Modeling of the photochemical reactions in the multi-molecular systems with a possible energy and charge transfer is a challenging problem that can rise in many fields. For example the light-induced charge transfer in the photosynthetic reaction centers is one (but not the only one) example of such a process. One possible way of such a modeling is the fragment-based treatment on the reference of wavefunctions of the molecules which are parts of the considered system. The non-orthogonal configuration interaction is one of the method for such a modeling. It is able to take into account fragment wavefunctions based on the localized orbitals that form a non-orthogonal set. Also the charge transferred states may be considered with their own orbital set which is not orthogonal to the initial one. The accuracy of the CI can be increased by the means of perturbation theory. The report will show the basic concept of the non-orthogonal CI and the easiest way of its expansion by the perturbation theory. The accuracy of the considered methods is tested on the complexes of small molecules and the results will be present in the report. The possible problems of the application of the considered methods to the large molecular aggregates will be discussed.