Ligand structures
The three-dimensional structures of the dATP, and the biologically
active forms of the drugs remdesivir triphosphate
[6,17] and
tenofovir
diphosphate[17], were
extracted from experimental structures containing these ligands in the
PDB. Prior to the docking simulations, these structures were prepared
and subjected to geometry optimization using the Becke-Lee-Yang-Parr
exchange correlation functional and the triple numerical plus
polarization basis set as implemented in the Dmol3 module of Materials
Studio (Dassault Systemes BIOVIA, v20.1.0). In all cases, the charge of
the molecules was -4, corresponding to the fully ionized triphosphate
groups.