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Yes, if you shut down the computer the USB port no longer outputs power to charge anything. If you are using a portable Mac, it should be able to charge a phone with USB port can cable after the computer switches to sleeping mode, or even after you close the clamp shell. So I think most likely a Magic Mouse 2 should be no exception, never tested though. But the charging speed is gonna be very very slow. But if the Mac is in the sleeping mode with shell closed, plugging the USB cable in it all by itself will neither wake up the computer nor the mobile device will be charged.