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Hypersonic vehicles generate shocks that can heat the air sufficiently to partially ionize the air and create an electrically conducting plasma that can be studied using the equations of single fluid magnetohydrodynamics (MHD). Introducing strong applied magnetic and electric fields into the flow could have beneficial effects such as reducing heat damage, providing a sort of MHD parachute, and generating electric power or thrust in the vehicle. The Low Diffusion E-CUSP (LDE) scheme with a fifth order WENO scheme has recently been developed by Zha et al. [1, 2]. The purpose of this work is to incorporate the low magnetic Reynolds number MHD model and the thermodynamics of high temperature air to the above CFD algorithm so that it can be used to simulate hypersonic flows with MHD effects. In this work we compare results treating air as chemically frozen, neglecting all high temperature real gas effects with results obtained treating the air as a real gas in thermodynamic equilibrium, whose thermodynamic properties are changed by the high temperature. The hypersonic flows at high altitudes considered in this study have low Reynolds numbers. The Reynolds numbers range from about 2000 to 5000 for Mach 6 flows and reach up to 1200000 for Mach 15 flows. Thus, the flows are treated as laminar for the former cases and as turbulent for the latter using the Baldwin-Lomax turbulence model.