data_A1I2I
# 
_chem_comp.id                                    A1I2I 
_chem_comp.name                                  "[[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H18 N3 O13 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-02-17 
_chem_comp.pdbx_modified_date                    2025-04-25 
_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                        481.184 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1I2I 
_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        9HFT 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              ? 
# 
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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
A1I2I "C1'"  C1  C 0 1 N N R N N N 89.179 76.890 85.722 -3.925 -0.482 1.324  "C1'"  A1I2I 1  
A1I2I C2     C2  C 0 1 N N N N N N 90.225 78.233 84.008 -4.910 0.354  -0.737 C2     A1I2I 2  
A1I2I "C2'"  C3  C 0 1 N N N N N N 87.729 76.909 86.155 -4.507 -1.906 1.220  "C2'"  A1I2I 3  
A1I2I "C3'"  C4  C 0 1 N N S N N N 87.617 75.732 87.008 -3.374 -2.731 0.562  "C3'"  A1I2I 4  
A1I2I C4     C5  C 0 1 N N N N N N 89.519 78.139 81.766 -6.348 2.161  -0.802 C4     A1I2I 5  
A1I2I "C4'"  C6  C 0 1 N N R N N N 88.772 74.846 86.737 -2.125 -1.862 0.859  "C4'"  A1I2I 6  
A1I2I C5     C7  C 0 1 N N N N N N 88.574 77.207 82.124 -6.240 2.295  0.597  C5     A1I2I 7  
A1I2I "C5'"  C8  C 0 1 N N N N N N 88.285 73.555 86.047 -1.023 -2.134 -0.167 "C5'"  A1I2I 8  
A1I2I C5A    C9  C 0 1 N N N N N N 87.624 76.615 81.043 -6.999 3.375  1.324  C5A    A1I2I 9  
A1I2I C6     C10 C 0 1 N N N N N N 88.463 76.796 83.430 -5.443 1.437  1.278  C6     A1I2I 10 
A1I2I N1     N1  N 0 1 N N N N N N 89.289 77.310 84.364 -4.781 0.459  0.598  N1     A1I2I 11 
A1I2I N3     N2  N 0 1 N N N N N N 90.334 78.645 82.693 -5.681 1.196  -1.422 N3     A1I2I 12 
A1I2I N4     N3  N 0 1 N N N N N N 89.628 78.573 80.374 -7.151 3.018  -1.519 N4     A1I2I 13 
A1I2I O1A    O1  O 0 1 N N N N N N 84.980 71.820 87.168 2.120  -2.954 -0.621 O1A    A1I2I 14 
A1I2I O1B    O2  O 0 1 N N N N N N 88.129 70.038 84.947 4.673  -0.674 -1.436 O1B    A1I2I 15 
A1I2I O1G    O3  O 0 1 N N N N N N 84.845 67.446 82.124 6.463  2.807  0.292  O1G    A1I2I 16 
A1I2I O2     O4  O 0 1 N N N N N N 90.958 78.691 84.828 -4.307 -0.525 -1.331 O2     A1I2I 17 
A1I2I O2A    O5  O 0 1 N N N N N N 85.153 73.837 85.759 1.228  -1.087 -2.066 O2A    A1I2I 18 
A1I2I O2B    O6  O 0 1 N N N N N N 86.057 69.359 86.094 3.486  1.553  -1.509 O2B    A1I2I 19 
A1I2I O2G    O7  O 0 1 N N N N N N 83.727 68.476 84.079 6.822  1.135  2.288  O2G    A1I2I 20 
A1I2I "O3'"  O8  O 0 1 N N N N N N 87.643 76.147 88.420 -3.258 -4.017 1.174  "O3'"  A1I2I 21 
A1I2I O3A    O9  O 0 1 N N N N N N 86.073 71.600 84.811 2.583  -0.432 -0.041 O3A    A1I2I 22 
A1I2I O3B    O10 O 0 1 N N N N N N 86.138 69.213 83.509 4.820  0.781  0.622  O3B    A1I2I 23 
A1I2I O3G    O11 O 0 1 N N N N N N 85.565 66.861 84.423 7.211  0.429  -0.104 O3G    A1I2I 24 
A1I2I "O4'"  O12 O 0 1 N N N N N N 89.692 75.528 85.871 -2.616 -0.511 0.731  "O4'"  A1I2I 25 
A1I2I "O5'"  O13 O 0 1 N N N N N N 87.315 72.918 86.855 0.154  -1.411 0.195  "O5'"  A1I2I 26 
A1I2I PA     P1  P 0 1 N N N N N N 85.838 72.557 86.165 1.515  -1.463 -0.664 PA     A1I2I 27 
A1I2I PB     P2  P 0 1 N N N N N N 86.624 70.041 84.873 3.907  0.286  -0.609 PB     A1I2I 28 
A1I2I PG     P3  P 0 1 N N N N N N 85.047 67.972 83.535 6.348  1.270  0.756  PG     A1I2I 29 
A1I2I "H1'"  H1  H 0 1 N N N N N N 89.751 77.569 86.372 -3.852 -0.188 2.371  "H1'"  A1I2I 30 
A1I2I "H2'1" H2  H 0 0 N N N N N N 87.498 77.826 86.717 -4.737 -2.297 2.211  "H2'1" A1I2I 31 
A1I2I "H2'2" H3  H 0 0 N N N N N N 87.058 76.832 85.287 -5.397 -1.910 0.591  "H2'2" A1I2I 32 
A1I2I "H3'"  H4  H 0 1 N N N N N N 86.680 75.198 86.793 -3.535 -2.826 -0.512 "H3'"  A1I2I 33 
A1I2I "H4'"  H5  H 0 1 N N N N N N 89.265 74.579 87.684 -1.762 -2.045 1.870  "H4'"  A1I2I 34 
A1I2I "H5'2" H6  H 0 0 N N N N N N 87.841 73.807 85.073 -0.802 -3.201 -0.189 "H5'2" A1I2I 35 
A1I2I "H5'1" H7  H 0 0 N N N N N N 89.138 72.877 85.897 -1.358 -1.813 -1.154 "H5'1" A1I2I 36 
