data_FDV
# 
_chem_comp.id                                    FDV 
_chem_comp.name                                  "5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]thymidine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H21 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                        494.222 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     FDV 
_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        6CTJ 
_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 
FDV N1    N1  N 0 1 N N N 54.622 8.446 9.765  5.003  -0.443 0.471  N1    FDV 1  
FDV C2    C1  C 0 1 N N N 55.369 8.867 8.760  5.206  -0.319 -0.853 C2    FDV 2  
FDV O2    O1  O 0 1 N N N 54.840 9.159 7.732  4.635  0.562  -1.467 O2    FDV 3  
FDV N3    N2  N 0 1 N N N 56.690 8.984 8.859  6.034  -1.155 -1.508 N3    FDV 4  
FDV C4    C2  C 0 1 N N N 57.304 8.667 9.991  6.675  -2.136 -0.841 C4    FDV 5  
FDV O4    O2  O 0 1 N N N 58.501 8.769 10.084 7.424  -2.893 -1.433 O4    FDV 6  
FDV C5    C3  C 0 1 N N N 56.567 8.206 11.105 6.469  -2.279 0.552  C5    FDV 7  
FDV C7    C4  C 0 1 N N N 57.238 7.816 12.447 7.173  -3.368 1.320  C7    FDV 8  
FDV C6    C5  C 0 1 N N N 55.184 8.115 10.937 5.634  -1.426 1.183  C6    FDV 9  
FDV PA    P1  P 0 1 N N N 53.285 6.070 14.193 -1.351 1.360  -0.807 PA    FDV 10 
FDV PB    P2  P 0 1 N N N 52.208 3.457 13.540 -4.001 0.063  -0.523 PB    FDV 11 
FDV PG    P3  P 0 1 N N N 52.429 2.095 16.204 -6.373 -1.415 0.501  PG    FDV 12 
FDV "C1'" C6  C 0 1 N N R 53.296 8.342 9.586  4.101  0.486  1.157  "C1'" FDV 13 
FDV O1A   O3  O 0 1 N N N 52.264 6.151 15.263 -1.005 1.091  -2.356 O1A   FDV 14 
FDV O2B   O4  O 0 1 N N N 51.985 2.965 12.114 -4.277 -0.104 -1.968 O2B   FDV 15 
FDV O1G   O5  O 0 1 N N N 51.980 3.472 16.624 -7.012 -1.414 -0.977 O1G   FDV 16 
FDV "C2'" C7  C 0 1 N N N 52.892 6.892 9.190  4.627  1.933  1.036  "C2'" FDV 17 
FDV O2A   O6  O 0 1 N N N 54.674 6.305 14.732 -1.922 2.717  -0.657 O2A   FDV 18 
FDV O1B   O7  O 0 1 N N N 50.918 3.944 14.194 -4.793 1.351  0.029  O1B   FDV 19 
FDV C4B   C8  C 0 1 N N N 54.369 1.928 14.260 -3.947 -1.424 1.781  C4B   FDV 20 
FDV O2G   O8  O 0 1 N N N 53.633 1.690 17.065 -6.862 -2.727 1.296  O2G   FDV 21 
FDV "C3'" C9  C 0 1 N N S 52.580 6.340 10.305 3.348  2.785  0.872  "C3'" FDV 22 
FDV "O3'" O9  O 0 1 N N N 51.745 5.126 10.171 3.224  3.714  1.950  "O3'" FDV 23 
FDV O3A   O10 O 0 1 N N N 53.276 4.675 13.416 -2.420 0.268  -0.299 O3A   FDV 24 
FDV C3B   C10 C 0 1 N N S 52.883 2.011 14.443 -4.555 -1.423 0.377  C3B   FDV 25 
FDV O3G   O11 O 0 1 N N N 51.320 1.066 16.397 -6.813 -0.204 1.230  O3G   FDV 26 
FDV "C4'" C11 C 0 1 N N R 51.789 7.549 11.077 2.201  1.751  0.913  "C4'" FDV 27 
FDV "O4'" O12 O 0 1 N N N 52.470 8.606 10.876 2.811  0.506  0.508  "O4'" FDV 28 
FDV "C5'" C12 C 0 1 N N N 51.678 7.224 12.551 1.093  2.145  -0.066 "C5'" FDV 29 
FDV "O5'" O13 O 0 1 N N N 52.973 7.228 13.142 -0.007 1.243  0.071  "O5'" FDV 30 
FDV H1    H1  H 0 1 N N N 57.222 9.312 8.078  6.169  -1.051 -2.463 H1    FDV 31 
FDV H2    H2  H 0 1 N N N 56.468 7.489 13.161 7.797  -3.947 0.640  H2    FDV 32 
FDV H3    H3  H 0 1 N N N 57.951 6.996 12.276 7.796  -2.921 2.095  H3    FDV 33 
FDV H4    H4  H 0 1 N N N 57.772 8.686 12.857 6.433  -4.023 1.781  H4    FDV 34 
FDV H5    H5  H 0 1 N N N 54.564 7.777 11.754 5.465  -1.519 2.246  H5    FDV 35 
FDV H6    H6  H 0 1 N N N 52.942 9.027 8.801  3.994  0.205  2.205  H6    FDV 36 
FDV H7    H7  H 0 1 N N N 52.688 6.338 16.092 -0.626 0.219  -2.529 H7    FDV 37 
FDV H8    H8  H 0 1 N N N 51.082 3.433 16.932 -6.766 -2.180 -1.512 H8    FDV 38 
FDV H9    H9  H 0 1 N N N 52.032 6.900 8.504  5.164  2.221  1.939  H9    FDV 39 
FDV H10   H10 H 0 1 N N N 53.735 6.367 8.716  5.268  2.035  0.160  H10   FDV 40 
FDV H11   H11 H 0 1 N N N 50.197 3.850 13.582 -4.658 1.522  0.971  H11   FDV 41 
FDV H12   H12 H 0 1 N N N 54.758 1.057 14.807 -2.860 -1.429 1.706  H12   FDV 42 
FDV H13   H13 H 0 1 N N N 54.601 1.823 13.190 -4.271 -0.532 2.318  H13   FDV 43 
FDV H14   H14 H 0 1 N N N 54.838 2.844 14.649 -4.278 -2.312 2.319  H14   FDV 44 
FDV H15   H15 H 0 1 N N N 53.433 0.888 17.533 -7.822 -2.789 1.400  H15   FDV 45 
