Table 2. Energy Analysis for the 2J0S Model^a.

homology model	ligand	delta energy (kJ/mol)	delta vdW (kJ/mol)	delta Coulomb (kJ/mol)
2j0s	ATP removed	134.44	18.23	99.84
2j0s	ATP redocked	–585.07	–367.68	–220.59

^aATP was removed from the 2J0S homology model and molecular dynamics were run so that the structure would adopt an open conformation. Prime MMGBSA was used to calculate the change in total energy, vDw energy, and Coulombic energy from the initial structure. ATP was then redocked into the model and MD simulations were run to promote domain closure. Prime was then used to calculate the change in energies upon domain closure. This demonstrates the creation of a dynamic eIF4A1 model and that ATP binding causes major energetic transformations to a low energy, stable system.