  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$$2\times 10^{49}$ erg by adopting an averaged gas density of
$\sim$$650\pm200$ 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.
