In this computational work, the structure of the active center of the enzyme glutathione peroxidase (in three forms -SeH, -SeOH and -Se(O)OH) and the non-covalent interactions in it were investigated using modern quantum chemistry methods. The non-covalent interactions are described in detail. The presence of σ-hole interactions (chalcogen, tetrel and pnictogen bonds) formed mostly by a selenium atom as an electrophile in the glutathione peroxidase active center is confirmed for the first time. It is shown that a number of non-covalent interactions stabilize intermediates along the catalytic cycle and that modelling of the whole enzyme active center is necessary for accurate predictions of thermodynamic parameters, in particular, activation barriers.