## 3 Results and Discussion
### Molecular Dynamics Simulation Analysis  
Figure 6 shows the root-mean-square deviation (RMSD) for the three studied complexes (Figure 6A) and for every ligand (Figure 6B). For all the systems, the RMSD reached a stable point after 75 ns, however, amongst the three curves; the one corresponding to MAY presented the highest variations, showing even a slight tendency to increase with time, (red curve in Figure 6A). This could be understood by observing the RMSD calculated only for the atoms of the MAY structure (red curve, Figure 6B). The time evolution of the RMSD suggests that MAY has not found a stable point inside the active site pocket of the protein; probably, the MAY molecule is \"trying to leave\" the hydrophilic zone. Figure 6 also shows that the NtMGAM-ACA complex achieved a more stable conformation (black curve) earlier. After 25 ns, the RMSD corresponding to the ACA ligand oscillates around a constant value (\(\sim\)0.3 nm). Hence, it could be assumed that ACA bonding to the protein is stronger than the MAY interaction. In the case of the NtMGAM-LUT complex, the RMSD curve (blue in Figure 6B) showed that the ligand is oscillating between two different binding conformations inside the active site pocket. The fact that the RMSD value of LUT is smaller (\(\sim\)0.2 nm) than the one corresponding to ACA, could be related to the geometry of Luteolin, because this molecule presents fewer torsion angles in the structure, while the acarbose exhibits a non-planar geometry with several dihedral angles. So, from the RMSD analysis, the order in stability for the studied complexes is ACA > LUT > MAY. \begin{table}
\begin{tabular}{c c c c c} \hline \hline
**Ligand** & **Active Site** & \(\eta\) & \(\mu\) & \(\Delta\)**N** \\ \hline \multirow{8}{*}{ACA} & Asp203 & 2.90 & \(-\)2.78 & 0.033 \\  & Thr205 & 2.36 & \(-\)3.11 & 0.006 \\  & Tyr299 & 2.67 & \(-\)3.61 & \(-\)0.039 \\  & Asp327 & 2.71 & \(-\)2.81 & 0.032 \\  & Asp443-Met444 & 2.85 & \(-\)2.85 & 0.027 \\  & Arg526 & 3.43 & \(-\)3.82 & \(-\)0.051 \\  & Trp539 & 2.58 & \(-\)3.19 & \(-\)0.002 \\  & Asp542 & 2.71 & \(-\)2.99 & 0.016 \\  & Thr544 & 3.27 & \(-\)3.81 & \(-\)0.051 \\  & Phe575-Ala576 & 2.89 & \(-\)3.50 & \(-\)0.028 \\  & His600 & 2.90 & \(-\)3.60 & \(-\)0.037 \\ \hline \multirow{8}{*}{MAY} & Arg202-Asp203 & 2.51 & \(-\)3.43 & 0.067 \\  & Thr204-Thr205 & 2.33 & \(-\)3.24 & 0.090 \\  & Tyr299 & 2.67 & \(-\)3.61 & 0.047 \\  & Asp327 & 2.71 & \(-\)2.81 & 0.127 \\ \(-\)3.85 & Trp406 & 2.56 & \(-\)3.37 & 0.072 \\  & Asp443 & 2.84 & \(-\)2.84 & 0.123 \\  & Lys480 & 2.97 & \(-\)3.63 & 0.042 \\  & Asp542 & 2.71 & \(-\)2.94 & 0.113 \\ \hline \multirow{8}{*}{LUT} & Tyr299 & 2.67 & \(-\)3.61 & 0.047 \\  & Ile364 & 3.33 & \(-\)3.62 & 0.036 \\ \cline{1-1}  & Trp406 & 2.56 & \(-\)3.37 & 0.068 \\ \cline{1-1}  & Asp443 & 2.77 & \(-\)2.74 & 0.127 \\ \cline{1-1}  & Ser448 & 3.31 & \(-\)3.96 & 0.006 \\ \cline{1-1}  & Arg526 & 3.43 & \(-\)3.82 & 0.018 \\ \cline{1-1}  & Phe575 & 2.91 & \(-\)3.70 & 0.032 \\ \cline{1-1}  & Gln603 & 3.20 & \(-\)3.95 & 0.007 \\ \hline \hline \end{tabular}
\end{table} 
Table 3: Reactivity parameters and charge transfer descriptor calculated for amino acids of the maltase-glucoamylase (NtMGAM) interacting with acarbose (ACA), maysin (MAY), and luteolin (LUT). Chemical hardness (\(\eta\)), chemical potential (\(\mu\)), and charge transfer (\(\Delta\)N). The values of \(\eta\) and \(\mu\) are presented in eV. Now, to understand better the behavior of RMSD values, the interaction between each ligand and the amino acids inside the active site pocket was analyzed. Hydrogen bond occupancies, shown in Table 4, were calculated from the MD trajectories. In the case of ACA, the occupancies were 98.3% and 81.09% with the residues Asp443 and Asp327, respectively, showing that ACA remained close to these residues during almost the whole simulation. Nevertheless, there is evidence of a rearrangement of the complex.