Protein-Ligand Free Energy Perturbation on Quantum Hardware
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Quantum Physics arXiv:2604.09857 (quant-ph) [Submitted on 10 Apr 2026] Title:Protein-Ligand Free Energy Perturbation on Quantum Hardware Authors:Zhen Li, Milana Bazayeva, Thaddeus Pellegrini, Mario Motta, Subhamoy Bhowmik, Susanta Das, Danil Kaliakin, Fangchun Liang, Akhil Shajan, Kenneth M.
Merz Jr View a PDF of the paper titled Protein-Ligand Free Energy Perturbation on Quantum Hardware, by Zhen Li and 9 other authors View PDF HTML (experimental) Abstract:The use of free energy perturbation (FEP) methods to study protein-ligand complexes is one of the most important tools in structure-based drug design. Because FEP methods typically rely on force fields, they may suffer from force field parameter-related issues. Herein, we present a quantum mechanics/molecular mechanics (QM/MM) hybrid method to overcome deficiencies in force-field models by using QM bookending approaches on both classical and quantum hardware. In the MM part of this QM/MM FEP method, AMBER is used to simulate the protein receptor and the unperturbed moiety of the ligand, with the ff19SB and GAFF2 force fields. In the QM part, QUICK was used to conduct Hartree-Fock (HF) calculations, followed by heat-bath configuration interaction (HCI) as a benchmark on classical devices. To enable the HCI function in QUICK, we developed a Python-based interface to execute HCI from IBM's qiskit-addon-dice-solver. Moreover, the same interface also enabled this work to execute QM/MM FEP calculations on quantum hardware using the Local Unitary Cluster Jastrow (LUCJ) ansatz, followed by sample-based diagonalization (SQD) and extended-SQD (extSQD) post-processing. Using a series of thermolysis inhibitors as an example, we find reasonable agreement with experiment between the classical HCI method and the LUCJ-SQD/extSQD method, with the latter yielding a result closer to the experimental value. The execution time between the HCI-based FEP method and the LUCJ-SQD/extSQD-based FEP method is also comparable, indicating a high potential for utility in the noisy intermediate-scale quantum (NISQ) era. Subjects: Quantum Physics (quant-ph) Cite as: arXiv:2604.09857 [quant-ph] (or arXiv:2604.09857v1 [quant-ph] for this version) https://doi.org/10.48550/arXiv.2604.09857 Focus to learn more arXiv-issued DOI via DataCite (pending registration) Submission history From: Akhil Shajan [view email] [v1] Fri, 10 Apr 2026 19:37:19 UTC (3,564 KB) Full-text links: Access Paper: View a PDF of the paper titled Protein-Ligand Free Energy Perturbation on Quantum Hardware, by Zhen Li and 9 other authorsView PDFHTML (experimental)TeX Source view license Current browse context: quant-ph new | recent | 2026-04 References & Citations INSPIRE HEP NASA ADSGoogle Scholar Semantic Scholar export BibTeX citation Loading... BibTeX formatted citation × loading... Data provided by: Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Code, Data and Media Associated with this Article alphaXiv Toggle alphaXiv (What is alphaXiv?) Links to Code Toggle CatalyzeX Code Finder for Papers (What is CatalyzeX?) DagsHub Toggle DagsHub (What is DagsHub?) GotitPub Toggle Gotit.pub (What is GotitPub?) Huggingface Toggle Hugging Face (What is Huggingface?) ScienceCast Toggle ScienceCast (What is ScienceCast?) Demos Demos Replicate Toggle Replicate (What is Replicate?) Spaces Toggle Hugging Face Spaces (What is Spaces?) Spaces Toggle TXYZ.AI (What is TXYZ.AI?) Related Papers Recommenders and Search Tools Link to Influence Flower Influence Flower (What are Influence Flowers?) Core recommender toggle CORE Recommender (What is CORE?) Author Venue Institution Topic About arXivLabs arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs. Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)