data_S6M
#

_chem_comp.id                                   S6M
_chem_comp.name                                 "[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-[1-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)-1,2,3-triazol-4-yl]oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C20 H31 N6 O9 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-01-25
_chem_comp.pdbx_modified_date                   2020-02-07
_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                       530.469
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    S6M
_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       6QJS
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
S6M  P      P1   P  0  1  N  N  N   5.682  26.015   99.866   4.779  -3.756   0.229  P      S6M   1  
S6M  OP1    O1   O  0  1  N  N  N   5.291  26.828   98.669   4.240  -4.911  -0.524  OP1    S6M   2  
S6M  "O5'"  O2   O  0  1  N  N  N   5.394  24.503   99.503   3.630  -2.642   0.399  "O5'"  S6M   3  
S6M  "C5'"  C1   C  0  1  N  N  N   5.877  23.470  100.348   2.916  -2.085  -0.707  "C5'"  S6M   4  
S6M  "C4'"  C2   C  0  1  N  N  R   5.130  22.201  100.030   1.901  -1.061  -0.195  "C4'"  S6M   5  
S6M  "C3'"  C3   C  0  1  N  N  S   5.392  21.678   98.659   1.085  -0.479  -1.371  "C3'"  S6M   6  
S6M  "O3'"  O3   O  0  1  N  N  N   6.645  20.972   98.651  -0.177  -1.141  -1.481  "O3'"  S6M   7  
S6M  "C2'"  C4   C  0  1  N  N  R   4.202  20.775   98.339   0.890   1.006  -0.993  "C2'"  S6M   8  
S6M  "C1'"  C5   C  0  1  N  N  R   3.101  21.360   99.198   1.611   1.146   0.366  "C1'"  S6M   9  
S6M  "O4'"  O4   O  0  1  N  N  N   3.713  22.337  100.138   2.580   0.075   0.381  "O4'"  S6M  10  
S6M  N1     N1   N  0  1  N  N  N   2.034  22.076   98.505   2.284   2.444   0.456  N1     S6M  11  
S6M  C6     C6   C  0  1  N  N  N   2.132  23.353   98.283   1.870   3.359   1.385  C6     S6M  12  
S6M  C5     C7   C  0  1  N  N  N   1.056  24.041   97.783   2.490   4.556   1.467  C5     S6M  13  
S6M  C4     C8   C  0  1  N  N  N  -0.116  23.379   97.581   3.561   4.839   0.586  C4     S6M  14  
S6M  N3     N2   N  0  1  N  N  N  -0.213  22.059   97.885   3.939   3.910  -0.316  N3     S6M  15  
S6M  C2     C9   C  0  1  N  N  N   0.873  21.398   98.258   3.306   2.724  -0.373  C2     S6M  16  
S6M  O2     O5   O  0  1  N  N  N   0.829  20.185   98.522   3.658   1.896  -1.191  O2     S6M  17  
S6M  O4     O6   O  0  1  N  N  N  -1.128  24.022   97.210   4.136   5.911   0.641  O4     S6M  18  
S6M  OP2    O7   O  0  1  N  N  N   7.101  26.205  100.183   5.271  -4.246   1.682  OP2    S6M  19  
S6M  C11    C10  C  0  1  Y  N  N   4.541  19.359   98.803  -0.576   1.326  -0.849  C11    S6M  20  
S6M  C12    C11  C  0  1  Y  N  N   3.869  18.279   98.240  -1.543   0.500  -0.389  C12    S6M  21  
