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Modern high-performance computing system design is becoming increasingly aware of the energy proportional computing to lower the operational costs and raise reliability. At the same time, high-performance application developers are taking pro-active steps towards less energy consumption without a significant performance loss. One way to accomplish this is to change the processor frequency dynamically during application execution. In this paper, a representative computationally-intensive HPC application GAMESS is considered with the aim to investigate the energy saving potential of its various stages. GAMESS is a quantum chemistry software package used worldwide to perform ab initio electronic structure calculations. This paper presents energy consumption characteristics of two Self-Consistent Field method implementations in GAMESS, which radically differ in their computer resource usages. The dynamic frequency scaling optimization is applied to these implementations and serves as verification for the proposed general energy savings model. The developed model provides the minimum of on the compute node energy consumption under a given performance loss tolerance for various processor frequencies.