data_5F4U
#
_model_server_result.job_id            30q8iDnH9KvjPU4gXJltoQ 
_model_server_result.datetime_utc      '2024-11-29 10:45:47' 
_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          5f4u 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":508}' 
#
_entry.id    5F4U 
#
_exptl.entry_id    5F4U 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              488.946 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-[[carbamimidoyl(methyl)amino]methyl]-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide" 
_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            5F4U 
_cell.length_a            67.439 
_cell.length_b            128.123 
_cell.length_c            193.599 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5F4U 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 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,G,H,I,J,K,L,M,N,O,P,Q 
_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
? 3 I N N 
? 3 Q N 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
disulf ? disulf1 A SG CYS 6 A CYS 54 1_555 A SG CYS 26 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf2 A SG CYS 71 A CYS 119 1_555 A SG CYS 84 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf3 A SG CYS 97 A CYS 218 1_555 A SG CYS 126 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 A SG CYS 107 A CYS 228 1_555 A SG CYS 118 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf5 A SG CYS 175 A CYS 296 1_555 A SG CYS 194 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf6 A SG CYS 240 A CYS 378 1_555 A SG CYS 304 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf7 A SG CYS 247 A CYS 385 1_555 A SG CYS 277 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf8 B SG CYS 6 B CYS 54 1_555 B SG CYS 26 B CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf9 B SG CYS 71 B CYS 119 1_555 B SG CYS 84 B CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf10 B SG CYS 97 B CYS 218 1_555 B SG CYS 126 B CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf11 B SG CYS 107 B CYS 228 1_555 B SG CYS 118 B CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf12 B SG CYS 175 B CYS 296 1_555 B SG CYS 194 B CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf13 B SG CYS 240 B CYS 378 1_555 B SG CYS 304 B CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf14 B SG CYS 247 B CYS 385 1_555 B SG CYS 277 B CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
#
_chem_comp.formula           'C22 H26 Cl F N8 O2' 
_chem_comp.formula_weight    488.946 
_chem_comp.id                5VH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-[[carbamimidoyl(methyl)amino]methyl]-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide" 
_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
CAF CAG 5VH doub 1 n y 
CAF CAD 5VH sing 2 n y 
NBD CBC 5VH doub 3 n n 
CAG CAH 5VH sing 4 n y 
NBB CBC 5VH sing 5 n n 
NBB CBA 5VH sing 6 n n 
CBC NBE 5VH sing 7 n n 
CLAE CAD 5VH sing 8 n n 
CAD CAB 5VH doub 9 n y 
CBA CAZ 5VH sing 10 n n 
CAH NAI 5VH sing 11 n n 
CAH CAA 5VH doub 12 n y 
CAZ CAY 5VH sing 13 n n 
CAZ CAO 5VH sing 14 n n 
NAI CAJ 5VH sing 15 n n 
CAY CAX 5VH sing 16 n n 
OAM CAL 5VH doub 17 n n 
CAJ CAL 5VH sing 18 n n 
CAJ OAK 5VH doub 19 n n 
CAL NAN 5VH sing 20 n n 
CAB CAA 5VH sing 21 n y 
CAB FAC 5VH sing 22 n n 
NAN CAO 5VH sing 23 n n 
CAO CAP 5VH sing 24 n n 
CAX CAW 5VH doub 25 n y 
CAX CAP 5VH sing 26 n y 
CAW CAV 5VH sing 27 n y 
CAP CAQ 5VH doub 28 n y 
CAQ CAR 5VH sing 29 n y 
CAV CAR 5VH doub 30 n y 
CAR CAS 5VH sing 31 n n 
CAU NAT 5VH sing 32 n n 
CAS NAT 5VH sing 33 n n 
NAT CBF 5VH sing 34 n n 
CBF NBH 5VH doub 35 n n 
CBF NBG 5VH sing 36 n n 
CAA H1 5VH sing 37 n n 
CAF H2 5VH sing 38 n n 
CAG H3 5VH sing 39 n n 
NAI H4 5VH sing 40 n n 
NAN H5 5VH sing 41 n n 
CAO H6 5VH sing 42 n n 
CAQ H7 5VH sing 43 n n 
CAS H8 5VH sing 44 n n 
CAS H9 5VH sing 45 n n 
CAU H10 5VH sing 46 n n 
CAU H11 5VH sing 47 n n 
CAU H12 5VH sing 48 n n 
NBH H13 5VH sing 49 n n 
NBG H14 5VH sing 50 n n 
NBG H15 5VH sing 51 n n 
CAV H16 5VH sing 52 n n 
CAW H17 5VH sing 53 n n 
CAY H18 5VH sing 54 n n 
CAY H19 5VH sing 55 n n 
CAZ H20 5VH sing 56 n n 
CBA H21 5VH sing 57 n n 
CBA H22 5VH sing 58 n n 
NBB H23 5VH sing 59 n n 
NBE H24 5VH sing 60 n n 
NBE H25 5VH sing 61 n n 
NBD H26 5VH sing 62 n n 
#
_atom_sites.entry_id                     5F4U 
_atom_sites.fract_transf_matrix[1][1]    0.014828 
_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]    0.007805 
_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]    0.005165 
_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 NAG A 1 501 503 NAG NAG . 
D 2 NAG A 1 502 504 NAG NAG . 
E 2 NAG A 1 503 505 NAG NAG . 
F 2 NAG A 1 504 506 NAG NAG . 
G 2 NAG A 1 505 507 NAG NAG . 
