data_D5D
# 
_chem_comp.id                                    D5D 
_chem_comp.name                                  "[(1S)-1-[(2S,3S,4R,5R)-5-[2,4-bis(oxidanylidene)-1,3-diazinan-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]ethyl] dihydrogen phosphate" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H17 N2 O9 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                        340.224 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     D5D 
_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 
D5D O2     O1  O 0 1 N N N N N N 225.680 251.695 210.667 -1.002 -1.231 0.319  O2     D5D 1  
D5D O4     O2  O 0 1 N N N N N N 224.079 253.979 207.348 -5.344 -2.060 0.266  O4     D5D 2  
D5D "C1'"  C1  C 0 1 N N R N N N 225.322 253.714 212.523 -1.191 1.350  -0.336 "C1'"  D5D 3  
D5D C2     C2  C 0 1 N N N N N N 225.078 252.685 210.323 -2.139 -0.813 0.221  C2     D5D 4  
D5D "C2'"  C3  C 0 1 N N R N N N 226.445 254.643 212.955 -0.272 1.473  0.906  "C2'"  D5D 5  
D5D "C3'"  C4  C 0 1 N N S N N N 226.118 254.828 214.427 1.093  1.824  0.266  "C3'"  D5D 6  
D5D C34    C5  C 0 1 N N N N N N 222.574 255.874 214.092 1.837  -0.240 -2.913 C34    D5D 7  
D5D C4     C6  C 0 1 N N N N N N 224.483 253.866 208.482 -4.420 -1.308 0.044  C4     D5D 8  
D5D "C4'"  C7  C 0 1 N N S N N N 224.597 254.880 214.414 0.960  1.346  -1.192 "C4'"  D5D 9  
D5D C5     C8  C 0 1 N N N N N N 225.073 255.046 209.183 -4.674 0.030  -0.604 C5     D5D 10 
D5D "C5'"  C9  C 0 1 N N S N N N 224.017 256.267 214.370 2.052  0.320  -1.505 "C5'"  D5D 11 
D5D C6     C10 C 0 1 N N N N N N 224.632 255.063 210.630 -3.688 1.056  -0.048 C6     D5D 12 
D5D N1     N1  N 0 1 N N N N N N 225.015 253.755 211.089 -2.339 0.488  -0.045 N1     D5D 13 
D5D N3     N2  N 0 1 N N N N N N 224.453 252.739 209.163 -3.166 -1.666 0.377  N3     D5D 14 
D5D "O2'"  O3  O 0 1 N N N N N N 227.713 254.090 212.703 -0.717 2.522  1.768  "O2'"  D5D 15 
D5D "O3'"  O4  O 0 1 N N N N N N 226.543 253.683 215.161 1.319  3.234  0.312  "O3'"  D5D 16 
D5D "O4'"  O5  O 0 1 N N N N N N 224.183 254.150 213.231 -0.337 0.742  -1.328 "O4'"  D5D 17 
D5D "O5'"  O6  O 0 1 N N N N N N 224.267 256.894 213.126 1.990  -0.745 -0.555 "O5'"  D5D 18 
D5D OP1    O7  O 0 1 N N N N N N 223.585 259.263 213.418 4.429  -1.375 -0.391 OP1    D5D 19 
D5D OP2    O8  O 0 1 N N N N N N 226.007 258.527 213.843 3.492  0.096  1.433  OP2    D5D 20 
D5D P      P1  P 0 1 N N N N N N 224.748 258.400 213.052 3.216  -1.123 0.418  P      D5D 21 
D5D "H1'"  H1  H 0 1 N N N N N N 225.582 252.685 212.814 -1.523 2.334  -0.666 "H1'"  D5D 22 
D5D "H2'"  H2  H 0 1 N N N N N N 226.332 255.607 212.438 -0.217 0.526  1.445  "H2'"  D5D 23 
D5D "H3'"  H3  H 0 1 N N N N N N 226.545 255.764 214.816 1.900  1.293  0.772  "H3'"  D5D 24 
D5D H4     H4  H 0 1 N N N N N N 222.161 255.349 214.966 1.883  0.573  -3.638 H4     D5D 25 
D5D H5     H5  H 0 1 N N N N N N 221.980 256.778 213.893 2.614  -0.970 -3.136 H5     D5D 26 
D5D H6     H6  H 0 1 N N N N N N 222.537 255.211 213.215 0.860  -0.720 -2.968 H6     D5D 27 
D5D "H4'"  H7  H 0 1 N N N N N N 224.222 254.367 215.312 1.046  2.196  -1.870 "H4'"  D5D 28 
D5D H51    H8  H 0 1 N N N N N N 226.170 254.985 209.137 -4.537 -0.055 -1.682 H51    D5D 29 
D5D H52    H9  H 0 1 N N N N N N 224.736 255.969 208.689 -5.694 0.350  -0.391 H52    D5D 30 
D5D "H5'"  H10 H 0 1 N N N N N N 224.170 256.872 215.276 3.028  0.801  -1.451 "H5'"  D5D 31 
D5D H61    H11 H 0 1 N N N N N N 225.153 255.850 211.195 -3.705 1.951  -0.671 H61    D5D 32 
