In this paper, we explore mutual information based stock networks to build regular vine copula structure on high frequency log returns of stocks and use it for the estimation of Value at Risk (VaR) of a portfolio of stocks. Our model is a data driven model that learns from a high frequency time series data of log returns of top 50 stocks listed on the National Stock Exchange (NSE) in India for the year 2014. The Ljung-Box test revealed the presence of Autocorrelation as well as Heteroscedasticity in the underlying time series data. Analysing the goodness of fit of a number of variants of the GARCH model on each working day of the year 2014, that is, 229 days in all, it was observed that ARMA(1,1)-EGARCH(1,1) demonstrated the best fit. The joint probability distribution of the portfolio is computed by constructed an R-Vine copula structure on the data with the mutual information guided minimum spanning tree as the key building block. The joint PDF is then fed into the Monte-Carlo simulation procedure to compute the VaR. If we replace the mutual information by the Kendall's Tau in the construction of the R-Vine copula structure, the resulting VaR estimations were found to be inferior suggesting the presence of non-linear relationships among stock returns.