data_05A
# 
_chem_comp.id                                    05A 
_chem_comp.name                                  "[(1R,3R,4R,7S)-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-[2-[[(1S,3R,4R,7S)-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-1-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                               "C24 H30 N5 O14 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                        643.494 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     05A 
_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        7OOO 
_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 
05A C4     C1  C 0 1 N N N -1.279 -17.045 -3.306 -2.906 1.202  2.083  C4     05A 1  
05A "C1'"  C2  C 0 1 N N R 0.786  -23.179 -3.402 5.456  1.233  -0.697 "C1'"  05A 2  
05A C7     C3  C 0 1 N N N -0.806 -23.125 -1.204 3.466  1.271  -2.568 C7     05A 3  
05A C2     C4  C 0 1 N N N 2.223  -24.081 -5.228 7.649  1.203  0.352  C2     05A 4  
05A "C2'"  C5  C 0 1 N N R 0.789  -24.296 -2.371 5.663  0.638  -2.125 "C2'"  05A 5  
05A C21    C6  C 0 1 N N N 0.778  -20.241 -6.613 -4.022 -3.690 1.150  C21    05A 6  
05A C11    C7  C 0 1 N N N 0.755  -17.954 -1.635 -1.168 0.791  -0.180 C11    05A 7  
05A "C3'"  C8  C 0 1 N N S 1.456  -23.624 -1.211 4.762  -0.643 -1.991 "C3'"  05A 8  
05A C41    C9  C 0 1 N N N 2.781  -20.212 -7.721 -4.841 -4.625 -0.828 C41    05A 9  
05A "C4'"  C10 C 0 1 N N S 0.543  -22.455 -1.261 3.529  0.173  -1.460 "C4'"  05A 10 
05A C8     C11 C 0 1 N N N 4.188  -23.080 -5.883 8.253  -0.380 1.961  C8     05A 11 
05A C51    C12 C 0 1 N N N 3.039  -18.868 -7.204 -5.053 -3.324 -1.342 C51    05A 12 
05A "C5'"  C13 C 0 1 N N N 0.859  -21.422 -0.202 2.241  -0.614 -1.208 "C5'"  05A 13 
05A C5     C14 C 0 1 N N N 3.976  -22.044 -4.865 6.969  -0.964 1.852  C5     05A 14 
05A C6     C15 C 0 1 N N N 2.847  -22.112 -4.077 6.076  -0.433 0.990  C6     05A 15 
05A C61    C16 C 0 1 N N N 2.093  -18.283 -6.395 -4.731 -2.256 -0.581 C61    05A 16 
05A C5A    C17 C 0 1 N N N 4.310  -18.161 -7.558 -5.625 -3.132 -2.723 C5A    05A 17 
05A C5M    C18 C 0 1 N N N 4.975  -20.940 -4.697 6.602  -2.164 2.688  C5M    05A 18 
05A C1     C19 C 0 1 N N N 1.318  -19.273 -1.192 -0.065 -0.161 -0.564 C1     05A 19 
05A N1     N1  N 0 1 N N N 1.987  -23.115 -4.236 6.425  0.656  0.239  N1     05A 20 
05A N11    N2  N 0 1 N N N 0.986  -18.956 -6.097 -4.213 -2.447 0.671  N11    05A 21 
05A "N5'"  N3  N 0 1 N N N 0.453  -20.120 -0.661 1.168  0.311  -0.835 "N5'"  05A 22 
05A N3     N4  N 0 1 N N N 3.296  -24.042 -6.006 8.558  0.693  1.204  N3     05A 23 
05A N31    N5  N 0 1 N N N 1.666  -20.824 -7.397 -4.329 -4.772 0.411  N31    05A 24 
05A O2     O1  O 0 1 N N N 1.429  -25.014 -5.403 7.940  2.168  -0.329 O2     05A 25 
05A O21    O2  O 0 1 N N N -0.256 -20.867 -6.346 -3.560 -3.837 2.266  O21    05A 26 
05A "O2'"  O3  O 0 1 N N N -1.268 -18.471 -3.330 -2.108 0.040  2.387  "O2'"  05A 27 
