data_B8H
#

_chem_comp.id                                   B8H
_chem_comp.name                                 "[(2~{R},3~{S},4~{R},5~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H15 N2 O9 P"
_chem_comp.mon_nstd_parent_comp_id              U
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-09-25
_chem_comp.pdbx_modified_date                   2019-05-06
_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                       338.208
_chem_comp.one_letter_code                      U
_chem_comp.three_letter_code                    B8H
_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       6EK0
_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
B8H  N1     N1   N  0  1  N  N  N  260.734  293.041  219.842  -4.314  -0.877  -0.749  N1     B8H   1  
B8H  C2     C1   C  0  1  N  N  N  260.266  294.152  220.561  -4.280  -1.467   0.460  C2     B8H   2  
B8H  C4     C2   C  0  1  N  N  N  260.861  295.594  218.858  -2.209  -0.491   0.925  C4     B8H   3  
B8H  "C1'"  C3   C  0  1  N  N  S  261.934  294.687  216.721  -1.088   1.013  -0.783  "C1'"  B8H   4  
B8H  "C2'"  C4   C  0  1  N  N  R  263.409  295.076  216.824  -1.013   2.260   0.118  "C2'"  B8H   5  
B8H  "C3'"  C5   C  0  1  N  N  S  264.073  293.721  216.654   0.408   2.202   0.729  "C3'"  B8H   6  
B8H  "C4'"  C6   C  0  1  N  N  R  263.206  293.077  215.594   1.154   1.283  -0.271  "C4'"  B8H   7  
B8H  C5     C7   C  0  1  N  N  N  261.352  294.457  218.069  -2.230   0.132  -0.346  C5     B8H   8  
B8H  "C5'"  C8   C  0  1  N  N  N  263.259  291.577  215.522   2.346   0.604   0.407  "C5'"  B8H   9  
B8H  C6     C9   C  0  1  N  N  N  261.239  293.199  218.634  -3.286  -0.074  -1.161  C6     B8H  10  
B8H  CN1    C10  C  0  1  N  N  N  260.660  291.685  220.383  -5.460  -1.102  -1.634  CN1    B8H  11  
B8H  N3     N2   N  0  1  N  N  N  260.340  295.380  220.061  -3.240  -1.279   1.293  N3     B8H  12  
B8H  O2     O1   O  0  1  N  N  N  259.781  294.000  221.696  -5.203  -2.180   0.805  O2     B8H  13  
B8H  "O2'"  O2   O  0  1  N  N  N  263.725  295.919  215.730  -1.179   3.448  -0.657  "O2'"  B8H  14  
B8H  "O3'"  O3   O  0  1  N  N  N  265.446  293.767  216.323   1.000   3.502   0.768  "O3'"  B8H  15  
B8H  O4     O4   O  0  1  N  N  N  260.931  296.746  218.391  -1.268  -0.320   1.678  O4     B8H  16  
B8H  "O4'"  O5   O  0  1  N  N  N  261.867  293.509  215.944   0.156   0.307  -0.640  "O4'"  B8H  17  
B8H  "O5'"  O6   O  0  1  N  N  N  262.699  290.975  216.675   3.022  -0.227  -0.538  "O5'"  B8H  18  
B8H  OP1    O7   O  0  1  N  N  N  261.822  289.002  217.966   4.897  -1.801  -1.498  OP1    B8H  19  
B8H  OP2    O8   O  0  1  N  N  N  262.931  288.743  215.634   5.365  -0.206   0.402  OP2    B8H  20  
B8H  P      P1   P  0  1  N  N  N  262.061  289.525  216.579   4.327  -1.095  -0.168  P      B8H  21  
B8H  O1     O9   O  0  1  N  Y  N  260.657  289.767  215.844   3.933  -2.222   0.912  O1     B8H  22  
B8H  H1     H1   H  0  1  N  N  N  261.388  295.503  216.225  -1.229   1.314  -1.821  H1     B8H  23  
B8H  H2     H2   H  0  1  N  N  N  263.642  295.524  217.801  -1.768   2.209   0.903  H2     B8H  24  
B8H  H3     H3   H  0  1  N  N  N  263.942  293.158  217.590   0.386   1.757   1.724  H3     B8H  25  
B8H  H4     H4   H  0  1  N  N  N  263.482  293.490  214.613   1.479   1.849  -1.143  H4     B8H  26  
B8H  H5     H5   H  0  1  N  N  N  262.697  291.243  214.637   3.033   1.363   0.780  H5     B8H  27  
B8H  H6     H6   H  0  1  N  N  N  264.309  291.262  215.430   1.992  -0.006   1.239  H6     B8H  28  
