# Bond angles in PDB

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.

This is what I got from optimisation.

• My eyesight must be poor. I don't see any 90° bond angle in the figure. – LDC3 Apr 22 '14 at 4:17
• 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. – BH2017 Apr 22 '14 at 4:26
• He said it should be tetrahedral, not trigonal planar. – BH2017 Apr 22 '14 at 21:06
• 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. – LDC3 Apr 23 '14 at 1:02
• Thank you! I agree, this guy is pretty strict when it comes to chem drawing; he's almost blocked me for my images. – BH2017 Apr 23 '14 at 1:36

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.

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)

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.

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)

• There's no double bonds in this PDB file. Could you please fix this? – BH2017 Jul 4 '14 at 8:28
• 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. – Martin - マーチン Jul 4 '14 at 9:27
• 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. – BH2017 Jul 4 '14 at 10:38
• 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. – Martin - マーチン Jul 4 '14 at 11:09

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.

• How could I do this? – BH2017 Apr 22 '14 at 21:14
• @BrentonHorne Info on geometry optimization added to answer. – Klaus-Dieter Warzecha Apr 22 '14 at 21:19
• How do I select the force field? – BH2017 Apr 22 '14 at 21:21
• @BrentonHorne Menu: Erweiterungen->Molekül-Mechanik->Kraftfeld einrichten. My Avogadro is in German. – Klaus-Dieter Warzecha Apr 22 '14 at 21:24
• Nvm I found out myself; but the amine still has a ~109-120 degree bond angle. – BH2017 Apr 22 '14 at 21:24

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.