Commander left in charge is a pain (5)
I believe the answer is:
colic
'pain' is the definition.
(I know that colic is a type of pain)
'commander left in charge' is the wordplay.
'commander' becomes 'co' (commanding officer).
'left' becomes 'l' (common abbreviation).
'in charge' becomes 'ic' (abbreviation for 'in charge').
'co'+'l'+'ic'='COLIC'
'is a' is the link.
(Other definitions for colic that I've seen before include "Gripe" , "Intestinal pain" , "Gastric pain" , "Abdominal pain spasms" , "Spasmodic abdominal pain" .)