data_1VRO
#
_model_server_result.job_id            -8cxjNCeXDApTSvOcRO5zA 
_model_server_result.datetime_utc      '2024-10-19 22:37:02' 
_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          1vro 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":201}' 
#
_entry.id    1VRO 
#
_exptl.entry_id    1VRO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              202.34 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            SPERMINE 
_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            1VRO 
_cell.length_a            17.778 
_cell.length_b            31.348 
_cell.length_c            44.116 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1VRO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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                             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
covale ? covale1 A O3' DC 1 A DC 1 1_555 A P GMS 2 A GMS 2 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.599 ? 
covale ? covale2 A O3' DC 1 A DC 1 1_555 A P GMS 2 A GMS 2 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.587 ? 
covale ? covale3 A O3' GMS 2 A GMS 2 1_555 A P DC 3 A DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? 
covale ? covale4 B O3' DC 1 B DC 107 1_555 B P GMS 2 B GMS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.586 ? 
covale ? covale5 B O3' GMS 2 B GMS 108 1_555 B P DC 3 B DC 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.637 ? 
metalc ? metalc1 B N7 DG 6 B DG 112 1_555 D MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? 
metalc ? metalc2 D MG MG . B MG 301 1_555 F O HOH . B HOH 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? 
metalc ? metalc3 D MG MG . B MG 301 1_555 F O HOH . B HOH 420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc4 D MG MG . B MG 301 1_555 F O HOH . B HOH 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc5 D MG MG . B MG 301 1_555 F O HOH . B HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
metalc ? metalc6 D MG MG . B MG 301 1_555 F O HOH . B HOH 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? 
hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 6 B DG 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 6 B DG 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 6 B DG 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N1 GMS 2 A GMS 2 1_555 B N3 DC 5 B DC 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N2 GMS 2 A GMS 2 1_555 B O2 DC 5 B DC 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O6 GMS 2 A GMS 2 1_555 B N4 DC 5 B DC 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 4 B DG 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 4 B DG 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 4 B DG 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 3 B DC 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 3 B DC 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 3 B DC 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A N3 DC 5 A DC 5 1_555 B N1 GMS 2 B GMS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N4 DC 5 A DC 5 1_555 B O6 GMS 2 B GMS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A O2 DC 5 A DC 5 1_555 B N2 GMS 2 B GMS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A N1 DG 6 A DG 6 1_555 B N3 DC 1 B DC 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N2 DG 6 A DG 6 1_555 B O2 DC 1 B DC 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A O6 DG 6 A DG 6 1_555 B N4 DC 1 B DC 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'C10 H26 N4' 
_chem_comp.formula_weight    202.34 
_chem_comp.id                SPM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              SPERMINE 
_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
N1 C2 SPM sing 116 n n 
N1 HN11 SPM sing 117 n n 
N1 HN12 SPM sing 118 n n 
C2 C3 SPM sing 119 n n 
C2 H21 SPM sing 120 n n 
C2 H22 SPM sing 121 n n 
C3 C4 SPM sing 122 n n 
C3 H31 SPM sing 123 n n 
C3 H32 SPM sing 124 n n 
C4 N5 SPM sing 125 n n 
C4 H41 SPM sing 126 n n 
C4 H42 SPM sing 127 n n 
N5 C6 SPM sing 128 n n 
N5 HN5 SPM sing 129 n n 
C6 C7 SPM sing 130 n n 
C6 H61 SPM sing 131 n n 
C6 H62 SPM sing 132 n n 
C7 C8 SPM sing 133 n n 
C7 H71 SPM sing 134 n n 
C7 H72 SPM sing 135 n n 
C8 C9 SPM sing 136 n n 
C8 H81 SPM sing 137 n n 
C8 H82 SPM sing 138 n n 
C9 N10 SPM sing 139 n n 
C9 H91 SPM sing 140 n n 
C9 H92 SPM sing 141 n n 
N10 C11 SPM sing 142 n n 
N10 HN0 SPM sing 143 n n 
C11 C12 SPM sing 144 n n 
C11 H111 SPM sing 145 n n 
C11 H112 SPM sing 146 n n 
C12 C13 SPM sing 147 n n 
C12 H121 SPM sing 148 n n 
C12 H122 SPM sing 149 n n 
C13 N14 SPM sing 150 n n 
C13 H131 SPM sing 151 n n 
C13 H132 SPM sing 152 n n 
N14 HN41 SPM sing 153 n n 
N14 HN42 SPM sing 154 n n 
#
_atom_sites.entry_id                     1VRO 
_atom_sites.fract_transf_matrix[1][1]    0.056249 
_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]    0.0319 
_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]    0.022668 
_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 SPM A 1 201 201 SPM SPM . 
D 3 MG B 1 301 301 MG MG . 
E 4 HOH A 1 401 401 HOH HOH . 
E 4 HOH A 2 402 402 HOH HOH . 
E 4 HOH A 3 405 405 HOH HOH . 
E 4 HOH A 4 406 406 HOH HOH . 
E 4 HOH A 5 407 407 HOH HOH . 
E 4 HOH A 6 408 408 HOH HOH . 
E 4 HOH A 7 410 410 HOH HOH . 
E 4 HOH A 8 411 411 HOH HOH . 
E 4 HOH A 9 415 415 HOH HOH . 
E 4 HOH A 10 416 416 HOH HOH . 
E 4 HOH A 11 417 417 HOH HOH . 
E 4 HOH A 12 419 419 HOH HOH . 
E 4 HOH A 13 424 424 HOH HOH . 
