data_4L3J
#
_model_server_result.job_id            '_leq7JbUPf0pwXgHWTMYxQ' 
_model_server_result.datetime_utc      '2024-10-19 03:46:47' 
_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          4l3j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    4L3J 
#
_exptl.entry_id    4L3J 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              390.405 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole 
_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            4L3J 
_cell.length_a            70.511 
_cell.length_b            70.511 
_cell.length_c            150.484 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4L3J 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_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 
#
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 SG CYS 169 A CYS 217 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc2 A ND1 HIS 174 A HIS 222 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc3 A ND1 HIS 180 A HIS 228 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc4 A SG CYS 183 A CYS 231 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
#
_chem_comp.formula           'C19 H21 F3 N6' 
_chem_comp.formula_weight    390.405 
_chem_comp.id                5FI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole 
_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
FAB CBB 5FI sing 1 n n 
FAD CBB 5FI sing 2 n n 
CBB FAC 5FI sing 3 n n 
CBB CAU 5FI sing 4 n n 
CAU CAI 5FI doub 5 n y 
CAU CAE 5FI sing 6 n y 
CAI CAX 5FI sing 7 n y 
CAE CAF 5FI doub 8 n y 
CAX NAR 5FI sing 9 n y 
CAX CAY 5FI doub 10 n y 
NAR CAV 5FI doub 11 n y 
CAA CAJ 5FI sing 12 n n 
CAJ C5 5FI sing 13 n n 
CAF CAY 5FI sing 14 n y 
CAY NAS 5FI sing 15 n y 
CAV NAS 5FI sing 16 n y 
CAV CAO 5FI sing 17 n n 
CAM CAK 5FI sing 18 n n 
CAM NBA 5FI sing 19 n n 
C5 C6 5FI doub 20 n y 
C5 C4 5FI sing 21 n y 
CAO NAZ 5FI sing 22 n n 
CAK NAZ 5FI sing 23 n n 
C6 N1 5FI sing 24 n y 
NAZ CAL 5FI sing 25 n n 
NBA C4 5FI sing 26 n n 
NBA CAN 5FI sing 27 n n 
C4 N3 5FI doub 28 n y 
N1 C2 5FI doub 29 n y 
CAN CAL 5FI sing 30 n n 
N3 C2 5FI sing 31 n y 
C6 H1 5FI sing 32 n n 
CAE H2 5FI sing 33 n n 
CAF H3 5FI sing 34 n n 
CAI H4 5FI sing 35 n n 
CAO H7 5FI sing 36 n n 
CAO H8 5FI sing 37 n n 
CAL H10 5FI sing 38 n n 
CAL H11 5FI sing 39 n n 
CAN H12 5FI sing 40 n n 
CAN H13 5FI sing 41 n n 
CAK H14 5FI sing 42 n n 
CAK H15 5FI sing 43 n n 
CAM H16 5FI sing 44 n n 
CAM H17 5FI sing 45 n n 
CAJ H18 5FI sing 46 n n 
CAJ H19 5FI sing 47 n n 
CAA H20 5FI sing 48 n n 
CAA H21 5FI sing 49 n n 
CAA H22 5FI sing 50 n n 
C2 H23 5FI sing 51 n n 
NAS H5 5FI sing 52 n n 
#
_atom_sites.entry_id                     4L3J 
_atom_sites.fract_transf_matrix[1][1]    0.014182 
_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]    0.014182 
_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]    0.006645 
_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 5FI A 1 401 1 5FI DRG . 
C 3 ZN A 1 402 1 ZN ZN . 
D 4 HOH A 1 501 1 HOH HOH . 
D 4 HOH A 2 502 2 HOH HOH . 
D 4 HOH A 3 503 3 HOH HOH . 
D 4 HOH A 4 504 4 HOH HOH . 
D 4 HOH A 5 505 5 HOH HOH . 
D 4 HOH A 6 506 6 HOH HOH . 
D 4 HOH A 7 507 7 HOH HOH . 
D 4 HOH A 8 508 8 HOH HOH . 
D 4 HOH A 9 509 9 HOH HOH . 
D 4 HOH A 10 510 10 HOH HOH . 
D 4 HOH A 11 511 11 HOH HOH . 
D 4 HOH A 12 512 12 HOH HOH . 
D 4 HOH A 13 513 13 HOH HOH . 
D 4 HOH A 14 514 14 HOH HOH . 
D 4 HOH A 15 515 15 HOH HOH . 
D 4 HOH A 16 516 16 HOH HOH . 
D 4 HOH A 17 517 17 HOH HOH . 
D 4 HOH A 18 518 18 HOH HOH . 
D 4 HOH A 19 519 19 HOH HOH . 
D 4 HOH A 20 520 20 HOH HOH . 
D 4 HOH A 21 521 21 HOH HOH . 
D 4 HOH A 22 522 22 HOH HOH . 
D 4 HOH A 23 523 23 HOH HOH . 
