SQL error: misuse of aggregate

Short-version fix for this is:

When you're using function like COUNT/SUM, you need to use HAVING instead of WHERE.

When using an aggregate function (sum / count / ... ), you also have to make use of the GROUP BY clause.

Next to that, when you want to filter on the result of an aggregate , you cannot do that in the WHERE clause, but you have to do that in the HAVING clause.

SELECT p1.domain_id, p2.domain_id, COUNT(p1.domain_id) AS d1, COUNT(p2.domain_id) AS d2
    FROM PDB as p1, Interacting_PDBs as i1, PDB as p2, Interacting_PDBs as i2
    WHERE p1.id = i1.PDB_first_id
    AND p2.id = i2.PDB_second_id
    AND i1.id = i2.id
GROUP BY p1.domain_Id, p2.domain_Id
HAVING d1 > 100 AND d2 > 100
ORDER BY d1, d2;