data_T8K
# 
_chem_comp.id                                    T8K 
_chem_comp.name                                  "[1-[(3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-3-methyl-imidazol-1-ium-2-yl]-nitrooxy-tris(oxidanyl)ruthenium" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H19 N3 O11 Ru" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "(4'~{R},6'~{S},7'~{S})-17'-fluoranyl-4',6'-dimethyl-13'-[(4~{S})-4-methyl-2-oxidanylidene-1,3-oxazolidin-3-yl]spiro[1,3-diazinane-5,8'-5,15-dioxa-2,14-diazatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(17),10,12(16),13-tetraene]-2,4,6-trione" 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2023-01-04 
_chem_comp.pdbx_modified_date                    2024-01-05 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        458.341 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     T8K 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        8C39 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
T8K O1  O1  O  0  1 N N N N N N 14.857 -36.059 -14.686 -3.660 -2.053 0.775  O1  T8K 1  
T8K O2  O2  O  -1 1 N N N N N N 14.355 -36.524 -12.466 -5.358 -0.871 1.184  O2  T8K 2  
T8K O3  O3  O  0  1 N N N N N N 12.641 -35.835 -13.892 -3.449 0.209  0.550  O3  T8K 3  
T8K N3  N1  N  0  1 Y N N N N N 11.874 -38.639 -12.890 -0.898 2.616  -0.833 N3  T8K 4  
T8K O4  O4  O  0  1 N N N N N N 12.223 -34.975 -11.058 -1.191 0.012  1.827  O4  T8K 5  
T8K O5  O5  O  0  1 N N N N N N 10.520 -33.860 -13.341 -1.072 -1.842 0.006  O5  T8K 6  
T8K N4  N2  N  1  1 Y N N N N N 11.323 -38.393 -10.763 0.802  1.388  -0.324 N4  T8K 7  
T8K O6  O6  O  0  1 N N N N N N 9.972  -36.612 -14.077 -2.218 -0.243 -1.697 O6  T8K 8  
T8K RU  RU1 RU 0  0 N N N N N N 11.027 -35.830 -12.638 -1.704 -0.115 0.065  RU  T8K 9  
T8K O11 O7  O  0  1 N N N N N N 8.857  -38.911 -9.978  0.634  -1.195 -1.564 O11 T8K 10 
T8K C37 C1  C  0  1 N N R N N N 9.645  -38.497 -8.980  1.875  -0.675 -1.083 C37 T8K 11 
T8K C36 C2  C  0  1 N N S N N N 8.724  -37.627 -7.984  2.776  -1.831 -0.637 C36 T8K 12 
T8K O13 O8  O  0  1 N N N N N N 7.547  -38.272 -7.227  3.084  -2.659 -1.760 O13 T8K 13 
T8K C35 C3  C  0  1 N N R N N N 9.614  -37.333 -6.906  4.071  -1.258 -0.052 C35 T8K 14 
T8K O15 O9  O  0  1 N N N N N N 9.503  -38.335 -5.891  4.776  -0.539 -1.066 O15 T8K 15 
T8K C34 C4  C  0  1 N N R N N N 11.035 -37.328 -7.355  3.726  -0.312 1.101  C34 T8K 16 
T8K C38 C5  C  0  1 N N N N N N 11.640 -37.974 -6.142  5.010  0.311  1.652  C38 T8K 17 
T8K O17 O10 O  0  1 N N N N N N 11.476 -37.106 -5.066  4.701  1.103  2.800  O17 T8K 18 
T8K O10 O11 O  0  1 N N N N N N 11.810 -37.580 -8.642  2.861  0.722  0.624  O10 T8K 19 
T8K C33 C6  C  0  1 N N R N N N 10.960 -38.091 -9.528  1.615  0.249  0.109  C33 T8K 20 
T8K C29 C7  C  0  1 Y N N N N N 11.483 -37.755 -11.933 -0.501 1.401  -0.395 C29 T8K 21 
T8K C32 C8  C  0  1 Y N N N N N 11.630 -39.674 -10.940 1.279  2.580  -0.709 C32 T8K 22 
T8K C31 C9  C  0  1 Y N N N N N 11.960 -39.830 -12.197 0.231  3.363  -1.032 C31 T8K 23 
T8K C30 C10 C  0  1 N N N N N N 12.153 -38.509 -14.194 -2.279 3.050  -1.059 C30 T8K 24 
T8K N   N3  N  1  1 N N N N N N 14.000 -36.115 -13.744 -4.190 -0.960 0.850  N   T8K 25 
T8K H4  H4  H  0  1 N N N N N N 8.013  -39.172 -9.628  0.724  -1.794 -2.318 H4  T8K 26 
T8K H5  H5  H  0  1 N N N N N N 9.868  -39.396 -8.386  2.368  -0.116 -1.878 H5  T8K 27 
T8K H6  H6  H  0  1 N N N N N N 8.390  -36.715 -8.501  2.262  -2.422 0.122  H6  T8K 28 
T8K H7  H7  H  0  1 N N N N N N 7.118  -37.616 -6.690  3.652  -3.412 -1.549 H7  T8K 29 
T8K H8  H8  H  0  1 N N N N N N 9.371  -36.347 -6.482  4.694  -2.072 0.319  H8  T8K 30 
T8K H9  H9  H  0  1 N N N N N N 10.098 -38.132 -5.179  5.022  -1.078 -1.830 H9  T8K 31 
T8K H10 H10 H  0  1 N N N N N N 11.299 -36.276 -7.171  3.224  -0.869 1.892  H10 T8K 32 
T8K H11 H11 H  0  1 N N N N N N 11.132 -38.927 -5.934  5.706  -0.480 1.932  H11 T8K 33 
T8K H12 H12 H  0  1 N N N N N N 12.711 -38.159 -6.312  5.465  0.941  0.887  H12 T8K 34 
