The shooting all took place in a North San Jose neighborhood Oct. 2.
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The Santa Clara County District Attorney's Office filed its complaint last week.
Now Monday, the suspect, 66-year-old Mark Henry Waters pleaded not guilty.
Waters is White and the victim is Black, law enforcement is investigating potential hate crime allegations - for now he faces more than 20 years on what he is charged with.
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"Assault with a semi-automatic firearm," Deputy DA Aidan Welsh listed off following Monday's court date, "He's also charged with personal infliction of great bodily injury, as well as use of a firearm."
The Santa Clara County District Attorney's office says the shooting happened when the 21-year-old victim left an Airbnb rental to walk to a grocery store.
They say surveillance video shows that as the victim crossed the street, he saw the suspect, Waters, leave his house and quickly approach him while holding a gun.
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In court Monday, the suspect's defense attorney did not deny claims that the suspect knew the victim tried to get away.
The prosecutor says Waters shot him while his back was turned.
The victim suffered a broken femur.
"He comprehended and knew that the victim was running away, and he shot him anyway," Welsh said, "There was nothing that would cause him to fear the victim, the victim had not stepped foot at his front door on his driveway in his front yard."
Multiple attempts have been made since Friday to get Waters' attorney, Jose Badillo, to comment to ABC7 in Waters' defense including at court Monday, he declined.
To the judge though, the lawyer said that Water's car was broken into a couple of nights before the shooting and that his garage door openers were stolen.
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Badillo said Waters initially believed the victim could have been one of the suspects and thought the victim was carrying a gun which later turned out to be headphones.
Still, the judge clarified Monday that there is no evidence that the victim, who was not in court, was in any way connected to those previous crimes nor did he resemble a suspect description Waters gave when the break in happened.
Several family members, friends and neighbors showed up in support of Waters and issued character statements to the court.
His attorney telling the judge that Waters had no prior criminal record, is a caretaker for his grandchildren and has been a role model for youth in his community.
Still, the judge said that the evidence showed that Waters was too dangerous to be out in the public and he was taken back into custody.
Waters next court appearance is set for Dec. 22.