You can do it the same way as when you use "Ligand Docking". The question is not very clear.

IFD output only includes the ligand in the whole structure and shows the ligand as a ligand in the Structure Hierarchy field. If your ligand has a peptide bond or if your ligand is very large, your ligand may appear under "protein structure" in rare cases, but this does not usually happen. Then double click on your ligand and the image in the large area will move closer to your ligand. You can measure the distances between two atoms using the "Measure" tool.