data_5EQY
#
_model_server_result.job_id            '_rWEUuqJWFtTOM6HJYY5rg' 
_model_server_result.datetime_utc      '2024-10-19 16:39:24' 
_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          5eqy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    5EQY 
#
_exptl.entry_id    5EQY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              431.616 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-[(4-methyl-1,4-diazepan-1-yl)methyl]-2-[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]benzenecarbonitrile 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            5EQY 
_cell.length_a            55.523 
_cell.length_b            121.532 
_cell.length_c            130.467 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5EQY 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C27 H37 N5' 
_chem_comp.formula_weight    431.616 
_chem_comp.id                5RA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-[(4-methyl-1,4-diazepan-1-yl)methyl]-2-[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]benzenecarbonitrile 
_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
C51 C50 5RA sing 1 n n 
C51 N52 5RA sing 2 n n 
C6 N2 5RA sing 3 n n 
C6 C7 5RA sing 4 n n 
C8 C7 5RA sing 5 n n 
C8 N9 5RA sing 6 n n 
C10 N9 5RA sing 7 n n 
C10 C11 5RA sing 8 n n 
N2 C11 5RA sing 9 n n 
N9 C22 5RA sing 10 n n 
C22 C23 5RA sing 11 n n 
C23 C26 5RA doub 12 n y 
C23 C30 5RA sing 13 n y 
C26 C27 5RA sing 14 n y 
C27 C28 5RA doub 15 n y 
C27 C44 5RA sing 16 n n 
C28 C29 5RA sing 17 n y 
C28 C34 5RA sing 18 n n 
C29 C30 5RA doub 19 n y 
C34 C35 5RA doub 20 n y 
C34 C39 5RA sing 21 n y 
C35 C36 5RA sing 22 n y 
C36 C37 5RA doub 23 n y 
C37 C38 5RA sing 24 n y 
C37 C46 5RA sing 25 n n 
C38 C39 5RA doub 26 n y 
C44 N45 5RA trip 27 n n 
C46 N47 5RA sing 28 n n 
N47 C50 5RA sing 29 n n 
N47 C55 5RA sing 30 n n 
N52 C53 5RA sing 31 n n 
N52 C66 5RA sing 32 n n 
C53 C54 5RA sing 33 n n 
C54 C55 5RA sing 34 n n 
N2 C1 5RA sing 35 n n 
C1 H1 5RA sing 36 n n 
C1 H2 5RA sing 37 n n 
C1 H3 5RA sing 38 n n 
C51 H4 5RA sing 39 n n 
C51 H5 5RA sing 40 n n 
C6 H6 5RA sing 41 n n 
C6 H7 5RA sing 42 n n 
C8 H8 5RA sing 43 n n 
C8 H9 5RA sing 44 n n 
C10 H10 5RA sing 45 n n 
C10 H11 5RA sing 46 n n 
C7 H13 5RA sing 47 n n 
C7 H14 5RA sing 48 n n 
C11 H16 5RA sing 49 n n 
C11 H17 5RA sing 50 n n 
C22 H18 5RA sing 51 n n 
C22 H19 5RA sing 52 n n 
C26 H20 5RA sing 53 n n 
C29 H21 5RA sing 54 n n 
C30 H22 5RA sing 55 n n 
C35 H23 5RA sing 56 n n 
C36 H24 5RA sing 57 n n 
C38 H25 5RA sing 58 n n 
C39 H26 5RA sing 59 n n 
C46 H27 5RA sing 60 n n 
C46 H28 5RA sing 61 n n 
C50 H30 5RA sing 62 n n 
C50 H31 5RA sing 63 n n 
C53 H33 5RA sing 64 n n 
C53 H34 5RA sing 65 n n 
C54 H35 5RA sing 66 n n 
C54 H36 5RA sing 67 n n 
C55 H37 5RA sing 68 n n 
C55 H38 5RA sing 69 n n 
C66 H39 5RA sing 70 n n 
C66 H40 5RA sing 71 n n 
C66 H41 5RA sing 72 n n 
#
_atom_sites.entry_id                     5EQY 
_atom_sites.fract_transf_matrix[1][1]    0.018011 
_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]    0.008228 
_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]    0.007665 
_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 5RA A 1 501 1 5RA AP3 . 
D 2 5RA B 1 501 1 5RA AP3 . 
E 3 HOH A 1 601 2 HOH WAT . 
E 3 HOH A 2 602 41 HOH WAT . 
