data_05H
# 
_chem_comp.id                                    05H 
_chem_comp.name                                  "[(1R,3R,4R,7S)-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-[2-[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylamino]-2-oxidanylidene-ethyl]-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C23 H30 N5 O13 P" 
_chem_comp.mon_nstd_parent_comp_id               "DT, DT" 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-05-28 
_chem_comp.pdbx_modified_date                    2023-03-09 
_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                        615.484 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     05H 
_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        7OOQ 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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.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 
05H C1     C1  C 0 1 N N N 10.014 16.377 5.858  0.110  -0.472 -0.849 C1     05H 1  
05H "C1'"  C2  C 0 1 N N R 8.011  19.341 2.849  5.673  0.135  -1.378 "C1'"  05H 2  
05H C5A    C3  C 0 1 N N N 14.800 20.918 5.875  -5.825 -3.225 -2.036 C5A    05H 3  
05H C2     C4  C 0 1 N N N 9.450  20.771 1.340  6.448  -0.489 0.840  C2     05H 4  
05H "C2'"  C5  C 0 1 N N N 7.196  18.623 1.783  5.983  -1.230 -2.030 "C2'"  05H 5  
05H C21    C6  C 0 1 N N N 10.648 21.722 5.783  -3.935 -3.276 1.747  C21    05H 6  
05H C3     C7  C 0 1 N N N 9.198  18.389 9.389  -2.359 1.575  1.732  C3     05H 7  
05H "C3'"  C8  C 0 1 N N S 7.446  17.165 2.071  4.602  -1.748 -2.491 "C3'"  05H 8  
05H C4     C9  C 0 1 N N N 11.762 20.611 1.378  8.097  0.710  1.981  C4     05H 9  
05H "C4'"  C10 C 0 1 N N R 7.639  17.116 3.562  3.621  -0.634 -2.062 "C4'"  05H 10 
05H C41    C11 C 0 1 N N N 12.726 22.093 4.837  -5.000 -4.447 0.029  C41    05H 11 
05H C5     C12 C 0 1 N N N 11.659 19.575 2.417  8.192  1.601  0.885  C5     05H 12 
05H "C5'"  C13 C 0 1 N N N 8.571  15.975 3.906  2.303  -1.243 -1.579 "C5'"  05H 13 
05H C51    C14 C 0 1 N N N 13.328 21.207 5.851  -5.150 -3.236 -0.689 C51    05H 14 
05H C6     C15 C 0 1 N N N 10.409 19.211 2.858  7.403  1.403  -0.193 C6     05H 15 
05H C61    C16 C 0 1 N N N 12.504 20.636 6.791  -4.681 -2.091 -0.149 C61    05H 16 
05H C5M    C17 C 0 1 N N N 12.885 18.926 2.987  9.161  2.755  0.920  C5M    05H 17 
05H C11    C18 C 0 1 N N N 10.026 16.563 7.346  -0.873 0.631  -0.552 C11    05H 18 
05H N1     N1  N 0 1 N N N 9.317  19.777 2.339  6.529  0.350  -0.208 N1     05H 19 
05H N11    N2  N 0 1 N N N 11.191 20.872 6.763  -4.071 -2.118 1.075  N11    05H 20 
05H N3     N3  N 0 1 N N N 10.649 21.147 0.903  7.223  -0.315 1.927  N3     05H 21 
05H N31    N4  N 0 1 N N N 11.417 22.297 4.862  -4.393 -4.432 1.233  N31    05H 22 
05H "N5'"  N5  N 0 1 N N N 8.830  16.170 5.313  1.347  -0.171 -1.291 "N5'"  05H 23 
05H O2     O1  O 0 1 N N N 8.463  21.337 0.832  5.661  -1.415 0.807  O2     05H 24 
