## 3 Results
### Molecular Docking  
The molecular docking outcomes for the plant defense VLP of _N. tabucum_ with PGN and \(\beta\)-glucan revealed significant differences in binding affinity, RMSD, and interaction profiles (Table 4). The binding affinity of VLP with PGN was \(-10.16\) kcal/mol, with an RMSD of 2.3 A, indicating a slightly higher deviation from the ideal docking pose, as shown in Figure 4. An RMSD value of 2.3 A suggests the binding pose is relatively stable. However, it is not as optimal as lower RMSD values. Key amino acid residues involved in the interaction included Ser152, which formed a conventional hydrogen bond and two carbon-hydrogen bonds with bond lengths of 2.99 A, 3.50 A, and 3.38 A, respectively. Additionally, Ser150 formed an unfavorable donor-donor bond (2.38 A), while Ser262 formed a conventional hydrogen bond (2.69 A). Ser264 and Ser331 each formed a carbon-hydrogen bond, with bond lengths of 3.26 A and 3.71 A, respectively. Last, Phe265 formed a pi-alkyl bond (5.41 A), and Arg289 formed two unfavorable donor-donor bonds (2.23 A and 2.02 A). Figure 3: Comparative validation of 3D structures of plant defense VLP of _N. tabucum_ generated by RoseTTAFold (**left**) and AlphaFold (**right**). The RoseTTAFold model (Z-score: \(-4.79\)) exhibited better structural quality and greater similarity to native X-ray structures than the AlphaFold model (Z-score: \(-3.01\)), indicating a more reliable prediction. \begin{table}
\begin{tabular}{c c 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 Hi Alkyl & 5.41 \\  & & & Arg289 & 2 Unfavourable donor–donor & 2.23, 2.02 \\  & & & Ser331 & 1 Carbon hydrogen bond & 3.71 \\  & & & 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 & 3.00, 2.25, 2.44 \\ \hline \hline \end{tabular}
\end{table} 
Table 4: Systematic examination of molecular docking outcomes involving plant defense VLP of _N. tabacum_ with PGN and \(\beta\)-glucan. Abbreviations: VLP—Vitellogenin-like Protein; PGN—Peptidoglycan; RMSD—Root Mean Square Deviation; Å—Angstrom. \begin{table}
\begin{tabular}{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, Ser55, Ser56, Ser57, Ser58, Thr59, Ser61, Phe62, Arg63, Ser64, Ser74, Thr75, Leu76, Pro77, Val78, Leu79, Thr81, Asn82, Gln85, Thr86, Ser91, Ser139, Ser143, Ile145, Ser146, Met147, Lys418, Lys148, Arg149, Ser150, Lys151, 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, Ser255, Arg254, Ser255, Arg256, Gly259, Cys260, Gly261, Ser262, Arg263, Ser264, Phe265, Gly266, Gly27, Phe269, Glu271, Ile273, Asp279, Thr281, Leu282, Arg283, Val285, Glu286, Arg289, Leu323, Phe324, Met328, Thr330, Ser331, His341, Leu364, and His366.