This article presents a circuit level representation from gated diode which is developed from Thymine single wall nanotube-like structure using density functional theory and non-equilibrium Green’s function. Electrical doping process has been introduced to form the p and n region of this gated diode. This p–n junction diode is originated from the single wall Thymine bio-molecular nanotube-like structure. The atomically thin three-dimensional diode that can be realized from a single wall Thymine nanotube-like structure with optimum process step in 300 K. The operating frequency of this device is 1000 THz. The quantum-ballistic carrier transmission is analyzed using molecular projected self-consistent Hamiltonian and Hilbert space spanned basis functions quantum simulation process which ensures that this device acts as a diode and also shows strong non-linear current–voltage characteristics. Due to electrical doping process, no impurity or dopants are added externally to form p and n junction of the gated diode. A metallic gate has been incorporated to this theoretical model to vary the channel current of the diode. By varying the potential at the p and n side of the gated diode, the doping concentration can be varied. The 3.75 nm long and 1.42 nm wide Thymine single wall nanotube-like structure gated diode shows maximum 99.3 µA current at + 1 V applied bias voltage. This diode is used to implement the basic logic gates like AND, OR and NOR gate. First principle results and the available experimental results are therefore validated using atomistic simulation of the test bed molecules. These results suggested that this bio-molecular nano diode is capable for circuit level realization like implementation of logic gates and logic circuits, in high operating frequency oscillator, switches, memory devices etc. This theoretical study is an approach to implement circuit level modeling of molecules.