[Dock-fans] Docked ligand folded to sterically improbable conformation

Dan Hsu dkhsu at ucdavis.edu
Mon Aug 25 10:43:56 PDT 2014


Hello

On re-docking wetlab-validated compounds it was disconcerting to see a 
few ligands (interactionsrankedhigh) appear withbondscrossing the same 
3D space (before & after docking structures are enclosed). I don't 
believe any ligand parameters have been drastically changed, but can 
anyone suggest what might cause this to happen and what to try fixing 
the issue? These structures are produced with, or without GB/SA scoring.

Thank you!
Dan

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@<TRIPOS>MOLECULE
ZINC03477122
   50    53     0     0     0
SMALL
USER_CHARGES

@<TRIPOS>ATOM
      1 C1         -0.0167    1.3781    0.0096 C.ar      1 <0>        -0.0618
      2 C2          1.1709    2.0855    0.0021 C.ar      1 <0>        -0.1382
      3 C3          2.3773    1.4107   -0.0130 C.ar      1 <0>        -0.0213
      4 C4          2.3960    0.0285   -0.0201 C.ar      1 <0>        -0.6788
      5 C5          1.2084   -0.6789   -0.0117 C.ar      1 <0>        -0.0223
      6 C6          0.0021   -0.0041    0.0020 C.ar      1 <0>        -0.1387
      7 S1          3.9337   -0.8316   -0.0405 S.o2      1 <0>         2.6893
      8 O1          3.6744   -2.1140   -0.5951 O.2       1 <0>        -0.9497
      9 O2          4.8903    0.0598   -0.5970 O.2       1 <0>        -0.9487
     10 N1          4.3776   -1.0785    1.5357 N.pl3     1 <0>        -0.9972
     11 C7          5.1905   -0.0831    2.2485 C.3       1 <0>         0.1048
     12 C8          4.4540    0.3236    3.5309 C.3       1 <0>         0.0982
     13 N2          4.0416   -0.8946    4.2420 N.am      1 <0>        -0.6081
     14 C9          3.2287   -1.8900    3.5292 C.3       1 <0>         0.0866
     15 C10         3.9605   -2.2941    2.2485 C.3       1 <0>         0.1028
     16 C11         4.4029   -1.0956    5.5248 C.2       1 <0>         0.5207
     17 O3          5.0742   -0.2671    6.1027 O.2       1 <0>        -0.5079
     18 C12         3.9726   -2.3496    6.2412 C.3       1 <0>         0.0376
     19 O4          4.4756   -2.3307    7.5786 O.3       1 <0>        -0.2832
     20 C13         4.1755   -3.3964    8.3655 C.ar      1 <0>         0.1583
     21 C14         3.4161   -4.4417    7.8558 C.ar      1 <0>        -0.2131
     22 C15         3.1092   -5.5245    8.6512 C.ar      1 <0>        -0.0203
     23 C16         3.5630   -5.5701    9.9708 C.ar      1 <0>        -0.0692
     24 C17         4.3266   -4.5175   10.4793 C.ar      1 <0>        -0.0385
     25 C18         4.6337   -3.4406    9.6759 C.ar      1 <0>        -0.1470
     26 C19         3.2358   -6.7291   10.8272 C.2       1 <0>         0.2198
     27 N3          2.5354   -7.7828   10.4772 N.2       1 <0>        -0.2823
     28 N4          2.4525   -8.5882   11.4771 N.2       1 <0>        -0.2871
     29 C20         3.0908   -8.0852   12.4962 C.2       1 <0>         0.1458
