data_2NLM
#
_model_server_result.job_id            Kvy1fi9KLrXhCa106-m-vA 
_model_server_result.datetime_utc      '2025-03-04 23:08:32' 
_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          2nlm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":25}' 
#
_entry.id    2NLM 
#
_exptl.entry_id    2NLM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              354.408 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2-{4'-[AMINO(IMINO)METHYL]BIPHENYL-3-YL}-1H-BENZIMIDAZOLE-6-CARBOXIMIDAMIDE" 
_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            2NLM 
_cell.length_a            24.726 
_cell.length_b            40.065 
_cell.length_c            65.556 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2NLM 
_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                      3 
_struct_asym.id                             D 
_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 C MG MG . A MG 26 1_555 E O HOH . A HOH 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc2 C MG MG . A MG 26 1_555 E O HOH . A HOH 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
metalc ? metalc3 C MG MG . A MG 26 1_555 E O HOH . A HOH 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
metalc ? metalc4 C MG MG . A MG 26 1_555 F O HOH . B HOH 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc5 C MG MG . A MG 26 1_555 F O HOH . B HOH 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc6 C MG MG . A MG 26 1_555 F O HOH . B HOH 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A N1 DA 5 A DA 5 1_555 B N3 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N6 DA 5 A DA 5 1_555 B O4 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A N1 DA 6 A DA 6 1_555 B N3 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A N6 DA 6 A DA 6 1_555 B O4 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N3 DT 7 A DT 7 1_555 B N1 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A O4 DT 7 A DT 7 1_555 B N6 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog19 A N3 DT 8 A DT 8 1_555 B N1 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog20 A O4 DT 8 A DT 8 1_555 B N6 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog21 A N3 DC 9 A DC 9 1_555 B N1 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog22 A N4 DC 9 A DC 9 1_555 B O6 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog23 A O2 DC 9 A DC 9 1_555 B N2 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog24 A N1 DG 10 A DG 10 1_555 B N3 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog25 A N2 DG 10 A DG 10 1_555 B O2 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog26 A O6 DG 10 A DG 10 1_555 B N4 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog27 A N3 DC 11 A DC 11 1_555 B N1 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog28 A N4 DC 11 A DC 11 1_555 B O6 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog29 A O2 DC 11 A DC 11 1_555 B N2 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog30 A N1 DG 12 A DG 12 1_555 B N3 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog31 A N2 DG 12 A DG 12 1_555 B O2 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog32 A O6 DG 12 A DG 12 1_555 B N4 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'C21 H18 N6' 
