data_HHX
# 
_chem_comp.id                                    HHX 
_chem_comp.name                                  "[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-[methanoyl(methyl)amino]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H16 N3 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-01-13 
_chem_comp.pdbx_modified_date                    2025-01-17 
_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                        365.233 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     HHX 
_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        7DS9 
_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 
HHX "C1'"  C1  C 0 1 N N R N N N -10.879 11.055 -18.954 1.087  -0.225 -0.339 "C1'" HHX 1  
HHX C2     C2  C 0 1 N N N N N N -8.873  11.983 -17.989 3.038  1.069  -0.993 C2    HHX 2  
HHX "C2'"  C3  C 0 1 N N R N N N -10.772 11.217 -20.585 1.168  -1.281 0.786  "C2'" HHX 3  
HHX "C3'"  C4  C 0 1 N N S N N N -11.077 10.065 -21.018 -0.300 -1.711 1.003  "C3'" HHX 4  
HHX C4     C5  C 0 1 N N N N N N -7.356  10.651 -16.867 3.874  2.828  0.299  C4    HHX 5  
HHX "C4'"  C6  C 0 1 N N R N N N -12.092 9.381  -19.994 -1.094 -0.864 -0.015 "C4'" HHX 6  
HHX C5     C7  C 0 1 N N N N N N -8.129  9.527  -17.140 2.845  2.606  1.245  C5    HHX 7  
HHX "C5'"  C8  C 0 1 N N N N N N -12.057 7.972  -19.958 -2.435 -0.432 0.581  "C5'" HHX 8  
HHX C6     C9  C 0 1 N N N N N N -9.294  9.703  -17.865 1.952  1.617  1.026  C6    HHX 9  
HHX "C6'"  C10 C 0 1 N N N N N N -13.160 12.340 -20.793 3.191  -2.779 1.109  "C6'" HHX 10 
HHX "C7'"  C11 C 0 1 N N N N N N -11.148 13.636 -21.431 1.620  -3.145 -0.718 "C7'" HHX 11 
HHX N1     N1  N 0 1 N N N N N N -9.631  10.920 -18.269 2.056  0.848  -0.101 N1    HHX 12 
HHX "N2'"  N2  N 0 1 N N N N N N -11.716 12.394 -20.944 1.982  -2.422 0.361  "N2'" HHX 13 
HHX N3     N3  N 0 1 N N N N N N -7.747  11.837 -17.310 3.941  2.048  -0.800 N3    HHX 14 
HHX O2     O1  O 0 1 N N N N N N -9.171  13.078 -18.364 3.114  0.371  -1.986 O2    HHX 15 
HHX "O3'"  O2  O 0 1 N N N N N N -11.741 10.068 -22.350 -0.460 -3.104 0.729  "O3'" HHX 16 
HHX O4     O3  O 0 1 N N N N N N -6.176  10.527 -16.141 4.690  3.714  0.474  O4    HHX 17 
HHX "O4'"  O4  O 0 1 N N N N N N -11.661 10.012 -18.709 -0.261 0.289  -0.266 "O4'" HHX 18 
HHX "O5'"  O5  O 0 1 N N N N N N -10.838 7.479  -19.484 -3.202 0.250  -0.414 "O5'" HHX 19 
HHX "O6'"  O6  O 0 1 N N N N N N -11.869 14.542 -21.700 2.294  -4.089 -1.069 "O6'" HHX 20 
HHX OP1    O7  O 0 1 N N N N N N -11.205 4.914  -19.797 -4.620 1.758  1.031  OP1   HHX 21 
HHX OP2    O8  O 0 1 N N N N N N -9.303  5.775  -18.363 -5.178 1.655  -1.429 OP2   HHX 22 
HHX P      P1  P 0 1 N N N N N N -10.716 5.973  -18.837 -4.671 0.845  -0.133 P     HHX 23 
HHX H1     H1  H 0 1 N N N N N N -11.367 11.973 -18.596 1.266  -0.688 -1.309 H1    HHX 24 
HHX H2     H2  H 0 1 N N N N N N -9.738  11.508 -20.824 1.576  -0.840 1.696  H2    HHX 25 
HHX H3     H3  H 0 1 N N N N N N -10.194 9.411  -21.077 -0.618 -1.482 2.020  H3    HHX 26 
HHX H4     H4  H 0 1 N N N N N N -13.105 9.730  -20.242 -1.253 -1.427 -0.935 H4    HHX 27 
HHX H5     H5  H 0 1 N N N N N N -7.829  8.548  -16.797 2.774  3.220  2.131  H5    HHX 28 
HHX H6     H6  H 0 1 N N N N N N -12.862 7.616  -19.298 -2.981 -1.311 0.922  H6    HHX 29 
HHX H7     H7  H 0 1 N N N N N N -12.221 7.589  -20.976 -2.259 0.236  1.425  H7    HHX 30 
HHX H8     H8  H 0 1 N N N N N N -9.923  8.857  -18.100 1.160  1.433  1.737  H8    HHX 31 
HHX H9     H9  H 0 1 N N N N N N -13.453 11.348 -20.419 4.046  -2.246 0.692  H9    HHX 32 
