Results from today are exciting in a good way - they seem to be confirming that the method is valid. Philip & I had been mystified by a hydrogen bond that both PBD Ligand Explorer and GOLD were showing in the X-ray structure from the original research group. It appears to be linking an ether group in the ligand to the O=C of the residue Asn 51, which is strange because you can't have hydrogen bonds without hydrogen - but we didn't think that either the amide or the ether oxygens would get protonated at pH 6.5. The joy of having two supervisors is that when I showed it to Katherine, she suggested it could be tautomerism - something like keto-enol. I just looked it up and there's such a thing as amide-imidic acid tautomerism. I can't find anything more useful from a quick Google search, but I'll add it to the list of things to look up in the huge 11-volume heterocycle book OF DOOM.
I'm feeling a bit better emotionally today. It took me forever to settle down to work, but I've eventually got quite a bit done. Yay.