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people I've been trying to adjust the bond angles in a protein data bank (PDB) file, but I'm a novice when it comes to computing so I would like to ask your assistance. I have a file for metamizole, but as has been pointed out by a user on Wikipedia the 90 degree bond angle in it isn't consistent with the trigonal planar geometry of the nitrogen atom in the molecule. Here is my PDB file:

COMPND    UNNAMED
AUTHOR    GENERATED BY OPEN BABEL 2.3.2
HETATM    1  C   LIG     1      -0.971  -5.437  -1.069  1.00  0.00           C  
HETATM    2  N   LIG     1      -1.931  -4.484  -0.575  1.00  0.00           N  
HETATM    3  C   LIG     1      -3.342  -4.804  -0.629  1.00  0.00           C  
HETATM    4  S   LIG     1      -4.562  -3.540  -0.090  1.00  0.00           S  
HETATM    5  O   LIG     1      -4.430  -2.149  -1.074  1.00  0.00           O  
HETATM    6  O   LIG     1      -4.326  -3.106   1.433  1.00  0.00           O  
HETATM    7  O   LIG     1      -6.044  -4.127  -0.251  1.00  0.00           O  
HETATM    8  C   LIG     1      -1.479  -3.307  -0.058  1.00  0.00           C  
HETATM    9  C   LIG     1      -1.218  -3.011   1.277  1.00  0.00           C  
HETATM   10  C   LIG     1      -1.353  -3.951   2.413  1.00  0.00           C  
HETATM   11  N   LIG     1      -0.863  -1.703   1.337  1.00  0.00           N  
HETATM   12  C   LIG     1      -0.731  -0.968   2.567  1.00  0.00           C  
HETATM   13  N   LIG     1      -0.775  -1.218   0.118  1.00  0.00           N  
HETATM   14  C   LIG     1      -1.185  -2.152  -0.766  1.00  0.00           C  
HETATM   15  O   LIG     1      -1.262  -2.037  -2.012  1.00  0.00           O  
HETATM   16  C   LIG     1      -0.309   0.020  -0.235  1.00  0.00           C  
HETATM   17  C   LIG     1      -1.201   0.998  -0.733  1.00  0.00           C  
HETATM   18  C   LIG     1      -0.737   2.291  -1.040  1.00  0.00           C  
HETATM   19  C   LIG     1       0.619   2.617  -0.856  1.00  0.00           C  
HETATM   20  C   LIG     1       1.520   1.640  -0.390  1.00  0.00           C  
HETATM   21  C   LIG     1       1.059   0.346  -0.078  1.00  0.00           C  
HETATM   22  H   LIG     1      -1.483  -6.301  -1.438  1.00  0.00           H  
HETATM   23  H   LIG     1      -0.312  -5.724  -0.276  1.00  0.00           H  
HETATM   24  H   LIG     1      -0.403  -4.993  -1.861  1.00  0.00           H  
HETATM   25  H   LIG     1      -3.492  -5.667  -0.014  1.00  0.00           H  
HETATM   26  H   LIG     1      -3.539  -4.923  -1.674  1.00  0.00           H  
HETATM   27  H   LIG     1      -3.538  -1.778  -0.991  1.00  0.00           H  
HETATM   28  H   LIG     1      -1.646  -4.913   2.048  1.00  0.00           H  
HETATM   29  H   LIG     1      -2.094  -3.586   3.092  1.00  0.00           H  
HETATM   30  H   LIG     1      -0.414  -4.034   2.920  1.00  0.00           H  
HETATM   31  H   LIG     1      -0.853  -1.635   3.395  1.00  0.00           H  
HETATM   32  H   LIG     1      -1.481  -0.206   2.610  1.00  0.00           H  
HETATM   33  H   LIG     1       0.238  -0.518   2.611  1.00  0.00           H  
HETATM   34  H   LIG     1      -2.196   0.763  -0.872  1.00  0.00           H  
HETATM   35  H   LIG     1      -1.394   3.001  -1.399  1.00  0.00           H  
HETATM   36  H   LIG     1       0.954   3.571  -1.064  1.00  0.00           H  
HETATM   37  H   LIG     1       2.519   1.873  -0.276  1.00  0.00           H  
HETATM   38  H   LIG     1       1.721  -0.367   0.265  1.00  0.00           H  
CONECT    1    2   22   23   24                                       
CONECT    1                                                           
CONECT    2    1    3    8                                            
CONECT    3    2    4   25   26                                       
CONECT    3                                                           
CONECT    4    3    5    6    7                                       
CONECT    4                                                           
CONECT    5    4   27                                                 
CONECT    6    4                                                      
CONECT    7    4                                                      
CONECT    8    2    9   14                                            
CONECT    9    8   10   11                                            
CONECT   10    9   28   29   30                                       
CONECT   10                                                           
CONECT   11    9   12   13                                            
CONECT   12   11   31   32   33                                       
CONECT   12                                                           
CONECT   13   11   14   16                                            
CONECT   14   13    8   15                                            
CONECT   15   14                                                      
CONECT   16   13   17   21                                            
CONECT   17   16   18   34                                            
CONECT   18   17   19   35                                            
CONECT   19   18   20   36                                            
CONECT   20   19   21   37                                            
CONECT   21   20   16   38                                            
CONECT   22    1                                                      
CONECT   23    1                                                      
CONECT   24    1                                                      
CONECT   25    3                                                      
CONECT   26    3                                                      
CONECT   27    5                                                      
CONECT   28   10                                                      
CONECT   29   10                                                      
CONECT   30   10                                                      
CONECT   31   12                                                      
CONECT   32   12                                                      
CONECT   33   12                                                      
CONECT   34   17                                                      
CONECT   35   18                                                      
CONECT   36   19                                                      
CONECT   37   20                                                      
CONECT   38   21                                                      
MASTER        0    0    0    0    0    0    0    0   38    0   38    0
END

