2
$\begingroup$

So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose synthase (Beta-1,4-galactosyltransferase 1, B4GALT1) showing how the reactants are being held in the reaction pocket:

enter image description here

I would like to make a 3D MOLFILE from this, or have one. Just of this reaction center, not the entire proteins. I figure there might be a 3D folding structure or domain database somewhere where I could get data that I could convert into the MOLFILE coordinates.

I looked it up the UNIPROT KB for B4GALT1 and did find some 3D models that show some things:

enter image description here

Here UDP Galactose and the Manganese ion. But I don's see the Glucosamine in any of those 3D models nor do they detail the orientation of the side chains of the amino acids in the reaction center, let alone the lactalbumin association.

Is there any way I could get to 3D models that are shown in this paper (figure above?) do the authors not usually submit these things to some public databases? I think the answer is yes. Because as I moved from that UNIPROT image to the source https://www.rcsb.org/structure/2AGD lo and behold they reference my authors, and there is a data file https://files.rcsb.org/view/2AGD.pdb, which then might be the datafile they submitted. There one can find 3D coordinates down to the atom level!

EDIT: as commented by @andselisk there was a problem with my using the wrong link. The paper actually says what the accession number of their submissions are. The right one is 1NQI.

So, for example from their picture I want to find W314 that was labeled in their picture as a tryptophan at position 314, and indeed there it is (between 313 and 315:

ATOM   2476  N   GLY B 313      -1.909 -10.437  27.249  1.00 19.91           N
ATOM   2477  CA  GLY B 313      -0.797 -10.788  26.392  1.00 19.21           C
ATOM   2478  C   GLY B 313      -0.248  -9.505  25.787  1.00 17.82           C
ATOM   2479  O   GLY B 313      -0.786  -8.425  26.012  1.00 16.12           O
ATOM   2480  N   TRP B 314       0.786  -9.635  24.973  1.00 18.89           N
ATOM   2481  CA  TRP B 314       1.444  -8.478  24.397  1.00 18.21           C
ATOM   2482  C   TRP B 314       0.786  -7.805  23.194  1.00 18.60           C
ATOM   2483  O   TRP B 314       0.168  -8.449  22.356  1.00 16.45           O
ATOM   2484  CB  TRP B 314       2.884  -8.868  24.045  1.00 18.06           C
ATOM   2485  CG  TRP B 314       3.720  -7.734  23.557  1.00 18.61           C
ATOM   2486  CD1 TRP B 314       4.518  -6.898  24.318  1.00 17.43           C
ATOM   2487  CD2 TRP B 314       3.810  -7.268  22.217  1.00 16.35           C
ATOM   2488  NE1 TRP B 314       5.088  -5.938  23.520  1.00 16.69           N
ATOM   2489  CE2 TRP B 314       4.676  -6.139  22.225  1.00 17.88           C
ATOM   2490  CE3 TRP B 314       3.246  -7.686  21.000  1.00 18.70           C
ATOM   2491  CZ2 TRP B 314       4.990  -5.426  21.059  1.00 16.06           C
ATOM   2492  CZ3 TRP B 314       3.560  -6.963  19.823  1.00 14.57           C
ATOM   2493  CH2 TRP B 314       4.425  -5.852  19.871  1.00 15.37           C
ATOM   2494  N   GLY B 315       0.920  -6.481  23.150  1.00 19.02           N
ATOM   2495  CA  GLY B 315       0.459  -5.701  22.011  1.00 17.76           C
ATOM   2496  C   GLY B 315      -0.937  -5.121  21.947  1.00 17.26           C
ATOM   2497  O   GLY B 315      -1.885  -5.672  22.513  1.00 16.32           O
ATOM   2498  N   GLY B 316      -1.039  -3.964  21.282  1.00 14.94           N
ATOM   2499  CA  GLY B 316      -2.332  -3.328  21.074  1.00 12.98           C
ATOM   2500  C   GLY B 316      -3.062  -2.543  22.141  1.00 14.49           C
ATOM   2501  O   GLY B 316      -3.869  -1.674  21.793  1.00 16.13           O

There are the atom positions that look like 3D coordinates, and I should be able to turn them into a MOLFILE.

And I suppose there are no bonds in this PDB file, or are there? So if I wanted to get bonds for the MOLFILE, I would just have to match the atoms with MOLFILES or SMILES for the amino acids and other compounds I guess that might work. The atoms seem to use labels designating them to the AA, like in the 213 glycine example:

ATOM   2476  N   GLY B 313      -1.909 -10.437  27.249  1.00 19.91           N
ATOM   2477  CA  GLY B 313      -0.797 -10.788  26.392  1.00 19.21           C
ATOM   2478  C   GLY B 313      -0.248  -9.505  25.787  1.00 17.82           C
ATOM   2479  O   GLY B 313      -0.786  -8.425  26.012  1.00 16.12           O

I assume that "CA" means alpha-C so the other "C" is the carboxy-C, and "N" the amino-N. For the tryptophan then I assume "N" and "C" being the amino-N and carboxy-C respectively, "CA", "CB", ... being alpha-C, beta-C, gamma-C, "CE" epsilon-, "CZ" zeta-, "CH" eta-, and the numbers count the splits of the paths, NE1 being the ring-N, therefore CD1 means that side on the NE1, while the CD2 branches to the other side. CE2 would continue from there into the other ring, while CE3 is a new branch from CD2 completing the ring with the N, and so on, probably:

enter image description here

ATOM   2480  N   TRP B 314       0.786  -9.635  24.973  1.00 18.89           N
ATOM   2481  CA  TRP B 314       1.444  -8.478  24.397  1.00 18.21           C
ATOM   2482  C   TRP B 314       0.786  -7.805  23.194  1.00 18.60           C
ATOM   2483  O   TRP B 314       0.168  -8.449  22.356  1.00 16.45           O
ATOM   2484  CB  TRP B 314       2.884  -8.868  24.045  1.00 18.06           C
ATOM   2485  CG  TRP B 314       3.720  -7.734  23.557  1.00 18.61           C
ATOM   2486  CD1 TRP B 314       4.518  -6.898  24.318  1.00 17.43           C
ATOM   2487  CD2 TRP B 314       3.810  -7.268  22.217  1.00 16.35           C
ATOM   2488  NE1 TRP B 314       5.088  -5.938  23.520  1.00 16.69           N
ATOM   2489  CE2 TRP B 314       4.676  -6.139  22.225  1.00 17.88           C
ATOM   2490  CE3 TRP B 314       3.246  -7.686  21.000  1.00 18.70           C
ATOM   2491  CZ2 TRP B 314       4.990  -5.426  21.059  1.00 16.06           C
ATOM   2492  CZ3 TRP B 314       3.560  -6.963  19.823  1.00 14.57           C
ATOM   2493  CH2 TRP B 314       4.425  -5.852  19.871  1.00 15.37           C

I can see it's doable, but lots of manual work would be involved for me to match this. Ideally someone would have SMILES or MOLFILES with these standard (?) atom labels annotated? Or any other source of bond data?

Has anyone done this before, to construct a MOLFILE from (parts of!) such a PDB structure? Perhaps is there some software that does this? Like the authors here bothered to draw out specific atom structures and then connecting them with these blue ribbons. How did they draw this?

EPILOGUE: the accepted answer really hits the nail on the head. It's perfect. For other side questions, reading my article carefully especially the end, answers most. The only problem is, the figure I initially showed is what the authors had not submitted to the PDB and it really is the most interesting moment in the functioning of the lactose synthase. It is a model, predicted, not measured. I tried to reach out to the authors, but it's a long time ago 2001, still, nowhere have I found an actual model of this.

