data_3NM1
#
_model_server_result.job_id            rWOQAbsKEQ-zecEoIF75aQ 
_model_server_result.datetime_utc      '2024-11-15 09:31:34' 
_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          3nm1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":542}' 
#
_entry.id    3NM1 
#
_exptl.entry_id    3NM1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              175.111 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-TRIFLUOROMETHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          102.1 
_cell.angle_gamma         90 
_cell.entry_id            3NM1 
_cell.length_a            104.938 
_cell.length_b            154.212 
_cell.length_c            148.704 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NM1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 H N N 
? 3 L N N 
? 3 P N N 
? 3 T N N 
? 3 X N N 
? 3 BA 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
metalc ? metalc1 A OD2 ASP 76 A ASP 76 1_555 J MG MG . A MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? 
metalc ? metalc2 A OD2 ASP 95 A ASP 95 1_555 J MG MG . A MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? 
metalc ? metalc3 I O6 POP . A POP 543 1_555 J MG MG . A MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc4 I O1 POP . A POP 543 1_555 J MG MG . A MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? 
metalc ? metalc5 I O4 POP . A POP 543 1_555 J MG MG . A MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? 
metalc ? metalc6 B OD2 ASP 95 B ASP 95 1_555 N MG MG . B MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? 
metalc ? metalc7 B OD1 ASP 95 B ASP 95 1_555 N MG MG . B MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? 
metalc ? metalc8 M O3 POP . B POP 543 1_555 N MG MG . B MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? 
metalc ? metalc9 M O4 POP . B POP 543 1_555 N MG MG . B MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? 
metalc ? metalc10 C OD1 ASP 76 C ASP 76 1_555 R MG MG . C MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? 
metalc ? metalc11 C OD2 ASP 95 C ASP 95 1_555 R MG MG . C MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
metalc ? metalc12 Q O6 POP . C POP 543 1_555 R MG MG . C MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? 
metalc ? metalc13 D OD1 ASP 76 D ASP 76 1_555 V MG MG . D MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? 
metalc ? metalc14 D OD2 ASP 95 D ASP 95 1_555 V MG MG . D MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
metalc ? metalc15 U O6 POP . D POP 543 1_555 V MG MG . D MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc16 U O3 POP . D POP 543 1_555 V MG MG . D MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? 
metalc ? metalc17 E OD2 ASP 76 E ASP 76 1_555 Z MG MG . E MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? 
metalc ? metalc18 E OD2 ASP 95 E ASP 95 1_555 Z MG MG . E MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? 
metalc ? metalc19 Y O6 POP . E POP 543 1_555 Z MG MG . E MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? 
metalc ? metalc20 Y O2 POP . E POP 543 1_555 Z MG MG . E MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? 
metalc ? metalc21 Y O3 POP . E POP 543 1_555 Z MG MG . E MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? 
metalc ? metalc22 F OD2 ASP 76 F ASP 76 1_555 DA MG MG . F MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
metalc ? metalc23 F OD2 ASP 95 F ASP 95 1_555 DA MG MG . F MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc24 CA O4 POP . F POP 543 1_555 DA MG MG . F MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? 
metalc ? metalc25 CA O3 POP . F POP 543 1_555 DA MG MG . F MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? 
metalc ? metalc26 CA O6 POP . F POP 543 1_555 DA MG MG . F MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.893 ? 
#
_chem_comp.formula           'C6 H4 F3 N3' 
_chem_comp.formula_weight    175.111 
_chem_comp.id                IFP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-TRIFLUOROMETHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     4-IMINO-5-METHIDYL-2-TRIFLUOROMETHYLPYRIMIDINE 
#
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
N1A C2A IFP sing 176 n n 
N1A C6A IFP doub 177 n n 
C2A CM2 IFP sing 178 n n 
C2A N3A IFP doub 179 n n 
CM2 F1 IFP sing 180 n n 
CM2 F2 IFP sing 181 n n 
CM2 F3 IFP sing 182 n n 
N3A C4A IFP sing 183 n n 
C4A N4A IFP doub 184 n n 
C4A C5A IFP sing 185 n n 
N4A HN4 IFP sing 186 n n 
C5A C6A IFP sing 187 n n 
C5A C7A IFP doub 188 n n 
C6A H6A1 IFP sing 189 n n 
C7A H7A1 IFP sing 190 n n 
C7A H7A2 IFP sing 191 n n 
#
_atom_sites.entry_id                     3NM1 
_atom_sites.fract_transf_matrix[1][1]    0.009529 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002043 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006485 
_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]    0.006878 
_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 2 3NM A 1 541 541 3NM 3NM . 
H 3 IFP A 1 542 542 IFP IFP . 
I 4 POP A 1 543 543 POP POP . 
J 5 MG A 1 544 544 MG MG . 
K 2 3NM B 1 541 541 3NM 3NM . 
L 3 IFP B 1 542 542 IFP IFP . 
M 4 POP B 1 543 543 POP POP . 
N 5 MG B 1 544 544 MG MG . 
O 2 3NM C 1 541 541 3NM 3NM . 
P 3 IFP C 1 542 542 IFP IFP . 
Q 4 POP C 1 543 543 POP POP . 
R 5 MG C 1 544 544 MG MG . 
S 2 3NM D 1 541 541 3NM 3NM . 
T 3 IFP D 1 542 542 IFP IFP . 
U 4 POP D 1 543 543 POP POP . 
V 5 MG D 1 544 544 MG MG . 
W 2 3NM E 1 541 541 3NM 3NM . 
X 3 IFP E 1 542 542 IFP IFP . 
Y 4 POP E 1 543 543 POP POP . 
Z 5 MG E 1 544 544 MG MG . 
AA 2 3NM F 1 541 541 3NM 3NM . 
BA 3 IFP F 1 542 542 IFP IFP . 
CA 4 POP F 1 543 543 POP POP . 
DA 5 MG F 1 544 544 MG MG . 
#
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 N1A IFP . . . P 3 8.659 39.303 52.562 1 62.59 ? N1A IFP 542 C 1 
HETATM 2 C C2A IFP . . . P 3 7.932 39.716 51.519 1 65.82 ? C2A IFP 542 C 1 
HETATM 3 C CM2 IFP . . . P 3 6.768 40.638 51.684 1 70.22 ? CM2 IFP 542 C 1 
HETATM 4 N N3A IFP . . . P 3 8.278 39.317 50.241 1 69.24 ? N3A IFP 542 C 1 
HETATM 5 C C4A IFP . . . P 3 9.362 38.509 50.027 1 69.16 ? C4A IFP 542 C 1 
HETATM 6 N N4A IFP . . . P 3 9.706 38.1 48.698 1 65.99 ? N4A IFP 542 C 1 
HETATM 7 C C5A IFP . . . P 3 10.109 38.094 51.102 1 66.07 ? C5A IFP 542 C 1 
HETATM 8 C C6A IFP . . . P 3 9.772 38.474 52.34 1 64.9 ? C6A IFP 542 C 1 
HETATM 9 C C7A IFP . . . P 3 11.292 37.215 50.876 1 64 ? C7A IFP 542 C 1 
HETATM 10 F F1 IFP . . . P 3 7.164 41.879 51.411 1 69.92 ? F1 IFP 542 C 1 
HETATM 11 F F2 IFP . . . P 3 5.833 40.304 50.801 1 74.99 ? F2 IFP 542 C 1 
HETATM 12 F F3 IFP . . . P 3 6.266 40.612 52.922 1 71.78 ? F3 IFP 542 C 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    36 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           12 
#