Ligplot is a software to display detailed protein-ligand interactions from 3-dimensional space to 2-dimensional scheme diagram. It generates useful information for data analyses and publication.
Now, LigPlot has been evolved to LigPlot+ (LigPlot Plus) and I am showing some examples generated by LigPlot+ v2.2 installed on my MacBook Pro.
First, obtain LigPlot+ from its office website. You need Java SE Runtime environment (JRE) to run LigPlot+.
SARS-CoV2 RNA-dependent RNA polymerase (RdRp) complexed with Remdesivir (PDB id: 7BV2) is used at here for demonstration. The program indicates this PDB file has 3 protein chains, 2 DNA/RNA chains, 2 ligands, 5 metal ions and 5 water molecules. One can choose the desired protein (or DNA/RNA)-ligands/water/ion pair to draw the schematic interactions.
I found LigPlot+ also provide scripts to display this annotated protein-ligand interactions in several molecular viewers, such as PyMOL and RasMOL. Here is a snapshot I output the RdRp-Remdesivir interactions in PyMOL. It is very helpful to generate some interaction schemes with depths or for readers to visualized the distances between ligand (center) and residues.