User 8feadbc205
21-04-2014 06:31:03
Hello,
I just have some questions about chemaxon calculating molecular properties of the same molecule at different formats, and seems like they give different results. Take ATP for example. I downloaded the mole file directly from KEGG database and calculate its water accessible surface area (ASA)
It gives me this
id Atom count Formal charge ASA ASA+ ASA- ASA_H ASA_P (mol file)
1 47 0 528.45 271.24 257.21 213.18 315.27
When I converted the mole file to smiles string and inchi strings and calculated the same properties again. I got this:
NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O (smiles string chemaxon)
id Atom count Formal charge ASA ASA+ ASA- ASA_H ASA_P
1 47 0 536.16 274.93 261.23 217.84 318.32
InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 (inchi string chemaxon)
id Atom count Formal charge ASA ASA+ ASA- ASA_H ASA_P
1 47 0 611.34 334.02 277.32 229.53 381.81
I also have another chemistry toolbox called open babel and they have different way of writing smiles string and inchi string than chemaxon, the result is again quite different.
C([C@@H]1[C@H]([C@H]([C@H](n2cnc3c(N)ncnc23)O1)O)O)OP(=O)(O)OP(=O)(O)OP(=O)(O)O (smiles string open babel)
id Atom count Formal charge ASA ASA+ ASA- ASA_H ASA_P
1 47 0 530.93 273.18 257.75 214.46 316.47
InChI=1/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1/f/h18-19,21,23H,11H2 (inchi string open babel)
id Atom count Formal charge ASA ASA+ ASA- ASA_H ASA_P
1 47 0 611.34 334.02 277.32 229.53 381.81
The difference is actually quite significant. Could you give me some explanations for such discrepancy and any possible work around for this? Is the way of writing smiles and inchi strings correct in both chemaxon and open babel?
Thank you for your time and help!
Bin