data_5YJ8
#
_model_server_result.job_id            PhVplzuqMqRP5XJDeycDtg 
_model_server_result.datetime_utc      '2025-02-05 04:43:27' 
_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          5yj8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":701}' 
#
_entry.id    5YJ8 
#
_exptl.entry_id    5YJ8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              191.23 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-(aminomethyl)-1,3-dimethyl-benzimidazol-2-one 
_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         120 
_cell.entry_id            5YJ8 
_cell.length_a            50.974 
_cell.length_b            50.974 
_cell.length_c            42.087 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YJ8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
_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 
_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 
#
_chem_comp.formula           'C10 H13 N3 O' 
_chem_comp.formula_weight    191.23 
_chem_comp.id                8W9 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-(aminomethyl)-1,3-dimethyl-benzimidazol-2-one 
_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
C12 C6 8W9 doub 1 n y 
C12 C11 8W9 sing 2 n y 
C6 C5 8W9 sing 3 n y 
C15 C11 8W9 sing 4 n n 
C15 N14 8W9 sing 5 n n 
C10 N3 8W9 sing 6 n n 
C11 C8 8W9 doub 7 n y 
C5 N3 8W9 sing 8 n n 
C5 C4 8W9 doub 9 n y 
N3 C1 8W9 sing 10 n n 
C8 C4 8W9 sing 11 n y 
C4 N2 8W9 sing 12 n n 
C1 N2 8W9 sing 13 n n 
C1 O7 8W9 doub 14 n n 
N2 C9 8W9 sing 15 n n 
C6 H1 8W9 sing 16 n n 
C8 H2 8W9 sing 17 n n 
C9 H3 8W9 sing 18 n n 
C9 H4 8W9 sing 19 n n 
C9 H5 8W9 sing 20 n n 
C10 H6 8W9 sing 21 n n 
C10 H7 8W9 sing 22 n n 
C10 H8 8W9 sing 23 n n 
C12 H9 8W9 sing 24 n n 
C15 H10 8W9 sing 25 n n 
C15 H11 8W9 sing 26 n n 
N14 H12 8W9 sing 27 n n 
N14 H13 8W9 sing 28 n n 
#
_atom_sites.entry_id                     5YJ8 
_atom_sites.fract_transf_matrix[1][1]    0.019618 
_atom_sites.fract_transf_matrix[1][2]    0.011326 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022653 
_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]    0.02376 
_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 8W9 A 1 701 1 8W9 DRG . 
C 3 SO4 A 1 702 1 SO4 SO4 . 
D 4 HOH A 1 801 7 HOH HOH . 
D 4 HOH A 2 802 15 HOH HOH . 
D 4 HOH A 3 803 11 HOH HOH . 
D 4 HOH A 4 804 10 HOH HOH . 
D 4 HOH A 5 805 5 HOH HOH . 
D 4 HOH A 6 806 17 HOH HOH . 
D 4 HOH A 7 807 6 HOH HOH . 
D 4 HOH A 8 808 34 HOH HOH . 
D 4 HOH A 9 809 24 HOH HOH . 
D 4 HOH A 10 810 28 HOH HOH . 
D 4 HOH A 11 811 8 HOH HOH . 
D 4 HOH A 12 812 18 HOH HOH . 
D 4 HOH A 13 813 39 HOH HOH . 
D 4 HOH A 14 814 3 HOH HOH . 
D 4 HOH A 15 815 9 HOH HOH . 
D 4 HOH A 16 816 14 HOH HOH . 
D 4 HOH A 17 817 16 HOH HOH . 
D 4 HOH A 18 818 19 HOH HOH . 
D 4 HOH A 19 819 47 HOH HOH . 
D 4 HOH A 20 820 38 HOH HOH . 
D 4 HOH A 21 821 29 HOH HOH . 
D 4 HOH A 22 822 36 HOH HOH . 
D 4 HOH A 23 823 2 HOH HOH . 
D 4 HOH A 24 824 43 HOH HOH . 
D 4 HOH A 25 825 45 HOH HOH . 
D 4 HOH A 26 826 21 HOH HOH . 
D 4 HOH A 27 827 33 HOH HOH . 
D 4 HOH A 28 828 4 HOH HOH . 
D 4 HOH A 29 829 32 HOH HOH . 
D 4 HOH A 30 830 35 HOH HOH . 
D 4 HOH A 31 831 22 HOH HOH . 
D 4 HOH A 32 832 46 HOH HOH . 
D 4 HOH A 33 833 12 HOH HOH . 
D 4 HOH A 34 834 30 HOH HOH . 
D 4 HOH A 35 835 37 HOH HOH . 
D 4 HOH A 36 836 27 HOH HOH . 
D 4 HOH A 37 837 13 HOH HOH . 
D 4 HOH A 38 838 42 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 C4 8W9 . . . B 2 -5.233 10.483 4.182 1 27.59 ? C4 8W9 701 A 1 
HETATM 2 C C5 8W9 . . . B 2 -5.776 11.293 3.252 1 27.01 ? C5 8W9 701 A 1 
HETATM 3 C C6 8W9 . . . B 2 -5.095 11.725 2.189 1 30.01 ? C6 8W9 701 A 1 
HETATM 4 C C11 8W9 . . . B 2 -3.222 10.49 2.967 1 35.58 ? C11 8W9 701 A 1 
HETATM 5 C C8 8W9 . . . B 2 -3.982 10.063 4.051 1 33.34 ? C8 8W9 701 A 1 
HETATM 6 C C9 8W9 . . . B 2 -6.017 9.421 6.34 1 26.51 ? C9 8W9 701 A 1 
HETATM 7 C C10 8W9 . . . B 2 -7.989 12.432 2.866 1 21.95 ? C10 8W9 701 A 1 
HETATM 8 C C12 8W9 . . . B 2 -3.78 11.319 2.019 1 33.6 ? C12 8W9 701 A 1 
HETATM 9 N N2 8W9 . . . B 2 -6.156 10.233 5.114 1 25.93 ? N2 8W9 701 A 1 
HETATM 10 N N3 8W9 . . . B 2 -7.04 11.561 3.624 1 22.53 ? N3 8W9 701 A 1 
HETATM 11 C C1 8W9 . . . B 2 -7.271 10.917 4.763 1 24.65 ? C1 8W9 701 A 1 
HETATM 12 O O7 8W9 . . . B 2 -8.359 10.964 5.376 1 22.94 ? O7 8W9 701 A 1 
HETATM 13 C C15 8W9 . . . B 2 -1.898 10.053 2.83 1 41.65 ? C15 8W9 701 A 1 
HETATM 14 N N14 8W9 . . . B 2 -1.476 9.996 1.42 1 44 ? N14 8W9 701 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           243 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           14 
#