Quantum dots patterned by atomically precise placement of phosphorus donors in single crystal silicon have long spin lifetimes, advantages in addressability, large exchange tunability, and are readily available few-electron systems. To be utilized as quantum bits, it is important to non-invasively characterise these donor quantum dots post fabrication and extract the number of bound electron and nuclear spins as well as their locations. Here, we propose a metrology technique based on electron spin resonance (ESR) measurements with the on-chip circuitry already needed for qubit manipulation to obtain atomic scale information about donor quantum dots and their spin configurations. Using atomistic tight-binding technique and Hartree self-consistent field approximation, we show that the ESR transition frequencies are directly related to the number of donors, electrons, and their locations through the electron-nuclear hyperfine interaction.