We study the energy landscape and thermodynamics of the zwitterionic variant of the widely studied TC5b Trp-cage protein using replica exchange molecular dynamics simulations. We show that the addition of two charge groups at the termini has dramatic consequences to the folding landscape. First, the addition of charged ends increases the equilibration time of the simulation by a factor of 2.5 over a variant with terminal capping. Second, we identify the formation of two long-lived metastable states not present in the capped ends variant structural ensemble. The population of these metastable states is higher at lower temperatures; furthermore, these states are determined to be low energy states, relative to the folded state. The first of the metastable states is a folding intermediate structure which is characterized by a non-native charge pair. The second is characterized by significant β sheet content. We show through potential of mean force (PMF) calculations that the PMF between two charge groups is a poor predictor of the prevalence of a particular ion pair in the unfolded structural ensemble. Finally, by analyzing the energy differences between the folded state, unfolded states, and the metastable states, we show that the stabilization of these metastable states is not only due to favorable Coulomb interactions but also due to strain in the dihedral angles. Our results show that, even for a simple protein, the folding landscape can be extremely complex and significantly altered by simple changes to the charge states of the sequence.