
#######################################################
#                                                     #
#                        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    6 (   51),  selected    6 , name T0321TS074_3-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected  148 , name T0321_D2.pdb
# PARAMETERS: T0321TS074_3-D2.T0321_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    -       -      V      97           -
LGA    -       -      I      98           -
LGA    -       -      F      99           -
LGA    -       -      S     100           -
LGA    -       -      D     101           -
LGA    -       -      A     102           -
LGA    -       -      N     110           -
LGA    -       -      D     111           -
LGA    -       -      P     112           -
LGA    -       -      F     113           -
LGA    -       -      I     114           -
LGA    -       -      M     115           -
LGA    -       -      S     116           -
LGA    -       -      Q     117           -
LGA    -       -      N     118           -
LGA    -       -      E     119           -
LGA    -       -      V     120           -
LGA    -       -      K     121           -
LGA    -       -      G     122           -
LGA    V      97      K     123          0.572
LGA    I      98      K     124          0.814
LGA    F      99      V     125          0.589
LGA    S     100      G     126          1.007
LGA    D     101      V     127          1.520
LGA    -       -      V     128           -
LGA    -       -      G     129           -
LGA    -       -      H     130           -
LGA    -       -      F     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      E     135           -
LGA    -       -      S     136           -
LGA    -       -      L     137           -
LGA    -       -      L     138           -
LGA    -       -      E     139           -
LGA    -       -      P     140           -
LGA    -       -      I     141           -
LGA    -       -      C     142           -
LGA    -       -      D     143           -
LGA    -       -      L     144           -
LGA    A     102      S     145          1.100
LGA    -       -      I     146           -
LGA    -       -      L     147           -
LGA    -       -      E     148           -
LGA    -       -      W     149           -
LGA    -       -      S     150           -
LGA    -       -      P     151           -
LGA    -       -      E     152           -
LGA    -       -      E     153           -
LGA    -       -      G     154           -
LGA    -       -      D     155           -
LGA    -       -      Y     156           -
LGA    -       -      P     157           -
LGA    -       -      L     158           -
LGA    -       -      P     159           -
LGA    -       -      A     160           -
LGA    -       -      S     161           -
LGA    -       -      E     162           -
LGA    -       -      F     163           -
LGA    -       -      I     164           -
LGA    -       -      L     165           -
LGA    -       -      P     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      D     169           -
LGA    -       -      Y     170           -
LGA    -       -      V     171           -
LGA    -       -      Y     172           -
LGA    -       -      I     173           -
LGA    -       -      T     174           -
LGA    -       -      C     175           -
LGA    -       -      A     176           -
LGA    -       -      S     177           -
LGA    -       -      V     178           -
LGA    -       -      V     179           -
LGA    -       -      D     180           -
LGA    -       -      K     181           -
LGA    -       -      T     182           -
LGA    -       -      L     183           -
LGA    -       -      P     184           -
LGA    -       -      R     185           -
LGA    -       -      L     186           -
LGA    -       -      L     187           -
LGA    -       -      E     188           -
LGA    -       -      L     189           -
LGA    -       -      S     190           -
LGA    -       -      R     191           -
LGA    -       -      N     192           -
LGA    -       -      A     193           -
LGA    -       -      R     194           -
LGA    -       -      R     195           -
LGA    -       -      I     196           -
LGA    -       -      T     197           -
LGA    -       -      L     198           -
LGA    -       -      V     199           -
LGA    -       -      G     200           -
LGA    -       -      P     201           -
LGA    -       -      G     202           -
LGA    -       -      T     203           -
LGA    -       -      P     204           -
LGA    -       -      L     205           -
LGA    -       -      A     206           -
LGA    -       -      P     207           -
LGA    -       -      V     208           -
LGA    -       -      L     209           -
LGA    -       -      F     210           -
LGA    -       -      E     211           -
LGA    -       -      H     212           -
LGA    -       -      G     213           -
LGA    -       -      L     214           -
LGA    -       -      Q     215           -
LGA    -       -      E     216           -
LGA    -       -      L     217           -
LGA    -       -      S     218           -
LGA    -       -      G     219           -
LGA    -       -      F     220           -
LGA    -       -      M     221           -
LGA    -       -      V     222           -
LGA    -       -      K     223           -
LGA    -       -      D     224           -