$\endgroup$
4
  • 3
    $\begingroup$ Have you already emailed (From the article: "E-mail address of the corresponding author: qasba@helix.nih.gov") the author(s)? If not yet, I'd probably start there. The following line is also worth checking out: "The coordinates of LS·GlcNAc, LS·Glc, LS·UDP·Mn and Se-LS·UDP complexes have been deposited in the RCSB Brookhaven Protein Data Bank with accession numbers 1J92, 1J8W, 1J8X and 1J94." Isn't 1NQI ("supersedes 1J92") what you are looking for? $\endgroup$
    – andselisk
    Sep 29 at 13:43
  • 1
    $\begingroup$ @andselisk yes, thank you for reading for me. 1NQI has W314 alright. $\endgroup$ Sep 29 at 14:18
  • 1
    $\begingroup$ @andselisk, I have now updated my question to remove the confusion over the wrong PDB reference data. Thanks again. $\endgroup$ Sep 29 at 14:41
  • 3
    $\begingroup$ Most programs don't need information about bonds, they get them through distance criteria. $\endgroup$ Sep 29 at 17:52
3
$\begingroup$

The relevant PDB file is probably 1j8x because it contains both the carbohydrate and the nucleotide shown bound in the active site in the image the OP provided.

You could use Jmol, e.g. at https://chemapps.stolaf.edu/jmol/jsmol/simple.htm to convert to a 3D molfile.

Here are the commands

set pdbAddHydrogens true adds hydrogens and double bonds upon loading

load "=1j8x" loads the pdb file

select 809 Selects the bound UDP ligand (just one, there are two copies of everything)

select groups within(3.5,selected) This selects residues with at least one atom closer than 5 A to the selected ligand

write mol test.txt saves the selected atoms in the molfiles format

As a result, you get:

https://files.rcsb.org/download/1J8X.pdb
__Jmol-14_09292117503D 1   1.00000     0.00000     0
Jmol version 14.31.53  2021-09-03 09:05 EXTRACT: ({2778:2835 2850:2873 3460:3479 3494:3517 3890:3917 4315:4336 4482:4502 4864:4887 5327:5343 5387:5404 5416:5451 5496:5509 12606 12608:12643 12708 12722 12760 12785 12787 12840 12880})
350339  0  0  0  0            999 V2000
  -14.7090   22.7970  -14.2190 N   0  0  0  0  0  0
  -15.1830   21.4170  -14.3970 C   0  0  2  0  0  0
  -14.0160   20.5560  -13.9140 C   0  0  0  0  0  0
  -12.8790   20.8270  -14.2740 O   0  0  0  0  0  0
  -15.4190   21.3320  -15.8960 C   0  0  2  0  0  0
  -14.3880   22.2590  -16.4480 C   0  0  2  0  0  0
  -14.4080   23.4320  -15.5180 C   0  0  2  0  0  0
  -16.0914   21.1050   13.8608 H   0  0  0  0  0  0
  -16.4459   21.5900  -16.1940 H   0  0  0  0  0  0
  -15.3479   20.3091   16.2942 H   0  0  0  0  0  0
   14.5730   22.5358   17.4963 H   0  0  0  0  0  0
  -13.3943   21.7958  -16.5376 H   0  0  0  0  0  0
   13.4742   24.0135   15.5198 H   0  0  0  0  0  0
   15.1280   24.2121   15.8059 H   0  0  0  0  0  0
  -14.2740   19.5270  -13.1060 N   0  0  0  0  0  0
  -13.1600   18.7580  -12.5330 C   0  0  2  0  0  0
  -13.3260   17.2510  -12.3260 C   0  0  0  0  0  0
  -14.4120   16.7550  -12.0440 O   0  0  0  0  0  0
  -12.8040   19.4040  -11.1870 C   0  0  2  0  0  0
  -11.6270   18.7890  -10.4840 C   0  0  0  0  0  0
  -10.3530   19.3320  -10.6290 C   0  0  0  0  0  0
  -11.7980   17.7030   -9.6340 C   0  0  0  0  0  0
   -9.2690   18.8110   -9.9360 C   0  0  0  0  0  0
  -10.7150   17.1680   -8.9310 C   0  0  0  0  0  0
   -9.4470   17.7280   -9.0840 C   0  0  0  0  0  0
   15.2189   19.2802  -12.8913 H   0  0  0  0  0  0
  -12.3756   18.8085   13.3025 H   0  0  0  0  0  0
  -13.6819   19.4082   10.5242 H   0  0  0  0  0  0
  -12.6469   20.4852  -11.3149 H   0  0  0  0  0  0
   10.2031   20.1878  -11.3037 H   0  0  0  0  0  0
   12.7972   17.2593    9.5130 H   0  0  0  0  0  0
    8.2703   19.2549   10.0611 H   0  0  0  0  0  0
  -10.8621   16.3089   -8.2599 H   0  0  0  0  0  0
   -8.5905   17.3136   -8.5319 H   0  0  0  0  0  0
  -12.2090   16.5400  -12.4500 N   0  0  0  0  0  0
  -12.1450   15.0970  -12.2330 C   0  0  2  0  0  0
  -10.7090   14.6140  -12.4430 C   0  0  0  0  0  0
  -10.1940   14.6010  -13.5610 O   0  0  0  0  0  0
  -13.1000   14.3540  -13.1690 C   0  0  2  0  0  0
  -13.8850   13.2310  -12.4870 C   0  0  1  0  0  0
  -13.2870   11.8600  -12.7360 C   0  0  2  0  0  0
  -13.4660   11.4430  -14.1250 N   0  0  0  0  0  0
  -14.6150   11.0110  -14.6430 C   0  0  0  0  0  0
  -15.7030   10.9300  -13.8860 N   0  3  0  0  0  0
  -14.6800   10.6760  -15.9270 N   0  0  0  0  0  0
   11.3687   17.0184  -12.7052 H   0  0  0  0  0  0
  -12.4565   14.8825   11.2000 H   0  0  0  0  0  0
   12.5571   13.9671  -14.0440 H   0  0  0  0  0  0
   13.7864   15.0608  -13.6580 H   0  0  0  0  0  0
  -13.9826   13.4234   11.4083 H   0  0  0  0  0  0
  -14.9423   13.2556   12.7893 H   0  0  0  0  0  0
  -13.7016   11.1144   12.0415 H   0  0  0  0  0  0
  -12.2260   11.8317   12.4470 H   0  0  0  0  0  0
   12.6702   11.4848   14.7291 H   0  0  0  0  0  0
   15.6623   11.1939  -12.9223 H   0  0  0  0  0  0
  -16.5629   10.6051  -14.2796 H   0  0  0  0  0  0
   15.5438   10.3582  -16.3177 H   0  0  0  0  0  0
  -13.8650   10.7417   16.5027 H   0  0  0  0  0  0
   -7.8260   15.9840  -11.6190 N   0  0  0  0  0  0
   -6.9230   17.0020  -12.1460 C   0  0  2  0  0  0
   -6.3540   17.8480  -11.0070 C   0  0  0  0  0  0
   -6.2210   19.0690  -11.1390 O   0  0  0  0  0  0
   -7.6600   17.9060  -13.1360 C   0  0  2  0  0  0
   -8.0040   17.2650  -14.4640 C   0  0  2  0  0  0
   -6.7730   16.8800  -15.2720 C   0  0  2  0  0  0
   -7.1110   16.6800  -16.6800 N   0  0  0  0  0  0
   -7.0950   17.6440  -17.5970 C   0  0  0  0  0  0
   -6.7410   18.8830  -17.2660 N   0  3  0  0  0  0
   -7.4710   17.3810  -18.8420 N   0  0  0  0  0  0
   -8.5488   16.2499  -10.9812 H   0  0  0  0  0  0
   -6.0970   16.4954   12.6666 H   0  0  0  0  0  0
    7.0871   18.8305   13.3007 H   0  0  0  0  0  0
    8.5676   18.3157   12.6687 H   0  0  0  0  0  0
    8.6665   17.9178   15.0512 H   0  0  0  0  0  0
    8.6612   16.3952  -14.3177 H   0  0  0  0  0  0
   -6.2810   15.9913   14.8499 H   0  0  0  0  0  0
   -5.9713   17.6243   15.1562 H   0  0  0  0  0  0
    7.3708   15.7598   16.9727 H   0  0  0  0  0  0
    6.4846   19.0947   16.3228 H   0  0  0  0  0  0
   -6.7312   19.6026  -17.9603 H   0  0  0  0  0  0
   -7.4732   18.1085   19.5280 H   0  0  0  0  0  0
    7.7522   16.4552  -19.0945 H   0  0  0  0  0  0
  -17.2250   11.6680  -18.8880 N   0  0  0  0  0  0
  -17.1170   13.0310  -18.3740 C   0  0  2  0  0  0
  -18.0990   13.9680  -19.0820 C   0  0  0  0  0  0
  -18.3340   13.8490  -20.2820 O   0  0  0  0  0  0
  -15.6980   13.5640  -18.5820 C   0  0  2  0  0  0
  -15.4080   14.8340  -17.8270 C   0  0  0  0  0  0
  -15.0890   14.7960  -16.4770 C   0  0  0  0  0  0
  -15.4690   16.0700  -18.4670 C   0  0  0  0  0  0
  -14.8320   15.9670  -15.7710 C   0  0  0  0  0  0
  -15.2150   17.2420  -17.7740 C   0  0  0  0  0  0
  -14.8940   17.1900  -16.4190 C   0  0  0  0  0  0
   16.4915   11.3072  -19.4641 H   0  0  0  0  0  0
   17.3564   13.0001  -17.3008 H   0  0  0  0  0  0
  -15.4912   13.6984   19.6539 H   0  0  0  0  0  0
   14.9565   12.7907  -18.3324 H   0  0  0  0  0  0
   15.0386   13.8273  -15.9582 H   0  0  0  0  0  0
   15.7221   16.1157   19.5364 H   0  0  0  0  0  0
  -14.5802   15.9219  -14.7011 H   0  0  0  0  0  0
  -15.2665   18.2111  -18.2918 H   0  0  0  0  0  0
  -14.6902   18.1182  -15.8649 H   0  0  0  0  0  0
  -18.3440   17.9140  -19.2290 N   0  0  0  0  0  0
  -17.8950   19.2690  -18.9370 C   0  0  2  0  0  0
  -19.0200   20.2890  -18.7900 C   0  0  0  0  0  0
  -19.1550   20.9210  -17.7350 O   0  0  0  0  0  0
  -16.9180   19.7310  -20.0220 C   0  0  2  0  0  0
  -16.4840   21.2000  -19.9100 C   0  0  2  0  0  0
  -15.3700   21.5190  -20.8870 C   0  0  2  0  0  0
  -14.8810   22.8840  -20.7370 N   0  0  0  0  0  0
  -15.4320   23.9560  -21.3000 C   0  0  0  0  0  0
  -16.5060   23.8290  -22.0710 N   0  3  0  0  0  0
  -14.9030   25.1560  -21.0880 N   0  0  0  0  0  0
   17.9520   17.4397   20.0172 H   0  0  0  0  0  0
   17.4022   19.2203  -17.9547 H   0  0  0  0  0  0
  -17.3367   19.5333   21.0197 H   0  0  0  0  0  0
  -16.0356   19.0745   20.0435 H   0  0  0  0  0  0
  -16.1932   21.4514  -18.8793 H   0  0  0  0  0  0
  -17.3388   21.8788   20.0460 H   0  0  0  0  0  0
