Advogadro2 saves molecule in unrealistic conformation

I believe this to be a bug with Avogadro

Environment Information

Avogadro version: 2
Operating system and version: SDGRID in linux

Expected Behavior

saving molecule in the same conformation that we see in advogadro screen

Actual Behavior

saving molecule in unrealistic conformation.

Steps to Reproduce

design molecule, optimize geometry, save molecule

Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin)

Can you please share the file? I haven’t seen anything like this.

Being a student, seeing such results is quite unusual for me. Can you please share the file?