data_L2B
#

_chem_comp.id                                   L2B
_chem_comp.name                                 "3'-DEOXYURIDINE-5'-MONOPHOSPHATE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H13 N2 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "[(2~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-07-16
_chem_comp.pdbx_modified_date                   2020-11-13
_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                       308.182
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    L2B
_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       6SA1
_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
L2B  "C1'"  C1   C  0  1  N  N  R  -32.450  -19.402  27.822   1.270   0.991   0.388  "C1'"  L2B   1  
L2B  C2     C2   C  0  1  N  N  N  -33.297  -21.124  26.207   3.364  -0.084   0.996  C2     L2B   2  
L2B  "C2'"  C3   C  0  1  N  N  R  -31.308  -18.754  27.046   1.221   2.103  -0.683  "C2'"  L2B   3  
L2B  "C3'"  C4   C  0  1  N  N  N  -31.102  -17.382  27.666  -0.288   2.359  -0.890  "C3'"  L2B   4  
L2B  C4     C5   C  0  1  N  N  N  -35.453  -21.011  25.330   4.415  -1.658  -0.373  C4     L2B   5  
L2B  "C4'"  C6   C  0  1  N  N  S  -32.004  -17.373  28.891  -0.973   1.371   0.080  "C4'"  L2B   6  
L2B  C5     C7   C  0  1  N  N  N  -35.692  -19.848  26.055   3.366  -1.525  -1.313  C5     L2B   7  
L2B  "C5'"  C8   C  0  1  N  N  N  -32.672  -16.015  29.078  -2.250   0.808  -0.547  "C5'"  L2B   8  
L2B  C6     C9   C  0  1  N  N  N  -34.696  -19.324  26.873   2.358  -0.664  -1.055  C6     L2B   9  
L2B  N1     N1   N  0  1  N  N  N  -33.511  -19.941  26.953   2.364   0.057   0.108  N1     L2B  10  
L2B  N3     N2   N  0  1  N  N  N  -34.266  -21.621  25.424   4.384  -0.930   0.762  N3     L2B  11  
L2B  O2     O1   O  0  1  N  N  N  -32.196  -21.716  26.276   3.349   0.567   2.024  O2     L2B  12  
L2B  "O2'"  O2   O  0  1  N  N  N  -30.112  -19.524  27.197   1.869   3.284  -0.208  "O2'"  L2B  13  
L2B  O4     O3   O  0  1  N  N  N  -36.343  -21.491  24.594   5.337  -2.425  -0.585  O4     L2B  14  
L2B  "O4'"  O4   O  0  1  N  N  N  -32.987  -18.387  28.673  -0.004   0.319   0.281  "O4'"  L2B  15  
L2B  "O5'"  O5   O  0  1  N  N  N  -33.337  -15.982  30.340  -2.928  -0.011   0.408  "O5'"  L2B  16  
L2B  OP1    O6   O  0  1  N  N  N  -35.293  -15.680  31.914  -5.471   0.320  -0.170  OP1    L2B  17  
L2B  OP2    O7   O  0  1  N  N  N  -35.156  -14.279  29.889  -4.148  -1.609  -1.118  OP2    L2B  18  
L2B  P      P1   P  0  1  N  N  N  -34.913  -15.660  30.452  -4.312  -0.768   0.088  P      L2B  19  
L2B  O1     O8   O  0  1  N  Y  N  -35.302  -17.151  30.681  -4.718  -1.697   1.339  O1     L2B  20  
L2B  H1     H1   H  0  1  N  N  N  -32.036  -20.218  28.433   1.388   1.425   1.381  H1     L2B  21  
L2B  H2     H2   H  0  1  N  N  N  -31.586  -18.650  25.987   1.684   1.761  -1.610  H2     L2B  22  
L2B  H3     H3   H  0  1  N  N  N  -30.051  -17.242  27.957  -0.540   3.387  -0.630  H3     L2B  23  
L2B  H4     H4   H  0  1  N  N  N  -31.396  -16.590  26.962  -0.575   2.144  -1.919  H4     L2B  24  
L2B  H5     H5   H  0  1  N  N  N  -31.404  -17.605  29.783  -1.201   1.865   1.025  H5     L2B  25  
