*2.4. Molecular Dynamics (MD) Simulation*

was used to examine the docked poses that resulted.

The optimal receptor–ligand complex pose for SRX and [(SRX)(TCNQ)] with a maximum docking score was acquired through the molecular docking investigation. The GROMACS package version (2019.2) was used to accomplish MD simulation analysis via GROMOS96 43a1 force field. The parameter files and topologies were created with the most recent CGenFF through CHARMM-GUI [31,32]. The SPC water models that prolonged 10 Å from the receptor were utilized to explain receptor–ligand structures [33]. To neutralize the systems, 59 Na<sup>+</sup> and 64 Cl<sup>−</sup> ions (0.15 M salt) were injected to simulate physiological salt concentrations (Figure 2). *2.4. Molecular Dynamics (MD) Simulation*  The optimal receptor–ligand complex pose for SRX and [(SRX)(TCNQ)] with a maximum docking score was acquired through the molecular docking investigation. The GROMACS package version (2019.2) was used to accomplish MD simulation analysis via GROMOS96 43a1 force field. The parameter files and topologies were created with the most recent CGenFF through CHARMM-GUI [31,32]. The SPC water models that prolonged 10 Å from the receptor were utilized to explain receptor–ligand structures [33]. To neutralize the systems, 59 Na<sup>+</sup> and 64 Cl<sup>−</sup> ions (0.15 M salt) were injected to simulate physiological salt concentrations (Figure 2).

**Figure 2.** Receptor–ligand complex (**a**) SRXD and (**b**) CTcD in triclinic box solvated with water molecules and neutralized with 59 Na<sup>+</sup> and 64 Cl<sup>−</sup> ions (0.15 M salt). **Figure 2.** Receptor–ligand complex (**a**) SRXD and (**b**) CTcD in triclinic box solvated with water molecules and neutralized with 59 Na<sup>+</sup> and 64 Cl<sup>−</sup> ions (0.15 M salt).

Both systems were exposed to periodic boundary conditions at a continuous temperature (300 K) and pressure (1.0 bar) for 100 ns simulation time with a Leap-frog MD integrator [34]. To minimize poor contact inside the system, energy reduction with 5000 steps was performed [35]. The gmx hbond device was used to investigate hydrogen bonding. The gyration radius was measured using gmx gyrate tool, while the solvent-accessible surface area was calculated by gmx sasa. The root mean square deviation (RMSD) of the protein was designed using the gmx rms tools. The GROMACS analytic tools [36] were used to accomplish trajectory analysis. Grace Software was used to compute the plots, while PyMol/VMD was utilized to visualize them [37]. Both systems were exposed to periodic boundary conditions at a continuous temperature (300 K) and pressure (1.0 bar) for 100 ns simulation time with a Leap-frog MD integrator [34]. To minimize poor contact inside the system, energy reduction with 5000 steps was performed [35]. The gmx hbond device was used to investigate hydrogen bonding. The gyration radius was measured using gmx gyrate tool, while the solvent-accessible surface area was calculated by gmx sasa. The root mean square deviation (RMSD) of the protein was designed using the gmx rms tools. The GROMACS analytic tools [36] were used to accomplish trajectory analysis. Grace Software was used to compute the plots, while PyMol/VMD was utilized to visualize them [37].
