Crystallineorganic compound,2-(methacryloyloxy)ethyl-6amino-5-cyano-2-methyl-4-(thiophen-2-yl)-4H-pyran-3-carboxylate (ACMP) was synthesized by one-pot three components reaction. The title compound is characterized by spectral techniques and single-crystal XRD. 2D and 3D Hirshfeld surface analysies were studied to understand the intermolecular contacts. The study revealed that H…H, OÀ H…N, and NÀ H…O are the most significant contributor towards crystal packing with a percentage contribution of 45.1, 13.2 and 16.8 %, respectively. Further, to get more insight into the electronic properties of the molecular structure of ACMP compound, chemical stability and reactivity have been well explored by the frontier molecular orbital (FMO) approach. Despite, the molecular docking study was employed to predict the binding affinity between the ACMP and COVID-19 M pro and spike protease. The analysis showed that the several interactions including H-bond, pi-alkyl and pi-pi interactions with the active sites of amino acid residues of 6LU7 and 2AJF.