data_U4M
#

_chem_comp.id                                   U4M
_chem_comp.name                                 "1-{2,5-dideoxy-2-fluoro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}pyrimidine-2,4(1H,3H)-dione"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H14 F N2 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "2'-F,4'-alpha-methyl uridine 5--(dihydrogen phosphate)"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-04-06
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       340.199
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    U4M
_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       6CXZ
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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
U4M  "C1'"   C1    C  0  1  N  N  R   -7.304  -19.593  10.268   1.365  -1.033  -0.345  "C1'"   U4M   1  
U4M  C2      C2    C  0  1  N  N  N   -5.076  -19.294   9.397   3.421   0.208  -0.719  C2      U4M   2  
U4M  "C2'"   C3    C  0  1  N  N  R   -7.216  -20.255  11.641   1.088  -1.728   1.012  "C2'"   U4M   3  
U4M  "C3'"   C4    C  0  1  N  N  R   -7.899  -19.218  12.483  -0.241  -2.469   0.698  "C3'"   U4M   4  
U4M  C4      C5    C  0  1  N  N  N   -3.957  -17.168   9.232   3.794   2.329   0.189  C4      U4M   5  
U4M  "C4'"   C6    C  0  1  N  N  R   -9.091  -18.799  11.575  -0.938  -1.493  -0.275  "C4'"   U4M   6  
U4M  C5      C7    C  0  1  N  N  N   -5.075  -16.543   9.777   2.515   2.282   0.795  C5      U4M   7  
U4M  "C5'"   C8    C  0  1  N  N  N   -9.801  -17.596  12.069  -1.956  -0.641   0.486  "C5'"   U4M   8  
U4M  C6      C9    C  0  1  N  N  N   -6.181  -17.313  10.130   1.742   1.190   0.614  C6      U4M   9  
U4M  CM      C10   C  0  1  N  N  N  -10.175  -19.873  11.503  -1.644  -2.280  -1.381  CM      U4M  10  
U4M  "F2'"   F1    F  0  1  N  N  N   -7.870  -21.444  11.537   2.106  -2.632   1.333  "F2'"   U4M  11  
U4M  N1      N1    N  0  1  N  N  N   -6.151  -18.713   9.922   2.204   0.151  -0.148  N1      U4M  12  
U4M  N3      N2    N  0  1  N  N  N   -3.954  -18.541   9.039   4.213   1.285  -0.554  N3      U4M  13  
U4M  O2      O1    O  0  1  N  N  N   -5.063  -20.507   9.214   3.814  -0.728  -1.388  O2      U4M  14  
U4M  "O3'"   O2    O  0  1  N  N  N   -8.337  -19.746  13.709   0.015  -3.724   0.064  "O3'"   U4M  15  
U4M  O4      O3    O  0  1  N  N  N   -2.967  -16.513   8.908   4.509   3.303   0.338  O4      U4M  16  
U4M  "O4'"   O4    O  0  1  N  N  N   -8.483  -18.693  10.273   0.072  -0.652  -0.843  "O4'"   U4M  17  
U4M  "O5'"   O5    O  0  1  N  N  N   -8.713  -16.530  12.010  -2.678   0.176  -0.437  "O5'"   U4M  18  
U4M  OP1     O6    O  0  1  N  N  N   -9.984  -14.708  13.173  -5.070   0.378   0.636  OP1     U4M  19  
U4M  OP2     O7    O  0  1  N  N  N   -7.728  -14.227  12.080  -3.296   2.128   1.038  OP2     U4M  20  
U4M  P       P1    P  0  1  N  N  N   -9.017  -14.959  12.086  -3.833   1.202   0.017  P       U4M  21  
U4M  "H1'"   H1    H  0  1  N  N  N   -7.427  -20.368   9.497   1.846  -1.728  -1.034  "H1'"   U4M  22  
U4M  "H2'"   H2    H  0  1  N  N  N   -6.164  -20.370  11.943   0.950  -0.995   1.807  "H2'"   U4M  23  
U4M  "H3'"   H3    H  0  1  N  N  N   -7.234  -18.355  12.631  -0.831  -2.607   1.604  "H3'"   U4M  24  
U4M  H5      H4    H  0  1  N  N  N   -5.085  -15.473   9.925   2.163   3.108   1.395  H5      U4M  25  
U4M  H6L     H5    H  0  1  N  N  N  -10.648  -17.337  11.417  -2.651  -1.292   1.017  H6L     U4M  26  
U4M  "H5'"   H6    H  0  1  N  N  N  -10.162  -17.741  13.098  -1.434  -0.006   1.202  "H5'"   U4M  27  
U4M  H6      H7    H  0  1  N  N  N   -7.055  -16.845  10.559   0.763   1.136   1.067  H6      U4M  28  
U4M  HM3     H8    H  0  1  N  N  N  -10.657  -19.975  12.487  -2.131  -1.586  -2.066  HM3     U4M  29  
