A previous study of diatomic molecules revealed that variational second-order density matrix theory has serious problems in the dissociation limit when the N-representability is imposed at the level of the usual two-index (P,Q,G) or even three-index (T1,T2) conditions [ H. Van Aggelen et al., Phys. Chem. Chem. Phys. 11, 5558 (2009) ]. Heteronuclear molecules tend to dissociate into fractionally charged atoms. In this paper we introduce a general class of N-representability conditions, called subsystem constraints, and show that they cure the dissociation problem at little additional computational cost. As a numerical example the singlet potential energy surface of Be B+ is studied. The extension to polyatomic molecules, where more subsystem choices can be identified, is also discussed.