A1I2I H5A3   H8  H 0 0 N N N N N N 86.941 75.891 81.511 -7.579 3.956  0.607  H5A3   A1I2I 37 
A1I2I H5A2   H9  H 0 0 N N N N N N 87.040 77.426 80.584 -7.671 2.920  2.052  H5A2   A1I2I 38 
A1I2I H5A1   H10 H 0 0 N N N N N N 88.220 76.109 80.269 -6.296 4.030  1.839  H5A1   A1I2I 39 
A1I2I H1     H11 H 0 1 N N N N N N 87.718 76.065 83.707 -5.343 1.520  2.351  H1     A1I2I 40 
A1I2I HN42   H12 H 0 0 N N N N N N 90.315 79.251 80.114 -7.644 3.717  -1.061 HN42   A1I2I 41 
A1I2I HN41   H13 H 0 0 N N N N N N 89.015 78.191 79.682 -7.223 2.924  -2.481 HN41   A1I2I 42 
A1I2I H2     H14 H 0 1 N N N N N N 84.188 72.317 87.334 2.332  -3.267 0.269  H2     A1I2I 43 
A1I2I H4     H15 H 0 1 N N N N N N 85.086 66.528 82.090 5.922  3.417  0.812  H4     A1I2I 44 
A1I2I H3     H16 H 0 1 N N N N N N 86.768 69.070 86.655 2.980  2.224  -1.031 H3     A1I2I 45 
A1I2I H5     H17 H 0 1 N N N N N N 83.501 67.990 84.863 7.735  1.412  2.443  H5     A1I2I 46 
A1I2I "HO3'" H18 H 0 0 N N N N N N 87.570 75.381 88.977 -4.051 -4.564 1.093  "HO3'" A1I2I 47 
# 
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 
A1I2I N1    C2     SING N N 1  
A1I2I N1    C6     SING N N 2  
A1I2I N1    "C1'"  SING N N 3  
A1I2I C2    N3     SING N N 4  
A1I2I C2    O2     DOUB N N 5  
A1I2I N3    C4     DOUB N N 6  
A1I2I C4    C5     SING N N 7  
A1I2I C4    N4     SING N N 8  
A1I2I C5    C6     DOUB N N 9  
A1I2I C5    C5A    SING N N 10 
A1I2I "C1'" "C2'"  SING N N 11 
A1I2I "C1'" "O4'"  SING N N 12 
A1I2I "C2'" "C3'"  SING N N 13 
A1I2I "C3'" "C4'"  SING N N 14 
A1I2I "C3'" "O3'"  SING N N 15 
A1I2I "C4'" "O4'"  SING N N 16 
A1I2I "C4'" "C5'"  SING N N 17 
A1I2I "C5'" "O5'"  SING N N 18 
A1I2I "O5'" PA     SING N N 19 
A1I2I PA    O1A    SING N N 20 
A1I2I PA    O2A    DOUB N N 21 
A1I2I PA    O3A    SING N N 22 
A1I2I O3A   PB     SING N N 23 
A1I2I PB    O1B    DOUB N N 24 
A1I2I PB    O2B    SING N N 25 
A1I2I PB    O3B    SING N N 26 
A1I2I O3B   PG     SING N N 27 
A1I2I PG    O1G    SING N N 28 
A1I2I PG    O2G    SING N N 29 
A1I2I PG    O3G    DOUB N N 30 
A1I2I "C1'" "H1'"  SING N N 31 
A1I2I "C2'" "H2'1" SING N N 32 
A1I2I "C2'" "H2'2" SING N N 33 
A1I2I "C3'" "H3'"  SING N N 34 
A1I2I "C4'" "H4'"  SING N N 35 
A1I2I "C5'" "H5'2" SING N N 36 
A1I2I "C5'" "H5'1" SING N N 37 
A1I2I C5A   H5A3   SING N N 38 
A1I2I C5A   H5A2   SING N N 39 
A1I2I C5A   H5A1   SING N N 40 
A1I2I C6    H1     SING N N 41 
A1I2I N4    HN42   SING N N 42 
A1I2I N4    HN41   SING N N 43 
A1I2I O1A   H2     SING N N 44 
A1I2I O1G   H4     SING N N 45 
A1I2I O2B   H3     SING N N 46 
A1I2I O2G   H5     SING N N 47 
A1I2I "O3'" "HO3'" SING N N 48 
# 
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 
A1I2I InChI            InChI                1.06  "InChI=1S/C10H18N3O13P3/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,14H,2,4H2,1H3,(H,19,20)(H,21,22)(H2,11,12,15)(H2,16,17,18)" 
A1I2I InChIKey         InChI                1.06  NGYHUCPPLJOZIX-UHFFFAOYSA-N                                                                                                                                                   
A1I2I SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)N=C1N"                                                                                              
A1I2I SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)N=C1N"                                                                                                  
A1I2I SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O"                                                                                                    
A1I2I SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N=C1N)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O"                                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           A1I2I 
_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},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-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 
A1I2I "Create component" 2025-02-17 PDBE 
A1I2I "Initial release"  2025-04-30 RCSB 
# 
