data_A1I59
# 
_chem_comp.id                                    A1I59 
_chem_comp.name                                  "[(2~{R},3~{S},4~{R},5~{R})-5-[4-azanyl-5-[(1~{S})-1-azanyl-3,3-bis(oxidanyl)propyl]-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H21 N4 O10 P" 
_chem_comp.mon_nstd_parent_comp_id               C 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-03-17 
_chem_comp.pdbx_modified_date                    2025-10-31 
_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                        412.290 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     A1I59 
_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        9QF6 
_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 
A1I59 C1     C1  C 0 1 N N N N N N 217.740 246.208 269.876 4.860  -1.367 0.457  C1    A1I59 1  
A1I59 "C1'"  C2  C 0 1 N N R N N N 213.399 242.433 269.300 -0.311 1.235  0.534  "C1'" A1I59 2  
A1I59 C2     C3  C 0 1 N N N N N N 213.738 244.145 267.658 0.814  0.629  -1.536 C2    A1I59 3  
A1I59 "C2'"  C4  C 0 1 N N R N N N 214.229 241.236 268.839 -0.833 2.597  0.024  "C2'" A1I59 4  
A1I59 C3     C5  C 0 1 N N N N N N 218.603 247.265 270.565 6.258  -1.543 1.055  C3    A1I59 5  
A1I59 "C3'"  C6  C 0 1 N N S N N N 215.142 241.037 270.039 -2.370 2.457  0.086  "C3'" A1I59 6  
A1I59 C4     C7  C 0 1 N N N N N N 215.020 246.005 267.979 3.060  0.097  -1.638 C4    A1I59 7  
A1I59 "C4'"  C8  C 0 1 N N R N N N 214.217 241.340 271.206 -2.595 1.027  0.627  "C4'" A1I59 8  
A1I59 C5     C9  C 0 1 N N N N N N 215.302 245.574 269.248 3.170  0.305  -0.248 C5    A1I59 9  
A1I59 "C5'"  C10 C 0 1 N N N N N N 214.885 241.757 272.490 -3.809 0.387  -0.051 "C5'" A1I59 10 
A1I59 C6     C11 C 0 1 N N N N N N 214.760 244.382 269.687 2.069  0.674  0.449  C6    A1I59 11 
A1I59 O1     O1  O 0 1 N N N N N N 218.936 246.834 271.863 6.555  -2.936 1.168  O1    A1I59 12 
A1I59 CM5    C12 C 0 1 N N S N N N 216.222 246.414 270.183 4.492  0.118  0.451  CM5   A1I59 13 
A1I59 N1     N1  N 0 1 N N N N N N 213.991 243.714 268.858 0.887  0.835  -0.209 N1    A1I59 14 
A1I59 O4     O2  O 0 1 N N N N N N 217.883 248.472 270.647 7.221  -0.918 0.205  O4    A1I59 15 
A1I59 N3     N2  N 0 1 N N N N N N 214.239 245.272 267.214 1.887  0.265  -2.236 N3    A1I59 16 
A1I59 N4     N3  N 0 1 N N N N N N 215.584 247.284 267.470 4.162  -0.279 -2.371 N4    A1I59 17 
A1I59 O2     O3  O 0 1 N N N N N N 213.038 243.504 266.947 -0.254 0.773  -2.108 O2    A1I59 18 
A1I59 "O2'"  O4  O 0 1 N N N N N N 213.361 240.125 268.679 -0.391 3.654  0.878  "O2'" A1I59 19 
A1I59 "O3'"  O5  O 0 1 N N N N N N 215.724 239.747 270.110 -2.925 3.423  0.981  "O3'" A1I59 20 
A1I59 "O4'"  O6  O 0 1 N N N N N N 213.375 242.415 270.713 -1.390 0.309  0.283  "O4'" A1I59 21 
A1I59 "O5'"  O7  O 0 1 N N N N N N 215.899 242.723 272.258 -4.069 -0.886 0.544  "O5'" A1I59 22 
A1I59 OP2    O8  O 0 1 N N N N N N 217.526 242.002 274.036 -5.193 -3.241 0.867  OP1   A1I59 23 