D 4 HOH A 24 524 24 HOH HOH . 
D 4 HOH A 25 525 25 HOH HOH . 
D 4 HOH A 26 526 26 HOH HOH . 
D 4 HOH A 27 527 27 HOH HOH . 
D 4 HOH A 28 528 28 HOH HOH . 
D 4 HOH A 29 529 29 HOH HOH . 
D 4 HOH A 30 530 30 HOH HOH . 
D 4 HOH A 31 531 31 HOH HOH . 
D 4 HOH A 32 532 32 HOH HOH . 
D 4 HOH A 33 533 33 HOH HOH . 
D 4 HOH A 34 534 34 HOH HOH . 
D 4 HOH A 35 535 35 HOH HOH . 
D 4 HOH A 36 536 36 HOH HOH . 
D 4 HOH A 37 537 37 HOH HOH . 
D 4 HOH A 38 538 38 HOH HOH . 
D 4 HOH A 39 539 39 HOH HOH . 
D 4 HOH A 40 540 40 HOH HOH . 
D 4 HOH A 41 541 41 HOH HOH . 
D 4 HOH A 42 542 42 HOH HOH . 
D 4 HOH A 43 543 43 HOH HOH . 
D 4 HOH A 44 544 44 HOH HOH . 
D 4 HOH A 45 545 45 HOH HOH . 
D 4 HOH A 46 546 46 HOH HOH . 
D 4 HOH A 47 547 47 HOH HOH . 
D 4 HOH A 48 548 48 HOH HOH . 
D 4 HOH A 49 549 49 HOH HOH . 
D 4 HOH A 50 550 50 HOH HOH . 
D 4 HOH A 51 551 51 HOH HOH . 
D 4 HOH A 52 552 52 HOH HOH . 
D 4 HOH A 53 553 53 HOH HOH . 
D 4 HOH A 54 554 54 HOH HOH . 
D 4 HOH A 55 555 55 HOH HOH . 
D 4 HOH A 56 556 56 HOH HOH . 
D 4 HOH A 57 557 57 HOH HOH . 
D 4 HOH A 58 558 58 HOH HOH . 
D 4 HOH A 59 559 59 HOH HOH . 
D 4 HOH A 60 560 60 HOH HOH . 
D 4 HOH A 61 561 61 HOH HOH . 
D 4 HOH A 62 562 62 HOH HOH . 
D 4 HOH A 63 563 63 HOH HOH . 
D 4 HOH A 64 564 64 HOH HOH . 
D 4 HOH A 65 565 65 HOH HOH . 
D 4 HOH A 66 566 66 HOH HOH . 
D 4 HOH A 67 567 67 HOH HOH . 
D 4 HOH A 68 568 68 HOH HOH . 
D 4 HOH A 69 569 69 HOH HOH . 
D 4 HOH A 70 570 70 HOH HOH . 
D 4 HOH A 71 571 71 HOH HOH . 
D 4 HOH A 72 572 72 HOH HOH . 
D 4 HOH A 73 573 73 HOH HOH . 
D 4 HOH A 74 574 74 HOH HOH . 
D 4 HOH A 75 575 75 HOH HOH . 
D 4 HOH A 76 576 76 HOH HOH . 
D 4 HOH A 77 577 77 HOH HOH . 
D 4 HOH A 78 578 78 HOH HOH . 
D 4 HOH A 79 579 79 HOH HOH . 
D 4 HOH A 80 580 80 HOH HOH . 
D 4 HOH A 81 581 81 HOH HOH . 
D 4 HOH A 82 582 82 HOH HOH . 
D 4 HOH A 83 583 83 HOH HOH . 
D 4 HOH A 84 584 84 HOH HOH . 
D 4 HOH A 85 585 85 HOH HOH . 
D 4 HOH A 86 586 86 HOH HOH . 
D 4 HOH A 87 587 87 HOH HOH . 
D 4 HOH A 88 588 88 HOH HOH . 
D 4 HOH A 89 589 89 HOH HOH . 
D 4 HOH A 90 590 90 HOH HOH . 
D 4 HOH A 91 591 91 HOH HOH . 
D 4 HOH A 92 592 92 HOH HOH . 
D 4 HOH A 93 593 93 HOH HOH . 
D 4 HOH A 94 594 94 HOH HOH . 
D 4 HOH A 95 595 95 HOH HOH . 
D 4 HOH A 96 596 96 HOH HOH . 
D 4 HOH A 97 597 97 HOH HOH . 
D 4 HOH A 98 598 98 HOH HOH . 
D 4 HOH A 99 599 99 HOH HOH . 
D 4 HOH A 100 600 100 HOH HOH . 
D 4 HOH A 101 601 101 HOH HOH . 
D 4 HOH A 102 602 102 HOH HOH . 
D 4 HOH A 103 603 103 HOH HOH . 
D 4 HOH A 104 604 104 HOH HOH . 
D 4 HOH A 105 605 105 HOH HOH . 
