C7790 Introduction to Molecular Modelling -1Lesson
10
Structure
Petr Kulhánek
kulhanek@chemi.muni.cz
National Centre for Biomolecular Research, Faculty of Science
Masaryk University, Kamenice 5, CZ-62500 Brno
JS/2022 Present Form of Teaching: Rev2
C7790 Introduction to Molecular
Modelling
TSM Modelling Molecular Structures
C9087 Computational Chemistry for Structural Biology
C7790 Introduction to Molecular Modelling -2-
Context
microworldmacroworld
equilibrium (equilibrium constant)
kinetics (rate constant)
free energy
(Gibbs/Helmholtz)
partition function
phenomenological thermodynamics
statistical thermodynamics
microstates
(mechanical properties, E)
states
(thermodynamic properties, G, T,…)
microstate ≠ microworld
Description levels (model chemistry):
• quantum mechanics
• semiempirical methods
• ab initio methods
• post-HF methods
• DFT methods
• molecular mechanics
• coarse-grained mechanics
Structure
EnergyFunction
Simulations:
• molecular dynamics
• Monte Carlo simulations
• docking
• …
C7790 Introduction to Molecular Modelling -3-
Structure
C7790 Introduction to Molecular Modelling -4Configuration
Space
)(RE R = point in 3N dimensional space (N is the number of atoms)
},,,....,,,,,,{ 222111 NNN zyxzyxzyx=R
Cartesian coordinates
of the first atom
Every point in the configuration space represents
a unique structure of the system.
Cartesian coordinates
of the last atom
C7790 Introduction to Molecular Modelling -5Models
- Small Molecules
line model
tube model
CPK model
vdW model
same structure
other visualization
C7790 Introduction to Molecular Modelling -6Models
- Biomolecules
line model line model with the
backbone of protein
Cartoon model
surface of the biomolecule
same structure
other visualization
Different models are used to highlight certain
structural information or internal properties
of a molecule or group of molecules, which
facilitates an easier understanding of the
studied problem.
C7790 Introduction to Molecular Modelling -7Coarse-grained
Models
C7790 Introduction to Molecular Modelling -8Computer
Representation of Models
The structure can be represented in various ways. More than 100 formats are
used in chemistry. They are either text or binary files.
The format describes:
➢ the geometry of the system
➢ the names of atoms
➢ groups of atoms
➢ connectivity between atoms (bonds)
➢ and other information
The system geometry is usually provided as:
➢ Cartesian coordinates
➢ internal coordinates
➢ variants of internal coordinates
C7790 Introduction to Molecular Modelling -9Cartesian
vs Internal Coordinates
O
H 1 0.974298
O 1 1.454349 2 96.868054
H 3 0.974298 1 96.868054 2 239.552651
Cartesian coordinates
Internal coordinates (Z-matrix)
bond length bond angle torsion angle
3N
3N-6
3N-5
Number of degrees of freedom:
Number of degrees of freedom:
(linear diatomic molecule)
x y z
O -0.180077 -0.046023 -0.062789
H 0.196208 -0.747659 0.498793
O 0.006537 1.047922 0.877207
H -0.931885 1.299156 0.951390
C7790 Introduction to Molecular Modelling -10Internal
Coordinates
1 O
2 H 1 0.974298
3 O 1 1.454349 2 96.868054
4 H 3 0.974298 1 96.868054 2 239.552651
2-1
4-3 4-3-1
3-1-2 4-3-1-2
bond length (a) bond angle (b) torsion angle (c)
http://www.ccl.net/cca/documents/molecular-modeling/node4.html
C7790 Introduction to Molecular Modelling -11XYZ
format
number of atoms
comment
element xyz
element xyz
...................
element xyz
The xyz format is a free-formatting text file (values ​​in columns can be separated by any
number of spaces or other whitespace).
The format only describes the geometry of the system. It does not contain information
about bonds in the system. A program that works with the format must calculate this
information (e.g., using atomic radii).
positions are in angstroms (Å)
24
chorismate
C -1.86100 -0.57700 0.31800
O -2.56800 0.47600 0.32600
O -2.20900 -1.75300 0.64200
C -0.38900 -0.41000 -0.18800
................................................