05A "O3'"  O4  O 0 1 N N N 1.331  -24.347 0.034  4.506  -1.267 -3.251 "O3'"  05A 28 
05A O31    O5  O 0 1 N N N -0.555 -24.340 -1.913 4.833  1.479  -2.976 O31    05A 29 
05A O41    O6  O 0 1 N N N 3.606  -20.770 -8.448 -5.120 -5.604 -1.497 O41    05A 30 
05A "O4'"  O7  O 0 1 N N N 0.716  -22.011 -2.594 4.115  0.862  -0.320 "O4'"  05A 31 
05A O4     O8  O 0 1 N N N 5.189  -23.057 -6.613 9.075  -0.842 2.731  O4     05A 32 
05A O1     O9  O 0 1 N N N 2.496  -19.526 -1.336 -0.286 -1.352 -0.628 O1     05A 33 
05A "O5'"  O10 O 0 1 N N N 1.951  -15.283 -3.896 -4.955 2.881  0.689  "O5'"  05A 34 
05A OP1    O11 O 0 1 N N N 2.442  -13.132 -2.672 -4.608 5.163  -0.332 OP1    05A 35 
05A OP2    O12 O 0 1 N N N 4.160  -13.999 -4.241 -6.648 3.869  -1.063 OP2    05A 36 
05A P      P1  P 0 1 N N N 2.693  -13.872 -3.944 -5.650 4.229  0.148  P      05A 37 
05A "C1'1" C20 C 0 0 N N R -0.030 -18.351 -5.248 -3.864 -1.289 1.496  "C1'1" 05A 38 
05A "C2'1" C21 C 0 0 N N R 0.003  -18.867 -3.824 -2.353 -0.932 1.332  "C2'1" 05A 39 
05A "C3'1" C22 C 0 0 N N S 0.889  -17.878 -3.133 -2.456 0.004  0.073  "C3'1" 05A 40 
05A "C4'1" C23 C 0 0 N N R 0.140  -16.725 -3.702 -3.587 0.890  0.713  "C4'1" 05A 41 
05A "C5'1" C24 C 0 0 N N N 0.673  -15.373 -3.302 -4.062 2.094  -0.101 "C5'1" 05A 42 
05A "O4'1" O13 O 0 0 N N N 0.229  -16.965 -5.089 -4.597 -0.105 1.046  "O4'1" 05A 43 
05A HC31   H1  H 0 0 N N N -1.512 -16.662 -2.301 -3.661 1.354  2.854  HC31   05A 44 
05A HC32   H2  H 0 0 N N N -2.000 -16.637 -4.030 -2.272 2.084  1.997  HC32   05A 45 
05A "H1'"  H3  H 0 1 N N N -0.109 -23.269 -4.034 5.555  2.319  -0.723 "H1'"  05A 46 
05A H71    H4  H 0 1 N N N -1.576 -22.520 -1.705 2.869  0.923  -3.411 H71    05A 47 
05A H72    H5  H 0 1 N N N -1.112 -23.322 -0.166 3.047  2.192  -2.163 H72    05A 48 
05A "H2'1" H6  H 0 0 N N N 1.241  -25.243 -2.702 6.694  0.494  -2.446 "H2'1" 05A 49 
05A H2     H7  H 0 1 N N N 1.315  -17.131 -1.167 -0.887 1.327  0.726  H2     05A 50 
05A H3     H8  H 0 1 N N N -0.305 -17.885 -1.350 -1.331 1.503  -0.988 H3     05A 51 
05A "H3'"  H9  H 0 1 N N N 2.496  -23.347 -1.439 5.147  -1.349 -1.254 "H3'"  05A 52 
05A "H5'1" H10 H 0 0 N N N 0.318  -21.669 0.723  1.960  -1.151 -2.114 "H5'1" 05A 53 
05A "H5'2" H11 H 0 0 N N N 1.941  -21.419 -0.004 2.404  -1.327 -0.399 "H5'2" 05A 54 
05A H6     H12 H 0 1 N N N 2.661  -21.353 -3.332 5.091  -0.865 0.893  H6     05A 55 
05A H61    H13 H 0 1 N N N 2.248  -17.287 -6.006 -4.886 -1.255 -0.957 H61    05A 56 
05A H5A1   H14 H 0 0 N N N 4.325  -17.170 -7.080 -5.813 -4.106 -3.177 H5A1   05A 57 
05A H5A2   H15 H 0 0 N N N 5.168  -18.751 -7.205 -6.560 -2.576 -2.656 H5A2   05A 58 
05A H5A3   H16 H 0 0 N N N 4.371  -18.042 -8.650 -4.915 -2.577 -3.337 H5A3   05A 59 
05A H51    H17 H 0 1 N N N 4.646  -20.266 -3.892 7.449  -2.441 3.315  H51    05A 60 
05A H52    H18 H 0 1 N N N 5.955  -21.368 -4.439 5.747  -1.920 3.318  H52    05A 61 
05A H53    H19 H 0 1 N N N 5.058  -20.375 -5.637 6.346  -2.997 2.034  H53    05A 62 
