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The planar hexagon graphene nanoflakes can deform their shape to be distorted after the single vacancy site creation. In this work, density functional theory (DFT) calculations are performed massively on a series sizes of graphene flake with all possible single vacancy site to determine its energetic, structural and electronic properties. It is found that the planar original graphene nanoflakes deform after a single vacancy is generated, and the deformation of graphene nanoflakes decreases with the increase of flake diameter. The formation energy of graphene nanoflakes with single vacancy indicates the stability increases with the size graphene nanoflakes increases. The HOMO-LUMO (Highest Occupied Molecular Orbital and Lowest Unoccupied Molecular Orbital) gap values are only highly related to the size of the system and much less related to different migration locations. The calculate the root mean squared deviation (RMSD) is also calculated to quantify the geometric distortion between original atomic structure and the structures after the creation of single vacancy. The results provide insights into better understanding of the relationship between the formation energy and the size, as well as the distortion change as a function of the graphene flake size, and sufficiently perspective into quantifying the uncertainties in these measurements.