
#######################################################
#                                                     #
#                        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   10 (   79),  selected   10 , name T0318TS021_2_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected  335 , name T0318_D2.pdb
# PARAMETERS: T0318TS021_2_1-D2.T0318_D2.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    -       -      T     156           -
LGA    -       -      N     157           -
LGA    -       -      E     158           -
LGA    -       -      D     159           -
LGA    -       -      A     160           -
LGA    -       -      V     161           -
LGA    -       -      F     162           -
LGA    -       -      L     163           -
LGA    -       -      T     164           -
LGA    -       -      D     165           -
LGA    -       -      L     166           -
LGA    -       -      S     167           -
LGA    -       -      E     168           -
LGA    -       -      S     169           -
LGA    -       -      V     170           -
LGA    -       -      R     171           -
LGA    -       -      E     172           -
LGA    -       -      T     173           -
LGA    -       -      A     174           -
LGA    -       -      R     175           -
LGA    -       -      L     176           -
LGA    -       -      I     177           -
LGA    -       -      D     178           -
LGA    -       -      T     179           -
LGA    -       -      P     180           -
LGA    -       -      A     181           -
LGA    -       -      N     182           -
LGA    -       -      I     183           -
LGA    -       -      L     184           -
LGA    -       -      T     185           -
LGA    -       -      T     186           -
LGA    -       -      D     187           -
LGA    -       -      A     188           -
LGA    -       -      L     189           -
LGA    -       -      V     190           -
LGA    -       -      D     191           -
LGA    -       -      E     192           -
LGA    -       -      A     193           -
LGA    -       -      V     194           -
LGA    -       -      K     195           -
LGA    -       -      V     196           -
LGA    -       -      G     197           -
LGA    -       -      N     198           -
LGA    -       -      A     199           -
LGA    -       -      T     200           -
LGA    -       -      G     201           -
LGA    -       -      S     202           -
LGA    -       -      K     203           -
LGA    -       -      I     204           -
LGA    -       -      T     205           -
LGA    -       -      V     206           -
LGA    -       -      I     207           -
LGA    -       -      R     208           -
LGA    -       -      G     209           -
LGA    -       -      E     210           -
LGA    -       -      E     211           -
LGA    -       -      L     212           -
LGA    -       -      L     213           -
LGA    -       -      K     214           -
LGA    -       -      A     215           -
LGA    -       -      G     216           -
LGA    -       -      F     217           -
LGA    -       -      G     218           -
LGA    -       -      G     219           -
LGA    -       -      I     220           -
LGA    -       -      Y     221           -
LGA    -       -      H     222           -
LGA    -       -      V     223           -
LGA    -       -      G     224           -
LGA    -       -      K     225           -
LGA    -       -      A     226           -
LGA    -       -      G     227           -
LGA    -       -      P     228           -
LGA    -       -      T     229           -
LGA    -       -      P     230           -
LGA    -       -      P     231           -
LGA    -       -      A     232           -
LGA    -       -      F     233           -
LGA    -       -      V     234           -
LGA    -       -      V     235           -
LGA    -       -      L     236           -
LGA    -       -      S     237           -
LGA    -       -      H     238           -
LGA    -       -      E     239           -
LGA    -       -      V     240           -
LGA    -       -      P     241           -
LGA    -       -      G     242           -
LGA    -       -      S     243           -
LGA    -       -      T     244           -
LGA    -       -      E     245           -
LGA    -       -      H     246           -
LGA    -       -      I     247           -
