Library of Cumulative Atomic Multipole Moments for AminoAcds

Beta version

Description

This database allows one to get precalculated Cumulative Atomic Multipole Moments for aminoacid residue with provided PDB coordinates. It consists of Python package rotabase.

Requirements

In order to use the library, you have to install a Pymolecule module, which is used to manipulate atomic multipole data. It also requires BioPython for handling the PDB files.

Raw multipoles

Raw CAMM arrays may be downloaded here. At the moment, available multipoles vere derived from Hartree-Fock density within 6-311G(3d,2p) and 6-31G(d) basis sets.
In order to generate CAMM for new molecule or apply electron density obtained in other method or basis set one may use GAMESS program released on Oct 1, 2010 or its any later version with option $ELMOM IAMM=n CUM=.TRUE. $END (with multipole rank n not greater than 12).
Rotamer definitions follow those from Dynameonics database (2015, backbone-independent); names are given in numerical notation (substitutions g+→ 0, t → 1, g- → 2 and similar). They are stored as serialized Pymolecule objects- in order to read them, the module must be read first, then the particular file has to be decompressed (either externally or within a Python script with module gzip), and, finally, loaded using Python pickle (or cPickle) module.

Example of loading molecule: 
from pymolecule import multipoles as m
import cPickle as pic
import gzip

with gzip.open('desired_file.pkl.gz','rb') as f: mol_camm=pic.load(f)

How to use

Download

The rotabase package can be downloaded here. Multipole moments calculated with HF/6-31G* and MP2/6-31G* densities are provided at the moment. Unfortunatelly, Windows compatibility hasn't been assured.

Although it should not happen, different Python versions may cause problems with serializes (pickle) files. This database was prepared with Python version 2.7.6 [GCC 4.8.4]. In case of problems, please contact with the author or the current maintainer.

Installation

Remember to install SciPy and fortran compiler (gfortran for instance) first. Than you should be able to build and install PyMolecule.
Note that currently rotabase still requires Python 2, but pymolecule has been updated to Python 3. Until the rotabase itself will be updated, one should download the older, Python 2 compatible version of pymolecule: 
git clone --branch v0.2.0 https://bitbucket.org/mmqc/pymolecule.git
cd pymolecule
python2 setup.py build
sudo python2 setup.py install --prefix=/usr/local
Next, install BioPython. Finally, after extraction of rotabase you can simply run a command:

sudo python2 setup.py install --prefix=/usr/local
in the package directory. Live long and prosper!

Literature related to Cumulative Atomic Multipole Moment (CAMM) technique and its applications in molecular modeling

  • Cumulative Atomic Multipole Representation of the Molecular Charge-Distribution and Its Basis Set Dependence, Sokalski, W.A.,Poirier, R.A., CHEMICAL PHYSICS LETTERS, 98, 86-92 (1983) link

  • Correlated Molecular and Cumulative Atomic Multipole Moments, Sokalski, W.A., Sawaryn, A., JOURNAL OF CHEMICAL PHYSICS, 87, 526-534 (1987). link

  • Cumulative Atomic Multipole Moments and Point-Charge Models Describing Molecular Charge Distribution, Sawaryn, A., Sokalski, W.A., COMPUTER PHYSICS COMMUNICATIONS, 52, 397-408 (1989). link

  • Fortran code calculating CAMM using RWF files generated by Gaussian-82 or Gaussian-86 package can be dowloaded here

  • Cumulative Atomic Multipole Moments for Molecular Crystals from Ab-Initio Crystal Orbital Wave-Functions and for Molecules in Excited States from Ab Initio Wave Functions, Sokalski, WA, Keegstra, PB; Roszak, S, Kaufman,J.J., INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY ,QUANTUM CHEMISTRY SYMPOSIUM, 24, 51-63 (1990). link

