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The project in Germany involves the modernization of 9,000 km of railway track over six years.
Mikel Merino scored the winner in the 119th minute to make it 2-1 for Spain.
The gesture is linked to the 'Grey Wolves', an ultra-nationalist youth branch of Turkey's Nationalist Movement Party, an ally of President Tayyip Erdogan's ruling AK Party.
The suspects had threatened to publish the data on the dark web unless they received millions of euros, said prosecutors.
Hosts Germany meet Spain in the first quarterfinal, while Portugal take on France in another mouth-watering clash.
The game was suspended for 20 minutes in the first half due to the weather before Danish defender Joachim Andersen went from hero to zero when his close-range finish was disallowed for offside and he conceded a penalty.
The knock-out phase action begins on Saturday.
The Germans will find out their last 16 opponents on Tuesday.
The two men from the western German city of Wuppertal were arrested on Wednesday and had been seeking millions of euros, Bild reported.
Jamal Musiala and Gundogan scored in a 2-0 win for Germany.