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I am using the Morphine mol file and I'm attempting to create a matrix which contains a table of the atoms and how they bond similar to a ball and stick format. In the mol file bond block listed bellow what do the type place holders mean?

  7  1  1  0  0  0  0
  1  2  1  0  0  0  0
  2 12  1  0  0  0  0
  1  3  2  0  0  0  0
  3 14  1  0  0  0  0
  2  4  2  0  0  0  0
  4 18  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  6  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  7 22  1  1  0  0  0
  8 10  1  0  0  0  0
  8 11  1  0  0  0  0
  8 20  1  1  0  0  0
  9 12  1  6  0  0  0
  9 13  1  0  0  0  0
 10 15  1  1  0  0  0
 10 14  1  0  0  0  0
 11 16  2  0  0  0  0
 13 17  1  6  0  0  0
 13 16  1  0  0  0  0
 15 19  1  0  0  0  0
 21 15  1  0  0  0  0
 22 21  1  0  0  0  0

This is the format I'm trying to create but not all the atoms have the full amount of bonds. What is wrong?

C   7   2   3   
C   1   12  4   12
C   1   14  5   5
C   2   18  6   18
C   3   6   3   6
C   4   5   4   5
C   1   8   9   22
C   7   10  11  20
C   7   12  13  12
C   8   15  14  15
C   8   16      16
O   2   9   2   9
C   9   17  16  16
C   3   10      10
N   10  19  21  
C   11  13  11  13
O   13          
O   4   4       
C   15          
H   8           
C   15  22  22  22
C   7   21  21  21
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The self-accepted answer given here is wrong.

Each line in a bond block of a MOL file represents one bond between two atoms.

A line in a bond block has the following compact format:

111222tttsssxxxrrrccc

With other words, each entry (=different number or letter) in such a line can take up to three spaces. If it needs less. e.g. when the atom number is smaller than 100, the data is right-aligned.

111 is the number of the first atom

222 is the number of the second atom

These atom numbers refer to the position of the atom in the atom block in the same file, where the cartesian coordinates and the atom type (element) are given.

ttt is the number decoding the bond type: 1=single, 2=double, 3=triple, etc.

sss describes the stereochemistry, 1 is a single bond pointing up, 6 is a single bond pointing down, etc.

The latter are used in the flat 2D MOL file of morphine cited in the question, e.g. for the only hydrogen atom in the file: a bridgehead H-atom.

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The bond block has the number of the atoms followed by the number of bonds mol files support up to three bonds. Not all the atoms are supposed to have all their bonds filled.

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  • $\begingroup$ Ah, so you had a problem and solved it yourself? That's great! (also, welcome to Chemistry.SE). It would be nice if you elaborated your answer though.. :) $\endgroup$ – ManishEarth Apr 9 '13 at 7:05

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