LGA    -       -      A     248           -
LGA    -       -      L     249           -
LGA    -       -      V     250           -
LGA    -       -      G     251           -
LGA    -       -      K     252           -
LGA    -       -      G     253           -
LGA    -       -      V     254           -
LGA    -       -      V     255           -
LGA    -       -      Y     256           -
LGA    -       -      D     257           -
LGA    -       -      T     258           -
LGA    -       -      G     259           -
LGA    -       -      G     260           -
LGA    -       -      L     261           -
LGA    -       -      Q     262           -
LGA    -       -      I     263           -
LGA    -       -      K     264           -
LGA    -       -      T     265           -
LGA    -       -      K     266           -
LGA    -       -      T     267           -
LGA    -       -      G     268           -
LGA    -       -      M     269           -
LGA    -       -      P     270           -
LGA    -       -      N     271           -
LGA    -       -      M     272           -
LGA    -       -      K     273           -
LGA    -       -      R     274           -
LGA    -       -      D     275           -
LGA    -       -      M     276           -
LGA    -       -      G     277           -
LGA    -       -      G     278           -
LGA    -       -      A     279           -
LGA    -       -      A     280           -
LGA    -       -      G     281           -
LGA    -       -      M     282           -
LGA    -       -      L     283           -
LGA    -       -      E     284           -
LGA    -       -      A     285           -
LGA    -       -      Y     286           -
LGA    -       -      S     287           -
LGA    -       -      A     288           -
LGA    -       -      L     289           -
LGA    -       -      V     290           -
LGA    -       -      K     291           -
LGA    -       -      H     292           -
LGA    -       -      G     293           -
LGA    -       -      F     294           -
LGA    -       -      S     295           -
LGA    -       -      Q     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      H     299           -
LGA    -       -      A     300           -
LGA    -       -      C     301           -
LGA    -       -      L     302           -
LGA    -       -      C     303           -
LGA    -       -      I     304           -
LGA    -       -      V     305           -
LGA    -       -      E     306           -
LGA    -       -      N     307           -
LGA    -       -      N     308           -
LGA    -       -      V     309           -
LGA    -       -      S     310           -
LGA    -       -      P     311           -
LGA    -       -      I     312           -
LGA    -       -      A     313           -
LGA    -       -      N     314           -
LGA    -       -      K     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      D     318           -
LGA    -       -      I     319           -
LGA    -       -      I     320           -
LGA    -       -      K     321           -
LGA    -       -      M     322           -
LGA    -       -      L     323           -
LGA    -       -      S     324           -
LGA    -       -      G     325           -
LGA    -       -      K     326           -
LGA    -       -      T     327           -
LGA    -       -      V     328           -
LGA    -       -      E     329           -
LGA    -       -      I     330           -
LGA    -       -      N     331           -
LGA    -       -      N     332           -
LGA    -       -      T     333           -
LGA    -       -      D     334           -
LGA    -       -      A     335           -
LGA    -       -      E     336           -
LGA    -       -      G     337           -
LGA    -       -      R     338           -
LGA    -       -      L     339           -
LGA    -       -      I     340           -
LGA    -       -      L     341           -
LGA    -       -      A     342           -
LGA    -       -      D     343           -
LGA    -       -      G     344           -
LGA    -       -      V     345           -
LGA    -       -      F     346           -
LGA    -       -      Y     347           -
LGA    -       -      A     348           -
LGA    -       -      K     349           -
LGA    -       -      E     350           -
LGA    -       -      T     351           -
LGA    -       -      L     352           -
