
#######################################################
#                                                     #
#                        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_2_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS268_2_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    N     228      E     250          0.640
LGA    N     229      I     251          2.135
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    S     230      A     254          2.048
LGA    L     231      F     255          0.753
LGA    P     232      G     256          1.054
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    1.47     0.00      6.333     0.318

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.060544 * X  +   0.933743 * Y  +  -0.352786 * Z  + -74.020912
  Y_new =   0.967755 * X  +   0.031665 * Y  +   0.249895 * Z  + -23.391535
  Z_new =   0.244509 * X  +  -0.356540 * Y  +  -0.901717 * Z  +  41.042164 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.765057    0.376536  [ DEG:  -158.4261     21.5739 ]
  Theta =  -0.247013   -2.894580  [ DEG:   -14.1528   -165.8472 ]
  Phi   =   1.508316   -1.633277  [ DEG:    86.4201    -93.5799 ]
 
# 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_2_2-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS268_2_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   1.47    0.00   6.333
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS268_2_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT 1ni5_A
ATOM   1861  N   ASN   228      -1.188  19.158  12.742  1.00  0.00
ATOM   1862  CA  ASN   228      -2.229  20.121  12.914  1.00  0.00
ATOM   1863  C   ASN   228      -1.653  21.441  12.540  1.00  0.00
ATOM   1864  O   ASN   228      -0.458  21.680  12.707  1.00  0.00
ATOM   1865  CB  ASN   228      -2.707  20.139  14.367  1.00  0.00
ATOM   1866  CG  ASN   228      -3.490  18.895  14.739  1.00  0.00
ATOM   1867  OD1 ASN   228      -4.013  18.197  13.871  1.00  0.00
ATOM   1868  ND2 ASN   228      -3.573  18.614  16.034  1.00  0.00
ATOM   1869  N   ASN   229      -2.499  22.331  11.994  1.00  0.00
ATOM   1870  CA  ASN   229      -2.016  23.618  11.606  1.00  0.00
ATOM   1871  C   ASN   229      -1.746  24.369  12.863  1.00  0.00
ATOM   1872  O   ASN   229      -2.275  24.037  13.923  1.00  0.00
ATOM   1873  CB  ASN   229      -3.061  24.350  10.762  1.00  0.00
ATOM   1874  CG  ASN   229      -3.220  23.749   9.380  1.00  0.00
ATOM   1875  OD1 ASN   229      -2.350  23.015   8.908  1.00  0.00
ATOM   1876  ND2 ASN   229      -4.332  24.058   8.725  1.00  0.00
ATOM   1877  N   SER   230      -0.887  25.399  12.779  1.00  0.00
ATOM   1878  CA  SER   230      -0.585  26.145  13.960  1.00  0.00
ATOM   1879  C   SER   230      -1.851  26.800  14.389  1.00  0.00
ATOM   1880  O   SER   230      -2.756  27.020  13.585  1.00  0.00
ATOM   1881  CB  SER   230       0.487  27.198  13.669  1.00  0.00
ATOM   1882  OG  SER   230      -0.015  28.216  12.820  1.00  0.00
ATOM   1883  N   LEU   231      -1.956  27.111  15.694  1.00  0.00
ATOM   1884  CA  LEU   231      -3.154  27.720  16.179  1.00  0.00
ATOM   1885  C   LEU   231      -3.194  29.106  15.639  1.00  0.00
ATOM   1886  O   LEU   231      -2.167  29.755  15.441  1.00  0.00
ATOM   1887  CB  LEU   231      -3.157  27.752  17.709  1.00  0.00
ATOM   1888  CG  LEU   231      -3.177  26.395  18.415  1.00  0.00
ATOM   1889  CD1 LEU   231      -3.056  26.571  19.921  1.00  0.00
ATOM   1890  CD2 LEU   231      -4.475  25.658  18.125  1.00  0.00
ATOM   1891  N   PRO   232      -4.384  29.551  15.361  1.00  0.00
ATOM   1892  CA  PRO   232      -4.543  30.881  14.852  1.00  0.00
ATOM   1893  C   PRO   232      -4.567  31.831  15.998  1.00  0.00
ATOM   1894  O   PRO   232      -5.386  31.611  16.931  1.00  0.00
ATOM   1895  CB  PRO   232      -5.877  30.833  14.104  1.00  0.00
ATOM   1896  CG  PRO   232      -6.711  29.876  14.888  1.00  0.00
ATOM   1897  CD  PRO   232      -5.780  28.786  15.339  1.00  0.00
TER
END