E 3 HOH A 3 603 13 HOH WAT . 
E 3 HOH A 4 604 14 HOH WAT . 
E 3 HOH A 5 605 20 HOH WAT . 
E 3 HOH A 6 606 32 HOH WAT . 
E 3 HOH A 7 607 52 HOH WAT . 
E 3 HOH A 8 608 18 HOH WAT . 
E 3 HOH A 9 609 4 HOH WAT . 
E 3 HOH A 10 610 34 HOH WAT . 
E 3 HOH A 11 611 61 HOH WAT . 
E 3 HOH A 12 612 66 HOH WAT . 
E 3 HOH A 13 613 6 HOH WAT . 
E 3 HOH A 14 614 30 HOH WAT . 
E 3 HOH A 15 615 53 HOH WAT . 
E 3 HOH A 16 616 25 HOH WAT . 
E 3 HOH A 17 617 37 HOH WAT . 
E 3 HOH A 18 618 29 HOH WAT . 
E 3 HOH A 19 619 40 HOH WAT . 
E 3 HOH A 20 620 19 HOH WAT . 
E 3 HOH A 21 621 57 HOH WAT . 
E 3 HOH A 22 622 35 HOH WAT . 
E 3 HOH A 23 623 49 HOH WAT . 
E 3 HOH A 24 624 31 HOH WAT . 
E 3 HOH A 25 625 16 HOH WAT . 
E 3 HOH A 26 626 15 HOH WAT . 
E 3 HOH A 27 627 50 HOH WAT . 
E 3 HOH A 28 628 47 HOH WAT . 
E 3 HOH A 29 629 42 HOH WAT . 
E 3 HOH A 30 630 62 HOH WAT . 
E 3 HOH A 31 631 54 HOH WAT . 
E 3 HOH A 32 632 10 HOH WAT . 
E 3 HOH A 33 633 7 HOH WAT . 
F 3 HOH B 1 601 8 HOH WAT . 
F 3 HOH B 2 602 1 HOH WAT . 
F 3 HOH B 3 603 60 HOH WAT . 
F 3 HOH B 4 604 26 HOH WAT . 
F 3 HOH B 5 605 9 HOH WAT . 
F 3 HOH B 6 606 36 HOH WAT . 
F 3 HOH B 7 607 63 HOH WAT . 
F 3 HOH B 8 608 38 HOH WAT . 
F 3 HOH B 9 609 48 HOH WAT . 
F 3 HOH B 10 610 27 HOH WAT . 
F 3 HOH B 11 611 44 HOH WAT . 
F 3 HOH B 12 612 39 HOH WAT . 
F 3 HOH B 13 613 12 HOH WAT . 
F 3 HOH B 14 614 33 HOH WAT . 
F 3 HOH B 15 615 17 HOH WAT . 
F 3 HOH B 16 616 56 HOH WAT . 
F 3 HOH B 17 617 59 HOH WAT . 
F 3 HOH B 18 618 2 HOH HOH . 
F 3 HOH B 19 619 5 HOH WAT . 
F 3 HOH B 20 620 3 HOH WAT . 
F 3 HOH B 21 621 5 HOH HOH . 
F 3 HOH B 22 622 68 HOH WAT . 
F 3 HOH B 23 623 51 HOH WAT . 
F 3 HOH B 24 624 24 HOH WAT . 
F 3 HOH B 25 625 3 HOH HOH . 
F 3 HOH B 26 626 6 HOH HOH . 
F 3 HOH B 27 627 55 HOH WAT . 
F 3 HOH B 28 628 23 HOH WAT . 
F 3 HOH B 29 629 45 HOH WAT . 
F 3 HOH B 30 630 46 HOH WAT . 
F 3 HOH B 31 631 7 HOH HOH . 
F 3 HOH B 32 632 58 HOH WAT . 
F 3 HOH B 33 633 11 HOH WAT . 
F 3 HOH B 34 634 4 HOH HOH . 
F 3 HOH B 35 635 21 HOH WAT . 
F 3 HOH B 36 636 22 HOH WAT . 
F 3 HOH B 37 637 43 HOH WAT . 
F 3 HOH B 38 638 1 HOH HOH . 
F 3 HOH B 39 639 65 HOH WAT . 
F 3 HOH B 40 640 67 HOH WAT . 
F 3 HOH B 41 641 28 HOH WAT . 
F 3 HOH B 42 642 64 HOH WAT . 
