data_X0F
# 
_chem_comp.id                                    X0F 
_chem_comp.name                                  
;2-oxo-2-hydroadenosine 5'-(tetrahydrogen triphosphate)
;
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H16 N5 O14 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-05-25 
_chem_comp.pdbx_modified_date                    2023-12-22 
_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                        523.180 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     X0F 
_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        8SY5 
_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 
X0F C14 C1  C 0 1 N N N N N N 133.272 146.192 132.409 -0.178 -2.565 -0.192 C14 X0F 1  
X0F C15 C2  C 0 1 N N R N N N 131.882 146.238 133.068 -1.445 -2.192 0.580  C15 X0F 2  
X0F C16 C3  C 0 1 N N S N N N 132.050 146.543 134.596 -2.546 -3.252 0.352  C16 X0F 3  
X0F C17 C4  C 0 1 N N R N N N 130.852 145.773 135.256 -3.852 -2.429 0.288  C17 X0F 4  
X0F C18 C5  C 0 1 N N R N N N 130.692 144.725 134.526 -3.386 -0.970 0.485  C18 X0F 5  
X0F C20 C6  C 0 1 N N N N N N 132.294 142.855 134.394 -4.197 -0.039 -1.719 C20 X0F 6  
X0F C22 C7  C 0 1 N N N N N N 132.144 142.044 136.406 -5.561 1.516  -1.066 C22 X0F 7  
X0F C23 C8  C 0 1 N N N N N N 132.258 141.251 137.730 -6.476 2.560  -0.914 C23 X0F 8  
X0F C26 C9  C 0 1 N N N N N N 130.586 142.760 138.766 -6.280 2.332  1.418  C26 X0F 9  
X0F C29 C10 C 0 1 N N N N N N 131.302 143.105 136.316 -5.031 0.909  0.090  C29 X0F 10 
X0F N19 N1  N 0 1 N N N N N N 131.399 143.605 135.069 -4.177 -0.064 -0.353 N19 X0F 11 
X0F N21 N2  N 0 1 N N N N N N 132.752 141.895 135.221 -5.008 0.887  -2.136 N21 X0F 12 
X0F N24 N3  N 0 1 N N N N N N 133.158 140.118 137.826 -7.018 3.180  -2.007 N24 X0F 13 
X0F N25 N4  N 0 1 N N N N N N 131.478 141.633 138.865 -6.817 2.947  0.349  N25 X0F 14 
X0F N28 N5  N 0 1 N N N N N N 130.480 143.505 137.513 -5.409 1.338  1.291  N28 X0F 15 
X0F O02 O1  O 0 1 N N N N N N 131.831 145.181 129.447 2.241  -1.737 -1.989 O02 X0F 16 
X0F O03 O2  O 0 1 N N N N N N 134.187 144.560 129.126 3.056  -3.081 -0.013 O03 X0F 17 
X0F O04 O3  O 0 1 N N N N N N 133.595 147.039 129.571 3.205  -0.456 -0.039 O04 X0F 18 
X0F O06 O4  O 0 1 N N N N N N 134.846 148.972 130.724 5.499  -0.767 -1.046 O06 X0F 19 
X0F O07 O5  O 0 1 N N N N N N 135.943 146.775 130.584 4.151  1.215  -1.836 O07 X0F 20 
X0F O08 O6  O 0 1 N N N N N N 135.751 148.205 128.438 5.199  1.144  0.575  O08 X0F 21 
X0F O10 O7  O 0 1 N N N N N N 137.392 147.684 126.518 7.695  0.923  0.277  O10 X0F 22 
X0F O11 O8  O 0 1 N N N N N N 136.461 145.800 127.798 6.693  3.217  -0.046 O11 X0F 23 
X0F O12 O9  O 0 1 N N N N N N 135.029 147.067 126.239 6.880  2.128  2.340  O12 X0F 24 
X0F O13 O10 O 0 1 N N N N N N 133.350 145.136 131.499 0.862  -1.638 0.123  O13 X0F 25 
X0F O27 O11 O 0 1 N N N N N N 129.938 143.078 139.703 -6.602 2.699  2.537  O27 X0F 26 
X0F O30 O12 O 0 1 N N N N N N 131.299 145.079 133.005 -2.004 -0.964 0.066  O30 X0F 27 
X0F O31 O13 O 0 1 N N N N N N 129.633 146.620 135.223 -4.740 -2.817 1.338  O31 X0F 28 
X0F O32 O14 O 0 1 N N N N N N 131.946 147.840 134.817 -2.587 -4.173 1.444  O32 X0F 29 
X0F P01 P1  P 0 1 N N N N N N 133.243 145.459 129.887 2.339  -1.728 -0.512 P01 X0F 30 
X0F P05 P2  P 0 1 N N N N N N 135.050 147.752 129.860 4.535  0.261  -0.596 P05 X0F 31 
X0F P09 P3  P 0 1 N N N N N N 136.166 147.166 127.227 6.640  1.833  0.776  P09 X0F 32 
X0F H1  H1  H 0 1 N N N N N N 133.453 147.139 131.880 0.135  -3.571 0.087  H1  X0F 33 
X0F H2  H2  H 0 1 N N N N N N 134.037 146.055 133.188 -0.382 -2.533 -1.263 H2  X0F 34 
X0F H3  H3  H 0 1 N N N N N N 131.289 147.042 132.608 -1.226 -2.095 1.643  H3  X0F 35 
X0F H4  H4  H 0 1 N N N N N N 132.999 146.116 134.952 -2.380 -3.779 -0.587 H4  X0F 36 
X0F H5  H5  H 0 1 N N N N N N 131.115 145.537 136.298 -4.332 -2.549 -0.683 H5  X0F 37 
X0F H6  H6  H 0 1 N N N N N N 129.630 144.469 134.394 -3.467 -0.683 1.533  H6  X0F 38 
X0F H8  H8  H 0 1 N N N N N N 132.593 142.999 133.366 -3.619 -0.691 -2.359 H8  X0F 39 
X0F H9  H9  H 0 1 N N N N N N 133.105 139.727 138.745 -6.768 2.896  -2.900 H9  X0F 40 
