• On the dashboard, search for "Journal Entry List" and filter for entries whose entry type is "Contra Entry"  (Refer Figure as shown) 

• Open the respective "Payment Entry" for which you want to book the charges and select  "Book Bank Charges" under "Make" button (Refer figure as shown)

In contra entry there is one popup will open for selecting bank account once you click on "Book Bank Charges"
Once you select the Account you will be redirected to Purchase invoice Page for creating the invoice

You will see page of  "Purchase Invoice" open up with all the basic details such as Supplier (Bank which has deducted the charges) ,Branch (Your company's branch for which charges has been deducted) , Cost center , Address of the bank and account currency auto-filled as per the payment entry you have made

Note: Bank accounts must be linked with Bank as supplier in Address reference table

In case, its not linked, Refer article "How to Link Bank Account with Bank Supplier address" 

Scroll down to the "Update Stock" section 

Bank charges as "Item" would be autofilled and you only need to fill amount of bank charge amount.
All tax and charges will be auto-filled based on the address of the supplier and calculation will be based on the rate you enter in respect to "Bank Charges" item 

Payment section will also be auto-filled

• Mode of payment and Cash/bank account  will remain the  same as the  mode of payment and ledger account of selected bank account mentioned while making "Payment entry"

In case no mode of payment is entered, it will remain "Wire Transfer" by default

Here paid amount is autofill on save and submit of purchase invoice

How to see Ledger of this Purchase Invoice

In case you want to see the ledger entry of this purchase invoice, you can do so by directly clicking" the Ledger option given on the same page