Modeling 3D dynamics is a fundamental problem in multi-body systems across scientific and engineering domains and has important practical implications in object trajectory prediction and simulation. While recent GNN-based approaches have achieved strong performance by enforcing geometric symmetries, encoding high-order features or incorporating neural-ODE mechanics, they typically depend on explicitly observed structures and inherently fail to capture the unobserved interactions that are crucial to complex physical behaviors and dynamics mechanism. In this paper, we propose PAINET, a principled SE(3)-equivariant transformer for learning all-pair interactions in multi-body systems. The model comprises: (1) a novel physics-inspired attention network derived from the minimization trajectory of an energy function, and (2) a parallel decoder that preserves equivariance while enabling efficient inference. Empirical results on diverse real-world benchmarks, including human motion capture, molecular dynamics, and large-scale protein simulations, show that PAINET consistently outperforms recently proposed models, yielding 4.7% to 41.5% error reductions in 3D dynamics prediction with comparable computation costs in terms of time and memory. Our codes, baseline models and datasets are available at https://github.com/Icarus1411/PAINET.