I wonder if there is a way to customize hydrogen bond in Avogadro. For example, intermolecular contacts between C-H∙∙∙S and N-H∙∙∙S were found in crystal structure but these interactions are not recognized in Avagadro.

At the moment, Avogadro only recognizes "classical" hydrogen bonds. Certainly if people have other interactions they'd like to classify, I'm open to broader interpretations.

I think in Avogadro 2.x, we're also open to the idea of a "zero-order" bond to classify things like coordination to metal centers, agostic interactions, etc. These would largely be manual assignments, but make it nicer for publication-quality images. :-)

Besides, what is function of "object" available in the configuration option? I tried to click on selected atoms and bonds from the drop down lists but nothing was happen to the molecular structure.

This isn't so useful for the hydrogen bond engine. But it allows you to hide certain atoms or bonds or to assign some atoms and bonds to particular display types but not others.

Hope that helps,