Can a rectangle/square be drawn from just knowing end coordinates of one of its diagonals? If yes, how? Also could someone post a link/something that I has good examples of opengl programming in java?

yes.

imagine the 4 corners are ABCD. you know point A and C (diagonal).

so B is :

B.x = A.x

B.y = C.y

and D is :

B.x = C.x

B.y = A.y

Try first with GL_LINES.

opengl+java :

https://jogl-demos.dev.java.net/

https://jogl-demos.dev.java.net/source/browse/jogl-demos/