
#######################################################
#                                                     #
#                        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   11 (  109),  selected   11 , name T0320TS083_4-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS083_4-D2.T0320_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    -       -      N     228           -
LGA    -       -      N     229           -
LGA    N     228      S     230          3.470
LGA    N     229      L     231          2.021
LGA    S     230      P     232          1.928
LGA    L     231      N     233          2.040
LGA    P     232      P     234          0.830
LGA    N     233      H     235          3.357
LGA    -       -      L     236           -
LGA    P     234      R     237          2.179
LGA    H     235      K     238          2.092
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    L     236      N     242          4.084
LGA    R     237      P     243          3.211
LGA    K     238      A     244          3.636
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    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
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)   11   73    5.0     11    2.78     9.09     11.506     0.381

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.965392 * X  +   0.249885 * Y  +   0.074673 * Z  + -82.825882
  Y_new =   0.255444 * X  +   0.848227 * Y  +   0.463960 * Z  + -62.001862
  Z_new =   0.052597 * X  +   0.466978 * Y  +  -0.882703 * Z  +  84.411034 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.654990   -0.486603  [ DEG:   152.1197    -27.8803 ]
  Theta =  -0.052622   -3.088971  [ DEG:    -3.0150   -176.9850 ]
  Phi   =   2.882919   -0.258674  [ DEG:   165.1791    -14.8209 ]
 
# 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: T0320TS083_4-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS083_4-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11   73   5.0   11   2.78    9.09  11.506
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS083_4-D2
PFRMAT TS
TARGET T0320
MODEL 4
PARENT 1bvp_1
ATOM   2117  H   ASN   228      20.376  21.279   8.858  1.00  1.00              
ATOM   2118  N   ASN   228      21.097  21.114   8.276  1.00  2.56              
ATOM   2119  CA  ASN   228      21.625  19.765   8.190  1.00  1.00              
ATOM   2120  CB  ASN   228      21.293  18.978   9.462  1.00  1.00              
ATOM   2121  C   ASN   228      21.001  19.081   6.976  1.00  1.03              
ATOM   2122  O   ASN   228      19.961  19.520   6.481  1.00  2.23              
ATOM   2123  CG  ASN   228      22.000  19.525  10.689  1.00  1.00              
ATOM   2124  ND2 ASN   228      21.324  19.491  11.830  1.00  1.00              
ATOM   2125 HD21 ASN   228      20.451  19.137  11.826  1.00  1.00              
ATOM   2126 HD22 ASN   228      21.724  19.823  12.617  1.00  1.00              
ATOM   2127  OD1 ASN   228      23.141  19.989  10.608  1.00  1.00              
ATOM   2128  H   ASN   229      22.345  17.652   6.980  1.00  1.00              
ATOM   2129  N   ASN   229      21.606  17.997   6.511  1.00  1.84              
ATOM   2130  CA  ASN   229      21.171  17.312   5.295  1.00  1.83              
ATOM   2131  CB  ASN   229      22.069  16.089   5.059  1.00  1.00              
ATOM   2132  C   ASN   229      19.724  16.840   5.361  1.00  2.29              
ATOM   2133  O   ASN   229      19.292  16.250   6.354  1.00  1.75              
ATOM   2134  CG  ASN   229      23.515  16.447   4.769  1.00  1.00              
ATOM   2135  ND2 ASN   229      24.419  15.494   4.981  1.00  1.00              
