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Existing approaches each have limitations: finite-size correction methods rely on approximate dielectric models and Poisson\u2013Boltzmann (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\u2013environment linear electrostatic interaction under the neutral-environment condition with an analytical correction for the residual periodic-boundary offset. By separating the physical ligand\u2013environment 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\u2013ligand 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.<\/jats:p>","DOI":"10.1021\/acs.jctc.6c00930","type":"journal-article","created":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T14:04:10Z","timestamp":1785852250000},"page":"7981-7992","source":"Crossref","is-referenced-by-count":1,"title":["Charged Systems\nin Absolute Binding Free Energy Calculations:\nAn Analytical Electrostatic Approach"],"prefix":"10.1021","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8446-0404","authenticated-orcid":true,"given":"Runduo","family":"Liu","sequence":"first","affiliation":[{"name":"Sun Yat-sen University , , ,","place":["Guangzhou, P. R. 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China, 572000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0024-9530","authenticated-orcid":true,"given":"Chuanfei","family":"Jin","sequence":"additional","affiliation":[{"name":"Sunshine Lake Pharma Co. Ltd. , ,","place":["Dongguan, P. R. China, 523871"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gefei","family":"Hao","sequence":"additional","affiliation":[{"name":"Guizhou University , , ,","place":["Guiyang, P. R. China, 550025"]},{"name":"Central China Normal University , , ,","place":["Wuhan, P. R. China, 430079"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9357-6839","authenticated-orcid":true,"given":"Zhe","family":"Li","sequence":"additional","affiliation":[{"name":"Sun Yat-sen University , , ,","place":["Guangzhou, P. R. 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Chem."},{"issue":"2","key":"2026081111095093500_cit29","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1021\/ct100578z","article-title":"PROPKA3: Consistent Treatment of\nInternal and Surface\nResidues in Empirical pKa Predictions","volume":"7","author":"Olsson","year":"2011","journal-title":"J. Chem.\nTheory Comput."},{"issue":"12","key":"2026081111095093500_cit30","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1007\/s10822-007-9133-z","article-title":"Epik: A Software Program for pKaprediction\nand Protonation State Generation for Drug-like Molecules","volume":"21","author":"Shelley","year":"2007","journal-title":"J. Comput. Aided Mol. Des"},{"issue":"9","key":"2026081111095093500_cit31","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1002\/jcc.20035","article-title":"Development\nand Testing of a General Amber Force Field","volume":"25","author":"Wang","year":"2004","journal-title":"J. Comput. 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Phys."},{"issue":"2","key":"2026081111095093500_cit36","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1002\/prot.20304","article-title":"A Molecular\nDynamics Study of the Structural Stability of HIV-1 Protease under\nPhysiological Conditions: The Role of Na+ Ions in Stabilizing the\nActive Site","volume":"58","author":"Kovalskyy","year":"2005","journal-title":"Proteins"},{"issue":"10","key":"2026081111095093500_cit37","doi-asserted-by":"publisher","first-page":"2352","DOI":"10.1016\/j.bpj.2018.02.042","article-title":"Open-Boundary\nMolecular Dynamics of a DNA Molecule in a Hybrid Explicit\/Implicit\nSalt Solution","volume":"114","author":"Zavadlav","year":"2018","journal-title":"Biophys. 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Model."},{"issue":"1","key":"2026081111095093500_cit41","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1021\/acs.jpclett.4c02656","article-title":"RED-E-Function-Based\nEquilibrium Parameter Finder: Finding the Best Restraint Parameters\nin Absolute Binding Free Energy Calculations","volume":"16","author":"Huang","year":"2025","journal-title":"J. Phys. Chem. Lett."},{"issue":"10","key":"2026081111095093500_cit42","doi-asserted-by":"publisher","first-page":"3637","DOI":"10.1021\/ct3000876","article-title":"Efficient\nAlgorithms for Langevin and DPD Dynamics","volume":"8","author":"Goga","year":"2012","journal-title":"J.\nChem. Theory Comput."},{"issue":"1\u20133","key":"2026081111095093500_cit43","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1016\/0010-4655(95)00059-O","article-title":"Isothermal-Isobaric\nMolecular Dynamics Simulations\nwith Monte Carlo Volume Sampling","volume":"91","author":"Chow","year":"1995","journal-title":"Comput. Phys.\nCommun."},{"issue":"12","key":"2026081111095093500_cit44","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle Mesh Ewald:\nAn N\u00b7log(N)\nMethod for Ewald Sums in Large Systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem.\nPhys."},{"issue":"2","key":"2026081111095093500_cit45","doi-asserted-by":"publisher","first-page":"434","DOI":"10.1021\/ct900463w","article-title":"Constant Constraint Matrix Approximation: A Robust,\nParallelizable Constraint Method for Molecular Simulations","volume":"6","author":"Eastman","year":"2010","journal-title":"J. Chem. Theory Comput."},{"issue":"1","key":"2026081111095093500_cit46","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1021\/acs.jctc.4c01389","article-title":"Equilibrium\nand Nonequilibrium Ensemble Methods for\nAccurate, Precise and Reproducible Absolute Binding Free Energy Calculations","volume":"21","author":"Bhati","year":"2025","journal-title":"J. Chem. Theory Comput."},{"issue":"4","key":"2026081111095093500_cit47","doi-asserted-by":"publisher","first-page":"1799","DOI":"10.1021\/acs.jctc.5b00784","article-title":"A Simple\nMethod for Automated Equilibration Detection in Molecular Simulations","volume":"12","author":"Chodera","year":"2016","journal-title":"J. Chem. Theory Comput."}],"container-title":["Journal of Chemical Theory\nand Computation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jctc.6c00930","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jctcce\/article-pdf\/22\/15\/7981\/66350275\/acs.jctc.6c00930.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jctcce\/article-pdf\/22\/15\/7981\/66350275\/acs.jctc.6c00930.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T15:43:29Z","timestamp":1786463009000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jctcce\/article\/22\/15\/7981\/5238065\/Charged-Systems-in-Absolute-Binding-Free-Energy"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,31]]},"references-count":47,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2026,7,31]]},"published-print":{"date-parts":[[2026,8,11]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jctc.6c00930","relation":{},"ISSN":["1549-9618","1549-9626"],"issn-type":[{"value":"1549-9618","type":"print"},{"value":"1549-9626","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,31]]}}}