T8K H13 H13 H  0  1 N N N N N N 11.852 -37.495 -4.285  5.470  1.529  3.203  H13 T8K 35 
T8K H14 H14 H  0  1 N N N N N N 10.586 -37.099 -9.822  1.086  -0.301 0.887  H14 T8K 36 
T8K H15 H15 H  0  1 N N N N N N 11.611 -40.445 -10.184 2.320  2.864  -0.753 H15 T8K 37 
T8K H16 H16 H  0  1 N N N N N N 12.261 -40.770 -12.636 0.275  4.384  -1.382 H16 T8K 38 
T8K H17 H17 H  0  1 N N N N N N 12.006 -37.462 -14.498 -2.569 2.821  -2.085 H17 T8K 39 
T8K H18 H18 H  0  1 N N N N N N 13.198 -38.800 -14.376 -2.941 2.528  -0.369 H18 T8K 40 
T8K H19 H19 H  0  1 N N N N N N 11.484 -39.158 -14.778 -2.354 4.124  -0.892 H19 T8K 41 
T8K H2  H2  H  0  1 N N N N N N 10.930 -33.209 -12.784 -0.162 -1.939 0.319  H2  T8K 42 
T8K H3  H3  H  0  1 N N N N N N 9.080  -36.747 -13.779 -1.503 -0.495 -2.298 H3  T8K 43 
T8K H1  H1  H  0  1 N N N N N N 13.123 -35.264 -11.150 -0.243 -0.116 1.971  H1  T8K 44 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
T8K O1  N   DOUB N N 1  
T8K C30 N3  SING N N 2  
T8K O6  RU  SING N N 3  
T8K O3  N   SING N N 4  
T8K O3  RU  SING N N 5  
T8K N   O2  SING N N 6  
T8K O5  RU  SING N N 7  
T8K N3  C31 SING Y N 8  
T8K N3  C29 SING Y N 9  
T8K RU  C29 SING N N 10 
T8K RU  O4  SING N N 11 
T8K C31 C32 DOUB Y N 12 
T8K C29 N4  DOUB Y N 13 
T8K C32 N4  SING Y N 14 
T8K N4  C33 SING N N 15 
T8K O11 C37 SING N N 16 
T8K C33 C37 SING N N 17 
T8K C33 O10 SING N N 18 
T8K C37 C36 SING N N 19 
T8K O10 C34 SING N N 20 
T8K C36 O13 SING N N 21 
T8K C36 C35 SING N N 22 
T8K C34 C35 SING N N 23 
T8K C34 C38 SING N N 24 
T8K C35 O15 SING N N 25 
T8K C38 O17 SING N N 26 
T8K O11 H4  SING N N 27 
T8K C37 H5  SING N N 28 
T8K C36 H6  SING N N 29 
T8K O13 H7  SING N N 30 
T8K C35 H8  SING N N 31 
T8K O15 H9  SING N N 32 
T8K C34 H10 SING N N 33 
T8K C38 H11 SING N N 34 
T8K C38 H12 SING N N 35 
T8K O17 H13 SING N N 36 
T8K C33 H14 SING N N 37 
T8K C32 H15 SING N N 38 
T8K C31 H16 SING N N 39 
T8K C30 H17 SING N N 40 
T8K C30 H18 SING N N 41 
T8K C30 H19 SING N N 42 
T8K O5  H2  SING N N 43 
T8K O6  H3  SING N N 44 
T8K O4  H1  SING N N 45 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
T8K InChI            InChI                1.06  "InChI=1S/C10H16N2O5.NO3.3H2O.Ru/c1-11-2-3-12(5-11)10-9(16)8(15)7(14)6(4-13)17-10;2-1(3)4;;;;/h2-3,6-10,13-16H,4H2,1H3;;3*1H2;/q+1;-1;;;;+4/p-3/t6-,7+,8+,9-,10-;;;;;/m1...../s1" 
T8K InChIKey         InChI                1.06  YHWXYWLAKQRSBE-BYNJHPACSA-K                                                                                                                                                       
T8K SMILES_CANONICAL CACTVS               3.385 "Cn1cc[n+]([C@@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)c1[Ru](O)(O)(O)O[N+]([O-])=O"                                                                                                 
T8K SMILES           CACTVS               3.385 "Cn1cc[n+]([CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)c1[Ru](O)(O)(O)O[N+]([O-])=O"                                                                                                       
T8K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cn1cc[n+](c1[Ru](O)(O)(O)O[N+](=O)[O-])C2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)O)O"                                                                                                   
T8K SMILES           "OpenEye OEToolkits" 2.0.7 "Cn1cc[n+](c1[Ru](O)(O)(O)O[N+](=O)[O-])C2C(C(C(C(O2)CO)O)O)O"                                                                                                                    
# 
_pdbx_chem_comp_identifier.comp_id           T8K 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "[1-[(3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-3-methyl-imidazol-1-ium-2-yl]-nitrooxy-tris(oxidanyl)ruthenium" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
T8K "Create component" 2023-01-04 PDBE 
T8K "Initial release"  2024-01-10 RCSB 
# 
