
#######################################################
#                                                     #
#                        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    9 (   36),  selected    9 , name T0356TS383_1-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS383_1-D1.T0356_D1.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.

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

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    -       -      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      K      23           -
LGA    -       -      R      24           -
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    D     314      P      70          2.495
LGA    F     340      K      71          1.199
LGA    V     341      R      72          2.169
LGA    P     342      V      73          3.001
LGA    I     343      A      74          4.639
LGA    -       -      M      75           -
LGA    L     344      G      76          0.442
LGA    Q     345      M      77          3.512
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    K     346      E      80          1.164
LGA    Q     347      D      81          2.064
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    -       -      A     335           -
LGA    -       -      L     336           -
LGA    -       -      N     337           -
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    -       -      F     340           -
LGA    -       -      V     341           -
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9  124    5.0      9    2.60     0.00      5.168     0.333

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.228085 * X  +  -0.583298 * Y  +  -0.779577 * Z  + 113.018684
  Y_new =   0.221201 * X  +  -0.810789 * Y  +   0.541934 * Z  + 104.526016
  Z_new =  -0.948181 * X  +  -0.048836 * Y  +   0.313955 * Z  + 101.466660 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.154315    2.987278  [ DEG:    -8.8416    171.1584 ]
  Theta =   1.247462    1.894131  [ DEG:    71.4743    108.5257 ]
  Phi   =   2.371516   -0.770077  [ DEG:   135.8779    -44.1222 ]
 
# 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: T0356TS383_1-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS383_1-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9  124   5.0    9   2.60    0.00   5.168
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS383_1-D1
PFRMAT TS
TARGET t0356
MODEL 1
PARENT 1ejeA
ATOM    609  N   ASP   314      56.278  76.723  79.371  1.00  0.00
ATOM    610  CA  ASP   314      56.273  76.823  77.924  1.00  0.00
ATOM    611  C   ASP   314      56.894  78.088  77.362  1.00  0.00
ATOM    612  O   ASP   314      56.914  78.283  76.148  1.00  0.00
ATOM    613  N   PHE   340      57.413  78.952  78.225  1.00  0.00
ATOM    614  CA  PHE   340      58.007  80.200  77.756  1.00  0.00
ATOM    615  C   PHE   340      59.480  80.061  77.400  1.00  0.00
ATOM    616  O   PHE   340      60.084  80.988  76.856  1.00  0.00
ATOM    617  N   VAL   341      60.056  78.901  77.700  1.00  0.00
ATOM    618  CA  VAL   341      61.461  78.652  77.407  1.00  0.00
ATOM    619  C   VAL   341      61.674  77.544  76.379  1.00  0.00
ATOM    620  O   VAL   341      61.174  76.431  76.535  1.00  0.00
ATOM    621  N   PRO   342      62.434  77.857  75.338  1.00  0.00
ATOM    622  CA  PRO   342      62.732  76.898  74.281  1.00  0.00
ATOM    623  C   PRO   342      64.246  76.776  74.123  1.00  0.00
ATOM    624  O   PRO   342      64.897  77.666  73.574  1.00  0.00
ATOM    625  N   ILE   343      64.792  75.669  74.619  1.00  0.00
ATOM    626  CA  ILE   343      66.225  75.397  74.565  1.00  0.00
ATOM    627  C   ILE   343      67.039  76.394  75.375  1.00  0.00
ATOM    628  O   ILE   343      68.144  76.769  74.984  1.00  0.00
ATOM    629  N   LEU   344      66.487  76.817  76.507  1.00  0.00
ATOM    630  CA  LEU   344      67.179  77.753  77.371  1.00  0.00
ATOM    631  C   LEU   344      66.960  79.211  77.024  1.00  0.00
ATOM    632  O   LEU   344      67.377  80.094  77.773  1.00  0.00
ATOM    633  N   GLN   345      66.302  79.466  75.894  1.00  0.00
ATOM    634  CA  GLN   345      66.040  80.832  75.445  1.00  0.00
ATOM    635  C   GLN   345      64.558  81.167  75.556  1.00  0.00
ATOM    636  O   GLN   345      63.719  80.274  75.664  1.00  0.00
ATOM    637  N   LYS   346      64.235  82.456  75.533  1.00  0.00
ATOM    638  CA  LYS   346      62.843  82.873  75.609  1.00  0.00
ATOM    639  C   LYS   346      62.173  82.404  74.330  1.00  0.00
ATOM    640  O   LYS   346      62.577  82.795  73.238  1.00  0.00
ATOM    641  N   GLN   347      61.163  81.551  74.463  1.00  0.00
ATOM    642  CA  GLN   347      60.456  81.034  73.294  1.00  0.00
ATOM    643  C   GLN   347      59.679  82.161  72.622  1.00  0.00
ATOM    644  O   GLN   347      58.455  82.221  72.709  1.00  0.00
TER
END
