data_9V9
#

_chem_comp.id                                   9V9
_chem_comp.name                                 "1-{2,5-anhydro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}-5-methyl-2-sulfanylidene-2,3-dihydropyrimidin-4(1H)-one"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C11 H15 N2 O8 P S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-08-16
_chem_comp.pdbx_modified_date                   2019-03-22
_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                       366.284
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    9V9
_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       6ADV
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
9V9  C4     C1   C  0  1  N  N  N   1.592  -1.368  -1.261  -4.235  -1.727   0.053  C4     9V9   1  
9V9  C5     C2   C  0  1  N  N  N   2.942  -0.937  -1.686  -2.912  -2.112   0.375  C5     9V9   2  
9V9  C6     C3   C  0  1  N  N  N   3.157   0.426  -1.804  -1.905  -1.235   0.173  C6     9V9   3  
9V9  P      P1   P  0  1  N  N  N   7.425   2.489  -3.821   4.589  -0.763  -0.393  P      9V9   4  
9V9  OP1    O1   O  0  1  N  N  N   8.247   3.747  -4.060   5.403  -0.284   0.747  OP1    9V9   5  
9V9  OP2    O2   O  0  1  N  N  N   8.011   1.213  -3.326   4.352  -2.349  -0.254  OP2    9V9   6  
9V9  "O5'"  O3   O  0  1  N  N  N   6.236   2.825  -2.793   3.169  -0.005  -0.393  "O5'"  9V9   7  
9V9  "C5'"  C4   C  0  1  N  N  N   5.557   4.041  -3.099   2.291   0.003   0.734  "C5'"  9V9   8  
9V9  "C4'"  C5   C  0  1  N  N  R   4.261   4.080  -2.334   1.035   0.810   0.397  "C4'"  9V9   9  
9V9  "O4'"  O4   O  0  1  N  N  N   3.406   3.022  -2.749   0.174   0.259  -0.640  "O4'"  9V9  10  
9V9  "C1'"  C6   C  0  1  N  N  R   2.435   2.806  -1.679  -1.085   0.956  -0.554  "C1'"  9V9  11  
9V9  N1     N1   N  0  1  N  N  N   2.187   1.335  -1.546  -2.178   0.004  -0.336  N1     9V9  12  
9V9  C2     C7   C  0  1  N  N  N   0.899   0.888  -1.139  -3.440   0.359  -0.637  C2     9V9  13  
9V9  N3     N2   N  0  1  N  N  N   0.652  -0.429  -1.013  -4.462  -0.497  -0.451  N3     9V9  14  
9V9  O4     O5   O  0  1  N  N  N   1.332  -2.584  -1.134  -5.160  -2.500   0.226  O4     9V9  15  
9V9  C5M    C8   C  0  1  N  N  N   4.014  -1.972  -1.970  -2.630  -3.483   0.935  C5M    9V9  16  
9V9  S1     S1   S  0  1  N  N  N  -0.259   1.958  -0.830  -3.750   1.918  -1.273  S1     9V9  17  
9V9  "C2'"  C9   C  0  1  N  N  R   2.937   3.779  -0.645  -0.946   1.911   0.673  "C2'"  9V9  18  
9V9  "O2'"  O6   O  0  1  N  N  N   2.606   5.096  -1.188  -0.043   2.952   0.202  "O2'"  9V9  19  
9V9  "C6'"  C10  C  0  1  N  N  N   3.425   5.343  -2.334   1.256   2.297  -0.022  "C6'"  9V9  20  
9V9  "C3'"  C11  C  0  1  N  N  S   4.399   3.852  -0.847   0.005   1.032   1.563  "C3'"  9V9  21  
9V9  "O3'"  O7   O  0  1  N  N  N   4.803   5.001  -0.125   0.569   1.747   2.664  "O3'"  9V9  22  
9V9  H1     H1   H  0  1  N  N  N   4.131   0.776  -2.112  -0.888  -1.512   0.413  H1     9V9  23  
9V9  H2     H2   H  0  1  N  N  N   8.945   1.323  -3.194   3.825  -2.732  -0.969  H3     9V9  24  
9V9  H4     H4   H  0  1  N  N  N   6.183   4.897  -2.808   2.010  -1.020   0.984  H4     9V9  25  
9V9  H5     H5   H  0  1  N  N  N   5.350   4.087  -4.178   2.798   0.459   1.586  H5     9V9  26  
9V9  H6     H6   H  0  1  N  N  N   1.488   3.231  -2.043  -1.262   1.530  -1.464  H6     9V9  27  
9V9  H7     H7   H  0  1  N  N  N  -0.259  -0.723  -0.726  -5.366  -0.227  -0.677  H7     9V9  28  
9V9  H8     H8   H  0  1  N  N  N   3.604  -2.980  -1.807  -3.564  -4.038   1.024  H8     9V9  29  
9V9  H9     H9   H  0  1  N  N  N   4.348  -1.877  -3.014  -1.953  -4.016   0.268  H9     9V9  30  
