
#######################################################
#                                                     #
#                        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 T0372TS021_1_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS021_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    K     290      R      25          1.600
LGA    Y     291      N      26          0.881
LGA    M     292      C      27          1.717
LGA    A     293      D      28          1.916
LGA    -       -      L      29           -
LGA    C     294      S      30          1.616
LGA    L     295      F      31          1.673
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    K     296      L      34          0.645
LGA    D     297      C      35          0.975
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    H     298      R      38          1.603
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    -       -      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    1.46     0.00      6.774     0.575

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.812459 * X  +  -0.570712 * Y  +   0.119154 * Z  +  98.432594
  Y_new =   0.216667 * X  +  -0.105824 * Y  +   0.970493 * Z  +  16.909706
  Z_new =  -0.541262 * X  +   0.814303 * Y  +   0.209632 * Z  +  26.477274 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.318830   -1.822763  [ DEG:    75.5634   -104.4366 ]
  Theta =   0.571938    2.569655  [ DEG:    32.7696    147.2304 ]
  Phi   =   2.880977   -0.260616  [ DEG:   165.0678    -14.9322 ]
 
# 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: T0372TS021_1_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS021_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:    9  126   5.0    9   1.46    0.00   6.774
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS021_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM   1225  N   LYS   290      30.793  53.592  12.577  1.00108.36       1SG1226
ATOM   1226  CA  LYS   290      29.707  53.147  13.405  1.00108.36       1SG1227
ATOM   1227  CB  LYS   290      28.372  53.048  12.648  1.00108.36       1SG1228
ATOM   1228  CG  LYS   290      27.897  54.386  12.081  1.00108.36       1SG1229
ATOM   1229  CD  LYS   290      27.728  55.480  13.137  1.00108.36       1SG1230
ATOM   1230  CE  LYS   290      27.276  56.822  12.555  1.00108.36       1SG1231
ATOM   1231  NZ  LYS   290      27.305  57.864  13.602  1.00108.36       1SG1232
ATOM   1232  C   LYS   290      30.041  51.779  13.895  1.00108.36       1SG1233
ATOM   1233  O   LYS   290      29.887  51.475  15.077  1.00108.36       1SG1234
ATOM   1234  N   TYR   291      30.548  50.927  12.992  1.00148.84       1SG1235
ATOM   1235  CA  TYR   291      30.960  49.616  13.382  1.00148.84       1SG1236
ATOM   1236  CB  TYR   291      30.837  48.571  12.264  1.00148.84       1SG1237
ATOM   1237  CG  TYR   291      29.359  48.408  12.244  1.00148.84       1SG1238
ATOM   1238  CD1 TYR   291      28.563  49.320  11.592  1.00148.84       1SG1239
ATOM   1239  CD2 TYR   291      28.771  47.361  12.913  1.00148.84       1SG1240
ATOM   1240  CE1 TYR   291      27.196  49.182  11.599  1.00148.84       1SG1241
ATOM   1241  CE2 TYR   291      27.404  47.216  12.926  1.00148.84       1SG1242
ATOM   1242  CZ  TYR   291      26.617  48.130  12.267  1.00148.84       1SG1243
ATOM   1243  OH  TYR   291      25.214  47.993  12.281  1.00148.84       1SG1244
ATOM   1244  C   TYR   291      32.345  49.798  13.883  1.00148.84       1SG1245
ATOM   1245  O   TYR   291      32.901  50.874  13.709  1.00148.84       1SG1246
ATOM   1246  N   MET   292      32.918  48.823  14.608  1.00196.46       1SG1247
ATOM   1247  CA  MET   292      34.188  49.115  15.210  1.00196.46       1SG1248
ATOM   1248  CB  MET   292      34.738  47.958  16.062  1.00196.46       1SG1249
ATOM   1249  CG  MET   292      35.962  48.349  16.893  1.00196.46       1SG1250
ATOM   1250  SD  MET   292      36.354  47.203  18.249  1.00196.46       1SG1251
