In the area of biology and chemistry, at the molecular level, our group is trying to understand the structure-function relationship of macromolecules. There are virtually no areas of biological and biomedical sciences that are unaffected by such advances, and molecular-level understanding of the phenomena involved in the function of biological systems has become a must in modern biological Studies. Proteins and enzymes show different chemical and biological activities towards different drug molecules, ions, ligands, etc. Understanding the proper mechanism of these processes at the molecular level will give one the route to control the activity of these biomacromolecules. We utilize molecular modeling, Molecular Docking, and simulation technologies to investigate the various types of biomolecular systems. Cystathionine beta-synthase (CBS) enzyme utilizes the Homocysteine and produces Cystathionine. Homocystinuria disease causes adverse effects like Scoliosis, Thromboembolism, Severe myopia, etc. in the body, due to mutation of the CBS enzyme. It is unclear what was happen in the protein then so it lost the enzymatic activity. To address this question, we study various mechanisms in the wild and mutant type protein by which the enzyme can restore its activity through the classical molecular dynamics simulation. It helps in understanding domain change and activity of heme with PLP through quantum mechanics. Performing for the classical molecular dynamics simulation we are also involved in force field preparation of protein cofactor Heme and PLP.