The data set contains: Nuclear repulsion energy: xyz coordinates of CHA and BEA energies given in json file (CHA-NRE.json and BEA-NRE.jon) Structures: xyz coordinates of the DFT optimized structures of either Pd-exchanged zeolite (CHA or BEA) or proton compensating zeolite (also CHA and BEA) xyz coordinates are given for the full QM/MM atom and the QM atoms energy.json: the calculated DFT energy of the optimized structures qm_region: xyz coordinates of the optimized DFT structures at different number of atoms in the QM region data are given for both the full QM/MM atoms and the QM atoms gas_traj: xyz coordinates of the optimized DFT structures of various adsorbates on Pd-exchanged CHA The nomenclature used to tabulate the data is as follow: zeolite name (CHA or BEA) - a number representing structure with a unique Al arrangement - adsorbate name (Pd+2, Pd+H+, Pd+, H+ or H+H+) - a number representing an initial position of the adsorbate - level of theory (GGA or hGGA) - type of calculations (opt for optimization and sp for single point calculation). Note that a different H+H+ reference (with different number of qm atoms) was used for the following CHA: CHA-2, CHA-3, CHA-6 and CHA-9. To reproduce the reaction energies in the paper for the following Pd+2-exchanged CHA, the following values should be used for H+H+ energy (which are the DFT energies using hGGA): CHA-2: -169459.651 CHA-3: -169459.387 CHA-6: -213371.676 CHA-9: -169459.530