
#######################################################
#                                                     #
#                        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 (   75),  selected    9 , name T0372TS022_4_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS022_4_2-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    K     290      G      69          2.476
LGA    -       -      N      70           -
LGA    Y     291      G      71          2.695
LGA    M     292      D      72          2.689
LGA    A     293      L      73          2.981
LGA    -       -      K      74           -
LGA    C     294      A      75          0.959
LGA    L     295      V      76          1.458
LGA    K     296      L      77          1.974
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    D     297      L      80          1.583
LGA    H     298      I      81          1.209
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9  126    5.0      9    2.12     0.00      5.880     0.406

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.402042 * X  +   0.630784 * Y  +  -0.663682 * Z  +  24.148432
  Y_new =   0.555639 * X  +  -0.744200 * Y  +  -0.370718 * Z  +  62.334518
  Z_new =  -0.727755 * X  +  -0.219723 * Y  +  -0.649688 * Z  +  24.660074 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.815470    0.326122  [ DEG:  -161.3146     18.6854 ]
  Theta =   0.815043    2.326550  [ DEG:    46.6985    133.3015 ]
  Phi   =   0.944428   -2.197165  [ DEG:    54.1118   -125.8883 ]
 
# 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: T0372TS022_4_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_4_2-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9  126   5.0    9   2.12    0.00   5.880
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT 1qst_A
ATOM   2148  N   LYS   290      35.331  60.739   2.460  1.00  0.00
ATOM   2149  CA  LYS   290      34.834  61.738   3.353  1.00  0.00
ATOM   2150  C   LYS   290      34.371  62.902   2.543  1.00  0.00
ATOM   2151  O   LYS   290      33.326  63.481   2.831  1.00  0.00
ATOM   2152  CB  LYS   290      35.934  62.189   4.317  1.00  0.00
ATOM   2153  CG  LYS   290      35.479  63.222   5.337  1.00  0.00
ATOM   2154  CD  LYS   290      36.596  63.566   6.309  1.00  0.00
ATOM   2155  CE  LYS   290      36.152  64.619   7.310  1.00  0.00
ATOM   2156  NZ  LYS   290      37.242  64.977   8.259  1.00  0.00
ATOM   2157  N   TYR   291      35.113  63.271   1.484  1.00  0.00
ATOM   2158  CA  TYR   291      34.649  64.397   0.734  1.00  0.00
ATOM   2159  C   TYR   291      33.541  63.918  -0.142  1.00  0.00
ATOM   2160  O   TYR   291      33.704  62.984  -0.924  1.00  0.00
ATOM   2161  CB  TYR   291      35.781  64.976  -0.118  1.00  0.00
ATOM   2162  CG  TYR   291      35.382  66.193  -0.921  1.00  0.00
ATOM   2163  CD1 TYR   291      35.295  67.443  -0.321  1.00  0.00
ATOM   2164  CD2 TYR   291      35.093  66.089  -2.276  1.00  0.00
ATOM   2165  CE1 TYR   291      34.932  68.561  -1.046  1.00  0.00
ATOM   2166  CE2 TYR   291      34.728  67.197  -3.016  1.00  0.00
ATOM   2167  CZ  TYR   291      34.648  68.440  -2.389  1.00  0.00
ATOM   2168  OH  TYR   291      34.286  69.552  -3.114  1.00  0.00
ATOM   2169  N   MET   292      32.366  64.565  -0.022  1.00  0.00
ATOM   2170  CA  MET   292      31.203  64.125  -0.734  1.00  0.00
ATOM   2171  C   MET   292      31.224  64.639  -2.135  1.00  0.00
