Atomic Charge Calculator III: a modern platform for calculating partial atomic charges

Partial atomic charges provide a simplified description of the molecular electrostatic distribution that governs interactions with the surrounding environment. Owing to their widespread use in computational chemistry, chemoinformatics, and bioinformatics, fast and reasonably accurate empirical approaches remain highly relevant. Here, we introduce Atomic Charge Calculator III (ACC III), a web application for computing partial atomic charges for diverse molecular systems, including small organic molecules and proteins. ACC III builds on previous releases and implements 20 widely used empirical charge calculation methods, including the state-of-the-art SQE+qp approach with updated parameters. The platform integrates the modern Mol* viewer for interactive visualization and supports embedding computed charges directly into mmCIF files using a formally defined extension, enabling distribution of results in a community-standard, FAIR structural format. In addition to the web interface, ACC III provides a programmatic API for automated workflows and an enhanced command-line version for local deployment. The service is freely available at https://acc.biodata.ceitec.cz, with no login required, including for commercial use.