data_A0I
# 
_chem_comp.id                                    A0I 
_chem_comp.name                                  "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[oxidanyl(phosphonooxy)phosphoryl]phosphonamidic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H17 N4 O13 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-07-17 
_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                        482.172 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A0I 
_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        8PSZ 
_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 
A0I C1  C1  C 0 1 N N N N N N 134.184 129.442 124.867 -7.366 -0.920 -0.710 C1  A0I 1  
A0I C2  C2  C 0 1 N N N N N N 135.145 130.040 125.587 -6.436 0.016  -1.010 C2  A0I 2  
A0I C3  C3  C 0 1 N N N N N N 135.683 127.970 126.666 -5.054 -0.831 0.691  C3  A0I 3  
A0I C4  C4  C 0 1 N N N N N N 133.979 128.050 125.065 -7.106 -1.833 0.333  C4  A0I 4  
A0I C5  C5  C 0 1 N N R N N N 136.960 130.008 127.283 -4.258 1.061  -0.614 C5  A0I 5  
A0I C6  C6  C 0 1 N N R N N N 138.366 129.421 127.093 -4.035 2.007  0.593  C6  A0I 6  
A0I C7  C7  C 0 1 N N S N N N 138.875 130.276 125.930 -2.597 2.522  0.340  C7  A0I 7  
A0I C8  C8  C 0 1 N N R N N N 138.326 131.646 126.329 -1.979 1.469  -0.599 C8  A0I 8  
A0I C9  C9  C 0 1 N N N N N N 138.268 132.669 125.222 -0.729 0.866  0.045  C9  A0I 9  
A0I N1  N1  N 0 1 N N N N N N 135.900 129.338 126.477 -5.274 0.053  -0.299 N1  A0I 10 
A0I N2  N2  N 0 1 N N N N N N 134.718 127.357 125.942 -5.960 -1.758 0.999  N2  A0I 11 
A0I N3  N3  N 0 1 N N N N N N 133.048 127.398 124.385 -8.034 -2.794 0.660  N3  A0I 12 
A0I N4  N4  N 0 1 N N N N N N 139.296 132.482 122.185 2.544  0.236  -0.448 N4  A0I 13 
A0I O1  O1  O 0 1 N N N N N N 136.379 127.357 127.484 -4.009 -0.784 1.317  O1  A0I 14 
A0I O10 O2  O 0 1 N N N N N N 139.235 134.526 119.521 7.319  -0.785 -0.482 O10 A0I 15 
A0I O11 O3  O 0 1 N N N N N N 136.818 131.947 121.744 1.091  -1.523 0.766  O11 A0I 16 
A0I O12 O4  O 0 1 N N N N N N 140.291 130.293 125.799 -2.628 3.802  -0.294 O12 A0I 17 
A0I O13 O5  O 0 1 N N N N N N 139.123 129.622 128.271 -4.973 3.085  0.577  O13 A0I 18 
A0I O2  O6  O 0 1 N N N N N N 137.019 131.355 126.868 -2.967 0.444  -0.802 O2  A0I 19 
A0I O3  O7  O 0 1 N N N N N N 137.596 132.113 124.073 -0.097 -0.023 -0.879 O3  A0I 20 
A0I O4  O8  O 0 1 N N N N N N 137.440 134.216 122.792 1.529  -1.924 -1.687 O4  A0I 21 
A0I O5  O9  O 0 1 N N N N N N 141.854 132.332 122.534 4.254  -1.573 -1.145 O5  A0I 22 
A0I O6  O10 O 0 1 N N N N N N 140.545 134.193 123.753 3.827  -1.320 1.330  O6  A0I 23 
A0I O7  O11 O 0 1 N N N N N N 140.955 134.237 121.337 5.187  0.483  -0.016 O7  A0I 24 
A0I O8  O12 O 0 1 N N N N N N 139.204 136.011 121.578 6.999  0.116  1.854  O8  A0I 25 
A0I O9  O13 O 0 1 N N N N N N 141.032 136.251 119.873 7.505  1.713  -0.173 O9  A0I 26 
A0I P1  P1  P 0 1 N N N N N N 137.734 132.757 122.612 1.249  -0.835 -0.534 P1  A0I 27 
A0I P2  P2  P 0 1 N N N N N N 140.682 133.267 122.581 3.975  -0.574 -0.089 P2  A0I 28 
A0I P3  P3  P 0 1 N N N N N N 140.047 135.308 120.532 6.765  0.357  0.279  P3  A0I 29 
A0I H1  H1  H 0 1 N N N N N N 133.587 130.000 124.161 -8.296 -0.965 -1.258 H1  A0I 30 
A0I H2  H2  H 0 1 N N N N N N 135.323 131.097 125.459 -6.612 0.725  -1.805 H2  A0I 31 
A0I H5  H3  H 0 1 N N N N N N 136.696 129.948 128.349 -4.545 1.629  -1.499 H5  A0I 32 
A0I H6  H4  H 0 1 N N N N N N 138.309 128.361 126.803 -4.093 1.458  1.533  H6  A0I 33 
A0I H7  H5  H 0 1 N N N N N N 138.396 129.947 124.996 -2.040 2.572  1.276  H7  A0I 34 
A0I H8  H6  H 0 1 N N N N N N 138.964 132.045 127.132 -1.721 1.929  -1.553 H8  A0I 35 