05H "O2'"  O2  O 0 1 N N N 8.570  18.780 8.163  -1.632 0.410  2.171  "O2'"  05H 25 
05H O21    O3  O 0 1 N N N 9.425  21.952 5.765  -3.386 -3.279 2.832  O21    05H 26 
05H O1     O4  O 0 1 N N N 11.044 16.436 5.215  -0.210 -1.630 -0.684 O1     05H 27 
05H "O3'"  O5  O 0 1 N N N 6.389  16.276 1.647  4.579  -1.917 -3.910 "O3'"  05H 28 
05H O4     O6  O 0 1 N N N 12.871 20.976 0.950  8.798  0.869  2.964  O4     05H 29 
05H "O4'"  O7  O 0 1 N N N 8.221  18.380 3.891  4.288  0.047  -0.978 "O4'"  05H 30 
05H O41    O8  O 0 1 N N N 13.426 22.637 3.964  -5.415 -5.493 -0.437 O41    05H 31 
05H "O5'"  O9  O 0 1 N N N 12.889 17.632 9.246  -4.435 3.155  0.213  "O5'"  05H 32 
05H OP1    O10 O 0 1 N N N 14.023 16.203 11.000 -5.892 4.008  -1.663 OP1    05H 33 
05H OP2    O11 O 0 1 N N N 15.561 17.326 9.311  -6.018 5.227  0.543  OP2    05H 34 
05H P      P1  P 0 1 N N N 14.189 17.399 10.157 -5.080 4.443  -0.504 P      05H 35 
05H "C1'1" C19 C 0 0 N N R 10.304 20.266 7.758  -3.562 -0.876 1.661  "C1'1" 05H 36 
05H "C2'1" C20 C 0 0 N N R 9.610  19.030 7.233  -2.049 -0.697 1.321  "C2'1" 05H 37 
05H "C3'1" C21 C 0 0 N N S 10.587 17.947 7.560  -2.191 0.023  -0.069 "C3'1" 05H 38 
05H "C4'1" C22 C 0 0 N N R 10.659 18.381 8.990  -3.184 1.106  0.493  "C4'1" 05H 39 
05H "C5'1" C23 C 0 0 N N N 11.601 17.555 9.841  -3.636 2.195  -0.482 "C5'1" 05H 40 
05H "O4'1" O12 O 0 0 N N N 11.047 19.745 8.859  -4.224 0.264  1.069  "O4'1" 05H 41 
05H "H1'"  H1  H 0 1 N N N 7.443  20.205 3.225  5.809  0.941  -2.100 "H1'"  05H 42 
05H H5A1   H2  H 0 0 N N N 15.027 20.238 6.709  -6.131 -4.238 -2.297 H5A1   05H 43 
05H H5A2   H3  H 0 0 N N N 15.096 20.446 4.927  -6.701 -2.579 -1.999 H5A2   05H 44 
05H H5A3   H4  H 0 0 N N N 15.356 21.858 6.006  -5.129 -2.851 -2.788 H5A3   05H 45 
05H "H2'1" H5  H 0 0 N N N 7.545  18.890 0.775  6.648  -1.103 -2.885 "H2'1" 05H 46 
05H "H2'2" H6  H 0 0 N N N 6.127  18.864 1.876  6.423  -1.911 -1.301 "H2'2" 05H 47 
05H HC31   H7  H 0 0 N N N 9.004  19.117 10.190 -3.026 1.923  2.520  HC31   05H 48 
05H HC32   H8  H 0 0 N N N 8.864  17.392 9.712  -1.666 2.367  1.446  HC32   05H 49 
05H "H3'"  H9  H 0 1 N N N 8.388  16.869 1.586  4.359  -2.685 -1.990 "H3'"  05H 50 
05H "H4'"  H10 H 0 1 N N N 6.671  16.978 4.066  3.442  0.053  -2.889 "H4'"  05H 51 
05H "H5'1" H11 H 0 0 N N N 8.088  15.003 3.725  1.897  -1.893 -2.354 "H5'1" 05H 52 
05H "H5'2" H12 H 0 0 N N N 9.501  16.036 3.322  2.481  -1.824 -0.674 "H5'2" 05H 53 
05H H6     H13 H 0 1 N N N 10.310 18.462 3.630  7.462  2.072  -1.038 H6     05H 54 
05H H61    H14 H 0 1 N N N 12.920 19.995 7.554  -4.787 -1.157 -0.682 H61    05H 55 
05H H52    H16 H 0 1 N N N 12.590 18.185 3.744  9.703  2.745  1.866  H52    05H 56 
05H H53    H17 H 0 1 N N N 13.443 18.425 2.182  9.868  2.661  0.096  H53    05H 57 
05H HN3    H22 H 0 1 N N N 10.711 21.853 0.197  7.152  -0.929 2.674  HN3    05H 58 
05H H31    H23 H 0 1 N N N 11.000 22.894 4.177  -4.287 -5.258 1.730  H31    05H 59 