  • Efficient Method for the Generation and Display of Electrostatic Potential Surfaces from Ab-Intion Wave-Functions, Sokalski, WA, Sneddon, SF, JOURNAL OF MOLECULAR GRAPHICS, 9, 74-77 (1991). link

  • Ab Initio Study of the Electrostatic Multipole Nature of Torsional Potentials in CH3SSCH3, CH3SSH, AND HOOH, Sokalski, WA, Lai, J, Luo, N, Sun, S, Shibata, M, Ornstein, R, Rein, R, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 40, 61-71 Supplement: 18 (1991). link

  • Cumulative Multicenter Multipole Moment Databases and their Applications, Sokalski, WA, Sawaryn, A., JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 88, 91-112 (1992). link

  • Cumulative Atomic Multipole Moments Complement any Atomic Charge Model to Obtain More Accurate Electrostatic Properties, Sokalski, WA, Shibata, M, Ornstein, RL; Rein, R, JOURNAL OF COMPUTATIONAL CHEMISTRY, 13, 883-887 (1992). link

  • Correlated Molecular and Multicenter Multipole Moments in Ground and Excited-States from Multiple Reference Double-Excitation Configuration-Interaction Calculations, Roszak, S); Sokalski, WA,Kaufman, JJ, JOURNAL OF COMPUTATIONAL CHEMISTRY, 13, 944-951 (1992). link

  • Intramolecular Electrostatic Interactions Studied by Cumulative Atomic Multipole Moment Expansion with Improved Convergence, Strasburger, K, Sokalski, WA, CHEMICAL PHYSICS LETTERS, 221,129-135 (1994). link

  • Electrostatic models of inhibitory activity, Grembecka, J, Kedzierski, P, Sokalski, WA, Leszczynski, J, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 83,180-192 (2001) link

  • Analysis of the transferability of atomic multipoles for amino acids in modeling macromolecular charge distribution from fragments, Kedzierski, P, Sokalski, WA JOURNAL OF COMPUTATIONAL CHEMISTRY, 22,1082-1097 (2001). link

  • Intriguing relations of interaction energy components in stacked nucleic acids, Langner, Karol M., Sokalski, W. Andrzej, Leszczynski, J., JOURNAL OF CHEMICAL PHYSICS, 127, 111102 (2007). link

  • Low-Cost Prediction of Relative Stabilities of HydrogenBonded Complexes from Atomic Multipole Moments for Overly Short Intermolecular Distances, Beker, Wiktor, Langner, Karol M., Dyguda-Kazimierowicz, Edyta, Feliks, Mikolaj, Sokalski, W. Andrzej, JOURNAL OF COMPUTATIONAL CHEMISTRY, 34,1797-1799 (2013). link

  • Physical Nature of Fatty Acid Amide Hydrolase Interactions with Its Inhibitors: Testing a Simple Nonempirical Scoring Model, Giedroyc-Piasecka, Wiktoria, Dyguda-Kazimierowicz, Edyta, Beker, Wiktor, Mor, Marco, Lodola, Alessio, Sokalski, W. Andrzej, JOURNAL OF PHYSICAL CHEMISTRY B, 118, 14727-14736 (2014). link

  • Universal short-range ab initio atom-atom potentials for interaction energy contributions with an optimal repulsion functional form, Konieczny, Jan K, Sokalski, W. Andrzej, JOURNAL OF MOLECULAR MODELING, 21,197 (2015). link

  • Tracking molecular charge distribution along reaction paths with atomic multipole moments, Langner, Karol M., Beker, Wiktor L., Dyguda-Kazimierowicz, Edyta, Sokalski, W. Andrzej, STRUCTURAL CHEMISTRY, 27, 429-438 (2016). link

  • Rapid Estimation of Catalytic Efficiency by Cumulative Atomic Multipole Moments: Application to Ketosteroid Isomerase Mutants, Beker, Wiktor, van der Kamp, Marc W., Mulholland, Adrian J., Sokalski, W. Andrzej, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13, 945-955 (2017). link

