
#######################################################
#                                                     #
#                        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   13 (   52),  selected   13 , name T0320AL333_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320AL333_2-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    P     232      S     273          1.191
LGA    N     233      V     274          0.924
LGA    P     234      V     275          0.960
LGA    H     235      D     276          0.295
LGA    L     236      K     277          0.746
LGA    R     237      E     278          1.205
LGA    K     238      R     279          1.457
LGA    D     239      F     280          1.681
LGA    S     240      S     281          1.735
LGA    N     241      K     282          1.249
LGA    N     242      Y     283          1.204
LGA    P     243      H     284          1.806
LGA    A     244      D     285          2.356
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   13   73    5.0     13    1.39     7.69     16.973     0.873

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.419502 * X  +   0.905362 * Y  +  -0.065867 * Z  + -107.769958
  Y_new =  -0.204959 * X  +   0.165155 * Y  +   0.964736 * Z  + -11.864305
  Z_new =   0.884314 * X  +  -0.391208 * Y  +   0.254844 * Z  +  49.191704 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.993418    2.148175  [ DEG:   -56.9186    123.0814 ]
  Theta =  -1.085022   -2.056571  [ DEG:   -62.1672   -117.8328 ]
  Phi   =  -0.454467    2.687126  [ DEG:   -26.0390    153.9610 ]
 
# 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: T0320AL333_2-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320AL333_2-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   13   73   5.0   13   1.39    7.69  16.973
REMARK  ---------------------------------------------------------- 
MOLECULE T0320AL333_2-D2
REMARK Aligment from pdb entry: 1ojx_A
ATOM    733  N   PRO   232      21.953  34.844   3.438  1.00  0.00              
ATOM    734  CA  PRO   232      20.772  34.320   2.745  1.00  0.00              
ATOM    735  C   PRO   232      21.063  33.788   1.345  1.00  0.00              
ATOM    736  O   PRO   232      20.634  32.681   1.005  1.00  0.00              
ATOM    737  N   ASN   233      21.783  34.565   0.535  1.00  0.00              
ATOM    738  CA  ASN   233      22.009  34.196  -0.860  1.00  0.00              
ATOM    739  C   ASN   233      22.955  32.991  -0.972  1.00  0.00              
ATOM    740  O   ASN   233      22.701  32.085  -1.752  1.00  0.00              
ATOM    741  N   PRO   234      24.029  32.982  -0.182  1.00  0.00              
ATOM    742  CA  PRO   234      24.971  31.865  -0.187  1.00  0.00              
ATOM    743  C   PRO   234      24.271  30.559   0.186  1.00  0.00              
ATOM    744  O   PRO   234      24.393  29.558  -0.521  1.00  0.00              
ATOM    745  N   HIS   235      23.521  30.572   1.284  1.00  0.00              
ATOM    746  CA  HIS   235      22.826  29.369   1.724  1.00  0.00              
ATOM    747  C   HIS   235      21.721  28.923   0.744  1.00  0.00              
ATOM    748  O   HIS   235      21.541  27.728   0.523  1.00  0.00              
ATOM    749  N   LEU   236      20.999  29.882   0.164  1.00  0.00              
ATOM    750  CA  LEU   236      20.014  29.610  -0.887  1.00  0.00              
ATOM    751  C   LEU   236      20.638  28.878  -2.093  1.00  0.00              
ATOM    752  O   LEU   236      20.048  27.959  -2.659  1.00  0.00              
ATOM    753  N   ARG   237      21.843  29.278  -2.478  1.00  0.00              
ATOM    754  CA  ARG   237      22.526  28.642  -3.606  1.00  0.00              
ATOM    755  C   ARG   237      22.968  27.210  -3.266  1.00  0.00              
ATOM    756  O   ARG   237      22.982  26.337  -4.136  1.00  0.00              
ATOM    757  N   LYS   238      23.310  26.963  -2.003  1.00  0.00              
ATOM    758  CA  LYS   238      23.655  25.608  -1.546  1.00  0.00              
ATOM    759  C   LYS   238      22.419  24.688  -1.518  1.00  0.00              
ATOM    760  O   LYS   238      22.493  23.493  -1.858  1.00  0.00              
ATOM    761  N   ASP   239      21.274  25.246  -1.140  1.00  0.00              
ATOM    762  CA  ASP   239      20.010  24.508  -1.196  1.00  0.00              
ATOM    763  C   ASP   239      19.672  24.086  -2.631  1.00  0.00              
ATOM    764  O   ASP   239      19.293  22.937  -2.864  1.00  0.00              
ATOM    765  N   SER   240      19.809  25.013  -3.579  1.00  0.00              
ATOM    766  CA  SER   240      19.577  24.727  -5.001  1.00  0.00              
ATOM    767  C   SER   240      20.489  23.619  -5.538  1.00  0.00              
ATOM    768  O   SER   240      20.054  22.776  -6.315  1.00  0.00              
ATOM    769  N   ASN   241      21.759  23.635  -5.147  1.00  0.00              
ATOM    770  CA  ASN   241      22.686  22.594  -5.582  1.00  0.00              
ATOM    771  C   ASN   241      22.227  21.216  -5.107  1.00  0.00              
ATOM    772  O   ASN   241      22.294  20.243  -5.856  1.00  0.00              
ATOM    773  N   ASN   242      21.748  21.150  -3.867  1.00  0.00              
ATOM    774  CA  ASN   242      21.300  19.892  -3.277  1.00  0.00              
ATOM    775  C   ASN   242      20.028  19.386  -3.945  1.00  0.00              
ATOM    776  O   ASN   242      19.962  18.225  -4.331  1.00  0.00              
ATOM    777  N   PRO   243      19.029  20.262  -4.080  1.00  0.00              
ATOM    778  CA  PRO   243      17.697  19.884  -4.556  1.00  0.00              
ATOM    779  C   PRO   243      17.676  19.618  -6.070  1.00  0.00              
ATOM    780  O   PRO   243      17.079  18.640  -6.521  1.00  0.00              
ATOM    781  N   ALA   244      18.307  20.494  -6.848  1.00  0.00              
ATOM    782  CA  ALA   244      18.346  20.366  -8.309  1.00  0.00              
ATOM    783  C   ALA   244      19.536  19.518  -8.756  1.00  0.00              
ATOM    784  O   ALA   244      19.637  19.164  -9.924  1.00  0.00              
END
