data_9DWD
#
_model_server_result.job_id            bYwzqf1nsQgGDjwStMYbQw 
_model_server_result.datetime_utc      '2024-12-01 01:14:08' 
_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          9dwd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":301}' 
#
_entry.id    9DWD 
#
_exptl.entry_id    9DWD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              968.282 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-[(1S)-1-(3-{4-chloro-3-[(methylsulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-methyl-3-(methylsulfonyl)but-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide 
_entity.pdbx_number_of_molecules    18 
_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            9DWD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9DWD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    octadecameric 
_pdbx_struct_assembly.oligomeric_count      18 
_pdbx_struct_assembly.details               author_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,EA,FA,GA,HA,IA,JA,KA 
_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    ? 
_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 S N N 
? 2 T N N 
? 2 U N N 
? 2 V N N 
? 2 W N N 
? 2 X N N 
? 2 Z N N 
? 2 AA N N 
? 2 BA N N 
? 2 CA N N 
? 2 DA N N 
? 2 EA N N 
? 2 FA N N 
? 2 GA N N 
? 2 HA N N 
? 2 IA N N 
? 2 JA N N 
? 2 KA N N 
#
_chem_comp.formula           'C39 H32 Cl F10 N7 O5 S2' 
_chem_comp.formula_weight    968.282 
_chem_comp.id                QNG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-[(1S)-1-(3-{4-chloro-3-[(methylsulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-methyl-3-(methylsulfonyl)but-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Lenacapavir 
#
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
C39 C36 QNG sing 329 n n 
C39 C37 QNG sing 330 n n 
F53 C40 QNG sing 331 n n 
F52 C40 QNG sing 332 n n 
C36 C37 QNG sing 333 n n 
C36 C31 QNG sing 334 n n 
C40 C35 QNG sing 335 n n 
C40 F64 QNG sing 336 n n 
C37 C38 QNG sing 337 n n 
C31 C35 QNG sing 338 n y 
C31 C32 QNG doub 339 n y 
C35 N34 QNG doub 340 n y 
F42 C38 QNG sing 341 n n 
C38 C32 QNG sing 342 n n 
C38 F41 QNG sing 343 n n 
C32 N33 QNG sing 344 n y 
N34 N33 QNG sing 345 n y 
N33 C30 QNG sing 346 n n 
F26 C24 QNG sing 347 n n 
C30 C28 QNG sing 348 n n 
C24 C23 QNG doub 349 n y 
C24 C25 QNG sing 350 n y 
C23 C22 QNG sing 351 n y 
C25 C20 QNG doub 352 n y 
C28 O29 QNG doub 353 n n 
C28 N43 QNG sing 354 n n 
C22 F27 QNG sing 355 n n 
C22 C21 QNG doub 356 n y 
N43 C01 QNG sing 357 n n 
O50 S48 QNG doub 358 n n 
