We present a three-dimensional computational model based on an immersed boundary (IB) method to study the hydrodynamic features of a solid flexible cylindrical rod in a viscous fluid driven at one side by a tiny motor. The elastic rod is modelled by a number of circular cross-sections with twelve IB points on each cross-section. Three types of elastic links are created from each IB point to obtain an elastic network model of the rod and the first cross-section is modelled as the motor part. The elastic forces are computed based on an elastic energy approach and the motor forces are obtained from the applied angular frequency of rotation of the motor. The Stokes equations governing the fluid are solved on a staggered Cartesian grid system using the fractional-step based finite-volume method. Numerical simulations are performed to demonstrate the three dynamical stages of rod motion- twirling, whirling and overwhirling for different rotational frequency of the motor. It is revealed that for low rotational frequencies, the rod undergoes stable rigid body motion known as twirling. For high rotational frequencies of the motor, it is observed that the rod initially undergoes whirling motion and attains an unstable helical shape. Further, it is noticed that a discontinuous shape transition occurs for the rod and it folds back on itself. This unstable motion is referred to as overwhirling. It is also found that there exists a critical value of angular frequency of rotation of the motor below which the rod is subjected to twirling motion and above which it undergoes overwhirling motion.