CF forget the neutral conductor. It's not needed with a 3-wire transformer primary. We don't even know if the bus duct has a neutral. Unless the OP is feeding other equipment down stream of the ATS, the equipment ground conductor with the feeder to the transformer via the ATS will carry the fault current back to the gen set. With no solid tie to the utility the gen set becomes a SDS.See if this sounds better:
If the plant 480V system is grounded Y and is bonded at the main switchgear, and you use a 3W transfer switch to the gen:
Then the gen neutral needs to be connected to the plant neutral, and the gen frame is connected to the plant grounding system, and no neutral/ground bonding jumper at the gen. For this case the gen is not an SDS.
CF said:Even though not used, the gen neutral must be connected. Otherwise, when running under the gen a ground fault will not get back to the gen neutral and trip a CB.
cf
The equipment ground conductor will acomplish this as well with the system bonding jumper installed.
Rick