data_LV2
#

_chem_comp.id                                   LV2
_chem_comp.name                                 "[(2~{R},3~{S},4~{R},5~{R})-5-[4-(dimethylamino)-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C11 H18 N3 O8 P"
_chem_comp.mon_nstd_parent_comp_id              C
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-09-10
_chem_comp.pdbx_modified_date                   2020-07-24
_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                       351.250
_chem_comp.one_letter_code                      C
_chem_comp.three_letter_code                    LV2
_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       6SKG
_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
LV2  P      P1   P  0  1  N  N  N  205.474  279.251  190.612   4.525   1.375   0.128  P      LV2   1  
LV2  OP1    O1   O  0  1  N  N  N  205.961  279.758  189.279   5.642   0.579  -0.430  OP1    LV2   2  
LV2  OP2    O2   O  0  1  N  N  N  206.378  279.326  191.815   4.033   2.449  -0.966  OP2    LV2   3  
LV2  "O5'"  O3   O  0  1  N  N  N  204.108  279.997  190.946   3.305   0.395   0.505  "O5'"  LV2   4  
LV2  "C5'"  C1   C  0  1  N  N  N  203.040  280.025  190.009   2.710  -0.504  -0.433  "C5'"  LV2   5  
LV2  "C4'"  C2   C  0  1  N  N  R  201.729  280.327  190.689   1.584  -1.282   0.250  "C4'"  LV2   6  
LV2  "O4'"  O4   O  0  1  N  N  N  201.445  279.289  191.657   0.471  -0.407   0.538  "O4'"  LV2   7  
LV2  "C3'"  C3   C  0  1  N  N  S  201.691  281.618  191.493   1.009  -2.349  -0.707  "C3'"  LV2   8  
LV2  "C2'"  C4   C  0  1  N  N  R  200.638  281.335  192.558  -0.507  -2.348  -0.405  "C2'"  LV2   9  
LV2  "O2'"  O5   O  0  1  N  N  N  199.333  281.546  192.041  -0.923  -3.629   0.072  "O2'"  LV2  10  
LV2  "C1'"  C5   C  0  1  N  N  R  200.823  279.837  192.796  -0.668  -1.280   0.700  "C1'"  LV2  11  
LV2  N1     N1   N  0  1  N  N  N  201.668  279.526  193.971  -1.914  -0.533   0.509  N1     LV2  12  
LV2  C2     C6   C  0  1  N  N  N  201.065  279.154  195.188  -2.097   0.189  -0.612  C2     LV2  13  
LV2  O2     O6   O  0  1  N  N  N  199.820  279.118  195.281  -1.220   0.213  -1.460  O2     LV2  14  
LV2  N3     N2   N  0  1  N  N  N  201.827  278.842  196.256  -3.220   0.877  -0.811  N3     LV2  15  
LV2  C4     C7   C  0  1  N  N  N  203.170  278.873  196.164  -4.189   0.867   0.094  C4     LV2  16  
LV2  N4     N3   N  0  1  N  N  N  203.942  278.546  197.280  -5.345   1.581  -0.123  N4     LV2  17  
LV2  C5     C8   C  0  1  N  N  N  203.780  279.227  194.969  -4.029   0.121   1.280  C5     LV2  18  
LV2  C6     C9   C  0  1  N  N  N  202.999  279.550  193.869  -2.884  -0.578   1.465  C6     LV2  19  
LV2  CM4    C10  C  0  1  N  N  N  203.290  278.015  198.464  -5.460   2.449  -1.298  CM4    LV2  20  
LV2  "O3'"  O7   O  0  1  N  N  N  201.383  282.741  190.686   1.574  -3.631  -0.426  "O3'"  LV2  21  
LV2  C1     C11  C  0  1  N  N  N  205.386  278.720  197.256  -6.460   1.474   0.821  C1     LV2  22  
LV2  H2     H2   H  0  1  N  N  N  207.208  279.714  191.564   3.302   3.007  -0.667  H2     LV2  23  
LV2  H3     H3   H  0  1  N  N  N  202.971  279.045  189.514   2.305   0.061  -1.272  H3     LV2  24  
LV2  H4     H4   H  0  1  N  N  N  203.242  280.802  189.257   3.465  -1.202  -0.796  H4     LV2  25  
LV2  H5     H5   H  0  1  N  N  N  200.932  280.358  189.931   1.947  -1.750   1.165  H5     LV2  26  
LV2  H6     H6   H  0  1  N  N  N  202.664  281.758  191.986   1.191  -2.069  -1.745  H6     LV2  27  
LV2  H7     H7   H  0  1  N  N  N  200.833  281.910  193.475  -1.073  -2.067  -1.293  H7     LV2  28  
LV2  H8     H8   H  0  1  N  N  N  198.691  281.365  192.717  -0.787  -4.347  -0.561  H8     LV2  29  
LV2  H9     H9   H  0  1  N  N  N  199.831  279.383  192.938  -0.652  -1.747   1.684  H9     LV2  30  