U4M  HM1     H9    H  0  1  N  N  N  -10.928  -19.585  10.754  -0.912  -2.875  -1.927  HM1     U4M  30  
U4M  HM2     H10   H  0  1  N  N  N   -9.721  -20.833  11.216  -2.391  -2.939  -0.938  HM2     U4M  31  
U4M  H3      H11   H  0  1  N  N  N   -3.152  -18.991   8.645   5.088   1.309  -0.972  H3      U4M  32  
U4M  H6M     H12   H  0  1  N  N  N   -7.585  -19.990  14.236   0.529  -4.340   0.603  H6M     U4M  33  
U4M  H1      H13   H  0  1  N  N  N   -9.628  -14.062  13.772  -5.472  -0.250   0.020  H1      U4M  34  
U4M  OP3     OP3   O  0  1  N  Y  N   -9.776  -14.665  10.695  -4.334   2.044  -1.260  OP3     U4M  35  
U4M  HOP3    HOP3  H  0  0  N  Y  N   -9.245  -14.087  10.160  -5.032   2.684  -1.060  HOP3    U4M  36  
#   #
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
U4M  O4     C4      DOUB  N  N   1  
U4M  N3     C4      SING  N  N   2  
U4M  N3     C2      SING  N  N   3  
U4M  O2     C2      DOUB  N  N   4  
U4M  C4     C5      SING  N  N   5  
U4M  C2     N1      SING  N  N   6  
U4M  C5     C6      DOUB  N  N   7  
U4M  N1     C6      SING  N  N   8  
U4M  N1     "C1'"   SING  N  N   9  
U4M  "C1'"  "O4'"   SING  N  N  10  
U4M  "C1'"  "C2'"   SING  N  N  11  
U4M  "O4'"  "C4'"   SING  N  N  12  
U4M  CM     "C4'"   SING  N  N  13  
U4M  "F2'"  "C2'"   SING  N  N  14  
U4M  "C4'"  "C5'"   SING  N  N  15  
U4M  "C4'"  "C3'"   SING  N  N  16  
U4M  "C2'"  "C3'"   SING  N  N  17  
U4M  "O5'"  "C5'"   SING  N  N  18  
U4M  "O5'"  P       SING  N  N  19  
U4M  OP2    P       DOUB  N  N  20  
U4M  P      OP1     SING  N  N  21  
U4M  "C3'"  "O3'"   SING  N  N  22  
U4M  "C1'"  "H1'"   SING  N  N  23  
U4M  "C2'"  "H2'"   SING  N  N  24  
U4M  "C3'"  "H3'"   SING  N  N  25  
U4M  C5     H5      SING  N  N  26  
U4M  "C5'"  H6L     SING  N  N  27  
U4M  "C5'"  "H5'"   SING  N  N  28  
U4M  C6     H6      SING  N  N  29  
U4M  CM     HM3     SING  N  N  30  
U4M  CM     HM1     SING  N  N  31  
U4M  CM     HM2     SING  N  N  32  
U4M  N3     H3      SING  N  N  33  
U4M  "O3'"  H6M     SING  N  N  34  
U4M  OP1    H1      SING  N  N  35  
U4M  P      OP3     SING  N  N  36  
U4M  OP3    HOP3    SING  N  N  37  
#   #
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
U4M  SMILES            ACDLabs               12.01  "C1(OC(C(C1F)O)(COP(O)(=O)O)C)N2C(NC(C=C2)=O)=O"  
U4M  InChI             InChI                 1.03   "InChI=1S/C10H14FN2O8P/c1-10(4-20-22(17,18)19)7(15)6(11)8(21-10)13-3-2-5(14)12-9(13)16/h2-3,6-8,15H,4H2,1H3,(H,12,14,16)(H2,17,18,19)/t6-,7+,8-,10-/m1/s1"  
U4M  InChIKey          InChI                 1.03   ZQJMYOGITIALJZ-IBCQBUCCSA-N  
U4M  SMILES_CANONICAL  CACTVS                3.385  "C[C@]1(CO[P](O)(O)=O)O[C@H]([C@H](F)[C@@H]1O)N2C=CC(=O)NC2=O"  
U4M  SMILES            CACTVS                3.385  "C[C]1(CO[P](O)(O)=O)O[CH]([CH](F)[CH]1O)N2C=CC(=O)NC2=O"  
U4M  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "C[C@]1([C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)F)O)COP(=O)(O)O"  
U4M  SMILES            "OpenEye OEToolkits"  2.0.6  "CC1(C(C(C(O1)N2C=CC(=O)NC2=O)F)O)COP(=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
U4M  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-{2,5-dideoxy-2-fluoro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}pyrimidine-2,4(1H,3H)-dione"  
U4M  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-2-methyl-3-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
U4M  "Create component"  2018-04-06  RCSB  
U4M  "Modify synonyms"   2018-04-12  RCSB  
U4M  "Initial release"   2018-08-29  RCSB  
U4M  "Modify synonyms"   2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     U4M
_pdbx_chem_comp_synonyms.name        "2'-F,4'-alpha-methyl uridine 5--(dihydrogen phosphate)"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