H -0.50900 1.67900 -0.44800
C7790 Introduction to Molecular Modelling -12-
..................................................................
ATOM 7 CB SER 1 5.814 16.335 8.213 1.00 0.00
ATOM 8 HB2 SER 1 6.870 16.427 7.958 1.00 0.00
ATOM 9 HB3 SER 1 5.610 16.900 9.123 1.00 0.00
ATOM 10 OG SER 1 5.491 14.946 8.427 1.00 0.00
ATOM 11 HG SER 1 6.026 14.600 9.145 1.00 0.00
ATOM 12 C SER 1 3.604 16.323 6.927 1.00 0.00
ATOM 13 O SER 1 2.605 16.742 7.521 1.00 0.00
ATOM 14 N GLN 2 3.567 15.251 6.134 1.00 0.00
ATOM 15 H GLN 2 4.401 14.914 5.675 1.00 0.00
..................................................................
PDB format
The pdb format is employed to store the structures of biomolecules and their complexes.
It is widely used but it has several limitations. Therefore, it is slowly substituted by more
advanced formats such as PDBx/mmCIF and others.
keyword
atom number
atom name
Cartesian coordinates of atoms
residue number
residue name
The pdb format does not usually contain information about bods in the system. The program
that works with the format must calculate this information (based on template structures).
For non-standard residues, the CONECT keyword can be used.
in angstroms (Å)
C7790 Introduction to Molecular Modelling -13Djungle
of formats I
acr -- ACR format
adf -- ADF cartesian input format
adfout -- ADF output format
alc -- Alchemy format
arc -- Accelrys/MSI Biosym/Insight II CAR format
bgf -- MSI BGF format
box -- Dock 3.5 Box format
bs -- Ball and Stick format
c3d1 -- Chem3D Cartesian 1 format
c3d2 -- Chem3D Cartesian 2 format
cac -- CAChe MolStruct format
caccrt -- Cacao Cartesian format
cache -- CAChe MolStruct format
cacint -- Cacao Internal format
can -- Canonical SMILES format.
car -- Accelrys/MSI Biosym/Insight II CAR format
ccc -- CCC format
cdx -- ChemDraw binary format
cdxml -- ChemDraw CDXML format
cht -- Chemtool format
cif -- Crystallographic Information File
ck -- ChemKin format
cml -- Chemical Markup Language
cmlr -- CML Reaction format
com -- Gaussian 98/03 Input
copy -- Copies raw text
crk2d -- Chemical Resource Kit diagram(2D)
crk3d -- Chemical Resource Kit 3D format
csr -- Accelrys/MSI Quanta CSR format
cssr -- CSD CSSR format
ct -- ChemDraw Connection Table format
cub -- OpenDX cube format for APBS
cube -- OpenDX cube format for APBS
dmol -- DMol3 coordinates format
dx -- OpenDX cube format for APBS
ent -- Protein Data Bank format
fa -- FASTA format
fasta -- FASTA format
fch -- Gaussian formatted checkpoint file format
fchk -- Gaussian formatted checkpoint file format
fck -- Gaussian formatted checkpoint file format
feat -- Feature format
fh -- Fenske-Hall Z-Matrix format
fix -- SMILES FIX format
fpt -- Fingerprint format
fract -- Free Form Fractional format
fs -- FastSearching
fsa -- FASTA format
g03 -- Gaussian98/03 Output
g92 -- Gaussian98/03 Output
g94 -- Gaussian98/03 Output
g98 -- Gaussian98/03 Output
gal -- Gaussian98/03 Output
gam -- GAMESS Output
gamin -- GAMESS Input
gamout -- GAMESS Output
C7790 Introduction to Molecular Modelling -14Djungle
of formats II
gau -- Gaussian 98/03 Input
gjc -- Gaussian 98/03 Input
gjf -- Gaussian 98/03 Input
gpr -- Ghemical format
gr96 -- GROMOS96 format
gukin -- GAMESS-UK Input
gukout -- GAMESS-UK Output
gzmat -- Gaussian Z-Matrix Input
hin -- HyperChem HIN format
inchi -- InChI format
inp -- GAMESS Input
ins -- ShelX format
