I have a cyclophosphamide molecule and I want to change the bond order on one phosphorus-oxygen bond from single to double. How would I achieve this? I have tried to find the answer myself by playing around with Avogadro, looking through menus trying different tools, etc. Also tried searching this site for “how to change bond order” in the ‘Support’ category and it returned no results.
I was hoping that Avogadro would have a tool to auto-detect bond order. The fact there’s no hydrogen hanging off the oxygen suggests it’s a double bond, so an auto-detect tool would realize that and change the bond order to double.
You can change the bond order in the draw tool and either left click on the bond, or “re-draw” by dragging over the bond to change the order.
In the case of file formats that don’t support bond orders (e.g., PDB, XYZ) Avogadro will perceive bond orders using Open Babel. In your case, you’re using an SDF file, which should have the correct bond orders in the first place - so Open Babel will not re-perceive bond orders.
Incidentally, in Avogadro v2, I’m breaking out “perceive bond connectivity” and “perceive bond orders” into separate commands, to allow perception to be fixed.
