This paper presents a discussion of the interaction energies for selected conformers of chiral l-cysteine and their (1:1) complexes with water at the B3LYP/aug-cc-pVDZ level. From among more than forty calculated 1:1 complexes three groups of complexes were singled out and examined by the B3LYP/aug-cc-pVDZ calculated vibrational circular dichroism (VCD) spectra. On the basis of analysis of the nu(OmicronEta) and nu(NuEta) and beta(OH2) and beta(NH2) ranges, the VCD spectra were found to be sensitive to conformational changes and water arrangement in cysteine complexes, and to be especially useful for discriminating between different chiral forms of intermolecular hydrogen-bonding complexes. In particular, we show that the VCD modes of an achiral water molecule after complex formation acquire significant rotational strengths whose signs change in line with the geometry of the complex. Moreover, for some water arrangements the VCD spectra can be sensitive to water-wagging conformers and, in temperatures low enough, the intensive nu(OmicronEtaWfree) and beta(H2O) VCD bands may be sufficiently separated to be splitted into pair of oppositely directed bands.