1) Don't bury the TNT ligand too deeply, this may disrupt the overall protein structure.
2) Avoid using charged residues (ASP, GLU, ARG, LYS, HIS) to make hydrogen bonds when possible (although one or two may be fine).
3) Make sure that the tail of the ligand has a way to get out of the binding site. The tail is the end of the ligand that is directed away from the center of the protein initially. (The linker isn't modeled in, but that tail is connected to more atoms, so make sure it can get out!)
4. It would be desirable if when you move the entire ligand away from the protein and repack, that the side chains which were making the ligand interactions don't move much. A less stringent test would be to just to repack with the ligand still there and make sure that the hydrogen bonding residues don't move away.
5. If you can "back up" residues that interact with the ligand, that would help to "glue" them into place (which is desirable). When I say "back up", I mean you want to be making good hydrogen bonds not only to the ligand, but to the residues which interact with the ligand.
And remember! We log all moves and filter through and all designs you generate, so if you really want to make a useful protein, try to follow these hints as well as try to get a good score!
For testing new strategies it would be helpful to have this puzzle (and others with mutable segments) as a contest template. Thanks !