Try this, it is milliseconds!
(Finer granularity that milliseconds in node-RED is not really practical, because of delays in the way which the system runs node-RED)
[{"id":"b39ddfe2f43f3986","type":"inject","z":"b3b413d1.05b1b","name":"","props":[{"p":"payload"}],"repeat":"","crontab":"","once":false,"onceDelay":0.1,"topic":"","payload":"2021-09-24T16:01:14.979695752Z","payloadType":"str","x":170,"y":1540,"wires":[["d3de07c8de8a5263"]]},{"id":"7918130156c85d93","type":"debug","z":"b3b413d1.05b1b","name":"","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"false","statusVal":"","statusType":"auto","x":500,"y":1540,"wires":[]},{"id":"d3de07c8de8a5263","type":"change","z":"b3b413d1.05b1b","name":"","rules":[{"t":"set","p":"payload","pt":"msg","to":"$moment(payload).format('YYYY-MM-DD HH:mm:ss.SSS')","tot":"jsonata"}],"action":"","property":"","from":"","to":"","reg":false,"x":330,"y":1540,"wires":[["7918130156c85d93"]]}]
The input is "2021-09-24T16:01:14.979695752Z"
The output is "2021-09-24 17:01:14.979"
Or if you want it to create the output based upon current time/date, try;
[{"id":"32ca630295eac4aa","type":"inject","z":"b3b413d1.05b1b","name":"","props":[{"p":"payload"}],"repeat":"","crontab":"","once":false,"onceDelay":0.1,"topic":"","payloadType":"str","x":165,"y":1625,"wires":[["980aa508d76b5348"]]},{"id":"ee4f62696d2a6f79","type":"debug","z":"b3b413d1.05b1b","name":"","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"false","statusVal":"","statusType":"auto","x":495,"y":1625,"wires":[]},{"id":"980aa508d76b5348","type":"change","z":"b3b413d1.05b1b","name":"","rules":[{"t":"set","p":"payload","pt":"msg","to":"$moment($now()).format('YYYY-MM-DD HH:mm:ss.SSS')","tot":"jsonata"}],"action":"","property":"","from":"","to":"","reg":false,"x":325,"y":1625,"wires":[["ee4f62696d2a6f79"]]}]