A1I59 OP3    O9  O 0 1 N Y N N N N 217.681 244.369 272.913 -6.684 -1.127 0.400  OP2   A1I59 24 
A1I59 P      P1  P 0 1 N N N N N N 216.841 243.218 273.441 -5.278 -1.842 0.076  P     A1I59 25 
A1I59 N5     N4  N 0 1 N N N N N N 215.965 246.037 271.557 4.387  0.603  1.834  N5    A1I59 26 
A1I59 H1     H1  H 0 1 N N N N N N 218.044 245.212 270.231 4.851  -1.748 -0.564 H1    A1I59 27 
A1I59 H2     H2  H 0 1 N N N N N N 217.896 246.273 268.789 4.136  -1.918 1.057  H2    A1I59 28 
A1I59 "H1'"  H3  H 0 1 N N N N N N 212.380 242.338 268.895 -0.095 1.287  1.601  H3    A1I59 29 
A1I59 "H2'"  H4  H 0 1 N N N N N N 214.803 241.471 267.930 -0.507 2.771  -1.001 H4    A1I59 30 
A1I59 "H3'"  H5  H 0 1 N N N N N N 215.931 241.803 270.009 -2.804 2.565  -0.908 H5    A1I59 31 
A1I59 "H4'"  H6  H 0 1 N N N N N N 213.599 240.451 271.402 -2.732 1.047  1.708  H6    A1I59 32 
A1I59 "H5'"  H7  H 0 1 N N N N N N 214.129 242.187 273.163 -4.678 1.032  0.075  H7    A1I59 33 
A1I59 "H5''" H8  H 0 1 N N N N N N 215.336 240.872 272.962 -3.605 0.256  -1.114 H8    A1I59 34 
A1I59 H6     H9  H 0 1 N N N N N N 214.962 244.011 270.681 2.128  0.839  1.515  H9    A1I59 35 
A1I59 H10    H10 H 0 1 N N N N N N 219.472 247.493 272.288 7.428  -3.123 1.541  H10   A1I59 36 
A1I59 H11    H11 H 0 1 N N N N N N 215.983 247.478 270.038 5.263  0.682  -0.074 H11   A1I59 37 
A1I59 H12    H12 H 0 1 N N N N N N 218.417 249.131 271.075 7.247  -1.278 -0.692 H12   A1I59 38 
A1I59 H41    H13 H 0 1 N N N N N N 215.370 247.591 266.542 5.036  -0.310 -1.952 H13   A1I59 39 
A1I59 H42    H14 H 0 1 N N N N N N 216.177 247.837 268.055 4.065  -0.512 -3.308 H14   A1I59 40 
A1I59 "HO2'" H15 H 0 1 N N N N N N 213.862 239.370 268.392 -0.691 4.532  0.604  H15   A1I59 41 
A1I59 "HO3'" H16 H 0 1 N Y N N N N 216.279 239.691 270.879 -2.760 4.340  0.721  H16   A1I59 42 
A1I59 HOP2   H17 H 0 1 N N N N N N 217.253 241.895 274.940 -5.892 -3.868 0.635  H17   A1I59 43 
A1I59 HOP3   H18 H 0 1 N N N N N N 217.382 245.183 273.300 -6.820 -0.933 1.337  H18   A1I59 44 
A1I59 H19    H19 H 0 1 N N N N N N 216.552 246.572 272.165 4.113  1.574  1.857  H19   A1I59 45 
A1I59 H20    H20 H 0 1 N N N N N N 215.006 246.215 271.778 3.748  0.034  2.369  H20   A1I59 46 
A1I59 OP1    OP3 O 0 1 N N N N N N 215.816 244.052 274.450 -5.175 -2.091 -1.379 OP3   A1I59 47 
A1I59 H22    H22 H 0 1 N N N N N N 219.516 247.410 269.969 6.291  -1.082 2.042  H22   A1I59 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 
A1I59 O2    C2     DOUB N N 1  
A1I59 N3    C2     SING N N 2  
A1I59 N3    C4     DOUB N N 3  
A1I59 N4    C4     SING N N 4  
A1I59 C2    N1     SING N N 5  
A1I59 C4    C5     SING N N 6  
A1I59 "O2'" "C2'"  SING N N 7  
A1I59 "C2'" "C1'"  SING N N 8  
A1I59 "C2'" "C3'"  SING N N 9  
A1I59 N1    "C1'"  SING N N 10 
A1I59 N1    C6     SING N N 11 
A1I59 C5    C6     DOUB N N 12 
A1I59 C5    CM5    SING N N 13 
