The study of the properties of defects in silicon forming under irradiation condition has been carried out for many years, however, many open questions remain. Particularly, there are not comprehensive results for variety of radiation centers calculated at the same level of theory. For example the previously calculated transition levels and formation energies show a large scatter. In this work, we focus on the important radiation-induced defect complexes in Si: double vacancy, vacancy-oxygen, vacancy-phosphorus. Additionally, the phosphorus–vacancy-oxygen complex was studied. Formation energy, charge transition levels and binding energy were calculated from first-principles using the hybrid exchange–correlation functional HSE06. Spin-polarized calculations and large supercells allows us to obtain charge transition levels which agree well with experimental measurements.