How does X-Seed decide what constitutes a hydrogen bond?
A. X-Seed generates hydrogen bonds using very simple criteria that you can customize according to your personal preference (see the “Program Settings” dialog). Only atoms in the “Valid Donor/Acceptor Elements” list are considered. A hydrogen bond is taken to be any contact between two such atoms that are closer than (vD + vA + n) to one another, where vD and vA are the van der Waals radii of the donor and acceptor atoms respectively and n is a tolerance value that you can specify. When you install X-Seed, n is set to zero by default and the “Valid Donor/Acceptor Elements” list contains N, O, F, Cl, Br, I and H. Upon request, X-Seed will thus generate hydrogen bonds between these atoms if they are closer together than the sum of their van der Waals radii. I have found that if H is in the donor/acceptor list and n = -0.5, you will get more sensible hydrogen bonds – i.e. H-bonds will involve the hydrogen atoms. Note that it is your responsibility to inspect the hydrogen bonds in order to
