data_6BM7
#
_model_server_result.job_id            RJaDA3o7De1_uloGKDNhsg 
_model_server_result.datetime_utc      '2024-10-15 16:21:35' 
_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          6bm7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":402}' 
#
_entry.id    6BM7 
#
_exptl.entry_id    6BM7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              359.04 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-amino-4-[(3,5-dibromophenyl)amino]-6-methylpyrimidin-1-ium 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          102.426 
_cell.angle_gamma         90 
_cell.entry_id            6BM7 
_cell.length_a            81.09 
_cell.length_b            96.25 
_cell.length_c            98.84 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6BM7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    'P 2yb' 
_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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 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,F,G,H,N,O,P,Q,T 1 1 
C,D,E,I,J,K,L,M,R,S 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
? 5 H N N 
? 5 J N 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 B C PYR 1 B PYR 86 1_555 B N SER 2 B SER 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale2 D C PYR 1 D PYR 86 1_555 D N SER 2 D SER 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
#
_chem_comp.formula           'C11 H11 Br2 N4 1' 
_chem_comp.formula_weight    359.04 
_chem_comp.id                DY7 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-amino-4-[(3,5-dibromophenyl)amino]-6-methylpyrimidin-1-ium 
_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
BR2 C11 DY7 sing 127 n n 
BR9 C08 DY7 sing 128 n n 
C10 C11 DY7 doub 129 n y 
C10 C08 DY7 sing 130 n y 
C11 C13 DY7 sing 131 n y 
C08 C07 DY7 doub 132 n y 
C13 C06 DY7 doub 133 n y 
C07 C06 DY7 sing 134 n y 
C06 N05 DY7 sing 135 n n 
N05 C04 DY7 sing 136 n n 
N03 C04 DY7 doub 137 n y 
N03 C02 DY7 sing 138 n y 
C04 C14 DY7 sing 139 n y 
N01 C02 DY7 sing 140 n n 
C02 N17 DY7 doub 141 n y 
C14 C15 DY7 doub 142 n y 
N17 C15 DY7 sing 143 n y 
C15 C16 DY7 sing 144 n n 
C10 H101 DY7 sing 145 n n 
C14 H141 DY7 sing 146 n n 
N01 H011 DY7 sing 147 n n 
N01 H012 DY7 sing 148 n n 
N05 H051 DY7 sing 149 n n 
C07 H071 DY7 sing 150 n n 
C13 H131 DY7 sing 151 n n 
C16 H162 DY7 sing 152 n n 
C16 H161 DY7 sing 153 n n 
C16 H163 DY7 sing 154 n n 
N17 H171 DY7 sing 155 n n 
#
_atom_sites.entry_id                     6BM7 
_atom_sites.fract_transf_matrix[1][1]    0.012332 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002717 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01039 
_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]    0.01036 
_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
G 4 B3P B 1 401 1 B3P B3P . 
H 5 DY7 B 1 402 4 DY7 56H . 
I 4 B3P D 1 401 2 B3P B3P . 
J 5 DY7 D 1 402 3 DY7 56H . 
K 6 PUT E 1 401 3 PUT PUT . 
L 7 PGE E 1 402 1 PGE PGE . 
M 7 PGE E 1 403 2 PGE PGE . 
N 6 PUT F 1 401 4 PUT PUT . 
O 8 PG4 F 1 402 3 PG4 PG4 . 
P 9 HOH A 1 101 14 HOH HOH . 
Q 9 HOH B 1 501 2 HOH HOH . 
R 9 HOH C 1 101 4 HOH HOH . 
S 9 HOH D 1 501 8 HOH HOH . 
S 9 HOH D 2 502 5 HOH HOH . 
T 9 HOH F 1 501 13 HOH HOH . 