X0F H10 H10 H 0 1 N N N N N N 132.895 139.426 137.154 -7.653 3.904  -1.888 H10 X0F 41 
X0F H12 H12 H 0 1 N N N N N N 133.691 144.010 128.531 3.154  -3.143 0.947  H12 X0F 42 
X0F H13 H13 H 0 1 N N N N N N 136.187 147.134 131.429 3.521  1.914  -1.613 H13 X0F 43 
X0F H14 H14 H 0 1 N N N N N N 137.355 145.556 127.590 6.027  3.863  0.228  H14 X0F 44 
X0F H15 H15 H 0 1 N Y N N N N 135.327 147.351 125.383 7.731  2.544  2.536  H15 X0F 45 
X0F H17 H17 H 0 1 N N N N N N 128.910 146.151 135.623 -5.016 -3.743 1.298  H17 X0F 46 
X0F H18 H18 H 0 1 N N N N N N 132.049 148.013 135.745 -3.261 -4.861 1.353  H18 X0F 47 
X0F H7  H7  H 0 1 N N N N N N 131.551 141.122 139.721 -7.451 3.670  0.477  H7  X0F 48 
# 
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 
X0F C14 C15 SING N N 1  
X0F C14 O13 SING N N 2  
X0F C15 C16 SING N N 3  
X0F C15 O30 SING N N 4  
X0F C16 C17 SING N N 5  
X0F C16 O32 SING N N 6  
X0F C17 C18 SING N N 7  
X0F C17 O31 SING N N 8  
X0F C18 N19 SING N N 9  
X0F C20 N19 SING N N 10 
X0F C20 N21 DOUB N N 11 
X0F C22 C23 DOUB N N 12 
X0F C22 C29 SING N N 13 
X0F C22 N21 SING N N 14 
X0F C23 N24 SING N N 15 
X0F C23 N25 SING N N 16 
X0F C26 N25 SING N N 17 
X0F C26 N28 SING N N 18 
X0F C26 O27 DOUB N N 19 
X0F C29 N19 SING N N 20 
X0F C29 N28 DOUB N N 21 
X0F O02 P01 DOUB N N 22 
X0F O03 P01 SING N N 23 
X0F O04 P01 SING N N 24 
X0F O04 P05 SING N N 25 
X0F O06 P05 DOUB N N 26 
X0F O07 P05 SING N N 27 
X0F O08 P05 SING N N 28 
X0F O08 P09 SING N N 29 
X0F O10 P09 DOUB N N 30 
X0F O11 P09 SING N N 31 
X0F O12 P09 SING N N 32 
X0F O13 P01 SING N N 33 
X0F C14 H1  SING N N 34 
X0F C14 H2  SING N N 35 
X0F C15 H3  SING N N 36 
X0F C16 H4  SING N N 37 
X0F C17 H5  SING N N 38 
X0F C18 H6  SING N N 39 
X0F C20 H8  SING N N 40 
X0F N24 H9  SING N N 41 
X0F N24 H10 SING N N 42 
X0F O03 H12 SING N N 43 
X0F O07 H13 SING N N 44 
X0F O11 H14 SING N N 45 
X0F O12 H15 SING N N 46 
X0F O31 H17 SING N N 47 
X0F O32 H18 SING N N 48 
X0F O30 C18 SING N N 49 
X0F N25 H7  SING N N 50 
# 
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 
X0F SMILES           ACDLabs              12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(N2C=NC3=C(N)NC(=O)N=C32)C(O)C1O"                                                                                                                                             
X0F InChI            InChI                1.06  "InChI=1S/C10H16N5O14P3/c11-7-4-8(14-10(18)13-7)15(2-12-4)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1" 
X0F InChIKey         InChI                1.06  DJHOBIUAJLDRDQ-UUOKFMHZSA-N                                                                                                                                                                                     
X0F SMILES_CANONICAL CACTVS               3.385 "NC1=C2N=CN([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)C2=NC(=O)N1"                                                                                                                     
X0F SMILES           CACTVS               3.385 "NC1=C2N=CN([CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O)C2=NC(=O)N1"                                                                                                                           
X0F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=NC2=C(NC(=O)N=C2N1C3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N"                                                                                                                             
X0F SMILES           "OpenEye OEToolkits" 2.0.7 "C1=NC2=C(NC(=O)N=C2N1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N"                                                                                                                                           
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
X0F "SYSTEMATIC NAME" ACDLabs              12.01 
;2-oxo-2-hydroadenosine 5'-(tetrahydrogen triphosphate)
;
X0F "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R})-5-(6-azanyl-2-oxidanylidene-1~{H}-purin-9-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 
X0F "Create component" 2023-05-25 RCSB 
X0F "Initial release"  2023-12-27 RCSB 
# 
