
#######################################################
#                                                     #
#                        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    8 (   65),  selected    8 , name T0372TS022_1_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS022_1_2-D1.T0372_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.

#      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    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
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    K     290      V      96          1.274
LGA    Y     291      C      97          0.347
LGA    M     292      S      98          1.323
LGA    A     293      N      99          0.735
LGA    C     294      M     100          0.622
LGA    L     295      R     101          1.422
LGA    K     296      A     102          3.619
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    D     297      F     114          4.018
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)    8  126    5.0      8    2.11     0.00      5.532     0.362

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.237941 * X  +   0.764265 * Y  +   0.599403 * Z  +  13.960481
  Y_new =  -0.781366 * X  +   0.215950 * Y  +  -0.585519 * Z  +  63.089596
  Z_new =  -0.576932 * X  +  -0.607672 * Y  +   0.545788 * Z  +   1.550968 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.838998    2.302595  [ DEG:   -48.0710    131.9290 ]
  Theta =   0.614968    2.526625  [ DEG:    35.2351    144.7649 ]
  Phi   =  -1.866393    1.275199  [ DEG:  -106.9365     73.0635 ]
 
# 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_1_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_1_2-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8  126   5.0    8   2.11    0.00   5.532
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT 1ne9_A
ATOM   2233  N   LYS   290      28.277  50.380   3.828  1.00  0.00
ATOM   2234  CA  LYS   290      28.299  50.922   5.149  1.00  0.00
ATOM   2235  C   LYS   290      26.899  50.890   5.651  1.00  0.00
ATOM   2236  O   LYS   290      25.989  50.471   4.937  1.00  0.00
ATOM   2237  CB  LYS   290      28.824  52.359   5.131  1.00  0.00
ATOM   2238  CG  LYS   290      30.254  52.490   4.635  1.00  0.00
ATOM   2239  CD  LYS   290      30.755  53.919   4.765  1.00  0.00
ATOM   2240  CE  LYS   290      32.191  54.048   4.282  1.00  0.00
ATOM   2241  NZ  LYS   290      32.700  55.440   4.418  1.00  0.00
ATOM   2242  N   TYR   291      26.707  51.320   6.913  1.00  0.00
ATOM   2243  CA  TYR   291      25.412  51.292   7.517  1.00  0.00
ATOM   2244  C   TYR   291      24.427  51.952   6.619  1.00  0.00
ATOM   2245  O   TYR   291      24.768  52.805   5.802  1.00  0.00
ATOM   2246  CB  TYR   291      25.431  52.030   8.858  1.00  0.00
ATOM   2247  CG  TYR   291      26.145  51.279   9.960  1.00  0.00
ATOM   2248  CD1 TYR   291      27.408  51.671  10.384  1.00  0.00
ATOM   2249  CD2 TYR   291      25.553  50.182  10.572  1.00  0.00
ATOM   2250  CE1 TYR   291      28.068  50.991  11.390  1.00  0.00
ATOM   2251  CE2 TYR   291      26.198  49.490  11.579  1.00  0.00
ATOM   2252  CZ  TYR   291      27.465  49.904  11.986  1.00  0.00
ATOM   2253  OH  TYR   291      28.120  49.226  12.988  1.00  0.00
ATOM   2254  N   MET   292      23.163  51.518   6.753  1.00  0.00
ATOM   2255  CA  MET   292      22.071  51.893   5.908  1.00  0.00
ATOM   2256  C   MET   292      21.926  53.374   5.975  1.00  0.00
ATOM   2257  O   MET   292      21.540  54.015   4.999  1.00  0.00
ATOM   2258  CB  MET   292      20.777  51.225   6.377  1.00  0.00
ATOM   2259  CG  MET   292      20.749  49.718   6.182  1.00  0.00
ATOM   2260  SD  MET   292      20.918  49.237   4.453  1.00  0.00
ATOM   2261  CE  MET   292      19.364  49.823   3.785  1.00  0.00
ATOM   2262  N   ALA   293      22.221  53.967   7.140  1.00  0.00
ATOM   2263  CA  ALA   293      22.030  55.380   7.242  1.00  0.00
ATOM   2264  C   ALA   293      22.881  56.078   6.222  1.00  0.00
ATOM   2265  O   ALA   293      22.408  56.997   5.557  1.00  0.00
ATOM   2266  CB  ALA   293      22.420  55.869   8.628  1.00  0.00
ATOM   2267  N   CYS   294      24.151  55.660   6.038  1.00  0.00
ATOM   2268  CA  CYS   294      24.967  56.389   5.105  1.00  0.00
ATOM   2269  C   CYS   294      24.365  56.342   3.741  1.00  0.00
ATOM   2270  O   CYS   294      24.089  57.381   3.144  1.00  0.00
ATOM   2271  CB  CYS   294      26.372  55.787   5.037  1.00  0.00
ATOM   2272  SG  CYS   294      27.493  56.634   3.900  1.00  0.00
ATOM   2273  N   LEU   295      24.116  55.129   3.216  1.00  0.00
ATOM   2274  CA  LEU   295      23.611  55.043   1.877  1.00  0.00
ATOM   2275  C   LEU   295      22.393  54.185   1.898  1.00  0.00
ATOM   2276  O   LEU   295      22.286  53.258   2.697  1.00  0.00
ATOM   2277  CB  LEU   295      24.659  54.428   0.947  1.00  0.00
ATOM   2278  CG  LEU   295      25.971  55.201   0.798  1.00  0.00
ATOM   2279  CD1 LEU   295      26.981  54.397  -0.005  1.00  0.00
ATOM   2280  CD2 LEU   295      25.738  56.523   0.083  1.00  0.00
ATOM   2281  N   LYS   296      21.425  54.489   1.019  1.00  0.00
ATOM   2282  CA  LYS   296      20.243  53.684   1.004  1.00  0.00
ATOM   2283  C   LYS   296      20.580  52.489   0.177  1.00  0.00
ATOM   2284  O   LYS   296      21.147  52.630  -0.904  1.00  0.00
ATOM   2285  CB  LYS   296      19.075  54.459   0.391  1.00  0.00
ATOM   2286  CG  LYS   296      17.758  53.699   0.392  1.00  0.00
ATOM   2287  CD  LYS   296      16.630  54.548  -0.174  1.00  0.00
ATOM   2288  CE  LYS   296      15.314  53.789  -0.171  1.00  0.00
ATOM   2289  NZ  LYS   296      14.200  54.607  -0.725  1.00  0.00
ATOM   2290  N   ASP   297      20.208  51.290   0.678  1.00  0.00
ATOM   2291  CA  ASP   297      20.462  49.995   0.100  1.00  0.00
ATOM   2292  C   ASP   297      21.728  49.972  -0.750  1.00  0.00
ATOM   2293  O   ASP   297      22.787  50.422  -0.237  1.00  0.00
ATOM   2294  CB  ASP   297      19.300  49.574  -0.802  1.00  0.00
ATOM   2295  CG  ASP   297      19.391  48.122  -1.229  1.00  0.00
ATOM   2296  OD1 ASP   297      20.192  47.375  -0.629  1.00  0.00
ATOM   2297  OD2 ASP   297      18.660  47.730  -2.163  1.00  0.00
TER
END
