Supermassive black holes (SMBHs) are fundamental keys to understand the formation and evolution of their host galaxies. However, the formation and growth of SMBHs are not yet well understood. One of the proposed formation scenarios is the growth of SMBHs from seed intermediate-mass black holes (IMBHs, 10^2 to 10^5 M_{odot}) formed in star clusters. In this context, and also with respect to the low mass end of the M-sigma relation for galaxies, globular clusters are in a mass range that make them ideal systems to look for IMBHs. Among Galactic star clusters, the massive cluster $omega$ Centauri is a special target due to its central high velocity dispersion and also its multiple stellar populations. We study the central structure and dynamics of the star cluster $omega$ Centauri to examine whether an IMBH is necessary to explain the observed velocity dispersion and surface brightness profiles. We perform direct N-body simulations to follow the dynamical evolution of $omega$ Centauri. The simulations are compared to the most recent data-sets in order to explain the present-day conditions of the cluster and to constrain the initial conditions leading to the observed profiles. We find that starting from isotropic spherical multi-mass King models and within our canonical assumptions, a model with a central IMBH mass of 2% of the cluster stellar mass, i.e. a 5x10^4 M_{odot} IMBH, provides a satisfactory fit to both the observed shallow cusp in surface brightness and the continuous rise towards the center of the radial velocity dispersion profile. In our isotropic spherical models, the predicted proper motion dispersion for the best-fit model is the same as the radial velocity dispersion one. (abridged)