something like this

To display a rotated molecule the rotation must be done brfore the translation. Any way the code below rotates the molecule about the vertical axis.

1. import processing.opengl.*;
2. 
   
3. H20 myH20;
4. 
   
5. void setup() {
6.   size(800, 600, OPENGL); 
7.   myH20 = new H20();
8. }
9. 
   
10. void draw() {
11.   background(0);
12.   myH20.display();
13.   myH20.move();
14.   myH20.turn(0.1);
15. }
16. 
    
17. class H20 {
18.   color c;
19.   float xpos = width/2;
20.   float ypos = height/2;
21.   float xspeed =5;
22.   float yspeed =5;
23.   float rot = 0;
24. 
    
25.   H20() {
26.     c = color(255);  
27.     xpos = width/2;  
28.     ypos = height/2;  
29.     xspeed = 1;
30.   }
31. 
    
32.   void display() {
33.     lights();  
34.     pushMatrix();
35.     // translate to centre of molecule (oxygen atom)
36.     translate(xpos, ypos, 50);
37.     // Rotate the molecule
38.     rotateY(rot);
39.     // Oxygen
40.     noStroke();
41.     fill(255, 100, 100);   
42.     sphere(50);
43.     // Hydrogen 1
44.     pushMatrix();
45.     lights();     
46.     translate(40, -35, 0);
47.     noStroke();
48.     fill(90);
49.     sphere(35);
50.     popMatrix();
51.     // Hydrogen 2
52.     pushMatrix();
53.     translate(-40, -35, 0);
54.     noStroke();
55.     fill(90);
56.     sphere(35);
57.     popMatrix();
58.     popMatrix();
59.   }
60. 
    
61.   void move() {
62.     xpos = xpos + xspeed;
63.     ypos = ypos + yspeed;
64.     if (xpos > width-100 || xpos <=100) {
65.       xspeed=xspeed*-1;
66.     }
67.     if (ypos > height-100 || ypos <= 100) {
68.       yspeed=yspeed*-1;
69.     }
70.   }
71. 
    
72.   void turn(float deltaRot) {
73.     rot += deltaRot;
74.   }
75. }