B8H  H7     H7   H  0  1  N  N  N  261.569  292.334  218.078  -3.319   0.392  -2.135  H7     B8H  29  
B8H  H8     H8   H  0  1  N  N  N  260.220  291.715  221.391  -6.173  -1.765  -1.144  H8     B8H  30  
B8H  H9     H9   H  0  1  N  N  N  260.033  291.063  219.728  -5.942  -0.149  -1.852  H9     B8H  31  
B8H  H10    H10  H  0  1  N  N  N  261.672  291.257  220.438  -5.118  -1.557  -2.563  H10    B8H  32  
B8H  H11    H11  H  0  1  N  N  N  259.999  296.153  220.597  -3.233  -1.709   2.162  H11    B8H  33  
B8H  H12    H12  H  0  1  N  N  N  263.304  296.763  215.848  -1.140   4.265  -0.140  H12    B8H  34  
B8H  H13    H13  H  0  1  N  N  N  265.929  294.181  217.029   0.516   4.139   1.311  H13    B8H  35  
B8H  H14    H14  H  0  1  N  N  N  262.286  288.181  218.080   5.685  -2.342  -1.349  H14    B8H  36  
B8H  H15    H15  H  0  1  N  N  N  260.678  289.369  214.982   3.256  -2.841   0.605  H15    B8H  37  
#   #
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
B8H  "C5'"  "C4'"  SING  N  N   1  
B8H  "C5'"  "O5'"  SING  N  N   2  
B8H  "C4'"  "O4'"  SING  N  N   3  
B8H  "C4'"  "C3'"  SING  N  N   4  
B8H  OP2    P      DOUB  N  N   5  
B8H  "O2'"  "C2'"  SING  N  N   6  
B8H  "O4'"  "C1'"  SING  N  N   7  
B8H  "O3'"  "C3'"  SING  N  N   8  
B8H  P      "O5'"  SING  N  N   9  
B8H  P      OP1    SING  N  N  10  
B8H  "C3'"  "C2'"  SING  N  N  11  
B8H  "C1'"  "C2'"  SING  N  N  12  
B8H  "C1'"  C5     SING  N  N  13  
B8H  C5     C6     DOUB  N  N  14  
B8H  C5     C4     SING  N  N  15  
B8H  O4     C4     DOUB  N  N  16  
B8H  C6     N1     SING  N  N  17  
B8H  C4     N3     SING  N  N  18  
B8H  N1     CN1    SING  N  N  19  
B8H  N1     C2     SING  N  N  20  
B8H  N3     C2     SING  N  N  21  
B8H  C2     O2     DOUB  N  N  22  
B8H  P      O1     SING  N  N  23  
B8H  "C1'"  H1     SING  N  N  24  
B8H  "C2'"  H2     SING  N  N  25  
B8H  "C3'"  H3     SING  N  N  26  
B8H  "C4'"  H4     SING  N  N  27  
B8H  "C5'"  H5     SING  N  N  28  
B8H  "C5'"  H6     SING  N  N  29  
B8H  C6     H7     SING  N  N  30  
B8H  CN1    H8     SING  N  N  31  
B8H  CN1    H9     SING  N  N  32  
B8H  CN1    H10    SING  N  N  33  
B8H  N3     H11    SING  N  N  34  
B8H  "O2'"  H12    SING  N  N  35  
B8H  "O3'"  H13    SING  N  N  36  
B8H  OP1    H14    SING  N  N  37  
B8H  O1     H15    SING  N  N  38  
#   #
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
B8H  InChI             InChI                 1.03   "InChI=1S/C10H15N2O9P/c1-12-2-4(9(15)11-10(12)16)8-7(14)6(13)5(21-8)3-20-22(17,18)19/h2,5-8,13-14H,3H2,1H3,(H,11,15,16)(H2,17,18,19)/t5-,6-,7-,8+/m1/s1"  
B8H  InChIKey          InChI                 1.03   VORAOZTXNOXTGQ-XUTVFYLZSA-N  
B8H  SMILES_CANONICAL  CACTVS                3.385  "CN1C=C([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)NC1=O"  
B8H  SMILES            CACTVS                3.385  "CN1C=C([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)NC1=O"  
B8H  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "CN1C=C(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"  
B8H  SMILES            "OpenEye OEToolkits"  2.0.6  "CN1C=C(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          B8H
_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~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(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
B8H  "Create component"        2017-09-25  EBI   
B8H  "Other modification"      2017-11-02  EBI   
B8H  "Initial release"         2018-01-24  RCSB  
B8H  "Modify one letter code"  2019-05-06  EBI   
##
