you have to deduct tds on actual amount payable if total purchase value exceeds 50 Lakh, once you deduct TDS then you have deposit it within 30 days from a month in which TDS deducted i.e. 30 July in your case.
You are suppose to pay 1,00,05,000(including proposed 5000) so TDS liability will be 1,00,050. but you have already paid 1 Cr without deducting TDS so you have to treat as already paid amount is net of TDS and it will be treated as 99%.
You can also club 5000 payment with amount already paid.
Now you have to pay TDS from your own pocket and reduced this amount from next payment to builder.
Total TDS will be 1,01,061(1,00,05,000 is 99%then 100% 1,01,06,061)
Hope it will be help ful
CA Varun Chawla