I understand your question now.
I don’t think it’s possible to specify BindingSite constraints via the constraint file; you’d have to write C++ code into FloppyTail to generate the constraint from the coordinates of some “reference state” where the binding was as you wish it to be.
You can use multiple AtomPair constraints to get essentially the same effect. You can also use AmbiguousConstraint or MultiConstraint to combine groups of other constraints to get effects like “this residue needs to hydrogen bond to any of these three partners, but it doesn’t matter which one” or “this quartet of residues has to form this particular geometry”.
I’ve attached an example of a file defining one complex AmbiguousConstraint, since the documentation on it is a little vague. I believe it is compatible with the FloppyTail demo (it was two years ago, but it may have drifted since then).