Molecular Properties     Download MoPro Suite

Christian Jelsch, Benoît Guillot, Cristian Iordache

MoPro is a cristallographic least square refinement package allowing structural or charge density studies of cristal stuctures of variable sizes, ranging from small molecules to biological macromolecules.

 

The MoProSuite software package

MoProSuite is a software package dedicated to the charge density modeling of crystal structures. It is constituted by two main computational components (MoPro and VMoPro), themselves interfaced by convenient graphical user interfaces (MoProGUI and MoProViewer, respectively).

 

MoPro is a crystallographic refinement and molecular modeling package. It allows structural and charge density studies of crystal structures of variable sizes, ranging from small molecules to biological macromolecules.It implements the Hansen & Coppens multipolar atom model of electron density. This is necessary to take into account the deformation of electron density arising from the interatomic interactions. These details become visible and quantifiable at subatomic resolution (0.5 Angstrom typically).

Deformation electron density in the plane of a peptide bond of the 0.62Å resolution RD1 antifreeze protein.

Deformation electron density in the plane of a peptide bond of the 0.62Å resolution RD1 antifreeze protein.

MoPro possesses its own graphical user interface MoProGUI allowing in a user-friendly way to define refinement strategies and to configure a refinement procedure. MoPro is also interfaced with the ELMAM2 experimental multipolar database, which groups the multipolar parameters necessary to describe the charge density of protein and common chemical groups. Hence, the transfer of these parameters allows computing derived electrostatic properties of crystal structures and notably biological macromolecules determined only at usual atomic resolution.

The VMoPro module allows the computation of derived properties based on the multipolar formalism, as molecular electrostatic potential, topological properties or intermolecular interaction energies. It relies on a molecular structure file generated by MoPro and is also interfaced. Its graphical user interface is MoProViewer, a molecular viewer specifically developed for the charge density research which allows, among many features, to graphically configure and execute electron density derived properties computations.

The MoProSuite software has the following most important features:

  • Multipolar (Hansen & Copppens) and spherical (IAM) models of atomic electron density to refine X-ray structures and charge distribution.
  • Lest squares refinement with full matrix inversion or preconditionned conjugate gradients
  • Isotropic, anisotropic and anharmonic modeling of atomic thermal motion
  • Simple and powerful script language
  • Restraints/Constraints on stereochemistry, thermal motion and charge density parameters
  • Automated generation of local axes systems
  • Automated generation of charge density symmetry and chemical equivalence constraints/restraints
  • Automated geometrical constraints/restraints
  • Electroneutrality constrain
  • For protein crystals, correction of disordered solvent scattering by exponential scaling model or bulk methods
  • Analysis tools (stereochemistry, charge density, hydrogen bonding, thermal motion)
  • Crystal, molecular or fragments Electrostatic Potential computation
  • Total, deformation, valence or multipolar (dipolar, quadripolar ..) electron density computation
  • Topological analysis of electron density/ electrostatic potential/Laplacian:

critical points, bond ellipticity, Laplacian, energy density Gcp, Vcp.

  • Atomic basins and charge integration
  • Electric field gradient
  • Electrostatic interaction energy computation
  • Refinement of Neutron and Electron diffraction crystal structure
  • Several file format import/export for molecular structure definition (PDB, Shelxl, CIF…)
  • Output Properties displayed in 2D plane, or given sampled on 3D grid (XPLOR or GAUSSIAN CUBE file formats)
  • Computation of Hirshfeld surface and contact enrichment ratios
  • Modeling of electron density by charged spherical real+virtual atoms
  • Estimation of errors on charge density derived properties using the sample standard deviation method.

 

References:

Fournier, B., Guillot, B., Lecomte, C., Escudero-Adán, E. C., & Jelsch, C. Acta Crystallographica Section A: Foundations and Advances, 74(3), 170-183.  A method to estimate statistical errors of properties derived from charge-density modelling

Nassour, A., Domagala, S.,  Guillot, B., Leduc, T &, Lecomte & Jelsch C. (2017)  Acta Cryst. B73, 610–625. A theoretical-electron-density databank using a model of real and virtual spherical atoms.

Domagala S.,  Fournier B,  Liebschner D.,  Guillot B. and  Jelsch C  Acta Cryst. (2012). A68, 337-351. An improved experimental databank of transferable multipolar atom models – ELMAM2.  Construction details and applications.

Guillot B., Jelsch C., Podjarny A. & Lecomte C. (2008) Acta Cryst. D.  D64, 567-588. Charge density analysis of a protein structure at subatomic resolution: the human Aldose Reductase case.

Jelsch, C.,  Guillot, B., Lagoutte, A. & Lecomte, C., (2005). J. Appl. Cryst. 38, 38-54. Advances in Proteins and Small Molecules. Charge Density Refinement Methods using software MoPro