S6M  N13    N3   N  0  1  Y  N  N   4.335  17.163   98.889  -2.696   1.207  -0.435  N13    S6M  22  
S6M  N14    N4   N  0  1  Y  N  N   5.243  17.529   99.869  -2.432   2.380  -0.894  N14    S6M  23  
S6M  N15    N5   N  0  1  Y  N  N   5.323  18.956   99.796  -1.175   2.485  -1.145  N15    S6M  24  
S6M  C17    C12  C  0  1  N  N  N   4.122  15.667   98.778  -4.022   0.719  -0.032  C17    S6M  25  
S6M  C18    C13  C  0  1  N  N  N   2.711  15.299   99.186  -4.658  -0.030  -1.204  C18    S6M  26  
S6M  C19    C14  C  0  1  N  N  N   2.453  13.785   99.121  -6.041  -0.544  -0.799  C19    S6M  27  
S6M  N20    N6   N  0  1  N  N  N   3.113  13.075   97.943  -5.986  -1.324   0.425  N20    S6M  28  
S6M  C21    C15  C  0  1  N  N  N   4.167  13.773   97.083  -5.219  -0.823   1.551  C21    S6M  29  
S6M  C22    C16  C  0  1  N  N  N   4.372  15.242   97.354  -3.866  -0.251   1.139  C22    S6M  30  
S6M  C23    C17  C  0  1  N  N  N   2.960  13.114  100.383  -7.023   0.623  -0.691  C23    S6M  31  
S6M  C24    C18  C  0  1  N  N  N   0.952  13.532   99.041  -6.541  -1.467  -1.932  C24    S6M  32  
S6M  C25    C19  C  0  1  N  N  N   5.460  13.041   97.356  -6.004   0.225   2.345  C25    S6M  33  
S6M  C26    C20  C  0  1  N  N  N   3.832  13.636   95.565  -4.949  -2.009   2.506  C26    S6M  34  
S6M  O27    O8   O  0  1  N  N  N   2.156  12.317   97.161  -5.715  -2.737   0.162  O27    S6M  35  
S6M  H2     H2   H  0  1  N  N  N   6.953  23.321  100.173   3.618  -1.595  -1.382  H2     S6M  36  
S6M  H3     H3   H  0  1  N  N  N   5.711  23.744  101.400   2.394  -2.880  -1.239  H3     S6M  37  
S6M  H4     H4   H  0  1  N  N  N   5.461  21.435  100.747   1.238  -1.519   0.539  H4     S6M  38  
S6M  H5     H5   H  0  1  N  N  N   5.416  22.512   97.942   1.643  -0.566  -2.303  H5     S6M  39  
S6M  H6     H6   H  0  1  N  N  N   7.350  21.575   98.855  -0.110  -2.089  -1.658  H6     S6M  40  
S6M  H7     H7   H  0  1  N  N  N   3.947  20.802   97.269   1.350   1.654  -1.740  H7     S6M  41  
S6M  H8     H8   H  0  1  N  N  N   2.656  20.544   99.786   0.902   1.028   1.186  H8     S6M  42  
S6M  H9     H9   H  0  1  N  N  N   3.057  23.870   98.491   1.050   3.126   2.048  H9     S6M  43  
S6M  H10    H10  H  0  1  N  N  N   1.138  25.093   97.553   2.173   5.287   2.196  H10    S6M  44  
S6M  H11    H11  H  0  1  N  N  N  -1.095  21.591   97.828   4.672   4.097  -0.923  H11    S6M  45  
S6M  H12    H12  H  0  1  N  N  N   7.487  26.810   99.560   5.965  -4.919   1.656  H12    S6M  46  
S6M  H13    H13  H  0  1  N  N  N   3.131  18.312   97.452  -1.420  -0.519  -0.052  H13    S6M  47  
S6M  H14    H14  H  0  1  N  N  N   4.834  15.152   99.440  -4.636   1.567   0.258  H14    S6M  48  
S6M  H15    H15  H  0  1  N  N  N   2.542  15.641  100.218  -4.758   0.646  -2.055  H15    S6M  49  
S6M  H16    H16  H  0  1  N  N  N   2.006  15.806   98.511  -4.025  -0.872  -1.485  H16    S6M  50  
