . B 2 57.583 14.26 -275.445 1 50.5 ? O5 NMY 305 A 1 
HETATM 11 C C6 NMY . . . B 2 56.091 12.422 -275.086 1 49.52 ? C6 NMY 305 A 1 
HETATM 12 C C7 NMY . . . B 2 56.615 18.567 -279.362 1 50.66 ? C7 NMY 305 A 1 
HETATM 13 N N7 NMY . . . B 2 55.875 19.839 -279.587 1 45.64 ? N7 NMY 305 A 1 
HETATM 14 C C12 NMY . . . B 2 57.546 18.792 -278.175 1 54 ? C12 NMY 305 A 1 
HETATM 15 C C11 NMY . . . B 2 58.343 17.503 -277.901 1 57.93 ? C11 NMY 305 A 1 
HETATM 16 O O11 NMY . . . B 2 59.203 17.743 -276.782 1 68.71 ? O11 NMY 305 A 1 
HETATM 17 C C10 NMY . . . B 2 57.356 16.334 -277.558 1 53.64 ? C10 NMY 305 A 1 
HETATM 18 C C9 NMY . . . B 2 56.285 16.178 -278.668 1 50.78 ? C9 NMY 305 A 1 
HETATM 19 N N9 NMY . . . B 2 55.237 15.265 -278.129 1 48.68 ? N9 NMY 305 A 1 
HETATM 20 C C8 NMY . . . B 2 55.572 17.507 -278.995 1 49.71 ? C8 NMY 305 A 1 
HETATM 21 C C13 NMY . . . B 2 60.519 18.121 -277.25 1 76.71 ? C13 NMY 305 A 1 
HETATM 22 C C14 NMY . . . B 2 61.032 19.233 -276.374 1 80.32 ? C14 NMY 305 A 1 
HETATM 23 C C15 NMY . . . B 2 62.029 18.565 -275.464 1 82.85 ? C15 NMY 305 A 1 
HETATM 24 C C16 NMY . . . B 2 62.371 17.281 -276.174 1 81.96 ? C16 NMY 305 A 1 
HETATM 25 O O16 NMY . . . B 2 61.277 16.947 -277.022 1 78.85 ? O16 NMY 305 A 1 
HETATM 26 C C17 NMY . . . B 2 62.58 16.17 -275.178 1 82.52 ? C17 NMY 305 A 1 
HETATM 27 C C21 NMY . . . B 2 66.035 20.324 -273.513 1 93.75 ? C21 NMY 305 A 1 
HETATM 28 C C20 NMY . . . B 2 65.384 21.115 -274.622 1 92.97 ? C20 NMY 305 A 1 
HETATM 29 C C19 NMY . . . B 2 63.936 21.377 -274.249 1 91.57 ? C19 NMY 305 A 1 
HETATM 30 C C18 NMY . . . B 2 63.194 20.052 -274.114 1 90.58 ? C18 NMY 305 A 1 
HETATM 31 O O18 NMY . . . B 2 63.214 19.342 -275.357 1 87.5 ? O18 NMY 305 A 1 
HETATM 32 C C22 NMY . . . B 2 65.312 18.989 -273.242 1 93.27 ? C22 NMY 305 A 1 
HETATM 33 O O22 NMY . . . B 2 63.84 19.122 -273.185 1 92.51 ? O22 NMY 305 A 1 
HETATM 34 C C23 NMY . . . B 2 65.663 17.913 -274.257 1 93.12 ? C23 NMY 305 A 1 
HETATM 35 N N6 NMY . . . B 2 55.092 13.541 -275.151 1 51.28 ? N6 NMY 305 A 1 
HETATM 36 O O14 NMY . . . B 2 61.696 20.175 -277.211 1 79.8 ? O14 NMY 305 A 1 
HETATM 37 O O20 NMY . . . B 2 66.054 22.361 -274.736 1 94.15 ? O20 NMY 305 A 1 
HETATM 38 O O21 NMY . . . B 2 67.389 20.055 -273.892 1 94.1 ? O21 NMY 305 A 1 
HETATM 39 O O17 NMY . . . B 2 63.738 15.447 -275.588 1 83.57 ? O17 NMY 305 A 1 
HETATM 40 O O12 NMY . . . B 2 58.448 19.842 -278.514 1 54.83 ? O12 NMY 305 A 1 
HETATM 41 N N19 NMY . . . B 2 65.389 16.64 -273.516 1 93.43 ? N19 NMY 305 A 1 
HETATM 42 N N23 NMY . . . B 2 63.32 22.098 -275.402 1 91.54 ? N23 NMY 305 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           42 
#