LGA    -       -      K     353           -
LGA    -       -      A     354           -
LGA    -       -      T     355           -
LGA    -       -      T     356           -
LGA    -       -      I     357           -
LGA    -       -      F     358           -
LGA    -       -      D     359           -
LGA    -       -      M     360           -
LGA    -       -      A     361           -
LGA    -       -      T     362           -
LGA    -       -      L     363           -
LGA    -       -      T     364           -
LGA    -       -      G     365           -
LGA    -       -      A     366           -
LGA    -       -      Q     367           -
LGA    -       -      A     368           -
LGA    -       -      W     369           -
LGA    -       -      L     370           -
LGA    -       -      S     371           -
LGA    -       -      G     372           -
LGA    -       -      R     373           -
LGA    -       -      L     374           -
LGA    -       -      H     375           -
LGA    -       -      G     376           -
LGA    -       -      A     377           -
LGA    -       -      A     378           -
LGA    -       -      M     379           -
LGA    -       -      T     380           -
LGA    -       -      N     381           -
LGA    -       -      D     382           -
LGA    -       -      E     383           -
LGA    -       -      Q     384           -
LGA    -       -      L     385           -
LGA    -       -      E     386           -
LGA    -       -      N     387           -
LGA    -       -      E     388           -
LGA    -       -      I     389           -
LGA    -       -      I     390           -
LGA    -       -      K     391           -
LGA    -       -      A     392           -
LGA    -       -      G     393           -
LGA    -       -      K     394           -
LGA    -       -      A     395           -
LGA    -       -      S     396           -
LGA    -       -      G     397           -
LGA    -       -      D     398           -
LGA    -       -      L     399           -
LGA    -       -      V     400           -
LGA    -       -      A     401           -
LGA    -       -      P     402           -
LGA    -       -      M     403           -
LGA    -       -      L     404           -
LGA    -       -      F     405           -
LGA    -       -      A     406           -
LGA    -       -      P     407           -
LGA    -       -      D     408           -
LGA    -       -      L     409           -
LGA    -       -      F     410           -
LGA    -       -      F     411           -
LGA    -       -      G     412           -
LGA    -       -      D     413           -
LGA    -       -      L     414           -
LGA    -       -      K     415           -
LGA    -       -      S     416           -
LGA    -       -      S     417           -
LGA    -       -      I     418           -
LGA    -       -      A     419           -
LGA    -       -      D     420           -
LGA    -       -      M     421           -
LGA    -       -      K     422           -
LGA    -       -      N     423           -
LGA    -       -      S     424           -
LGA    -       -      N     425           -
LGA    -       -      L     426           -
LGA    -       -      G     427           -
LGA    -       -      K     428           -
LGA    -       -      M     429           -
LGA    -       -      D     430           -
LGA    -       -      G     431           -
LGA    -       -      P     432           -
LGA    -       -      P     433           -
LGA    -       -      S     434           -
LGA    -       -      A     435           -
LGA    -       -      V     436           -
LGA    -       -      A     437           -
LGA    -       -      G     438           -
LGA    -       -      L     439           -
LGA    -       -      L     440           -
LGA    -       -      I     441           -
LGA    -       -      G     442           -
LGA    -       -      A     443           -
LGA    -       -      H     444           -
LGA    -       -      I     445           -
LGA    -       -      G     446           -
LGA    -       -      F     447           -
LGA    -       -      G     448           -
LGA    -       -      E     449           -
LGA    -       -      G     450           -
LGA    -       -      L     451           -
LGA    T     156      R     452          0.829
LGA    N     157      W     453          0.701
LGA    E     158      L     454          1.145