S6M  H17    H17  H  0  1  N  N  N   5.412  15.494   97.100  -3.201  -1.068   0.845  H17    S6M  51  
S6M  H18    H18  H  0  1  N  N  N   3.688  15.808   96.704  -3.420   0.274   1.987  H18    S6M  52  
S6M  H19    H19  H  0  1  N  N  N   2.508  13.596  101.262  -7.097   1.126  -1.655  H19    S6M  53  
S6M  H20    H20  H  0  1  N  N  N   2.686  12.049  100.367  -8.005   0.246  -0.402  H20    S6M  54  
S6M  H21    H21  H  0  1  N  N  N   4.055  13.210  100.435  -6.669   1.328   0.061  H21    S6M  55  
S6M  H22    H22  H  0  1  N  N  N   0.450  14.034   99.881  -5.846  -2.298  -2.056  H22    S6M  56  
S6M  H23    H23  H  0  1  N  N  N   0.563  13.929   98.091  -7.528  -1.854  -1.676  H23    S6M  57  
S6M  H24    H24  H  0  1  N  N  N   0.759  12.450   99.092  -6.602  -0.901  -2.861  H24    S6M  58  
S6M  H25    H25  H  0  1  N  N  N   5.712  13.127   98.423  -6.159   1.109   1.726  H25    S6M  59  
S6M  H26    H26  H  0  1  N  N  N   5.343  11.980   97.091  -6.970  -0.188   2.637  H26    S6M  60  
S6M  H27    H27  H  0  1  N  N  N   6.266  13.483   96.752  -5.442   0.501   3.238  H27    S6M  61  
S6M  H28    H28  H  0  1  N  N  N   3.673  12.576   95.318  -4.402  -1.654   3.379  H28    S6M  62  
S6M  H29    H29  H  0  1  N  N  N   2.919  14.206   95.338  -5.896  -2.444   2.822  H29    S6M  63  
S6M  H30    H30  H  0  1  N  N  N   4.668  14.030   94.968  -4.357  -2.764   1.988  H30    S6M  64  
S6M  H31    H31  H  0  1  N  N  N   1.527  11.906   97.742  -5.672  -3.284   0.957  H31    S6M  65  
S6M  O1     O9   O  0  1  N  N  N       ?       ?        ?   6.024  -3.125  -0.574  O1     S6M  66  
S6M  H1     H1   H  0  1  N  N  N       ?       ?        ?   6.428  -2.363  -0.137  H1     S6M  67  
#   #
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
S6M  C26    C21    SING  N  N   1  
S6M  C21    C22    SING  N  N   2  
S6M  C21    C25    SING  N  N   3  
S6M  C21    N20    SING  N  N   4  
S6M  O27    N20    SING  N  N   5  
S6M  O4     C4     DOUB  N  N   6  
S6M  C22    C17    SING  N  N   7  
S6M  C4     C5     SING  N  N   8  
S6M  C4     N3     SING  N  N   9  
S6M  C5     C6     DOUB  N  N  10  
S6M  N3     C2     SING  N  N  11  
S6M  N20    C19    SING  N  N  12  
S6M  C12    C11    DOUB  Y  N  13  
S6M  C12    N13    SING  Y  N  14  
S6M  C2     N1     SING  N  N  15  
S6M  C2     O2     DOUB  N  N  16  
S6M  C6     N1     SING  N  N  17  
S6M  "C2'"  "C3'"  SING  N  N  18  
S6M  "C2'"  C11    SING  N  N  19  
S6M  "C2'"  "C1'"  SING  N  N  20  
S6M  N1     "C1'"  SING  N  N  21  
S6M  "O3'"  "C3'"  SING  N  N  22  
S6M  "C3'"  "C4'"  SING  N  N  23  
S6M  OP1    P      DOUB  N  N  24  
S6M  C17    N13    SING  N  N  25  
S6M  C17    C18    SING  N  N  26  
S6M  C11    N15    SING  Y  N  27  
S6M  N13    N14    SING  Y  N  28  
S6M  C24    C19    SING  N  N  29  
S6M  C19    C18    SING  N  N  30  
