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I am using the transport, freight, lorry 7.5 - 16 metric ton, EURO6 from ecoinvent as my transport process. In the database it is mentioned that truck consumes 0.047 kg/ton.km diesel fuel. I have calculated one example truck that carries 1 ton waste by the distance of 100 km and the result is 4.7 kg/100 km.Which is similar fuel consumption of a small passenger car. From the Volvo truck's EURO6 document, the consumption of the smallest truck is 20 liters/100 km when empty and 30 liters/100 km when fully loaded. 

I have also checked all the references mentioned in the ecoinvent document about the fuel consumption of the transport. But I did not find how the database fuel consumption has been calculated. 

I want to become clear how the number 0.047 kg/ton.km diesel fuel in this database has been calculated?

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If I am not mistaken ecoinvent uses the TREMOVE (https://www.tmleuven.be/en/navigation/TREMOVE) model for calculating the emissions of transport. Evidently however the ton-km unit is a very rough measure; an almost empty truck is terribly inefficient and uses a lot of fuel per transported good; ecoinvent always assumes a 50% payload. You can of course try to implement this differently (see e.g. https://www.ifeu.de/en/methods/models/tremod/ with its specific load-based factors, or just enter a value that you think is good) especially for your foreground / important processes.
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