A0I H10 H7  H 0 1 N N N N N N 139.291 132.960 124.941 -0.037 1.665  0.312  H10 A0I 36 
A0I H9  H8  H 0 1 N N N N N N 137.718 133.555 125.573 -1.012 0.316  0.942  H9  A0I 37 
A0I H3  H9  H 0 1 N N N N N N 132.914 126.418 124.534 -8.871 -2.846 0.172  H3  A0I 38 
A0I H4  H10 H 0 1 N N N N N N 132.479 127.885 123.723 -7.852 -3.420 1.378  H4  A0I 39 
A0I H11 H11 H 0 1 N N N N N N 139.279 132.518 121.186 2.364  0.968  0.223  H11 A0I 40 
A0I H12 H12 H 0 1 N N N N N N 140.597 129.428 125.551 -3.008 4.503  0.253  H12 A0I 41 
A0I H13 H13 H 0 1 N N N N N N 138.777 129.076 128.967 -4.873 3.704  1.313  H13 A0I 42 
A0I H14 H14 H 0 1 N N N N N N 136.661 134.446 122.299 1.643  -1.543 -2.568 H14 A0I 43 
A0I H15 H15 H 0 1 N N N N N N 141.269 134.055 124.352 3.642  -0.725 2.070  H15 A0I 44 
A0I H16 H16 H 0 1 N N N N N N 138.285 135.835 121.415 6.660  0.827  2.415  H16 A0I 45 
A0I H17 H17 H 0 1 N N N N N N 140.958 136.177 118.929 8.460  1.708  -0.024 H17 A0I 46 
# 
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 
A0I O10 P3  DOUB N N 1  
A0I O9  P3  SING N N 2  
A0I P3  O7  SING N N 3  
A0I P3  O8  SING N N 4  
A0I O7  P2  SING N N 5  
A0I O11 P1  DOUB N N 6  
A0I N4  P2  SING N N 7  
A0I N4  P1  SING N N 8  
A0I O5  P2  DOUB N N 9  
A0I P2  O6  SING N N 10 
A0I P1  O4  SING N N 11 
A0I P1  O3  SING N N 12 
A0I O3  C9  SING N N 13 
A0I N3  C4  SING N N 14 
A0I C1  C4  SING N N 15 
A0I C1  C2  DOUB N N 16 
A0I C4  N2  DOUB N N 17 
A0I C9  C8  SING N N 18 
A0I C2  N1  SING N N 19 
A0I O12 C7  SING N N 20 
A0I C7  C8  SING N N 21 
A0I C7  C6  SING N N 22 
A0I N2  C3  SING N N 23 
A0I C8  O2  SING N N 24 
A0I N1  C3  SING N N 25 
A0I N1  C5  SING N N 26 
A0I C3  O1  DOUB N N 27 
A0I O2  C5  SING N N 28 
A0I C6  C5  SING N N 29 
A0I C6  O13 SING N N 30 
A0I C1  H1  SING N N 31 
A0I C2  H2  SING N N 32 
A0I C5  H5  SING N N 33 
A0I C6  H6  SING N N 34 
A0I C7  H7  SING N N 35 
A0I C8  H8  SING N N 36 
A0I C9  H10 SING N N 37 
A0I C9  H9  SING N N 38 
A0I N3  H3  SING N N 39 
A0I N3  H4  SING N N 40 
A0I N4  H11 SING N N 41 
A0I O12 H12 SING N N 42 
A0I O13 H13 SING N N 43 
A0I O4  H14 SING N N 44 
A0I O6  H15 SING N N 45 
A0I O8  H16 SING N N 46 
A0I O9  H17 SING N N 47 
# 
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 
A0I InChI            InChI                1.06  "InChI=1S/C9H17N4O13P3/c10-5-1-2-13(9(16)11-5)8-7(15)6(14)4(25-8)3-24-27(17,18)12-28(19,20)26-29(21,22)23/h1-2,4,6-8,14-15H,3H2,(H2,10,11,16)(H2,21,22,23)(H3,12,17,18,19,20)/t4-,6-,7-,8-/m1/s1" 
A0I InChIKey         InChI                1.06  HVZVBWDHTKBLAI-XVFCMESISA-N                                                                                                                                                                       
A0I SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O"                                                                                                             
A0I SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O"                                                                                                                   
A0I SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O"                                                                                                                 
A0I SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O"                                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           A0I 
_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-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[oxidanyl(phosphonooxy)phosphoryl]phosphonamidic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A0I "Create component" 2023-07-17 PDBE 
A0I "Initial release"  2023-12-27 RCSB 
# 
