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Context. The Galactic Center (GC) region has been studied in gamma rays in the past decades - the GC excess detected by Fermi is still not fully understood and the first detection of a PeVatron by H.E.S.S. indicates the existence of sources that can accelerate cosmic rays up to a PeV or higher. Aims. In this paper, we are investigating the origin of the PeVatron emission detected by H.E.S.S. by, for the first time, simulating cosmic rays in the GC in a realistic three-dimensional gas and photon field distribution and large-scale magnetic field. Methods. We solve the 3D transport equation with an anisotropic diffusion tensor using the approach of stochastic differential equations as implemented in the propagation software CRPropa 3.1 (Merten et al. 2017). We test five different source distributions for four different configurations of the diffusion tensor, i.e. with ratios of the perpendicular to parallel components $ε= 0.001,\ 0.01,\ 0.1,\ 0.3$. Results. We find that the two-dimensional distribution of gamma rays as measured by H.E.S.S. is best fit by a model that considers three cosmic-ray sources, i.e. a central source, the SNR G0.9+0.1 and the source HESS J1746-285. The fit indicates that propagation is dominated by parallel diffusion with $ \espilon = 0.001 $. Conclusions. We find that the 3D propagation in the 3D gas and B-field configurations taken from Guenduez et al. (2020) can explain the general features of the data well. We predict that CTA should be able to identify emission from SgrB2 and the six dust ridge clouds that are included in our simulations and that should be detectable with a the expected resolution of CTA of 0.033$^\circ$.