Space-borne missions CoRoT and Kepler have provided a rich harvest of high-quality photometric data for solar-like pulsators. It is now possible to measure damping rates for hundreds of main-sequence and thousands of red-giant. However, among the seismic parameters, mode damping rates remain poorly understood and thus barely used for inferring the physical properties of stars. Previous approaches to model mode damping rates were based on mixing-length theory or a Reynolds-stress approach to model turbulent convection. While able to grasp the main physics of the problem, those approaches are of little help to provide quantitative estimates as well as a definitive answer on the relative contribution of each physical mechanism. Our aim is thus to assess the ability of 3D hydrodynamical simulations to infer the physical mechanisms responsible for damping of solar-like oscillations. To this end, a solar high-spatial resolution and long-duration hydrodynamical 3D simulation computed with the ANTARES code allows probing the coupling between turbulent convection and the normal modes of the simulated box. Indeed, normal modes of the simulation experience realistic driving and damping in the super-adiabatic layers of the simulation. Therefore, investigating the properties of the normal modes in the simulation provides a unique insight into the mode physics. We demonstrate that such an approach provides constraints on the solar damping rates and is able to disentangle the relative contribution related to the perturbation of the turbulent pressure, the gas pressure, the radiative flux, and the convective flux contributions. Finally, we conclude that using the normal modes of a 3D numerical simulation is possible and is potentially able to unveil the respective role of the different physical mechanisms responsible for mode damping provided the time-duration of the simulation is long enough.