
#######################################################
#                                                     #
#                        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_1_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS268_1_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    -       -      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    N     228      S     265          0.457
LGA    N     229      A     266          0.771
LGA    S     230      I     267          0.774
LGA    L     231      N     268          0.464
LGA    P     232      T     269          0.740
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    0.66     0.00      6.849     0.660

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.950614 * X  +  -0.309837 * Y  +  -0.018259 * Z  + -31.760582
  Y_new =   0.085132 * X  +   0.203720 * Y  +   0.975321 * Z  + -49.824955
  Z_new =  -0.298471 * X  +  -0.928708 * Y  +   0.220036 * Z  +  -0.100389 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.338159    1.803434  [ DEG:   -76.6709    103.3291 ]
  Theta =   0.303090    2.838502  [ DEG:    17.3658    162.6342 ]
  Phi   =   0.089317   -3.052276  [ DEG:     5.1175   -174.8825 ]
 
# 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_1_2-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS268_1_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   0.66    0.00   6.849
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS268_1_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT 1sur
ATOM   1861  N   ASN   228      -1.616  24.144   3.617  1.00  0.00
ATOM   1862  CA  ASN   228      -1.693  25.192   4.585  1.00  0.00
ATOM   1863  C   ASN   228      -0.266  25.495   4.896  1.00  0.00
ATOM   1864  O   ASN   228       0.427  24.696   5.525  1.00  0.00
ATOM   1865  CB  ASN   228      -2.456  24.722   5.824  1.00  0.00
ATOM   1866  CG  ASN   228      -2.714  25.844   6.811  1.00  0.00
ATOM   1867  OD1 ASN   228      -1.971  26.824   6.859  1.00  0.00
ATOM   1868  ND2 ASN   228      -3.771  25.703   7.602  1.00  0.00
ATOM   1869  N   ASN   229       0.203  26.677   4.460  1.00  0.00
ATOM   1870  CA  ASN   229       1.591  26.994   4.593  1.00  0.00
ATOM   1871  C   ASN   229       1.929  27.131   6.037  1.00  0.00
ATOM   1872  O   ASN   229       1.213  27.769   6.807  1.00  0.00
ATOM   1873  CB  ASN   229       1.911  28.309   3.879  1.00  0.00
ATOM   1874  CG  ASN   229       3.393  28.626   3.881  1.00  0.00
ATOM   1875  OD1 ASN   229       3.972  28.932   4.923  1.00  0.00
ATOM   1876  ND2 ASN   229       4.014  28.555   2.708  1.00  0.00
ATOM   1877  N   SER   230       3.044  26.492   6.436  1.00  0.00
ATOM   1878  CA  SER   230       3.532  26.600   7.774  1.00  0.00
ATOM   1879  C   SER   230       4.442  27.782   7.767  1.00  0.00
ATOM   1880  O   SER   230       4.689  28.381   6.724  1.00  0.00
ATOM   1881  CB  SER   230       4.286  25.329   8.173  1.00  0.00
ATOM   1882  OG  SER   230       5.481  25.188   7.426  1.00  0.00
ATOM   1883  N   LEU   231       4.956  28.166   8.949  1.00  0.00
ATOM   1884  CA  LEU   231       5.843  29.287   8.982  1.00  0.00
ATOM   1885  C   LEU   231       7.100  28.851   8.311  1.00  0.00
ATOM   1886  O   LEU   231       7.493  27.688   8.385  1.00  0.00
ATOM   1887  CB  LEU   231       6.126  29.705  10.426  1.00  0.00
ATOM   1888  CG  LEU   231       4.929  30.218  11.229  1.00  0.00
ATOM   1889  CD1 LEU   231       5.324  30.482  12.673  1.00  0.00
ATOM   1890  CD2 LEU   231       4.400  31.515  10.636  1.00  0.00
ATOM   1891  N   PRO   232       7.720  29.764   7.621  1.00  0.00
ATOM   1892  CA  PRO   232       8.944  29.427   6.954  1.00  0.00
ATOM   1893  C   PRO   232      10.074  29.546   7.918  1.00  0.00
ATOM   1894  O   PRO   232       9.922  29.056   9.069  1.00  0.00
ATOM   1895  CB  PRO   232       9.040  30.448   5.818  1.00  0.00
ATOM   1896  CG  PRO   232       8.428  31.688   6.379  1.00  0.00
ATOM   1897  CD  PRO   232       7.268  31.236   7.221  1.00  0.00
TER
END