ATOM   1251  CE  MET   292      35.067  47.851  19.356  1.00196.46       1SG1252
ATOM   1252  C   MET   292      35.188  49.478  14.159  1.00196.46       1SG1253
ATOM   1253  O   MET   292      35.823  50.525  14.272  1.00196.46       1SG1254
ATOM   1254  N   ALA   293      35.287  48.665  13.085  1.00130.69       1SG1255
ATOM   1255  CA  ALA   293      36.176  48.939  11.988  1.00130.69       1SG1256
ATOM   1256  CB  ALA   293      35.679  50.070  11.071  1.00130.69       1SG1257
ATOM   1257  C   ALA   293      37.517  49.320  12.525  1.00130.69       1SG1258
ATOM   1258  O   ALA   293      38.041  50.383  12.198  1.00130.69       1SG1259
ATOM   1259  N   CYS   294      38.107  48.449  13.361  1.00 78.24       1SG1260
ATOM   1260  CA  CYS   294      39.356  48.772  13.982  1.00 78.24       1SG1261
ATOM   1261  CB  CYS   294      39.927  47.651  14.869  1.00 78.24       1SG1262
ATOM   1262  SG  CYS   294      38.917  47.314  16.341  1.00 78.24       1SG1263
ATOM   1263  C   CYS   294      40.349  49.015  12.903  1.00 78.24       1SG1264
ATOM   1264  O   CYS   294      40.098  48.716  11.736  1.00 78.24       1SG1265
ATOM   1265  N   LEU   295      41.502  49.604  13.278  1.00 46.69       1SG1266
ATOM   1266  CA  LEU   295      42.500  49.874  12.294  1.00 46.69       1SG1267
ATOM   1267  CB  LEU   295      43.803  50.457  12.871  1.00 46.69       1SG1268
ATOM   1268  CG  LEU   295      43.635  51.828  13.555  1.00 46.69       1SG1269
ATOM   1269  CD1 LEU   295      44.981  52.357  14.076  1.00 46.69       1SG1270
ATOM   1270  CD2 LEU   295      42.921  52.828  12.634  1.00 46.69       1SG1271
ATOM   1271  C   LEU   295      42.832  48.554  11.695  1.00 46.69       1SG1272
ATOM   1272  O   LEU   295      43.132  47.595  12.404  1.00 46.69       1SG1273
ATOM   1273  N   LYS   296      42.759  48.472  10.355  1.00 90.70       1SG1274
ATOM   1274  CA  LYS   296      43.038  47.227   9.717  1.00 90.70       1SG1275
ATOM   1275  CB  LYS   296      42.497  47.153   8.276  1.00 90.70       1SG1276
ATOM   1276  CG  LYS   296      40.972  47.018   8.216  1.00 90.70       1SG1277
ATOM   1277  CD  LYS   296      40.358  47.398   6.865  1.00 90.70       1SG1278
ATOM   1278  CE  LYS   296      41.035  46.746   5.657  1.00 90.70       1SG1279
ATOM   1279  NZ  LYS   296      40.328  47.127   4.413  1.00 90.70       1SG1280
ATOM   1280  C   LYS   296      44.513  47.066   9.684  1.00 90.70       1SG1281
ATOM   1281  O   LYS   296      45.243  47.943   9.225  1.00 90.70       1SG1282
ATOM   1282  N   ASP   297      44.986  45.922  10.206  1.00126.46       1SG1283
ATOM   1283  CA  ASP   297      46.388  45.655  10.216  1.00126.46       1SG1284
ATOM   1284  CB  ASP   297      46.750  44.350  10.952  1.00126.46       1SG1285
ATOM   1285  CG  ASP   297      46.130  43.175  10.205  1.00126.46       1SG1286
ATOM   1286  OD1 ASP   297      44.914  43.251   9.883  1.00126.46       1SG1287
ATOM   1287  OD2 ASP   297      46.866  42.183   9.950  1.00126.46       1SG1288
ATOM   1288  C   ASP   297      46.813  45.521   8.793  1.00126.46       1SG1289
ATOM   1289  O   ASP   297      47.880  45.996   8.405  1.00126.46       1SG1290
ATOM   1290  N   HIS   298      45.963  44.888   7.971  1.00156.53       1SG1291
ATOM   1291  CA  HIS   298      46.318  44.657   6.599  1.00156.53       1SG1292
ATOM   1292  ND1 HIS   298      46.767  42.266   4.380  1.00156.53       1SG1293
ATOM   1293  CG  HIS   298      45.863  43.296   4.522  1.00156.53       1SG1294
ATOM   1294  CB  HIS   298      45.326  43.760   5.845  1.00156.53       1SG1295
ATOM   1295  NE2 HIS   298      46.358  43.033   2.335  1.00156.53       1SG1296
ATOM   1296  CD2 HIS   298      45.626  43.756   3.262  1.00156.53       1SG1297
ATOM   1297  CE1 HIS   298      47.030  42.154   3.055  1.00156.53       1SG1298
ATOM   1298  C   HIS   298      46.392  45.988   5.910  1.00156.53       1SG1299
ATOM   1299  O   HIS   298      45.710  46.942   6.280  1.00156.53       1SG1300
TER
END
