These data comprise input and output files from first principles molecular dynamics calculations on the soil mineral kaolinite, detailing its interactions with four different veterinary antibiotics, namely enrofloxacin, florfenicol, ciprofloxacin and florfenicol amine. The dataset includes the final, complete molecular dynamics trajectories of the sorption process of each antibiotic on the mineral surfaces (Al-terminated or Si-terminated). The data were collected as part of the NERC Exploring the Frontiers grant (Grant No. NE/X009572/1), ‘Antibiotic chemistry in agricultural soils: modelling mineral-antibiotic interactions from first principles’. The work fits within the broad field of ‘emerging contaminants’ in the environment, and understanding drivers of antimicrobial resistance (AMR). Full details about this nonGeographicDataset can be found at https://doi.org/10.5285/ce86e353-5068-48a6-99bc-4898201d6e6b