data_M5Q
# 
_chem_comp.id                                    M5Q 
_chem_comp.name                                  "[(1S)-1-[(2S,3R,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]ethyl] dihydrogen phosphate" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H18 N3 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-12-15 
_chem_comp.pdbx_modified_date                    2025-11-07 
_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                        351.250 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     M5Q 
_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        8HMK 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_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_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 
M5Q "C1'"  C1  C 0 1 N N R N N N 231.600 261.679 220.869 -1.143 1.131  -0.760 "C1'"  M5Q 1  
M5Q C2     C2  C 0 1 N N N N N N 232.019 259.503 221.882 -2.062 -0.983 0.017  C2     M5Q 2  
M5Q "C2'"  C3  C 0 1 N N R N N N 232.582 261.601 219.704 -0.338 1.439  0.528  "C2'"  M5Q 3  
M5Q "C3'"  C4  C 0 1 N N R N N N 231.653 261.792 218.524 1.063  1.777  -0.038 "C3'"  M5Q 4  
M5Q C34    C5  C 0 1 N N N N N N 228.723 264.197 218.836 2.146  -0.606 -2.878 C34    M5Q 5  
M5Q C4     C6  C 0 1 N N N N N N 230.398 258.051 222.157 -4.330 -1.412 0.106  C4     M5Q 6  
M5Q "C4'"  C7  C 0 1 N N S N N N 230.684 262.814 219.056 1.072  1.128  -1.436 "C4'"  M5Q 7  
M5Q C5     C8  C 0 1 N N N N N N 229.431 258.913 221.599 -4.592 -0.118 -0.388 C5     M5Q 8  
M5Q "C5'"  C9  C 0 1 N N S N N N 229.374 262.915 218.334 2.220  0.122  -1.534 "C5'"  M5Q 9  
M5Q C6     C10 C 0 1 N N N N N N 229.851 260.102 221.183 -3.550 0.700  -0.668 C6     M5Q 10 
M5Q N1     N1  N 0 1 N N N N N N 231.163 260.351 221.339 -2.279 0.256  -0.461 N1     M5Q 11 
M5Q N3     N2  N 0 1 N N N N N N 231.672 258.295 222.320 -3.076 -1.802 0.292  N3     M5Q 12 
M5Q N4     N3  N 0 1 N N N N N N 229.959 256.867 222.557 -5.370 -2.266 0.394  N4     M5Q 13 
M5Q O2     O1  O 0 1 N N N N N N 233.199 259.801 222.006 -0.917 -1.365 0.197  O2     M5Q 14 
M5Q "O2'"  O2  O 0 1 N N N N N N 233.456 262.703 219.803 -0.892 2.560  1.220  "O2'"  M5Q 15 
M5Q "O3'"  O3  O 0 1 N N N N N N 232.303 262.207 217.341 1.235  3.192  -0.142 "O3'"  M5Q 16 
M5Q "O4'"  O4  O 0 1 N N N N N N 230.465 262.377 220.412 -0.188 0.454  -1.604 "O4'"  M5Q 17 
M5Q "O5'"  O5  O 0 1 N N N N N N 228.527 261.835 218.657 2.115  -0.827 -0.471 "O5'"  M5Q 18 
M5Q OP1    O6  O 0 1 N N N N N N 226.612 261.569 217.129 4.551  -1.326 -0.037 OP1    M5Q 19 
M5Q OP2    O7  O 0 1 N N N N N N 228.823 260.595 216.547 3.411  0.305  1.517  OP2    M5Q 20 
M5Q P      P1  P 0 1 N N N N N N 227.841 260.948 217.538 3.265  -1.035 0.636  P      M5Q 21 
M5Q CM2    C11 C 0 1 N N N N N N 234.766 262.350 220.089 -1.870 2.211  2.202  CM2    M5Q 22 
M5Q "H1'"  H1  H 0 1 N N N N N N 232.077 262.223 221.698 -1.484 2.054  -1.230 "H1'"  M5Q 23 
M5Q "H2'"  H2  H 0 1 N N N N N N 233.098 260.630 219.669 -0.295 0.566  1.178  "H2'"  M5Q 24 
M5Q "H3'"  H3  H 0 1 N N N N N N 231.112 260.851 218.346 1.841  1.343  0.590  "H3'"  M5Q 25 
M5Q H34    H4  H 0 1 N N N N N N 229.368 265.055 218.595 2.227  0.118  -3.688 H34    M5Q 26 
M5Q H35    H5  H 0 1 N N N N N N 227.744 264.326 218.350 2.964  -1.323 -2.948 H35    M5Q 27 
M5Q H36    H6  H 0 1 N N N N N N 228.586 264.136 219.926 1.195  -1.132 -2.954 H36    M5Q 28 
M5Q "H4'"  H7  H 0 1 N N N N N N 231.170 263.801 219.056 1.183  1.897  -2.200 "H4'"  M5Q 29 
M5Q H5     H8  H 0 1 N N N N N N 228.395 258.619 221.514 -5.608 0.214  -0.545 H5     M5Q 30 
M5Q "H5'"  H9  H 0 1 N N N N N N 229.544 262.983 217.249 3.172  0.648  -1.458 "H5'"  M5Q 31 
M5Q H6     H10 H 0 1 N N N N N N 229.179 260.826 220.746 -3.725 1.695  -1.052 H6     M5Q 32 