     30 O5          3.6056   -6.9041   12.1117 O.3       1 <0>        -0.2247
     31 H1         -0.9591    1.9053    0.0259 H         1 <0>         0.1322
     32 H2          1.1563    3.1654    0.0076 H         1 <0>         0.1344
     33 H3          3.3051    1.9634   -0.0196 H         1 <0>         0.1397
     34 H4          1.2231   -1.7588   -0.0176 H         1 <0>         0.1396
     35 H5         -0.9258   -0.5567    0.0082 H         1 <0>         0.1342
     36 H6          6.1578   -0.5158    2.5038 H         1 <0>         0.0859
     37 H7          5.3342    0.7927    1.6158 H         1 <0>         0.1073
     38 H8          5.1195    0.9097    4.1647 H         1 <0>         0.1105
     39 H9          3.5739    0.9139    3.2757 H         1 <0>         0.0778
     40 H10         3.0850   -2.7659    4.1619 H         1 <0>         0.0980
     41 H11         2.2614   -1.4573    3.2739 H         1 <0>         0.0834
     42 H12         3.2921   -2.8781    1.6158 H         1 <0>         0.1085
     43 H13         4.8382   -2.8878    2.5038 H         1 <0>         0.0861
     44 H14         2.8840   -2.4002    6.2632 H         1 <0>         0.0987
     45 H15         4.3662   -3.2206    5.7173 H         1 <0>         0.0994
     46 H16         3.0654   -4.4057    6.8350 H         1 <0>         0.1400
     47 H17         2.5180   -6.3366    8.2544 H         1 <0>         0.1455
     48 H18         4.6792   -4.5490   11.4996 H         1 <0>         0.1421
     49 H19         5.2280   -2.6281   10.0672 H         1 <0>         0.1456
     50 H20         3.1915   -8.5373   13.4719 H         1 <0>         0.2649
@<TRIPOS>BOND
     1    1    6 ar
     2    1    2 ar
     3    1   31 1
     4    2    3 ar
     5    2   32 1
     6    3    4 ar
     7    3   33 1
     8    4    5 ar
     9    4    7 1
    10    5    6 ar
    11    5   34 1
    12    6   35 1
    13    7    8 2
    14    7    9 2
    15    7   10 1
    16   10   15 1
    17   10   11 1
    18   11   12 1
    19   11   36 1
    20   11   37 1
    21   12   13 1
    22   12   38 1
    23   12   39 1
    24   13   14 1
    25   13   16 am
    26   14   15 1
    27   14   40 1
    28   14   41 1
    29   15   42 1
    30   15   43 1
    31   16   17 2
    32   16   18 1
    33   18   19 1
    34   18   44 1
    35   18   45 1
    36   19   20 1
    37   20   25 ar
    38   20   21 ar
    39   21   22 ar
    40   21   46 1
    41   22   23 ar
    42   22   47 1
    43   23   24 ar
    44   23   26 1
    45   24   25 ar
    46   24   48 1
    47   25   49 1
    48   26   30 1
    49   26   27 2
    50   27   28 1
    51   28   29 2
    52   29   30 1
    53   29   50 1
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########## Name:		ZINC03477122
##########    Grid Score:          -47.097813
##########      Grid_vdw:          -31.619627
##########       Grid_es:          -15.478187
@<TRIPOS>MOLECULE
ZINC03477122
50 53 1 0 0
SMALL
USER_CHARGES


