data_TLO
#

_chem_comp.id                                   TLO
_chem_comp.name                                 "5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H20 N2 O11 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "thymidine diphosphate phenol"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2010-10-29
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       478.284
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    TLO
_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       3PFG
_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
TLO  N1      N1      N  0  1  N  N  N   -4.972   5.207  35.692   4.821  -0.504   0.437  N1      TLO   1  
TLO  C2      C2      C  0  1  N  N  N   -3.884   5.847  36.170   4.856  -0.682  -0.896  C2      TLO   2  
TLO  O2      O2      O  0  1  N  N  N   -3.785   7.106  36.098   4.281   0.107  -1.621  O2      TLO   3  
TLO  N3      N3      N  0  1  N  N  N   -2.869   5.168  36.776   5.519  -1.720  -1.438  N3      TLO   4  
TLO  C4      C4      C  0  1  N  N  N   -2.947   3.806  36.856   6.162  -2.603  -0.648  C4      TLO   5  
TLO  O4      O4      O  0  1  N  N  N   -1.961   3.253  37.380   6.763  -3.542  -1.138  O4      TLO   6  
TLO  C5      C5      C  0  1  N  N  N   -4.059   3.108  36.354   6.133  -2.428   0.757  C5      TLO   7  
TLO  C6      C6      C  0  1  N  N  N   -5.057   3.859  35.752   5.460  -1.377   1.274  C6      TLO   8  
TLO  PA      PA      P  0  1  N  N  N   -9.358   1.816  32.709  -1.481   1.662  -0.484  PA      TLO   9  
TLO  PB      PB      P  0  1  N  N  N   -7.760   2.499  30.318  -3.863  -0.084  -0.242  PB      TLO  10  
TLO  CG      CG      C  0  1  Y  N  N   -7.376   0.326  28.949  -5.884  -1.122   0.786  CG      TLO  11  
TLO  CZ      CZ      C  0  1  Y  N  N   -5.780  -1.843  28.416  -8.384  -2.171   0.234  CZ      TLO  12  
TLO  "C1'"   "C1'"   C  0  1  N  N  R   -6.015   5.933  34.963   4.096   0.639   0.998  "C1'"   TLO  13  
TLO  O1A     O1A     O  0  1  N  N  N   -9.073   0.749  33.750  -2.074   3.153  -0.351  O1A     TLO  14  
TLO  O1B     O1B     O  0  1  N  N  N   -6.299   2.738  30.328  -3.534  -1.331  -1.206  O1B     TLO  15  
TLO  "C2'"   "C2'"   C  0  1  N  N  N   -5.933   5.607  33.454   4.716   1.965   0.502  "C2'"   TLO  16  
TLO  O2A     O2A     O  0  1  N  N  N  -10.606   1.699  31.858  -1.328   1.318  -1.916  O2A     TLO  17  
TLO  O2B     O2B     O  0  1  N  N  N   -8.670   3.709  30.151  -4.700   0.895  -0.971  O2B     TLO  18  
TLO  "C3'"   "C3'"   C  0  1  N  N  S   -7.389   5.598  33.006   3.499   2.895   0.298  "C3'"   TLO  19  
TLO  "O3'"   "O3'"   O  0  1  N  N  N   -7.808   6.984  32.817   3.594   4.037   1.152  "O3'"   TLO  20  
TLO  O3A     O3A     O  0  1  N  N  N   -8.074   1.797  31.740  -2.489   0.619   0.214  O3A     TLO  21  
TLO  O3B     O3B     O  0  1  N  N  N   -8.186   1.390  29.247  -4.657  -0.606   1.058  O3B     TLO  22  
TLO  "C4'"   "C4'"   C  0  1  N  N  R   -8.106   5.163  34.246   2.288   2.022   0.696  "C4'"   TLO  23  
TLO  "O4'"   "O4'"   O  0  1  N  N  N   -7.271   5.478  35.366   2.737   0.662   0.510  "O4'"   TLO  24  
TLO  "C5'"   "C5'"   C  0  1  N  N  N   -8.262   3.661  34.241   1.095   2.318  -0.215  "C5'"   TLO  25  