M5Q HN41   H11 H 0 0 N N N N N N 230.594 256.209 222.962 -5.186 -3.156 0.734  HN41   M5Q 33 
M5Q HN42   H12 H 0 0 N N N N N N 228.993 256.631 222.454 -6.286 -1.979 0.257  HN42   M5Q 34 
M5Q "HO3'" H13 H 0 0 N N N N N N 232.900 261.527 217.052 1.237  3.652  0.708  "HO3'" M5Q 35 
M5Q HOP2   H15 H 0 0 N N N N N N 228.505 260.838 215.685 2.604  0.556  1.987  HOP2   M5Q 36 
M5Q H16    H16 H 0 1 N N N N N N 235.386 263.257 220.151 -2.243 3.116  2.682  H16    M5Q 37 
M5Q H17    H17 H 0 1 N N N N N N 234.800 261.817 221.050 -2.697 1.689  1.721  H17    M5Q 38 
M5Q H18    H18 H 0 1 N N N N N N 235.152 261.696 219.293 -1.418 1.562  2.951  H18    M5Q 39 
M5Q OP3    O8  O 0 1 N N N N N N 227.467 259.613 218.322 2.870  -2.267 1.594  OP3    M5Q 40 
M5Q HOP3   H14 H 0 0 N N N N N N 226.522 259.516 218.350 3.520  -2.450 2.287  HOP3   M5Q 41 
# 
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 
M5Q OP2   P      SING N N 1  
M5Q OP1   P      DOUB N N 2  
M5Q "O3'" "C3'"  SING N N 3  
M5Q P     "O5'"  SING N N 4  
M5Q "C5'" "O5'"  SING N N 5  
M5Q "C5'" C34    SING N N 6  
M5Q "C5'" "C4'"  SING N N 7  
M5Q "C3'" "C4'"  SING N N 8  
M5Q "C3'" "C2'"  SING N N 9  
M5Q "C4'" "O4'"  SING N N 10 
M5Q "C2'" "O2'"  SING N N 11 
M5Q "C2'" "C1'"  SING N N 12 
M5Q "O2'" CM2    SING N N 13 
M5Q "O4'" "C1'"  SING N N 14 
M5Q "C1'" N1     SING N N 15 
M5Q C6    N1     SING N N 16 
M5Q C6    C5     DOUB N N 17 
M5Q N1    C2     SING N N 18 
M5Q C5    C4     SING N N 19 
M5Q C2    O2     DOUB N N 20 
M5Q C2    N3     SING N N 21 
M5Q C4    N3     DOUB N N 22 
M5Q C4    N4     SING N N 23 
M5Q "C1'" "H1'"  SING N N 24 
M5Q "C2'" "H2'"  SING N N 25 
M5Q "C3'" "H3'"  SING N N 26 
M5Q C34   H34    SING N N 27 
M5Q C34   H35    SING N N 28 
M5Q C34   H36    SING N N 29 
M5Q "C4'" "H4'"  SING N N 30 
M5Q C5    H5     SING N N 31 
M5Q "C5'" "H5'"  SING N N 32 
M5Q C6    H6     SING N N 33 
M5Q N4    HN41   SING N N 34 
M5Q N4    HN42   SING N N 35 
M5Q "O3'" "HO3'" SING N N 36 
M5Q OP2   HOP2   SING N N 37 
M5Q CM2   H16    SING N N 38 
M5Q CM2   H17    SING N N 39 
M5Q CM2   H18    SING N N 40 
M5Q P     OP3    SING N N 41 
M5Q OP3   HOP3   SING N N 42 
# 
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 
M5Q InChI            InChI                1.06  "InChI=1S/C11H18N3O8P/c1-5(22-23(17,18)19)8-7(15)9(20-2)10(21-8)14-4-3-6(12)13-11(14)16/h3-5,7-10,15H,1-2H3,(H2,12,13,16)(H2,17,18,19)/t5-,7+,8+,9+,10+/m0/s1" 
M5Q InChIKey         InChI                1.06  OBLDPPWBFVCFRR-BOHATCBPSA-N                                                                                                                                    
M5Q SMILES_CANONICAL CACTVS               3.385 "CO[C@@H]1[C@H](O)[C@H](O[C@H]1N2C=CC(=NC2=O)N)[C@H](C)O[P](O)(O)=O"                                                                                           
M5Q SMILES           CACTVS               3.385 "CO[CH]1[CH](O)[CH](O[CH]1N2C=CC(=NC2=O)N)[CH](C)O[P](O)(O)=O"                                                                                                 
M5Q SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]([C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)OC)O)OP(=O)(O)O"                                                                                         
M5Q SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C1C(C(C(O1)N2C=CC(=NC2=O)N)OC)O)OP(=O)(O)O"                                                                                                                
# 
_pdbx_chem_comp_identifier.comp_id           M5Q 
_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        "[(1~{S})-1-[(2~{S},3~{R},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]ethyl] 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 
M5Q "Create component" 2022-12-15 PDBJ 
M5Q "Initial release"  2025-11-12 RCSB 
# 
