You can have a search for 'mds'  (Molecular dot surface) code, based on M.L Connolly's publication in Science and J. App. Cryst. (1983).

In principle, you can calculate the solvent surface accessible area (the so called sasa) of ligand without protein and in complex with protein, then the difference will give the buried surface of ligand, which can be converted in percentage by dividing with total sasa of ligand.

Or you can try our two algorithms, the "Tangent Sphere Method" and the "Cutting Plane Method" -- please see S. Cheguri and V. M. Reyes here in ResearchGate or in arXiv.org (full text is available).

Thanks for your help!

You could use our software (buried surface area calculator):

http://shityakovlab.uphero.com/hardware-and-software.html

Hello, you could download this software:

https://github.com/nioroso-x3/dr_sasa_n

dr-sasa - Solvent Accessible Surface Area calculation software for biological molecules