diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index adaf99a..889c597 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -404,9 +404,15 @@
 		if not self.advance_tax_account:
 			frappe.throw(_("Advance TDS account is mandatory for advance TDS deduction"))
 
-		reference_doclist = []
 		net_total = self.paid_amount
-		included_in_paid_amount = 0
+
+		for reference in self.get("references"):
+			net_total_for_tds = 0
+			if reference.reference_doctype == 'Purchase Order':
+				net_total_for_tds += flt(frappe.db.get_value('Purchase Order', reference.reference_name, 'net_total'))
+		
+			if net_total_for_tds:
+				net_total = net_total_for_tds
 
 		# Adding args as purchase invoice to get TDS amount
 		args = frappe._dict({
@@ -423,7 +429,6 @@
 			return
 
 		tax_withholding_details.update({
-			'included_in_paid_amount': included_in_paid_amount,
 			'cost_center': self.cost_center or erpnext.get_default_cost_center(self.company)
 		})
 
@@ -509,18 +514,17 @@
 		self.base_total_allocated_amount = abs(base_total_allocated_amount)
 
 	def set_unallocated_amount(self):
-		self.unallocated_amount = 0
 		if self.party:
 			total_deductions = sum(flt(d.amount) for d in self.get("deductions"))
 			if self.payment_type == "Receive" \
-				and self.base_total_allocated_amount < self.base_received_amount_after_tax + total_deductions \
-				and self.total_allocated_amount < self.paid_amount_after_tax + (total_deductions / self.source_exchange_rate):
-				self.unallocated_amount = (self.received_amount_after_tax + total_deductions -
+				and self.base_total_allocated_amount < self.base_received_amount + total_deductions \
+				and self.total_allocated_amount < self.paid_amount + (total_deductions / self.source_exchange_rate):
+				self.unallocated_amount = (self.received_amount + total_deductions -
 					self.base_total_allocated_amount) / self.source_exchange_rate
 			elif self.payment_type == "Pay" \
-				and self.base_total_allocated_amount < (self.base_paid_amount_after_tax - total_deductions) \
-				and self.total_allocated_amount < self.received_amount_after_tax + (total_deductions / self.target_exchange_rate):
-				self.unallocated_amount = (self.base_paid_amount_after_tax - (total_deductions +
+				and self.base_total_allocated_amount < (self.base_paid_amount - total_deductions) \
+				and self.total_allocated_amount < self.received_amount + (total_deductions / self.target_exchange_rate):
+				self.unallocated_amount = (self.base_paid_amount - (total_deductions +
 					self.base_total_allocated_amount)) / self.target_exchange_rate
 
 	def set_difference_amount(self):
@@ -530,11 +534,11 @@
 		base_party_amount = flt(self.base_total_allocated_amount) + flt(base_unallocated_amount)
 
 		if self.payment_type == "Receive":
-			self.difference_amount = base_party_amount - self.base_received_amount_after_tax
+			self.difference_amount = base_party_amount - self.base_received_amount
 		elif self.payment_type == "Pay":
-			self.difference_amount = self.base_paid_amount_after_tax - base_party_amount
+			self.difference_amount = self.base_paid_amount - base_party_amount
 		else:
-			self.difference_amount = self.base_paid_amount_after_tax - flt(self.base_received_amount_after_tax)
+			self.difference_amount = self.base_paid_amount - flt(self.base_received_amount)
 
 		total_deductions = sum(flt(d.amount) for d in self.get("deductions"))
 
@@ -683,8 +687,8 @@
 					"account": self.paid_from,
 					"account_currency": self.paid_from_account_currency,
 					"against": self.party if self.payment_type=="Pay" else self.paid_to,
-					"credit_in_account_currency": self.paid_amount_after_tax,
-					"credit": self.base_paid_amount_after_tax,
+					"credit_in_account_currency": self.paid_amount,
+					"credit": self.base_paid_amount,
 					"cost_center": self.cost_center
 				}, item=self)
 			)
@@ -694,8 +698,8 @@
 					"account": self.paid_to,
 					"account_currency": self.paid_to_account_currency,
 					"against": self.party if self.payment_type=="Receive" else self.paid_from,
-					"debit_in_account_currency": self.received_amount_after_tax,
-					"debit": self.base_received_amount_after_tax,
+					"debit_in_account_currency": self.received_amount,
+					"debit": self.base_received_amount,
 					"cost_center": self.cost_center
 				}, item=self)
 			)
@@ -708,15 +712,17 @@
 
 			if self.payment_type in ('Pay', 'Internal Transfer'):
 				dr_or_cr = "debit" if d.add_deduct_tax == "Add" else "credit"
+				against = self.party or self.paid_from
 			elif self.payment_type == 'Receive':
 				dr_or_cr = "credit" if d.add_deduct_tax == "Add" else "debit"
+				against = self.party or self.paid_to
 
 			payment_or_advance_account = self.get_party_account_for_taxes()
 
 			gl_entries.append(
 				self.get_gl_dict({
 					"account": d.account_head,
-					"against": self.party if self.payment_type=="Receive" else self.paid_from,
+					"against": against,
 					dr_or_cr: d.base_tax_amount,
 					dr_or_cr + "_in_account_currency": d.base_tax_amount
 					if account_currency==self.company_currency
@@ -728,14 +734,12 @@
 			gl_entries.append(
 				self.get_gl_dict({
 					"account": payment_or_advance_account,
-					"against": self.party if self.payment_type=="Receive" else self.paid_from,
+					"against": against,
 					dr_or_cr: -1 * d.base_tax_amount,
 					dr_or_cr + "_in_account_currency": -1*d.base_tax_amount
 					if account_currency==self.company_currency
 					else d.tax_amount,
 					"cost_center": self.cost_center,
-					"party_type": self.party_type,
-					"party": self.party
 				}, account_currency, item=d))
 
 	def add_deductions_gl_entries(self, gl_entries):
@@ -760,9 +764,9 @@
 		if self.advance_tax_account:
 			return self.advance_tax_account
 		elif self.payment_type == 'Receive':
-			return self.paid_from
-		elif self.payment_type in ('Pay', 'Internal Transfer'):
 			return self.paid_to
+		elif self.payment_type in ('Pay', 'Internal Transfer'):
+			return self.paid_from
 
 	def update_advance_paid(self):
 		if self.payment_type in ("Receive", "Pay") and self.party:
@@ -1634,12 +1638,6 @@
 			if dt == "Employee Advance":
 				paid_amount = received_amount * doc.get('exchange_rate', 1)
 
-	if dt == "Purchase Order" and doc.apply_tds:
-		if party_account_currency == bank.account_currency:
-			paid_amount = received_amount = doc.base_net_total
-		else:
-			paid_amount = received_amount = doc.base_net_total * doc.get('exchange_rate', 1)
-
 	return paid_amount, received_amount
 
 def apply_early_payment_discount(paid_amount, received_amount, doc):