05H "HN5'" H24 H 0 0 N N N 8.043  16.146 5.929  1.605  0.756  -1.419 "HN5'" 05H 60 
05H "HO3'" H25 H 0 0 N Y N 6.622  15.381 1.863  5.219  -2.562 -4.240 "HO3'" 05H 61 
05H HOP2   H26 H 0 0 N N N 16.016 16.517 9.513  -6.441 6.017  0.178  HOP2   05H 62 
05H H1     H27 H 0 1 N N N 9.555  20.996 8.099  -3.710 -0.879 2.741  H1     05H 63 
05H HC21   H28 H 0 0 N N N 9.316  19.085 6.174  -1.436 -1.597 1.346  HC21   05H 64 
05H OP3    OP3 O 0 1 N Y N ?      ?      ?      -3.905 5.421  -1.010 OP3    05H 65 
05H HOP3   H29 H 0 0 N Y N ?      ?      ?      -3.333 5.746  -0.302 HOP3   05H 66 
05H H2     H30 H 0 1 N N N 9.007  16.491 7.753  -0.467 1.281  0.223  H2     05H 67 
05H H3     H31 H 0 1 N N N 10.666 15.808 7.825  -1.051 1.212  -1.457 H3     05H 68 
05H "H3'1" H32 H 0 0 N N N 11.546 18.085 7.039  -2.650 -0.615 -0.825 "H3'1" 05H 69 
05H HC52   H33 H 0 0 N N N 11.635 17.958 10.864 -4.222 1.746  -1.283 HC52   05H 70 
05H H51    H34 H 0 1 N N N 13.522 19.692 3.453  8.613  3.692  0.825  H51    05H 71 
05H HC51   H35 H 0 0 N N N 11.262 16.509 9.870  -2.761 2.689  -0.905 HC51   05H 72 
# 
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 
05H O2     C2     DOUB N N 1  
05H N3     C2     SING N N 2  
05H N3     C4     SING N N 3  
05H O4     C4     DOUB N N 4  
05H C2     N1     SING N N 5  
05H C4     C5     SING N N 6  
05H "O3'"  "C3'"  SING N N 7  
05H "C2'"  "C3'"  SING N N 8  
05H "C2'"  "C1'"  SING N N 9  
05H "C3'"  "C4'"  SING N N 10 
05H N1     "C1'"  SING N N 11 
05H N1     C6     SING N N 12 
05H C5     C6     DOUB N N 13 
05H C5     C5M    SING N N 14 
05H "C1'"  "O4'"  SING N N 15 
05H "C4'"  "O4'"  SING N N 16 
05H "C4'"  "C5'"  SING N N 17 
05H "C5'"  "N5'"  SING N N 18 
05H O41    C41    DOUB N N 19 
05H C41    N31    SING N N 20 
05H C41    C51    SING N N 21 
05H N31    C21    SING N N 22 
05H O1     C1     DOUB N N 23 
05H "N5'"  C1     SING N N 24 
05H O21    C21    DOUB N N 25 
05H C21    N11    SING N N 26 
05H C51    C5A    SING N N 27 
05H C51    C61    DOUB N N 28 
05H C1     C11    SING N N 29 
05H N11    C61    SING N N 30 
05H N11    "C1'1" SING N N 31 
05H "C2'1" "C3'1" SING N N 32 
05H "C2'1" "C1'1" SING N N 33 
05H "C2'1" "O2'"  SING N N 34 
05H C11    "C3'1" SING N N 35 
05H "C3'1" "C4'1" SING N N 36 
05H "C1'1" "O4'1" SING N N 37 
05H "O2'"  C3     SING N N 38 
05H "O4'1" "C4'1" SING N N 39 
05H "C4'1" C3     SING N N 40 
05H "C4'1" "C5'1" SING N N 41 
05H "O5'"  "C5'1" SING N N 42 
05H "O5'"  P      SING N N 43 
05H OP2    P      SING N N 44 
05H P      OP1    DOUB N N 45 
05H "C1'"  "H1'"  SING N N 46 
05H C5A    H5A1   SING N N 47 
05H C5A    H5A2   SING N N 48 
05H C5A    H5A3   SING N N 49 
05H "C2'"  "H2'1" SING N N 50 
05H "C2'"  "H2'2" SING N N 51 
05H C3     HC31   SING N N 52 
05H C3     HC32   SING N N 53 
05H "C3'"  "H3'"  SING N N 54 
05H "C4'"  "H4'"  SING N N 55 
05H "C5'"  "H5'1" SING N N 56 
05H "C5'"  "H5'2" SING N N 57 
05H C6     H6     SING N N 58 
