
#######################################################
#                                                     #
#                        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   16 (  117),  selected   16 , name T0316TS211_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS211_3-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      G     220           -
LGA    -       -      R     221           -
LGA    -       -      M     222           -
LGA    -       -      M     223           -
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    -       -      M     230           -
LGA    -       -      G     231           -
LGA    -       -      E     232           -
LGA    -       -      H     233           -
LGA    -       -      A     234           -
LGA    -       -      G     235           -
LGA    -       -      L     236           -
LGA    -       -      M     237           -
LGA    G     220      Y     238          1.787
LGA    R     221      Y     239          2.736
LGA    -       -      T     240           -
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    M     222      G     246          2.774
LGA    M     223      L     247          0.603
LGA    T     224      G     248          3.492
LGA    V     225      I     249          2.362
LGA    D     226      G     250          2.267
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    G     227      P     259          5.321
LGA    R     228      W     260          2.043
LGA    -       -      F     261           -
LGA    D     229      V     262          1.822
LGA    M     230      V     263          2.648
LGA    G     231      G     264          3.719
LGA    E     232      K     265           -
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    H     233      Q     276          4.424
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    A     234      H     280          1.033
LGA    G     235      D     281          0.766
LGA    -       -      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16   60    5.0     15    2.82     6.67     15.725     0.513

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.110285 * X  +   0.081862 * Y  +   0.990523 * Z  +  39.052643
  Y_new =   0.894032 * X  +   0.427226 * Y  +  -0.134850 * Z  +  42.730907
  Z_new =  -0.434216 * X  +   0.900431 * Y  +  -0.026071 * Z  + -34.635845 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.599742   -1.541851  [ DEG:    91.6585    -88.3415 ]
  Theta =   0.449168    2.692425  [ DEG:    25.7354    154.2646 ]
  Phi   =   1.448060   -1.693533  [ DEG:    82.9677    -97.0323 ]
 
# 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: T0316TS211_3-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS211_3-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16   60   5.0   15   2.82    6.67  15.725
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS211_3-D2
PFRMAT     TS
TARGET     T0316
MODEL      3 
PARENT     1vl2_B
ATOM   1700  N   GLY   220      39.907  27.178 -14.800  1.00  0.00           N  
ATOM   1701  CA  GLY   220      38.591  27.004 -14.148  1.00  0.00           C  
ATOM   1702  C   GLY   220      37.449  26.751 -15.162  1.00  0.00           C  
ATOM   1703  O   GLY   220      37.563  27.041 -16.358  1.00  0.00           O  
ATOM   1704  N   ARG   221      36.324  26.231 -14.663  1.00  0.00           N  
ATOM   1705  CA  ARG   221      35.079  26.095 -15.485  1.00  0.00           C  
ATOM   1706  C   ARG   221      34.462  27.438 -16.006  1.00  0.00           C  
ATOM   1707  O   ARG   221      33.900  27.474 -17.102  1.00  0.00           O  
ATOM   1708  CB  ARG   221      34.001  25.303 -14.713  1.00  0.00           C  
ATOM   1709  CG  ARG   221      34.390  23.866 -14.307  1.00  0.00           C  
ATOM   1710  CD  ARG   221      33.189  23.137 -13.693  1.00  0.00           C  
ATOM   1711  NE  ARG   221      33.530  21.729 -13.390  1.00  0.00           N  
ATOM   1712  CZ  ARG   221      32.685  20.856 -12.821  1.00  0.00           C  
ATOM   1713  NH1 ARG   221      33.100  19.621 -12.647  1.00  0.00           N  
ATOM   1714  NH2 ARG   221      31.457  21.169 -12.425  1.00  0.00           N  