jin -- Jaguar input format
jout -- Jaguar output format
k -- Compare molecules using InChI
mcdl -- MCDL format
mcif -- Macromolecular Crystallographic Information
mdl -- MDL MOL format
ml2 -- Sybyl Mol2 format
mmcif -- Macromolecular Crystallographic Information
mmd -- MacroModel format
mmod -- MacroModel format
mol -- MDL MOL format
mol2 -- Sybyl Mol2 format
molden -- Molden input format
molreport -- Open Babel molecule report
moo -- MOPAC Output format
mop -- MOPAC Cartesian format
mopcrt -- MOPAC Cartesian format
mopin -- MOPAC Internal
mopout -- MOPAC Output format
mpc -- MOPAC Cartesian format
mpd -- Sybyl descriptor format
mpqc -- MPQC output format
mpqcin -- MPQC simplified input format
msi -- Accelrys/MSI Cerius II MSI format
msms -- M.F. Sanner's MSMS input format
nw -- NWChem input format
nwo -- NWChem output format
outmol -- DMol3 coordinates format
pc -- PubChem format
pcm -- PCModel Format
pdb -- Protein Data Bank format
png -- PNG files with embedded data
pov -- POV-Ray input format
pqr -- PQR format
pqs -- Parallel Quantum Solutions format
prep -- Amber Prep format
qcin -- Q-Chem input format
qcout -- Q-Chem output format
report -- Open Babel report format
res -- ShelX format
rsmi -- Reaction SMILES format
rxn -- MDL RXN format
sd -- MDL MOL format
sdf -- MDL MOL format
C7790 Introduction to Molecular Modelling -15Djungle
of formats III
The formats usually contain, in addition to the 3D/2D structure, also accompanying
information such as connectivity, force field parameters, atomic partial charges, various
properties, etc.
http://openbabel.org/wiki/Main_Page
OpenBabel is a chemical toolbox designed to speak the many languages ​​of chemical data.
It's an open, collaborative project allowing anyone to search, convert,
analyze, or store data from molecular modeling, chemistry, solid-state
materials, biochemistry, or related areas.
smi -- SMILES format
smiles -- SMILES format
sy2 -- Sybyl Mol2 format
t41 -- ADF TAPE41 format
tdd -- Thermo format
test -- Test format
therm -- Thermo format
tmol -- TurboMole Coordinate format
txt -- Title format
txyz -- Tinker MM2 format
unixyz -- UniChem XYZ format
vmol -- ViewMol format
xed -- XED format
xml -- General XML format
xtc -- XTC format
xyz -- XYZ cartesian coordinates format
yob -- YASARA.org YOB format
zin -- ZINDO input format
How to convert?
C7790 Introduction to Molecular Modelling -16Software
for visualizations
In addition to molecular modelling software (Avogadro, Nemesis, etc.), there are special
software serving only for visualizing structures and results.
Visual Molecular Dynamics (VMD) PyMOL
https://www.ks.uiuc.edu/Research/vmd
https://en.wikipedia.org/wiki/PyMOL
➢ scriptable (TCL, Python)
➢ advanced rendering
➢ available for MS Windows, Linux, macOS
https://en.wikipedia.org/wiki/List_of_molecular_graphics_systems
Overview of software:
C7790 Introduction to Molecular Modelling -17-
Summary
➢ Structures (Models) can be visualized in different ways.
➢ Visualization type is typically based on the intended description of studied
phenomenon/property.
➢ Geometry can be represented in Cartesian and/or internal coordinates.
➢ Computational chemistry (molecular modelling) employs huge number of formats
describing models, which complicates interoperability between different software.
Homework:
Is there a principal advantage of using
Cartesian or internal coordinates?