data_FDJ
# 
_chem_comp.id                                    FDJ 
_chem_comp.name                                  "5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H18 Cl 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                        514.641 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     FDJ 
_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        6CTM 
_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 
FDJ C2    C1  C  0 1 N N N 55.206 8.991 8.639  -5.298 -0.409 0.865  C2    FDJ 1  
FDJ C4    C2  C  0 1 N N N 57.151 8.801 9.863  -6.682 -2.289 0.775  C4    FDJ 2  
FDJ C5    C3  C  0 1 N N N 56.438 8.275 10.959 -6.521 -2.326 -0.631 C5    FDJ 3  
FDJ C6    C4  C  0 1 N N N 55.046 8.140 10.788 -5.749 -1.394 -1.229 C6    FDJ 4  
FDJ C7    C5  C  0 1 N N N 57.143 7.846 12.281 -7.202 -3.393 -1.450 C7    FDJ 5  
FDJ O2    O1  O  0 1 N N N 54.679 9.312 7.592  -4.742 0.451  1.521  O2    FDJ 6  
FDJ N1    N1  N  0 1 N N N 54.456 8.499 9.622  -5.137 -0.433 -0.470 N1    FDJ 7  
FDJ N3    N2  N  0 1 N N N 56.505 9.149 8.737  -6.063 -1.326 1.487  N3    FDJ 8  
FDJ O4    O2  O  0 1 N N N 58.359 8.960 9.930  -7.374 -3.120 1.337  O4    FDJ 9  
FDJ PA    P1  P  0 1 N N N 53.190 6.206 14.118 1.171  1.565  0.737  PA    FDJ 10 
FDJ PB    P2  P  0 1 N N N 52.283 3.548 13.479 3.864  0.410  0.287  PB    FDJ 11 
FDJ PG    P3  P  0 1 N N N 52.622 2.378 16.199 6.257  -1.154 -0.543 PG    FDJ 12 
FDJ "C1'" C6  C  0 1 N N R 53.138 8.350 9.431  -4.299 0.579  -1.118 "C1'" FDJ 13 
FDJ O1A   O3  O  0 1 N N N 52.177 6.221 15.218 0.888  1.179  2.274  O1A   FDJ 14 
FDJ O2B   O4  O  0 1 N N N 52.120 2.906 12.117 4.194  0.161  1.709  O2B   FDJ 15 
FDJ O1G   O5  O  0 1 N N N 52.226 3.755 16.633 6.616  -1.426 1.003  O1G   FDJ 16 
FDJ "C2'" C7  C  0 1 N N N 52.779 6.858 9.098  -4.883 1.990  -0.885 "C2'" FDJ 17 
FDJ O2A   O6  O  0 1 N N N 54.581 6.430 14.620 1.679  2.953  0.662  O2A   FDJ 18 
FDJ O1B   O7  O  0 1 N N N 50.950 3.848 14.067 4.582  1.766  -0.200 O1B   FDJ 19 
FDJ CL1   CL1 CL 0 0 N N N 53.441 0.891 13.792 3.648  -2.505 -0.181 CL1   FDJ 20 
FDJ O2G   O8  O  0 1 N N N 53.646 1.829 17.166 6.775  -2.388 -1.439 O2G   FDJ 21 
FDJ "C3'" C8  C  0 1 N N S 52.424 6.339 10.212 -3.637 2.885  -0.702 "C3'" FDJ 22 
FDJ "O3'" O9  O  0 1 N N N 51.533 5.168 10.126 -3.587 3.888  -1.718 "O3'" FDJ 23 
FDJ O3A   O10 O  0 1 N N N 53.186 4.839 13.304 2.269  0.558  0.125  O3A   FDJ 24 
FDJ C3B   C9  C  0 1 N N R 53.314 2.484 14.526 4.451  -0.986 -0.727 C3B   FDJ 25 
FDJ O3G   O11 O  0 1 N N N 51.393 1.485 16.171 6.917  0.093  -0.991 O3G   FDJ 26 
FDJ "C4'" C10 C  0 1 N N R 51.668 7.577 10.954 -2.448 1.909  -0.847 "C4'" FDJ 27 
FDJ "O4'" O12 O  0 1 N N N 52.357 8.626 10.726 -2.991 0.614  -0.508 "O4'" FDJ 28 
FDJ "C5'" C11 C  0 1 N N N 51.559 7.260 12.448 -1.327 2.287  0.123  "C5'" FDJ 29 
FDJ "O5'" O13 O  0 1 N N N 52.856 7.334 13.052 -0.195 1.446  -0.107 "O5'" FDJ 30 
FDJ H1    H1  H  0 1 N N N 54.444 7.747 11.594 -5.615 -1.406 -2.300 H1    FDJ 31 
FDJ H2    H2  H  0 1 N N N 56.393 7.467 12.991 -7.775 -4.046 -0.791 H2    FDJ 32 
FDJ H3    H3  H  0 1 N N N 57.876 7.055 12.065 -7.873 -2.925 -2.170 H3    FDJ 33 
FDJ H4    H4  H  0 1 N N N 57.658 8.713 12.720 -6.451 -3.979 -1.980 H4    FDJ 34 
FDJ H5    H5  H  0 1 N N N 57.018 9.531 7.968  -6.168 -1.294 2.451  H5    FDJ 35 
FDJ H6    H6  H  0 1 N N N 52.755 8.998 8.628  -4.215 0.373  -2.186 H6    FDJ 36 
FDJ H7    H7  H  0 1 N N N 52.613 6.373 16.048 0.553  0.281  2.399  H7    FDJ 37 
FDJ H8    H8  H  0 1 N N N 51.291 3.779 16.799 6.216  -2.228 1.365  H8    FDJ 38 
FDJ H9    H9  H  0 1 N N N 51.954 6.813 8.372  -5.461 2.313  -1.750 H9    FDJ 39 
FDJ H10   H10 H  0 1 N N N 53.655 6.333 8.690  -5.499 2.004  0.015  H10   FDJ 40 
