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Abstract We study spin dynamics and quantum magnetism with ultracold highly-magnetic atoms. In particular, we focus on the interactions among rare-earth atoms localized in a site of an optical-lattice potential, modeled as a cylindrically symmetric harmonic oscillator in the presence of a weak external magnetic field. The interactions between the atoms are modeled using a multi-channel Hamiltonian containing multiple spin–spin and anisotropic spin–orbit interactions with strengths that depend on the separation between the atoms. We studied the eigenenergies of the atom pair in a site for different lattice geometries and magnetic field strengths. In parallel, we compared these energies to those found from a simplified approach, where the complex-collisional physics is replaced by a two-length-scale pseudopotential containing the contact and magnetic dipole–dipole interactions. The eigenenergies of this model can be computed analytically within the Born approximation as well as non-perturbatively for strong contact interactions. We have shown that the pseudopotential model can accurately represent the multi-channel Hamiltonian in certain parameter regimes of the shape of the site of an optical lattice. The pseudopotential forms the starting point for many-body, condensed matter simulations involving many atom pairs in different sites of an optical lattice.