C20 C21 QNG sing 359 n y 
C20 C19 QNG sing 360 n n 
C01 C19 QNG sing 361 n n 
C01 C05 QNG sing 362 n n 
O51 S48 QNG doub 363 n n 
S48 N17 QNG sing 364 n n 
S48 C49 QNG sing 365 n n 
N17 C16 QNG sing 366 n n 
C56 C46 QNG sing 367 n n 
N15 C16 QNG doub 368 n y 
N15 N14 QNG sing 369 n y 
C16 C09 QNG sing 370 n y 
C18 N14 QNG sing 371 n n 
C18 C60 QNG sing 372 n n 
N14 C08 QNG sing 373 n y 
C05 N06 QNG doub 374 n y 
C05 C13 QNG sing 375 n y 
N06 C02 QNG sing 376 n y 
C09 C08 QNG doub 377 n y 
C09 C10 QNG sing 378 n y 
O59 S55 QNG doub 379 n n 
C08 C07 QNG sing 380 n y 
F63 C60 QNG sing 381 n n 
CL47 C10 QNG sing 382 n n 
C60 F61 QNG sing 383 n n 
C60 F62 QNG sing 384 n n 
C10 C11 QNG doub 385 n y 
C46 C45 QNG sing 386 n n 
C46 S55 QNG sing 387 n n 
C46 C54 QNG sing 388 n n 
C07 C13 QNG sing 389 n n 
C07 C12 QNG doub 390 n y 
C45 C44 QNG trip 391 n n 
C13 C04 QNG doub 392 n y 
C44 C02 QNG sing 393 n n 
C02 C03 QNG doub 394 n y 
S55 O57 QNG doub 395 n n 
S55 C58 QNG sing 396 n n 
C11 C12 QNG sing 397 n y 
C04 C03 QNG sing 398 n y 
C01 H1 QNG sing 399 n n 
C03 H2 QNG sing 400 n n 
C04 H3 QNG sing 401 n n 
C11 H4 QNG sing 402 n n 
C12 H5 QNG sing 403 n n 
C18 H6 QNG sing 404 n n 
C18 H7 QNG sing 405 n n 
C19 H8 QNG sing 406 n n 
C19 H9 QNG sing 407 n n 
C21 H10 QNG sing 408 n n 
C23 H11 QNG sing 409 n n 
C25 H12 QNG sing 410 n n 
C30 H13 QNG sing 411 n n 
C30 H14 QNG sing 412 n n 
C36 H15 QNG sing 413 n n 
C37 H16 QNG sing 414 n n 
C39 H17 QNG sing 415 n n 
C39 H18 QNG sing 416 n n 
C49 H19 QNG sing 417 n n 
C49 H20 QNG sing 418 n n 
C49 H21 QNG sing 419 n n 
C54 H22 QNG sing 420 n n 
C54 H23 QNG sing 421 n n 
C54 H24 QNG sing 422 n n 
C56 H25 QNG sing 423 n n 
C56 H26 QNG sing 424 n n 
C56 H27 QNG sing 425 n n 
C58 H28 QNG sing 426 n n 
C58 H29 QNG sing 427 n n 
C58 H30 QNG sing 428 n n 
N17 H31 QNG sing 429 n n 
N43 H32 QNG sing 430 n n 
#
_atom_sites.entry_id                     9DWD 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
S 2 QNG A 1 301 402 QNG QNG . 
T 2 QNG B 1 301 402 QNG QNG . 
U 2 QNG C 1 301 402 QNG QNG . 
V 2 QNG D 1 301 402 QNG QNG . 
W 2 QNG E 1 301 402 QNG QNG . 
X 2 QNG F 1 301 402 QNG QNG . 
Y 3 IHP G 1 401 401 IHP IHP . 
Z 2 QNG G 1 402 402 QNG QNG . 
AA 2 QNG H 1 301 402 QNG QNG . 
BA 2 QNG I 1 301 402 QNG QNG . 
CA 2 QNG J 1 301 402 QNG QNG . 
DA 2 QNG K 1 301 402 QNG QNG . 
EA 2 QNG L 1 301 402 QNG QNG . 
FA 2 QNG M 1 301 402 QNG QNG . 
GA 2 QNG N 1 301 402 QNG QNG . 
HA 2 QNG O 1 301 402 QNG QNG . 
IA 2 QNG P 1 301 402 QNG QNG . 
JA 2 QNG Q 1 301 402 QNG QNG . 
KA 2 QNG R 1 301 402 QNG QNG . 