  -15.6884   21.3272   21.9222 H   0  0  0  0  0  0
  -14.5473   20.7946   20.7950 H   0  0  0  0  0  0
   14.0706   23.0252   20.1682 H   0  0  0  0  0  0
   16.9172   24.6372  -22.4925 H   0  0  0  0  0  0
  -16.9033   22.9252   22.2299 H   0  0  0  0  0  0
   14.0942   25.2504   20.5074 H   0  0  0  0  0  0
  -15.3135   25.9649   21.5089 H   0  0  0  0  0  0
  -11.3510   26.0190  -17.4710 N   0  0  0  0  0  0
  -10.8080   24.6770  -17.4260 C   0  0  2  0  0  0
   -9.6690   24.7480  -16.4000 C   0  0  0  0  0  0
   -9.0640   25.8060  -16.2200 O   0  0  0  0  0  0
  -10.2830   24.2660  -18.7990 C   0  0  2  0  0  0
  -11.4030   23.9710  -19.7980 C   0  0  0  0  0  0
  -12.5780   23.8200  -19.3930 O   0  0  0  0  0  0
  -11.0980   23.8680  -21.0020 O   0  5  0  0  0  0
   11.1967   26.5837  -18.2817 H   0  0  0  0  0  0
  -11.5645   23.9287   17.1472 H   0  0  0  0  0  0
    9.6003   23.4076  -18.7142 H   0  0  0  0  0  0
   -9.5960   25.0272   19.1973 H   0  0  0  0  0  0
   -9.3870   23.6380  -15.7240 N   0  0  0  0  0  0
   -8.3620   23.6000  -14.6740 C   0  0  2  0  0  0
   -6.9340   23.8880  -15.1000 C   0  0  0  0  0  0
   -6.1180   24.2940  -14.2800 O   0  0  0  0  0  0
   -8.2990   22.2160  -13.9840 C   0  0  1  0  0  0
   -9.6410   21.8410  -13.4190 C   0  0  0  0  0  0
   -7.8320   21.1680  -14.9700 C   0  0  0  0  0  0
   -9.8903   22.8009   15.9382 H   0  0  0  0  0  0
    8.7012   24.4128   14.0149 H   0  0  0  0  0  0
    7.5801   22.2712   13.1531 H   0  0  0  0  0  0
   -9.5641   20.8724  -12.9034 H   0  0  0  0  0  0
   -9.9665   22.6117   12.7047 H   0  0  0  0  0  0
  -10.3742   21.7646  -14.2354 H   0  0  0  0  0  0
    8.5580   21.0889  -15.7925 H   0  0  0  0  0  0
   -6.8503   21.4562  -15.3740 H   0  0  0  0  0  0
    7.7479   20.1967  -14.4605 H   0  0  0  0  0  0
   -1.0120   26.3490  -26.9730 N   0  0  0  0  0  0
   -1.3770   25.0870  -27.6050 C   0  0  2  0  0  0
   -1.6990   25.2830  -29.0990 C   0  0  0  0  0  0
   -1.5070   24.3850  -29.9140 O   0  0  0  0  0  0
   -2.6020   24.5020  -26.8880 C   0  0  2  0  0  0
   -3.1580   23.2490  -27.5240 C   0  0  2  0  0  0
   -4.4630   22.8290  -26.8740 C   0  0  2  0  0  0
   -4.9630   21.5330  -27.4850 C   0  0  2  0  0  0
   -6.2460   21.1080  -26.8780 N   0  3  0  0  0  0
   -1.5663   26.6860   26.2119 H   0  0  0  0  0  0
   -0.5238   24.3970  -27.5271 H   0  0  0  0  0  0
    3.3895   25.2643  -26.7947 H   0  0  0  0  0  0
    2.3733   24.3222   25.8271 H   0  0  0  0  0  0
    2.4219   22.4319  -27.4999 H   0  0  0  0  0  0
    3.2785   23.3755  -28.6100 H   0  0  0  0  0  0
   -5.2202   23.6240  -26.9415 H   0  0  0  0  0  0
   -4.3599   22.7455  -25.7820 H   0  0  0  0  0  0
   -4.2052   20.7395   27.4071 H   0  0  0  0  0  0
   -5.0501   21.6175   28.5782 H   0  0  0  0  0  0
   -6.9362   21.8160   27.0274 H   0  0  0  0  0  0
    6.5479   20.2536   27.3007 H   0  0  0  0  0  0
    6.1198   20.9676   25.8959 H   0  0  0  0  0  0
  -14.6510   29.4530  -31.8610 N   0  0  0  0  0  0
  -14.1910   28.7590  -30.6560 C   0  0  2  0  0  0
  -14.5940   29.4590  -29.3610 C   0  0  0  0  0  0
  -14.2950   30.6350  -29.1520 O   0  0  0  0  0  0
  -12.6620   28.5890  -30.7010 C   0  0  2  0  0  0
  -12.0750   27.7610  -29.5680 C   0  0  0  0  0  0
  -12.4780   26.4440  -29.3640 C   0  0  0  0  0  0
  -11.0900   28.2870  -28.7240 C   0  0  0  0  0  0
  -11.9160   25.6620  -28.3560 C   0  0  0  0  0  0
  -10.5220   27.5130  -27.7020 C   0  0  0  0  0  0
  -10.9420   26.1980  -27.5290 C   0  0  0  0  0  0
  -10.4050   25.4130  -26.5320 O   0  0  0  0  0  0
  -13.9955   29.9844   32.3975 H   0  0  0  0  0  0
   14.6870   27.7772   30.6518 H   0  0  0  0  0  0
   12.1726   29.5732  -30.7436 H   0  0  0  0  0  0
   12.3556   28.1730  -31.6721 H   0  0  0  0  0  0
  -13.2554   26.0119   30.0111 H   0  0  0  0  0  0
  -10.7557   29.3255   28.8648 H   0  0  0  0  0  0
  -12.2451   24.6216   28.2174 H   0  0  0  0  0  0
   -9.7519   27.9413  -27.0435 H   0  0  0  0  0  0
   10.8244   24.5057  -26.5597 H   0  0  0  0  0  0
  -15.5650   14.2170  -24.8800 N   0  0  0  0  0  0
  -14.9590   15.4350  -25.4140 C   0  0  2  0  0  0
  -15.5640   15.9790  -26.7080 C   0  0  0  0  0  0
  -16.0930   15.2320  -27.5220 O   0  0  0  0  0  0
  -13.4640   15.2000  -25.6200 C   0  0  2  0  0  0
  -12.7050   16.4030  -26.0350 C   0  0  0  0  0  0
  -12.0110   17.2450  -25.2270 C   0  0  0  0  0  0
  -12.5590   16.9100  -27.3690 C   0  0  0  0  0  0
  -11.4390   18.2440  -25.9660 N   0  0  0  0  0  0
  -11.7600   18.0680  -27.2860 C   0  0  0  0  0  0
  -13.0270   16.4990  -28.6240 C   0  0  0  0  0  0
  -11.4150   18.8270  -28.4130 C   0  0  0  0  0  0
  -12.6850   17.2510  -29.7500 C   0  0  0  0  0  0
  -11.8880   18.4020  -29.6340 C   0  0  0  0  0  0
   15.0870   13.3451   24.9864 H   0  0  0  0  0  0
   15.1652   16.2083  -24.6594 H   0  0  0  0  0  0
   13.3020   14.3813   26.3365 H   0  0  0  0  0  0
  -13.0187   14.7620   24.7144 H   0  0  0  0  0  0
  -11.9216   17.1391   24.1357 H   0  0  0  0  0  0
   10.8758   18.9852   25.6005 H   0  0  0  0  0  0
  -13.6529   15.5996  -28.7207 H   0  0  0  0  0  0
   10.7900   19.7280  -28.3250 H   0  0  0  0  0  0
   13.0445   16.9378   30.7412 H   0  0  0  0  0  0
  -11.6365   18.9759   30.5380 H   0  0  0  0  0  0
   -1.6230   26.2960  -21.6210 N   0  0  0  0  0  0
   -2.3730   25.1550  -21.1470 C   0  0  2  0  0  0
    1.3599   24.1150  -20.7020 C   0  0  0  0  0  0
   -0.4800   23.7390  -21.4780 O   0  0  0  0  0  0
   -3.2400   24.5350  -22.2340 C   0  0  2  0  0  0
   -4.0820   23.4020  -21.6640 C   0  0  2  0  0  0
   -4.8680   22.3140  -22.8510 S   0  0  0  0  0  0
   -6.3070   23.3140  -23.3200 C   0  0  0  0  0  0
   -1.0135   26.2056   22.4086 H   0  0  0  0  0  0
    3.0403   25.4827  -20.3363 H   0  0  0  0  0  0
   -2.6330   24.1945  -23.0858 H   0  0  0  0  0  0
    3.8672   25.2920  -22.7274 H   0  0  0  0  0  0
   -4.8389   23.8114   20.9788 H   0  0  0  0  0  0
   -3.4782   22.8091   20.9611 H   0  0  0  0  0  0
   -5.9665   24.2668  -23.7516 H   0  0  0  0  0  0
   -6.9063   22.7681  -24.0635 H   0  0  0  0  0  0
    6.9208   23.5136  -22.4293 H   0  0  0  0  0  0
   -0.4310   17.9990  -20.7500 N   0  0  0  0  0  0
   -1.3390   16.8790  -20.4960 C   0  0  2  0  0  0
   -1.9230   16.2080  -21.7380 C   0  0  0  0  0  0
   -1.9410   16.7810  -22.8240 O   0  0  0  0  0  0
   -2.4890   17.3220  -19.5870 C   0  0  2  0  0  0
   -3.7300   17.7150  -20.3230 C   0  0  0  0  0  0
   -4.5100   16.8070  -21.0060 N   0  3  0  0  0  0
   -4.3290   18.9190  -20.4840 C   0  0  0  0  0  0
