
#######################################################
#                                                     #
#                        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   11 (   55),  selected   11 , name T0356TS245_1-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS245_1-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    D     314      L      50          0.882
LGA    A     315      L      51          3.595
LGA    I     316      F      52           -
LGA    F     340      E      53          2.449
LGA    V     341      N      54          2.059
LGA    P     342      P      55          1.837
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    I     343      Y      58          0.412
LGA    L     344      S      59          0.511
LGA    Q     345      M      60          0.701
LGA    K     346      P      61          0.511
LGA    Q     347      V      62          3.247
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
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)   11  124    5.0     10    1.98    10.00      7.240     0.482

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.452451 * X  +  -0.704323 * Y  +  -0.547007 * Z  + 127.401222
  Y_new =  -0.474899 * X  +  -0.328884 * Y  +   0.816276 * Z  +  87.014778
  Z_new =  -0.754824 * X  +   0.629098 * Y  +  -0.185679 * Z  +  93.842278 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.857798   -1.283794  [ DEG:   106.4440    -73.5560 ]
  Theta =   0.855386    2.286207  [ DEG:    49.0100    130.9900 ]
  Phi   =  -2.331993    0.809600  [ DEG:  -133.6133     46.3867 ]
 
# 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: T0356TS245_1-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS245_1-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11  124   5.0   10   1.98   10.00   7.240
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS245_1-D1
PFRMAT TS
TARGET t0356
MODEL 1
PARENT 1ejeA
ATOM    751  N   ASP   314      61.922  74.201  92.570  1.00  0.00
ATOM    752  CA  ASP   314      61.691  73.619  91.253  1.00  0.00
ATOM    753  C   ASP   314      62.293  74.399  90.127  1.00  0.00
ATOM    754  O   ASP   314      62.179  74.290  88.886  1.00  0.00
ATOM    755  CB  ASP   314      60.174  73.521  91.074  1.00  0.00
ATOM    756  N   ALA   315      63.359  75.270  90.792  1.00  0.00
ATOM    757  CA  ALA   315      64.458  76.151  90.405  1.00  0.00
ATOM    758  C   ALA   315      64.382  76.614  88.964  1.00  0.00
ATOM    759  O   ALA   315      64.113  77.266  89.996  1.00  0.00
ATOM    760  CB  ALA   315      65.757  75.379  90.640  1.00  0.00
ATOM    761  N   ILE   316      64.157  77.884  85.925  1.00  0.00
ATOM    762  CA  ILE   316      63.940  78.304  87.319  1.00  0.00
ATOM    763  C   ILE   316      63.991  77.138  88.320  1.00  0.00
ATOM    764  O   ILE   316      63.327  78.134  87.959  1.00  0.00
ATOM    765  CB  ILE   316      62.574  78.989  87.377  1.00  0.00
ATOM    766  N   PHE   340      64.695  73.742  99.209  1.00  0.00
ATOM    767  CA  PHE   340      64.504  73.684 100.653  1.00  0.00
ATOM    768  C   PHE   340      65.302  72.617 101.332  1.00  0.00
ATOM    769  O   PHE   340      64.748  72.720 100.217  1.00  0.00
ATOM    770  CB  PHE   340      63.010  73.455 100.892  1.00  0.00
ATOM    771  N   VAL   341      66.150  72.113 101.472  1.00  0.00
ATOM    772  CA  VAL   341      67.380  71.335 101.465  1.00  0.00
ATOM    773  C   VAL   341      67.016  69.867 101.570  1.00  0.00
ATOM    774  O   VAL   341      65.782  70.071 101.537  1.00  0.00
ATOM    775  CB  VAL   341      68.257  71.746 102.650  1.00  0.00
ATOM    776  N   PRO   342      67.459  68.939 101.285  1.00  0.00
ATOM    777  CA  PRO   342      67.357  67.590 100.807  1.00  0.00
ATOM    778  C   PRO   342      68.685  67.023 101.013  1.00  0.00
ATOM    779  O   PRO   342      69.233  67.207  99.904  1.00  0.00
ATOM    780  CB  PRO   342      66.993  67.545  99.321  1.00  0.00
ATOM    781  N   ILE   343      69.188  66.405 101.883  1.00  0.00
ATOM    782  CA  ILE   343      70.463  65.714 101.977  1.00  0.00
ATOM    783  C   ILE   343      71.620  66.641 101.635  1.00  0.00
ATOM    784  O   ILE   343      71.056  66.849 100.539  1.00  0.00
ATOM    785  CB  ILE   343      70.436  64.527 101.012  1.00  0.00
ATOM    786  N   LEU   344      72.268  67.470 102.201  1.00  0.00
ATOM    787  CA  LEU   344      72.590  68.844 101.856  1.00  0.00
ATOM    788  C   LEU   344      72.481  69.549 100.526  1.00  0.00
ATOM    789  O   LEU   344      73.419  70.344 100.310  1.00  0.00
ATOM    790  CB  LEU   344      74.041  68.860 102.341  1.00  0.00
ATOM    791  N   GLN   345      71.652  69.260  99.688  1.00  0.00
ATOM    792  CA  GLN   345      71.495  69.694  98.311  1.00  0.00
ATOM    793  C   GLN   345      70.201  70.475  98.218  1.00  0.00
ATOM    794  O   GLN   345      69.502  69.752  98.961  1.00  0.00
ATOM    795  CB  GLN   345      71.445  68.480  97.382  1.00  0.00
ATOM    796  N   LYS   346      69.799  71.235  97.618  1.00  0.00
ATOM    797  CA  LYS   346      68.892  72.120  96.987  1.00  0.00
ATOM    798  C   LYS   346      67.543  71.569  96.956  1.00  0.00
ATOM    799  O   LYS   346      68.150  71.283  95.901  1.00  0.00
ATOM    800  CB  LYS   346      69.389  72.376  95.563  1.00  0.00
ATOM    801  N   GLN   347      66.714  71.112  97.241  1.00  0.00
ATOM    802  CA  GLN   347      65.650  70.140  97.086  1.00  0.00
ATOM    803  C   GLN   347      64.873  70.567  95.844  1.00  0.00
ATOM    804  O   GLN   347      63.795  71.196  95.914  1.00  0.00
ATOM    805  CB  GLN   347      64.729  70.135  98.307  1.00  0.00
TER
END