_chem_comp.formula_weight    354.408 
_chem_comp.id                DB9 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2-{4'-[AMINO(IMINO)METHYL]BIPHENYL-3-YL}-1H-BENZIMIDAZOLE-6-CARBOXIMIDAMIDE" 
_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 DB9 doub 39 n y 
C1 C6 DB9 sing 40 n y 
C1 H1 DB9 sing 41 n n 
C2 C13 DB9 sing 42 n n 
C2 C3 DB9 sing 43 n y 
C3 C4 DB9 doub 44 n y 
C3 H3 DB9 sing 45 n n 
C4 C5 DB9 sing 46 n y 
C4 H4 DB9 sing 47 n n 
C5 C6 DB9 doub 48 n y 
C5 C7 DB9 sing 49 n y 
C6 H6 DB9 sing 50 n n 
C7 C8 DB9 doub 51 n y 
C7 C12 DB9 sing 52 n y 
C8 C9 DB9 sing 53 n y 
C8 H8 DB9 sing 54 n n 
C9 C10 DB9 doub 55 n y 
C9 H9 DB9 sing 56 n n 
C10 C11 DB9 sing 57 n y 
C10 H10 DB9 sing 58 n n 
C11 C12 DB9 doub 59 n y 
C11 C16 DB9 sing 60 n y 
C12 H12 DB9 sing 61 n n 
C13 N14 DB9 sing 62 n n 
C13 N15 DB9 doub 63 e n 
N14 H141 DB9 sing 64 n n 
N14 H142 DB9 sing 65 n n 
N15 HN15 DB9 sing 66 n n 
C16 N17 DB9 sing 67 n y 
C16 N20 DB9 doub 68 n y 
N17 C18 DB9 sing 69 n y 
N17 HN17 DB9 sing 70 n n 
C18 C19 DB9 doub 71 n y 
C18 C24 DB9 sing 72 n y 
C19 N20 DB9 sing 73 n y 
C19 C21 DB9 sing 74 n y 
C21 C22 DB9 doub 75 n y 
C21 H21 DB9 sing 76 n n 
C22 C23 DB9 sing 77 n y 
C22 H22 DB9 sing 78 n n 
C23 C24 DB9 doub 79 n y 
C23 C25 DB9 sing 80 n n 
C24 H24 DB9 sing 81 n n 
C25 N26 DB9 sing 82 n n 
C25 N27 DB9 doub 83 e n 
N26 H261 DB9 sing 84 n n 
N26 H262 DB9 sing 85 n n 
N27 HN27 DB9 sing 86 n n 
#
_atom_sites.entry_id                     2NLM 
_atom_sites.fract_transf_matrix[1][1]    0.040443 
_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]    0.024959 
_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]    0.015254 
_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 MG A 1 26 26 MG MG . 
D 3 DB9 B 1 25 25 DB9 DB9 . 
E 4 HOH A 1 27 27 HOH HOH . 
E 4 HOH A 2 28 29 HOH HOH . 
E 4 HOH A 3 29 31 HOH HOH . 
E 4 HOH A 4 30 32 HOH HOH . 
E 4 HOH A 5 31 33 HOH HOH . 
E 4 HOH A 6 32 34 HOH HOH . 
E 4 HOH A 7 33 35 HOH HOH . 
E 4 HOH A 8 34 36 HOH HOH . 
E 4 HOH A 9 35 37 HOH HOH . 
E 4 HOH A 10 36 38 HOH HOH . 
E 4 HOH A 11 37 39 HOH HOH . 
E 4 HOH A 12 38 41 HOH HOH . 
E 4 HOH A 13 39 42 HOH HOH . 
E 4 HOH A 14 40 44 HOH HOH . 
E 4 HOH A 15 41 49 HOH HOH . 
E 4 HOH A 16 42 55 HOH HOH . 
E 4 HOH A 17 43 58 HOH HOH . 
E 4 HOH A 18 44 60 HOH HOH . 
E 4 HOH A 19 45 61 HOH HOH . 
E 4 HOH A 20 46 62 HOH HOH . 
E 4 HOH A 21 47 63 HOH HOH . 
E 4 HOH A 22 48 64 HOH HOH . 
E 4 HOH A 23 49 65 HOH HOH . 
E 4 HOH A 24 50 67 HOH HOH . 
E 4 HOH A 25 51 68 HOH HOH . 
E 4 HOH A 26 52 71 HOH HOH . 
F 4 HOH B 1 26 28 HOH HOH . 
F 4 HOH B 2 27 30 HOH HOH . 
F 4 HOH B 3 28 40 HOH HOH . 
F 4 HOH B 4 29 43 HOH HOH . 
F 4 HOH B 5 30 45 HOH HOH . 
F 4 HOH B 6 31 46 HOH HOH . 
F 4 HOH B 7 32 47 HOH HOH . 
F 4 HOH B 8 33 48 HOH HOH . 
F 4 HOH B 9 34 50 HOH HOH . 
F 4 HOH B 10 35 51 HOH HOH . 
F 4 HOH B 11 36 52 HOH HOH . 
F 4 HOH B 12 37 53 HOH HOH . 
F 4 HOH B 13 38 54 HOH HOH . 
F 4 HOH B 14 39 56 HOH HOH . 
F 4 HOH B 15 40 57 HOH HOH . 
F 4 HOH B 16 41 59 HOH HOH . 