#
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 5RA . . . D 2 33.803 38.306 36.948 1 32.12 ? C1 5RA 501 B 1 
HETATM 2 C C51 5RA . . . D 2 44.901 28.671 45.361 1 74.92 ? C51 5RA 501 B 1 
HETATM 3 C C6 5RA . . . D 2 33.603 36.833 35.55 1 33.95 ? C6 5RA 501 B 1 
HETATM 4 C C8 5RA . . . D 2 34.596 34.449 35.46 1 37.71 ? C8 5RA 501 B 1 
HETATM 5 C C10 5RA . . . D 2 35.817 35.501 37.42 1 36.37 ? C10 5RA 501 B 1 
HETATM 6 N N2 5RA . . . D 2 33.613 36.595 36.979 1 34.86 ? N2 5RA 501 B 1 
HETATM 7 C C7 5RA . . . D 2 33.926 35.596 34.691 1 36.97 ? C7 5RA 501 B 1 
HETATM 8 N N9 5RA . . . D 2 35.882 34.816 36.08 1 39.26 ? N9 5RA 501 B 1 
HETATM 9 C C11 5RA . . . D 2 34.91 36.711 37.622 1 34.97 ? C11 5RA 501 B 1 
HETATM 10 C C22 5RA . . . D 2 36.892 33.702 35.928 1 41.2 ? C22 5RA 501 B 1 
HETATM 11 C C23 5RA . . . D 2 37.752 33.346 37.135 1 44.08 ? C23 5RA 501 B 1 
HETATM 12 C C26 5RA . . . D 2 37.187 32.717 38.276 1 44.3 ? C26 5RA 501 B 1 
HETATM 13 C C27 5RA . . . D 2 37.973 32.386 39.405 1 47.65 ? C27 5RA 501 B 1 
HETATM 14 C C28 5RA . . . D 2 39.381 32.653 39.429 1 49.02 ? C28 5RA 501 B 1 
HETATM 15 C C29 5RA . . . D 2 39.933 33.283 38.284 1 46.35 ? C29 5RA 501 B 1 
HETATM 16 C C30 5RA . . . D 2 39.142 33.619 37.149 1 44.77 ? C30 5RA 501 B 1 
HETATM 17 C C34 5RA . . . D 2 40.292 32.332 40.599 1 55.52 ? C34 5RA 501 B 1 
HETATM 18 C C35 5RA . . . D 2 40.667 30.995 40.906 1 58.27 ? C35 5RA 501 B 1 
HETATM 19 C C36 5RA . . . D 2 41.519 30.699 42.01 1 61.48 ? C36 5RA 501 B 1 
HETATM 20 C C37 5RA . . . D 2 42.027 31.738 42.842 1 63.12 ? C37 5RA 501 B 1 
HETATM 21 C C38 5RA . . . D 2 41.648 33.067 42.532 1 60.98 ? C38 5RA 501 B 1 
HETATM 22 C C39 5RA . . . D 2 40.804 33.354 41.44 1 58.29 ? C39 5RA 501 B 1 
HETATM 23 C C44 5RA . . . D 2 37.254 31.761 40.493 1 48.5 ? C44 5RA 501 B 1 
HETATM 24 N N45 5RA . . . D 2 36.694 31.276 41.392 1 48.89 ? N45 5RA 501 B 1 
HETATM 25 C C46 5RA . . . D 2 42.945 31.456 44.016 1 65.83 ? C46 5RA 501 B 1 
HETATM 26 N N47 5RA . . . D 2 43.934 30.389 43.735 1 69.85 ? N47 5RA 501 B 1 
HETATM 27 C C50 5RA . . . D 2 43.757 29.073 44.4 1 72.62 ? C50 5RA 501 B 1 
HETATM 28 N N52 5RA . . . D 2 46.003 29.662 45.347 1 75.13 ? N52 5RA 501 B 1 
HETATM 29 C C53 5RA . . . D 2 46.922 29.616 44.182 1 72.85 ? C53 5RA 501 B 1 
HETATM 30 C C54 5RA . . . D 2 46.26 29.678 42.794 1 70.44 ? C54 5RA 501 B 1 
HETATM 31 C C55 5RA . . . D 2 45.007 30.586 42.704 1 69.45 ? C55 5RA 501 B 1 
HETATM 32 C C66 5RA . . . D 2 46.655 29.911 46.641 1 75.63 ? C66 5RA 501 B 1 
#
_model_server_stats.io_time_ms              65 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           32 
#