Abstract Solar energetic particles (SEPs) can pose hazardous radiation risks to both humans and spacecraft electronics in space. Numerical modeling based on first principles offers valuable insights into the underlying physics of SEPs and provides synthetic observables for SEPs at any time and location in the inner heliosphere. In this work, we present a numerical scheme, which conserves the number of particles based on integral relations for Poisson brackets, to solve the kinetic equation for particle acceleration and transport processes. We implement this scheme within the Space Weather Modeling Framework, developed at the University of Michigan. In addition, we develop a new shock-capturing tool to study the coronal mass ejection-driven shock originating from the low solar corona. These methodological advancements are applied to conduct a comprehensive study of a historical SEP event on 2013 April 11. Observations from multiple spacecraft, including the Solar and Heliospheric Observatory, Solar Dynamics Observatory, Geostationary Operational Environmental Satellite, Advanced Composition Explorer near Earth, and STEREO-A/B, are used for model–data comparison and validation. We show synthetic observables, including extreme ultraviolet and white-light images, proton time–intensity profiles, and energy spectra, and discuss their differences and probable explanations compared to observations. Our simulation results demonstrate the application of the Poisson bracket scheme with a particle solver to simulating a historical SEP event. We also show the capability of extracting the complex shock surface using our shock-capturing tool and understand how the complex shock surface affects the particle acceleration process.