Nanomechanics of individual collagen fibrils govern the mechanical behavior of the majority of connective tissues, yet the current models lack significant details. Majority of the current models assume a rod-shape molecule with homogenous mechanical properties. Recent X-ray crystallography revealed significantly different microstructures in the D-period of collagen microfibrils, markedly different from the conventionally assumed rod-shaped molecule. Motivated by this recent microstructure, the nanomechanics of hydrated collagen molecules are investigated through molecular dynamics simulations. The results reveal significant mechanical heterogeneity in individual collagen molecules, which is expected to significantly impact the biomechanics of collagen fibrils in healthy and diseased tissues.