The electronic structure in unconventional superconductors holds a key to understand the momentum-dependent pairing interactions and the resulting superconducting gap function. In superconducting Fe-based chalcogenides, there have been controversial results regarding the importance of the $k_z$ dependence of the electronic dispersion, the gap structure and the pairing mechanisms of iron-based superconductivity. Here, we present a detailed investigation of the van der Waals interaction in FeSe and its interplay with magnetic disorder and real space structural properties. Using density functional theory we show that they need to be taken into account upon investigation of the 3-dimensional effects, including non-trivial topology, of FeSe$_{1-x}$Te$_x$ and FeSe$_{1-x}$S$_x$ systems. In addition, the impact of paramagnetic (PM) disorder is considered within the spin-space average approach. Our calculations show that the PM relaxed structure supports the picture of different competing ordered magnetic states in the nematic regime, yielding magnetic frustration.
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