HHX H10    H10 H 0 1 N N N N N N -13.483 13.112 -20.079 3.066  -2.502 2.155  H10   HHX 33 
HHX H11    H11 H 0 1 N N N N N N -13.637 12.520 -21.768 3.361  -3.853 1.035  H11   HHX 34 
HHX H12    H12 H 0 1 N N N N N N -10.079 13.737 -21.548 0.729  -2.882 -1.269 H12   HHX 35 
HHX H13    H13 H 0 1 N N N N N N -7.179  12.639 -17.127 4.643  2.194  -1.453 H13   HHX 36 
HHX "HO3'" H14 H 0 1 N Y N N N N -11.939 9.175  -22.608 -1.363 -3.428 0.849  H14   HHX 37 
HHX HOP2   H16 H 0 1 N N N N N N -8.942  4.991  -18.760 -6.059 2.042  -1.331 H16   HHX 38 
HHX OP3    O9  O 0 1 N Y N N N N -11.764 5.972  -17.622 -5.689 -0.363 0.177  O1    HHX 39 
HHX HOP3   H15 H 0 1 N N N N N N -12.436 5.320  -17.783 -5.773 -1.002 -0.544 H15   HHX 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 
HHX "O3'" "C3'"  SING N N 1  
HHX "O6'" "C7'"  DOUB N N 2  
HHX "C7'" "N2'"  SING N N 3  
HHX "C3'" "C2'"  SING N N 4  
HHX "C3'" "C4'"  SING N N 5  
HHX "N2'" "C6'"  SING N N 6  
HHX "N2'" "C2'"  SING N N 7  
HHX "C2'" "C1'"  SING N N 8  
HHX "C4'" "C5'"  SING N N 9  
HHX "C4'" "O4'"  SING N N 10 
HHX "C5'" "O5'"  SING N N 11 
HHX OP1   P      DOUB N N 12 
HHX "O5'" P      SING N N 13 
HHX "C1'" "O4'"  SING N N 14 
HHX "C1'" N1     SING N N 15 
HHX P     OP2    SING N N 16 
HHX O2    C2     DOUB N N 17 
HHX N1    C2     SING N N 18 
HHX N1    C6     SING N N 19 
HHX C2    N3     SING N N 20 
HHX C6    C5     DOUB N N 21 
HHX N3    C4     SING N N 22 
HHX C5    C4     SING N N 23 
HHX C4    O4     DOUB N N 24 
HHX "C1'" H1     SING N N 25 
HHX "C2'" H2     SING N N 26 
HHX "C3'" H3     SING N N 27 
HHX "C4'" H4     SING N N 28 
HHX C5    H5     SING N N 29 
HHX "C5'" H6     SING N N 30 
HHX "C5'" H7     SING N N 31 
HHX C6    H8     SING N N 32 
HHX "C6'" H9     SING N N 33 
HHX "C6'" H10    SING N N 34 
HHX "C6'" H11    SING N N 35 
HHX "C7'" H12    SING N N 36 
HHX N3    H13    SING N N 37 
HHX "O3'" "HO3'" SING N N 38 
HHX OP2   HOP2   SING N N 39 
HHX P     OP3    SING N N 40 
HHX OP3   HOP3   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 
HHX InChI            InChI                1.03  "InChI=1S/C11H16N3O9P/c1-13(5-15)8-9(17)6(4-22-24(19,20)21)23-10(8)14-3-2-7(16)12-11(14)18/h2-3,5-6,8-10,17H,4H2,1H3,(H,12,16,18)(H2,19,20,21)/t6-,8-,9-,10-/m1/s1" 
HHX InChIKey         InChI                1.03  CCDZTXGHNXOAPJ-PEBGCTIMSA-N                                                                                                                                         
HHX SMILES_CANONICAL CACTVS               3.385 "CN(C=O)[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O"                                                                                                 
HHX SMILES           CACTVS               3.385 "CN(C=O)[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O"                                                                                                       
HHX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN(C=O)[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O"                                                                                                   
HHX SMILES           "OpenEye OEToolkits" 2.0.7 "CN(C=O)C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O"                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           HHX 
_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-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-[methanoyl(methyl)amino]-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 
HHX "Create component" 2021-01-13 PDBJ 
HHX "Initial release"  2025-01-22 RCSB 
# 
