data_8BY0
#
_model_server_result.job_id            vSyOqBPwJ2x147rOW9dQNg 
_model_server_result.datetime_utc      '2025-01-10 16:36:43' 
_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          8by0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    8BY0 
#
_exptl.entry_id    8BY0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              847.487 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "tert-butyl 7'-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-1-chloranyl-2,3,4,5,6-pentamethyl-spiro[1$l^{8}-iridapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexane-1,2'-3-aza-1-azonia-2$l^{8}-iridatricyclo[6.3.1.0^{4,12}]dodeca-1(11),4,6,8(12),9-pentaene]-3'-carboxylate" 
_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            8BY0 
_cell.length_a            57.428 
_cell.length_b            57.428 
_cell.length_c            183.123 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8BY0 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        98 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 41 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 8_665 -y+1,-x+1,-z 0 -1 0 -1 0 0 0 0 -1 57.428 57.428 0 
3 'crystal symmetry operation' 10_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 57.428 57.428 0 
4 'crystal symmetry operation' 15_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 
#
_chem_comp.formula           'C34 H45 Cl Ir N5 O4 S 1' 
_chem_comp.formula_weight    847.487 
_chem_comp.id                NOF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "tert-butyl 7'-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-1-chloranyl-2,3,4,5,6-pentamethyl-spiro[1$l^{8}-iridapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexane-1,2'-3-aza-1-azonia-2$l^{8}-iridatricyclo[6.3.1.0^{4,12}]dodeca-1(11),4,6,8(12),9-pentaene]-3'-carboxylate" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'iridium catalyst for CH activation' 
#
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
N1 C12 NOF sing 224 n y 
N1 IR1 NOF sing 225 n n 
N1 C18 NOF doub 226 n y 
N3 C26 NOF sing 227 n n 
N3 C29 NOF sing 228 n n 
C4 C3 NOF sing 229 n n 
C5 C6 NOF sing 230 n n 
C5 C7 NOF sing 231 n n 
C5 C3 NOF sing 232 n n 
C5 IR1 NOF sing 233 n n 
C7 C8 NOF sing 234 n n 
C7 C9 NOF sing 235 n n 
C7 IR1 NOF sing 236 n n 
C10 C9 NOF sing 237 n n 
C13 C15 NOF sing 238 n y 
C13 C11 NOF doub 239 n y 
C15 C16 NOF doub 240 n y 
C17 C14 NOF sing 241 n y 
C17 C19 NOF doub 242 n y 
C20 C21 NOF sing 243 n n 
C20 N2 NOF sing 244 n n 
C20 O1 NOF doub 245 n n 
C21 C22 NOF sing 246 n n 
C22 C23 NOF sing 247 n n 
C24 C23 NOF sing 248 n n 
C24 C25 NOF sing 249 n n 
C26 C28 NOF sing 250 n n 
C26 C25 NOF sing 251 n n 
C28 C27 NOF sing 252 n n 
C28 N4 NOF sing 253 n n 
C1 C2 NOF sing 254 n n 
C1 C3 NOF sing 255 n n 
C1 C9 NOF sing 256 n n 
C1 IR1 NOF sing 257 n n 
C3 IR1 NOF sing 258 n n 
C9 IR1 NOF sing 259 n n 
C11 C12 NOF sing 260 n y 
C11 N5 NOF sing 261 n n 
C12 C14 NOF doub 262 n y 
IR1 N5 NOF sing 263 n n 
