data_S9F
# 
_chem_comp.id                                    S9F 
_chem_comp.name                                  "[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-1$l^{4},3,5,7-tetrazabicyclo[4.3.0]nona-1(6),3,8-trien-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H17 N5 O14 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    -1 
_chem_comp.pdbx_initial_date                     2023-08-24 
_chem_comp.pdbx_modified_date                    2024-01-19 
_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                        524.188 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     S9F 
_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        8TXO 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
S9F O13 O1  O 0  1 N N N N N N 123.422 128.215 138.120 0.943  1.512  0.006  O13 S9F 1  
S9F O25 O2  O 0  1 N N N N N N 124.178 130.244 130.902 -7.032 -3.254 1.589  O25 S9F 2  
S9F C14 C1  C 0  1 N N N N N N 123.486 126.959 137.443 -0.137 2.358  0.408  C14 S9F 3  
S9F C15 C2  C 0  1 N N R N N N 122.067 126.574 136.993 -1.387 2.007  -0.401 C15 S9F 4  
S9F C16 C3  C 0  1 N N S N N N 122.127 125.754 135.645 -2.533 2.991  -0.072 C16 S9F 5  
S9F C17 C4  C 0  1 N N R N N N 120.987 126.379 134.779 -3.802 2.109  -0.093 C17 S9F 6  
S9F C19 C5  C 0  1 N N R N N N 120.984 127.633 135.122 -3.273 0.698  -0.432 C19 S9F 7  
S9F C21 C6  C 0  1 N N N N N N 122.931 129.060 134.821 -3.660 -0.882 1.513  C21 S9F 8  
S9F C22 C7  C 0  1 N N N N N N 123.611 129.626 133.754 -4.613 -1.762 1.845  C22 S9F 9  
S9F C24 C8  C 0  1 N N N N N N 123.271 129.569 131.196 -6.706 -2.451 0.730  C24 S9F 10 
S9F C27 C9  C 0  1 N N N N N N 121.342 128.231 130.549 -7.156 -1.406 -1.279 C27 S9F 11 
S9F C30 C10 C 0  1 N N N N N N 121.959 128.494 132.980 -5.200 -0.880 -0.062 C30 S9F 12 
S9F N20 N1  N 0  1 N N N N N N 121.939 128.377 134.355 -4.022 -0.319 0.310  N20 S9F 13 
S9F N23 N2  N -1 1 N N N N N N 122.995 129.264 132.645 -5.560 -1.755 0.868  N23 S9F 14 
S9F N26 N3  N 0  1 N N N N N N 122.432 129.040 130.196 -7.490 -2.270 -0.338 N26 S9F 15 
S9F N28 N4  N 0  1 N N N N N N 120.481 127.682 129.535 -7.966 -1.230 -2.368 N28 S9F 16 
S9F N29 N5  N 0  1 N N N N N N 121.083 127.942 131.932 -6.001 -0.690 -1.162 N29 S9F 17 
S9F O02 O3  O 0  1 N N N N N N 123.037 127.862 140.671 2.320  1.462  2.121  O02 S9F 18 
S9F O03 O4  O 0  1 N N N N N N 124.533 129.693 139.946 3.072  3.029  0.290  O03 S9F 19 
S9F O04 O5  O 0  1 N N N N N N 125.379 127.254 139.713 3.336  0.424  0.057  O04 S9F 20 
S9F O06 O6  O 0  1 N N N N N N 124.264 124.946 139.919 5.615  0.734  1.095  O06 S9F 21 
S9F O07 O7  O 0  1 N N N N N N 126.675 125.110 140.303 4.356  -1.374 1.681  O07 S9F 22 
S9F O08 O8  O 0  1 N N N N N N 125.088 126.039 142.066 5.396  -1.020 -0.707 O08 S9F 23 
S9F O10 O9  O 0  1 N N N N N N 125.705 128.529 142.396 7.881  -0.720 -0.383 O10 S9F 24 
S9F O11 O10 O 0  1 N N N N N N 125.496 127.082 144.405 6.980  -3.076 -0.291 O11 S9F 25 
S9F O12 O11 O 0  1 N N N N N N 127.438 126.805 142.852 7.116  -1.750 -2.557 O12 S9F 26 
S9F O18 O12 O 0  1 N N N N N N 119.706 125.756 135.145 -4.707 2.560  -1.102 O18 S9F 27 
S9F O31 O13 O 0  1 N N N N N N 121.380 127.656 136.738 -1.891 0.711  -0.012 O31 S9F 28 
S9F O32 O14 O 0  1 N N N N N N 121.878 124.460 135.872 -2.616 4.012  -1.068 O32 S9F 29 
S9F P01 P1  P 0  1 N N N N N N 124.080 128.288 139.652 2.415  1.604  0.651  P01 S9F 30 
S9F P05 P2  P 0  1 N N N N N N 125.350 125.796 140.488 4.696  -0.287 0.544  P05 S9F 31 
S9F P09 P3  P 0  1 N N N N N N 125.944 127.135 142.948 6.866  -1.622 -0.972 P09 S9F 32 
S9F H1  H1  H 0  1 N N N N N N 124.143 127.044 136.565 -0.337 2.210  1.469  H1  S9F 33 
S9F H2  H2  H 0  1 N N N N N N 123.881 126.190 138.124 0.132  3.399  0.230  H2  S9F 34 
S9F H3  H3  H 0  1 N N N N N N 121.600 125.946 137.766 -1.166 2.026  -1.468 H3  S9F 35 
S9F H4  H4  H 0  1 N N N N N N 123.097 125.926 135.156 -2.388 3.429  0.915  H4  S9F 36 
S9F H5  H5  H 0  1 N N N N N N 121.207 126.216 133.714 -4.285 2.112  0.884  H5  S9F 37 