05H C61    H61    SING N N 59 
05H C5M    H52    SING N N 60 
05H C5M    H53    SING N N 61 
05H N3     HN3    SING N N 62 
05H N31    H31    SING N N 63 
05H "N5'"  "HN5'" SING N N 64 
05H "O3'"  "HO3'" SING N N 65 
05H OP2    HOP2   SING N N 66 
05H "C1'1" H1     SING N N 67 
05H "C2'1" HC21   SING N N 68 
05H P      OP3    SING N N 69 
05H OP3    HOP3   SING N N 70 
05H C11    H2     SING N N 71 
05H C11    H3     SING N N 72 
05H "C3'1" "H3'1" SING N N 73 
05H "C5'1" HC52   SING N N 74 
05H C5M    H51    SING N N 75 
05H "C5'1" HC51   SING N N 76 
# 
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 
05H InChI            InChI                1.06  "InChI=1S/C23H30N5O13P/c1-10-6-27(21(33)25-18(10)31)16-4-13(29)14(40-16)5-24-15(30)3-12-17-20(28-7-11(2)19(32)26-22(28)34)41-23(12,8-38-17)9-39-42(35,36)37/h6-7,12-14,16-17,20,29H,3-5,8-9H2,1-2H3,(H,24,30)(H,25,31,33)(H,26,32,34)(H2,35,36,37)/t12-,13-,14+,16+,17+,20+,23+/m0/s1" 
05H InChIKey         InChI                1.06  ITNKNYJNRRELEH-CDWNFYEKSA-N                                                                                                                                                                                                                                                            
05H SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CNC(=O)C[C@H]3[C@H]4OC[C@]3(CO[P](O)(O)=O)O[C@H]4N5C=C(C)C(=O)NC5=O)O2)C(=O)NC1=O"                                                                                                                                                                       
05H SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](O)[CH](CNC(=O)C[CH]3[CH]4OC[C]3(CO[P](O)(O)=O)O[CH]4N5C=C(C)C(=O)NC5=O)O2)C(=O)NC1=O"                                                                                                                                                                               
05H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CNC(=O)C[C@H]3[C@@H]4[C@@H](O[C@]3(CO4)COP(=O)(O)O)N5C=C(C(=O)NC5=O)C)O"                                                                                                                                                                     
05H SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CNC(=O)CC3C4C(OC3(CO4)COP(=O)(O)O)N5C=C(C(=O)NC5=O)C)O"                                                                                                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           05H 
_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~{R},3~{R},4~{R},7~{S})-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-[2-[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylamino]-2-oxidanylidene-ethyl]-2,5-dioxabicyclo[2.2.1]heptan-1-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 
05H "Create component"         2021-05-28 PDBE 
05H "Initial release"          2022-08-03 RCSB 
05H "Modify leaving atom flag" 2023-03-09 PDBE 
# 
