Charged Systems in Absolute Binding Free Energy Calculations: An Analytical Electrostatic Approach

Abstract

Alchemical free energy perturbation (FEP) is one of the most rigorous methods for predicting protein–ligand binding affinities, yet charged-ligand calculations suffer from finite-size electrostatic artifacts introduced by periodic boundary conditions, which can bias results by several kcal·mol–1. Existing approaches each have limitations: finite-size correction methods rely on approximate dielectric models and Poisson–Boltzmann (PB) calculations, while alchemical co-ion methods introduce alchemically transformed particles, causing spurious interactions and sampling difficulties. Here we present Electrostatic Interaction Decoupling (EID), a postprocessing approach that combines an exact algebraic isolation of the ligand–environment linear electrostatic interaction under the neutral-environment condition with an analytical correction for the residual periodic-boundary offset. By separating the physical ligand–environment interaction from artifact-contaminated terms, EID corrects charge-changing FEP results without PB/continuum-electrostatics calculations or alchemically transformed particles. In benchmarks across four charged protein–ligand systems, EID achieved improved predictive accuracy and more consistent cross-system performance than both comparison methods. Because EID operates as a postprocessing step requiring no additional simulations or PB calculations, it provides a rigorous, immediately deployable solution for charge-changing free energy calculations.