We present a dynamical spectral model for large-eddy simulation of the incompressible magnetohydrodynamic (MHD) equations based on the eddy damped quasinormal Markovian approximation. This model extends classical spectral large-eddy simulations for the Navier-Stokes equations to incorporate general (non-Kolmogorovian) spectra as well as eddy noise. We derive the model for MHD flows and show that the introduction of an eddy damping time for the dynamics of spectral tensors, in the absence of equipartition between the velocity and magnetic fields, leads to better agreement with direct numerical simulations, an important point for dynamo computations.