LV2  H10    H10  H  0  1  N  N  N  204.857  279.251  194.896  -4.809   0.104   2.026  H10    LV2  31  
LV2  H11    H11  H  0  1  N  N  N  203.466  279.820  192.933  -2.739  -1.161   2.362  H11    LV2  32  
LV2  H12    H12  H  0  1  N  N  N  204.044  277.815  199.240  -5.872   1.880  -2.131  H12    LV2  33  
LV2  H13    H13  H  0  1  N  N  N  202.562  278.748  198.841  -6.120   3.286  -1.068  H13    LV2  34  
LV2  H14    H14  H  0  1  N  N  N  202.770  277.080  198.208  -4.475   2.827  -1.568  H14    LV2  35  
LV2  H15    H15  H  0  1  N  N  N  201.369  283.524  191.224   1.248  -4.339  -0.999  H15    LV2  36  
LV2  H16    H16  H  0  1  N  N  N  205.809  278.409  198.222  -6.160   0.860   1.670  H16    LV2  37  
LV2  H17    H17  H  0  1  N  N  N  205.816  278.104  196.452  -6.736   2.468   1.172  H17    LV2  38  
LV2  H18    H18  H  0  1  N  N  N  205.625  279.778  197.075  -7.314   1.014   0.324  H18    LV2  39  
LV2  OP3    OP3  O  0  1  N  Y  N  205.041  277.720  190.416   5.024   2.145   1.451  OP3    LV2  40  
LV2  H1     H1   H  0  1  N  N  N  205.183  277.464  189.512   5.760   2.754   1.298  H1     LV2  41  
#   #
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
LV2  OP1    P      DOUB  N  N   1  
LV2  "C5'"  "C4'"  SING  N  N   2  
LV2  "C5'"  "O5'"  SING  N  N   3  
LV2  P      "O5'"  SING  N  N   4  
LV2  P      OP2    SING  N  N   5  
LV2  "O3'"  "C3'"  SING  N  N   6  
LV2  "C4'"  "C3'"  SING  N  N   7  
LV2  "C4'"  "O4'"  SING  N  N   8  
LV2  "C3'"  "C2'"  SING  N  N   9  
LV2  "O4'"  "C1'"  SING  N  N  10  
LV2  "O2'"  "C2'"  SING  N  N  11  
LV2  "C2'"  "C1'"  SING  N  N  12  
LV2  "C1'"  N1     SING  N  N  13  
LV2  C6     N1     SING  N  N  14  
LV2  C6     C5     DOUB  N  N  15  
LV2  N1     C2     SING  N  N  16  
LV2  C5     C4     SING  N  N  17  
LV2  C2     O2     DOUB  N  N  18  
LV2  C2     N3     SING  N  N  19  
LV2  C4     N3     DOUB  N  N  20  
LV2  C4     N4     SING  N  N  21  
LV2  C1     N4     SING  N  N  22  
LV2  N4     CM4    SING  N  N  23  
LV2  OP2    H2     SING  N  N  24  
LV2  "C5'"  H3     SING  N  N  25  
LV2  "C5'"  H4     SING  N  N  26  
LV2  "C4'"  H5     SING  N  N  27  
LV2  "C3'"  H6     SING  N  N  28  
LV2  "C2'"  H7     SING  N  N  29  
LV2  "O2'"  H8     SING  N  N  30  
LV2  "C1'"  H9     SING  N  N  31  
LV2  C5     H10    SING  N  N  32  
LV2  C6     H11    SING  N  N  33  
LV2  CM4    H12    SING  N  N  34  
LV2  CM4    H13    SING  N  N  35  
LV2  CM4    H14    SING  N  N  36  
LV2  "O3'"  H15    SING  N  N  37  
LV2  C1     H16    SING  N  N  38  
LV2  C1     H17    SING  N  N  39  
LV2  C1     H18    SING  N  N  40  
LV2  P      OP3    SING  N  N  41  
LV2  OP3    H1     SING  N  N  42  
#   #
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
LV2  InChI             InChI                 1.03   "InChI=1S/C11H18N3O8P/c1-13(2)7-3-4-14(11(17)12-7)10-9(16)8(15)6(22-10)5-21-23(18,19)20/h3-4,6,8-10,15-16H,5H2,1-2H3,(H2,18,19,20)/t6-,8-,9-,10-/m1/s1"  
LV2  InChIKey          InChI                 1.03   PGVGGVCCRBGELR-PEBGCTIMSA-N  
LV2  SMILES_CANONICAL  CACTVS                3.385  "CN(C)C1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O"  
LV2  SMILES            CACTVS                3.385  "CN(C)C1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O"  
LV2  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CN(C)C1=NC(=O)N(C=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"  
LV2  SMILES            "OpenEye OEToolkits"  2.0.7  "CN(C)C1=NC(=O)N(C=C1)C2C(C(C(O2)COP(=O)(O)O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          LV2
_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       "[(2~{R},3~{S},4~{R},5~{R})-5-[4-(dimethylamino)-2-oxidanylidene-pyrimidin-1-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
LV2  "Create component"  2019-09-10  EBI   
LV2  "Initial release"   2020-07-29  RCSB  
##
