
#######################################################
#                                                     #
#                        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 (   41),  selected    6 , name T0382TS009_1_2-D1
# Molecule2: number of CA atoms  119 (  920),  selected  119 , name T0382_D1.pdb
# PARAMETERS: T0382TS009_1_2-D1.T0382_D1.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    -       -      L       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      M       9           -
LGA    -       -      T      10           -
LGA    -       -      T      11           -
LGA    -       -      Q      12           -
LGA    -       -      D      13           -
LGA    -       -      L      14           -
LGA    -       -      V      15           -
LGA    -       -      A      16           -
LGA    -       -      L      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      K      20           -
LGA    -       -      V      21           -
LGA    -       -      T      22           -
LGA    -       -      V      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      D      26           -
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    -       -      L      29           -
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    -       -      Q      33           -
LGA    -       -      I      34           -
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    -       -      F      37           -
LGA    -       -      N      38           -
LGA    -       -      R      39           -
LGA    -       -      L      40           -
LGA    -       -      F      41           -
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    -       -      M      44           -
LGA    -       -      A      45           -
LGA    -       -      E      46           -
LGA    -       -      I      47           -
LGA    -       -      A      48           -
LGA    -       -      D      49           -
LGA    -       -      E      50           -
LGA    -       -      L      51           -
LGA    -       -      K      52           -
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    -       -      D      55           -
LGA    -       -      G      56           -
LGA    -       -      D      57           -
LGA    -       -      Q      58           -
LGA    -       -      R      59           -
LGA    -       -      T      60           -
LGA    -       -      A      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      S      64           -
LGA    -       -      L      65           -
LGA    -       -      F      66           -
LGA    -       -      E      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      N      70           -
LGA    -       -      M      71           -
LGA    -       -      Q      72           -
LGA    -       -      V      73           -
LGA    -       -      R      74           -
LGA    -       -      L      75           -
LGA    -       -      Q      76           -
LGA    -       -      A      77           -
LGA    -       -      A      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      T      81           -
LGA    -       -      L      82           -
LGA    E      94      A      83          1.062
LGA    A      95      V      84          1.988
LGA    I      96      A      85          1.099
LGA    V      97      P      86          1.578
LGA    S      98      V      87          1.870
LGA    -       -      K      88           -
LGA    -       -      A      89           -
LGA    -       -      R      90           -
LGA    S      99      E      91          1.842
LGA    -       -      Q      92           -
LGA    -       -      L      93           -
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    -       -      I      96           -
LGA    -       -      V      97           -
LGA    -       -      S      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      W     101           -
LGA    -       -      F     102           -
LGA    -       -      P     103           -
LGA    -       -      Q     104           -
LGA    -       -      A     105           -
LGA    -       -      G     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      G     109           -
LGA    -       -      M     110           -
LGA    -       -      C     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    -       -      P     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6  119    5.0      6    1.62     0.00      4.780     0.350

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.313275 * X  +   0.818186 * Y  +  -0.482110 * Z  +  15.624226
  Y_new =   0.737650 * X  +  -0.110084 * Y  +  -0.666149 * Z  +  48.644703
  Z_new =  -0.598106 * X  +  -0.564316 * Y  +  -0.569048 * Z  + -21.820303 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.360369    0.781223  [ DEG:  -135.2392     44.7608 ]
  Theta =   0.641136    2.500457  [ DEG:    36.7344    143.2656 ]
  Phi   =   1.972408   -1.169185  [ DEG:   113.0106    -66.9894 ]
 
# 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: T0382TS009_1_2-D1                             
REMARK     2: T0382_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_1_2-D1.T0382_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6  119   5.0    6   1.62    0.00   4.780
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_1_2-D1
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                            
ATOM    731  N   GLU    94     -12.951  54.620  -4.604  1.00  0.00              
ATOM    732  CA  GLU    94     -13.447  55.450  -3.514  1.00  0.00              
ATOM    733  C   GLU    94     -14.756  56.133  -3.891  1.00  0.00              
ATOM    734  O   GLU    94     -15.592  56.415  -3.032  1.00  0.00              
ATOM    735  CB  GLU    94     -13.638  54.612  -2.248  1.00  0.00              
ATOM    736  CG  GLU    94     -12.492  54.721  -1.253  1.00  0.00              
ATOM    737  CD  GLU    94     -12.795  54.028   0.061  1.00  0.00              
ATOM    738  OE1 GLU    94     -12.410  52.849   0.213  1.00  0.00              
ATOM    739  OE2 GLU    94     -13.416  54.663   0.938  1.00  0.00              
ATOM    740  N   ALA    95     -14.929  56.399  -5.182  1.00  0.00              
ATOM    741  CA  ALA    95     -16.137  57.049  -5.676  1.00  0.00              
ATOM    742  C   ALA    95     -17.307  56.839  -4.722  1.00  0.00              
ATOM    743  O   ALA    95     -17.942  57.796  -4.282  1.00  0.00              
ATOM    744  CB  ALA    95     -15.890  58.536  -5.884  1.00  0.00              
ATOM    745  N   ILE    96     -17.586  55.578  -4.405  1.00  0.00              
ATOM    746  CA  ILE    96     -18.705  55.232  -3.482  1.00  0.00              
ATOM    747  C   ILE    96     -18.585  55.988  -2.163  1.00  0.00              
ATOM    748  O   ILE    96     -17.483  56.281  -1.702  1.00  0.00              
ATOM    749  CB  ILE    96     -20.075  55.536  -4.116  1.00  0.00              
ATOM    750  CG2 ILE    96     -20.478  54.424  -5.072  1.00  0.00              
ATOM    751  CG1 ILE    96     -20.041  56.884  -4.838  1.00  0.00              
ATOM    752  CD1 ILE    96     -20.902  56.933  -6.081  1.00  0.00              
ATOM    753  N   VAL    97     -19.729  56.301  -1.561  1.00  0.00              
ATOM    754  CA  VAL    97     -19.756  57.040  -0.266  1.00  0.00              
ATOM    755  C   VAL    97     -21.186  57.253   0.217  1.00  0.00              
ATOM    756  O   VAL    97     -22.120  57.307  -0.582  1.00  0.00              
ATOM    757  CB  VAL    97     -18.960  56.297   0.824  1.00  0.00              
ATOM    758  CG1 VAL    97     -17.465  56.482   0.612  1.00  0.00              
ATOM    759  CG2 VAL    97     -19.325  54.821   0.837  1.00  0.00              
ATOM    760  N   SER    98     -21.349  57.374   1.530  1.00  0.00              
ATOM    761  CA  SER    98     -22.664  57.581   2.124  1.00  0.00              
ATOM    762  C   SER    98     -22.589  57.587   3.646  1.00  0.00              
ATOM    763  O   SER    98     -21.503  57.640   4.224  1.00  0.00              
ATOM    764  CB  SER    98     -23.278  58.891   1.622  1.00  0.00              
ATOM    765  OG  SER    98     -24.648  58.722   1.300  1.00  0.00              
ATOM    766  N   SER    99     -23.750  57.532   4.292  1.00  0.00              
ATOM    767  CA  SER    99     -23.817  57.531   5.749  1.00  0.00              
ATOM    768  C   SER    99     -25.261  57.590   6.234  1.00  0.00              
ATOM    769  O   SER    99     -25.552  58.172   7.279  1.00  0.00              
ATOM    770  CB  SER    99     -23.122  56.292   6.316  1.00  0.00              
ATOM    771  OG  SER    99     -22.309  56.628   7.427  1.00  0.00              
TER
END
