Vacancy ACE (VACE) is one of the ACE methods, and has been used to study binding interactions between different biomolecules. Thermodynamic binding constants can be estimated with nonlinear regression methods. With a highly efficient computer simulation program (SimDCCE), it is possible to demonstrate the detailed behaviors of each species during the interaction process under different conditions. In this work, thirteen scenarios in four different combinations of migration orders of the free protein, free drug, and complex formed are studied. The detailed interaction process between protein and ligand is discussed and illustrated based on the mass balance equation, also called mass transfer equation. By properly setting the parameters in the simulation model, the influence of different factors during the interaction process can be well understood.