05A "HN5'" H20 H 0 0 N N N -0.506 -19.850 -0.576 1.345  1.263  -0.783 "HN5'" 05A 63 
05A HN3    H21 H 0 1 N N N 3.430  -24.753 -6.696 9.437  1.099  1.272  HN3    05A 64 
05A H31    H22 H 0 1 N N N 1.487  -21.743 -7.748 -4.180 -5.660 0.770  H31    05A 65 
05A "HO3'" H23 H 0 0 N Y N 1.774  -23.868 0.725  5.301  -1.580 -3.704 "HO3'" 05A 66 
05A HOP2   H25 H 0 0 N N N 4.661  -13.578 -3.552 -7.358 3.259  -0.820 HOP2   05A 67 
05A H1     H26 H 0 1 N N N -1.031 -18.516 -5.674 -4.083 -1.493 2.544  H1     05A 68 
05A HC21   H27 H 0 0 N N N 0.283  -19.924 -3.709 -1.659 -1.771 1.277  HC21   05A 69 
05A "H3'1" H28 H 0 0 N N N 1.934  -17.926 -3.472 -2.793 -0.528 -0.817 "H3'1" 05A 70 
05A HC51   H29 H 0 0 N N N 0.751  -15.299 -2.207 -4.580 1.746  -0.996 HC51   05A 71 
05A HC52   H30 H 0 0 N N N 0.017  -14.574 -3.678 -3.204 2.699  -0.391 HC52   05A 72 
05A OP3    OP3 O 0 1 N Y N ?      ?       ?      -6.482 4.920  1.341  OP3    05A 73 
05A HOP3   H31 H 0 0 N Y N ?      ?       ?      -6.928 5.739  1.086  HOP3   05A 74 
# 
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 
05A O41    C41    DOUB N N 1  
05A C41    N31    SING N N 2  
05A C41    C51    SING N N 3  
05A C5A    C51    SING N N 4  
05A N31    C21    SING N N 5  
05A C51    C61    DOUB N N 6  
05A C21    O21    DOUB N N 7  
05A C21    N11    SING N N 8  
05A O4     C8     DOUB N N 9  
05A C61    N11    SING N N 10 
05A N11    "C1'1" SING N N 11 
05A N3     C8     SING N N 12 
05A N3     C2     SING N N 13 
05A C8     C5     SING N N 14 
05A O2     C2     DOUB N N 15 
05A "C1'1" "O4'1" SING N N 16 
05A "C1'1" "C2'1" SING N N 17 
05A C2     N1     SING N N 18 
05A "O4'1" "C4'1" SING N N 19 
05A C5     C5M    SING N N 20 
05A C5     C6     DOUB N N 21 
05A OP2    P      SING N N 22 
05A N1     C6     SING N N 23 
05A N1     "C1'"  SING N N 24 
05A P      "O5'"  SING N N 25 
05A P      OP1    DOUB N N 26 
05A "O5'"  "C5'1" SING N N 27 
05A "C2'1" "O2'"  SING N N 28 
05A "C2'1" "C3'1" SING N N 29 
05A "C4'1" C4     SING N N 30 
05A "C4'1" "C5'1" SING N N 31 
05A "C4'1" "C3'1" SING N N 32 
05A "C1'"  "O4'"  SING N N 33 
05A "C1'"  "C2'"  SING N N 34 
05A "O2'"  C4     SING N N 35 
05A "C3'1" C11    SING N N 36 
05A "O4'"  "C4'"  SING N N 37 
05A "C2'"  O31    SING N N 38 
05A "C2'"  "C3'"  SING N N 39 
05A O31    C7     SING N N 40 
05A C11    C1     SING N N 41 
05A O1     C1     DOUB N N 42 
05A "C4'"  "C3'"  SING N N 43 
05A "C4'"  C7     SING N N 44 
05A "C4'"  "C5'"  SING N N 45 
05A "C3'"  "O3'"  SING N N 46 
05A C1     "N5'"  SING N N 47 
05A "N5'"  "C5'"  SING N N 48 
05A C4     HC31   SING N N 49 
05A C4     HC32   SING N N 50 
05A "C1'"  "H1'"  SING N N 51 
05A C7     H71    SING N N 52 
05A C7     H72    SING N N 53 
05A "C2'"  "H2'1" SING N N 54 
05A C11    H2     SING N N 55 
05A C11    H3     SING N N 56 
05A "C3'"  "H3'"  SING N N 57 
05A "C5'"  "H5'1" SING N N 58 
05A "C5'"  "H5'2" SING N N 59 
05A C6     H6     SING N N 60 
05A C61    H61    SING N N 61 
