
#######################################################
#                                                     #
#                        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   10 (   81),  selected   10 , name T0320TS105_2_1-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS105_2_1-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    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
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    N     228      E     278          2.040
LGA    N     229      R     279          1.063
LGA    S     230      F     280          2.043
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    L     231      Y     283          0.629
LGA    P     232      H     284          1.846
LGA    -       -      D     285           -
LGA    N     233      N     286          1.053
LGA    P     234      Y     287          1.799
LGA    H     235      Y     288          1.260
LGA    L     236      P     289          1.268
LGA    R     237      G     290          1.316
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)   10   73    5.0     10    1.50    10.00     13.062     0.624

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.999107 * X  +  -0.039460 * Y  +   0.015129 * Z  + -12.999779
  Y_new =   0.018649 * X  +   0.090422 * Y  +  -0.995729 * Z  + 109.633965
  Z_new =   0.037923 * X  +   0.995122 * Y  +   0.091077 * Z  + -12.312418 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.479527   -1.662066  [ DEG:    84.7707    -95.2293 ]
  Theta =  -0.037932   -3.103660  [ DEG:    -2.1734   -177.8266 ]
  Phi   =   0.018664   -3.122929  [ DEG:     1.0694   -178.9306 ]
 
# 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: T0320TS105_2_1-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS105_2_1-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10   73   5.0   10   1.50   10.00  13.062
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS105_2_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT 1sur
ATOM   1865  N   ASN   228      24.756  30.964  -1.737  1.00222.96       1SG1866
ATOM   1866  CA  ASN   228      23.971  29.773  -1.692  1.00222.96       1SG1867
ATOM   1867  CB  ASN   228      22.601  29.913  -2.381  1.00222.96       1SG1868
ATOM   1868  CG  ASN   228      21.693  30.762  -1.501  1.00222.96       1SG1869
ATOM   1869  OD1 ASN   228      21.991  31.025  -0.337  1.00222.96       1SG1870
ATOM   1870  ND2 ASN   228      20.534  31.186  -2.070  1.00222.96       1SG1871
ATOM   1871  C   ASN   228      24.639  28.591  -2.310  1.00222.96       1SG1872
ATOM   1872  O   ASN   228      25.529  28.699  -3.154  1.00222.96       1SG1873
ATOM   1873  N   ASN   229      24.193  27.414  -1.824  1.00269.50       1SG1874
ATOM   1874  CA  ASN   229      24.545  26.102  -2.280  1.00269.50       1SG1875
ATOM   1875  CB  ASN   229      25.263  25.261  -1.208  1.00269.50       1SG1876
ATOM   1876  CG  ASN   229      25.846  24.023  -1.869  1.00269.50       1SG1877
ATOM   1877  OD1 ASN   229      26.564  24.123  -2.862  1.00269.50       1SG1878
ATOM   1878  ND2 ASN   229      25.542  22.825  -1.299  1.00269.50       1SG1879
ATOM   1879  C   ASN   229      23.211  25.473  -2.542  1.00269.50       1SG1880
ATOM   1880  O   ASN   229      22.211  25.906  -1.970  1.00269.50       1SG1881
ATOM   1881  N   SER   230      23.117  24.459  -3.424  1.00236.37       1SG1882
ATOM   1882  CA  SER   230      21.775  24.012  -3.667  1.00236.37       1SG1883
ATOM   1883  CB  SER   230      21.190  24.559  -4.978  1.00236.37       1SG1884
ATOM   1884  OG  SER   230      21.191  25.979  -4.967  1.00236.37       1SG1885
ATOM   1885  C   SER   230      21.713  22.524  -3.794  1.00236.37       1SG1886
ATOM   1886  O   SER   230      22.639  21.877  -4.278  1.00236.37       1SG1887
ATOM   1887  N   LEU   231      20.586  21.951  -3.320  1.00284.74       1SG1888
ATOM   1888  CA  LEU   231      20.273  20.562  -3.505  1.00284.74       1SG1889
ATOM   1889  CB  LEU   231      20.357  19.695  -2.238  1.00284.74       1SG1890
ATOM   1890  CG  LEU   231      20.008  18.215  -2.497  1.00284.74       1SG1891
ATOM   1891  CD1 LEU   231      20.988  17.573  -3.489  1.00284.74       1SG1892
ATOM   1892  CD2 LEU   231      19.890  17.427  -1.183  1.00284.74       1SG1893
