data_FDY
# 
_chem_comp.id                                    FDY 
_chem_comp.name                                  "5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H18 F N2 O13 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-03-26 
_chem_comp.pdbx_modified_date                    2018-06-15 
_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                        498.186 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     FDY 
_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        6CTK 
_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 
FDY C2    C1  C 0 1 N N N 7.769  7.940  9.331  -5.193 -0.414 0.863  C2    FDY 1  
FDY C4    C2  C 0 1 N N N 9.664  7.561  10.658 -6.610 -2.269 0.768  C4    FDY 2  
FDY C5    C3  C 0 1 N N N 8.857  7.032  11.700 -6.450 -2.305 -0.638 C5    FDY 3  
FDY C6    C4  C 0 1 N N N 7.458  6.991  11.452 -5.661 -1.385 -1.233 C6    FDY 4  
FDY O4    O1  O 0 1 N N N 10.856 7.617  10.804 -7.316 -3.089 1.327  O4    FDY 5  
FDY C7    C5  C 0 1 N N N 9.454  6.507  13.036 -7.151 -3.356 -1.460 C7    FDY 6  
FDY N3    N1  N 0 1 N N N 9.079  8.015  9.508  -5.974 -1.319 1.482  N3    FDY 7  
FDY O2    O2  O 0 1 N N N 7.275  8.335  8.267  -4.621 0.433  1.521  O2    FDY 8  
FDY N1    N2  N 0 1 N N N 6.953  7.449  10.288 -5.032 -0.438 -0.472 N1    FDY 9  
FDY "C1'" C6  C 0 1 N N R 5.544  7.351  10.033 -4.177 0.561  -1.118 "C1'" FDY 10 
FDY "C2'" C7  C 0 1 N N N 5.261  6.126  9.669  -4.734 1.982  -0.879 "C2'" FDY 11 
FDY "C3'" C8  C 0 1 N N S 4.625  5.455  10.836 -3.473 2.854  -0.694 "C3'" FDY 12 
FDY "O3'" O3  O 0 1 N N N 3.725  4.392  10.575 -3.406 3.859  -1.707 "O3'" FDY 13 
FDY "O4'" O4  O 0 1 N N N 4.687  7.614  11.351 -2.868 0.571  -0.507 "O4'" FDY 14 
FDY "C4'" C9  C 0 1 N N R 3.903  6.665  11.503 -2.302 1.857  -0.842 "C4'" FDY 15 
FDY "C5'" C10 C 0 1 N N N 3.699  6.367  13.012 -1.174 2.212  0.129  "C5'" FDY 16 
FDY "O5'" O5  O 0 1 N N N 5.073  6.102  13.517 -0.057 1.352  -0.104 "O5'" FDY 17 
FDY PA    P1  P 0 1 N N N 5.287  4.909  14.592 1.311  1.444  0.740  PA    FDY 18 
FDY O1A   O6  O 0 1 N N N 4.302  5.008  15.716 1.021  1.059  2.276  O1A   FDY 19 
FDY O2A   O7  O 0 1 N N N 6.689  5.002  15.102 1.843  2.823  0.669  O2A   FDY 20 
FDY O3A   O8  O 0 1 N N N 5.202  3.506  13.828 2.391  0.420  0.125  O3A   FDY 21 
FDY PB    P2  P 0 1 N N N 3.975  2.592  13.631 3.983  0.242  0.287  PB    FDY 22 
FDY O2B   O9  O 0 1 N N N 3.856  2.264  12.135 4.308  -0.017 1.707  O2B   FDY 23 
FDY O1B   O10 O 0 1 N N N 2.693  3.214  14.139 4.724  1.587  -0.197 O1B   FDY 24 
FDY C3B   C11 C 0 1 N N R 4.369  1.004  14.572 4.544  -1.161 -0.732 C3B   FDY 25 
FDY F2B   F1  F 0 1 N N N 4.040  -0.033 13.801 3.900  -2.330 -0.312 F2B   FDY 26 
FDY PG    P3  P 0 1 N N N 3.499  0.993  16.140 6.347  -1.362 -0.549 PG    FDY 27 
FDY O3G   O11 O 0 1 N N N 2.024  0.707  15.888 7.029  -0.126 -0.993 O3G   FDY 28 
FDY O2G   O12 O 0 1 N N N 4.082  -0.013 17.042 6.701  -1.644 0.996  O2G   FDY 29 
FDY O1G   O13 O 0 1 N N N 3.618  2.374  16.749 6.843  -2.602 -1.448 O1G   FDY 30 
FDY H1    H1  H 0 1 N N N 6.793  6.589  12.202 -5.527 -1.397 -2.305 H1    FDY 31 
FDY H2    H2  H 0 1 N N N 8.642  6.148  13.685 -7.736 -4.001 -0.804 H2    FDY 32 
FDY H3    H3  H 0 1 N N N 10.149 5.680  12.827 -7.813 -2.873 -2.179 H3    FDY 33 
FDY H4    H4  H 0 1 N N N 9.994  7.321  13.541 -6.411 -3.954 -1.992 H4    FDY 34 
FDY H5    H5  H 0 1 N N N 9.650  8.410  8.789  -6.078 -1.288 2.446  H5    FDY 35 
FDY H6    H6  H 0 1 N N N 5.243  8.090  9.276  -4.096 0.357  -2.185 H6    FDY 36 
FDY H7    H7  H 0 1 N N N 4.566  6.137  8.816  -5.307 2.317  -1.744 H7    FDY 37 
FDY H8    H8  H 0 1 N N N 6.182  5.595  9.385  -5.350 2.005  0.020  H8    FDY 38 
FDY H9    H9  H 0 1 N N N 5.415  5.113  11.521 -3.464 3.308  0.297  H9    FDY 39 
FDY H10   H10 H 0 1 N N N 3.872  3.692  11.200 -4.149 4.477  -1.698 H10   FDY 40 
FDY H11   H11 H 0 1 N N N 2.922  6.807  11.026 -1.934 1.854  -1.868 H11   FDY 41 