If you can also give me a general method of correcting this problem it will be much appreciated. Here is the gif file I get out of this PDB file from Jmol.

enter image description here

This is what I got from optimisation. enter image description here

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7
  • $\begingroup$ My eyesight must be poor. I don't see any 90° bond angle in the figure. $\endgroup$
    – LDC3
    Apr 22, 2014 at 4:17
  • $\begingroup$ Good point! I'll say that and see what response this guy has. I think he might have an inflamed ego, thinking he's the chem God. Thanks, Chem isn't my strong suit so I'm kind of letting this guy walk all over me. $\endgroup$
    – Josh Pinto
    Apr 22, 2014 at 4:26
  • $\begingroup$ He said it should be tetrahedral, not trigonal planar. $\endgroup$
    – Josh Pinto
    Apr 22, 2014 at 21:06
  • 1
    $\begingroup$ I made the molecule in ACD ChemSketch and it made the nitrogen almost planer. The C=C-N-C(-SO2CH3) torsion angle is 22.34° and -178.68° to the other carbon. So, your configuration should be OK. If he still thinks it should be tetrahedral, ask him for the molecular modeling calculation. $\endgroup$
    – LDC3
    Apr 23, 2014 at 1:02
  • $\begingroup$ Thank you! I agree, this guy is pretty strict when it comes to chem drawing; he's almost blocked me for my images. $\endgroup$
    – Josh Pinto
    Apr 23, 2014 at 1:36

3 Answers 3

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The crystal structure of metamizole can be found in Acta Cryst. (1979). B35, 612-615. It is also available via the ​Cambridge Crystallographic Data Centre (CCDC) database, entering the DOI: 10.1107/S0567740879004271.
metamizole
There are essentially two conformations. The phenyl ring is rotated of plane of the pyrazolone moiety by about $42.5/44.5^\circ$. The nitrogen(4) bound to the phenyl moiety is slightly out of plane of the surrounding atoms ($-0.17/-0.18~\mathring{\mathrm{A}}$), so is the neighbouring nitrogen(5) ($0.39~\mathring{\mathrm{A}}$). The methylaminomethane group is also pyramidalised [nitrogen(9)], as can be seen by the dihedral angles with respect to the pyrazolone ring, $\ce{C(3)-C(2)-N(9)-C(12)}$ and $\ce{C(3)-C(2)-N(9)-C(12)}$, being $89.3/104.6^\circ$ and $-43/-42.2^\circ$.