F 4 HOH B 17 42 66 HOH HOH . 
F 4 HOH B 18 43 69 HOH HOH . 
F 4 HOH B 19 44 70 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 DB9 . . . D 3 9.687 25.874 5.4 1 53.8 ? C1 DB9 25 B 1 
HETATM 2 C C2 DB9 . . . D 3 10.659 24.908 5.181 1 54.32 ? C2 DB9 25 B 1 
HETATM 3 C C3 DB9 . . . D 3 10.537 23.661 5.775 1 54.35 ? C3 DB9 25 B 1 
HETATM 4 C C4 DB9 . . . D 3 9.442 23.377 6.59 1 56.38 ? C4 DB9 25 B 1 
HETATM 5 C C5 DB9 . . . D 3 8.465 24.341 6.814 1 56.32 ? C5 DB9 25 B 1 
HETATM 6 C C6 DB9 . . . D 3 8.589 25.586 6.219 1 58.05 ? C6 DB9 25 B 1 
HETATM 7 C C7 DB9 . . . D 3 7.338 24.014 7.665 1 50.1 ? C7 DB9 25 B 1 
HETATM 8 C C8 DB9 . . . D 3 6.092 24.584 7.454 1 56.99 ? C8 DB9 25 B 1 
HETATM 9 C C9 DB9 . . . D 3 5.018 24.259 8.279 1 59.28 ? C9 DB9 25 B 1 
HETATM 10 C C10 DB9 . . . D 3 5.195 23.355 9.322 1 61.06 ? C10 DB9 25 B 1 
HETATM 11 C C11 DB9 . . . D 3 6.44 22.773 9.548 1 54.75 ? C11 DB9 25 B 1 
HETATM 12 C C12 DB9 . . . D 3 7.502 23.111 8.709 1 52.28 ? C12 DB9 25 B 1 
HETATM 13 C C13 DB9 . . . D 3 11.804 25.176 4.34 1 58.22 ? C13 DB9 25 B 1 
HETATM 14 N N14 DB9 . . . D 3 11.915 26.349 3.683 1 58.55 ? N14 DB9 25 B 1 
HETATM 15 N N15 DB9 . . . D 3 12.759 24.23 4.207 1 66.64 ? N15 DB9 25 B 1 
HETATM 16 C C16 DB9 . . . D 3 6.636 21.827 10.634 1 46.18 ? C16 DB9 25 B 1 
HETATM 17 N N17 DB9 . . . D 3 7.845 21.343 11.049 1 45.36 ? N17 DB9 25 B 1 
HETATM 18 C C18 DB9 . . . D 3 7.617 20.485 12.085 1 43.37 ? C18 DB9 25 B 1 
HETATM 19 C C19 DB9 . . . D 3 6.239 20.468 12.277 1 47.23 ? C19 DB9 25 B 1 
HETATM 20 N N20 DB9 . . . D 3 5.684 21.305 11.366 1 49.58 ? N20 DB9 25 B 1 
HETATM 21 C C21 DB9 . . . D 3 5.69 19.677 13.275 1 44.18 ? C21 DB9 25 B 1 
HETATM 22 C C22 DB9 . . . D 3 6.525 18.903 14.077 1 42.16 ? C22 DB9 25 B 1 
HETATM 23 C C23 DB9 . . . D 3 7.902 18.922 13.881 1 47.31 ? C23 DB9 25 B 1 
HETATM 24 C C24 DB9 . . . D 3 8.451 19.717 12.881 1 44.52 ? C24 DB9 25 B 1 
HETATM 25 C C25 DB9 . . . D 3 8.767 18.117 14.719 1 46.57 ? C25 DB9 25 B 1 
HETATM 26 N N26 DB9 . . . D 3 10.101 18.294 14.643 1 41.94 ? N26 DB9 25 B 1 
HETATM 27 N N27 DB9 . . . D 3 8.242 17.218 15.578 1 30.77 ? N27 DB9 25 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           27 
#