I wouldnt send payment yet but do write a letter explaining why you've only been able to do it - inland revenue are actually quite nice.
From Inland Rev website:
What happens if my tax return is late?
If you miss the filing date a penalty will be imposed.
Whatever stage you are at, we can help you get your affairs in order and stop them getting worse.
When are penalties imposed? How much are they?
Fixed penalties for individuals and trustees
Please send your tax return to reach us by 31 January. If we do not receive your return by 1 February we will charge a £100 penalty.
There is a second fixed penalty of another £100 if your tax return is still outstanding six months later. This is usually 31 July, but in the example where the deadline was 14 February, the second penalty would be imposed if the return was not received in the Tax Office by 14 August.
Reduction of fixed penalties
If, when the tax return comes in, the correct amount of tax payable at the due date is less than the fixed penalties, then they will be reduced to the amount of that tax. The correct amount of tax payable does not include any payments on account for the following year.
Daily penalty for individuals and trustees
We can ask the Appeal Commissioners to allow us to impose a daily penalty of up to £60 a day. If we do this within six months of the filing date, then we do not impose the second fixed penalty. We expect to ask for daily penalties only rarely, for example, where we believe that fixed penalties alone will not result in someone sending back his or her return.
Tax-based penalty for individuals and trustees
We can also impose a penalty up to the amount of tax