Connection Table File Format

---

The connection table format file described in this section is generated for the cyclohexanol structure shown below. All references to atom serial numbers are based on the Atom Numbering shown.

The following is a sample Connection Table file produced for cyclohexanol using ChemDraw. The line numbers are added for purposes of discussion only.

Line 1	Cyclohexanol
Line 2	7 7
Line 3	0.0000	0.5000	0.0000	C
Line 4	-0.8667	0.0000	0.0000	C
Line 5	-0.8667	-1.0000	0.0000	C
Line 6	0.0000	-1.5000	0.0000	C
Line 7	0.8667	-1.0000	0.0000	C
Line 8	0.8667	0.0000	0.0000	C
Line 9	0.0000	1.5000	0.0000	O
Line 10	1 2 1 1
Line 11	2 3 1 1
Line 12	3 4 1 1
Line 13	4 5 1 1
Line 14	5 6 1 1
Line 15	1 6 1 1
Line 16	6 7 1 1

Each line represents a data record containing one or more fields of information about the structure. Individual fields are delimited by space(s) or a tab. The fields in the Connection Table format file used by ChemDraw are discussed below. The field value for Carbon 6 from the example file is included in parentheses for reference.

• Line 1 is the molecule name. The molecule name is the file name when the file was created using ChemDraw.
• Line 2 contains two fields: the first field is the number of atom labels, and the second field is the number of bonds. These fields must be separated by at least one space.
• Lines 3-9 each contain 4 fields describing information about the individual atoms: the first field is the X Cartesian coordinate (0.8667), the second field is the Y Cartesian coordinate (0.0000), the third field is the Z Cartesian coordinate (0.0000), and the fourth field is the atom label (C).

The spacing of these fields is very important. Any data outside the following columns (especially data overlapping the ranges) may render a file unreadable.

• Field 1: Columns 0-9
• Field 2: Columns 10-19
• Field 3: Columns 20-29
• Field 4: Columns 31-end

• Lines 10-16 each contain four fields describing information about the individual bonds between the atoms: the first two fields represent the serial numbers of the atoms that are connected by this bond (atom 1 and atom 6), the third field is the bond order (1) and the fourth field is the bond type (1).

The bond types for the Connection Table format are as follows:

value	bond type
1	Single.
2	Dashed.
3	Hashed.
4	Wedged hash with first atom at narrow end.
5	Wedged hash with second atom at narrow end.
6	Bold.
7	Wedged with first atom at narrow end.
8	Wedged with second atom at narrow end.
9	Wavy.
10	Hollow wedge with narrow end towards 1st atom.
11	Hollow wedge with narrow end towards 2nd atom.
12	Dative bond with arrow towards 2nd atom.
13	Dative bond with arrow towards 1st atom.
14	Any (bond property).
15	Single/Double (bond property).
16	Double/Aromatic (bond property).
17	Single/Aromatic (bond property).

Double bonds are bit encoded using a bitmask. The default value (0) indicates a normal (two solid lines) double bond, with the second line on the right (looking from the first atom to the second). Other values are as follows:

value	bond type/position
1	The second line is on the left (looking from the first atom to the second).
2	The two lines are centered.
4	A double bond with one dashed and one solid line.
8	A modifier to the previous two values, indicating that the user specifically set the positioning. If this bit is not present, ChemDraw calculated the positioning automatically.
16	A double bond with one bold and one solid line.
32	A crossed bond.
64	A double bond with two dashed lines.

So, for example, a bitmask value of 13 (= 1 + 4 + 8) means a double bond with one dashed and one solid line (4), where the user specifically wants (8) the second line to be on the left (1).

NOTE: This connection table format is obsolete, and is documented here for historical purposes only. This format should never be used for critical work where chemical information is important.