H 2 NAG A 1 506 508 NAG NAG . 
I 3 5VH A 1 507 1 5VH DRG . 
J 2 NAG B 1 501 502 NAG NAG . 
K 2 NAG B 1 502 503 NAG NAG . 
L 2 NAG B 1 503 504 NAG NAG . 
M 2 NAG B 1 504 505 NAG NAG . 
N 2 NAG B 1 505 506 NAG NAG . 
O 2 NAG B 1 506 507 NAG NAG . 
P 2 NAG B 1 507 508 NAG NAG . 
Q 3 5VH B 1 508 2 5VH DRG . 
#
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 CAA 5VH . . . Q 3 -23.353 -6.263 21.227 1 20 ? CAA 5VH 508 B 1 
HETATM 2 C CAB 5VH . . . Q 3 -23.544 -7.629 21.406 1 20 ? CAB 5VH 508 B 1 
HETATM 3 F FAC 5VH . . . Q 3 -23.517 -8.161 22.657 1 20 ? FAC 5VH 508 B 1 
HETATM 4 C CAD 5VH . . . Q 3 -23.766 -8.449 20.304 1 20 ? CAD 5VH 508 B 1 
HETATM 5 CL CLAE 5VH . . . Q 3 -24.003 -10.144 20.528 1 20 ? CLAE 5VH 508 B 1 
HETATM 6 C CAF 5VH . . . Q 3 -23.795 -7.905 19.027 1 20 ? CAF 5VH 508 B 1 
HETATM 7 C CAG 5VH . . . Q 3 -23.604 -6.54 18.848 1 20 ? CAG 5VH 508 B 1 
HETATM 8 C CAH 5VH . . . Q 3 -23.383 -5.72 19.948 1 20 ? CAH 5VH 508 B 1 
HETATM 9 N NAI 5VH . . . Q 3 -23.198 -4.402 19.775 1 20 ? NAI 5VH 508 B 1 
HETATM 10 C CAJ 5VH . . . Q 3 -22.167 -3.789 20.439 1 20 ? CAJ 5VH 508 B 1 
HETATM 11 O OAK 5VH . . . Q 3 -21.415 -4.394 21.212 1 20 ? OAK 5VH 508 B 1 
HETATM 12 C CAL 5VH . . . Q 3 -21.853 -2.265 20.271 1 20 ? CAL 5VH 508 B 1 
HETATM 13 O OAM 5VH . . . Q 3 -22.58 -1.649 19.494 1 20 ? OAM 5VH 508 B 1 
HETATM 14 N NAN 5VH . . . Q 3 -20.855 -1.597 20.909 1 20 ? NAN 5VH 508 B 1 
HETATM 15 C CAO 5VH . . . Q 3 -20.47 -0.181 20.818 1 20 ? CAO 5VH 508 B 1 
HETATM 16 C CAP 5VH . . . Q 3 -19.734 0.188 21.948 1 20 ? CAP 5VH 508 B 1 
HETATM 17 C CAQ 5VH . . . Q 3 -20.174 0.515 23.163 1 20 ? CAQ 5VH 508 B 1 
HETATM 18 C CAR 5VH . . . Q 3 -19.283 0.858 24.17 1 20 ? CAR 5VH 508 B 1 
HETATM 19 C CAS 5VH . . . Q 3 -19.741 1.197 25.439 1 20 ? CAS 5VH 508 B 1 
HETATM 20 N NAT 5VH . . . Q 3 -20.032 2.638 25.485 1 20 ? NAT 5VH 508 B 1 
HETATM 21 C CAU 5VH . . . Q 3 -19.747 3.486 24.317 1 20 ? CAU 5VH 508 B 1 
HETATM 22 C CBF 5VH . . . Q 3 -20.561 3.221 26.579 1 20 ? CBF 5VH 508 B 1 
HETATM 23 N NBH 5VH . . . Q 3 -20.825 4.54 26.617 1 20 ? NBH 5VH 508 B 1 
HETATM 24 N NBG 5VH . . . Q 3 -20.835 2.479 27.664 1 20 ? NBG 5VH 508 B 1 
HETATM 25 C CAV 5VH . . . Q 3 -17.93 0.856 23.886 1 20 ? CAV 5VH 508 B 1 
HETATM 26 C CAW 5VH . . . Q 3 -17.523 0.511 22.607 1 20 ? CAW 5VH 508 B 1 
HETATM 27 C CAX 5VH . . . Q 3 -18.415 0.186 21.671 1 20 ? CAX 5VH 508 B 1 
HETATM 28 C CAY 5VH . . . Q 3 -18.2 -0.184 20.342 1 20 ? CAY 5VH 508 B 1 
HETATM 29 C CAZ 5VH . . . Q 3 -19.524 0.019 19.667 1 20 ? CAZ 5VH 508 B 1 
HETATM 30 C CBA 5VH . . . Q 3 -19.692 0.889 19.014 1 20 ? CBA 5VH 508 B 1 
HETATM 31 N NBB 5VH . . . Q 3 -20.93 0.605 17.986 1 20 ? NBB 5VH 508 B 1 
HETATM 32 C CBC 5VH . . . Q 3 -22.078 1.257 17.374 1 20 ? CBC 5VH 508 B 1 
HETATM 33 N NBE 5VH . . . Q 3 -22.611 1.884 18.189 1 20 ? NBE 5VH 508 B 1 
HETATM 34 N NBD 5VH . . . Q 3 -23.332 1.098 16.553 1 20 ? NBD 5VH 508 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           34 
#