  • Bottom-Up Nonempirical Approach To Reducing Search Space in Enzyme Design Guided by Catalytic Fields, Beker, Wiktor; Sokalski, W. Andrzej JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 16, 3420-3429 (2020). link

  • Catalytic Fields as a Tool to Analyze Enzyme Reaction Mechanisms Variants and Reaction Steps, Kedzierski, Pawel, Moskal, Martyna, Sokalski, W. Andrzej, JOURNAL OF PHYSICAL CHEMISTRY B, 125, 11606-11616 (2021). link

CATALYTIC FIELDS

Literature related to Catalytic Field technique

  • Theoretical Model for Exploration of Catalytic Activity of Enzymes and Design of New Catalysts: CO2 Hydration Reaction, Sokalski, W. Andrzej INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 20, 231 - 240 (1981). link

  • The Physical Nature of Catalytic Activity Due to Molecular Environment in Terms of Intermolecular Interactions Theory: Derivation of Simplified Models, Sokalski, W. Andrzej JOURNAL OF MOLECULAR CATALYSIS, 30, 395 - 410 (1985). link

  • Nonempirical Modeling of the Static and Dynamic Properties of the Optimum Environment for Chemical Reactions, Sokalski, W. Andrzej JOURNAL OF MOLECULAR STRUCTURE (THEOCHEM), 138, 77 - 87 (1986). link

  • Nonempirical analysis of the catalytic activity of the molecular environment – optimal static and dynamic catalytic fields for double proton transfer in formamide–formamidine complex, Dziekonski, Paweł, Sokalski, W. Andrzej, Podolyan, Evgeniy, CHEMICAL PHYSICS LETTERS, 367, 367 - 375 (2003). link

  • Differential Transition State Stabilization in Enzyme Catalysis: Quantum Chemical Analysis of Interactions in the Chorismate Mutase Reaction and Prediction of the Optimal Catalytic Field, Szefczyk, Borys,; Mulholland, Adrian J.;, Ranaghan, Kara,; Sokalski, W. Andrzej, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 126, 16148-16159 (2004). link

  • Double-Proton Transfer in Adenine−Thymine and Guanine−Cytosine Base Pairs. A Post-Hartree−Fock ab Initio Study, Gorb, Leonid, Podolyan, Yevgenii, Sokalski, W. Andrzej,Leszczynski, Jerzy, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 126, 10119-10129 (2004). link

  • Predicting substituent effects on activation energy changes by static catalytic fields, Chojnacka, Martyna, Feliks, Mikołaj, Beker, Wiktor, Sokalski, W. Andrzej, JOURNAL OF MOLECULAR MODELING, 24, 28 (2018). link

  • Extreme Catalytic Power of Ketosteroid Isomerase Related to the Reversal of Proton Dislocations in Hydrogen-Bond Network, Kedzierski, Pawel, Maria Zaczkowska, Sokalski, W. Andrzej, JOURNAL OF PHYSICAL CHEMISTRY B, 124, 3661-3666 (2020). link

  • Bottom-Up Nonempirical Approach To Reducing Search Space in Enzyme Design Guided by Catalytic Fields, Beker, Wiktor; Sokalski, W. Andrzej JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 16, 3420-3429 (2020). link

  • Catalytic Fields as a Tool to Analyze Enzyme Reaction Mechanisms Variants and Reaction Steps, Kedzierski, Pawel, Moskal, Martyna, Sokalski, W. Andrzej, JOURNAL OF PHYSICAL CHEMISTRY B, 125, 11606-11616 (2021). link

  • Extension of an Atom-Atom Dispersion Function to Halogen Bonds and its use for Rational Design of Drugs and Biocatalysts, Jedwabny, Wiktoria, Dyguda-Kazimierowicz, Edyta, Pernal, Katarzyna, Szalewicz, Krzysztof, JOURNAL OF PHYSICAL CHEMISTRY A, 125, 1787-1799 (2021). link