Ligands not part of a thermodynamic cycle on perturbation mapping

[David-Araripe]

While working with Lomap I noticed that some of the ligands in the perturbation mapping weren't part of a thermodynamic cycle, with only one edge connecting them to the rest of the network. I tried using the radial parameter but still observed the same.

Is there a way to force this behavior so that all ligands are part of a thermodynamic cycle?

I also noticed a slight misalignment between some of my ligands (3D coordinates). Could that play a role in the scoring from Lomap since they're obtained from gufe?