ATOM   2172  O   MET   292      31.834  65.664  -2.432  1.00  0.00
ATOM   2173  CB  MET   292      29.932  64.634  -0.052  1.00  0.00
ATOM   2174  CG  MET   292      29.735  64.110   1.362  1.00  0.00
ATOM   2175  SD  MET   292      29.552  62.317   1.420  1.00  0.00
ATOM   2176  CE  MET   292      27.956  62.113   0.633  1.00  0.00
ATOM   2177  N   ALA   293      30.532  63.889  -3.016  1.00  0.00
ATOM   2178  CA  ALA   293      30.307  64.141  -4.411  1.00  0.00
ATOM   2179  C   ALA   293      31.576  64.319  -5.179  1.00  0.00
ATOM   2180  O   ALA   293      32.509  65.009  -4.775  1.00  0.00
ATOM   2181  CB  ALA   293      29.488  65.409  -4.596  1.00  0.00
ATOM   2182  N   CYS   294      31.623  63.646  -6.341  1.00  0.00
ATOM   2183  CA  CYS   294      32.699  63.756  -7.276  1.00  0.00
ATOM   2184  C   CYS   294      33.944  63.199  -6.673  1.00  0.00
ATOM   2185  O   CYS   294      34.995  63.194  -7.310  1.00  0.00
ATOM   2186  CB  CYS   294      32.939  65.220  -7.646  1.00  0.00
ATOM   2187  SG  CYS   294      31.507  66.053  -8.371  1.00  0.00
ATOM   2188  N   LEU   295      33.871  62.691  -5.430  1.00  0.00
ATOM   2189  CA  LEU   295      35.060  62.111  -4.894  1.00  0.00
ATOM   2190  C   LEU   295      34.650  60.788  -4.346  1.00  0.00
ATOM   2191  O   LEU   295      34.186  60.691  -3.210  1.00  0.00
ATOM   2192  CB  LEU   295      35.642  63.001  -3.794  1.00  0.00
ATOM   2193  CG  LEU   295      36.987  62.564  -3.210  1.00  0.00
ATOM   2194  CD1 LEU   295      38.065  62.566  -4.283  1.00  0.00
ATOM   2195  CD2 LEU   295      37.422  63.508  -2.098  1.00  0.00
ATOM   2196  N   LYS   296      34.801  59.726  -5.157  1.00  0.00
ATOM   2197  CA  LYS   296      34.400  58.434  -4.687  1.00  0.00
ATOM   2198  C   LYS   296      35.178  57.406  -5.434  1.00  0.00
ATOM   2199  O   LYS   296      35.680  57.659  -6.529  1.00  0.00
ATOM   2200  CB  LYS   296      32.903  58.218  -4.924  1.00  0.00
ATOM   2201  CG  LYS   296      32.508  58.174  -6.391  1.00  0.00
ATOM   2202  CD  LYS   296      31.003  58.307  -6.562  1.00  0.00
ATOM   2203  CE  LYS   296      30.274  57.100  -5.995  1.00  0.00
ATOM   2204  NZ  LYS   296      28.797  57.229  -6.134  1.00  0.00
ATOM   2205  N   ASP   297      35.321  56.212  -4.827  1.00  0.00
ATOM   2206  CA  ASP   297      36.015  55.140  -5.472  1.00  0.00
ATOM   2207  C   ASP   297      35.071  54.541  -6.459  1.00  0.00
ATOM   2208  O   ASP   297      33.861  54.527  -6.243  1.00  0.00
ATOM   2209  CB  ASP   297      36.446  54.089  -4.448  1.00  0.00
ATOM   2210  CG  ASP   297      37.579  54.569  -3.562  1.00  0.00
ATOM   2211  OD1 ASP   297      38.185  55.611  -3.885  1.00  0.00
ATOM   2212  OD2 ASP   297      37.861  53.901  -2.544  1.00  0.00
ATOM   2213  N   HIS   298      35.600  54.044  -7.591  1.00  0.00
ATOM   2214  CA  HIS   298      34.727  53.434  -8.546  1.00  0.00
ATOM   2215  C   HIS   298      35.279  52.077  -8.826  1.00  0.00
ATOM   2216  O   HIS   298      36.488  51.860  -8.820  1.00  0.00
ATOM   2217  CB  HIS   298      34.675  54.263  -9.830  1.00  0.00
ATOM   2218  CG  HIS   298      34.156  55.653  -9.632  1.00  0.00
ATOM   2219  ND1 HIS   298      32.810  55.948  -9.603  1.00  0.00
ATOM   2220  CD2 HIS   298      34.754  56.965  -9.432  1.00  0.00
ATOM   2221  CE1 HIS   298      32.657  57.270  -9.411  1.00  0.00
ATOM   2222  NE2 HIS   298      33.817  57.887  -9.307  1.00  0.00
TER
END