D 4 HOH A 106 606 106 HOH HOH . 
D 4 HOH A 107 607 107 HOH HOH . 
D 4 HOH A 108 608 108 HOH HOH . 
D 4 HOH A 109 609 109 HOH HOH . 
D 4 HOH A 110 610 110 HOH HOH . 
D 4 HOH A 111 611 111 HOH HOH . 
D 4 HOH A 112 612 112 HOH HOH . 
D 4 HOH A 113 613 113 HOH HOH . 
D 4 HOH A 114 614 114 HOH HOH . 
D 4 HOH A 115 615 115 HOH HOH . 
D 4 HOH A 116 616 116 HOH HOH . 
D 4 HOH A 117 617 117 HOH HOH . 
D 4 HOH A 118 618 118 HOH HOH . 
D 4 HOH A 119 619 119 HOH HOH . 
D 4 HOH A 120 620 120 HOH HOH . 
D 4 HOH A 121 621 121 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 5FI . . . B 2 25.291 -20.726 14.907 1 53.17 ? C4 5FI 401 A 1 
HETATM 2 C C5 5FI . . . B 2 26.495 -20.939 14.237 1 53.24 ? C5 5FI 401 A 1 
HETATM 3 C C6 5FI . . . B 2 27.663 -20.708 14.959 1 52.68 ? C6 5FI 401 A 1 
HETATM 4 N N1 5FI . . . B 2 27.618 -20.307 16.223 1 50.07 ? N1 5FI 401 A 1 
HETATM 5 N N3 5FI . . . B 2 25.358 -20.31 16.196 1 53.59 ? N3 5FI 401 A 1 
HETATM 6 F FAB 5FI . . . B 2 19.975 -28.75 10.051 1 69.21 ? FAB 5FI 401 A 1 
HETATM 7 C CBB 5FI . . . B 2 19.562 -27.686 9.384 1 67.52 ? CBB 5FI 401 A 1 
HETATM 8 F FAC 5FI . . . B 2 18.392 -27.951 8.872 1 65.99 ? FAC 5FI 401 A 1 
HETATM 9 F FAD 5FI . . . B 2 20.377 -27.427 8.36 1 69.37 ? FAD 5FI 401 A 1 
HETATM 10 C CAU 5FI . . . B 2 19.398 -26.487 10.35 1 65.04 ? CAU 5FI 401 A 1 
HETATM 11 C CAE 5FI . . . B 2 18.559 -26.622 11.456 1 61.74 ? CAE 5FI 401 A 1 
HETATM 12 C CAF 5FI . . . B 2 18.38 -25.559 12.334 1 61.6 ? CAF 5FI 401 A 1 
HETATM 13 C CAI 5FI . . . B 2 20.062 -25.284 10.121 1 61.73 ? CAI 5FI 401 A 1 
HETATM 14 C CAX 5FI . . . B 2 19.873 -24.221 11 1 60.08 ? CAX 5FI 401 A 1 
HETATM 15 C CAY 5FI . . . B 2 19.041 -24.352 12.092 1 59.87 ? CAY 5FI 401 A 1 
HETATM 16 N NAS 5FI . . . B 2 19.058 -23.201 12.739 1 57.89 ? NAS 5FI 401 A 1 
HETATM 17 N NAR 5FI . . . B 2 20.364 -22.996 11.035 1 58.51 ? NAR 5FI 401 A 1 
HETATM 18 C CAV 5FI . . . B 2 19.865 -22.378 12.088 1 58.24 ? CAV 5FI 401 A 1 
HETATM 19 C CAO 5FI . . . B 2 20.161 -20.928 12.496 1 57.92 ? CAO 5FI 401 A 1 
HETATM 20 N NAZ 5FI . . . B 2 21.456 -20.775 13.167 1 56.87 ? NAZ 5FI 401 A 1 
HETATM 21 C CAL 5FI . . . B 2 21.578 -21.533 14.424 1 56.02 ? CAL 5FI 401 A 1 
HETATM 22 C CAN 5FI . . . B 2 22.837 -21.095 15.201 1 54.33 ? CAN 5FI 401 A 1 
HETATM 23 C CAK 5FI . . . B 2 22.587 -20.996 12.258 1 54.97 ? CAK 5FI 401 A 1 
HETATM 24 C CAM 5FI . . . B 2 23.835 -20.399 12.889 1 56.05 ? CAM 5FI 401 A 1 
HETATM 25 N NBA 5FI . . . B 2 24.015 -20.837 14.323 1 52.65 ? NBA 5FI 401 A 1 
HETATM 26 C CAJ 5FI . . . B 2 26.69 -21.396 12.783 1 57.95 ? CAJ 5FI 401 A 1 
HETATM 27 C CAA 5FI . . . B 2 26.443 -22.893 12.647 1 53.08 ? CAA 5FI 401 A 1 
HETATM 28 C C2 5FI . . . B 2 26.488 -20.115 16.84 1 49.81 ? C2 5FI 401 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#