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Quantum chemical calculations at the M06L-GD3/def2-TZVPP level were done to investigate hydrogen bonds between amino acid metal complexes and a free water molecule. Octahedral nickel(II) and square planar palladium(II) complexes of glycine, cysteine, phenylalanine, and serine with different charges of metal complexes (+1, 0, and −1) were investigated. The following hydrogen bonds were considered: NH/O (amino acid is a H-donor), O1/HO (coordinated O1 oxygen from amino acid is a H-acceptor), and O2/HO (non-coordinated O2 oxygen from amino acid is a H-acceptor). Amino acid type has a small influence on interaction energies, both for octahedral nickel(II) and square planar palladium(II) complexes. The influence is the largest for NH/O and the smallest for O2/HO hydrogen bonds. For NH/O interaction, palladium(II) complexes showed stronger hydrogen bonds than nickel(II), up to −11.8 kcal mol−1 for singly positively charged complexes. Nickel(II) complexes demonstrated higher O1/HO hydrogen bond strength than palladium(II) with interaction energies up to −8.9 kcal mol−1 for singly negative complexes. With up to −9.0 kcal mol−1 interaction energy for singly negative complexes, O2/HO interactions were also stronger for nickel(II) complexes than palladium(II). [ABSTRACT FROM AUTHOR]