05A C5A    H5A1   SING N N 62 
05A C5A    H5A2   SING N N 63 
05A C5A    H5A3   SING N N 64 
05A C5M    H51    SING N N 65 
05A C5M    H52    SING N N 66 
05A C5M    H53    SING N N 67 
05A "N5'"  "HN5'" SING N N 68 
05A N3     HN3    SING N N 69 
05A N31    H31    SING N N 70 
05A "O3'"  "HO3'" SING N N 71 
05A OP2    HOP2   SING N N 72 
05A "C1'1" H1     SING N N 73 
05A "C2'1" HC21   SING N N 74 
05A "C3'1" "H3'1" SING N N 75 
05A "C5'1" HC51   SING N N 76 
05A "C5'1" HC52   SING N N 77 
05A P      OP3    SING N N 78 
05A OP3    HOP3   SING N N 79 
# 
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 
05A InChI            InChI                1.06  "InChI=1S/C24H30N5O14P/c1-10-4-28(21(34)26-17(10)32)19-14-12(24(43-19,8-39-14)9-41-44(36,37)38)3-13(30)25-6-23-7-40-15(16(23)31)20(42-23)29-5-11(2)18(33)27-22(29)35/h4-5,12,14-16,19-20,31H,3,6-9H2,1-2H3,(H,25,30)(H,26,32,34)(H,27,33,35)(H2,36,37,38)/t12-,14+,15+,16-,19+,20+,23-,24+/m0/s1" 
05A InChIKey         InChI                1.06  ZPMMRXCRABIQDW-XVYZCTGRSA-N                                                                                                                                                                                                                                                                       
05A SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@@H]2O[C@@]3(CNC(=O)C[C@H]4[C@H]5OC[C@]4(CO[P](O)(O)=O)O[C@H]5N6C=C(C)C(=O)NC6=O)CO[C@@H]2[C@@H]3O)C(=O)NC1=O"                                                                                                                                                                          
05A SMILES           CACTVS               3.385 "CC1=CN([CH]2O[C]3(CNC(=O)C[CH]4[CH]5OC[C]4(CO[P](O)(O)=O)O[CH]5N6C=C(C)C(=O)NC6=O)CO[CH]2[CH]3O)C(=O)NC1=O"                                                                                                                                                                                      
05A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2[C@H]3[C@@H]([C@@](O2)(CO3)COP(=O)(O)O)CC(=O)NC[C@]45CO[C@H]([C@@H]4O)[C@@H](O5)N6C=C(C(=O)NC6=O)C"                                                                                                                                                                      
05A SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2C3C(C(O2)(CO3)COP(=O)(O)O)CC(=O)NCC45COC(C4O)C(O5)N6C=C(C(=O)NC6=O)C"                                                                                                                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           05A 
_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-[[(1~{S},3~{R},4~{R},7~{S})-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-1-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 
05A "Create component"         2021-05-28 PDBE 
05A "Initial release"          2022-08-03 RCSB 
05A "Modify leaving atom flag" 2023-03-09 PDBE 
# 