C14 C16 NOF sing 264 n y 
C16 N2 NOF sing 265 n n 
C18 C19 NOF sing 266 n y 
C25 S1 NOF sing 267 n n 
S1 C27 NOF sing 268 n n 
N4 C29 NOF sing 269 n n 
C29 O2 NOF doub 270 n n 
N5 C30 NOF sing 271 n n 
C30 O3 NOF doub 272 n n 
C30 O4 NOF sing 273 n n 
O4 C31 NOF sing 274 n n 
C31 C32 NOF sing 275 n n 
C31 C33 NOF sing 276 n n 
C31 C34 NOF sing 277 n n 
IR1 CL46 NOF sing 278 n n 
N3 H1 NOF sing 279 n n 
C4 H2 NOF sing 280 n n 
C4 H3 NOF sing 281 n n 
C4 H4 NOF sing 282 n n 
C6 H5 NOF sing 283 n n 
C6 H6 NOF sing 284 n n 
C6 H7 NOF sing 285 n n 
C8 H8 NOF sing 286 n n 
C8 H9 NOF sing 287 n n 
C8 H10 NOF sing 288 n n 
C10 H11 NOF sing 289 n n 
C10 H12 NOF sing 290 n n 
C10 H13 NOF sing 291 n n 
C13 H14 NOF sing 292 n n 
C15 H15 NOF sing 293 n n 
C17 H16 NOF sing 294 n n 
C21 H17 NOF sing 295 n n 
C21 H18 NOF sing 296 n n 
C22 H19 NOF sing 297 n n 
C22 H20 NOF sing 298 n n 
C24 H21 NOF sing 299 n n 
C24 H22 NOF sing 300 n n 
C26 H23 NOF sing 301 n n 
C28 H24 NOF sing 302 n n 
C2 H25 NOF sing 303 n n 
C2 H26 NOF sing 304 n n 
C2 H27 NOF sing 305 n n 
C18 H28 NOF sing 306 n n 
C19 H29 NOF sing 307 n n 
N2 H30 NOF sing 308 n n 
C23 H31 NOF sing 309 n n 
C23 H32 NOF sing 310 n n 
C25 H33 NOF sing 311 n n 
C27 H34 NOF sing 312 n n 
C27 H35 NOF sing 313 n n 
N4 H36 NOF sing 314 n n 
C32 H37 NOF sing 315 n n 
C32 H38 NOF sing 316 n n 
C32 H39 NOF sing 317 n n 
C33 H40 NOF sing 318 n n 
C33 H41 NOF sing 319 n n 
C33 H42 NOF sing 320 n n 
C34 H43 NOF sing 321 n n 
C34 H44 NOF sing 322 n n 
C34 H45 NOF sing 323 n n 
#
_atom_sites.entry_id                     8BY0 
_atom_sites.fract_transf_matrix[1][1]    0.017413 
_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]    0.017413 
_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]    0.005461 
_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 NOF A 1 201 201 NOF LIG . 
C 3 SO4 A 1 202 1 SO4 SO4 . 
D 3 SO4 A 1 203 2 SO4 SO4 . 
E 4 HOH A 1 301 12 HOH HOH . 
E 4 HOH A 2 302 1 HOH HOH . 
E 4 HOH A 3 303 11 HOH HOH . 
E 4 HOH A 4 304 5 HOH HOH . 
E 4 HOH A 5 305 13 HOH HOH . 
E 4 HOH A 6 306 8 HOH HOH . 
E 4 HOH A 7 307 2 HOH HOH . 
E 4 HOH A 8 308 7 HOH HOH . 
E 4 HOH A 9 309 6 HOH HOH . 
E 4 HOH A 10 310 9 HOH HOH . 
E 4 HOH A 11 311 10 HOH HOH . 
E 4 HOH A 12 312 3 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 N N1 NOF . . . B 2 24.331 26.945 -16.007 1 71.32 0 N1 NOF 201 A 1 
HETATM 2 N N3 NOF . . . B 2 15.894 29.039 -9.741 1 39.49 0 N3 NOF 201 A 1 
HETATM 3 C C4 NOF . . . B 2 27.295 27.469 -14.717 1 68.38 0 C4 NOF 201 A 1 
HETATM 4 C C5 NOF . . . B 2 27.83 26.437 -16.979 1 69.57 0 C5 NOF 201 A 1 
HETATM 5 C C6 NOF . . . B 2 28.374 25.094 -16.571 1 67.77 0 C6 NOF 201 A 1 
HETATM 6 C C7 NOF . . . B 2 27.783 26.811 -18.317 1 76.28 0 C7 NOF 201 A 1 
HETATM 7 C C8 NOF . . . B 2 28.25 25.96 -19.479 1 73.15 0 C8 NOF 201 A 1 
HETATM 8 C C10 NOF . . . B 2 27.003 28.803 -19.755 1 69.33 0 C10 NOF 201 A 1 
HETATM 9 C C13 NOF . . . B 2 23.547 23.241 -16.57 1 57.41 0 C13 NOF 201 A 1 