LGA    D     159      H     455          0.854
LGA    A     160      L     456          0.807
LGA    V     161      D     457          1.902
LGA    F     162      I     458          0.865
LGA    L     163      A     459          1.876
LGA    -       -      A     460           -
LGA    -       -      P     461           -
LGA    T     164      A     462          3.316
LGA    D     165      E     463          1.453
LGA    -       -      V     464           -
LGA    -       -      G     465           -
LGA    -       -      D     466           -
LGA    -       -      R     467           -
LGA    -       -      G     468           -
LGA    -       -      T     469           -
LGA    -       -      G     470           -
LGA    -       -      Y     471           -
LGA    -       -      G     472           -
LGA    -       -      P     473           -
LGA    -       -      A     474           -
LGA    -       -      L     475           -
LGA    -       -      F     476           -
LGA    -       -      S     477           -
LGA    -       -      T     478           -
LGA    -       -      L     479           -
LGA    -       -      L     480           -
LGA    -       -      G     481           -
LGA    -       -      K     482           -
LGA    -       -      Y     483           -
LGA    -       -      T     484           -
LGA    -       -      S     485           -
LGA    -       -      V     486           -
LGA    -       -      P     487           -
LGA    -       -      M     488           -
LGA    -       -      L     489           -
LGA    -       -      K     490           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   10  335    5.0     10    1.58     0.00      2.852     0.596

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.173426 * X  +   0.918845 * Y  +   0.354468 * Z  + -26.062626
  Y_new =  -0.710293 * X  +  -0.366016 * Y  +   0.601263 * Z  +  81.611382
  Z_new =   0.682208 * X  +  -0.147502 * Y  +   0.716125 * Z  +  -6.848931 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.203131    2.938462  [ DEG:   -11.6385    168.3615 ]
  Theta =  -0.750778   -2.390814  [ DEG:   -43.0164   -136.9836 ]
  Phi   =  -1.810272    1.331321  [ DEG:  -103.7209     76.2791 ]
 
# 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: T0318TS021_2_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS021_2_1-D2.T0318_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10  335   5.0   10   1.58    0.00   2.852
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS021_2_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM   1201  N   THR   156      -4.184  35.651  17.497  1.00200.09       1SG1202
ATOM   1202  CA  THR   156      -4.774  36.705  16.716  1.00200.09       1SG1203
ATOM   1203  CB  THR   156      -6.180  37.025  17.147  1.00200.09       1SG1204
ATOM   1204  OG1 THR   156      -6.841  37.822  16.175  1.00200.09       1SG1205
ATOM   1205  CG2 THR   156      -6.126  37.773  18.490  1.00200.09       1SG1206
ATOM   1206  C   THR   156      -3.957  37.954  16.821  1.00200.09       1SG1207
ATOM   1207  O   THR   156      -2.855  37.951  17.366  1.00200.09       1SG1208
ATOM   1208  N   ASN   157      -4.493  39.057  16.255  1.00146.88       1SG1209
ATOM   1209  CA  ASN   157      -3.820  40.320  16.186  1.00146.88       1SG1210
ATOM   1210  CB  ASN   157      -4.457  41.322  15.204  1.00146.88       1SG1211
ATOM   1211  CG  ASN   157      -4.199  40.871  13.771  1.00146.88       1SG1212
ATOM   1212  OD1 ASN   157      -5.042  40.234  13.143  1.00146.88       1SG1213
ATOM   1213  ND2 ASN   157      -3.003  41.228  13.232  1.00146.88       1SG1214
ATOM   1214  C   ASN   157      -3.808  40.989  17.513  1.00146.88       1SG1215
ATOM   1215  O   ASN   157      -4.737  40.874  18.307  1.00146.88       1SG1216
ATOM   1216  N   GLU   158      -2.698  41.705  17.767  1.00293.46       1SG1217
ATOM   1217  CA  GLU   158      -2.537  42.494  18.945  1.00293.46       1SG1218
ATOM   1218  CB  GLU   158      -1.562  41.879  19.965  1.00293.46       1SG1219
ATOM   1219  CG  GLU   158      -1.382  42.703  21.241  1.00293.46       1SG1220
ATOM   1220  CD  GLU   158      -0.471  41.914  22.171  1.00293.46       1SG1221
ATOM   1221  OE1 GLU   158      -0.874  40.796  22.586  1.00293.46       1SG1222
ATOM   1222  OE2 GLU   158       0.644  42.417  22.474  1.00293.46       1SG1223
ATOM   1223  C   GLU   158      -1.968  43.790  18.465  1.00293.46       1SG1224
ATOM   1224  O   GLU   158      -1.263  43.824  17.459  1.00293.46       1SG1225