T 9 HOH F 2 502 12 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 C15 DY7 . . . H 5 25.798 26.665 34.683 1 67.18 ? C15 DY7 402 B 1 
HETATM 2 C C11 DY7 . . . H 5 25.062 24.908 41.73 1 77.17 ? C11 DY7 402 B 1 
HETATM 3 C C10 DY7 . . . H 5 25.062 26.154 42.342 1 68.79 ? C10 DY7 402 B 1 
HETATM 4 C C14 DY7 . . . H 5 26.107 25.964 35.782 1 63.16 ? C14 DY7 402 B 1 
HETATM 5 N N17 DY7 . . . H 5 25.461 28.028 34.812 1 68.11 1 N17 DY7 402 B 1 
HETATM 6 N N01 DY7 . . . H 5 25.158 29.824 36.244 1 69.23 ? N01 DY7 402 B 1 
HETATM 7 C C02 DY7 . . . H 5 25.48 28.555 36.155 1 62.85 ? C02 DY7 402 B 1 
HETATM 8 N N03 DY7 . . . H 5 25.807 27.767 37.232 1 57.96 ? N03 DY7 402 B 1 
HETATM 9 C C04 DY7 . . . H 5 26.137 26.439 37.126 1 64.92 ? C04 DY7 402 B 1 
HETATM 10 N N05 DY7 . . . H 5 26.485 25.65 38.273 1 72.01 ? N05 DY7 402 B 1 
HETATM 11 C C06 DY7 . . . H 5 26.001 25.816 39.658 1 72.05 ? C06 DY7 402 B 1 
HETATM 12 C C07 DY7 . . . H 5 25.996 27.098 40.296 1 72.39 ? C07 DY7 402 B 1 
HETATM 13 C C08 DY7 . . . H 5 25.529 27.234 41.61 1 69.79 ? C08 DY7 402 B 1 
HETATM 14 BR BR9 DY7 . . . H 5 25.54 29.03 42.438 1 103.62 ? BR9 DY7 402 B 1 
HETATM 15 BR BR2 DY7 . . . H 5 24.403 23.331 42.717 1 122.97 ? BR2 DY7 402 B 1 
HETATM 16 C C13 DY7 . . . H 5 25.521 24.721 40.414 1 76.83 ? C13 DY7 402 B 1 
HETATM 17 C C16 DY7 . . . H 5 25.734 26.24 33.237 1 82.98 ? C16 DY7 402 B 1 
HETATM 18 H H101 DY7 . . . H 5 24.751 26.254 43.213 1 82.55 ? H101 DY7 402 B 1 
HETATM 19 H H141 DY7 . . . H 5 26.329 25.065 35.689 1 75.79 ? H141 DY7 402 B 1 
HETATM 20 H H011 DY7 . . . H 5 25.724 30.457 36.11 1 83.07 ? H011 DY7 402 B 1 
HETATM 21 H H012 DY7 . . . H 5 24.408 30.2 36.432 1 83.07 ? H012 DY7 402 B 1 
HETATM 22 H H051 DY7 . . . H 5 27.158 25.124 38.167 1 86.41 ? H051 DY7 402 B 1 
HETATM 23 H H071 DY7 . . . H 5 26.298 27.857 39.852 1 86.86 ? H071 DY7 402 B 1 
HETATM 24 H H131 DY7 . . . H 5 25.503 23.868 40.043 1 92.2 ? H131 DY7 402 B 1 
HETATM 25 H H162 DY7 . . . H 5 25.996 25.31 33.155 1 99.58 ? H162 DY7 402 B 1 
HETATM 26 H H161 DY7 . . . H 5 24.869 26.269 32.797 1 99.58 ? H161 DY7 402 B 1 
HETATM 27 H H163 DY7 . . . H 5 26.309 26.692 32.6 1 99.58 ? H163 DY7 402 B 1 
HETATM 28 H H171 DY7 . . . H 5 25.251 28.519 34.137 1 81.73 1 H171 DY7 402 B 1 
#
_model_server_stats.io_time_ms              34 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    49 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#