S6M  C19    C23    SING  N  N  31  
S6M  "C1'"  "O4'"  SING  N  N  32  
S6M  "O5'"  P      SING  N  N  33  
S6M  "O5'"  "C5'"  SING  N  N  34  
S6M  N15    N14    DOUB  Y  N  35  
S6M  P      OP2    SING  N  N  36  
S6M  "C4'"  "O4'"  SING  N  N  37  
S6M  "C4'"  "C5'"  SING  N  N  38  
S6M  "C5'"  H2     SING  N  N  39  
S6M  "C5'"  H3     SING  N  N  40  
S6M  "C4'"  H4     SING  N  N  41  
S6M  "C3'"  H5     SING  N  N  42  
S6M  "O3'"  H6     SING  N  N  43  
S6M  "C2'"  H7     SING  N  N  44  
S6M  "C1'"  H8     SING  N  N  45  
S6M  C6     H9     SING  N  N  46  
S6M  C5     H10    SING  N  N  47  
S6M  N3     H11    SING  N  N  48  
S6M  OP2    H12    SING  N  N  49  
S6M  C12    H13    SING  N  N  50  
S6M  C17    H14    SING  N  N  51  
S6M  C18    H15    SING  N  N  52  
S6M  C18    H16    SING  N  N  53  
S6M  C22    H17    SING  N  N  54  
S6M  C22    H18    SING  N  N  55  
S6M  C23    H19    SING  N  N  56  
S6M  C23    H20    SING  N  N  57  
S6M  C23    H21    SING  N  N  58  
S6M  C24    H22    SING  N  N  59  
S6M  C24    H23    SING  N  N  60  
S6M  C24    H24    SING  N  N  61  
S6M  C25    H25    SING  N  N  62  
S6M  C25    H26    SING  N  N  63  
S6M  C25    H27    SING  N  N  64  
S6M  C26    H28    SING  N  N  65  
S6M  C26    H29    SING  N  N  66  
S6M  C26    H30    SING  N  N  67  
S6M  O27    H31    SING  N  N  68  
S6M  P      O1     SING  N  N  69  
S6M  O1     H1     SING  N  N  70  
#   #
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
S6M  InChI             InChI                 1.03   "InChI=1S/C20H31N6O9P/c1-19(2)7-11(8-20(3,4)26(19)30)25-9-12(22-23-25)15-16(28)13(10-34-36(31,32)33)35-17(15)24-6-5-14(27)21-18(24)29/h5-6,9,11,13,15-17,28,30H,7-8,10H2,1-4H3,(H,21,27,29)(H2,31,32,33)/t13-,15-,16-,17-/m1/s1"  
S6M  InChIKey          InChI                 1.03   YUAIZSADZZEHSX-MWQQHZPXSA-N  
S6M  SMILES_CANONICAL  CACTVS                3.385  "CC1(C)CC(CC(C)(C)N1O)n2cc(nn2)[C@@H]3[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]3N4C=CC(=O)NC4=O"  
S6M  SMILES            CACTVS                3.385  "CC1(C)CC(CC(C)(C)N1O)n2cc(nn2)[CH]3[CH](O)[CH](CO[P](O)(O)=O)O[CH]3N4C=CC(=O)NC4=O"  
S6M  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "CC1(CC(CC(N1O)(C)C)n2cc(nn2)[C@@H]3[C@@H]([C@H](O[C@H]3N4C=CC(=O)NC4=O)COP(=O)(O)O)O)C"  
S6M  SMILES            "OpenEye OEToolkits"  2.0.6  "CC1(CC(CC(N1O)(C)C)n2cc(nn2)C3C(C(OC3N4C=CC(=O)NC4=O)COP(=O)(O)O)O)C"  
#
_pdbx_chem_comp_identifier.comp_id          S6M
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.6
_pdbx_chem_comp_identifier.identifier       "[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-[1-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)-1,2,3-triazol-4-yl]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
S6M  "Create component"  2019-01-25  EBI   
S6M  "Initial release"   2020-02-12  RCSB  
##
