

PFRMAT DKF1
TARGET T0041
AUTHOR 1414-3771-3305
MODEL 1   CONFIDENCE  .7
REMARK  Inhibitor only, protein will be sent separately due to hydrogen 
REMARK complications.  Inhibitor is in reference frame of trypsin in 
REMARK target 33 crystal structure.  
REMARK 
REMARK Confidence level is based on calculated inhibitor-trypsin interaction
REMARK energy relative to model 2. 
REMARK
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 
BEGPDB
ATOM   3732  C1  INI     1      42.085  18.218  31.760  1.00 10.00              
ATOM   3734  C31 INI     1      42.774  17.355  30.993  1.00 10.00              
ATOM   3736  C32 INI     1      42.100  16.416  30.071  1.00 10.00              
ATOM   3738  C33 INI     1      42.802  15.498  29.396  1.00 10.00              
ATOM   3741  C2  INI     1      42.720  19.214  32.660  1.00 10.00              
ATOM   3742  C3  INI     1      44.053  19.084  33.112  1.00 10.00              
ATOM   3744  C4  INI     1      44.642  20.102  33.869  1.00 10.00              
ATOM   3746  C5  INI     1      43.917  21.252  34.190  1.00 10.00              
ATOM   3747  C6  INI     1      42.582  21.377  33.787  1.00 10.00              
ATOM   3749  C7  INI     1      41.978  20.354  33.038  1.00 10.00              
ATOM   3751  S8  INI     1      44.766  22.606  34.929  1.00 10.00              
ATOM   3752  O18 INI     1      45.212  23.494  33.792  1.00 10.00              
ATOM   3753  O19 INI     1      45.973  22.089  35.671  1.00 10.00              
ATOM   3754  N9  INI     1      43.897  23.428  36.067  1.00 10.00              
ATOM   3756  C10 INI     1      43.256  24.646  35.745  1.00 10.00              
ATOM   3759  C11 INI     1      43.574  25.740  36.723  1.00 10.00              
ATOM   3760  O20 INI     1      44.094  26.830  36.284  1.00 10.00              
ATOM   3761  N12 INI     1      43.184  25.620  38.007  1.00 10.00              
ATOM   3763  C13 INI     1      43.413  26.590  39.022  1.00 10.00              
ATOM   3765  C14 INI     1      44.370  26.072  40.072  1.00 10.00              
ATOM   3766  O25 INI     1      43.952  25.046  40.962  1.00 10.00              
ATOM   3767  C16 INI     1      45.039  24.136  41.239  1.00 10.00              
ATOM   3769  C34 INI     1      45.157  23.125  40.102  1.00 10.00              
ATOM   3773  C35 INI     1      44.679  23.497  42.568  1.00 10.00              
ATOM   3777  O17 INI     1      45.380  26.756  40.387  1.00 10.00              
ATOM   3778  C30 INI     1      42.070  26.973  39.690  1.00 10.00              
ATOM   3781  C21 INI     1      41.151  27.913  38.932  1.00 10.00              
ATOM   3782  C22 INI     1      39.935  28.319  39.526  1.00 10.00              
ATOM   3784  C23 INI     1      39.051  29.175  38.840  1.00 10.00              
ATOM   3786  C24 INI     1      39.367  29.640  37.547  1.00 10.00              
ATOM   3787  C25 INI     1      40.584  29.241  36.968  1.00 10.00              
ATOM   3789  C26 INI     1      41.460  28.405  37.651  1.00 10.00              
ATOM   3791  C27 INI     1      38.465  30.536  36.782  1.00 10.00              
ATOM   3792  N28 INI     1      38.822  31.107  35.699  1.00 10.00              
ATOM   3795  N29 INI     1      37.277  30.833  37.144  1.00 10.00              
TER    3800      INI     1
ENDMDL                                                                          
END                                                                             