#
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 QNG . . . S 2 175.46 150.287 193.918 1 113.92 ? C01 QNG 301 A 1 
HETATM 2 C C02 QNG . . . S 2 176.781 151.578 197.199 1 113.85 ? C02 QNG 301 A 1 
HETATM 3 C C03 QNG . . . S 2 175.895 150.97 198.087 1 112.83 ? C03 QNG 301 A 1 
HETATM 4 C C04 QNG . . . S 2 174.899 150.167 197.617 1 112.58 ? C04 QNG 301 A 1 
HETATM 5 C C05 QNG . . . S 2 175.674 150.579 195.402 1 113.83 ? C05 QNG 301 A 1 
HETATM 6 C C07 QNG . . . S 2 173.559 149.029 196.238 1 116.44 ? C07 QNG 301 A 1 
HETATM 7 C C08 QNG . . . S 2 172.17 149.191 196.067 1 116.62 ? C08 QNG 301 A 1 
HETATM 8 C C09 QNG . . . S 2 171.348 148.103 196.065 1 117.03 ? C09 QNG 301 A 1 
HETATM 9 C C10 QNG . . . S 2 171.895 146.811 196.217 1 116.86 ? C10 QNG 301 A 1 
HETATM 10 C C11 QNG . . . S 2 173.268 146.647 196.371 1 113.39 ? C11 QNG 301 A 1 
HETATM 11 C C12 QNG . . . S 2 174.104 147.757 196.377 1 114.81 ? C12 QNG 301 A 1 
HETATM 12 C C13 QNG . . . S 2 174.795 149.968 196.277 1 114.22 ? C13 QNG 301 A 1 
HETATM 13 C C16 QNG . . . S 2 170.046 148.561 195.897 1 117.78 ? C16 QNG 301 A 1 
HETATM 14 C C18 QNG . . . S 2 171.371 151.76 195.791 1 118.26 ? C18 QNG 301 A 1 
HETATM 15 C C19 QNG . . . S 2 176.562 149.375 193.364 1 112.95 ? C19 QNG 301 A 1 
HETATM 16 C C20 QNG . . . S 2 175.967 148.726 192.095 1 111.23 ? C20 QNG 301 A 1 
HETATM 17 C C21 QNG . . . S 2 176.042 149.386 190.879 1 116.45 ? C21 QNG 301 A 1 
HETATM 18 C C22 QNG . . . S 2 175.5 148.809 189.742 1 115.62 ? C22 QNG 301 A 1 
HETATM 19 C C23 QNG . . . S 2 174.877 147.574 189.82 1 111.81 ? C23 QNG 301 A 1 
HETATM 20 C C24 QNG . . . S 2 174.798 146.919 191.04 1 115.25 ? C24 QNG 301 A 1 
HETATM 21 C C25 QNG . . . S 2 175.338 147.493 192.179 1 111.79 ? C25 QNG 301 A 1 
HETATM 22 C C28 QNG . . . S 2 174.054 151.993 192.752 1 114.33 ? C28 QNG 301 A 1 
HETATM 23 C C30 QNG . . . S 2 173.894 153.252 191.873 1 114.24 ? C30 QNG 301 A 1 
HETATM 24 C C31 QNG . . . S 2 173.256 152.249 188.415 1 113.49 ? C31 QNG 301 A 1 
HETATM 25 C C32 QNG . . . S 2 174.022 152.92 189.398 1 114.41 ? C32 QNG 301 A 1 
HETATM 26 C C35 QNG . . . S 2 172.198 151.654 189.045 1 115.78 ? C35 QNG 301 A 1 
HETATM 27 C C36 QNG . . . S 2 173.94 152.463 187.03 1 115.71 ? C36 QNG 301 A 1 
HETATM 28 C C37 QNG . . . S 2 175.286 153.11 187.279 1 118.47 ? C37 QNG 301 A 1 
HETATM 29 C C38 QNG . . . S 2 175.244 153.606 188.68 1 119.24 ? C38 QNG 301 A 1 
HETATM 30 C C39 QNG . . . S 2 174.431 153.565 186.119 1 119.63 ? C39 QNG 301 A 1 
HETATM 31 C C40 QNG . . . S 2 171.103 150.819 188.368 1 120.18 ? C40 QNG 301 A 1 
HETATM 32 C C44 QNG . . . S 2 177.911 152.49 197.712 1 111.88 ? C44 QNG 301 A 1 
HETATM 33 C C45 QNG . . . S 2 178.808 153.196 198.078 1 113.4 ? C45 QNG 301 A 1 
