Cosmic rays (CRs) in our galaxy are thought to be generated via diffusive shock acceleration. Gamma-ray observations have revealed that protons and/or electrons are accelerated to energies up to 100 TeV in supernova remnants (SNRs), and hence SNRs are the most plausible source of CR production. Whereas low-energy cosmic rays (LECRs) below the MeV band have important information on the initial acceleration mechanism, there has been very little information on LECRs due to lack of an effective probe. Interacting with neutral iron atoms in the interstellar medium, LECRs produce fluorescent X-ray line emission at 6.40 keV. The 6.40 keV line observation can be a unique probe to investigate LECRs. Analyzing the Suzaku data, we discovered the 6.40 keV line emission from several SNRs interacting with molecular clouds (W28, W44, Kes 67, Kes 69, Kes 78, Kes 79, and 3C391). The 6.40 keV line emission would be produced by MeV protons with the energy density of $>10$ eV cm$^{-3}$. Furthermore, we discovered the 6.40 keV line emission from a giant molecular cloud located near the Galactic center. The energy density of MeV protons is estimated to be 80 eV cm$^{-3}$. The diffusion length of MeV protons is only a few tens of parsecs, and thus the MeV protons should be produced in situ. Surprisingly, there is no SNR in the vicinity. The LECRs would possibly be generated by stochastic acceleration via Alfven turbulence.