ATOM   1715  N   MET   222      34.630  28.532 -15.238  1.00  0.00           N  
ATOM   1716  CA  MET   222      34.410  29.933 -15.696  1.00  0.00           C  
ATOM   1717  C   MET   222      35.203  30.388 -16.971  1.00  0.00           C  
ATOM   1718  O   MET   222      34.711  31.240 -17.714  1.00  0.00           O  
ATOM   1719  CB  MET   222      34.733  30.883 -14.506  1.00  0.00           C  
ATOM   1720  CG  MET   222      33.997  30.627 -13.169  1.00  0.00           C  
ATOM   1721  SD  MET   222      32.205  30.524 -13.387  1.00  0.00           S  
ATOM   1722  CE  MET   222      31.788  32.244 -13.725  1.00  0.00           C  
ATOM   1723  N   MET   223      36.394  29.810 -17.238  1.00  0.00           N  
ATOM   1724  CA  MET   223      37.105  29.956 -18.535  1.00  0.00           C  
ATOM   1725  C   MET   223      36.426  29.314 -19.788  1.00  0.00           C  
ATOM   1726  O   MET   223      36.678  29.796 -20.895  1.00  0.00           O  
ATOM   1727  CB  MET   223      38.539  29.381 -18.369  1.00  0.00           C  
ATOM   1728  CG  MET   223      39.563  30.018 -19.318  1.00  0.00           C  
ATOM   1729  SD  MET   223      39.731  31.795 -19.006  1.00  0.00           S  
ATOM   1730  CE  MET   223      40.533  31.830 -17.388  1.00  0.00           C  
ATOM   1731  N   THR   224      35.599  28.251 -19.643  1.00  0.00           N  
ATOM   1732  CA  THR   224      34.921  27.589 -20.792  1.00  0.00           C  
ATOM   1733  C   THR   224      33.767  28.503 -21.310  1.00  0.00           C  
ATOM   1734  O   THR   224      32.755  28.724 -20.636  1.00  0.00           O  
ATOM   1735  CB  THR   224      34.434  26.153 -20.443  1.00  0.00           C  
ATOM   1736  OG1 THR   224      35.488  25.389 -19.863  1.00  0.00           O  
ATOM   1737  CG2 THR   224      33.960  25.379 -21.686  1.00  0.00           C  
ATOM   1738  N   VAL   225      34.013  29.064 -22.501  1.00  0.00           N  
ATOM   1739  CA  VAL   225      33.259  30.206 -23.077  1.00  0.00           C  
ATOM   1740  C   VAL   225      31.794  29.888 -23.547  1.00  0.00           C  
ATOM   1741  O   VAL   225      30.804  30.334 -22.971  1.00  0.00           O  
ATOM   1742  CB  VAL   225      33.554  31.624 -22.453  1.00  0.00           C  
ATOM   1743  CG1 VAL   225      33.553  31.760 -20.913  1.00  0.00           C  
ATOM   1744  CG2 VAL   225      34.884  32.225 -22.958  1.00  0.00           C  
ATOM   1745  N   ASP   226      31.695  29.129 -24.653  1.00  0.00           N  
ATOM   1746  CA  ASP   226      30.438  28.889 -25.417  1.00  0.00           C  
ATOM   1747  C   ASP   226      29.833  27.507 -25.061  1.00  0.00           C  
ATOM   1748  O   ASP   226      28.678  27.436 -24.631  1.00  0.00           O  
ATOM   1749  CB  ASP   226      30.761  29.029 -26.933  1.00  0.00           C  
ATOM   1750  CG  ASP   226      29.572  28.848 -27.886  1.00  0.00           C  
ATOM   1751  OD1 ASP   226      29.490  27.793 -28.552  1.00  0.00           O  
ATOM   1752  OD2 ASP   226      28.709  29.751 -27.953  1.00  0.00           O  
ATOM   1753  N   GLY   227      30.612  26.423 -25.253  1.00  0.00           N  
ATOM   1754  CA  GLY   227      30.194  25.065 -24.877  1.00  0.00           C  
ATOM   1755  C   GLY   227      30.007  24.884 -23.362  1.00  0.00           C  
ATOM   1756  O   GLY   227      30.736  25.442 -22.536  1.00  0.00           O  
ATOM   1757  N   ARG   228      29.045  24.027 -23.026  1.00  0.00           N  
ATOM   1758  CA  ARG   228      28.969  23.427 -21.671  1.00  0.00           C  
ATOM   1759  C   ARG   228      30.118  22.390 -21.498  1.00  0.00           C  
ATOM   1760  O   ARG   228      30.613  21.804 -22.471  1.00  0.00           O  
ATOM   1761  CB  ARG   228      27.591  22.742 -21.476  1.00  0.00           C  
ATOM   1762  CG  ARG   228      26.369  23.682 -21.550  1.00  0.00           C  
ATOM   1763  CD  ARG   228      25.051  22.919 -21.362  1.00  0.00           C  
ATOM   1764  NE  ARG   228      23.906  23.847 -21.509  1.00  0.00           N  
ATOM   1765  CZ  ARG   228      22.620  23.467 -21.565  1.00  0.00           C  
