We have established that relatively simple calculations of the Coulomb interaction in the lattice of doped lithium niobate (LN, LiNbO3) can confirm the physical properties of real crystals. We have developed a method for the double adjustment of real XRD data for calculations of Coulomb interaction in a LN cluster. The study considers two crystals doped with boron (LN:B); LN:B(1) has been grown from a charge with 0.02 mol% B2O3, boron has been introduced by homogeneous doping, LN:B(2) has been grown from a charge with 0.547 mol% B2O3, and boron has been introduced by direct solid-state doping. XRD and Rietveld method data have been obtained for these crystals. The obtained data have been used to build a model of the LN cluster; the cluster in the calculations consists of six oxygen octahedra of the LN structure. The cluster configuration has been chosen in such a way that the structure contains two tetrahedral voids. We have studied 10 variants of filling a cluster with intrinsic cations (Li, Nb), defects, and vacancies. There are 10 of them because, in addition to the basic cations in their positions, defects are present in the structure. In terms of the defects used (NbLi, NbV), we have used only those that Rietveld found for these exact LN:B crystals, and the vacancy in the niobium octahedron (VNb) compensates for these defects, according to the models known for LN. The energy of the Coulomb interaction between the cluster structure of a real crystal and the boron cation localized in it in different positions has been calculated for each of the configurations. Calculations have demonstrated that B is more likely to be embedded near a defect than in a regular structure. This means that boron positively influences the local substructure of doped LN crystals, not only structures the melt during crystal growth. Calculations have shown that the type and location of structural defects affect the position of boron in the structure of a LN crystal. Calculations have also shown that LN:B(1) has a more stable structure, including optical damage resistance. The photoinduced light scattering (PILS) patterns and conoscopic patterns confirm this conclusion for the studied LN:B crystals. The information obtained in this study may be useful for interpreting the defective structure of LN crystals co-doped with boron and metals (Mg, Zn, etc.). This will supplement the knowledge available in the literature regarding models that describe the structure of complexly doped LN crystals.