Re: CCL:ASSIGNMENT OF ATOM TYPES IN MMFF94

[Richard Gillilan <richard - at - tc.cornell.edu>]

First, the easy part:
 >2) Coordination no. (i.e. no of attached atoms) for all the 3 types
 (38)NPYD,
 >   (39)NPYL and (79)N5 is [2]. How is this possible? e.g. in pyrrole, the
 > nitrogen atom gets atom type (39)NPYL, then how does (39)NPYL have
 >  coordination no. [2]?
 If you are looking at table II of Halgren's first paper on MMFF94,
 the coordination number, [2], listed for NPYL is a typo. The
 properties table (I) in his paper V lists the coordination number
 as [3].
 ----- now the hard part
 If you don't already know, it is very informative to look at the
 assigned structures in the free validation suite available on the
 osc web page. I tripped over this problem last summer, so it's not too
 fresh in my mind, but here goes:
 > The following questions arise from these facts:
 > 1) If ring is a hetero-aromatic 5-ring, with respect to the base atom,
 > only 4 atoms  need to be addressed. Clearly 2 of them (the 2 atoms
 > directly connected to base atom) will be alpha to the base atom,
 > remaining 2 will be beta to the base atom. (If the hetero atom is N, it
 > would be of type (39)NPYL. Hence, any other N in the same 5-ring will
 > have the atom type (38)NPYD or (65)N5A or (66)N5B and C will have the
 > atom type (63)C5A or (64)C5B. Any other type of carbon can't exist if
 > 5-ring is an aromatic ring)
 >In this situation, where do the types (78)C5 and (79)N5 fit? Can any one
 >suggest me a structure in which atom types (78)C5 or (79)N5 would be
 >used?
 One example is GUANCH01 (protonated guanine) in the validation suite.
 The two carbons shared between the 5 and 6 membered rings are
 not part of the imidazolium resonance structure. Because of the
 imidazolium part, the position of the atoms relative to "the unique
 lone-pair
 heteroatom" is ambiguous and the L5 parameter in the aromatic substitution
 table gets a value of 4. At least, that's what works for me. The aromatic
 substitution
 table is a bit puzzling since several aromatic types (like C5A, for example)
 appear
 in the "OLD TYPE" column as if the substitution gets called more than
 once on a given
 structure. Perhaps now that Thomas Halgren is with another company, he can speak
 freely
 on the subject of implementation. There are many details like this that I have
 encountered
 and it makes me appreciate why he has requested that any implementation that
 does not pass the
 suite of 761 molecules be labeled as "partial".
 Richard Gillilan
 Cornell Theory Center