HETATM 34 C C46 QNG . . . S 2 179.98 154.086 198.537 1 121.07 ? C46 QNG 301 A 1 
HETATM 35 C C49 QNG . . . S 2 166.079 147.087 196.029 1 119.75 ? C49 QNG 301 A 1 
HETATM 36 C C54 QNG . . . S 2 180.925 153.256 199.431 1 118.57 ? C54 QNG 301 A 1 
HETATM 37 C C56 QNG . . . S 2 179.447 155.3 199.34 1 119.24 ? C56 QNG 301 A 1 
HETATM 38 C C58 QNG . . . S 2 182.412 155.568 197.57 1 116.24 ? C58 QNG 301 A 1 
HETATM 39 C C60 QNG . . . S 2 171.67 152.417 197.152 1 118.93 ? C60 QNG 301 A 1 
HETATM 40 F F26 QNG . . . S 2 174.186 145.701 191.12 1 126.1 ? F26 QNG 301 A 1 
HETATM 41 F F27 QNG . . . S 2 175.584 149.461 188.546 1 121.16 ? F27 QNG 301 A 1 
HETATM 42 F F41 QNG . . . S 2 176.403 153.284 189.328 1 119.06 ? F41 QNG 301 A 1 
HETATM 43 F F42 QNG . . . S 2 175.054 154.961 188.687 1 122.54 ? F42 QNG 301 A 1 
HETATM 44 F F52 QNG . . . S 2 170.101 151.641 187.936 1 120.85 ? F52 QNG 301 A 1 
HETATM 45 F F53 QNG . . . S 2 171.64 150.154 187.303 1 122.43 ? F53 QNG 301 A 1 
HETATM 46 F F61 QNG . . . S 2 172.688 153.313 196.987 1 119.39 ? F61 QNG 301 A 1 
HETATM 47 F F62 QNG . . . S 2 170.559 153.071 197.607 1 122.07 ? F62 QNG 301 A 1 
HETATM 48 F F63 QNG . . . S 2 172.04 151.46 198.055 1 115.42 ? F63 QNG 301 A 1 
HETATM 49 F F64 QNG . . . S 2 170.603 149.919 189.266 1 121.03 ? F64 QNG 301 A 1 
HETATM 50 N N06 QNG . . . S 2 176.664 151.375 195.86 1 114.76 ? N06 QNG 301 A 1 
HETATM 51 N N14 QNG . . . S 2 171.406 150.296 195.914 1 116.7 ? N14 QNG 301 A 1 
HETATM 52 N N15 QNG . . . S 2 170.079 149.891 195.8 1 116.88 ? N15 QNG 301 A 1 
HETATM 53 N N17 QNG . . . S 2 168.941 147.601 195.854 1 118.2 ? N17 QNG 301 A 1 
HETATM 54 N N33 QNG . . . S 2 173.432 152.737 190.576 1 113.05 ? N33 QNG 301 A 1 
HETATM 55 N N34 QNG . . . S 2 172.283 151.936 190.37 1 115.62 ? N34 QNG 301 A 1 
HETATM 56 N N43 QNG . . . S 2 175.39 151.492 193.115 1 113.68 ? N43 QNG 301 A 1 
HETATM 57 O O29 QNG . . . S 2 173.091 151.41 193.123 1 116.08 ? O29 QNG 301 A 1 
HETATM 58 O O50 QNG . . . S 2 167.194 149.557 195.716 1 120.82 ? O50 QNG 301 A 1 
HETATM 59 O O51 QNG . . . S 2 167.314 148.237 193.879 1 119.29 ? O51 QNG 301 A 1 
HETATM 60 O O57 QNG . . . S 2 180.046 155.501 196.201 1 124.58 ? O57 QNG 301 A 1 
HETATM 61 O O59 QNG . . . S 2 181.205 153.568 196.152 1 118.78 ? O59 QNG 301 A 1 
HETATM 62 S S48 QNG . . . S 2 167.397 148.152 195.342 1 126.66 ? S48 QNG 301 A 1 
HETATM 63 S S55 QNG . . . S 2 180.894 154.673 197.067 1 131.13 ? S55 QNG 301 A 1 
HETATM 64 CL CL47 QNG . . . S 2 171.253 145.145 196.277 1 127.36 ? CL47 QNG 301 A 1 
#
_model_server_stats.io_time_ms              42 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    36 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           64 
#