'We wanted to go 57, ' Thomas said.
The Team Jumbo Visna rider was not expected to be fighting for the win, but held off Slovenian Peter Sagan and Australian Caleb Ewan to take the stage by the narrowest of margins. "It's just one of those things".
Few riders lost time in the overall classification due to the crash being in the final three kilometres and so those riders' placing put Team Ineos at the bottom of the team ranking and so first off in the team time trial.
Initially it looked as though the 34-year-old Dane might lose touch, but his teammates helped him recover and he worked his way back to finish in the peloton.
A relatively uneventful 194km opener around the Wallonia and Flanders countryside exploded into life after the bunch reeled in an audacious late breakaway from French debutant Stephane Rossetto as the race re-entered Brussels.
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A total of 176 cyclists from 22 teams took part in the opening race of the day, departing from the Royal Square in central Brussels, through Charleroi, Waterloo and other cities in Belgium, before ending at the King's private palace on the outskirts of Brussels, rounding off a 194.5km opening day race.
With the first few stages likely to be the domain of the sprinters Nibali, who crashed out heavily a year ago in the Alps, said he would have more idea of his form after stage six which finishes with a brutal climb to La Planche des Belles Filles.
"After that I though, I'm still fresh and everyone was dying in the last meters, even Sagan, then I took him on the line. Hopefully when Dylan heard it was me who won he could still smile". "I might do okay in the GC but then be unable to win a stage".
Mark Cavendish won't get a chance this month to overhaul Eddy Merckx's record of 34 stage victories at the Tour de France.
Belgium's Olympic champion Greg van Avermaet made an early move to the front, much to the delight of local fans.