Yes. You can easily use a N99Panel VPS to run a MySQL server only. To use it in this way,

1. Create a system user
2. Create a MySQL DB and a MySQL User Pair
3. Grant remote access to the MySQL DB
4. 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.