Here is a stick model screenshot of this structure, hydrogen atoms are not included in the files. (grey: carbon; red: oxygen; blue-ish: nitrogen; yellow: sulfur; purple: sodium) crystal structure

A calculation (BP86/cc-pVTZ in gas phase at $O~\mathrm{K}$) based on one of the modifications in the crystal structure reveals the same picture.
gas phase optimisation of metamizole

And for completeness the xyz coordinates of the optimised compound.

  38
BVP86/cc-PVDZ scf done: -1369.314862
 C     0.634952    10.049072     4.900129
 C    -0.038364     9.052812     5.625610
 C    -0.843603     9.404086     6.721280
 C    -0.967888    10.746974     7.078721
 C    -0.317360    11.745954     6.347432
 C     0.482122    11.389915     5.258069
 N     0.088512     7.682548     5.283073
 N     0.524862     7.332867     3.979484
 C     1.016111     6.033439     4.052906
 C     1.037214     5.613638     5.356904
 C     0.456058     6.652593     6.201473
 C    -0.418749     7.686282     2.908454
 C     1.415171     5.281438     2.830834
 N     1.587824     4.410206     5.852441
 C     0.695266     3.536091     6.539780
 S     0.466632     1.963130     5.547604
 O     1.708338     1.174668     5.559744
 O     0.313685     6.699922     7.422867
 C     2.964673     4.465074     6.365693
 O    -0.210611     2.273661     4.290449
 O    -0.634313     1.159020     6.505778
 H    -0.141454     0.406631     6.889481
 H    -1.345054     8.622837     7.287776
 H    -1.589369    11.013825     7.934553
 H    -0.429995    12.793897     6.626878
 H     1.005549    12.158525     4.687515
 H     1.289838     9.765864     4.076298
 H    -1.364716     7.127508     2.998793
 H     0.053315     7.462436     1.945681
 H    -0.625790     8.761093     2.953974
 H     0.547989     5.057675     2.191339
 H     2.145811     5.841566     2.228931
 H     1.854760     4.324136     3.132627
 H    -0.315695     3.946934     6.648080
 H     1.067111     3.196537     7.517244
 H     3.601787     4.973633     5.631670
 H     3.344097     3.442734     6.490780
 H     3.030898     5.004553     7.327684

Upon request, I will also provide a pdb file. There are probably a million ways for easy conversion of *.xyz files to *.pdb files. For example on linux with openbabel via

PROMPT> babel <filename>.xyz -opdb <filename>.pdb

Much more easier, because with graphical user interface: Avogadro (because it has openbabel built in).

  • open the *.xyz via file - open or ctrl+o
  • save the file as *.pdb via file - save as or ctrl+shift+s
    make sure you select as filetype "common molecule formats" and enter the ending

And as a result you will get this beautiful file:

COMPND    METAMIZOLE scf done: -1369.314862 
AUTHOR    GENERATED BY OPEN BABEL 2.3.0
HETATM    1  C   LIG     1       0.635  10.049   4.900  1.00  0.00           C  
HETATM    2  C   LIG     1      -0.038   9.053   5.626  1.00  0.00           C  
HETATM    3  C   LIG     1      -0.844   9.404   6.721  1.00  0.00           C  
HETATM    4  C   LIG     1      -0.968  10.747   7.079  1.00  0.00           C  
HETATM    5  C   LIG     1      -0.317  11.746   6.347  1.00  0.00           C  
HETATM    6  C   LIG     1       0.482  11.390   5.258  1.00  0.00           C  
HETATM    7  N   LIG     1       0.089   7.683   5.283  1.00  0.00           N  
HETATM    8  N   LIG     1       0.525   7.333   3.979  1.00  0.00           N  
HETATM    9  C   LIG     1       1.016   6.033   4.053  1.00  0.00           C  
HETATM   10  C   LIG     1       1.037   5.614   5.357  1.00  0.00           C  
HETATM   11  C   LIG     1       0.456   6.653   6.201  1.00  0.00           C  
HETATM   12  C   LIG     1      -0.419   7.686   2.908  1.00  0.00           C  
HETATM   13  C   LIG     1       1.415   5.281   2.831  1.00  0.00           C  
HETATM   14  N   LIG     1       1.588   4.410   5.852  1.00  0.00           N  
HETATM   15  C   LIG     1       0.695   3.536   6.540  1.00  0.00           C  
HETATM   16  S   LIG     1       0.467   1.963   5.548  1.00  0.00           S  
HETATM   17  O   LIG     1       1.708   1.175   5.560  1.00  0.00           O  
HETATM   18  O   LIG     1       0.314   6.700   7.423  1.00  0.00           O  
HETATM   19  C   LIG     1       2.965   4.465   6.366  1.00  0.00           C  
HETATM   20  O   LIG     1      -0.211   2.274   4.290  1.00  0.00           O  
HETATM   21  O   LIG     1      -0.634   1.159   6.506  1.00  0.00           O  
HETATM   22  H   LIG     1      -0.141   0.407   6.889  1.00  0.00           H  
HETATM   23  H   LIG     1      -1.345   8.623   7.288  1.00  0.00           H  
HETATM   24  H   LIG     1      -1.589  11.014   7.935  1.00  0.00           H  
HETATM   25  H   LIG     1      -0.430  12.794   6.627  1.00  0.00           H  
HETATM   26  H   LIG     1       1.006  12.159   4.688  1.00  0.00           H  
HETATM   27  H   LIG     1       1.290   9.766   4.076  1.00  0.00           H  
HETATM   28  H   LIG     1      -1.365   7.128   2.999  1.00  0.00           H  
HETATM   29  H   LIG     1       0.053   7.462   1.946  1.00  0.00           H  
HETATM   30  H   LIG     1      -0.626   8.761   2.954  1.00  0.00           H  
HETATM   31  H   LIG     1       0.548   5.058   2.191  1.00  0.00           H  
HETATM   32  H   LIG     1       2.146   5.842   2.229  1.00  0.00           H  
HETATM   33  H   LIG     1       1.855   4.324   3.133  1.00  0.00           H  
HETATM   34  H   LIG     1      -0.316   3.947   6.648  1.00  0.00           H  
HETATM   35  H   LIG     1       1.067   3.197   7.517  1.00  0.00           H  
HETATM   36  H   LIG     1       3.602   4.974   5.632  1.00  0.00           H  
HETATM   37  H   LIG     1       3.344   3.443   6.491  1.00  0.00           H  
HETATM   38  H   LIG     1       3.031   5.005   7.328  1.00  0.00           H  
CONECT    1   27    6    2                                            
CONECT    2    1    7    3                                            
CONECT    3    2    4   23                                            
CONECT    4    5    3   24                                            
CONECT    5    6   25    4                                            
CONECT    6   26    1    5                                            
CONECT    7    8    2   11                                            
CONECT    8   12    9    7                                            
CONECT    9   13    8   10                                            
CONECT   10    9   14   11                                            
CONECT   11    7   10   18                                            
CONECT   12   29   30   28    8                                       
CONECT   12                                                           
CONECT   13   31   32   33    9                                       
CONECT   13                                                           
CONECT   14   10   19   15                                            
CONECT   15   16   14   34   35                                       
CONECT   15                                                           
CONECT   16   20   17   21   15                                       
CONECT   16                                                           
CONECT   17   16                                                      
CONECT   18   11                                                      
CONECT   19   36   14   37   38                                       
CONECT   19                                                           
CONECT   20   16                                                      
CONECT   21   16   22                                                 
CONECT   22   21                                                      
CONECT   23    3                                                      
CONECT   24    4                                                      
CONECT   25    5                                                      
CONECT   26    6                                                      
CONECT   27    1                                                      
CONECT   28   12                                                      
CONECT   29   12                                                      
CONECT   30   12                                                      
CONECT   31   13                                                      
CONECT   32   13                                                      
CONECT   33   13                                                      
CONECT   34   15                                                      
CONECT   35   15                                                      
CONECT   36   19                                                      
CONECT   37   19                                                      
CONECT   38   19                                                      
MASTER        0    0    0    0    0    0    0    0   38    0   38    0
END

