data_4NYM
#
_model_server_result.job_id            UJseS1-mPyLy3OxYbYsKww 
_model_server_result.datetime_utc      '2024-11-02 04:22:08' 
_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          4nym 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1101}' 
#
_entry.id    4NYM 
#
_exptl.entry_id    4NYM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              415.531 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]-L-tryptophanamide 
_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            4NYM 
_cell.length_a            186.805 
_cell.length_b            186.805 
_cell.length_c            178.684 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4NYM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        97 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             F 
_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 OG SER 17 Q SER 17 1_555 D MG MG . Q MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc2 A OG1 THR 35 Q THR 35 1_555 D MG MG . Q MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc3 D MG MG . Q MG 201 1_555 E O2G GNP . Q GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc4 D MG MG . Q MG 201 1_555 E O2B GNP . Q GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
#
_chem_comp.formula           'C25 H29 N5 O' 
_chem_comp.formula_weight    415.531 
_chem_comp.id                RND 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]-L-tryptophanamide 
_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
C15 C16 RND sing 326 n n 
C15 C14 RND sing 327 n n 
N22 C19 RND sing 328 n n 
C16 N11 RND sing 329 n n 
C30 C31 RND doub 330 n y 
C30 C29 RND sing 331 n y 
C14 N17 RND sing 332 n n 
C14 C13 RND sing 333 n n 
N17 C18 RND sing 334 n n 
C31 C26 RND sing 335 n y 
C18 C19 RND sing 336 n n 
C18 O20 RND doub 337 n n 
C19 C21 RND sing 338 n n 
C29 C28 RND doub 339 n y 
N11 C10 RND sing 340 n n 
N11 C12 RND sing 341 n n 
C10 C08 RND sing 342 n n 
C13 C12 RND sing 343 n n 
C26 C23 RND sing 344 n y 
C26 C27 RND doub 345 n y 
C21 C23 RND sing 346 n n 
C09 C08 RND doub 347 n y 
C09 N07 RND sing 348 n y 
C08 C06 RND sing 349 n y 
C28 C27 RND sing 350 n y 
C23 C25 RND doub 351 n y 
C27 N24 RND sing 352 n y 
N07 C05 RND sing 353 n y 
C06 C05 RND doub 354 n y 
C06 C01 RND sing 355 n y 
C25 N24 RND sing 356 n y 
C05 C04 RND sing 357 n y 
C01 C02 RND doub 358 n y 
C04 C03 RND doub 359 n y 
C02 C03 RND sing 360 n y 
C01 H1 RND sing 361 n n 
C02 H2 RND sing 362 n n 
C03 H3 RND sing 363 n n 
C04 H4 RND sing 364 n n 
N07 H5 RND sing 365 n n 
C09 H6 RND sing 366 n n 
C10 H7 RND sing 367 n n 
C10 H8 RND sing 368 n n 
C12 H10 RND sing 369 n n 
C12 H11 RND sing 370 n n 
C13 H12 RND sing 371 n n 
C13 H13 RND sing 372 n n 
C14 H14 RND sing 373 n n 
C15 H15 RND sing 374 n n 
C15 H16 RND sing 375 n n 
C16 H17 RND sing 376 n n 
C16 H18 RND sing 377 n n 
N17 H19 RND sing 378 n n 
C19 H20 RND sing 379 n n 
C21 H21 RND sing 380 n n 
C21 H22 RND sing 381 n n 
N22 H23 RND sing 382 n n 
N22 H24 RND sing 383 n n 
N24 H26 RND sing 384 n n 
C25 H27 RND sing 385 n n 
C28 H28 RND sing 386 n n 
C29 H29 RND sing 387 n n 
C30 H30 RND sing 388 n n 
C31 H31 RND sing 389 n n 
#
_atom_sites.entry_id                     4NYM 
_atom_sites.fract_transf_matrix[1][1]    0.005353 
_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]    0.005353 
_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]    0.005596 
_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
D 4 MG Q 1 201 1002 MG MG . 
E 5 GNP Q 1 202 1001 GNP GNP . 
F 6 RND S 1 1101 401 RND RND . 
