A method for constructing ab initio polarizable intermolecular potentials for flexible molecules within the NEMO scheme is presented. In this scheme the total interaction energy between two molecules is calculated from the properties of the interacting molecules. It is shown that the changes in the charge distribution of a flexible molecule due to conformational changes can be constructed from the interaction of a native charge distribution and a set of distributed polarizabilities. It is further shown that this extension of the model results in a straightforward way to calculate the interaction energy for a given conformation (inter- and intramolecular) of a molecular complex. As a test, we have constructed the intramolecular potential for the 1,2-dimethoxyethane (DME) molecule and the intermolecular potential between a flexible DME molecule and water. The potential obtained is compared to the results from ab initio quantum chemical calculations at the SCF level for the DME-water complex. For the free DME molecule, it is found that a conformation which is anti around all C-C and C-O bonds is favored, whereas inclusion of a water molecule favors anti-gauche-anti and anti-gauche(+)-gauche(-) around the C-O, C-C, and C-O bonds, respectively.