Structure based on 4k4i

Ideal structure
Name: [[(2r,5s)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Formula: C8 H13 F N3 O12 P3 S
Weight: 487.186
SMILES: "NC1=NC(=O)N(C=C1F)[CH]2CS[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2"
Spacial conformation based on PDB 4k4i.
Also present on 5c51, 5c52, 5tb9, 5u2t
RESIDUE   1RY     41
CONECT      OAC    2 PAZ  H1  
CONECT      PAZ    4 OAC  OAF  OAG  OAQ 
CONECT      OAF    2 PAZ  H2  
CONECT      OAG    1 PAZ 
CONECT      OAQ    2 PAZ  PBB 
CONECT      PBB    4 OAQ  OAI  OAE  OAR 
CONECT      OAI    2 PBB  H3  
CONECT      OAE    1 PBB 
CONECT      OAR    2 PBB  PBA 
CONECT      PBA    4 OAR  OAH  OAD  OAO 
CONECT      OAH    1 PBA 
CONECT      OAD    2 PBA  H4  
CONECT      OAO    2 PBA  CAL 
CONECT      CAL    4 OAO  CAW  H5   H6  
CONECT      CAW    4 CAL  OAP  SAS  H7  
CONECT      OAP    2 CAW  CAX 
CONECT      SAS    2 CAW  CAM 
CONECT      CAM    4 SAS  CAX  H8   H9  
CONECT      CAX    4 OAP  CAM  NAY  H10 
CONECT      NAY    3 CAX  CAK  CAV 
CONECT      CAK    3 NAY  CAU  H11 
CONECT      CAU    3 CAK  FAJ  CAT 
CONECT      FAJ    1 CAU 
CONECT      CAV    3 NAY  OAB  NAN 
CONECT      OAB    1 CAV 
CONECT      NAN    2 CAV  CAT 
CONECT      CAT    3 CAU  NAN  NAA 
CONECT      NAA    3 CAT  H12  H13 
CONECT      H1     1 OAC 
CONECT      H2     1 OAF 
CONECT      H3     1 OAI 
CONECT      H4     1 OAD 
CONECT      H5     1 CAL 
CONECT      H6     1 CAL 
CONECT      H7     1 CAW 
CONECT      H8     1 CAM 
CONECT      H9     1 CAM 
CONECT      H10    1 CAX 
CONECT      H11    1 CAK 
CONECT      H12    1 NAA 
CONECT      H13    1 NAA 
END   
HET    1RY             41
HETNAM     1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrim
HETNAM   2 1RY idin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phospho
HETNAM   3 1RY ryl] phosphono hydrogen phosphate
FORMUL      1RY    C8 H13 F1 N3 O12 P3 S1

This OCA MONOMER page
uses Jmol, developed by the Jmol Development Team (color reference)
OCA© by Jaime Prilusky, 1996-2004,2006,2010,2014
Bioinformatics Unit
Weizmann Institute of Science