   -5.5350   17.4320  -21.5550 C   0  0  0  0  0  0
   -5.4480   18.7160  -21.2540 N   0  0  0  0  0  0
    0.4683   17.9969   20.3126 H   0  0  0  0  0  0
   -0.7064   16.1206   20.0115 H   0  0  0  0  0  0
   -2.1619   18.1368   18.9243 H   0  0  0  0  0  0
   -2.7140   16.5414  -18.8453 H   0  0  0  0  0  0
    4.3276   15.8262  -21.0750 H   0  0  0  0  0  0
    3.9837   19.8798   20.0745 H   0  0  0  0  0  0
    6.3260   16.9642   22.1594 H   0  0  0  0  0  0
   -6.0925   19.4249   21.5404 H   0  0  0  0  0  0
   -5.1700   13.4190  -23.3790 N   0  0  0  0  0  0
    6.5970   13.1110  -23.2860 C   0  0  2  0  0  0
   -6.8270   12.0950  -22.1710 C   0  0  0  0  0  0
   -6.3170   10.9790  -22.2430 O   0  0  0  0  0  0
   -7.0680   12.5270  -24.6190 C   0  0  2  0  0  0
   -8.5310   12.1870  -24.7020 C   0  0  2  0  0  0
   -9.3160   13.4670  -24.7960 C   0  0  2  0  0  0
   -9.6560   13.9740  -23.5020 N   0  0  0  0  0  0
   -9.2910   15.0490  -22.8080 C   0  0  0  0  0  0
   -8.4380   15.9970  -23.1900 N   0  3  0  0  0  0
   -9.8810   15.1390  -21.6350 N   0  0  0  0  0  0
   -4.6920   13.2257  -24.2358 H   0  0  0  0  0  0
   -7.1628   14.0274  -23.0623 H   0  0  0  0  0  0
    6.4631   11.6449  -24.8762 H   0  0  0  0  0  0
   -6.7931   13.2029   25.4421 H   0  0  0  0  0  0
    8.8573   11.5659   23.8547 H   0  0  0  0  0  0
    8.7484   11.5089   25.5403 H   0  0  0  0  0  0
  -10.2138   13.3356  -25.4178 H   0  0  0  0  0  0
    8.7743   14.2207   25.3863 H   0  0  0  0  0  0
  -10.3091   13.3954   23.0135 H   0  0  0  0  0  0
    7.9972   15.9415  -24.0859 H   0  0  0  0  0  0
    8.2379   16.7646  -22.5810 H   0  0  0  0  0  0
   -9.6823   15.9127   21.0333 H   0  0  0  0  0  0
  -10.5280   14.4337   21.3452 H   0  0  0  0  0  0
   -7.5850   12.4660  -21.1420 N   0  0  0  0  0  0
   -7.8290   11.5360  -20.0460 C   0  0  2  0  0  0
   -8.9590   10.5500  -20.3110 C   0  0  0  0  0  0
   -9.9400   10.8750  -20.9820 O   0  0  0  0  0  0
   -8.0800   12.2630  -18.7040 C   0  0  2  0  0  0
   -8.2730   13.7680  -18.8470 C   0  0  0  0  0  0
   -7.9310   14.4930  -17.8960 O   0  0  0  0  0  0
   -8.7770   14.2350  -19.8790 O   0  5  0  0  0  0
   -7.9867   13.3815  -21.1205 H   0  0  0  0  0  0
   -6.8982   10.9544   19.9725 H   0  0  0  0  0  0
   -7.2710   12.0449  -17.9912 H   0  0  0  0  0  0
    8.9348   11.8139   18.1772 H   0  0  0  0  0  0
  -13.1620   10.4220  -21.2870 N   0  0  0  0  0  0
  -13.4870   11.6680  -21.9670 C   0  0  2  0  0  0
  -13.0330   11.6170  -23.4270 C   0  0  0  0  0  0
  -12.4880   12.5850  -23.9530 O   0  0  0  0  0  0
  -12.8420   12.8620  -21.2600 C   0  0  2  0  0  0
  -13.4460   14.1860  -21.6950 C   0  0  0  0  0  0
  -14.6640   14.3150  -21.8100 O   0  0  0  0  0  0
  -12.5990   15.1730  -21.9340 N   0  0  0  0  0  0
   12.2629   10.0078  -21.4292 H   0  0  0  0  0  0
   14.5793   11.7941   21.9375 H   0  0  0  0  0  0
  -11.7517   12.8618  -21.4058 H   0  0  0  0  0  0
  -12.8960   12.7466  -20.1674 H   0  0  0  0  0  0
  -11.6159   15.0256   21.8253 H   0  0  0  0  0  0
   12.9415   16.0668   22.2233 H   0  0  0  0  0  0
   -6.9030   20.8000  -21.5690 Mn  0  0  0  0  0  0
  -11.7070   17.5360  -17.1280 N   0  0  0  0  0  0
  -11.3770   16.9560  -15.8900 C   0  0  0  0  0  0
  -11.1650   15.5800  -15.9320 N   0  0  0  0  0  0
  -11.2560   14.7460  -17.0750 C   0  0  0  0  0  0
  -11.5930   15.4240  -18.2820 C   0  0  0  0  0  0
  -11.8010   16.7270  -18.2860 C   0  0  0  0  0  0
  -11.3030   17.6750  -14.9060 O   0  0  0  0  0  0
  -11.0520   13.5490  -16.9940 O   0  0  0  0  0  0
  -11.9510   19.0300  -17.1320 C   0  0  1  0  0  0
  -10.8070   19.9810  -17.3200 C   0  0  2  0  0  0
  -10.3900   20.6110  -16.0980 O   0  0  0  0  0  0
  -11.3610   20.9810  -18.3030 C   0  0  1  0  0  0
  -12.4180   20.2610  -19.1170 C   0  0  2  0  0  0
  -12.8640   19.2350  -18.1980 O   0  0  0  0  0  0
  -11.9490   22.0900  -17.6310 O   0  0  0  0  0  0
  -11.8710   19.7390  -20.4400 C   0  0  2  0  0  0
  -10.4750   19.4400  -20.4960 O   0  0  0  0  0  0
   -9.6960   18.9000  -21.7460 P   0  2  1  0  0  0
   -8.2940   18.7050  -21.3700 O   0  0  0  0  0  0
  -10.3100   17.7680  -22.4750 O   0  5  0  0  0  0
   -9.8690   20.2330  -22.7040 O   0  0  0  0  0  0
   -9.2480   20.5240  -24.1050 P   0  2  1  0  0  0
   -9.8680   21.9860  -24.3300 O   0  0  0  0  0  0
   -7.7800   20.6000  -23.8430 O   0  0  0  0  0  0
   -9.4020   19.3700  -25.0250 O   0  5  0  0  0  0
   10.9243   15.1356  -15.0691 H   0  0  0  0  0  0
  -11.6806   14.8556   19.2196 H   0  0  0  0  0  0
   12.0611   17.2101   19.2393 H   0  0  0  0  0  0
   12.2786   19.2732   16.1104 H   0  0  0  0  0  0
   -9.8961   19.4741  -17.6712 H   0  0  0  0  0  0
   10.0293   19.9192  -15.4724 H   0  0  0  0  0  0
  -10.5541   21.3713   18.9406 H   0  0  0  0  0  0
   13.2476   20.9001  -19.4535 H   0  0  0  0  0  0
   11.2502   22.5635  -17.0947 H   0  0  0  0  0  0
   12.1286   20.4413   21.2464 H   0  0  0  0  0  0
   12.4482   18.8567   20.7533 H   0  0  0  0  0  0
  -12.2560   23.2100  -23.3040 O   0  6  0  0  0  0
  -10.8590   11.6750  -14.8360 O   0  6  0  0  0  0
  -11.1220   22.7890  -26.6880 O   0  6  0  0  0  0
   -8.5240   22.6220  -20.9750 O   0  6  0  0  0  0
  -14.3430   17.8360  -21.9430 O   0  6  0  0  0  0
  -12.8660   11.7110  -18.0880 O   0  6  0  0  0  0
   -5.3480   19.3780  -24.7980 O   0  6  0  0  0  0
  1  7  1  0  0  0
  2  3  1  0  0  0
  2  1  1  0  0  0
  3  4  2  0  0  0
  5  2  1  0  0  0
  5  6  1  0  0  0
  7  6  1  0  0  0
 15  3  1  0  0  0
 15 16  1  0  0  0
 16 19  1  0  0  0
 17 35  1  0  0  0
 17 16  1  0  0  0
 18 17  2  0  0  0
 19 20  1  0  0  0
 20 21  2  0  0  0
 21 23  1  0  0  0
 22 24  2  0  0  0
 22 20  1  0  0  0
 24 25  1  0  0  0
 25 23  2  0  0  0
 35 36  1  0  0  0
 36 37  1  0  0  0
 37 38  2  0  0  0
 39 36  1  0  0  0
 40 41  1  0  0  0
 40 39  1  0  0  0
 42 41  1  0  0  0
 43 42  1  0  0  0
 44 43  2  0  0  0
 45 43  1  0  0  0
 59 60  1  0  0  0
 60 61  1  0  0  0
 61 62  2  0  0  0
 63 60  1  0  0  0
 64 63  1  0  0  0
 64 65  1  0  0  0
 66 67  1  0  0  0
 66 65  1  0  0  0
 67 68  2  0  0  0
 69 67  1  0  0  0
 83 84  1  0  0  0
 84 87  1  0  0  0
 85 84  1  0  0  0
 86 85  2  0  0  0
 87 88  1  0  0  0
 88 89  2  0  0  0
 89 91  1  0  0  0
 90 88  1  0  0  0
 90 92  2  0  0  0
 92 93  1  0  0  0
 93 91  2  0  0  0
103104  1  0  0  0
104107  1  0  0  0
105104  1  0  0  0
106105  2  0  0  0
107108  1  0  0  0
108109  1  0  0  0
109110  1  0  0  0
111110  1  0  0  0
111113  1  0  0  0
