## 3 Results
### Molecular Dynamic Simulation of TIM-1 and Lumateperone Docked Complex  
Figure 6a shows the main chain deformability of the TIM-1 and Lumateperone docked complex deformed at each of its residues. The location of the chain 'hinges' can be derived from the high deformability regions. The B-factor of the majority of the interacting residues was between 250-300 (Figure 6a). The iMOds finding confirms our docking results in Figure 3. \begin{table}
\begin{tabular}{c c c} \hline
**Receptor-Ligand Interaction** & **Type of Interaction** & **Interacting Residues** \\ \hline \multirow{4}{*}{S-protein–Lumateperone} & Pi-Donar Hydrogen Bond & Asn461 \\  & Pi Sigma & Ala349 \\  & Alkyl & Ilee26,Val353 \\  & Pi-Alkyl & Ala459 \\ \hline \multirow{4}{*}{TIM-1 receptor–Lumateperone} & Van der Waals & Thr241, Ilee246, Asn277, Ser201, Asn276, Asp271 \\  & Conventional Hydrogen Bond & Asn221 \\  & Carbon Hydrogen Bond & Asn275 \\  & Pi-Cation & Arg219 \\  & Pi–PI stacked & Trp274 \\  & Pi–Alkyl Bond & Ala245 \\ \hline \multirow{2}{*}{**Protein–Protein Interaction** **(S-Protein/TIM-1)**} & \multirow{2}{*}{**Type of Interaction**} & \multirow{2}{*}{**Interacting Residues**} \\  & & Lys56, Arg54, Asn461, Asn514, Asn463, Glu359, \\ \hline \multirow{2}{*}{S-protein residues TIM-1 receptor residues} & Hydrogen Bond Interaction & Ser363, Thr367, Val181, Asp632, Lys633, \\  & Thr363, Asp364, Gln278, Asn275, Trp274, \\ \cline{1-1}  & Lys317, Ser303, Ala339, Lys338, Gln336 \\ \hline \end{tabular} Note = Bold residues are residues of S-protein and TIM-1 protein that interact with Lumateperone.  
\end{table} 
Table 2: The interacting residues and bonding in protein–protein and protein–substrate interaction. Figure 3: **(a)** 2D representation of the S-protein/TIM-1 interaction showing the interacting residues of both proteins; the green circle shows the residues of the TIM-1 protein that were interacting with Lumateperone; the red circle shows the residues of the S-protein that were involved in interacting with Lumateperone; **(b)** 2D representation of Lumateperone and S-protein docking, while the red arrow shows the common interacting residue of the S-protein; **(c)** 2D representation of Lumateperone and TIM-1 docking; the green arrow shows the common interacting residues on the TIM-1 protein. Figure 4: S-protein/TIM-1 protein docked complex showing the 900 kJ/mol as the binding energy of the system in the absence of a Lumateperone molecule. Figure 5: (a) S-protein/TIM-1 protein docking complex showing the binding energy of the system in the presence of Lumateperone (Lumateperone is docked with the S-protein); (b) S-protein/TIM-1 protein docking complex showing the binding energy of the system in the presence of Lumateperone (Lumateperone is docked with the TIM-1 protein). Figure 6b shows the motion stiffness of the complex by normal mode linked with the eigenvalue. The motion stiffness value has a direct relation to the energy needed to distort the structure. Deformation is easier with a low eigenvalue. The eigenvalue of our complex was about 1.573330 \(\times\) 10\({}^{-6}\). This means that less energy will be required to deform the structure (as in Figure 6b). Figure 6c shows the covariance matrix, which indicates a connection among pairs of residues, i.e., whether they experience correlated (red), uncorrelated (white), or anti-correlated (blue) motions. From Figure 6c, you can see that most of the residues in the TIM-1 protein and Lumateperone correlated with each other, giving the best coupling matrix. Figure 6d reports the pairs of atoms that are linked by springs described by the elastic network model. Each dot in the graph represents one spring between the corresponding pair of atoms.