L2B  H6     H6   H  0  1  N  N  N  -36.649  -19.353  25.983   3.374  -2.100  -2.227  H6     L2B  26  
L2B  H7     H7   H  0  1  N  N  N  -31.909  -15.223  29.045  -2.900   1.629  -0.848  H7     L2B  27  
L2B  H8     H8   H  0  1  N  N  N  -33.404  -15.853  28.273  -1.992   0.209  -1.420  H8     L2B  28  
L2B  H9     H9   H  0  1  N  N  N  -34.878  -18.424  27.441   1.549  -0.549  -1.761  H9     L2B  29  
L2B  H10    H10  H  0  1  N  N  N  -34.099  -22.458  24.904   5.099  -1.016   1.411  H10    L2B  30  
L2B  H11    H11  H  0  1  N  N  N  -30.237  -20.383  26.810   1.816   4.034  -0.817  H11    L2B  31  
L2B  H12    H12  H  0  1  N  N  N  -35.605  -14.821  32.172  -5.634   0.907   0.581  H12    L2B  32  
L2B  H13    H13  H  0  1  N  N  N  -36.131  -17.332  30.254  -5.544  -2.184   1.216  H13    L2B  33  
#   #
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
L2B  O4     C4     DOUB  N  N   1  
L2B  C4     N3     SING  N  N   2  
L2B  C4     C5     SING  N  N   3  
L2B  N3     C2     SING  N  N   4  
L2B  C5     C6     DOUB  N  N   5  
L2B  C2     O2     DOUB  N  N   6  
L2B  C2     N1     SING  N  N   7  
L2B  C6     N1     SING  N  N   8  
L2B  N1     "C1'"  SING  N  N   9  
L2B  "C2'"  "O2'"  SING  N  N  10  
L2B  "C2'"  "C3'"  SING  N  N  11  
L2B  "C2'"  "C1'"  SING  N  N  12  
L2B  "C3'"  "C4'"  SING  N  N  13  
L2B  "C1'"  "O4'"  SING  N  N  14  
L2B  "O4'"  "C4'"  SING  N  N  15  
L2B  "C4'"  "C5'"  SING  N  N  16  
L2B  "C5'"  "O5'"  SING  N  N  17  
L2B  OP2    P      DOUB  N  N  18  
L2B  "O5'"  P      SING  N  N  19  
L2B  P      OP1    SING  N  N  20  
L2B  P      O1     SING  N  N  21  
L2B  "C1'"  H1     SING  N  N  22  
L2B  "C2'"  H2     SING  N  N  23  
L2B  "C3'"  H3     SING  N  N  24  
L2B  "C3'"  H4     SING  N  N  25  
L2B  "C4'"  H5     SING  N  N  26  
L2B  C5     H6     SING  N  N  27  
L2B  "C5'"  H7     SING  N  N  28  
L2B  "C5'"  H8     SING  N  N  29  
L2B  C6     H9     SING  N  N  30  
L2B  N3     H10    SING  N  N  31  
L2B  "O2'"  H11    SING  N  N  32  
L2B  OP1    H12    SING  N  N  33  
L2B  O1     H13    SING  N  N  34  
#   #
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
L2B  InChI             InChI                 1.03   "InChI=1S/C9H13N2O8P/c12-6-3-5(4-18-20(15,16)17)19-8(6)11-2-1-7(13)10-9(11)14/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1"  
L2B  InChIKey          InChI                 1.03   SEOHEWZQAGEAGZ-SHYZEUOFSA-N  
L2B  SMILES_CANONICAL  CACTVS                3.385  "O[C@@H]1C[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O"  
L2B  SMILES            CACTVS                3.385  "O[CH]1C[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O"  
L2B  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1[C@H](O[C@H]([C@@H]1O)N2C=CC(=O)NC2=O)COP(=O)(O)O"  
L2B  SMILES            "OpenEye OEToolkits"  2.0.7  "C1C(OC(C1O)N2C=CC(=O)NC2=O)COP(=O)(O)O"  
#
_pdbx_chem_comp_identifier.comp_id          L2B
_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~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     L2B
_pdbx_chem_comp_synonyms.name        "[(2~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
L2B  "Create component"  2019-07-16  PDBE  
L2B  "Modify synonyms"   2020-06-05  PDBE  
L2B  "Initial release"   2020-11-18  RCSB  
##
