Fig. 5
(a) [A] RMSD of Cα atoms of the protein backbone atoms. [B] RMSF of each residue of the protein backbone Cα atoms of protein residues ; (C) ROG of each protein residue’s Cα atoms; (D) solvent accessible surface area (SASA) of the Cα atoms relative (black) to the starting minimised over 100 ns for the main protease (Mpro) of SARS-CoV-2 protein with ligand Hexadecanoic acid (red), Kojic acid(green) , Octanoic acid(blue), 4(4Methylbenzylidene) cyclohexane-1,3-dione (Cyn). (b) PCA projection of Cα atom motion constructed by plotting the first two principal components (PC1 and PC2) in conformational space, apo (black ), Hexadecanoic acid (red), Kojic acid(blue) , Octanoic acid(pink), and 4(4-Methylbenzylidene) cyclohexane-1,3-dione (green) , respectively. (c) Dynamic cross-correlation matrix analyses for main protease enzyme Apo (A), Kojic acid(B) Hexadecanoic acid (C), Octanoic acid(D), and 4(4Methylbenzylidene) cyclohexane-1,3-dione (E). Numbers closer to 1 indicate high correlation, while those closer to -1 indicate anticorrelation between pairs of residues. X denoted the binding site region of the main protease of SARS-CoV-2 (Mpro) protein. (d) Conformational free energy landscape for Apo [A], Hexadecanoic acid [B], Kojic acid [C], Octanoic acid [D], 4(4-Methylbenzylidene)cyclohexane-1,3-dione [E] systems. (e) Per-residue decomposition plots showing the energy contributions to the binding and stabilization at the catalytic active site of the main protease of SARS-CoV-2 (Mpro) protein [A] Hexadecanoic acid, [B] Kojic acid,[C] Octanoic acid, [D] 4(4Methylbenzylidene) cyclohexane-1,3-dione.
