Protein xyz file

The coordinates of the protein are converted to an xyz file, and the polar hydrogen atoms are manually renamed to D (Recommended but not essential).

LigX estimates interaction energies using element-specific standardized Lennard-Jones and Coulomb parameters. For hydrogen, two parameters are adopted: nonpolar hydrogen H and polar hydrogen D.

To reduce computational cost, it is acceptable to manually remove atoms outside the region where ligands would be in close proximity.