The parameters of a classical embedding potential can be derived directly from QM calculations on the individual fragments that make up the environment, as is done in the fragment-based PE method. For solute-solvent systems (e.g., water as solvent), the solvent can usually be easily fragmented into individual solvent molecules, and the embedding parameters (i.e., multipoles and polarizabilities) can then be derived for each water molecule in isolation. However, because of the high computational cost, embedding parameters cannot be directly derived for environments composed of large molecules (e.g., proteins). Hence, a more elaborate fragmentation scheme must be used. One simple and effective approach is the molecular fractionation with conjugate caps (MFCC) method 12 that splits the system into small capped fragments with overlapping atoms and so-called concap fragments created by combining neighboring capping groups (i.e., the overlapping atoms). It was originally designed by Zhang and Zhang 12 for calculating protein-ligand interaction energies but has been extended by Söderhjelm and Ryde 13 for the calculation of localized or distributed properties, such as atom-centered multipoles and polarizabilities. The resulting embedding potentials are highly accurate, as has been shown for proteins, 14 nucleic acids, 15 and lipids. In this work, we present an extension of the MFCC approach used in the fragment-based PE method that preserves and considers the hydrogen bonds (HB) in the fragmentation (denoted MFCC(HB) in this work). While the original MFCC approach 12 did not consider hydrogen bonds in the fragmentation, it was added in a later extension aimed at calculating full protein energies. 17 Vornweg et al. 18 also include hydrogen bonds in their implementation of MFCC, which they combine with a second-order many-body expansion approach. The MFCC(HB) approach is implemented in the PyFraME package. The performance of the model is investigated in terms of electrostatic potentials on several molecular systems of different nature and complexity. The quality of the embedding potentials and the effects on dipole moments, excitation energies, oscillator strengths, and two-photon absorption (TPA) cross-sections are evaluated for different chromophores in water and complex protein environments.