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The paper investigates the harmonic interaction between the AC and DC sides of a three-level inverter used as a static synchronous VAr compensator (STATCOM). It is illustrated that due to the third harmonic voltage across each DC side capacitor, the conventional selective harmonic elimination modulation (SHEM) may not actually eliminate the target harmonics when the system is on load. A new modulation method, which dynamically adjusts the switching angles according to the operating point, is proposed to overcome this difficulty. The proposed method is verified using simulation and experimental tests.