In the present work we study transmission of electron through vibrat- ing molecular junction interacting with leads using a method of nonequilibrium Green functions. Our Green functions use combination of first quantization to treat vibrational levels and second quantization to treat electron processes. We treat the change of vibrational potential of junction induced by charging of junc- tion, we find a spectral function and a magnitude of current through the junction. We confirm the effect of Fermi sea and Frack-Condon factors on sharpening of peaks. We study these processes on model motivated by biphenyl molecule, in- troducing double well potential and study an effect of quasidegenerate energy levels. We present the shift of peaks, resulting from an increase of moment of inertia, to positions determined by Franck-Condon factors.