Path C - Module 30: Geometrical Measurements

To optimize a drug, you must know exactly how far it is from the key residues of the enzyme. In this module, you will learn to measure the geometric relationship between the N3 inhibitor and the SARS-CoV-2 Mpro active site.

import molsysmt as msm
from molsysmt import systems

# Load the complex
molsys = msm.convert('pdb:6LU7', to_form='molsysmt.MolSys', selection='molecule_type==["protein", "small molecule"]')

# Measure the distance between the inhibitor and the catalytic Cys145
distance = msm.get_distances(molsys, selection='molecule_type=="small molecule"', 
                             selection_2='group_id==145 and atom_name=="SG"')

print(f"Distance to catalytic Cysteine: {distance}")