Ignoring losses, the chemical energy in the cell went into the light emitted by the LED.
The conversion to electricity was not 100% efficient, so some energy went into heating the cell. The transmission of electricity was not 100% efficient, so some energy went into heating the wires. The conversion of electricity was not 100% efficient, so some energy went into heating the LED.
Some of the light emitted by the LED impacted on your retina where it caused chemical changes in your photoreceptors. Some of the light emitted by the LED caused other chemical changes when it hit the wall, the floor, the ceiling or your skin. (Perhaps you have a new melanoma). Some of the light emitted by the LED was reflected and was then absorbed by other surfaces. Most of the light absorbed on those surfaces went into heat. Some of the light emitted by the LED might have made it out through an open window and into the night sky where it may be whizzing past Neptune and Pluto now.
Some of the heat that was deposited in various places would have been re-radiated in the infrared. Some would have been conducted to other objects. Some would have heated up the air and convected away.
These effects seem minor and are easily ignored unless you are looking closely. But they add up to exactly match the chemical energy that was originally expended. Rest assured that the books balance. Energy is conserved.