A methodology for the configuration analysis of multi-configurational wave-functions of a closed-shell system is presented. The molecular system is partitioned in interacting fragments, the molecular orbitals are expanded in fragment orbitals and each Slater determinant is expanded in localized reactant electronic structures. Finally, to reduce the number of relevant coefficients, a transformation of orbitals is performed. The main advantage of employing configuration analysis lays in its simplicity and compactness, specially when extended basis sets are used. As a test, the wave-function at the transition state for some nucleophilic substitution reactions is analyzed.