FDY H12   H12 H 0 1 N N N 3.254  7.233  13.525 -0.873 3.248  -0.026 H12   FDY 42 
FDY H13   H13 H 0 1 N N N 3.054  5.487  13.153 -1.523 2.084  1.153  H13   FDY 43 
FDY H14   H14 H 0 1 N N N 4.768  5.111  16.538 0.670  0.166  2.398  H14   FDY 44 
FDY H15   H15 H 0 1 N N N 2.067  3.278  13.427 4.556  1.819  -1.121 H15   FDY 45 
FDY H16   H16 H 0 1 N N N 5.444  1.046  14.802 4.305  -0.970 -1.778 H16   FDY 46 
FDY H17   H17 H 0 1 N N N 3.415  -0.643 17.287 6.288  -2.441 1.355  H17   FDY 47 
FDY H18   H18 H 0 1 N N N 2.753  2.756  16.840 7.795  -2.767 -1.399 H18   FDY 48 
# 
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 
FDY O2    C2    DOUB N N 1  
FDY C2    N3    SING N N 2  
FDY C2    N1    SING N N 3  
FDY N3    C4    SING N N 4  
FDY "C2'" "C1'" SING N N 5  
FDY "C2'" "C3'" SING N N 6  
FDY "C1'" N1    SING N N 7  
FDY "C1'" "O4'" SING N N 8  
FDY N1    C6    SING N N 9  
FDY "O3'" "C3'" SING N N 10 
FDY C4    O4    DOUB N N 11 
FDY C4    C5    SING N N 12 
FDY "C3'" "C4'" SING N N 13 
FDY "O4'" "C4'" SING N N 14 
FDY C6    C5    DOUB N N 15 
FDY "C4'" "C5'" SING N N 16 
FDY C5    C7    SING N N 17 
FDY O2B   PB    DOUB N N 18 
FDY "C5'" "O5'" SING N N 19 
FDY "O5'" PA    SING N N 20 
FDY PB    O3A   SING N N 21 
FDY PB    O1B   SING N N 22 
FDY PB    C3B   SING N N 23 
FDY F2B   C3B   SING N N 24 
FDY O3A   PA    SING N N 25 
FDY C3B   PG    SING N N 26 
FDY PA    O2A   DOUB N N 27 
FDY PA    O1A   SING N N 28 
FDY O3G   PG    DOUB N N 29 
FDY PG    O1G   SING N N 30 
FDY PG    O2G   SING N N 31 
FDY C6    H1    SING N N 32 
FDY C7    H2    SING N N 33 
FDY C7    H3    SING N N 34 
FDY C7    H4    SING N N 35 
FDY N3    H5    SING N N 36 
FDY "C1'" H6    SING N N 37 
FDY "C2'" H7    SING N N 38 
FDY "C2'" H8    SING N N 39 
FDY "C3'" H9    SING N N 40 
FDY "O3'" H10   SING N N 41 
FDY "C4'" H11   SING N N 42 
FDY "C5'" H12   SING N N 43 
FDY "C5'" H13   SING N N 44 
FDY O1A   H14   SING N N 45 
FDY O1B   H15   SING N N 46 
FDY C3B   H16   SING N N 47 
FDY O2G   H17   SING N N 48 
FDY O1G   H18   SING N N 49 
# 
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 
FDY SMILES           ACDLabs              12.01 "C1(NC(=O)C(C)=CN1C2OC(C(C2)O)COP(=O)(O)OP(O)(C(P(O)(O)=O)F)=O)=O"                                                                                                                                      
FDY InChI            InChI                1.03  "InChI=1S/C11H18FN2O13P3/c1-5-3-14(11(17)13-9(5)16)8-2-6(15)7(26-8)4-25-30(23,24)27-29(21,22)10(12)28(18,19)20/h3,6-8,10,15H,2,4H2,1H3,(H,21,22)(H,23,24)(H,13,16,17)(H2,18,19,20)/t6-,7+,8+,10+/m0/s1" 
FDY InChIKey         InChI                1.03  XUHVKXPQGWCRQM-OKJYPTKPSA-N                                                                                                                                                                             
FDY SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@H](F)[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                 
FDY SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](F)[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                      
FDY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)([C@H](F)P(=O)(O)O)O)O"                                                                                                                       
FDY SMILES           "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(C(F)P(=O)(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 
FDY "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"                                                                                           
FDY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{R})-fluoranyl-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphonic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
FDY "Create component" 2018-03-26 RCSB 
FDY "Initial release"  2018-06-20 RCSB 
# 
