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FORMAT OF THE FCON FILE


The FCON file is the chemical connectivity file which was used by the program CONNSER in Versions 1/2 of the Cambridge Crystallographic Structural Database System.

The basic concepts associated with the encoding of chemical connectivity can be illustrated with respect to a simple example :

Residues

Sodium acetate dihydrate is said to have 3 residues, viz. the acetate anion, the sodium cation and the water molecule.

The number of units of each residue is the residue multiplier. Thus residues 1 and 2 each have a multiplier of 1, residue 3 has a multiplier of 2.

Residue 1 has a net charge of -1, residue 2 a net charge of +1 and residue 3 a net charge of 0.

All atoms, excluding terminal H atoms, are assigned a number, 1 to 6 in the above example.

Atom Properties

Each numbered atom can be described in terms of:

For our example we have:

atom no.		el	nca	nh	nch

1 C 1 3 0 2 C 3 0 0 3 O 1 0 0 4 O 1 0 -1 5 NA 0 0 +1 6 O 0 2 0

In FCON we combine nca, nh and nch to form an atom property number, APN:

APN = 1000(nca) + 100(nh) + nch + 50

Thus:

Bond Properties

Each bond in the structure must also be defined in terms of the 2 atoms, one at each end of the bond, and the bond type.

In our example we have:

atom i		atom j		bond type (bt)

1 2 1 2 3 2 2 4 1

Thus:

In FCON we combine the 3 integers defining a bond into a single number, the bond property number, BPN:

BPN = 106(50+bt) + 103(i) + j

Thus:

The full set of allowed bond types is:

In addition, the distinction is made between acyclic and cyclic bonds:

Thus aromatic bonds are always of bond type -5 but single bonds can be of bond type 1 or -1, etc.

Some examples of FCON entries are given at the end of this chapter, together with explanatory notes. These should be carefully studied with respect to the FCON format specifications.

Overall Entry Structure in FCON

Each entry is composed of up to 5 possible record types:

  1. Directory record
  2. Residue properties record
  3. Atom properties record
  4. Bond properties record
  5. Comment record

    Records 1-4 are always present.

    Record 5 is present in less than 10% of FCON entries - for details see below.

    Record Type 1 : Directory

    The format is: (4HCONN,4X,A8,5I4,I6)

    The contents of the record are:

    Cols.	1-4 	CONN
    	9-16	Reference code
    	17-20	NRES		the number of residues
    	21-24	NATM		the total number of atoms, excluding terminal H atoms>
    	25-28	NBON		the total number of bonds
    	29-32	NCOM		the number of 4-character words of comment
    	33-36	NPOL		the polymer flag
    	37-42	NDAT		the accession date
    

    Notes:

    Record Type 2 : Residue Properties

    The format is: (5(F8.3,2I4))

    The contents of the record are:

    Cols.	1-8	PMLR1	the multiplier for residue 1
    	9-12	KCHR1	the net charge for residue 1
    	13-16	NATR1	the number of atoms in residue 1
    	17-24	PMLR2	the multiplier for residue 2
    	25-28	KCHR2	the net charge for residue 2
    	29-32	NATR2	the number of atoms in residue 2
    	..............................................
    	77-80	NATR5	the number of atoms in residue 5
    

    Note:

    In the few cases where there are more than 5 residues then the information is continued on a second residue properties record.

    Record Type 3 : Atom Properties

    The format is: (10(A2,I5,1X))

    The contents of the record are:

    Cols.	1-2	Element symbol for atom 1
    	3-7	Atom property number (APN) for atom 1
    	9-10	Element symbol for atom 2
    	11-15	Atom property number (APN) for atom 2
    	............................................
    	75-79	Atom property number (APN) for atom 10
    

    Notes:

    Record Type 4 : Bond Properties

    The format is: (8(I8,2X))

    The contents of the record are:

    Cols.	1-8	Bond property number (BPN) for bond 1
    	11-18	Bond property number (BPN) for bond 2
    	......................................
    	71-78	Bond property number (BPN) for bond 8
    

    Notes:

    Record Type 5 : Comment

    The format is: (20A4)

    The contents of the record are:

    Cols.	1-4	First 4-character word of comment text
    	5-8	Second 4-character word of comment text>
    	.............................................
    	77-80	Twentieth 4-character word of comment text
    

    Notes:

    Examples of FCON entries

    EXAMPLE 1. AABHTZ

    CONN    AABHTZ     1  23  24   0   0770506
       1.000   0  23
    C  3050 N  3050 N  3050 N  2050 C  2150 N  2150 N  2050 C  3050 N  2050 C  3050
    C  2150 O  1050 C  1350 O  1050 C  1350 C  3050 C  3050 C  3050 C  2150 CL 1050
    C  2150 CL 1050 C  2150
    49001002  51001003  48001004  49002005  51002006  51003007  51003008  49004009
    48005009  51006010  52007011  52008012  51008013  52010014  51010015  51011016
    45016017  45016018  45017019  51017020  45018021  51018022  45019023  45021023
    

    The directory record indicates:

    The residue properties record indicates that residue 1 has:

    The next 3 lines contain the atom properties record.

    For example, atom 6 is N with APN = 2150, ie.

    The next 3 lines contain the bond properties record.

    For example:

    EXAMPLE 2. ACAMPT

    CONN    ACAMPT     1  17  16  10   0711231
       1.000   0  17
    PT 4050 N  2150 N  2150 CL 1050 CL 1050 C  3050 C  3050 C  4050 O  1150 C  4050
    O  1150 C  1350 C  1350 C  1350 C  1350 C  1350 C  1350
    51001002  51001003  51001004  51001005  52002006  52003007  51006008  51006009
    51007010  51007011  51008012  51008013  51008014  51010015  51010016  51010017
    MATCHING IMPOSSIBLE because of disorder
    

    EXAMPLE 3. ACMPCD

    CONN    ACMPCD     2  32  32   0   1790511
       1.000   0  31   1.500   0   1
    N  3050 CD 6050 C  3050 C  3050 O  1050 O  1050 O  1050 O  1050 O  1250 N  3050
    O  1050 C  2150 N  1250 C  3150 C  2150 C  3150 O  2050 C  3150 O  1150 C  3150
    O  1150 C  2250 O  2050 P  4050 O  3050 O  2050 O  2050 CD 1050 CD 1050 CD 1050
    CD 1050 O   250
    51001002  49001003  48001004  56002005  56002006  56002007  56002008  51002009
    49003010  52003011  49004012  51004013  51010014  49010015  48012015  49014016
    49014017  49016018  51016019  49017020  49018020  51018021  51020022  51022023
    51023024  51024025  51024026  52024027  56025028  56025029  56026030  56027031
    


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