9V9  H10    H10  H  0  1  N  N  N   4.868  -1.810  -1.296  -2.170  -3.386   1.918  H10    9V9  31  
9V9  H11    H11  H  0  1  N  N  N   2.605   3.583   0.385  -1.874   2.248   1.133  H11    9V9  32  
9V9  H12    H12  H  0  1  N  N  N   4.045   6.243  -2.207   2.043   2.747   0.583  H12    9V9  33  
9V9  H13    H13  H  0  1  N  N  N   2.826   5.437  -3.252   1.510   2.357  -1.080  H13    9V9  34  
9V9  H14    H14  H  0  1  N  N  N   4.935   2.926  -0.592  -0.477   0.106   1.878  H14    9V9  35  
9V9  H15    H15  H  0  1  N  N  N   4.870   4.788   0.798  -0.048   1.895   3.394  H15    9V9  36  
9V9  OP3    OP3  O  0  1  N  Y  N   6.646   2.166  -5.175   5.362  -0.454  -1.771  OP3    9V9  37  
9V9  H3     H3   H  0  1  N  Y  N   6.861   2.821  -5.829   6.228  -0.879  -1.841  H2     9V9  38  
#   #
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
9V9  OP1    P      DOUB  N  N   1  
9V9  P      OP2    SING  N  N   2  
9V9  P      "O5'"  SING  N  N   3  
9V9  "C5'"  "O5'"  SING  N  N   4  
9V9  "C5'"  "C4'"  SING  N  N   5  
9V9  "O4'"  "C4'"  SING  N  N   6  
9V9  "O4'"  "C1'"  SING  N  N   7  
9V9  "C6'"  "C4'"  SING  N  N   8  
9V9  "C6'"  "O2'"  SING  N  N   9  
9V9  "C4'"  "C3'"  SING  N  N  10  
9V9  C5M    C5     SING  N  N  11  
9V9  C6     C5     DOUB  N  N  12  
9V9  C6     N1     SING  N  N  13  
9V9  C5     C4     SING  N  N  14  
9V9  "C1'"  N1     SING  N  N  15  
9V9  "C1'"  "C2'"  SING  N  N  16  
9V9  N1     C2     SING  N  N  17  
9V9  C4     O4     DOUB  N  N  18  
9V9  C4     N3     SING  N  N  19  
9V9  "O2'"  "C2'"  SING  N  N  20  
9V9  C2     N3     SING  N  N  21  
9V9  C2     S1     DOUB  N  N  22  
9V9  "C3'"  "C2'"  SING  N  N  23  
9V9  "C3'"  "O3'"  SING  N  N  24  
9V9  C6     H1     SING  N  N  25  
9V9  OP2    H2     SING  N  N  26  
9V9  "C5'"  H4     SING  N  N  27  
9V9  "C5'"  H5     SING  N  N  28  
9V9  "C1'"  H6     SING  N  N  29  
9V9  N3     H7     SING  N  N  30  
9V9  C5M    H8     SING  N  N  31  
9V9  C5M    H9     SING  N  N  32  
9V9  C5M    H10    SING  N  N  33  
9V9  "C2'"  H11    SING  N  N  34  
9V9  "C6'"  H12    SING  N  N  35  
9V9  "C6'"  H13    SING  N  N  36  
9V9  "C3'"  H14    SING  N  N  37  
9V9  "O3'"  H15    SING  N  N  38  
9V9  P      OP3    SING  N  N  39  
9V9  OP3    H3     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
9V9  SMILES            ACDLabs               12.01  "C1(=O)NC(N(C=C1C)C2OC3(COP(O)(O)=O)C(C2OC3)O)=S"  
9V9  InChI             InChI                 1.03   "InChI=1S/C11H15N2O8PS/c1-5-2-13(10(23)12-8(5)15)9-6-7(14)11(21-9,3-19-6)4-20-22(16,17)18/h2,6-7,9,14H,3-4H2,1H3,(H,12,15,23)(H2,16,17,18)/t6-,7+,9-,11-/m1/s1"  
9V9  InChIKey          InChI                 1.03   OQJRNZAUGSRQOO-YRCORFKGSA-N  
9V9  SMILES_CANONICAL  CACTVS                3.385  "CC1=CN([C@@H]2O[C@]3(CO[C@@H]2[C@@H]3O)CO[P](O)(O)=O)C(=S)NC1=O"  
9V9  SMILES            CACTVS                3.385  "CC1=CN([CH]2O[C]3(CO[CH]2[CH]3O)CO[P](O)(O)=O)C(=S)NC1=O"  
9V9  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "CC1=CN(C(=S)NC1=O)[C@H]2[C@H]3[C@@H]([C@@](O2)(CO3)COP(=O)(O)O)O"  
9V9  SMILES            "OpenEye OEToolkits"  2.0.6  "CC1=CN(C(=S)NC1=O)C2C3C(C(O2)(CO3)COP(=O)(O)O)O"  
#   #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
9V9  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-{2,5-anhydro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}-5-methyl-2-sulfanylidene-2,3-dihydropyrimidin-4(1H)-one"  
9V9  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "[(1~{R},3~{R},4~{R},7~{S})-3-(5-methyl-4-oxidanylidene-2-sulfanylidene-pyrimidin-1-yl)-7-oxidanyl-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
9V9  "Create component"  2018-08-16  PDBJ  
9V9  "Initial release"   2019-03-27  RCSB  
##