ATOM   2136 HD21 ASN   229      24.125  14.655   5.293  1.00  1.00              
ATOM   2137 HD22 ASN   229      25.329  15.671   4.811  1.00  1.00              
ATOM   2138  OD1 ASN   229      23.817  17.561   4.333  1.00  1.37              
ATOM   2139  H   SER   230      19.324  17.671   3.620  1.00  1.00              
ATOM   2140  N   SER   230      18.975  17.139   4.305  1.00  5.11              
ATOM   2141  CA  SER   230      17.606  16.658   4.180  1.00  3.57              
ATOM   2142  CB  SER   230      16.940  17.247   2.939  1.00  1.00              
ATOM   2143  C   SER   230      17.725  15.145   4.054  1.00  4.08              
ATOM   2144  O   SER   230      18.842  14.656   3.866  1.00  2.64              
ATOM   2145  OG  SER   230      17.633  16.826   1.775  1.00  3.54              
ATOM   2146  H   LEU   231      15.797  14.767   4.315  1.00  1.00              
ATOM   2147  N   LEU   231      16.651  14.379   4.204  1.00  3.88              
ATOM   2148  CA  LEU   231      16.811  12.928   4.220  1.00  2.99              
ATOM   2149  CB  LEU   231      15.443  12.234   4.213  1.00  1.01              
ATOM   2150  C   LEU   231      17.614  12.525   2.986  1.00  2.42              
ATOM   2151  O   LEU   231      17.389  13.061   1.899  1.00  2.67              
ATOM   2152  CG  LEU   231      15.443  10.725   4.479  1.00  1.13              
ATOM   2153  CD1 LEU   231      15.818  10.445   5.928  1.00  1.70              
ATOM   2154  CD2 LEU   231      14.091  10.114   4.155  1.00  1.00              
ATOM   2155  N   PRO   232      18.592  11.619   3.135  1.00  3.15              
ATOM   2156  CA  PRO   232      19.409  11.195   1.998  1.00  2.81              
ATOM   2157  CB  PRO   232      20.562  10.420   2.635  1.00  1.00              
ATOM   2158  C   PRO   232      18.653  10.365   0.972  1.00  2.52              
ATOM   2159  O   PRO   232      19.188  10.071  -0.100  1.00  1.45              
ATOM   2160  CG  PRO   232      19.956   9.867   3.888  1.00  1.00              
ATOM   2161  CD  PRO   232      19.056  10.979   4.382  1.00  1.00              
ATOM   2162  H   ASN   233      17.059  10.141   2.128  1.00  1.00              
ATOM   2163  N   ASN   233      17.419   9.979   1.274  1.00  4.83              
ATOM   2164  CA  ASN   233      16.616   9.321   0.254  1.00  2.37              
ATOM   2165  CB  ASN   233      15.389   8.614   0.839  1.00  1.00              
ATOM   2166  C   ASN   233      16.226  10.451  -0.686  1.00  3.33              
ATOM   2167  O   ASN   233      16.078  11.582  -0.227  1.00  2.55              
ATOM   2168  CG  ASN   233      15.752   7.415   1.694  1.00  1.00              
ATOM   2169  ND2 ASN   233      14.870   7.053   2.619  1.00  1.43              
ATOM   2170 HD21 ASN   233      14.073   7.550   2.700  1.00  1.00              
ATOM   2171 HD22 ASN   233      15.055   6.313   3.173  1.00  1.00              
ATOM   2172  OD1 ASN   233      16.803   6.797   1.505  1.00  1.49              
ATOM   2173  N   PRO   234      15.983  10.234  -1.970  1.00  4.46              
ATOM   2174  CA  PRO   234      15.635  11.376  -2.808  1.00  4.01              
ATOM   2175  CB  PRO   234      15.569  10.769  -4.213  1.00  1.00              
ATOM   2176  C   PRO   234      14.291  12.000  -2.448  1.00  3.05              
ATOM   2177  O   PRO   234      14.134  13.218  -2.569  1.00  1.49              
ATOM   2178  CG  PRO   234      16.372   9.504  -4.126  1.00  1.06              
ATOM   2179  CD  PRO   234      16.090   8.982  -2.735  1.00  1.00              
ATOM   2180  H   HIS   235      13.442  10.277  -1.950  1.00  1.00              
