data_A1IC1
# 
_chem_comp.id                                    A1IC1 
_chem_comp.name                                  "[(2~{R},3~{R},4~{R},5~{R})-4-methoxy-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H17 N2 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               U 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-06-04 
_chem_comp.pdbx_modified_date                    2024-12-20 
_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                        352.234 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     A1IC1 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        9F67 
_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 
A1IC1 "C5'"  C1  C 0 1 N N N N N N 166.657 109.048 127.765 2.565  0.608  0.379  "C5'"  A1IC1 1  
A1IC1 O4     O1  O 0 1 N N N N N N 167.693 117.510 126.328 -4.986 -2.627 1.085  O4     A1IC1 2  
A1IC1 "O5'"  O2  O 0 1 N N N N N N 166.616 108.679 126.386 3.224  -0.333 -0.472 "O5'"  A1IC1 3  
A1IC1 OP3    O3  O 0 1 N Y N N N N 165.771 109.363 124.144 5.134  -1.925 -1.326 OP3    A1IC1 4  
A1IC1 C55    C2  C 0 1 N N N N N N 168.000 115.692 124.406 -5.248 -1.511 -1.361 C55    A1IC1 5  
A1IC1 C4     C3  C 0 1 N N N N N N 167.775 116.349 126.725 -4.078 -1.892 0.741  C4     A1IC1 6  
A1IC1 "C4'"  C4  C 0 1 N N R N N N 167.650 110.196 127.972 1.267  1.072  -0.285 "C4'"  A1IC1 7  
A1IC1 C50    C5  C 0 1 N N N N N N 167.405 113.609 131.131 -2.163 3.913  0.740  C50    A1IC1 8  
A1IC1 N1     N1  N 0 1 N N N N N N 167.946 113.766 127.520 -2.058 -0.249 -0.033 N1     A1IC1 9  
A1IC1 C5     C6  C 0 1 N N N N N N 167.699 116.073 128.076 -2.974 -1.670 1.599  C5     A1IC1 10 
A1IC1 C6     C7  C 0 1 N N N N N N 167.797 114.755 128.474 -1.981 -0.850 1.194  C6     A1IC1 11 
A1IC1 "C1'"  C8  C 0 1 N N R N N N 168.064 112.364 127.963 -0.980 0.641  -0.474 "C1'"  A1IC1 12 
A1IC1 "C2'"  C9  C 0 1 N N R N N N 167.481 112.155 129.317 -0.913 1.892  0.431  "C2'"  A1IC1 13 
A1IC1 "C3'"  C10 C 0 1 N N R N N N 167.607 110.643 129.425 0.599  2.182  0.558  "C3'"  A1IC1 14 
A1IC1 O2     O4  O 0 1 N N N N N N 168.155 113.225 125.378 -3.155 0.068  -1.930 O2     A1IC1 15 
A1IC1 C2     C11 C 0 1 N N N N N N 168.019 114.091 126.233 -3.110 -0.472 -0.842 C2     A1IC1 16 
A1IC1 N3     N2  N 0 1 N N N N N N 167.932 115.362 125.845 -4.114 -1.285 -0.462 N3     A1IC1 17 
A1IC1 "O4'"  O5  O 0 1 N N N N N N 167.317 111.389 127.239 0.302  -0.002 -0.310 "O4'"  A1IC1 18 
A1IC1 "O2'"  O6  O 0 1 N N N N N N 168.271 112.825 130.306 -1.584 2.993  -0.186 "O2'"  A1IC1 19 
A1IC1 OP1    O7  O 0 1 N N N N N N 164.222 108.291 125.865 5.629  0.013  0.214  OP1    A1IC1 20 
A1IC1 "O3'"  O8  O 0 1 N N N N N N 168.840 110.266 130.035 0.909  3.471  0.023  "O3'"  A1IC1 21 
A1IC1 P      P1  P 0 1 N N N N N N 165.368 109.166 125.548 4.623  -1.031 -0.088 P      A1IC1 22 
A1IC1 "H5'"  H1  H 0 1 N N N N N N 165.655 109.371 128.085 2.336  0.135  1.334  "H5'"  A1IC1 23 
A1IC1 "H5''" H2  H 0 0 N N N N N N 166.972 108.181 128.365 3.215  1.466  0.545  "H5''" A1IC1 24 
A1IC1 HOP3   H3  H 0 0 N Y N N N N 165.197 108.862 123.576 5.974  -2.376 -1.165 HOP3   A1IC1 25 
A1IC1 H4     H4  H 0 1 N N N N N N 167.912 116.781 124.274 -5.039 -2.368 -2.001 H4     A1IC1 26 
A1IC1 H1     H5  H 0 1 N N N N N N 168.962 115.350 123.997 -6.144 -1.707 -0.772 H1     A1IC1 27 
A1IC1 H2     H6  H 0 1 N N N N N N 167.177 115.191 123.876 -5.406 -0.626 -1.977 H2     A1IC1 28 
A1IC1 "H4'"  H7  H 0 1 N N N N N N 168.665 109.853 127.721 1.465  1.430  -1.295 "H4'"  A1IC1 29 
A1IC1 H8     H8  H 0 1 N N N N N N 167.999 114.130 131.896 -2.897 3.395  1.358  H8     A1IC1 30 
A1IC1 H9     H9  H 0 1 N N N N N N 166.878 114.348 130.510 -1.382 4.329  1.377  H9     A1IC1 31 
A1IC1 H10    H10 H 0 1 N N N N N N 166.672 112.952 131.621 -2.653 4.719  0.194  H10    A1IC1 32 
