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We present an original multi-state projective diabatization scheme based on the Green's function formalism that allows the systematic mapping of many-body ab initio calculations onto effective excitonic models. This method inherits the ability of the Bethe-Salpeter equation to describe Frenkel molecular excitons and intermolecular charge-transfer states equally well, as well as the possibility for an effective description of environmental effects in a QM/MM framework. The latter is found to be a crucial element in order to obtain accurate model parameters for condensed phases and to ensure their transferability to excitonic models for extended systems. The method is presented through a series of examples illustrating its quality, robustness, and internal consistency.