We establish guaranteed and practically computable a posteriori error bounds for source problems and eigenvalue problems involving linear Schrödinger operators with atom-centered potentials discretized with linear combinations of atomic orbitals. We show that the energy norm of the discretization error can be estimated by the dual energy norm of the residual, that further decomposes into atomic contributions, characterizing the error localized on atoms. Moreover, we show that the practical computation of the dual norms of atomic residuals involves diagonalizing radial Schrödinger operators which can easily be precomputed in practice. We provide numerical illustrations of the performance of such a posteriori analysis on several test cases, showing that the error bounds accurately estimate the error, and that the localized error components allow for optimized adaptive basis sets.