#
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 C01 RND . . . F 6 35.71 30.014 24.701 1 79.1 ? C01 RND 1101 S 1 
HETATM 2 C C02 RND . . . F 6 35.641 30.062 26.141 1 82.41 ? C02 RND 1101 S 1 
HETATM 3 C C03 RND . . . F 6 34.45 29.829 26.816 1 75.95 ? C03 RND 1101 S 1 
HETATM 4 C C04 RND . . . F 6 33.316 29.536 26.078 1 69.9 ? C04 RND 1101 S 1 
HETATM 5 C C05 RND . . . F 6 33.387 29.482 24.607 1 71.52 ? C05 RND 1101 S 1 
HETATM 6 C C06 RND . . . F 6 34.554 29.717 23.945 1 73.62 ? C06 RND 1101 S 1 
HETATM 7 N N07 RND . . . F 6 32.405 29.211 23.647 1 68.64 ? N07 RND 1101 S 1 
HETATM 8 C C08 RND . . . F 6 34.28 29.582 22.516 1 73.45 ? C08 RND 1101 S 1 
HETATM 9 C C09 RND . . . F 6 32.921 29.269 22.425 1 70.17 ? C09 RND 1101 S 1 
HETATM 10 C C10 RND . . . F 6 35.202 29.739 21.346 1 76.84 ? C10 RND 1101 S 1 
HETATM 11 N N11 RND . . . F 6 36.2 28.636 21.294 1 78.29 ? N11 RND 1101 S 1 
HETATM 12 C C12 RND . . . F 6 37.17 27.959 22.201 1 81.1 ? C12 RND 1101 S 1 
HETATM 13 C C13 RND . . . F 6 37.837 26.778 21.604 1 73.09 ? C13 RND 1101 S 1 
HETATM 14 C C14 RND . . . F 6 38.426 27.14 20.317 1 84.41 ? C14 RND 1101 S 1 
HETATM 15 C C15 RND . . . F 6 37.374 27.646 19.427 1 89.66 ? C15 RND 1101 S 1 
HETATM 16 C C16 RND . . . F 6 36.767 28.901 19.984 1 77.49 ? C16 RND 1101 S 1 
HETATM 17 N N17 RND . . . F 6 39.423 28.233 20.458 1 92.29 ? N17 RND 1101 S 1 
HETATM 18 C C18 RND . . . F 6 40.824 28.032 20.831 1 98.76 ? C18 RND 1101 S 1 
HETATM 19 C C19 RND . . . F 6 41.769 29.186 20.931 1 94.96 ? C19 RND 1101 S 1 
HETATM 20 O O20 RND . . . F 6 41.262 26.928 21.052 1 101.7 ? O20 RND 1101 S 1 
HETATM 21 C C21 RND . . . F 6 41.679 29.955 22.264 1 89.91 ? C21 RND 1101 S 1 
HETATM 22 N N22 RND . . . F 6 41.599 30.068 19.845 1 93.38 ? N22 RND 1101 S 1 
HETATM 23 C C23 RND . . . F 6 40.471 30.725 22.742 1 94.16 ? C23 RND 1101 S 1 
HETATM 24 N N24 RND . . . F 6 38.918 31.536 24.183 1 88.74 ? N24 RND 1101 S 1 
HETATM 25 C C25 RND . . . F 6 40.023 30.735 24.066 1 94.3 ? C25 RND 1101 S 1 
HETATM 26 C C26 RND . . . F 6 39.552 31.602 22.02 1 91.43 ? C26 RND 1101 S 1 
HETATM 27 C C27 RND . . . F 6 38.617 32.066 22.96 1 87.35 ? C27 RND 1101 S 1 
HETATM 28 C C28 RND . . . F 6 37.536 32.969 22.571 1 75.27 ? C28 RND 1101 S 1 
HETATM 29 C C29 RND . . . F 6 37.447 33.363 21.261 1 78.68 ? C29 RND 1101 S 1 
HETATM 30 C C30 RND . . . F 6 38.382 32.899 20.303 1 80.18 ? C30 RND 1101 S 1 
HETATM 31 C C31 RND . . . F 6 39.446 32.011 20.689 1 82.28 ? C31 RND 1101 S 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           314 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           31 
#