ATOM   1893  C   LEU   231      18.850  20.551  -3.952  1.00284.74       1SG1894
ATOM   1894  O   LEU   231      17.966  21.058  -3.259  1.00284.74       1SG1895
ATOM   1895  N   PRO   232      18.612  20.004  -5.103  1.00176.77       1SG1896
ATOM   1896  CA  PRO   232      17.287  20.007  -5.659  1.00176.77       1SG1897
ATOM   1897  CD  PRO   232      19.631  19.966  -6.137  1.00176.77       1SG1898
ATOM   1898  CB  PRO   232      17.451  19.733  -7.156  1.00176.77       1SG1899
ATOM   1899  CG  PRO   232      18.920  19.301  -7.321  1.00176.77       1SG1900
ATOM   1900  C   PRO   232      16.276  19.128  -4.995  1.00176.77       1SG1901
ATOM   1901  O   PRO   232      15.088  19.356  -5.213  1.00176.77       1SG1902
ATOM   1902  N   ASN   233      16.686  18.121  -4.202  1.00167.70       1SG1903
ATOM   1903  CA  ASN   233      15.696  17.227  -3.666  1.00167.70       1SG1904
ATOM   1904  CB  ASN   233      16.287  15.911  -3.136  1.00167.70       1SG1905
ATOM   1905  CG  ASN   233      16.863  15.169  -4.335  1.00167.70       1SG1906
ATOM   1906  OD1 ASN   233      16.673  15.581  -5.479  1.00167.70       1SG1907
ATOM   1907  ND2 ASN   233      17.586  14.048  -4.075  1.00167.70       1SG1908
ATOM   1908  C   ASN   233      14.945  17.894  -2.557  1.00167.70       1SG1909
ATOM   1909  O   ASN   233      15.516  18.476  -1.634  1.00167.70       1SG1910
ATOM   1910  N   PRO   234      13.645  17.831  -2.676  1.00113.15       1SG1911
ATOM   1911  CA  PRO   234      12.769  18.394  -1.681  1.00113.15       1SG1912
ATOM   1912  CD  PRO   234      13.037  17.842  -3.996  1.00113.15       1SG1913
ATOM   1913  CB  PRO   234      11.471  18.760  -2.407  1.00113.15       1SG1914
ATOM   1914  CG  PRO   234      11.532  17.978  -3.728  1.00113.15       1SG1915
ATOM   1915  C   PRO   234      12.546  17.434  -0.554  1.00113.15       1SG1916
ATOM   1916  O   PRO   234      12.784  16.240  -0.735  1.00113.15       1SG1917
ATOM   1917  N   HIS   235      12.101  17.940   0.617  1.00309.10       1SG1918
ATOM   1918  CA  HIS   235      11.778  17.105   1.736  1.00309.10       1SG1919
ATOM   1919  ND1 HIS   235      11.789  14.256   3.215  1.00309.10       1SG1920
ATOM   1920  CG  HIS   235      12.598  15.360   3.388  1.00309.10       1SG1921
ATOM   1921  CB  HIS   235      12.974  16.306   2.287  1.00309.10       1SG1922
ATOM   1922  NE2 HIS   235      12.368  14.292   5.362  1.00309.10       1SG1923
ATOM   1923  CD2 HIS   235      12.941  15.366   4.703  1.00309.10       1SG1924
ATOM   1924  CE1 HIS   235      11.685  13.655   4.426  1.00309.10       1SG1925
ATOM   1925  C   HIS   235      11.260  18.007   2.813  1.00309.10       1SG1926
ATOM   1926  O   HIS   235      11.475  19.218   2.776  1.00309.10       1SG1927
ATOM   1927  N   LEU   236      10.530  17.436   3.792  1.00337.57       1SG1928
ATOM   1928  CA  LEU   236       9.999  18.222   4.867  1.00337.57       1SG1929
ATOM   1929  CB  LEU   236       8.463  18.229   4.930  1.00337.57       1SG1930
ATOM   1930  CG  LEU   236       7.919  19.068   6.099  1.00337.57       1SG1931
ATOM   1931  CD1 LEU   236       8.374  20.534   6.005  1.00337.57       1SG1932
ATOM   1932  CD2 LEU   236       6.395  18.916   6.227  1.00337.57       1SG1933
ATOM   1933  C   LEU   236      10.489  17.636   6.147  1.00337.57       1SG1934
ATOM   1934  O   LEU   236      10.813  16.450   6.209  1.00337.57       1SG1935
ATOM   1935  N   ARG   237      10.579  18.465   7.208  1.00349.53       1SG1936
ATOM   1936  CA  ARG   237      11.012  17.954   8.472  1.00349.53       1SG1937
ATOM   1937  CB  ARG   237      12.295  18.594   9.018  1.00349.53       1SG1938
ATOM   1938  CG  ARG   237      12.698  18.004  10.371  1.00349.53       1SG1939
ATOM   1939  CD  ARG   237      13.688  18.866  11.154  1.00349.53       1SG1940
ATOM   1940  NE  ARG   237      12.901  19.939  11.826  1.00349.53       1SG1941
ATOM   1941  CZ  ARG   237      13.367  20.496  12.982  1.00349.53       1SG1942
ATOM   1942  NH1 ARG   237      14.548  20.069  13.514  1.00349.53       1SG1943
ATOM   1943  NH2 ARG   237      12.651  21.474  13.610  1.00349.53       1SG1944
ATOM   1944  C   ARG   237       9.968  18.281   9.488  1.00349.53       1SG1945
ATOM   1945  O   ARG   237       9.382  19.362   9.476  1.00349.53       1SG1946
TER
END