FDV H16   H16 H 0 1 N N N 53.468 6.098 10.908 3.357  3.307  -0.085 H16   FDV 46 
FDV H17   H17 H 0 1 N N N 51.944 4.525 10.879 3.950  4.349  2.008  H17   FDV 47 
FDV H18   H18 H 0 1 N N N 52.390 1.119 14.028 -4.231 -2.314 -0.160 H18   FDV 48 
FDV H19   H19 H 0 1 N N N 50.778 7.608 10.648 1.801  1.668  1.924  H19   FDV 49 
FDV H20   H20 H 0 1 N N N 51.048 7.978 13.045 0.760  3.160  0.151  H20   FDV 50 
FDV H21   H21 H 0 1 N N N 51.223 6.230 12.673 1.476  2.099  -1.085 H21   FDV 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 
FDV O2    C2    DOUB N N 1  
FDV C2    N3    SING N N 2  
FDV C2    N1    SING N N 3  
FDV N3    C4    SING N N 4  
FDV "C2'" "C1'" SING N N 5  
FDV "C2'" "C3'" SING N N 6  
FDV "C1'" N1    SING N N 7  
FDV "C1'" "O4'" SING N N 8  
FDV N1    C6    SING N N 9  
FDV C4    O4    DOUB N N 10 
FDV C4    C5    SING N N 11 
FDV "O3'" "C3'" SING N N 12 
FDV "C3'" "C4'" SING N N 13 
FDV "O4'" "C4'" SING N N 14 
FDV C6    C5    DOUB N N 15 
FDV "C4'" "C5'" SING N N 16 
FDV C5    C7    SING N N 17 
FDV O2B   PB    DOUB N N 18 
FDV "C5'" "O5'" SING N N 19 
FDV "O5'" PA    SING N N 20 
FDV O3A   PB    SING N N 21 
FDV O3A   PA    SING N N 22 
FDV PB    O1B   SING N N 23 
FDV PB    C3B   SING N N 24 
FDV PA    O2A   DOUB N N 25 
FDV PA    O1A   SING N N 26 
FDV C4B   C3B   SING N N 27 
FDV C3B   PG    SING N N 28 
FDV PG    O3G   DOUB N N 29 
FDV PG    O1G   SING N N 30 
FDV PG    O2G   SING N N 31 
FDV N3    H1    SING N N 32 
FDV C7    H2    SING N N 33 
FDV C7    H3    SING N N 34 
FDV C7    H4    SING N N 35 
FDV C6    H5    SING N N 36 
FDV "C1'" H6    SING N N 37 
FDV O1A   H7    SING N N 38 
FDV O1G   H8    SING N N 39 
FDV "C2'" H9    SING N N 40 
FDV "C2'" H10   SING N N 41 
FDV O1B   H11   SING N N 42 
FDV C4B   H12   SING N N 43 
FDV C4B   H13   SING N N 44 
FDV C4B   H14   SING N N 45 
FDV O2G   H15   SING N N 46 
FDV "C3'" H16   SING N N 47 
FDV "O3'" H17   SING N N 48 
FDV C3B   H18   SING N N 49 
FDV "C4'" H19   SING N N 50 
FDV "C5'" H20   SING N N 51 
FDV "C5'" H21   SING N N 52 
# 
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 
FDV SMILES           ACDLabs              12.01 "N1(C=C(C(NC1=O)=O)C)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(P(=O)(O)O)C)=O"                                                                                                                                      
FDV InChI            InChI                1.03  "InChI=1S/C12H21N2O13P3/c1-6-4-14(12(17)13-11(6)16)10-3-8(15)9(26-10)5-25-30(23,24)27-29(21,22)7(2)28(18,19)20/h4,7-10,15H,3,5H2,1-2H3,(H,21,22)(H,23,24)(H,13,16,17)(H2,18,19,20)/t7-,8-,9+,10+/m0/s1" 
FDV InChIKey         InChI                1.03  UWVKVMOYWXUGRK-AXTSPUMRSA-N                                                                                                                                                                             
FDV SMILES_CANONICAL CACTVS               3.385 "C[C@@H]([P](O)(O)=O)[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)N2C=C(C)C(=O)NC2=O"                                                                                                                  
FDV SMILES           CACTVS               3.385 "C[CH]([P](O)(O)=O)[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH](C[CH]1O)N2C=C(C)C(=O)NC2=O"                                                                                                                        
FDV 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](C)P(=O)(O)O)O)O"                                                                                                                      
FDV SMILES           "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(C(C)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 
FDV "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]thymidine"                                                                                             
FDV "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(1~{S})-1-[[[(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]ethyl]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 
FDV "Create component" 2018-03-26 RCSB 
FDV "Initial release"  2018-06-20 RCSB 
# 
