We give a survey on the application of the chemical fragmentation concept in computer modelling of extended covalent systems. It will be stressed that information on molecular topology, as well as location and composition of the reaction centre allows the construction of a reasonable initial guess for the wave function and thus facilitates the solution of the Schrödinger equation. For systems, where the chemical changes are localised to a few atoms, while others play the role of essentially electrostatic perturbation, a partition into active site and environment is possible providing a background to hybrid quantum mechanical/molecular mechanical (QM/MM) methods. Full molecular orbital treatment of large covalent systems at the minimal basis, semiempirical level becomes possible in the frame of the fragment self-consistent field (FSCF) method which was developed in the past two decades in our laboratory. As an application, we discuss the hydride shift reaction step in xylose isomerase catalysis.