TLO  "O5'"   "O5'"   O  0  1  N  N  N   -9.294   3.308  33.278  -0.045   1.588   0.241  "O5'"   TLO  26  
TLO  C5M     C5M     C  0  1  N  N  N   -4.093   1.586  36.515   6.843  -3.401   1.662  C5M     TLO  27  
TLO  CD1     CD1     C  0  1  Y  N  N   -7.414  -0.803  29.778  -6.024  -2.474   0.508  CD1     TLO  28  
TLO  CD2     CD2     C  0  1  Y  N  N   -6.546   0.386  27.851  -7.001  -0.298   0.792  CD2     TLO  29  
TLO  CE1     CE1     C  0  1  Y  N  N   -6.609  -1.902  29.529  -7.273  -2.996   0.233  CE1     TLO  30  
TLO  CE2     CE2     C  0  1  Y  N  N   -5.750  -0.719  27.603  -8.248  -0.825   0.516  CE2     TLO  31  
TLO  HN3     HN3     H  0  1  N  N  N   -2.083   5.657  37.154   5.534  -1.833  -2.402  HN3     TLO  32  
TLO  H6      H6      H  0  1  N  N  N   -5.914   3.360  35.325   5.428  -1.227   2.343  H6      TLO  33  
TLO  HZ      HZ      H  0  1  N  N  N   -5.148  -2.686  28.179  -9.359  -2.581   0.018  HZ      TLO  34  
TLO  "H1'"   "H1'"   H  0  1  N  N  N   -5.875   7.006  35.160   4.108   0.598   2.087  "H1'"   TLO  35  
TLO  HO1A    HO1A    H  0  0  N  N  N   -9.764   0.097  33.733  -2.200   3.446   0.562  HO1A    TLO  36  
TLO  HO1B    HO1B    H  0  0  N  N  N   -6.129   3.667  30.223  -2.987  -2.014  -0.793  HO1B    TLO  37  
TLO  "H2'"   "H2'"   H  0  1  N  N  N   -5.350   6.365  32.910   5.390   2.376   1.253  "H2'"   TLO  38  
TLO  "H2'A"  "H2'A"  H  0  0  N  N  N   -5.453   4.633  33.279   5.243   1.811  -0.440  "H2'A"  TLO  39  
TLO  "H3'"   "H3'"   H  0  1  N  N  N   -7.562   4.994  32.103   3.423   3.202  -0.745  "H3'"   TLO  40  
TLO  "HO3'"  "HO3'"  H  0  0  N  N  N   -8.715   7.006  32.537   4.371   4.589   0.985  "HO3'"  TLO  41  
TLO  "H4'"   "H4'"   H  0  1  N  N  N   -9.087   5.658  34.297   2.023   2.194   1.739  "H4'"   TLO  42  
TLO  "H5'"   "H5'"   H  0  1  N  N  N   -7.310   3.188  33.957   0.877   3.386  -0.191  "H5'"   TLO  43  
TLO  "H5'A"  "H5'A"  H  0  0  N  N  N   -8.553   3.313  35.243   1.334   2.019  -1.235  "H5'A"  TLO  44  
TLO  H5M     H5M     H  0  1  N  N  N   -5.020   1.191  36.074   7.323  -4.173   1.061  H5M     TLO  45  
TLO  H5MA    H5MA    H  0  0  N  N  N   -3.226   1.144  36.002   7.597  -2.871   2.244  H5MA    TLO  46  
TLO  H5MB    H5MB    H  0  0  N  N  N   -4.057   1.330  37.584   6.122  -3.862   2.337  H5MB    TLO  47  
TLO  HD1     HD1     H  0  1  N  N  N   -8.083  -0.816  30.626  -5.157  -3.118   0.506  HD1     TLO  48  
TLO  HD2     HD2     H  0  1  N  N  N   -6.518   1.256  27.212  -6.895   0.754   1.013  HD2     TLO  49  
TLO  HE1     HE1     H  0  1  N  N  N   -6.625  -2.769  30.173  -7.382  -4.047   0.012  HE1     TLO  50  
TLO  HE2     HE2     H  0  1  N  N  N   -5.086  -0.706  26.751  -9.116  -0.183   0.516  HE2     TLO  51  
#   #
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
TLO  "C1'"  N1      SING  N  N   1  
TLO  N1     C6      SING  N  N   2  
TLO  N1     C2      SING  N  N   3  
TLO  O2     C2      DOUB  N  N   4  
TLO  C2     N3      SING  N  N   5  
TLO  N3     C4      SING  N  N   6  
TLO  N3     HN3     SING  N  N   7  
TLO  C5     C4      SING  N  N   8  
TLO  C4     O4      DOUB  N  N   9  
TLO  C6     C5      DOUB  N  N  10  
TLO  C5     C5M     SING  N  N  11  
TLO  C6     H6      SING  N  N  12  
