Hi CK,
If you were using a Cloud SQL instance, you could have used a debugging article that covers most of the connection issues related to Cloud SQL instances.
Since your configuration is MySQL(in Windows) + Linux VM, I would also recommend you to refer to Google Cloud Platform's help center article about 'connectivity tests' which helps you to check(diagnose) some basic issues related to network services, inconsistent configuration, etc. To create and run connectivity tests, you could use this help center article.
As this is a forum meant for general discussion of the Google Cloud platform and or its connected resources, I would strongly recommend you to either discuss this concern with the help of your system administrator or should take a question like this to StackOverflow for additional assistance(in-depth technical assistance). While opening a question in stackoverflow.com, make sure to include all relevant details that would help somebody to debug it. An example of one such discussion thread can be found here.