The extremely localized molecular orbitals (ELMOs) are a set of molecular orbitals strictly localized only on a few atoms of a molecule. They are obtained in an a priori fashion through the direct application of the variation principle. Even if the theoretical aspects of their determination have been discussed already in the literature, stable and fast algorithms to obtain ELMOs are still not trivial and a comparison between different methods is reported. We furthermore investigate the applicability of ELMOs to quantum mechanics/molecular mechanics (QM/MM) methods which employ frozen localized orbitals to represent covalent bonds across the QM and the MM region. In addition it is shown that ELMOs can be used to describe species with intramolecular hydrogen bonds, where a correct elimination of the intramolecular basis set superposition error can be essential to perform accurate conformational studies.