ATOM   2181  N   HIS   235      13.311  11.211  -2.016  1.00  4.47              
ATOM   2182  CA  HIS   235      12.027  11.805  -1.665  1.00  1.73              
ATOM   2183  CB  HIS   235      11.126  11.895  -2.903  1.00  1.00              
ATOM   2184  C   HIS   235      11.257  11.146  -0.518  1.00  2.29              
ATOM   2185  O   HIS   235      11.143   9.919  -0.465  1.00  2.14              
ATOM   2186  CG  HIS   235       9.810  12.565  -2.637  1.00  1.15              
ATOM   2187  ND1 HIS   235       9.698  13.911  -2.365  1.00  1.33              
ATOM   2188  HD1 HIS   235      10.417  14.529  -2.292  1.00  1.00              
ATOM   2189  CE1 HIS   235       8.426  14.205  -2.149  1.00  1.00              
ATOM   2190  NE2 HIS   235       7.709  13.108  -2.323  1.00  1.16              
ATOM   2191  HE2 HIS   235       6.766  13.052  -2.204  1.00  1.00              
ATOM   2192  CD2 HIS   235       8.552  12.061  -2.598  1.00  1.00              
ATOM   2193  H   LEU   236      10.941  12.883   0.368  1.00  1.00              
ATOM   2194  N   LEU   236      10.743  11.960   0.408  1.00  6.39              
ATOM   2195  CA  LEU   236       9.877  11.476   1.487  1.00  5.20              
ATOM   2196  CB  LEU   236      10.649  11.033   2.732  1.00  2.83              
ATOM   2197  C   LEU   236       8.772  12.468   1.846  1.00  2.43              
ATOM   2198  O   LEU   236       9.013  13.676   1.900  1.00  2.35              
ATOM   2199  CG  LEU   236      10.690   9.521   2.969  1.00  3.73              
ATOM   2200  CD1 LEU   236      10.548   9.219   4.454  1.00  1.92              
ATOM   2201  CD2 LEU   236       9.577   8.843   2.182  1.00  1.05              
ATOM   2202  H   ARG   237       7.412  11.036   1.938  1.00  1.00              
ATOM   2203  N   ARG   237       7.561  11.967   2.073  1.00  4.76              
ATOM   2204  CA  ARG   237       6.452  12.806   2.522  1.00  1.38              
ATOM   2205  CB  ARG   237       5.204  12.534   1.678  1.00  1.00              
ATOM   2206  C   ARG   237       6.166  12.478   3.981  1.00  1.00              
ATOM   2207  O   ARG   237       5.500  13.237   4.687  1.00  1.00              
ATOM   2208  CG  ARG   237       5.369  12.874   0.203  1.00  1.00              
ATOM   2209  CD  ARG   237       4.103  12.578  -0.591  1.00  1.00              
ATOM   2210  NE  ARG   237       4.255  12.919  -2.004  1.00  1.00              
ATOM   2211  HE  ARG   237       5.085  13.291  -2.278  1.00  1.00              
ATOM   2212  CZ  ARG   237       3.318  12.758  -2.938  1.00  1.00              
ATOM   2213  NH1 ARG   237       2.142  12.220  -2.628  1.00  1.00              
ATOM   2214  NH2 ARG   237       3.544  13.159  -4.185  1.00  1.00              
ATOM   2215  H   LYS   238       7.123  10.758   3.808  1.00  1.00              
ATOM   2216  N   LYS   238       6.665  11.325   4.415  1.00  2.49              
ATOM   2217  CA  LYS   238       6.527  10.899   5.801  1.00  1.00              
ATOM   2218  CB  LYS   238       6.700   9.381   5.906  1.00  1.00              
ATOM   2219  C   LYS   238       7.541  11.597   6.703  1.00  1.00              
ATOM   2220  O   LYS   238       7.303  12.767   7.067  1.00  1.00              
ATOM   2221  OXT LYS   238       8.477  10.921   7.177  1.00  1.00              
ATOM   2222  CG  LYS   238       5.619   8.590   5.185  1.00  1.00              
ATOM   2223  CD  LYS   238       5.852   7.090   5.312  1.00  1.00              
ATOM   2224  CE  LYS   238       4.768   6.291   4.599  1.00  1.00              
ATOM   2225  NZ  LYS   238       4.995   4.821   4.715  1.00  1.00              
TER
END