HETATM 10 C C15 NOF . . . B 2 22.457 23.079 -15.651 1 58.13 0 C15 NOF 201 A 1 
HETATM 11 C C17 NOF . . . B 2 22.173 26.73 -14.171 1 70.91 0 C17 NOF 201 A 1 
HETATM 12 C C20 NOF . . . B 2 19.651 24.502 -14.281 1 40.08 0 C20 NOF 201 A 1 
HETATM 13 C C21 NOF . . . B 2 18.421 24.048 -13.518 1 38.35 0 C21 NOF 201 A 1 
HETATM 14 C C22 NOF . . . B 2 17.568 25.198 -13.01 1 35.74 0 C22 NOF 201 A 1 
HETATM 15 C C24 NOF . . . B 2 17.398 27.067 -11.34 1 33.12 0 C24 NOF 201 A 1 
HETATM 16 C C26 NOF . . . B 2 17.287 29.062 -9.682 1 36.69 0 C26 NOF 201 A 1 
HETATM 17 C C28 NOF . . . B 2 17.687 29.256 -8.118 1 39.95 0 C28 NOF 201 A 1 
HETATM 18 C C1 NOF . . . B 2 27.031 28.556 -17.127 1 70.19 0 C1 NOF 201 A 1 
HETATM 19 C C2 NOF . . . B 2 26.481 29.932 -16.821 1 69.16 0 C2 NOF 201 A 1 
HETATM 20 C C3 NOF . . . B 2 27.39 27.501 -16.229 1 70.2 0 C3 NOF 201 A 1 
HETATM 21 C C9 NOF . . . B 2 27.329 28.129 -18.422 1 76.23 0 C9 NOF 201 A 1 
HETATM 22 C C11 NOF . . . B 2 24.144 24.558 -16.69 1 62.06 0 C11 NOF 201 A 1 
HETATM 23 C C12 NOF . . . B 2 23.666 25.691 -15.878 1 61.62 0 C12 NOF 201 A 1 
HETATM 24 IR IR1 NOF . . . B 2 25.73 26.82 -17.518 1 65.94 0 IR1 NOF 201 A 1 
HETATM 25 C C14 NOF . . . B 2 22.585 25.542 -14.941 1 61.42 0 C14 NOF 201 A 1 
HETATM 26 C C16 NOF . . . B 2 21.99 24.2 -14.837 1 54.63 0 C16 NOF 201 A 1 
HETATM 27 C C18 NOF . . . B 2 23.926 28.134 -15.323 1 68.35 0 C18 NOF 201 A 1 
HETATM 28 C C19 NOF . . . B 2 22.844 28.031 -14.361 1 68.84 0 C19 NOF 201 A 1 
HETATM 29 N N2 NOF . . . B 2 20.883 23.76 -14.014 1 47.24 0 N2 NOF 201 A 1 
HETATM 30 O O1 NOF . . . B 2 19.577 25.598 -15.172 1 39.42 0 O1 NOF 201 A 1 
HETATM 31 C C23 NOF . . . B 2 18.234 25.877 -11.791 1 35.22 0 C23 NOF 201 A 1 
HETATM 32 C C25 NOF . . . B 2 18.015 27.779 -10.205 1 38.79 0 C25 NOF 201 A 1 
HETATM 33 S S1 NOF . . . B 2 17.829 26.68 -8.775 1 39.93 0 S1 NOF 201 A 1 
HETATM 34 C C27 NOF . . . B 2 18.409 27.855 -7.771 1 40.45 0 C27 NOF 201 A 1 
HETATM 35 N N4 NOF . . . B 2 16.382 29.342 -7.487 1 41.88 0 N4 NOF 201 A 1 
HETATM 36 C C29 NOF . . . B 2 15.349 29.185 -8.476 1 40.92 0 C29 NOF 201 A 1 
HETATM 37 O O2 NOF . . . B 2 14.14 29.197 -8.213 1 44.93 0 O2 NOF 201 A 1 
HETATM 38 N N5 NOF . . . B 2 25.264 24.799 -17.553 1 69.04 0 N5 NOF 201 A 1 
HETATM 39 C C30 NOF . . . B 2 25.494 24.109 -18.83 1 72.61 0 C30 NOF 201 A 1 
HETATM 40 O O3 NOF . . . B 2 25.656 24.796 -19.879 1 64.69 0 O3 NOF 201 A 1 
HETATM 41 O O4 NOF . . . B 2 26.137 22.845 -18.562 1 77.54 0 O4 NOF 201 A 1 
HETATM 42 C C31 NOF . . . B 2 25.575 21.659 -19.196 1 81.59 0 C31 NOF 201 A 1 
HETATM 43 C C32 NOF . . . B 2 25.761 20.455 -18.221 1 74.05 0 C32 NOF 201 A 1 
HETATM 44 C C33 NOF . . . B 2 24.076 21.793 -19.585 1 78.76 0 C33 NOF 201 A 1 
HETATM 45 C C34 NOF . . . B 2 26.349 21.357 -20.504 1 79.14 0 C34 NOF 201 A 1 
HETATM 46 CL CL46 NOF . . . B 2 24.616 27.331 -19.951 1 76.43 0 CL46 NOF 201 A 1 
HETATM 47 H H2 NOF . . . B 2 27.029 26.586 -14.427 1 68.82 0 H2 NOF 201 A 1 