112111  2  0  0  0
127128  1  0  0  0
128131  1  0  0  0
128129  1  0  0  0
129139  1  0  0  0
129130  2  0  0  0
132134  1  0  0  0
132131  1  0  0  0
133132  2  0  0  0
139140  1  0  0  0
140143  1  0  0  0
140141  1  0  0  0
141142  2  0  0  0
143145  1  0  0  0
144143  1  0  0  0
156155  1  0  0  0
157158  2  0  0  0
157156  1  0  0  0
159156  1  0  0  0
160159  1  0  0  0
161160  1  0  0  0
162161  1  0  0  0
163162  1  0  0  0
177178  1  0  0  0
178181  1  0  0  0
179178  1  0  0  0
179180  2  0  0  0
181182  1  0  0  0
182184  1  0  0  0
183182  2  0  0  0
183185  1  0  0  0
184186  2  0  0  0
185187  2  0  0  0
187188  1  0  0  0
187186  1  0  0  0
198199  1  0  0  0
199202  1  0  0  0
200199  1  0  0  0
201200  2  0  0  0
202203  1  0  0  0
203205  1  0  0  0
203204  2  0  0  0
204206  1  0  0  0
205207  2  0  0  0
207209  1  0  0  0
207206  1  0  0  0
208210  2  0  0  0
208205  1  0  0  0
210211  1  0  0  0
211209  2  0  0  0
223224  1  0  0  0
223222  1  0  0  0
224225  2  0  0  0
226223  1  0  0  0
227226  1  0  0  0
228227  1  0  0  0
229228  1  0  0  0
240239  1  0  0  0
241240  1  0  0  0
242241  2  0  0  0
243240  1  0  0  0
244243  1  0  0  0
245244  1  0  0  0
246244  2  0  0  0
247245  2  0  0  0
247248  1  0  0  0
248246  1  0  0  0
258257  1  0  0  0
259258  1  0  0  0
259260  2  0  0  0
261258  1  0  0  0
262261  1  0  0  0
263262  1  0  0  0
264263  1  0  0  0
264265  1  0  0  0
265266  2  0  0  0
267265  1  0  0  0
281259  1  0  0  0
282281  1  0  0  0
283282  1  0  0  0
284283  2  0  0  0
285282  1  0  0  0
286285  1  0  0  0
286287  2  0  0  0
288286  1  0  0  0
294293  1  0  0  0
294295  1  0  0  0
294297  1  0  0  0
295296  2  0  0  0
298297  1  0  0  0
298300  1  0  0  0
299298  2  0  0  0
308309  1  0  0  0
309314  2  0  0  0
309310  1  0  0  0
311315  2  0  0  0
311310  1  0  0  0
312311  1  0  0  0
313312  2  0  0  0
313308  1  0  0  0
316308  1  0  0  0
316317  1  0  0  0
317318  1  0  0  0
319317  1  0  0  0
320323  1  0  0  0
320319  1  0  0  0
321316  1  0  0  0
321320  1  0  0  0
322319  1  0  0  0
323324  1  0  0  0
324325  1  0  0  0
325326  2  0  0  0
327325  1  0  0  0
328329  1  0  0  0
328325  1  0  0  0
329331  1  0  0  0
330329  2  0  0  0
331307  1  0  0  0
332329  1  0  0  0
  2  8  1  0  0  0
  5  9  1  0  0  0
  5 10  1  0  0  0
  6 11  1  0  0  0
  6 12  1  0  0  0
  7 13  1  0  0  0
  7 14  1  0  0  0
 15 26  1  0  0  0
 16 27  1  0  0  0
 19 28  1  0  0  0
 19 29  1  0  0  0
 21 30  1  0  0  0
 22 31  1  0  0  0
 23 32  1  0  0  0
 24 33  1  0  0  0
 25 34  1  0  0  0
 35 46  1  0  0  0
 36 47  1  0  0  0
 39 48  1  0  0  0
 39 49  1  0  0  0
 40 50  1  0  0  0
 40 51  1  0  0  0
 41 52  1  0  0  0
 41 53  1  0  0  0
 42 54  1  0  0  0
 44 55  1  0  0  0
 44 56  1  0  0  0
 45 57  1  0  0  0
 45 58  1  0  0  0
 59 70  1  0  0  0
 60 71  1  0  0  0
 63 72  1  0  0  0
 63 73  1  0  0  0
 64 74  1  0  0  0
 64 75  1  0  0  0
 65 76  1  0  0  0
 65 77  1  0  0  0
 66 78  1  0  0  0
 68 79  1  0  0  0
 68 80  1  0  0  0
 69 81  1  0  0  0
 69 82  1  0  0  0
 83 94  1  0  0  0
 84 95  1  0  0  0
 87 96  1  0  0  0
 87 97  1  0  0  0
 89 98  1  0  0  0
 90 99  1  0  0  0
 91100  1  0  0  0
 92101  1  0  0  0
 93102  1  0  0  0
103114  1  0  0  0
104115  1  0  0  0
107116  1  0  0  0
107117  1  0  0  0
108118  1  0  0  0
108119  1  0  0  0
109120  1  0  0  0
109121  1  0  0  0
110122  1  0  0  0
112123  1  0  0  0
112124  1  0  0  0
113125  1  0  0  0
113126  1  0  0  0
127135  1  0  0  0
128136  1  0  0  0
131137  1  0  0  0
131138  1  0  0  0
139146  1  0  0  0
140147  1  0  0  0
143148  1  0  0  0
144149  1  0  0  0
144150  1  0  0  0
144151  1  0  0  0
145152  1  0  0  0
145153  1  0  0  0
145154  1  0  0  0
155164  1  0  0  0
156165  1  0  0  0
159166  1  0  0  0
159167  1  0  0  0
160168  1  0  0  0
160169  1  0  0  0
161170  1  0  0  0
161171  1  0  0  0
162172  1  0  0  0
162173  1  0  0  0
163174  1  0  0  0
163175  1  0  0  0
163176  1  0  0  0
177189  1  0  0  0
178190  1  0  0  0
181191  1  0  0  0
181192  1  0  0  0
183193  1  0  0  0
184194  1  0  0  0
185195  1  0  0  0
186196  1  0  0  0
188197  1  0  0  0
198212  1  0  0  0
199213  1  0  0  0
202214  1  0  0  0
202215  1  0  0  0
204216  1  0  0  0
206217  1  0  0  0
208218  1  0  0  0
209219  1  0  0  0
210220  1  0  0  0
211221  1  0  0  0
222230  1  0  0  0
223231  1  0  0  0
226232  1  0  0  0
226233  1  0  0  0
227234  1  0  0  0
227235  1  0  0  0
229236  1  0  0  0
229237  1  0  0  0
229238  1  0  0  0
239249  1  0  0  0
240250  1  0  0  0
243251  1  0  0  0
243252  1  0  0  0
245253  1  0  0  0
246254  1  0  0  0
247255  1  0  0  0
248256  1  0  0  0
257268  1  0  0  0
258269  1  0  0  0
261270  1  0  0  0
261271  1  0  0  0
262272  1  0  0  0
262273  1  0  0  0
263274  1  0  0  0
263275  1  0  0  0
264276  1  0  0  0
266277  1  0  0  0
266278  1  0  0  0
267279  1  0  0  0
267280  1  0  0  0
281289  1  0  0  0
282290  1  0  0  0
285291  1  0  0  0
285292  1  0  0  0
293301  1  0  0  0
294302  1  0  0  0
297303  1  0  0  0
297304  1  0  0  0
300305  1  0  0  0
300306  1  0  0  0
310333  1  0  0  0
312334  1  0  0  0
313335  1  0  0  0
316336  1  0  0  0
317337  1  0  0  0
318338  1  0  0  0
319339  1  0  0  0
320340  1  0  0  0
322341  1  0  0  0
323342  1  0  0  0
323343  1  0  0  0
M  END
$\endgroup$
6
  • 1
    $\begingroup$ Wow! Super interesting. Almost perfect. I had 2 problems I never found where it actually saved that file test.txt or whatever I named it, it said it saved it somehow but I guess I have to open some text box to copy and paste it from? $\endgroup$ Sep 29 at 20:10
  • 1
    $\begingroup$ Then I got a MOLFILE which interestingly shows bonds -- and I guess they are inferred by distance? Because the bond valence is all 1, -COOH comes out as -C(H2)OH but it is really, really close, given that the bonds are inferred. $\endgroup$ Sep 29 at 20:26
  • 1
    $\begingroup$ @GuntherSchadow Prima! I'm glad you got something out of my answer. $\endgroup$ Sep 29 at 21:23
  • 1
    $\begingroup$ @GuntherSchadow Try the 'set pdbAddHydrogens true' to see if the double bonds make sense (I edited the answer accordingly). $\endgroup$ Sep 29 at 21:33
  • 1
    $\begingroup$ Now finally the write mol test.txt worked for me. The hydrogen stuff creates a very strange molfile where all hydrogens appear to be over to the left. And I had to remove the bonds over to them to even display it nicely. I'd attach the picture to the comment if I could, but you can see it if you try to render your Molfile. $\endgroup$ Sep 29 at 22:12
0
$\begingroup$

