EM6351 - Contract Settlements: Letters of Offer: Detail - Interest Clause
The guidance about contract settlements at EM6000+ only relates to direct tax. You must never include VAT or VAT penalties in a contract settlement.
You should ensure the standard clauses providing for interest at the current statutory rate in the event of delay in payment, are included in all draft letters of offer unless there is nothing left to pay.
For instalment cases refer to EMapp1.