ATOM   1225  N   ASP   159      -2.299  44.902  19.152  1.00178.34       1SG1226
ATOM   1226  CA  ASP   159      -1.775  46.172  18.746  1.00178.34       1SG1227
ATOM   1227  CB  ASP   159      -2.722  47.355  19.013  1.00178.34       1SG1228
ATOM   1228  CG  ASP   159      -3.859  47.280  18.007  1.00178.34       1SG1229
ATOM   1229  OD1 ASP   159      -3.575  46.983  16.817  1.00178.34       1SG1230
ATOM   1230  OD2 ASP   159      -5.027  47.524  18.412  1.00178.34       1SG1231
ATOM   1231  C   ASP   159      -0.542  46.412  19.545  1.00178.34       1SG1232
ATOM   1232  O   ASP   159      -0.583  47.012  20.618  1.00178.34       1SG1233
ATOM   1233  N   ALA   160       0.598  45.918  19.039  1.00 81.91       1SG1234
ATOM   1234  CA  ALA   160       1.841  46.108  19.718  1.00 81.91       1SG1235
ATOM   1235  CB  ALA   160       2.907  45.065  19.341  1.00 81.91       1SG1236
ATOM   1236  C   ALA   160       2.362  47.446  19.325  1.00 81.91       1SG1237
ATOM   1237  O   ALA   160       2.025  47.973  18.267  1.00 81.91       1SG1238
ATOM   1238  N   VAL   161       3.178  48.056  20.200  1.00171.94       1SG1239
ATOM   1239  CA  VAL   161       3.751  49.306  19.825  1.00171.94       1SG1240
ATOM   1240  CB  VAL   161       2.911  50.493  20.177  1.00171.94       1SG1241
ATOM   1241  CG1 VAL   161       2.983  50.724  21.696  1.00171.94       1SG1242
ATOM   1242  CG2 VAL   161       3.380  51.676  19.323  1.00171.94       1SG1243
ATOM   1243  C   VAL   161       5.027  49.435  20.575  1.00171.94       1SG1244
ATOM   1244  O   VAL   161       5.227  48.794  21.605  1.00171.94       1SG1245
ATOM   1245  N   PHE   162       5.946  50.259  20.056  1.00118.56       1SG1246
ATOM   1246  CA  PHE   162       7.171  50.434  20.763  1.00118.56       1SG1247
ATOM   1247  CB  PHE   162       8.409  49.977  19.977  1.00118.56       1SG1248
ATOM   1248  CG  PHE   162       8.352  48.492  19.902  1.00118.56       1SG1249
ATOM   1249  CD1 PHE   162       7.498  47.861  19.026  1.00118.56       1SG1250
ATOM   1250  CD2 PHE   162       9.160  47.725  20.709  1.00118.56       1SG1251
ATOM   1251  CE1 PHE   162       7.451  46.488  18.960  1.00118.56       1SG1252
ATOM   1252  CE2 PHE   162       9.117  46.353  20.648  1.00118.56       1SG1253
ATOM   1253  CZ  PHE   162       8.260  45.729  19.774  1.00118.56       1SG1254
ATOM   1254  C   PHE   162       7.308  51.887  21.029  1.00118.56       1SG1255
ATOM   1255  O   PHE   162       6.777  52.727  20.305  1.00118.56       1SG1256
ATOM   1256  N   LEU   163       8.002  52.211  22.127  1.00233.65       1SG1257
ATOM   1257  CA  LEU   163       8.234  53.569  22.491  1.00233.65       1SG1258
ATOM   1258  CB  LEU   163       8.334  53.775  24.010  1.00233.65       1SG1259
ATOM   1259  CG  LEU   163       7.056  53.352  24.772  1.00233.65       1SG1260
ATOM   1260  CD1 LEU   163       5.842  54.202  24.362  1.00233.65       1SG1261
ATOM   1261  CD2 LEU   163       6.785  51.843  24.643  1.00233.65       1SG1262
ATOM   1262  C   LEU   163       9.541  53.925  21.871  1.00233.65       1SG1263
ATOM   1263  O   LEU   163      10.341  53.041  21.570  1.00233.65       1SG1264
ATOM   1264  N   THR   164       9.794  55.232  21.657  1.00366.25       1SG1265
ATOM   1265  CA  THR   164      11.025  55.613  21.029  1.00366.25       1SG1266
ATOM   1266  CB  THR   164      11.228  57.095  20.918  1.00366.25       1SG1267
ATOM   1267  OG1 THR   164      10.184  57.681  20.154  1.00366.25       1SG1268
ATOM   1268  CG2 THR   164      12.596  57.362  20.261  1.00366.25       1SG1269
ATOM   1269  C   THR   164      12.132  55.095  21.870  1.00366.25       1SG1270
ATOM   1270  O   THR   164      12.172  55.320  23.078  1.00366.25       1SG1271
ATOM   1271  N   ASP   165      13.068  54.370  21.236  1.00458.31       1SG1272
ATOM   1272  CA  ASP   165      14.145  53.825  21.998  1.00458.31       1SG1273
ATOM   1273  CB  ASP   165      14.952  52.762  21.237  1.00458.31       1SG1274
ATOM   1274  CG  ASP   165      14.057  51.543  21.067  1.00458.31       1SG1275
ATOM   1275  OD1 ASP   165      13.092  51.399  21.865  1.00458.31       1SG1276
ATOM   1276  OD2 ASP   165      14.326  50.737  20.137  1.00458.31       1SG1277
ATOM   1277  C   ASP   165      15.072  54.974  22.354  1.00458.31       1SG1278
ATOM   1278  O   ASP   165      14.835  56.099  21.840  1.00458.31       1SG1279
ATOM   1279  OXT ASP   165      16.022  54.748  23.150  1.00458.31       1SG1280
TER
END
