[EDIT: as I don't know what lib you're using, and as this question is not specific to Java, my answer is in pseudo-code.]
If I understand your question correctly, atan2 is not what you're looking for.
What you want to achieve is moving something (which has coordinates) from one point to another according to time. You just need to compute the vector between the player entity and the target.
What you need here is:
- the position (x,y) of the player (player_position).
- the position (x,y) of the target (target_position).
- the speed at which you want your bullet to travel (in unit per seconds) (bullet_speed).
- the time passed between two game updates (two frames) (deltaTime).
As you seem to have all of that, you seem ready to make that bullet move.
The vector from your player to the target, in pseudo code, is :
Vector2 diff_vector = player_position - target_position;
Then put your bullet at player_position and move it each frame alongside this vector you just computed using the deltaTime between frames. Something like:
new_bullet_position = bullet_position + diff_vector * deltaTime * bullet_speed;
Changing bullet position each frame accordingly to the diff_vector and the bullet_speed will make it move uniformly from player to target.
I hope it helps.