In this work, we continue our research of the problem concerning the proteins' functioning efficiency. The system under study, a three-dimensional harmonic oscillator, placed in a water "drop" which consists of 264 molecules, simulates the fluctuations of atomic groups in a non-stationary charge pattern field of an active center. The latter results in a break of chemical bonds. Damping time and Q-factor calculations of atomic fluctuations at various frequencies, intensities of interaction with the water environment, and also at various atomic weights are carried out. By means of the argon-like model of water molecules the Q-factor of atomic fluctuations is also estimated. The results obtained are compared with those calculated with the SP3-model.