D5D H62    H12 H 0 1 N N N N N N 223.545 255.210 210.712 -3.972 1.318  0.971  H62    D5D 33 
D5D HN3    H13 H 0 1 N N N N N N 223.966 251.941 208.808 -3.001 -2.552 0.734  HN3    D5D 34 
D5D "HO2'" H14 H 0 0 N N N N N N 228.386 254.698 212.986 -0.174 2.638  2.560  "HO2'" D5D 35 
D5D "HO3'" H15 H 0 0 N Y N N N N 226.337 253.802 216.081 1.352  3.598  1.208  "HO3'" D5D 36 
D5D HOP2   H16 H 0 0 N N N N N N 225.892 259.184 214.519 2.738  0.317  1.997  HOP2   D5D 37 
D5D OP3    OP3 O 0 1 N Y N N N N 225.033 258.641 211.494 2.846  -2.446 1.258  OP3    D5D 38 
D5D HOP3   H17 H 0 0 N N N N N N 224.409 259.270 211.151 3.541  -2.733 1.866  HOP3   D5D 39 
# 
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 
D5D O4    C4     DOUB N N 1  
D5D C4    N3     SING N N 2  
D5D C4    C5     SING N N 3  
D5D N3    C2     SING N N 4  
D5D C5    C6     SING N N 5  
D5D C2    O2     DOUB N N 6  
D5D C2    N1     SING N N 7  
D5D C6    N1     SING N N 8  
D5D N1    "C1'"  SING N N 9  
D5D "C1'" "C2'"  SING N N 10 
D5D "C1'" "O4'"  SING N N 11 
D5D "O2'" "C2'"  SING N N 12 
D5D "C2'" "C3'"  SING N N 13 
D5D P     "O5'"  SING N N 14 
D5D P     OP1    DOUB N N 15 
D5D P     OP2    SING N N 16 
D5D "O5'" "C5'"  SING N N 17 
D5D "O4'" "C4'"  SING N N 18 
D5D C34   "C5'"  SING N N 19 
D5D "C5'" "C4'"  SING N N 20 
D5D "C4'" "C3'"  SING N N 21 
D5D "C3'" "O3'"  SING N N 22 
D5D "C1'" "H1'"  SING N N 23 
D5D "C2'" "H2'"  SING N N 24 
D5D "C3'" "H3'"  SING N N 25 
D5D C34   H4     SING N N 26 
D5D C34   H5     SING N N 27 
D5D C34   H6     SING N N 28 
D5D "C4'" "H4'"  SING N N 29 
D5D C5    H51    SING N N 30 
D5D C5    H52    SING N N 31 
D5D "C5'" "H5'"  SING N N 32 
D5D C6    H61    SING N N 33 
D5D C6    H62    SING N N 34 
D5D N3    HN3    SING N N 35 
D5D "O2'" "HO2'" SING N N 36 
D5D "O3'" "HO3'" SING N N 37 
D5D OP2   HOP2   SING N N 38 
D5D P     OP3    SING N N 39 
D5D OP3   HOP3   SING N N 40 
# 
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 
D5D InChI            InChI                1.06  "InChI=1S/C10H17N2O9P/c1-4(21-22(17,18)19)8-6(14)7(15)9(20-8)12-3-2-5(13)11-10(12)16/h4,6-9,14-15H,2-3H2,1H3,(H,11,13,16)(H2,17,18,19)/t4-,6-,7+,8+,9+/m0/s1" 
D5D InChIKey         InChI                1.06  UTNZYCCMZBSWKD-IHMGDUAMSA-N                                                                                                                                   
D5D SMILES_CANONICAL CACTVS               3.385 "C[C@H](O[P](O)(O)=O)[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2CCC(=O)NC2=O"                                                                                            
D5D SMILES           CACTVS               3.385 "C[CH](O[P](O)(O)=O)[CH]1O[CH]([CH](O)[CH]1O)N2CCC(=O)NC2=O"                                                                                                  
D5D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]([C@@H]1[C@H]([C@H]([C@@H](O1)N2CCC(=O)NC2=O)O)O)OP(=O)(O)O"                                                                                          
D5D SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C1C(C(C(O1)N2CCC(=O)NC2=O)O)O)OP(=O)(O)O"                                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           D5D 
_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~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)-1,3-diazinan-1-yl]-3,4-bis(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 
D5D "Create component" 2022-12-15 PDBJ 
D5D "Initial release"  2025-11-12 RCSB 
# 
