## 3 Results
### Molecular Docking
\begin{table}
\begin{tabular}{c c c c c c} \hline \hline
**Functional Interaction Site** & **Area (SA) Å\({}^{2}\)** & **Volume (SA) Å\({}^{3}\)** & **Interaction Amino Acids** \\ \hline \hline  & & & Met1, Met3, Phe33, Gln36, Glu37, Leu39, Gly40, Lys41, Val43, Ser44, Ser49, Ile51, Phe52, Pr053, Ser54, Ser556, Ser57, Ser58, Thr59, Ser61, Phe62, Arg63, Ser64, Ser74, Thr75, Leu76, Pro77, Val78, Leu79, Thr81, Asn82, Gln85, Thr86, Ser91, Ser139, Ser143, Ile145, Ser146, Met147, Lys148, Arg149, Ser151, Ser152, Thr153, Thr154, Pr0156, Arg157, Phe183, Tyr185, Glu201, Ile204, Lys205, Met207, Ser208, Phe209, Ala210, Ser212, Ala215, Lys230, Glu233, Phe234, Val235, Glu245, Ala246, Ala247, Phe248, Arg250, Val252, Ser253, Arg254, Ser255, Arg256, Gly259, Cys260, Gly261, Ser262, Arg263, Ser264, Phe265, Gly267, Ile269, Glu271, Ile273, Asp279, Thr281, Leu282, Arg283, Val285, Glu286, Arg289, Leu323, Phe324, Met328, Thr330, Ser331, His341, Leu364, and His366.  
\begin{tabular}{c c c c c} \hline \hline
**Protein** & **Ligand** & **Binding Affinity** & **RMSD** & **Amino Acid** & **Number and Types of Bond** & **Bond Length** \\  & **(kcal/mol)** & **RMSD** & **Residues** & **Interaction** & **(A\({}^{\circ}\))** \\ \hline \hline VLP & PGN & \(-10.16\) & 2.3 & Ser150 & 1 Unfavourable donor–donor & 2.38 \\  & & & & Ser152 & 1 Conventional hydrogen bond, 2 & 2.99, 3.50, 3.38 \\  & & & & Ser262 & 1 Conventional hydrogen bond & 2.69 \\  & & & Ser264 & 1 Carbon hydrogen bond & 3.26 \\  & & & Phe265 & 1 Pi Alkyl & 5.41 \\  & & & Arg289 & 2 Unfavourable donor–donor & 2.23, 2.02 \\  & & & Ser331 & 1 Carbon hydrogen bond & 3.71 \\  & \(\beta\)-glucan & \(-7.19\) & 1.45 & Ile145 & 2 Carbon hydrogen bond & 2.51, 2.57 \\  & & & Met147 & 1 Conventional hydrogen bond & 2.03 \\  & & & Ser208 & 3 Carbon hydrogen bond & 2.35, 2.86, 3.48 \\  & & & Ala210 & 1 Carbon hydrogen bond & 3.42 \\  & & & Ser212 & 1 Conventional hydrogen bonds, 1 & 2.36, 3.3 \\  & & & Ser214 & 1 Conventional hydrogen bonds & 2.08 \\  & & & Glu233 & 2 Conventional hydrogen bonds, 1 & 2.00, 2.25, 2.44 \\  & & & Carbon hydrogen bond & 2.00, 2.25, 2.44 \\ \hline \hline \end{tabular}
\end{table} 
Table 3: Functional interaction site prediction of the 3D modeled structure of plant defense VLP of _N. tabacum_, predicted by RoseTTAFold using the CastP 3.0 server. In contrast, the binding affinity of VLP with \(\beta\)-glucan was significantly higher at \(-\)7.19 kcal/mol, with a much lower RMSD of 1.45 A, indicating a more stable and precise docking pose compared with PGN, as shown in Figure 5. An RMSD value of 1.45 A suggests that the interaction with \(\beta\)-glucan is highly stable, reflecting a more optimal docking conformation. The interactions involved Ile145, which formed two carbon-hydrogen bonds (2.51 and 2.57 A), Met147 with one conventional hydrogen bond (2.03 A), and Ser208 with three carbon-hydrogen bonds (2.35, 2.86, and 3.48 A). Additional interactions included Ala210 with one carbon-hydrogen bond (3.42 A), Ser212 with one conventional hydrogen bond and one carbon-hydrogen bond (2.36 and 3.3 A, respectively), Ser214 with one conventional hydrogen bond (2.08 A) and Glu233 with two conventional hydrogen bonds and one carbon-hydrogen bond (2.00, 2.25, and 2.44 A). These results highlight the more robust and diverse binding interactions of VLP with PGN compared with \(\beta\)-glucan, suggesting a potentially higher affinity and specificity of VLP towards fungal PAMPs. Figure 4: Molecular docking interactions of plant defense VLP of _N. tabacum_ with PGN. (**a**) 3D docked complex, 2D ligand interactions are shown by (**b**) MOE (initial docking and interaction profiles, highlighting key binding interactions), (**c**) Discovery Studio (detailed 2D interaction diagrams, showing spatial and interaction), and (**d**) Ligplot (simplified and clear 2D map, emphasizing specific ligand-receptor interactions such as hydrogen bonds and hydrophobic contacts).