# Generating mol files from a molecular structure image?

I have a question regarding mol files.For example I have this molecule-

The mol file for this is-

  Sample

22 23  0  0  0  0  0  0  0  0999 V2000
-2.5962    2.2535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-2.5962    0.7512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-1.2958    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
0.0000    0.7512    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
0.0000    2.2535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-1.2958    3.0047    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
-4.6479    1.7042    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
1.3005    3.0047    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-1.2958    4.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-1.2958   -1.5023    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
1.3005    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
1.3005   -1.5023    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
2.6009   -2.2535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
3.8967   -1.5023    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
3.8967    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
2.6009    0.7512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
5.1972   -2.2535    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
2.6009   -3.7559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-3.8967    3.0047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-5.1972    3.7559    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
-3.1455    4.3052    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
3.9014   -4.5070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
1  2  2  0  0  0  0
2  3  1  0  0  0  0
3  4  1  0  0  0  0
4  5  1  0  0  0  0
5  6  1  0  0  0  0
1  6  1  0  0  0  0
1 19  1  0  0  0  0
5  8  2  0  0  0  0
6  9  1  0  0  0  0
3 10  2  0  0  0  0
4 11  1  0  0  0  0
11 12  1  0  0  0  0
12 13  2  0  0  0  0
13 14  1  0  0  0  0
14 15  2  0  0  0  0
15 16  1  0  0  0  0
11 16  2  0  0  0  0
14 17  1  0  0  0  0
13 18  1  0  0  0  0
19  7  1  0  0  0  0
19 20  1  0  0  0  0
19 21  1  0  0  0  0
18 22  2  0  0  0  0
M  END


So,I have read that lines 5-26 are for atoms.first three columns represent x,y and z coordinates of atoms.So,my question is how are the coordinates of atoms decided?What is taken as the origin?Also,the atoms are large,so they may occupy more than one coordinate,so how do we decide what x,y,z value to take?Also,is H atoms not taken into account for creating mol files?

• which program did you use to create the mol file? – pH13 - Yet another Philipp Jun 27 '15 at 18:20
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• @PH13 I did not use any program.I got it from this site- scitouch.net/imago/report/report.html#g2 It is the first image under image2structure(statistics) – LifeIsGood Jun 27 '15 at 18:29
• because if you look closely, the protons of the CH3 and fluorine atoms of the CF3 group are missing – pH13 - Yet another Philipp Jun 27 '15 at 18:34
• Some programs for making 2D structures will store them in MOL files (with all atoms in a single plane), since the format stores all info needed to regenerate the (2D) structure. If you need 3D, you'll need something that can do basic molecular mechanics, at least geometry optimization. There are lots of options: I like [Avogadro](avogadro.cc), which is free, but there are lots of other options (both free and commercial). – j_foster Jun 27 '15 at 20:57

In MOL files, the presence of hydrogen atoms can be implied from valence and number of other bonds. (They can also be specified explicitly if needed.) In the long set of zeros at the end of each atom line (just after the element), the fourth zero specifies to add however many single bonds to hydrogen atoms are needed for the atom's valence. The sixth zero indicates to use the element's normal valence. For example, the carbon of the $\mathrm{CH_3}$ group has only one explicit bond, so three bonds to hydrogen are implied by carbon's normal valence of 4. How implicit hydrogens are handled depends on the software (e.g., this molecule has four implicit hydrogens that, per the usual convention for skeletal formulas, are not shown in your image).
• Thanks a lot.I I understand that coordinates for atom specify nucleus of the atom.But how do I assign the coordinates if I have to create a mol file.I was trying to generate mol files from the jpeg images of structures.So,in that case what coordinates for the atom should I use? – LifeIsGood Jun 27 '15 at 22:35