We carried out new CO($J$ = 2-1) observations toward the mixed-morphology supernova remnant (SNR) W49B with the Atacama Large Millimeter/submillimeter Array (ALMA). We found that CO clouds at $sim$10 km s$^{-1}$ show a good spatial correspondence with synchrotron radio continuum as well as an X-ray deformed shell. The bulk mass of molecular clouds accounts for the western part of the shell, not for the eastern shell where near-infrared H$_2$ emission is detected. The molecular clouds at $sim$10 km s$^{-1}$ show higher kinetic temperature of $sim$20-60 K, suggesting that modest shock-heating occurred. The expanding motion of the clouds with $Delta V sim$6 km s$^{-1}$ was formed by strong winds from the progenitor system. We argue that the barrel-like structure of Fe rich ejecta was possibly formed not only by an asymmetric explosion, but also by interactions with dense molecular clouds. We also found a negative correlation between the CO intensity and the electron temperature of recombining plasma, implying that the origin of the high-temperature recombining plasma in W49B can be understood as the thermal conduction model. The total energy of accelerated cosmic-ray protons $W_mathrm{p}$ is estimated to be $sim$$2times 10^{49}$ erg by adopting an averaged gas density of $sim$$650pm200$ cm$^{-3}$. The SNR age-$W_mathrm{p}$ diagram indicates that W49B shows one of the highest in-situ values of $W_mathrm{p}$ in the gamma-ray bright SNRs.
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