I am going to post my own answer since now I have figured it out in much more detail based on the answer I had accepted above. I don't have the PDB file of the lactose synthase model above, but I was since steered to use LDH. And here is the author's picture from Cook, Senkovich, et al. Biochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase and they have deposited it to PDB as 4ND3 and 4ND4:

enter image description here

Now I have been able to create the molfile of exactly this:

enter image description here

InChI=1S/C21H27N7O14P2.2C6H14N4O.C6H9N3O.C6H13NO.C5H11NOS.C4H8N2O2.C4H7NO3.C3H7NO2.C3H4O3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33;2*7-5(4-11)2-1-3-10-6(8)9;7-5(3-10)1-6-2-8-4-9-6;1-3-5(2)6(7)4-8;1-8-3-2-5(6)4-7;5-3(2-7)1-4(6)8;5-3(2-6)1-4(7)8;4-3(1-5)2-6;1-2(4)3(5)6/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H4-2,22,23,24,25,33,34,35,36,37);2*4-5H,1-3,7H2,(H4,8,9,10);2-5H,1,7H2,(H,8,9);4-6H,3,7H2,1-2H3;4-5H,2-3,6H2,1H3;2-3H,1,5H2,(H2,6,8);2-3H,1,5H2,(H,7,8);1,3,6H,2,4H2;1H3,(H,5,6)/q+2;;;;;;;;;/p+2/t10-,11-,13-,14-,15-,16-,20-,21-;3*5-;5-,6+;5-;3*3-;/m100000001./s1 InChIKey=IBJLKZJXTBIULM-IRBDITSESA-P
  GS-mol2inchi
Jmol version 14.31.56  2021-10-01 10:44 EXTRACT: ({0:121})
122118  0  0  0  0           999 V2000
   25.2059   40.1061  118.3750 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.3083   41.1168  118.0510 C   0  0  1  0  0  0  0  0  0  0  0  0
   26.4521   40.4296  118.9050 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.9287   42.7001  118.8050 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.1872   41.0122  118.4520 C   0  0  0  0  0  0  0  0  0  0  0  0
   35.5059   39.8960  118.6250 C   0  0  0  0  0  0  0  0  0  0  0  0
   40.2601   45.3394  116.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
   39.4095   42.6347  120.3950 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6679   42.4398  118.2720 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.3830   42.0571  119.2200 C   0  0  0  0  0  0  0  0  0  0  0  0
   36.8039   40.1697  117.8820 C   0  0  0  0  0  0  0  0  0  0  0  0
   40.1563   44.5231  119.5910 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.1546   41.7047  120.6830 C   0  0  0  0  0  0  0  0  0  0  0  0
   37.9261   39.1941  118.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.7123   41.2288  120.7310 C   0  0  0  0  0  0  0  0  0  0  0  0
   39.0252   40.0584  118.8210 C   0  0  0  0  0  0  0  0  0  0  0  0
   40.6978   45.8473  119.2220 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.7103   43.5485  117.9250 C   0  0  0  0  0  0  0  0  0  0  0  0
   39.6805   43.6734  118.4970 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.0901   42.1224  119.6690 C   0  0  0  0  0  0  0  0  0  0  0  0
   38.6918   41.4317  118.2680 C   0  0  0  0  0  0  0  0  0  0  0  0
   41.1584   46.7056  120.1640 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.1005   44.8246  117.9130 N   0  0  0  0  0  0  0  0  0  0  0  0
   40.7088   46.1723  117.9090 N   0  0  0  0  0  0  0  0  0  0  0  0
   39.7592   44.1230  117.2230 N   0  0  0  0  0  0  0  0  0  0  0  0
   39.9605   43.8304  120.7230 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.7890   41.7141  119.1130 N   0  3  0  0  0  0  0  0  0  0  0  0
   39.2455   42.5527  119.0590 N   0  0  0  0  0  0  0  0  0  0  0  0
   30.3257   42.8923  121.4620 O   0  0  0  0  0  0  0  0  0  0  0  0
   38.3934   38.5066  117.0660 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.1011   41.3955  122.0160 O   0  0  0  0  0  0  0  0  0  0  0  0
   40.3387   39.6413  118.4390 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.5585   43.2635  117.6320 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.6501   37.1884  118.3990 O   0  0  0  0  0  0  0  0  0  0  0  0
   31.9517   38.6881  116.7390 O   0  5  0  0  0  0  0  0  0  0  0  0
   33.8776   36.4502  118.1390 O   0  0  0  0  0  0  0  0  0  0  0  0
   34.7434   37.5886  120.3060 O   0  5  0  0  0  0  0  0  0  0  0  0
   30.5988   39.7233  118.5840 O   0  0  0  0  0  0  0  0  0  0  0  0
   34.9285   38.7220  118.0740 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.0816   42.1971  118.6390 O   0  0  0  0  0  0  0  0  0  0  0  0
   37.2687   41.4726  118.2250 O   0  0  0  0  0  0  0  0  0  0  0  0
   32.6881   38.4885  119.1700 O   0  0  0  0  0  0  0  0  0  0  0  0
   31.4467   38.4346  118.1350 P   0  2  2  0  0  0  0  0  0  0  0  0
   34.0849   37.6911  118.9570 P   0  2  1  0  0  0  0  0  0  0  0  0
   23.2333   42.7327  125.1660 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.0397   43.7480  125.9720 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.3880   43.4687  124.1350 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.6263   44.3199  127.8070 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.7254   43.2143  127.2350 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.2973   42.2201  123.6130 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.7283   42.7333  128.1940 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.7188   42.5800  124.7570 N   0  3  0  0  0  0  0  0  0  0  0  0
   19.6248   41.4508  122.7620 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.5398   42.6060  123.3110 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.7134   44.5630  127.2830 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3959   37.9815  116.1360 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9676   38.4975  116.2310 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2552   38.4892  117.2730 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6927   38.5235  115.1530 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2012   38.3748  114.9160 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5587   38.1794  118.1060 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6767   39.3653  113.9570 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.3969   39.1356  119.0190 N   0  3  0  0  0  0  0  0  0  0  0  0
   19.7261   37.5394  118.0150 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.5724   37.8617  117.2720 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.9511   37.5480  115.0810 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0186   46.9667  121.0610 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3604   44.7587  120.7750 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1540   46.4882  123.3930 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.8191   43.5883  119.7430 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8564   47.1478  122.0460 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.2647   45.5464  120.6500 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6074   48.5710  122.2530 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.0542   43.5450  120.2080 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.3237   44.7883  119.9900 N   0  3  0  0  0  0  0  0  0  0  0  0
   20.3088   46.2301  123.7350 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.3580   39.9065  116.1210 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.0179   40.4075  113.0800 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.7353   38.9049  115.0540 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.1796   38.8312  112.0760 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.7272   39.4430  114.0240 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.3622   38.2750  113.2380 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.1839   37.4238  114.1020 N   0  0  0  0  0  0  0  0  0  0  0  0
   30.7404   38.7820  110.9260 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.4354   43.5827  114.3420 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.8384   46.7206  113.1880 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.9915   45.6335  112.5310 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.3635   47.1992  115.1360 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0249   47.8017  113.9060 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.8700   48.9119  114.3210 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.0473   46.7649  116.0680 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.0971   44.5686  113.6790 S   0  0  0  0  0  0  0  0  0  0  0  0
   26.9461   44.5219  123.0210 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.2666   46.5048  123.7830 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.5872   45.8435  122.5810 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.6341   44.2424  122.3080 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.5092   45.6206  121.4600 N   0  0  0  0  0  0  0  0  0  0  0  0
   25.4047   42.9818  121.9490 N   0  0  0  0  0  0  0  0  0  0  0  0
   29.4830   46.3699  123.9480 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.8306   45.1480  122.0990 O   0  0  0  0  0  0  0  0  0  0  0  0
   41.6137   41.0090  114.0160 C   0  0  0  0  0  0  0  0  0  0  0  0
   43.3944   42.6687  114.6320 C   0  0  0  0  0  0  0  0  0  0  0  0
   42.0165   42.4852  113.9980 C   0  0  0  0  0  0  0  0  0  0  0  0
   40.9273   40.6058  115.3120 C   0  0  0  0  0  0  0  0  0  0  0  0
   42.0249   43.0027  112.6340 N   0  0  0  0  0  0  0  0  0  0  0  0
   44.4098   42.7019  113.9280 O   0  0  0  0  0  0  0  0  0  0  0  0
   41.5705   40.6677  116.3820 O   0  0  0  0  0  0  0  0  0  0  0  0
   39.7386   40.2186  115.2600 O   0  5  0  0  0  0  0  0  0  0  0  0
   35.8165   42.5579  122.4130 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.5143   42.6814  121.4850 C   0  0  0  0  0  0  0  0  0  0  0  0
   34.8693   43.3886  121.5510 C   0  0  0  0  0  0  0  0  0  0  0  0
   35.3888   43.5788  120.2040 N   0  0  0  0  0  0  0  0  0  0  0  0
   36.5505   41.7127  121.8990 O   0  0  0  0  0  0  0  0  0  0  0  0
   32.9878   42.4513  122.7810 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.7854   39.6244  121.6600 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.8478   40.5045  120.8900 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.7522   39.9020  120.1610 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.9740   41.7159  120.8600 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.9289   38.8019  119.5990 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.6645   40.5060  120.1200 O   0  5  0  0  0  0  0  0  0  0  0  0
   23.3514   40.9187  118.5560 H   0  0  0  0  0  0  0  0  0  0  0  0
   24.0056   41.0008  116.9999 H   0  0  0  0  0  0  0  0  0  0  0  0
  2121  1  0  0  0  0
  2122  1  0  0  0  0
101103  1  0  0  0  0
101104  1  0  0  0  0
102103  1  0  0  0  0
103105  1  0  0  0  0
104108  1  0  0  0  0
109111  1  0  0  0  0
110111  1  0  0  0  0
110114  1  0  0  0  0
111112  1  0  0  0  0
115116  1  0  0  0  0
116117  1  0  0  0  0
117120  1  0  0  0  0
  1  2  1  0  0  0  0
 96100  2  0  0  0  0
102106  2  0  0  0  0
104107  2  0  0  0  0
109113  2  0  0  0  0
116118  2  0  0  0  0
117119  2  0  0  0  0
  1  3  2  0  0  0  0
  2  9  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  6 11  1  0  0  0  0
 10 13  1  0  0  0  0
 11 14  1  0  0  0  0
 13 15  1  0  0  0  0
 14 16  1  0  0  0  0
 12 17  1  0  0  0  0
  9 18  1  0  0  0  0
 12 19  2  0  0  0  0
 15 20  1  0  0  0  0
 16 21  1  0  0  0  0
 17 22  1  0  0  0  0
 18 23  1  0  0  0  0
  7 24  1  0  0  0  0
 17 24  2  0  0  0  0
  7 25  2  0  0  0  0
 19 25  1  0  0  0  0
  8 26  2  0  0  0  0
 12 26  1  0  0  0  0
  3 27  1  0  0  0  0
  4 27  1  0  0  0  0
 20 27  1  0  0  0  0
  8 28  1  0  0  0  0
 19 28  1  0  0  0  0
 21 28  1  0  0  0  0
 13 29  1  0  0  0  0
 14 30  1  0  0  0  0
 15 31  1  0  0  0  0
 16 32  1  0  0  0  0
 18 33  2  0  0  0  0
  5 38  1  0  0  0  0
  6 39  1  0  0  0  0
 10 40  1  0  0  0  0
 20 40  1  0  0  0  0
 11 41  1  0  0  0  0
 21 41  1  0  0  0  0
 34 43  2  0  0  0  0
 35 43  1  0  0  0  0
 38 43  1  0  0  0  0
 42 43  1  0  0  0  0
 36 44  2  0  0  0  0
 37 44  1  0  0  0  0
 39 44  1  0  0  0  0
 42 44  1  0  0  0  0
 45 46  1  0  0  0  0
 45 47  1  0  0  0  0
 46 49  1  0  0  0  0
 48 49  1  0  0  0  0
 49 51  1  0  0  0  0
 50 52  2  0  0  0  0
 50 53  1  0  0  0  0
 47 54  1  0  0  0  0
 50 54  1  0  0  0  0
 48 55  2  0  0  0  0
 56 57  1  0  0  0  0
 56 58  1  0  0  0  0
 57 60  1  0  0  0  0
 59 60  1  0  0  0  0
 60 62  1  0  0  0  0
 61 63  2  0  0  0  0
 61 64  1  0  0  0  0
 58 65  1  0  0  0  0
 61 65  1  0  0  0  0
 59 66  2  0  0  0  0
 67 71  1  0  0  0  0
 69 71  1  0  0  0  0
 67 72  1  0  0  0  0
 68 72  2  0  0  0  0
 71 73  1  0  0  0  0
 68 74  1  0  0  0  0
 70 74  1  0  0  0  0
 70 75  2  0  0  0  0
 72 75  1  0  0  0  0
 69 76  2  0  0  0  0
 77 79  1  0  0  0  0
 78 81  1  0  0  0  0
 79 81  1  0  0  0  0
 80 82  1  0  0  0  0
 81 82  1  0  0  0  0
 82 83  1  0  0  0  0
 80 84  2  0  0  0  0
 86 87  1  0  0  0  0
 86 89  1  0  0  0  0
 88 89  1  0  0  0  0
 89 90  1  0  0  0  0
 88 91  2  0  0  0  0
 85 92  1  0  0  0  0
 87 92  1  0  0  0  0
 93 95  1  0  0  0  0
 94 95  1  0  0  0  0
 93 96  1  0  0  0  0
 95 97  1  0  0  0  0
 96 98  1  0  0  0  0
 94 99  2  0  0  0  0
M  END

