

PFRMAT DKF1
TARGET T0039
AUTHOR 6682-2204-3506 Bernd Kramer, GMD-SCAI, Bernd.Kramer@gmd.de
AUTHOR 6682-2204-3506 Thomas Lengauer, GMD-SCAI, Lengauer@gmd.de
AUTHOR 6682-2204-3506 Matthias Rarey, GMD-SCAI, Rarey@gmd.de
REMARK ===================================================================
REMARK 1.Preparation of input data
REMARK   The ligand is generated and energy minimized to fall in an 
REMARK   arbitrary low-energy conformation. Favorable torsion angles at 
REMARK   rotatable bonds, interaction types, and interaction geometries 
REMARK   are automatically assigned.
REMARK   The active site of the protein is selected manually by comparing
REMARK   the protein structure to complexes where the same protein is
REMARK   involved (typically 8-10 A around the ligand). Hydrogens at
REMARK   hydrogen bond donors and acceptors are added in standard 
REMARK   geometries automatically. Interaction types and interaction 
REMARK   geometries are also assigned automatically.
REMARK 2.Docking
REMARK   Complexes are generated using our docking software FlexX (see
REMARK   Ref.). FlexX is a docking tool based on an incremental 
REMARK   construction algorithm producing results in approximately
REMARK   1-3 minutes for one pair of a receptor and a ligand molecule. 
REMARK   No refinement of the produced structures is performed.
REMARK 3.Selection of models
REMARK   The selection of a set of models and the assignment of 
REMARK   confidences is done manually again. Here we have considered
REMARK   phenomena like intramolecular hydrogen bonds which are not 
REMARK   modeled yet. FlexX' energy predictions for the different models
REMARK   are used as a guideline for the selection.
REMARK ===================================================================
REMARK References: 
REMARK   Matthias Rarey, Stephan Wefing and Thomas Lengauer:
REMARK   Placement of medium-sized molecular fragments into active sites
REMARK   of proteins, JCAMD (1996) 10, 41--54
REMARK
REMARK   Matthias Rarey, Bernd Kramer, Thomas Lengauer and Gerhard Klebe: 
REMARK   A Fast Flexible Docking Method using an Incremental Construction 
REMARK   Algorithm, JMB (1996) 261, 470--489
REMARK ===================================================================
MODEL     3 CONFIDENCE 0.2
ATOM      1 C1   AIC   336      13.080  -3.042  90.214                
ATOM      2 N1   AIC   336      13.247  -2.535  91.607                
ATOM      3 C2   AIC   336      11.936  -2.221  92.084                
ATOM      4 N2   AIC   336      11.018  -2.533  91.005                
ATOM      5 C3   AIC   336      11.782  -3.035  89.880                
ATOM      6 C4   AIC   336      15.278  -0.583  91.322                
ATOM      7 C5   AIC   336      15.592  -2.018  91.712                
ATOM      8 C6   AIC   336      14.398  -2.330  92.465                
ATOM      9 O2   AIC   336      14.288  -1.148  93.326                
ATOM     10 C7   AIC   336      14.612  -0.009  92.561                
ATOM     11 C8   AIC   336      13.366   0.797  92.229                
ATOM     12 O3   AIC   336      16.437   0.148  90.985                
ATOM     13 O4   AIC   336      16.791  -2.125  92.447                
ATOM     14 N3   AIC   336      14.241  -3.450  89.447                
ATOM     15 C9   AIC   336      11.350  -3.509  88.502                
ATOM     16 N4   AIC   336      10.284  -3.000  87.949                
ATOM     17 O5   AIC   336      12.025  -4.364  87.950                
ATOM     18 O1   AIC   336      13.135   1.765  93.258                
ATOM     19 P1   AIC   336      12.888   1.346  94.783                
ATOM     20 O6   AIC   336      11.593   0.412  94.878                
ATOM     21 O7   AIC   336      14.162   0.547  95.330                
ATOM     22 O8   AIC   336      12.666   2.661  95.667                
TER      23      AIC   336 
ENDMDL