E 4 HOH A 14 426 426 HOH HOH . 
E 4 HOH A 15 430 430 HOH HOH . 
E 4 HOH A 16 432 432 HOH HOH . 
E 4 HOH A 17 433 433 HOH HOH . 
E 4 HOH A 18 436 436 HOH HOH . 
E 4 HOH A 19 438 438 HOH HOH . 
E 4 HOH A 20 441 441 HOH HOH . 
E 4 HOH A 21 442 442 HOH HOH . 
E 4 HOH A 22 443 443 HOH HOH . 
E 4 HOH A 23 446 446 HOH HOH . 
E 4 HOH A 24 447 447 HOH HOH . 
E 4 HOH A 25 450 450 HOH HOH . 
E 4 HOH A 26 451 451 HOH HOH . 
E 4 HOH A 27 453 453 HOH HOH . 
E 4 HOH A 28 454 454 HOH HOH . 
E 4 HOH A 29 455 455 HOH HOH . 
E 4 HOH A 30 457 457 HOH HOH . 
E 4 HOH A 31 458 458 HOH HOH . 
E 4 HOH A 32 459 459 HOH HOH . 
E 4 HOH A 33 460 460 HOH HOH . 
E 4 HOH A 34 461 461 HOH HOH . 
E 4 HOH A 35 463 463 HOH HOH . 
E 4 HOH A 36 464 464 HOH HOH . 
E 4 HOH A 37 469 469 HOH HOH . 
F 4 HOH B 1 403 403 HOH HOH . 
F 4 HOH B 2 404 404 HOH HOH . 
F 4 HOH B 3 409 409 HOH HOH . 
F 4 HOH B 4 412 412 HOH HOH . 
F 4 HOH B 5 413 413 HOH HOH . 
F 4 HOH B 6 414 414 HOH HOH . 
F 4 HOH B 7 418 418 HOH HOH . 
F 4 HOH B 8 420 420 HOH HOH . 
F 4 HOH B 9 421 421 HOH HOH . 
F 4 HOH B 10 422 422 HOH HOH . 
F 4 HOH B 11 423 423 HOH HOH . 
F 4 HOH B 12 425 425 HOH HOH . 
F 4 HOH B 13 427 427 HOH HOH . 
F 4 HOH B 14 428 428 HOH HOH . 
F 4 HOH B 15 429 429 HOH HOH . 
F 4 HOH B 16 431 431 HOH HOH . 
F 4 HOH B 17 434 434 HOH HOH . 
F 4 HOH B 18 435 435 HOH HOH . 
F 4 HOH B 19 437 437 HOH HOH . 
F 4 HOH B 20 439 439 HOH HOH . 
F 4 HOH B 21 440 440 HOH HOH . 
F 4 HOH B 22 444 444 HOH HOH . 
F 4 HOH B 23 445 445 HOH HOH . 
F 4 HOH B 24 448 448 HOH HOH . 
F 4 HOH B 25 449 449 HOH HOH . 
F 4 HOH B 26 452 452 HOH HOH . 
F 4 HOH B 27 456 456 HOH HOH . 
F 4 HOH B 28 462 462 HOH HOH . 
F 4 HOH B 29 465 465 HOH HOH . 
F 4 HOH B 30 466 466 HOH HOH . 
F 4 HOH B 31 467 467 HOH HOH . 
F 4 HOH B 32 468 468 HOH HOH . 
F 4 HOH B 33 470 470 HOH HOH . 
F 4 HOH B 34 471 471 HOH HOH . 
F 4 HOH B 35 472 472 HOH HOH . 
F 4 HOH B 36 473 473 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 N N1 SPM . . . C 2 -10.585 7.762 33.689 1 7.54 ? N1 SPM 201 A 1 
HETATM 2 C C2 SPM . . . C 2 -9.951 8.572 34.789 1 8.77 ? C2 SPM 201 A 1 
HETATM 3 C C3 SPM . . . C 2 -8.551 8.094 35.04 1 9.25 ? C3 SPM 201 A 1 
HETATM 4 C C4 SPM . . . C 2 -7.758 8.926 36.041 1 10.33 ? C4 SPM 201 A 1 
HETATM 5 N N5 SPM . . . C 2 -7.215 10.191 35.495 1 8.73 ? N5 SPM 201 A 1 
HETATM 6 C C6 SPM . . . C 2 -6.266 10.887 36.41 1 10.78 ? C6 SPM 201 A 1 
HETATM 7 C C7 SPM . . . C 2 -5.925 12.267 36.115 1 15.43 ? C7 SPM 201 A 1 
HETATM 8 C C8 SPM . . . C 2 -5.309 12.478 34.77 1 12.81 ? C8 SPM 201 A 1 
HETATM 9 C C9 SPM . . . C 2 -5.05 13.97 34.541 1 15.12 ? C9 SPM 201 A 1 
HETATM 10 N N10 SPM . . . C 2 -4.718 14.125 33.109 1 10.62 ? N10 SPM 201 A 1 
HETATM 11 C C11 SPM . . . C 2 -4.524 15.533 32.625 1 12.32 ? C11 SPM 201 A 1 
HETATM 12 C C12 SPM . . . C 2 -4.251 15.525 31.11 1 14.83 ? C12 SPM 201 A 1 
HETATM 13 C C13 SPM . . . C 2 -4.492 16.846 30.421 1 20.36 ? C13 SPM 201 A 1 
HETATM 14 N N14 SPM . . . C 2 -3.489 17.824 30.915 1 22.99 ? N14 SPM 201 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#