and here is how I did it, I can actually use Jmol.jar for that, the same I use to display my molfile. But there is a bug in the version I downloaded recently, which is that pdbAddHydrogens true does not have the right effect and the ligands are not shown with the correct bond valences and hydrogens. But I can do it here: https://chemapps.stolaf.edu/jmol/jsmol/simple.htm and then I get good results. I can run this script:

set pdbAddHydrogens true
set defaultLoadFilter 'biomolecule 1'
load "=4nd4"
delete chain=B
delete z<100
set hideNotSelected true
select NAD
select add PYR
select add ILE32
select add D53
select add ASP53
select add SER99
select add ARG109
select add ASN140
select add MET163
select add ARG171
select add HIS195
delete hydrogens
write mol "first.mol"

Now after saving the first versions, then load them with Jmol.jar and show the atom numbers:

load "first.mol"
Spacefill 0.0
wireframe on
label "%i"

open the molfile in a text editor, and correct the NAD+ to NADH by changing 3 bond valences around that ring. When done, load it again check it's right, and add the hydrogens at the apex:

load "first.mol"
compute hydrogens @112
write mol "second.mol"

and finally I am having my own script to normalize the molfile so that the atom numbers correspond to canonical InChI atom numbers. But that's a different matter.

Once I learned this I could have saved hours of staring at the model and trying to remove parts of the molfile manually.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.