TDS on property purchase from NRI

Dear Sir/Madam, I have made a sale agreement to NRI (through Power of Attorney) on 15th Jan 2018. I paid Rs. 100000/- as token amount. The Sale agreement was valid for 60 days (i.e. till 16th March 2018). 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 Feb 10th, 2018 but Seller got Lower TDS certificate 197(1), with 1% TDS deduction from AO Income-Tax on 20th March 2018. We both agree to finalize the deal as we planned. Now I need to pay TDS on the agreed total sum (say Rs. 5000000/-). My questions are, 1. Since I paid token amount on 15th Jan, 2018, and lower TDS certificate is only valid from 20 March 2018. 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.