> Is it possible to use bond order 0 to store H-bonds?

I think that's more of a question for Open Babel than Avogadro. The answer is 
"maybe." Yes, you can store them, but there's currently no guarantee that all 
of Open Babel is ready to accept bond orders of 0. For example, some code just 
checks for the number of bonds to an atom. This would cause problems with 
"extra" valence.

Hope that helps,
-Geoff
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