Arrange my monomer dictionary in a uniform way

I have a monomer DNA/RNA dictionary which are drawn as it is, sometimes the phosphate group is on the right sometimes on the left, see the attached examples (A.png, T.png).

I want to arrange my structures uniformly such a way to able to connect them nicely. So I rotate and flip them to have the phosphate group on the left and the hydroxyl group on the right so if I connect and move them one bond away the result will look nice.

 

/**

     * Rotate the monomer to have attach1 and attach2 atoms on a horizontal line

     * and attach1 at right, attach2 at left side.

     * @param m

     * @param attach1

     * @param attach2

     */

    private static void rotateMonomer(Molecule m, MolAtom attach1, MolAtom attach2){

        if (attach2.getX() < attach1.getX()){

            // flip

            CTransform3D flip = new CTransform3D();

            flip.m00 = -1;

            flip.m22 = -1;

            m.transform(flip);

        }

        DPoint3 p_point = attach2.getLocation();

        double angle = p_point.angle2D(attach1.getX(), attach1.getY());

        CTransform3D T = new CTransform3D();

        T.setRotationCenter(p_point);

        T.setRotation(0, 0, 1, -angle);

        m.transform(T);

    }