MOVES is designed to model fleet emissions, but the project scale in MOVES allows you to model a single vehicle on a link (road segment). The project scale requires the user to import detailed data, including vehicle population. By importing a vehicle population of one and importing a drive schedule with speeds (velocity) at each second of travel, you can define the entire vehicle behavior (acceleration, deceleration, cruise, and idle) and get emissions output for that one vehicle.
MOVES reports the results as an aggregate over an hour of operation, but you can also get activity (number of vehicles, number of hours, number of miles, etc.), so you can manually determine a rate (mass per vehicle, mass per mile, etc.).