A1I59 "C1'" "O4'"  SING N N 14 
A1I59 C1    CM5    SING N N 15 
A1I59 C1    C3     SING N N 16 
A1I59 "C3'" "O3'"  SING N N 17 
A1I59 "C3'" "C4'"  SING N N 18 
A1I59 CM5   N5     SING N N 19 
A1I59 C3    O4     SING N N 20 
A1I59 C3    O1     SING N N 21 
A1I59 "O4'" "C4'"  SING N N 22 
A1I59 "C4'" "C5'"  SING N N 23 
A1I59 "O5'" "C5'"  SING N N 24 
A1I59 "O5'" P      SING N N 25 
A1I59 OP3   P      SING N N 26 
A1I59 P     OP2    SING N N 27 
A1I59 C1    H1     SING N N 28 
A1I59 C1    H2     SING N N 29 
A1I59 "C1'" "H1'"  SING N N 30 
A1I59 "C2'" "H2'"  SING N N 31 
A1I59 "C3'" "H3'"  SING N N 32 
A1I59 "C4'" "H4'"  SING N N 33 
A1I59 "C5'" "H5'"  SING N N 34 
A1I59 "C5'" "H5''" SING N N 35 
A1I59 C6    H6     SING N N 36 
A1I59 O1    H10    SING N N 37 
A1I59 CM5   H11    SING N N 38 
A1I59 O4    H12    SING N N 39 
A1I59 N4    H41    SING N N 40 
A1I59 N4    H42    SING N N 41 
A1I59 "O2'" "HO2'" SING N N 42 
A1I59 "O3'" "HO3'" SING N N 43 
A1I59 OP2   HOP2   SING N N 44 
A1I59 OP3   HOP3   SING N N 45 
A1I59 N5    H19    SING N N 46 
A1I59 N5    H20    SING N N 47 
A1I59 P     OP1    DOUB N N 48 
A1I59 C3    H22    SING N N 49 
# 
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 
A1I59 InChI            InChI                1.06  "InChI=1S/C12H21N4O10P/c13-5(1-7(17)18)4-2-16(12(21)15-10(4)14)11-9(20)8(19)6(26-11)3-25-27(22,23)24/h2,5-9,11,17-20H,1,3,13H2,(H2,14,15,21)(H2,22,23,24)/t5-,6+,8+,9+,11+/m0/s1" 
A1I59 InChIKey         InChI                1.06  MVVSSDOMXIJOEA-DANLAGSESA-N                                                                                                                                                       
A1I59 SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CC(O)O)C1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N=C1N"                                                                                                    
A1I59 SMILES           CACTVS               3.385 "N[CH](CC(O)O)C1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N=C1N"                                                                                                            
A1I59 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)[C@H](CC(O)O)N"                                                                                                   
A1I59 SMILES           "OpenEye OEToolkits" 2.0.7 "C1=C(C(=NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)N)C(CC(O)O)N"                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           A1I59 
_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-5-[(1~{S})-1-azanyl-3,3-bis(oxidanyl)propyl]-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen 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 
A1I59 "Create component"         2025-03-17 PDBE 
A1I59 "Modify leaving atom flag" 2025-03-18 PDBE 
A1I59 "Initial release"          2025-11-05 RCSB 
# 
