We present a multi-scale approach to efficiently embed an ab initio correlated chemical fragment described by its energy-weighted density matrices, and entangled with a wider mean-field many-electron system. This approach, first presented in Phys. Rev. B, 98, 235132 (2018), is here extended to account for realistic long-range interactions and broken symmetry states. The scheme allows for a systematically improvable description in the range of correlated fluctuations out of the fragment into the system, via a self-consistent optimization of a coupled auxiliary mean-field system. It is discussed that the method has rigorous limits equivalent to existing quantum embedding approaches of both dynamical mean-field theory, as well as density matrix embedding theory, to which this method is compared, and the importance of these correlated fluctuations is demonstrated. We derive a self-consistent local energy functional within the scheme, and demonstrate the approach for Hydrogen rings, where quantitative accuracy is achieved despite only a single atom being explicitly treated. arXiv:1904.08019v2 [cond-mat.str-el]