I have a doubt about the "quarter note" melody:
https://www.guitartricks.com/lesson/29329 [3:25]

I am not sure how to play the second beat of measure 13

the thumb hits E and G and the index(or middle) the D,

OR

thumb hits E and index and middle play G and D?

Because, even in the following lessons, I have the same problem
(I tend to miss the second chord with the thumb) 

Thanks