Hi, I used MOE (molecular operating environment) Loop Modeler and generated a missing loop of protein PDB:1RYH in its center based on its sequence. I found the generated loop (green in the pic I attached) is not connected to the protein main chain (white and colorful in the pic I attached) and it has a small gap between the generated loop and the main chain. Except for this, everything looks fine to me.

How do I connect the generated-loop and the main chain?

while

I need to keep the H-bonds in between the ligand GNP and the binding pocket, which means the main chain's binding pocket area cannot be changed (so I guess no structure prep or minimization can be used).