ATOM   1766  NH1 ARG   228      21.707  24.402 -21.713  1.00  0.00           N  
ATOM   1767  NH2 ARG   228      22.220  22.204 -21.481  1.00  0.00           N  
ATOM   1768  N   ASP   229      30.511  22.128 -20.244  1.00  0.00           N  
ATOM   1769  CA  ASP   229      31.443  21.010 -19.939  1.00  0.00           C  
ATOM   1770  C   ASP   229      30.802  19.628 -20.273  1.00  0.00           C  
ATOM   1771  O   ASP   229      29.576  19.469 -20.279  1.00  0.00           O  
ATOM   1772  CB  ASP   229      31.889  21.080 -18.453  1.00  0.00           C  
ATOM   1773  CG  ASP   229      32.826  22.228 -18.045  1.00  0.00           C  
ATOM   1774  OD1 ASP   229      33.151  22.299 -16.842  1.00  0.00           O  
ATOM   1775  OD2 ASP   229      33.256  23.042 -18.893  1.00  0.00           O  
ATOM   1776  N   MET   230      31.648  18.624 -20.544  1.00  0.00           N  
ATOM   1777  CA  MET   230      31.195  17.213 -20.746  1.00  0.00           C  
ATOM   1778  C   MET   230      30.401  16.577 -19.551  1.00  0.00           C  
ATOM   1779  O   MET   230      29.448  15.831 -19.792  1.00  0.00           O  
ATOM   1780  CB  MET   230      32.414  16.336 -21.132  1.00  0.00           C  
ATOM   1781  CG  MET   230      33.055  16.639 -22.504  1.00  0.00           C  
ATOM   1782  SD  MET   230      31.866  16.462 -23.859  1.00  0.00           S  
ATOM   1783  CE  MET   230      31.595  14.678 -23.897  1.00  0.00           C  
ATOM   1784  N   GLY   231      30.751  16.916 -18.291  1.00  0.00           N  
ATOM   1785  CA  GLY   231      29.890  16.647 -17.110  1.00  0.00           C  
ATOM   1786  C   GLY   231      28.509  17.356 -17.032  1.00  0.00           C  
ATOM   1787  O   GLY   231      27.549  16.752 -16.549  1.00  0.00           O  
ATOM   1788  N   GLU   232      28.417  18.617 -17.492  1.00  0.00           N  
ATOM   1789  CA  GLU   232      27.130  19.371 -17.596  1.00  0.00           C  
ATOM   1790  C   GLU   232      26.255  19.079 -18.866  1.00  0.00           C  
ATOM   1791  O   GLU   232      25.077  19.451 -18.876  1.00  0.00           O  
ATOM   1792  CB  GLU   232      27.426  20.896 -17.528  1.00  0.00           C  
ATOM   1793  CG  GLU   232      28.145  21.403 -16.253  1.00  0.00           C  
ATOM   1794  CD  GLU   232      28.476  22.900 -16.212  1.00  0.00           C  
ATOM   1795  OE1 GLU   232      28.196  23.641 -17.182  1.00  0.00           O  
ATOM   1796  OE2 GLU   232      29.038  23.336 -15.184  1.00  0.00           O  
ATOM   1797  N   HIS   233      26.795  18.429 -19.922  1.00  0.00           N  
ATOM   1798  CA  HIS   233      26.036  18.060 -21.144  1.00  0.00           C  
ATOM   1799  C   HIS   233      24.993  16.928 -20.869  1.00  0.00           C  
ATOM   1800  O   HIS   233      25.095  16.171 -19.896  1.00  0.00           O  
ATOM   1801  CB  HIS   233      27.076  17.680 -22.245  1.00  0.00           C  
ATOM   1802  CG  HIS   233      26.522  17.701 -23.675  1.00  0.00           C  
ATOM   1803  ND1 HIS   233      26.161  18.868 -24.343  1.00  0.00           N  
ATOM   1804  CD2 HIS   233      26.183  16.565 -24.437  1.00  0.00           C  
ATOM   1805  CE1 HIS   233      25.612  18.308 -25.470  1.00  0.00           C  
ATOM   1806  NE2 HIS   233      25.582  16.948 -25.620  1.00  0.00           N  
ATOM   1807  N   ALA   234      23.987  16.820 -21.755  1.00  0.00           N  
ATOM   1808  CA  ALA   234      22.944  15.767 -21.674  1.00  0.00           C  
ATOM   1809  C   ALA   234      23.499  14.317 -21.814  1.00  0.00           C  
ATOM   1810  O   ALA   234      24.392  14.053 -22.628  1.00  0.00           O  
ATOM   1811  CB  ALA   234      21.906  16.053 -22.775  1.00  0.00           C  
ATOM   1812  N   GLY   235      22.958  13.399 -20.994  1.00  0.00           N  
ATOM   1813  CA  GLY   235      23.379  11.980 -20.994  1.00  0.00           C  
ATOM   1814  C   GLY   235      22.507  11.120 -21.914  1.00  0.00           C  
ATOM   1815  O   GLY   235      21.707  10.307 -21.400  1.00  0.00           O  
ATOM   1816  OXT GLY   235      22.622  11.244 -23.154  1.00  0.00           O  
TER
END