TLO  O3A    PA      SING  N  N  13  
TLO  O2A    PA      DOUB  N  N  14  
TLO  PA     "O5'"   SING  N  N  15  
TLO  PA     O1A     SING  N  N  16  
TLO  O3B    PB      SING  N  N  17  
TLO  O2B    PB      DOUB  N  N  18  
TLO  PB     O1B     SING  N  N  19  
TLO  PB     O3A     SING  N  N  20  
TLO  CD2    CG      DOUB  Y  N  21  
TLO  CG     O3B     SING  N  N  22  
TLO  CG     CD1     SING  Y  N  23  
TLO  CE2    CZ      DOUB  Y  N  24  
TLO  CZ     CE1     SING  Y  N  25  
TLO  CZ     HZ      SING  N  N  26  
TLO  "C2'"  "C1'"   SING  N  N  27  
TLO  "C1'"  "O4'"   SING  N  N  28  
TLO  "C1'"  "H1'"   SING  N  N  29  
TLO  O1A    HO1A    SING  N  N  30  
TLO  O1B    HO1B    SING  N  N  31  
TLO  "C3'"  "C2'"   SING  N  N  32  
TLO  "C2'"  "H2'"   SING  N  N  33  
TLO  "C2'"  "H2'A"  SING  N  N  34  
TLO  "O3'"  "C3'"   SING  N  N  35  
TLO  "C3'"  "C4'"   SING  N  N  36  
TLO  "C3'"  "H3'"   SING  N  N  37  
TLO  "O3'"  "HO3'"  SING  N  N  38  
TLO  "C5'"  "C4'"   SING  N  N  39  
TLO  "C4'"  "O4'"   SING  N  N  40  
TLO  "C4'"  "H4'"   SING  N  N  41  
TLO  "O5'"  "C5'"   SING  N  N  42  
TLO  "C5'"  "H5'"   SING  N  N  43  
TLO  "C5'"  "H5'A"  SING  N  N  44  
TLO  C5M    H5M     SING  N  N  45  
TLO  C5M    H5MA    SING  N  N  46  
TLO  C5M    H5MB    SING  N  N  47  
TLO  CE1    CD1     DOUB  Y  N  48  
TLO  CD1    HD1     SING  N  N  49  
TLO  CE2    CD2     SING  Y  N  50  
TLO  CD2    HD2     SING  N  N  51  
TLO  CE1    HE1     SING  N  N  52  
TLO  CE2    HE2     SING  N  N  53  
#   #
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
TLO  SMILES            ACDLabs               12.01  "O=P(Oc1ccccc1)(O)OP(=O)(O)OCC3OC(N2C(=O)NC(=O)C(=C2)C)CC3O"  
TLO  SMILES_CANONICAL  CACTVS                3.370  "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)Oc3ccccc3)O2)C(=O)NC1=O"  
TLO  SMILES            CACTVS                3.370  "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)Oc3ccccc3)O2)C(=O)NC1=O"  
TLO  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.0  "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)Oc3ccccc3)O"  
TLO  SMILES            "OpenEye OEToolkits"  1.7.0  "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)Oc3ccccc3)O"  
TLO  InChI             InChI                 1.03   "InChI=1S/C16H20N2O11P2/c1-10-8-18(16(21)17-15(10)20)14-7-12(19)13(27-14)9-26-30(22,23)29-31(24,25)28-11-5-3-2-4-6-11/h2-6,8,12-14,19H,7,9H2,1H3,(H,22,23)(H,24,25)(H,17,20,21)/t12-,13+,14+/m0/s1"  
TLO  InChIKey          InChI                 1.03   BANJVYKYIQPYKP-BFHYXJOUSA-N  
#   #
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
TLO  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine"  
TLO  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.0  "[hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] phenyl hydrogen 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
TLO  "Create component"      2010-10-29  RCSB  
TLO  "Modify aromatic_flag"  2011-06-04  RCSB  
TLO  "Modify descriptor"     2011-06-04  RCSB  
TLO  "Modify synonyms"       2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     TLO
_pdbx_chem_comp_synonyms.name        "thymidine diphosphate phenol"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