HETATM 48 H H3 NOF . . . B 2 26.64 28.119 -14.419 1 68.91 0 H3 NOF 201 A 1 
HETATM 49 H H4 NOF . . . B 2 28.16 27.686 -14.336 1 68.91 0 H4 NOF 201 A 1 
HETATM 50 H H5 NOF . . . B 2 27.878 24.392 -17.019 1 68.33 0 H5 NOF 201 A 1 
HETATM 51 H H6 NOF . . . B 2 28.29 24.984 -15.611 1 68.29 0 H6 NOF 201 A 1 
HETATM 52 H H7 NOF . . . B 2 29.309 25.032 -16.82 1 68.32 0 H7 NOF 201 A 1 
HETATM 53 H H8 NOF . . . B 2 29.211 26.065 -19.595 1 74.07 0 H8 NOF 201 A 1 
HETATM 54 H H9 NOF . . . B 2 27.795 26.221 -20.298 1 74.04 0 H9 NOF 201 A 1 
HETATM 55 H H10 NOF . . . B 2 28.071 25.023 -19.294 1 74.03 0 H10 NOF 201 A 1 
HETATM 56 H H11 NOF . . . B 2 26.684 28.146 -20.39 1 71.41 0 H11 NOF 201 A 1 
HETATM 57 H H12 NOF . . . B 2 27.797 29.208 -20.125 1 71.41 0 H12 NOF 201 A 1 
HETATM 58 H H13 NOF . . . B 2 26.328 29.488 -19.621 1 71.4 0 H13 NOF 201 A 1 
HETATM 59 H H14 NOF . . . B 2 24.062 22.497 -16.779 1 58.8 0 H14 NOF 201 A 1 
HETATM 60 H H15 NOF . . . B 2 21.9 22.346 -15.749 1 56.91 0 H15 NOF 201 A 1 
HETATM 61 H H16 NOF . . . B 2 21.539 26.638 -13.496 1 68.07 0 H16 NOF 201 A 1 
HETATM 62 H H17 NOF . . . B 2 18.715 23.527 -12.757 1 38.14 0 H17 NOF 201 A 1 
HETATM 63 H H18 NOF . . . B 2 17.881 23.486 -14.096 1 38.12 0 H18 NOF 201 A 1 
HETATM 64 H H19 NOF . . . B 2 16.7 24.855 -12.746 1 36.22 0 H19 NOF 201 A 1 
HETATM 65 H H20 NOF . . . B 2 17.449 25.851 -13.717 1 36.23 0 H20 NOF 201 A 1 
HETATM 66 H H21 NOF . . . B 2 16.519 26.75 -11.078 1 34.9 0 H21 NOF 201 A 1 
HETATM 67 H H22 NOF . . . B 2 17.302 27.684 -12.083 1 34.88 0 H22 NOF 201 A 1 
HETATM 68 H H25 NOF . . . B 2 25.513 29.914 -16.871 1 69.48 0 H25 NOF 201 A 1 
HETATM 69 H H26 NOF . . . B 2 26.815 30.562 -17.477 1 69.48 0 H26 NOF 201 A 1 
HETATM 70 H H27 NOF . . . B 2 26.758 30.206 -15.933 1 69.48 0 H27 NOF 201 A 1 
HETATM 71 H H28 NOF . . . B 2 24.531 28.831 -15.231 1 69.15 0 H28 NOF 201 A 1 
HETATM 72 H H29 NOF . . . B 2 22.801 28.66 -13.678 1 69.2 0 H29 NOF 201 A 1 
HETATM 73 H H30 NOF . . . B 2 21.038 23.431 -13.201 1 47 0 H30 NOF 201 A 1 
HETATM 74 H H31 NOF . . . B 2 19.12 26.186 -12.036 1 34.85 0 H31 NOF 201 A 1 
HETATM 75 H H32 NOF . . . B 2 18.306 25.231 -11.073 1 34.86 0 H32 NOF 201 A 1 
HETATM 76 H H34 NOF . . . B 2 18.941 27.7 -7.025 1 40.2 0 H34 NOF 201 A 1 
HETATM 77 H H37 NOF . . . B 2 26.643 20.501 -17.815 1 76.29 0 H37 NOF 201 A 1 
HETATM 78 H H38 NOF . . . B 2 25.675 19.623 -18.715 1 76.29 0 H38 NOF 201 A 1 
HETATM 79 H H39 NOF . . . B 2 25.083 20.491 -17.527 1 76.25 0 H39 NOF 201 A 1 
HETATM 80 H H40 NOF . . . B 2 23.62 22.423 -18.999 1 79.48 0 H40 NOF 201 A 1 
HETATM 81 H H41 NOF . . . B 2 23.643 20.917 -19.516 1 79.58 0 H41 NOF 201 A 1 
HETATM 82 H H42 NOF . . . B 2 24.01 22.111 -20.509 1 79.59 0 H42 NOF 201 A 1 
HETATM 83 H H43 NOF . . . B 2 27.266 21.123 -20.29 1 79.89 0 H43 NOF 201 A 1 
HETATM 84 H H44 NOF . . . B 2 26.34 22.142 -21.073 1 79.89 0 H44 NOF 201 A 1 
HETATM 85 H H45 NOF . . . B 2 25.926 20.617 -20.966 1 79.88 0 H45 NOF 201 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           85 
#