The electron density is an important object in quantum chemistry that is crucial for many downstream tasks in drug design. Recent deep learning approaches predict the electron density around a molecule from atom types and atom positions. Most of these methods use the plane wave (PW) numerical method as a source of ground-truth training data. However, the drug design field mostly uses the Linear Combination of Atomic Orbitals (LCAO) for computation of quantum properties. In this study, we focus on prediction of the electron density for drug-like substances and train- ing neural networks with LCAO-based datasets. Our experiments show that proper handling of large amplitudes of core orbitals is crucial for training on LCAO-based data. We propose to store the electron density with the stand- ard grids instead of the uniform grid. This allowed us to reduce the number of probing points per molecule by 43 times and reduce storage space requirements by 8 times. Finally, we propose a novel architecture based on the Deep- DFT model that we name LAGNet. It is specifically designed and tuned for drug-like substances and ∇2DFT dataset.