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After add
launchctl load ~/Library/LaunchAgents/org.mongodb.mongod.plist 

To add the file to the launchd service, and then you can run
launchctl start org.mongodb.mongod

Also you can add alias to your ~/.bash_profile to start/stop mongod service
alias mongostart="launchctl start org.mongodb.mongod"
alias mongostop="launchctl stop org.mongodb.mongod"

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
  <key>Label</key>
  <string>org.mongodb.mongod</string>
  <key>ProgramArguments</key>
  <array>
    <string>/usr/local/bin/mongod</string>
    <string>run</string>
    <string>--config</string>
    <string>/Users/atma/.mongodb/mongod.conf</string>
  </array>
  <key>RunAtLoad</key>
  <true/>
  <key>KeepAlive</key>
  <false/>
  <key>UserName</key>
  <string>{your_username}</string>
  <key>WorkingDirectory</key>
  <string>/usr/local</string>
  <key>StandardErrorPath</key>
  <string>/usr/local/var/log/mongodb/error.log</string>
  <key>StandardOutPath</key>
  <string>/usr/local/var/log/mongodb/output.log</string>
</dict>
</plist>