Abstract
This paper introduce a novel algorithm for rational drug design applying quantum mechanics to optimize target specificity and binding affinity. This algorithm strategically implement Configuration Cloning, substituent replacement and strategic functionalization, Manual Rotor Locking, and Structural Refinement to develop high-affinity, selective inhibitors. The mathematical model supporting this approach is developed using principles of Quantum Mechanics, Molecular Orbital Theory, and Conformational Entropy Minimization. Our results show that this approach
significantly enhances ligand-target interactions through precise electronic and steric modifications.