If you do not see any double bonds (or $\pi$ bonds as they should correctly be referred as) then you messed up your programs settings. (This is probably valid for any common molecular geometry file)

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4
  • $\begingroup$ There's no double bonds in this PDB file. Could you please fix this? $\endgroup$
    – Josh Pinto
    Jul 4, 2014 at 8:28
  • $\begingroup$ This is no PDB file, these are xyz atomic coordinates. They have no representation of bonds whatsoever. I consider the use of double bonds in the depiction of 3D structures of molecules as too incorrect, as it will never be close to the actual bonding picture (except for ethene maybe). I do not have any experience with PDB, so I cannot fix it. $\endgroup$
    – Martin - マーチン ♦
    Jul 4, 2014 at 9:27
  • $\begingroup$ OK, this question is about PDB files so I'm going to need a valid PDB file for me to accept your answer. Although if you know how to import these coordinates into avogadro, I could probably use it to create the PDB file I desire. $\endgroup$
    – Josh Pinto
    Jul 4, 2014 at 10:38
  • $\begingroup$ I have updated the answer with your desired pdb. I included also a short tutorial on how you can do it yourself. Just a note on the display of double bonds. There will be double bonds between sulfur and oxygen, which are wrong. There might be double bonds in the phenyl ring, which is absolutely not correct, since it is a delocalised electron system. $\endgroup$
    – Martin - マーチン ♦
    Jul 4, 2014 at 11:09
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Your interpretation of the remark on wikipedia is wrong.

It seems that you provided a pdb file of the structure as drawn and without any geometry optimization. As a result, N2, N3, and N13 are trigonal planar in your file, while there should in fact be pyramidalisation (there are lone pairs!).

Moreover, "the guy" isn't writing about bond angles, but about the dihedral angle formed by C1-N2-C8-C9, which is indeed close to 90° in your structure.

The criticism is justified.

Your should run a geometry optimization on the structure before you submit it.

In order to do that, open your pdb file in Avogadro, select MMFF94 as your force field and run a geometry optimization pressing AltCtrlO. If necessary, fiddle with the dihedral in question and repeat the optimization.

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8
  • $\begingroup$ How could I do this? $\endgroup$
    – Josh Pinto
    Apr 22, 2014 at 21:14
  • $\begingroup$ @BrentonHorne Info on geometry optimization added to answer. $\endgroup$
    – Klaus-Dieter Warzecha
    Apr 22, 2014 at 21:19
  • $\begingroup$ How do I select the force field? $\endgroup$
    – Josh Pinto
    Apr 22, 2014 at 21:21
  • $\begingroup$ @BrentonHorne Menu: Erweiterungen->Molekül-Mechanik->Kraftfeld einrichten. My Avogadro is in German. $\endgroup$
    – Klaus-Dieter Warzecha
    Apr 22, 2014 at 21:24
  • $\begingroup$ Nvm I found out myself; but the amine still has a ~109-120 degree bond angle. $\endgroup$
    – Josh Pinto
    Apr 22, 2014 at 21:24
0
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The nitrogen is trigonal planer with the lone pair orbitals aligned with the pi-bond orbitals on the 5-member ring. Also the benzene ring needs to be planer with the 5-member ring.

enter image description here

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