We demonstrate the conversion of an adsorbed precursor state of polychlorinated biphenyl (PCB) molecules on the Si(111)-7 x 7 surface at room temperature into a more stable configuration via site- and energy-selective atomic manipulation in the scanning tunneling microscope (STM). Whereas molecular desorption is maximized by electron injection into the chemisorbed molecular ring at low voltage, injection into the physisorbed molecular ring above a threshold voltage (2.5 V) favors the reconfiguration of the bonding. The results clearly demonstrate both intramolecular charge localization and intramolecular charge transportation as key ingredients in the atomic manipulation of individual polyatomic molecules.