LGA    -       -      N     225           -
LGA    -       -      A     226           -
LGA    -       -      R     227           -
LGA    -       -      A     228           -
LGA    -       -      F     229           -
LGA    -       -      R     230           -
LGA    -       -      I     231           -
LGA    -       -      V     232           -
LGA    -       -      A     233           -
LGA    -       -      G     234           -
LGA    -       -      A     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      V     238           -
LGA    -       -      K     239           -
LGA    -       -      I     240           -
LGA    -       -      Y     241           -
LGA    -       -      S     242           -
LGA    -       -      A     243           -
LGA    -       -      G     244           -
LGA    -       -      Q     245           -
LGA    -       -      K     246           -
LGA    -       -      V     247           -
LGA    -       -      T     248           -
LGA    -       -      I     249           -
LGA    -       -      K     250           -
LGA    -       -      K     251           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6  148    5.0      6    0.99     0.00      4.001     0.551

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.669178 * X  +   0.304753 * Y  +   0.677737 * Z  +   8.344560
  Y_new =  -0.387155 * X  +   0.921456 * Y  +  -0.032078 * Z  +  39.518822
  Z_new =  -0.634281 * X  +  -0.240923 * Y  +   0.734605 * Z  +  78.327660 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.316910    2.824683  [ DEG:   -18.1576    161.8424 ]
  Theta =   0.687078    2.454515  [ DEG:    39.3666    140.6334 ]
  Phi   =  -0.524501    2.617092  [ DEG:   -30.0517    149.9483 ]
 
# 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: T0321TS074_3-D2                               
REMARK     2: T0321_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS074_3-D2.T0321_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6  148   5.0    6   0.99    0.00   4.001
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS074_3-D2
PFRMAT TS
TARGET T0321
MODEL  3
PARENT N/A
ATOM    817  N   VAL    97      23.458  34.482  70.407  1.00  1.00
ATOM    818  CA  VAL    97      22.009  34.563  70.574  1.00  1.00
ATOM    819  C   VAL    97      21.475  35.090  69.248  1.00  1.00
ATOM    820  O   VAL    97      21.857  36.170  68.806  1.00  1.00
ATOM    821  HN  VAL    97      23.962  35.215  70.863  1.00  1.00
ATOM    822  CB  VAL    97      21.629  35.557  71.678  1.00  1.00
ATOM    823  CG1 VAL    97      22.182  35.217  73.037  1.00  1.00
ATOM    824  CG2 VAL    97      20.147  35.696  71.907  1.00  1.00
ATOM    825  N   ILE    98      20.594  34.330  68.582  1.00  1.00
ATOM    826  CA  ILE    98      20.047  34.797  67.300  1.00  1.00
ATOM    827  C   ILE    98      19.164  36.037  67.476  1.00  1.00
ATOM    828  O   ILE    98      18.288  36.065  68.340  1.00  1.00
ATOM    829  HN  ILE    98      20.247  33.439  68.871  1.00  1.00
ATOM    830  CB  ILE    98      19.272  33.582  66.798  1.00  1.00
ATOM    831  CG1 ILE    98      18.225  33.395  67.859  1.00  1.00
ATOM    832  CG2 ILE    98      20.289  32.465  66.527  1.00  1.00
ATOM    833  CD1 ILE    98      17.170  32.159  67.062  1.00  1.00
ATOM    834  N   PHE    99      19.400  37.056  66.657  1.00  1.00
ATOM    835  CA  PHE    99      18.633  38.299  66.735  1.00  1.00
ATOM    836  C   PHE    99      17.950  38.581  65.402  1.00  1.00
ATOM    837  O   PHE    99      18.611  38.844  64.397  1.00  1.00
ATOM    838  HN  PHE    99      20.100  37.054  65.943  1.00  1.00
ATOM    839  CB  PHE    99      19.548  39.485  67.084  1.00  1.00
ATOM    840  CG  PHE    99      20.120  39.301  68.479  1.00  1.00
ATOM    841  CD1 PHE    99      19.343  38.592  69.428  1.00  1.00
ATOM    842  CD2 PHE    99      21.039  40.215  68.992  1.00  1.00
ATOM    843  CE1 PHE    99      19.693  38.623  70.763  1.00  1.00
ATOM    844  CE2 PHE    99      21.423  40.251  70.307  1.00  1.00
ATOM    845  CZ  PHE    99      20.734  39.409  71.220  1.00  1.00
ATOM    846  N   SER   100      16.622  38.548  65.406  1.00  1.00
ATOM    847  CA  SER   100      15.842  38.777  64.185  1.00  1.00
ATOM    848  C   SER   100      15.752  40.259  63.800  1.00  1.00
ATOM    849  O   SER   100      15.336  40.581  62.688  1.00  1.00
ATOM    850  HN  SER   100      16.064  38.370  66.217  1.00  1.00
ATOM    851  CB  SER   100      14.428  38.197  64.341  1.00  1.00
ATOM    852  OG  SER   100      13.723  38.834  65.395  1.00  1.00
ATOM    853  N   ASP   101      16.114  41.152  64.723  1.00  1.00
ATOM    854  CA  ASP   101      16.212  42.599  64.443  1.00  1.00
ATOM    855  C   ASP   101      17.615  43.051  63.983  1.00  1.00
ATOM    856  O   ASP   101      17.832  44.247  63.763  1.00  1.00
ATOM    857  HN  ASP   101      16.342  40.902  65.664  1.00  1.00
ATOM    858  CB  ASP   101      15.799  43.422  65.681  1.00  1.00
ATOM    859  CG  ASP   101      16.707  43.174  66.892  1.00  1.00
ATOM    860  OD1 ASP   101      17.890  42.875  66.762  1.00  1.00
ATOM    861  OD2 ASP   101      16.205  43.182  68.019  1.00  1.00
ATOM    862  N   ALA   102      18.556  42.114  63.855  1.00  1.00
ATOM    863  CA  ALA   102      19.903  42.432  63.373  1.00  1.00
ATOM    864  C   ALA   102      19.802  43.118  62.025  1.00  1.00
ATOM    865  O   ALA   102      19.052  42.669  61.158  1.00  1.00
ATOM    866  HN  ALA   102      18.420  41.147  64.073  1.00  1.00
ATOM    867  CB  ALA   102      20.750  41.173  63.256  1.00  1.00
TER
END