A1IC1 H5     H11 H 0 1 N N N N N N 167.567 116.864 128.799 -2.927 -2.150 2.565  H5     A1IC1 33 
A1IC1 H6     H12 H 0 1 N N N N N N 167.758 114.499 129.522 -1.131 -0.669 1.834  H6     A1IC1 34 
A1IC1 "H1'"  H13 H 0 1 N N N N N N 169.127 112.080 127.984 -1.131 0.932  -1.513 "H1'"  A1IC1 35 
A1IC1 "H2'"  H14 H 0 1 N N N N N N 166.426 112.463 129.350 -1.345 1.680  1.409  "H2'"  A1IC1 36 
A1IC1 "H3'"  H15 H 0 1 N N N N N N 166.736 110.213 129.942 0.915  2.113  1.599  "H3'"  A1IC1 37 
A1IC1 "HO3'" H17 H 0 0 N N N N N N 168.838 110.535 130.946 1.853  3.680  0.023  "HO3'" A1IC1 38 
A1IC1 OP2    O9  O 0 1 N N N N N N ?       ?       ?       4.419  -1.969 1.204  OP2    A1IC1 39 
A1IC1 HOP2   H19 H 0 0 N N N N N N ?       ?       ?       3.772  -2.677 1.078  HOP2   A1IC1 40 
# 
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 
A1IC1 OP3   P      SING N N 1  
A1IC1 C55   N3     SING N N 2  
A1IC1 O2    C2     DOUB N N 3  
A1IC1 P     OP1    DOUB N N 4  
A1IC1 P     "O5'"  SING N N 5  
A1IC1 N3    C2     SING N N 6  
A1IC1 N3    C4     SING N N 7  
A1IC1 C2    N1     SING N N 8  
A1IC1 O4    C4     DOUB N N 9  
A1IC1 "O5'" "C5'"  SING N N 10 
A1IC1 C4    C5     SING N N 11 
A1IC1 "O4'" "C1'"  SING N N 12 
A1IC1 "O4'" "C4'"  SING N N 13 
A1IC1 N1    "C1'"  SING N N 14 
A1IC1 N1    C6     SING N N 15 
A1IC1 "C5'" "C4'"  SING N N 16 
A1IC1 "C1'" "C2'"  SING N N 17 
A1IC1 "C4'" "C3'"  SING N N 18 
A1IC1 C5    C6     DOUB N N 19 
A1IC1 "C2'" "C3'"  SING N N 20 
A1IC1 "C2'" "O2'"  SING N N 21 
A1IC1 "C3'" "O3'"  SING N N 22 
A1IC1 "O2'" C50    SING N N 23 
A1IC1 "C5'" "H5'"  SING N N 24 
A1IC1 "C5'" "H5''" SING N N 25 
A1IC1 OP3   HOP3   SING N N 26 
A1IC1 C55   H4     SING N N 27 
A1IC1 C55   H1     SING N N 28 
A1IC1 C55   H2     SING N N 29 
A1IC1 "C4'" "H4'"  SING N N 30 
A1IC1 C50   H8     SING N N 31 
A1IC1 C50   H9     SING N N 32 
A1IC1 C50   H10    SING N N 33 
A1IC1 C5    H5     SING N N 34 
A1IC1 C6    H6     SING N N 35 
A1IC1 "C1'" "H1'"  SING N N 36 
A1IC1 "C2'" "H2'"  SING N N 37 
A1IC1 "C3'" "H3'"  SING N N 38 
A1IC1 "O3'" "HO3'" SING N N 39 
A1IC1 P     OP2    SING N N 40 
A1IC1 OP2   HOP2   SING N N 41 
# 
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 
A1IC1 InChI            InChI                1.06  "InChI=1S/C11H17N2O9P/c1-12-7(14)3-4-13(11(12)16)10-9(20-2)8(15)6(22-10)5-21-23(17,18)19/h3-4,6,8-10,15H,5H2,1-2H3,(H2,17,18,19)/t6-,8-,9-,10-/m1/s1" 
A1IC1 InChIKey         InChI                1.06  DXHZPCMDHBXXMJ-PEBGCTIMSA-N                                                                                                                           
A1IC1 SMILES_CANONICAL CACTVS               3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)N(C)C2=O"                                                                                     
A1IC1 SMILES           CACTVS               3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)N(C)C2=O"                                                                                           
A1IC1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OC"                                                                                     
A1IC1 SMILES           "OpenEye OEToolkits" 2.0.7 "CN1C(=O)C=CN(C1=O)C2C(C(C(O2)COP(=O)(O)O)O)OC"                                                                                                       
# 
_pdbx_chem_comp_identifier.comp_id           A1IC1 
_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~{R},4~{R},5~{R})-4-methoxy-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-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 
A1IC1 "Create component"      2024-06-04 PDBE 
A1IC1 "Modify linking type"   2024-06-07 PDBE 
A1IC1 "Modify parent residue" 2024-06-07 PDBE 
A1IC1 "Initial release"       2024-12-25 RCSB 
# 