@<TRIPOS>ATOM
      1 C1         19.3985   37.3886   32.6400 C.ar      1 <0>   -0.0618
      2 C2         19.6729   38.7363   32.5012 C.ar      1 <0>   -0.1382
      3 C3         18.7100   39.5893   31.9949 C.ar      1 <0>   -0.0213
      4 C4         17.4729   39.0943   31.6269 C.ar      1 <0>   -0.6788
      5 C5         17.1988   37.7464   31.7648 C.ar      1 <0>   -0.0223
      6 C6         18.1612   36.8939   32.2724 C.ar      1 <0>   -0.1387
      7 S1         16.2452   40.1816   30.9826 S.o2      1 <0>    2.6893
      8 O1         15.0865   39.3929   30.7489 O.2       1 <0>   -0.9497
      9 O2         16.2312   41.3244   31.8272 O.2       1 <0>   -0.9487
     10 N1         16.7752   40.6952   29.5001 N.pl3     1 <0>   -0.9972
     11 C7         15.9881   40.4238   28.2892 C.3       1 <0>    0.1048
     12 C8         15.7122   41.7532   27.5759 C.3       1 <0>    0.0982
     13 N2         16.9779   42.4890   27.4478 N.am      1 <0>   -0.6081
     14 C9         17.7650   42.7604   28.6588 C.3       1 <0>    0.0866
     15 C10        18.0382   41.4358   29.3728 C.3       1 <0>    0.1028
     16 C11        17.4093   42.9069   26.2413 C.2       1 <0>    0.5207
     17 O3         16.6128   43.1108   25.3496 O.2       1 <0>   -0.5079
     18 C12        18.8813   43.1211   26.0001 C.3       1 <0>    0.0376
     19 O4         19.5917   42.9775   27.2317 O.3       1 <0>   -0.2832
     20 C13        18.9934   42.2457   28.2071 C.ar      1 <0>    0.1583
     21 C14        19.5725   42.1660   29.4670 C.ar      1 <0>   -0.2131
     22 C15        18.9687   41.4241   30.4592 C.ar      1 <0>   -0.0203
     23 C16        17.7732   40.7525   30.1967 C.ar      1 <0>   -0.0692
     24 C17        17.1939   40.8355   28.9289 C.ar      1 <0>   -0.0385
     25 C18        17.8012   41.5837   27.9436 C.ar      1 <0>   -0.1470
     26 C19        17.1226   39.9556   31.2576 C.2       1 <0>    0.2198
     27 N3         15.8310   39.8267   31.4534 N.2       1 <0>   -0.2823
     28 N4         15.6301   39.0593   32.4664 N.2       1 <0>   -0.2871
     29 C20        16.7752   38.6714   32.9534 C.2       1 <0>    0.1458
     30 O5         17.7448   39.2210   32.2013 O.3       1 <0>   -0.2247
     31 H1         20.1523   36.7216   33.0313 H         1 <0>    0.1322
     32 H2         20.6395   39.1231   32.7888 H         1 <0>    0.1344
     33 H3         18.9242   40.6423   31.8872 H         1 <0>    0.1397
     34 H4         16.2321   37.3599   31.4776 H         1 <0>    0.1396
     35 H5         17.9470   35.8408   32.3805 H         1 <0>    0.1342
     36 H6         16.5496   39.7637   27.6282 H         1 <0>    0.0859
     37 H7         15.0441   39.9535   28.5643 H         1 <0>    0.1073
     38 H8         15.3004   41.5584   26.5856 H         1 <0>    0.1105
     39 H9         15.0044   42.3417   28.1598 H         1 <0>    0.0778
     40 H10        18.7091   43.2307   28.3837 H         1 <0>    0.0980
     41 H11        17.2035   43.4205   29.3198 H         1 <0>    0.0834
     42 H12        18.4478   41.6336   30.3634 H         1 <0>    0.1085
     43 H13        18.7491   40.8494   28.7907 H         1 <0>    0.0861
     44 H14        19.2433   42.3835   25.2838 H         1 <0>    0.0987
     45 H15        19.0424   44.1231   25.6025 H         1 <0>    0.0994
     46 H16        20.4974   42.6857   29.6693 H         1 <0>    0.1400
     47 H17        19.4200   41.3620   31.4384 H         1 <0>    0.1455
     48 H18        16.2693   40.3172   28.7220 H         1 <0>    0.1421
     49 H19        17.3514   41.6520   26.9641 H         1 <0>    0.1456
     50 H20        16.9192   38.0224   33.8046 H         1 <0>    0.2649
@<TRIPOS>BOND
     1    1    6 ar
     2    1    2 ar
     3    1   31 1
     4    2    3 ar
     5    2   32 1
     6    3    4 ar
     7    3   33 1
     8    4    5 ar
     9    4    7 1
    10    5    6 ar
    11    5   34 1
    12    6   35 1
    13    7    8 2
    14    7    9 2
    15    7   10 1
    16   10   15 1
    17   10   11 1
    18   11   12 1
    19   11   36 1
    20   11   37 1
    21   12   13 1
    22   12   38 1
    23   12   39 1
    24   13   14 1
    25   13   16 am
    26   14   15 1
    27   14   40 1
    28   14   41 1
    29   15   42 1
    30   15   43 1
    31   16   17 2
    32   16   18 1
    33   18   19 1
    34   18   44 1
    35   18   45 1
    36   19   20 1
    37   20   25 ar
    38   20   21 ar
    39   21   22 ar
    40   21   46 1
    41   22   23 ar
    42   22   47 1
    43   23   24 ar
    44   23   26 1
    45   24   25 ar
    46   24   48 1
    47   25   49 1
    48   26   30 1
    49   26   27 2
    50   27   28 1
    51   28   29 2
    52   29   30 1
    53   29   50 1
@<TRIPOS>SUBSTRUCTURE
     1 <0>     1 RESIDUE           4 A     <0>     0 ROOT


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