Tds on token amount paid to nri while buying property

Dear Sir/Madam,

I have made a sale agreement to NRI (through Power of Attorney) on 13th July 2017. I paid Rs. 100000/- as token amount.  The Sale agreement was valid for 60 days (i.e. till 13th september 2017). Based on above Sale Agreement I applied for Home Loan and Sellar applied for Lower TDS (under section 195/197).

Now my home loan was approved on August 18th, 2017 but Seller got Lower TDS certificate 197(1), with 1% TDS deduction from AO Income-Tax on 25th september 2017. We both agree to finalize the deal as we planned.

Now I need to pay TDS on the agreed total sum (say Rs. 500000/-). My questions are,

1. Since I paid token amount on 13th July, 2017, and lower TDS certificate is only valid from 25 September 2017. How much amount of "TDS on the Token amount"  do I need to pay ? i.e. Should I pay 20.6 % of 100000 = Rs. 20,600 /-  or can I combined all the amount and pay 1% on the total Rs. 500000/- = Rs. 50000/-.

2. Do I need to pay penalty charge as well, if yes how much in both the cases discussed in point -1 above?

Could you please help.