S9F H6  H6  H 0  1 N N N N N N 119.987 128.088 135.026 -3.343 0.513  -1.504 H6  S9F 38 
S9F H8  H8  H 0  1 N N N N N N 123.187 129.171 135.864 -2.774 -0.652 2.086  H8  S9F 39 
S9F H9  H9  H 0  1 N N N N N N 124.489 130.252 133.819 -4.628 -2.373 2.736  H9  S9F 40 
S9F H10 H10 H 0  1 N N N N N N 120.658 127.876 128.570 -8.787 -1.740 -2.449 H10 S9F 41 
S9F H11 H11 H 0  1 N N N N N N 119.706 127.106 129.795 -7.719 -0.595 -3.058 H11 S9F 42 
S9F H12 H12 H 0  1 N N N N N N 120.306 127.365 132.184 -5.748 -0.052 -1.848 H12 S9F 43 
S9F H13 H13 H 0  1 N N N N N N 124.072 130.022 140.709 3.165  3.190  -0.659 H13 S9F 44 
S9F H14 H14 H 0  1 N N N N N N 126.543 124.279 139.862 3.757  -2.075 1.389  H14 S9F 45 
S9F H15 H15 H 0  1 N N N N N N 125.160 127.932 144.665 6.343  -3.720 -0.629 H15 S9F 46 
S9F H16 H16 H 0  1 N N N N N N 127.901 127.540 142.468 7.984  -2.106 -2.790 H16 S9F 47 
S9F H17 H17 H 0  1 N N N N N N 119.009 126.133 134.621 -5.024 3.464  -0.971 H17 S9F 48 
S9F H19 H19 H 0  1 N N N N N N 121.918 123.981 135.053 -3.319 4.658  -0.911 H19 S9F 49 
# 
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 
S9F O13 C14 SING N N 1  
S9F O13 P01 SING N N 2  
S9F O25 C24 DOUB N N 3  
S9F C14 C15 SING N N 4  
S9F C15 C16 SING N N 5  
S9F C15 O31 SING N N 6  
S9F C16 C17 SING N N 7  
S9F C16 O32 SING N N 8  
S9F C17 C19 SING N N 9  
S9F C17 O18 SING N N 10 
S9F C19 N20 SING N N 11 
S9F C21 C22 DOUB N N 12 
S9F C21 N20 SING N N 13 
S9F C22 N23 SING N N 14 
S9F C24 N23 SING N N 15 
S9F C24 N26 SING N N 16 
S9F C27 N26 DOUB N N 17 
S9F C27 N28 SING N N 18 
S9F C27 N29 SING N N 19 
S9F C30 N20 SING N N 20 
S9F C30 N23 DOUB N N 21 
S9F C30 N29 SING N N 22 
S9F O02 P01 DOUB N N 23 
S9F O03 P01 SING N N 24 
S9F O04 P01 SING N N 25 
S9F O04 P05 SING N N 26 
S9F O06 P05 DOUB N N 27 
S9F O07 P05 SING N N 28 
S9F O08 P05 SING N N 29 
S9F O08 P09 SING N N 30 
S9F O10 P09 DOUB N N 31 
S9F O11 P09 SING N N 32 
S9F O12 P09 SING N N 33 
S9F C14 H1  SING N N 34 
S9F C14 H2  SING N N 35 
S9F C15 H3  SING N N 36 
S9F C16 H4  SING N N 37 
S9F C17 H5  SING N N 38 
S9F C19 H6  SING N N 39 
S9F C21 H8  SING N N 40 
S9F C22 H9  SING N N 41 
S9F N28 H10 SING N N 42 
S9F N28 H11 SING N N 43 
S9F N29 H12 SING N N 44 
S9F O03 H13 SING N N 45 
S9F O07 H14 SING N N 46 
S9F O11 H15 SING N N 47 
S9F O12 H16 SING N N 48 
S9F O18 H17 SING N N 49 
S9F O32 H19 SING N N 50 
S9F C19 O31 SING N N 51 
# 
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 
S9F InChI            InChI                1.06  "InChI=1S/C10H17N5O14P3/c11-8-12-9-14(1-2-15(9)10(18)13-8)7-6(17)5(16)4(27-7)3-26-31(22,23)29-32(24,25)28-30(19,20)21/h1-2,4-7,16-17H,3H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,12,13,18)/q-1/t4-,5-,6-,7-/m1/s1" 
S9F InChIKey         InChI                1.06  QAJSSYBGBVOZGX-DBRKOABJSA-N                                                                                                                                                                                       
S9F SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)[N-]2=C(N1)N(C=C2)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O"                                                                                                                  
S9F SMILES           CACTVS               3.385 "NC1=NC(=O)[N-]2=C(N1)N(C=C2)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O"                                                                                                                        
S9F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C2=[N-]1C(=O)N=C(N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                      
S9F SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C2=[N-]1C(=O)N=C(N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           S9F 
_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        "[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-3,5,7-triaza-1-azanuidabicyclo[4.3.0]nona-1(6),3,8-trien-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
S9F "Create component" 2023-08-24 RCSB 
S9F "Initial release"  2024-01-24 RCSB 
# 
