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On 18/11/2011 3:11 AM, Ehud Schreiber wrote:
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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal">I have recently studied the hydrogen
database format of .hdb files (page 118, section 5.6.4 in the
manual version 4.5.4). I would like to make a few remarks
that, if correct, may need addressing.<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><span
style="mso-list:Ignore">1)<span style="font:7.0pt
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dir="LTR"></span>Method 3 of adding the hydrogens, that of
two planar hydrogens, gives -NH2 as the example. I think this
is misleading, as although this is true for an amide group
–C(=O)NH2 such as in an asparagine and glutamine side chains,
the nitrogen is tetrahedral in the R-NH2 case or in the amino
acid N-terminus.</p>
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<br>
True, though attempting to model pyramidal inversion with the usual
MM tool kit sounds like a recipe for trouble anyway.<br>
<br>
<blockquote
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<p class="MsoListParagraph" style="text-indent: -0.25in;"> A
better example for two planar hydrogens would be =CH2 such as
in ethylene or vinyls. <br>
</p>
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<br>
True, I'll add that to the manual ahead of amide -NH2.<br>
<br>
<blockquote
cite="mid:64E0EFC300379B4EB6A055D51941785401209BB6@cmail"
type="cite">
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<p class="MsoListParagraph"
style="text-indent:-.25in;mso-list:l1 level1 lfo2"><o:p></o:p></p>
<p class="MsoListParagraph"
style="text-indent:-.25in;mso-list:l1 level1 lfo2"><!--[if !supportLists]--><span
style="mso-list:Ignore">2)<span style="font:7.0pt
"Times New Roman""> </span></span><!--[endif]--><span
dir="LTR"></span>The provided methods for adding hydrogens
are not covering the whole set of possibilities. In
particular, it seems to me that three methods are lacking,
although admittedly they are less common:<o:p></o:p></p>
<p class="MsoListParagraph"
style="margin-left:1.0in;text-indent:-.25in;mso-list:l1 level2
lfo2"><!--[if !supportLists]--><span style="mso-list:Ignore">a.<span
style="font:7.0pt "Times New Roman""> </span></span><!--[endif]--><span
dir="LTR"></span>One tetrahedral hydrogen connected to atom
i which is in turn connected to two atoms j,k such that n is
on the plane bisecting angle j-i-k; n-i-j = n-i-k = 109.47
degrees; and dihedral n-i-j-l > 90 degrees. Example:
secondary amines R2NH. This case can be mimicked by method 2
with i,j,l atoms so is perhaps superfluous.<o:p></o:p></p>
<p class="MsoListParagraph"
style="margin-left:1.0in;text-indent:-.25in;mso-list:l1 level2
lfo2"><!--[if !supportLists]--><span style="mso-list:Ignore">b.<span
style="font:7.0pt "Times New Roman""> </span></span><!--[endif]--><span
dir="LTR"></span>One planar hydrogen connected to atom i
which is connected to only one other atom j such that n-i-j =
120 degrees and n-i-j-k is trans. Example: R2C=NH.<o:p></o:p></p>
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<br>
Yeah I'd use method 2 for both of these and rely on EM to fix it,
but some hints are in order.<br>
<br>
<blockquote
cite="mid:64E0EFC300379B4EB6A055D51941785401209BB6@cmail"
type="cite">
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<p class="MsoListParagraph"
style="margin-left:1.0in;text-indent:-.25in;mso-list:l1 level2
lfo2"><!--[if !supportLists]--><span style="mso-list:Ignore">c.<span
style="font:7.0pt "Times New Roman""> </span></span><!--[endif]--><span
dir="LTR"></span>One linear hydrogen such that n-i-j is a
straight line. Example: #CH where # is a triple bond.<o:p></o:p></p>
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<br>
That's a potentially useful feature, but method 2 would still be
acceptable with due care.<br>
<br>
<blockquote
cite="mid:64E0EFC300379B4EB6A055D51941785401209BB6@cmail"
type="cite">
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<p class="MsoListParagraph"
style="text-indent:-.25in;mso-list:l1 level1 lfo2"><!--[if !supportLists]--><span
style="mso-list:Ignore">3)<span style="font:7.0pt
"Times New Roman""> </span></span><!--[endif]--><span
dir="LTR"></span>I haven’t checked this, but can the k atom
be a hydrogen added in an earlier line of the same .hdb file?<o:p></o:p></p>
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<br>
I would think so.<br>
<br>
Mark<br>
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