Path C - Module 27: Conformational Engineering

Small molecules are flexible. To find the best binding pose, you might need to rotate its internal bonds. In this module, you will learn to change the conformation of the N3 inhibitor by rotating its dihedral angles.

import molsysmt as msm
from molsysmt import systems

# Load the ligand alone
ligand = msm.extract('pdb:6LU7', selection='molecule_type=="small molecule"')
msm.build.add_missing_bonds(ligand)

# Measure all dihedral angles of the ligand
dihedrals = msm.get(ligand, element='bond', dihedral_angle=True)
print(f"Ligand internal dihedrals: {dihedrals}")