Hi, 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.
1) 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. A better example for two planar hydrogens would be =CH2 such as in ethylene or vinyls. 2) 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: a. 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. b. 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. c. One linear hydrogen such that n-i-j is a straight line. Example: #CH where # is a triple bond. 3) I haven't checked this, but can the k atom be a hydrogen added in an earlier line of the same .hdb file? What do you say? Thanks, Ehud Schreiber.
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