

PFRMAT DKF1
TARGET T0040
AUTHOR 1414-3771-3305
MODEL 1   CONFIDENCE  .5
REMARK Model 1 is fragment docking followed by energy minimization. 
REMARK  Ligand built in AMMP  by the method of explosions.
REMARK  The coordinates of tar033 were used for the trypsin
REMARK  with the hydrogens built with AMMP. All crystal waters were kept.
REMARK  Both orientations of the meta-benzamidino group were 
REMARK  checked and the orientation with the least clashes used.
REMARK  The INH molecule was then built by using torsion searches around
REMARK  the internal torsions until a satisfactory model was found.
REMARK  This was followed by energy minimization using no cutoffs.
REMARK  waters 407 and 361 as well as gln 192 were allowed to adjust as
REMARK  well as the inhibitor.  The general procedure is
REMARK described in Weber, I.T. and Harrison, R.W. (1996) Molecular 
REMARK mechanics calculations on HIV-1 protease with peptide substrates
REMARK correlate with experimental data.  Protein Eng. 9, 679-690. and
REMARK Xu, L.Z., Weber, I.T., Harrison, R.W., Gidh-Jain, M. and Pilkis, S.J.
REMARK (1995) Biochem. 34, 6083-6092. 
REMARK
REMARK The chirality on C13 should be correct, but i would not be surprised
REMARK if we goofed.
REMARK
REMARK INH is residue1
REMARK the inserts in trypsin 64A etc are given numbers 964 ...
REMARK 
REMARK this is just the inhibitor, we want to send protein too but that has 
REMARK not worked yet - 
BEGPDB
ATOM   1630  C1  INH     1      46.455  29.066  45.642  1.00 10.00          
ATOM   1631  C2  INH     1      45.907  28.056  46.608  1.00 10.00          
ATOM   1632  C3  INH     1      46.636  26.888  46.906  1.00 10.00          
ATOM   1633  C4  INH     1      46.066  25.899  47.710  1.00 10.00          
ATOM   1634  C5  INH     1      44.784  26.072  48.240  1.00 10.00          
ATOM   1635  C6  INH     1      44.054  27.229  47.964  1.00 10.00          
ATOM   1636  C7  INH     1      44.616  28.231  47.158  1.00 10.00          
ATOM   1637  S8  INH     1      43.978  24.670  48.894  1.00 10.00          
ATOM   1638  O18 INH     1      43.385  24.124  47.632  1.00 10.00          
ATOM   1639  O19 INH     1      44.982  23.679  49.404  1.00 10.00          
ATOM   1640  N9  INH     1      42.711  24.766  49.938  1.00 10.00          
ATOM   1641  C10 INH     1      42.725  25.611  51.067  1.00 10.00          
ATOM   1642  C11 INH     1      43.379  25.027  52.288  1.00 10.00          
ATOM   1643  O20 INH     1      42.800  25.116  53.432  1.00 10.00          
ATOM   1644  N12 INH     1      44.650  24.613  52.189  1.00 10.00          
ATOM   1645  C13 INH     1      45.481  24.119  53.235  1.00 10.00          
ATOM   1646  C14 INH     1      45.919  25.187  54.229  1.00 10.00          
ATOM   1647  O15 INH     1      46.536  26.357  53.701  1.00 10.00          
ATOM   1648  C16 INH     1      45.551  27.425  53.695  1.00 10.00          
ATOM   1649  O17 INH     1      46.314  24.828  55.373  1.00 10.00          
ATOM   1650  C30 INH     1      44.903  22.829  53.859  1.00 10.00          
ATOM   1651  C21 INH     1      45.052  21.575  53.011  1.00 10.00          
ATOM   1652  C22 INH     1      44.555  21.510  51.695  1.00 10.00          
ATOM   1653  C23 INH     1      44.521  20.296  50.999  1.00 10.00          
ATOM   1654  C24 INH     1      44.965  19.122  51.622  1.00 10.00          
ATOM   1655  C25 INH     1      45.462  19.169  52.935  1.00 10.00          
ATOM   1656  C26 INH     1      45.519  20.397  53.612  1.00 10.00          
ATOM   1657  C27 INH     1      45.834  17.943  53.640  1.00 10.00          
ATOM   1658  N28 INH     1      45.480  16.780  53.254  1.00 10.00          
ATOM   1659  N29 INH     1      46.383  17.961  54.785  1.00 10.00          
ENDMDL                                                                          
END                                                                             


