.. _comparison_to_eh99:
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Comparing Grade2 and EH99 Restraints for amino acid side chains
***************************************************************
Introduction
============
Grade2 produces restraints for ligands that are based on information
from the Cambridge Structural Database
(`CSD `_)
of small molecule structures where possible.
This chapter examines the compatibility of Grade2 restraints
with the EH99
(`Engh and Huber, 2006 `_)
restraints for amino acids that are used in BUSTER refinements for proteins.
EH99 restraints were obtained by an analysis of CSD structures using different
methods when the CSD contained just over 200 thousand structures compared to
today when it has over 1.2 million structures
(`Statistics on the Cambridge Structural Database `_).
It is shown how Grade2 bond and angle restraint ideal values are consistent
with EH99 values.
Furthermore, the agreement between the sigma values is examined with the
conclusion that it is necessary to scale up Grade2 bond and angle restraint
sigmas for complete consistency with EH99.
We thank a Grade Web Server user for raising this matter.
Method
======
Grade2 restraint dictionaries were produced for 17 common proteinogenic
amino acids (excluding ``GLY``, ``ALA`` and ``PRO``). The bond and
bond angle restraints were compared to the EH99
(`Engh and Huber, 2006 `_)
restraints for each of the side chains. Data were analyzed
using `Jupyter Notebook `_ with
`matplotlib `_ and
`scipy.stats `_
Results
=======
.. figure:: images/grade2_eh99_comparison_bond_length.png
:width: 500
:align: center
:alt: EH99/Grade2 bond length comparison
Comparison between the ideal bond lengths of EH99 and Grade2 restraints for
amino acid side chains.
Blue circles are used to mark each ideal bond length.
The green dotted line marks equality.
As shown in the figure above, the ideal bond lengths are directly related
(Pearson's *r* (78) = 1.00, p < .001).
The root mean squared difference (rmsD) between the ideal bond lengths for the two sets
of restraints is 0.006Å. This can be compared to an mean bond sigma value
of 0.022Å for EH99 and 0.013Å for Grade2. The rmsD between the two sets is
therefore approximately half the lower of the mean sigma values.
It can be concluded that ideal bond
lengths of Grade2 reproduce EH99 values consistently, as would be expected
given they are both based on CSD structural information.
.. figure:: images/grade2_eh99_comparison_angle_ideal.png
:width: 500
:align: center
:alt: EH99/Grade2 ideal angle comparison
Comparison between the ideal angles in EH99 and Grade2 restraints for
amino acid side chains.
As shown in the figure above, the ideal bond angle in EH99 and Grade2
are also directly related
(Pearson's *r* (104) = .99, p < .001).
The rmsD between the ideal bond angles for the two sets
of restraints is 0.7º. This can be compared to an mean EH99 bond angle sigma value
of 1.7º and 1.4º for Grade2. Once again, the rmsD between the two sets is
therefore approximately half the lower of the mean sigma values.
It can be concluded that ideal bond angles also agree well.
.. figure:: images/grade2_eh99_comparison_bond_sigma.png
:width: 700
:align: center
:alt: EH99/Grade2 bond sigma comparison
Comparison between the bond sigma of EH99 and Grade2 restraints for
amino acid side chains.
Comparing the sigma values for bond lengths shows a moderate positive
correlation
(Pearson's *r* (78) = .58, p < .001).
The Grade2 value for sigma are smaller than corresponding EH99 value in
95% of bonds.
The mean sigma value for this set of bonds is 0.013Å
for Grade2 compared to 0.022Å for EH99. The ratio of the two means
is 1.68.
In a similar fashion the sigma values for bond angles (below) show a moderate positive
correlation
(Pearson's *r* (105) = .53, p < .001).
The Grade2 angle sigma 1.4º is smaller than than the mean EH99 angle sigma 1.7º
by a factor of 1.25.
.. figure:: images/grade2_eh99_comparison_angle_sigma.png
:width: 700
:align: center
:alt: EH99/Grade2 angle sigma comparison
Comparison between the bond angle sigma of EH99 and Grade2 restraints for
amino acid side chains.
A further investigation was conducted to find out why a
tighter distribution for both bond lengths and bond angles is produced
by Grade2 compared to EH99 values.
Grade2 uses a
`Mogul `_
option to only analyze CSD structures with an Rfactor <=5%. When this filter was
disabled, the mean amino acid bond sigma increased by a factor of 1.63 and
the mean angle sigma by 1.32. As these values are comparable to
the difference between Grade2 and EH99, the major difference between
Grade2 and EH99 is likely to be because Grade2 data is based on a selection
of the highest resolution CSD structures rather than a wider set.
.. _eh99_sigma_correction:
The ``--eh99_sigma_correction`` option
======================================
Grade2 from release :ref:`1.5.0 ` includes a
command line option ``--eh99_sigma_correction`` that scales up sigma values
for bonds and angles to
match the mean sigma values of the EH99 amino restraints:
* The sigma values for bonds, that do not involve hydrogen atoms,
are increased by a factor 1.68.
* The sigma values for bond angles, that do not involve hydrogen atoms,
are increased by a factor 1.25.
The ``--eh99_sigma_correction`` option can be used for refinements
where EH99 restraints
are used for protein residues, for instance in BUSTER.
If it is not used then ligand bond and angles will be restrained
to ideal values more strongly in comparison to protein residues
(for most users this will not be a problem).
The option should not be used if Grade2 restraints
are to be used with CCP4 restraints for amino acids. Comparing Grade2
and CCP4 restraints for amino acid bonds shows they have comparable
mean sigmas for both bond length and bond angles (Unpublished data).