Open the receptor/target protein and ligand separately in a single tab of Pymol, then you can visualise the interaction and contacts between the protein and ligand.

there is a simple way.when you use vina for docking , vina saves the best pose of your ligand .when you open that in pymol you can see it in best pose with the best geometry based on binding affinity results. you should open receptor file too and see that the ligand is in the best place after that you can use pymol to see the hydrogen bonds between ligand and receptor with their distances in angestroms.

I have a suggestion. when you opened ligand and receptor simultaneously, save the complex in .pdb format then use that in ligplot+, (it needs javaruntime in windows) when you opened it in ligplot+ you can see all bonds and receptoers neighbour amino acids residues.it have more graphical and more precise result

David Annaraj

AutoDock Vina generates several ligand binding poses and ranks them based on binding energy, with the most favorable (most negative binding energy) listed first. Since you are already using AutoDock Vina via the command line, you can include a command to automatically extract the top-scoring pose into a separate file within a subdirectory of your working directory. I can share the exact command if you would like. After that, you can load the receptor along with the best ligand pose to visualize the complex in PyMOL and generate 2D interaction plot using LigPlot from the complex.