We address the task of estimating the ground-state energy of Hamiltonians coming from chemistry. We study numerically the behavior of a digital-analog variational quantum eigensolver for the H2, LiH and BeH2 molecules, and we observe that one can estimate the energy to a few percent points of error leveraging on learning the atom register positions with respect to selected features of the molecular Hamiltonian and then an iterative pulse shaping optimization, where each step performs a derandomization energy estimation.