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sqlite3 PM_617794.db
DROP TABLE IF EXISTS pdbs;
...
INSERT INTO pdbs VALUES('2oa9','CD','CD', 913,'-','CL','CL', 801,'-',2
+.403);
.mode column pdbs
.width 4 2 2 4 1 2 2 4 1 5

SELECT   *, COUNT(PdbId) as c
FROM     pdbs
GROUP BY PdbId
HAVING   c >= 2
;

1nc7  MG  MG  1501  -  CL  CL  1402  -  2.66   2
2oa9  CD  CD  913   -  CL  CL  801   -  2.403  2

SELECT     pdbs.*
FROM       pdbs JOIN (
...
AND        pdbs.ResName = counter.ResName
WHERE      pdbs.ResName = 'CL'
;

1nc7  MG  MG  1501  -  CL  CL  1401  -  3.065
1nc7  MG  MG  1501  -  CL  CL  1402  -  2.66
2oa9  CD  CD  911   -  CL  CL  800   -  2.291
2oa9  CD  CD  913   -  CL  CL  801   -  2.403