FDJ H11   H11 H  0 1 N N N 50.269 3.574 13.464 4.409  1.992  -1.124 H11   FDJ 41 
FDJ H12   H12 H  0 1 N N N 53.313 1.033 17.563 7.730  -2.536 -1.389 H12   FDJ 42 
FDJ H13   H13 H  0 1 N N N 53.293 6.077 10.834 -3.637 3.342  0.288  H13   FDJ 43 
FDJ H14   H14 H  0 1 N N N 51.329 4.860 11.001 -4.342 4.493  -1.711 H14   FDJ 44 
FDJ H15   H15 H  0 1 N N N 54.318 2.929 14.592 4.208  -0.803 -1.773 H15   FDJ 45 
FDJ H16   H16 H  0 1 N N N 50.653 7.641 10.535 -2.079 1.911  -1.872 H16   FDJ 46 
FDJ H17   H17 H  0 1 N N N 50.889 7.988 12.929 -1.045 3.328  -0.035 H17   FDJ 47 
FDJ H18   H18 H  0 1 N N N 51.152 6.246 12.578 -1.674 2.156  1.148  H18   FDJ 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 
FDJ O2    C2    DOUB N N 1  
FDJ C2    N3    SING N N 2  
FDJ C2    N1    SING N N 3  
FDJ N3    C4    SING N N 4  
FDJ "C2'" "C1'" SING N N 5  
FDJ "C2'" "C3'" SING N N 6  
FDJ "C1'" N1    SING N N 7  
FDJ "C1'" "O4'" SING N N 8  
FDJ N1    C6    SING N N 9  
FDJ C4    O4    DOUB N N 10 
FDJ C4    C5    SING N N 11 
FDJ "O3'" "C3'" SING N N 12 
FDJ "C3'" "C4'" SING N N 13 
FDJ "O4'" "C4'" SING N N 14 
FDJ C6    C5    DOUB N N 15 
FDJ "C4'" "C5'" SING N N 16 
FDJ C5    C7    SING N N 17 
FDJ O2B   PB    DOUB N N 18 
FDJ "C5'" "O5'" SING N N 19 
FDJ "O5'" PA    SING N N 20 
FDJ O3A   PB    SING N N 21 
FDJ O3A   PA    SING N N 22 
FDJ PB    O1B   SING N N 23 
FDJ PB    C3B   SING N N 24 
FDJ CL1   C3B   SING N N 25 
FDJ PA    O2A   DOUB N N 26 
FDJ PA    O1A   SING N N 27 
FDJ C3B   PG    SING N N 28 
FDJ O3G   PG    DOUB N N 29 
FDJ PG    O1G   SING N N 30 
FDJ PG    O2G   SING N N 31 
FDJ C6    H1    SING N N 32 
FDJ C7    H2    SING N N 33 
FDJ C7    H3    SING N N 34 
FDJ C7    H4    SING N N 35 
FDJ N3    H5    SING N N 36 
FDJ "C1'" H6    SING N N 37 
FDJ O1A   H7    SING N N 38 
FDJ O1G   H8    SING N N 39 
FDJ "C2'" H9    SING N N 40 
FDJ "C2'" H10   SING N N 41 
FDJ O1B   H11   SING N N 42 
FDJ O2G   H12   SING N N 43 
FDJ "C3'" H13   SING N N 44 
FDJ "O3'" H14   SING N N 45 
FDJ C3B   H15   SING N N 46 
FDJ "C4'" H16   SING N N 47 
FDJ "C5'" H17   SING N N 48 
FDJ "C5'" 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 
FDJ SMILES           ACDLabs              12.01 "C1(NC(=O)C(C)=CN1C2OC(C(C2)O)COP(=O)(O)OP(O)(C(P(O)(O)=O)Cl)=O)=O"                                                                                                                                      
FDJ InChI            InChI                1.03  "InChI=1S/C11H18ClN2O13P3/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" 
FDJ InChIKey         InChI                1.03  AEQPCMIHLIQHEG-OKJYPTKPSA-N                                                                                                                                                                              
FDJ 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](Cl)[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                 
FDJ SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](Cl)[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                      
FDJ 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](P(=O)(O)O)Cl)O)O"                                                                                                                      
FDJ SMILES           "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(C(P(=O)(O)O)Cl)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 
FDJ "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"                                                                                           
FDJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{R})-chloranyl-[[[(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 
FDJ "Create component" 2018-03-26 RCSB 
FDJ "Initial release"  2018-06-20 RCSB 
# 
