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If you are doing VPC peering, you can refer to the security group of the peering destination as shown in the following document.
So try to put a setting in the Mongo DB security group to allow the EC2 security group.
https://docs.aws.amazon.com/vpc/latest/peering/vpc-peering-security-groups.html
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Agree.. I have done the exact same before when using VPC peering, you can specifiy a security group from another VPC