
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms    5 (   37),  selected    5 , name T0320TS268_5_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS268_5_2-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    N     228      I     251          0.601
LGA    N     229      I     252          0.753
LGA    S     230      H     253          0.834
LGA    L     231      A     254          0.599
LGA    P     232      F     255          0.535
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   73    5.0      5    0.67     0.00      6.849     0.646

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.097580 * X  +   0.137165 * Y  +   0.985730 * Z  + -50.954136
  Y_new =  -0.061427 * X  +   0.987738 * Y  +  -0.143526 * Z  + -23.659225
  Z_new =  -0.993330 * X  +  -0.074556 * Y  +  -0.087958 * Z  +  52.120899 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.438478    0.703114  [ DEG:  -139.7145     40.2855 ]
  Theta =   1.455234    1.686358  [ DEG:    83.3788     96.6212 ]
  Phi   =  -2.579763    0.561830  [ DEG:  -147.8095     32.1905 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0320TS268_5_2-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS268_5_2-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   73   5.0    5   0.67    0.00   6.849
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS268_5_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT 1kqp_A
ATOM   1861  N   ASN   228      -0.132  23.295   9.309  1.00  0.00
ATOM   1862  CA  ASN   228      -1.045  22.246   9.661  1.00  0.00
ATOM   1863  C   ASN   228      -2.407  22.746   9.302  1.00  0.00
ATOM   1864  O   ASN   228      -2.558  23.893   8.885  1.00  0.00
ATOM   1865  CB  ASN   228      -0.959  21.940  11.157  1.00  0.00
ATOM   1866  CG  ASN   228      -1.435  23.096  12.016  1.00  0.00
ATOM   1867  OD1 ASN   228      -1.893  24.116  11.503  1.00  0.00
ATOM   1868  ND2 ASN   228      -1.326  22.938  13.330  1.00  0.00
ATOM   1869  N   ASN   229      -3.441  21.892   9.421  1.00  0.00
ATOM   1870  CA  ASN   229      -4.757  22.349   9.087  1.00  0.00
ATOM   1871  C   ASN   229      -5.109  23.464  10.015  1.00  0.00
ATOM   1872  O   ASN   229      -5.569  24.517   9.576  1.00  0.00
ATOM   1873  CB  ASN   229      -5.772  21.214   9.237  1.00  0.00
ATOM   1874  CG  ASN   229      -5.654  20.177   8.136  1.00  0.00
ATOM   1875  OD1 ASN   229      -5.085  20.444   7.077  1.00  0.00
ATOM   1876  ND2 ASN   229      -6.191  18.989   8.384  1.00  0.00
ATOM   1877  N   SER   230      -4.889  23.281  11.329  1.00  0.00
ATOM   1878  CA  SER   230      -5.215  24.364  12.209  1.00  0.00
ATOM   1879  C   SER   230      -4.124  24.490  13.227  1.00  0.00
ATOM   1880  O   SER   230      -3.699  23.504  13.827  1.00  0.00
ATOM   1881  CB  SER   230      -6.547  24.098  12.914  1.00  0.00
ATOM   1882  OG  SER   230      -6.877  25.156  13.797  1.00  0.00
ATOM   1883  N   LEU   231      -3.628  25.726  13.436  1.00  0.00
ATOM   1884  CA  LEU   231      -2.599  25.937  14.411  1.00  0.00
ATOM   1885  C   LEU   231      -2.972  27.190  15.145  1.00  0.00
ATOM   1886  O   LEU   231      -3.469  28.139  14.541  1.00  0.00
ATOM   1887  CB  LEU   231      -1.239  26.095  13.728  1.00  0.00
ATOM   1888  CG  LEU   231      -0.053  26.410  14.643  1.00  0.00
ATOM   1889  CD1 LEU   231       0.271  25.219  15.532  1.00  0.00
ATOM   1890  CD2 LEU   231       1.184  26.743  13.825  1.00  0.00
ATOM   1891  N   PRO   232      -2.776  27.230  16.432  1.00  0.00
ATOM   1892  CA  PRO   232      -3.115  28.445  17.118  1.00  0.00
ATOM   1893  C   PRO   232      -2.072  29.480  16.861  1.00  0.00
ATOM   1894  O   PRO   232      -1.721  30.232  17.808  1.00  0.00
ATOM   1895  CB  PRO   232      -3.166  28.037  18.592  1.00  0.00
ATOM   1896  CG  PRO   232      -2.115  26.986  18.723  1.00  0.00
ATOM   1897  CD  PRO   232      -2.175  26.175  17.460  1.00  0.00
TER
END
