Input files for the simulations performed in the publication "Stability of point defects near MgO grain boundaries in FeCoB/MgO/FeCoB magnetic tunnel junctions". The oxygen point defects were generated by removing oxygen atoms in MgO grain boundary structures from a previous work Bean, J. J., Saito, M., Fukami, S., Sato, H., Ikeda, S., Ohno, H., … McKenna, K. P. (2017). Atomic structure and electronic properties of MgO grain boundaries in tunnelling magnetoresistive devices. Scientific Reports, 7(January), 45594. https://doi.org/10.1038/srep45594. The boron interstitials were generated by randomly guessing a position in the MgO grain boundary supercells, if the boron to be inserted was greater than 1.0 from nearby Mg and O ions it would be inserted. The software package (VASP) was used to perform the DFT calculations and hence results in the paper from these input structures. Input files for all simulations are included however output files could not be included due to their large size. There is an arbitrary naming system used to describe each point defect. Note that the output position files are also given in the form of CONTCAR files thus reoptimisation is not required.