In this work, a novel method to model off-diagonal disorder in organic materials has been developed. The off-diagonal disorder is taken directly from the geometry of the system, which includes both a distance and an orientational dependence on the constituent molecules, and does not rely on a parametric random distribution. The geometry of the system is generated by running molecular dynamics simulations on phenylene-vinylene oligomers packed into boxes. The effect of the kind of randomness generated in this way is then investigated by means of Monte Carlo simulations of the charge transport in these boxes and a comparison is made to the commonly used model of offdiagonal disorder, where only the distance dependence is accounted for. It is shown that this new refined way of treating the disorder has a significant impact on the charge transport, while still being compliant with previously published and confirmed results.