This dataset contains the representative 3D atomistic structures of the full-length SARS-CoV-2 Nucleocapsid (N) protein dimer in complex with the host cellular target, the G3BP1 NTF2L domain. The data files include the representative structural conformations for the wild-type (WT) complex, as well as the F17A and D22A mutant variants of the viral N protein. The provided structures were extracted from the dominant metastable basins (local free energy minima) identified on 2-dimensional free energy surfaces. These free energy landscapes were constructed using principal component analysis (PCA) applied to 500 ns all-atom molecular dynamics (MD) simulation trajectories. The MD simulations were performed using GROMACS 2024.4 with the AMBER14SB force field and TIP3P water model, starting from initial configurations modeled via AlphaFold3 and the HADDOCK webserver. The dataset inherently captures the spatial coordinates and atomistic details of the hierarchical binding mechanism, including the primary electrostatic anchor (Asp22) and the secondary hydrophobic interface (Phe17). The coordinate data captures distinct conformational states of the viral-host interface, including the complete allosteric collapse observed in the F17A mutant and the partial interaction network of the D22A mutant. Researchers can reuse these structural files for further atomistic structural evaluation, as validated starting configurations for advanced enhanced-sampling simulations, or for structure-based drug design and virtual screening efforts aimed at identifying novel inhibitors to disrupt the critical SARS-CoV-2 N protein-G3BP1 interaction. All structural data included in this dataset were generated entirely via in silico computational modeling and molecular dynamics simulations. The research does not involve any human or animal subjects. Therefore, there are no ethical or legal restrictions associated with the reuse of this dataset.