I think your friend Johannes is in
Manama, Bahrain
If we try to make sense of each of the 3-letter strings we see that
the only strings that do make sense are the last 6 ones.
They are TEHRAN, BAGHDAD, ABU DHABI, DOHA, KUWAIT, RIYADH. If we read these capital cities last three letter backwards we get the strings on the list.
The other strings OBA, OTI, SAC, ATR I couldn't make sense of I believe are simply just there to confuse.
Lastely
The thing all these capital cities respective country have in common is that they are all countries boardering the persian gulf. So the only capital city missing here is Manama which is in Bahrain.
Note
The second clue refers to 5 capitals and 7 countries who boarder the persian gulf. These are Abu Dhabi, Doha, Manama, Kuwait and Dubai (since it's capital of Emirate of Dubai). The countries are Iran, Iraq, Kuwait, Saudi Arabia, Qatar, Bahrain, United Arab Emirates. And even though Oman is said to boarder the gulf too I think the most fitting is Bahrain since it's more obvious when looking at the map.