If you are looking to compare with observed pKa's please use the Full Speciation option(macroconstants).
•Single pKa provides microconstants ONLY.
•The macroconstants are based on N*2(N-1) microconstants where N is the number of ionizable sites.
When you press the Select Atom button you will be presented with the molecule to be used for the calculation. The system will present the SMILES string you entered with the ionizable sites in red. Clicking one of the red atoms will select this atom as the ionizable site and circle it in yellow. Now pressing the Calculate button will show two tabs. The summary tab will show the graphical reaction and give the calculated pKa for that microconstant. The detail tab will show the mechanistic components that give rise to the calculated value.
Click here to watch a tutorial video.