Subject: ASSIGNMENT OF ATOM TYPES IN MMFF94

From: Sami Mukhopadhyay <[email-masked]>
Date: Tue, 15 Feb 2000 11:57:20 +0530

Dear CCL NETers,

Assignment of atom types in MMFF94
----------------------------------------

MMFF94 -- an atom based force field is known to be useful and is
supported by many software packages in market. A naive study of the
method -- especially for assigning atom types to C & N atoms-posed some
problems for a beginner like me.

Atoms in aromatic 5-rings are treated quite extensively in MMFF94.

Types (38)NPYD and (39)NPYL are aromatic 5 ring N atoms with sigma and
pi lone pair respectively.
Type      (65)N5A is for aromatic 5 ring N atom which is alpha to N: or
O: or S:
whereas (66)N5B is for aromatic 5 ring N atom which is  beta  to N: or
O: or S:
There is also an atom type (79)N5 which is general N in heteroaromatic
5-ring

Similarly for carbon:

Type    (63)C5A is for aromatic 5 ring C atom which is alpha to N: or O:
or S:
whereas (64)C5B is for aromatic 5 ring C atom which is  beta to N: or O:
or S:
There is also an atom type (78)C5 which is general C in heteroaromatic
5-ring

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?

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]?

Since, above mentioned problems were encountered by a non-chemist, there
is a possibility of missed out facts. Can anybody put some light on
this?

Thanks in advance,

-- Bhalchandra Gore