

PFRMAT DKF1
TARGET T0041
AUTHOR 1414-3771-3305
MODEL  2  CONFIDENCE  .8
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 1. 
REMARK
REMARK Model 2 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   3729  C1  INI     1      48.038  21.779  47.732  1.00 10.00              
ATOM   3731  C31 INI     1      47.828  20.573  48.285  1.00 10.00              
ATOM   3733  C32 INI     1      48.729  20.085  49.356  1.00 10.00              
ATOM   3735  C33 INI     1      48.604  18.868  49.892  1.00 10.00              
ATOM   3738  C2  INI     1      47.234  22.407  46.647  1.00 10.00              
ATOM   3739  C3  INI     1      46.148  21.782  45.981  1.00 10.00              
ATOM   3741  C4  INI     1      45.451  22.463  44.966  1.00 10.00              
ATOM   3743  C5  INI     1      45.839  23.761  44.606  1.00 10.00              
ATOM   3744  C6  INI     1      46.908  24.382  45.252  1.00 10.00              
ATOM   3746  C7  INI     1      47.598  23.716  46.265  1.00 10.00              
ATOM   3748  S8  INI     1      44.995  24.694  43.378  1.00 10.00              
ATOM   3749  O18 INI     1      44.690  26.041  43.966  1.00 10.00              
ATOM   3750  O19 INI     1      43.720  24.040  42.927  1.00 10.00              
ATOM   3751  N9  INI     1      45.976  25.015  42.096  1.00 10.00              
ATOM   3753  C10 INI     1      45.702  24.433  40.842  1.00 10.00              
ATOM   3756  C11 INI     1      44.804  25.310  40.022  1.00 10.00              
ATOM   3757  O20 INI     1      45.284  26.409  39.564  1.00 10.00              
ATOM   3758  N12 INI     1      43.559  24.887  39.730  1.00 10.00              
ATOM   3760  C13 INI     1      42.565  25.623  39.023  1.00 10.00              
ATOM   3762  C14 INI     1      42.824  25.751  37.525  1.00 10.00              
ATOM   3763  O25 INI     1      43.971  26.420  37.006  1.00 10.00              
ATOM   3764  C16 INI     1      44.720  25.561  36.119  1.00 10.00              
ATOM   3766  C34 INI     1      45.503  24.513  36.908  1.00 10.00              
ATOM   3770  C35 INI     1      45.667  26.490  35.380  1.00 10.00              
ATOM   3774  O17 INI     1      41.919  25.426  36.709  1.00 10.00              
ATOM   3775  C30 INI     1      42.219  26.921  39.788  1.00 10.00              
ATOM   3778  C21 INI     1      41.267  27.864  39.088  1.00 10.00              
ATOM   3779  C22 INI     1      39.964  28.105  39.571  1.00 10.00              
ATOM   3781  C23 INI     1      39.098  28.976  38.879  1.00 10.00              
ATOM   3783  C24 INI     1      39.524  29.627  37.699  1.00 10.00              
ATOM   3784  C25 INI     1      40.841  29.406  37.255  1.00 10.00              
ATOM   3786  C26 INI     1      41.704  28.558  37.949  1.00 10.00              
ATOM   3788  C27 INI     1      38.632  30.542  36.931  1.00 10.00              
ATOM   3789  N28 INI     1      39.023  31.199  35.906  1.00 10.00              
ATOM   3792  N29 INI     1      37.414  30.778  37.233  1.00 10.00              
TER    3800      INI     1
ENDMDL                                                                          
END                                                                             


