Yes. You can easily use a N99Panel VPS to run a MySQL server only. To use it in this way,
- Create a system user
- Create a MySQL DB and a MySQL User Pair
- Grant remote access to the MySQL DB
- Allow access to 3306 port
You can do all the above steps right from within the N99panel console
Ideally a standalone MySQL VPS should be used with another N99panel VPS instance so that they communicate on the private IP range. To setup a private IP, you would need to contact N99panel support team.