
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0363AL243_2-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL243_2-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    -       -      I      13           -
LGA    -       -      N      14           -
LGA    -       -      I      15           -
LGA    -       -      E      16           -
LGA    -       -      I      17           -
LGA    -       -      A      18           -
LGA    S      29      Y      19          4.045
LGA    -       -      A      20           -
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    F      30      Y      26          3.795
LGA    Q      31      L      27          1.750
LGA    V      32      K      28          1.256
LGA    D      33      S      29          2.089
LGA    E      34      F      30          2.670
LGA    -       -      Q      31           -
LGA    G      35      V      32          3.269
LGA    I      36      D      33          3.337
LGA    -       -      E      34           -
LGA    -       -      G      35           -
LGA    T      37      I      36          2.336
LGA    V      38      T      37          3.559
LGA    Q      39      V      38          3.577
LGA    -       -      Q      39           -
LGA    T      40      T      40          2.612
LGA    A      41      A      41          1.802
LGA    I      42      I      42          1.392
LGA    T      43      T      43          0.370
LGA    Q      44      Q      44          3.308
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    I      47      I      47          2.495
LGA    L      48      L      48          2.259
LGA    S      49      S      49          3.106
LGA    Q      50      Q      50          2.440
LGA    F      51      F      51          2.841
LGA    P      52      P      52          1.598
LGA    E      53      E      53          0.793
LGA    I      54      I      54          2.350
LGA    D      55      -       -           -
LGA    L      56      D      55          2.203
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   26   46    5.0     25    2.62    52.00     36.659     0.920

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.864001 * X  +   0.500773 * Y  +   0.052241 * Z  +  26.095627
  Y_new =  -0.422601 * X  +  -0.777681 * Y  +   0.465426 * Z  +  48.118420
  Z_new =   0.273700 * X  +   0.380051 * Y  +   0.883544 * Z  +  -7.843190 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.406220   -2.735373  [ DEG:    23.2747   -156.7253 ]
  Theta =  -0.277238   -2.864355  [ DEG:   -15.8846   -164.1154 ]
  Phi   =  -2.686686    0.454907  [ DEG:  -153.9358     26.0642 ]
 
# 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: T0363AL243_2-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL243_2-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   26   46   5.0   25   2.62   52.00  36.659
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL243_2-D1
REMARK Aligment from pdb entry: 1fmaD
ATOM      1  N   SER    29      25.982  24.444   2.088  1.00  0.00              
ATOM      2  CA  SER    29      24.991  23.362   2.160  1.00  0.00              
ATOM      3  C   SER    29      25.144  22.422   1.075  1.00  0.00              
ATOM      4  O   SER    29      25.459  22.884  -0.047  1.00  0.00              
ATOM      5  N   PHE    30      24.831  21.191   1.299  1.00  0.00              
ATOM      6  CA  PHE    30      24.853  20.219   0.264  1.00  0.00              
ATOM      7  C   PHE    30      23.928  19.098   0.585  1.00  0.00              
ATOM      8  O   PHE    30      23.495  18.918   1.681  1.00  0.00              
ATOM      9  N   GLN    31      23.589  18.313  -0.397  1.00  0.00              
ATOM     10  CA  GLN    31      22.730  17.142  -0.191  1.00  0.00              
ATOM     11  C   GLN    31      23.495  15.881  -0.415  1.00  0.00              
ATOM     12  O   GLN    31      24.345  15.823  -1.341  1.00  0.00              
ATOM     13  N   VAL    32      23.167  14.882   0.400  1.00  0.00              
ATOM     14  CA  VAL    32      23.678  13.530   0.318  1.00  0.00              
ATOM     15  C   VAL    32      22.538  12.468   0.397  1.00  0.00              
ATOM     16  O   VAL    32      21.447  12.661   0.928  1.00  0.00              
ATOM     17  N   ASP    33      22.703  11.329  -0.268  1.00  0.00              
ATOM     18  CA  ASP    33      21.674  10.273  -0.138  1.00  0.00              
ATOM     19  C   ASP    33      21.552   9.774   1.335  1.00  0.00              
ATOM     20  O   ASP    33      22.507   9.864   2.111  1.00  0.00              
ATOM     21  N   GLU    34      22.070   7.173   2.788  1.00  0.00              
ATOM     22  CA  GLU    34      22.741   5.896   2.825  1.00  0.00              
ATOM     23  C   GLU    34      23.747   5.858   3.929  1.00  0.00              
ATOM     24  O   GLU    34      24.768   5.205   3.732  1.00  0.00              
ATOM     25  N   GLY    35      23.541   6.598   5.023  1.00  0.00              
ATOM     26  CA  GLY    35      24.471   6.492   6.124  1.00  0.00              
ATOM     27  C   GLY    35      23.743   6.209   7.379  1.00  0.00              
ATOM     28  O   GLY    35      22.727   6.829   7.634  1.00  0.00              
ATOM     29  N   ILE    36      24.249   5.304   8.181  1.00  0.00              
ATOM     30  CA  ILE    36      23.479   4.959   9.365  1.00  0.00              
ATOM     31  C   ILE    36      23.517   6.028  10.447  1.00  0.00              
ATOM     32  O   ILE    36      22.589   6.074  11.200  1.00  0.00              
ATOM     33  N   THR    37      24.585   6.804  10.511  1.00  0.00              
ATOM     34  CA  THR    37      24.822   7.717  11.646  1.00  0.00              
ATOM     35  C   THR    37      25.455   8.948  11.099  1.00  0.00              
ATOM     36  O   THR    37      26.018   8.990  10.003  1.00  0.00              
ATOM     37  N   VAL    38      25.405   9.945  11.939  1.00  0.00              
ATOM     38  CA  VAL    38      26.116  11.216  11.701  1.00  0.00              
ATOM     39  C   VAL    38      27.575  10.920  11.461  1.00  0.00              
ATOM     40  O   VAL    38      28.197  11.513  10.567  1.00  0.00              
ATOM     41  N   GLN    39      28.168  10.070  12.261  1.00  0.00              
ATOM     42  CA  GLN    39      29.555   9.719  12.076  1.00  0.00              
ATOM     43  C   GLN    39      29.840   9.138  10.719  1.00  0.00              
ATOM     44  O   GLN    39      30.834   9.450  10.121  1.00  0.00              
ATOM     45  N   THR    40      29.023   8.230  10.264  1.00  0.00              
ATOM     46  CA  THR    40      29.235   7.611   8.966  1.00  0.00              
ATOM     47  C   THR    40      29.185   8.667   7.892  1.00  0.00              
ATOM     48  O   THR    40      29.969   8.704   6.948  1.00  0.00              
ATOM     49  N   ALA    41      28.243   9.580   8.044  1.00  0.00              
ATOM     50  CA  ALA    41      28.148  10.696   7.095  1.00  0.00              
ATOM     51  C   ALA    41      29.381  11.599   7.175  1.00  0.00              
ATOM     52  O   ALA    41      29.978  11.946   6.156  1.00  0.00              
ATOM     53  N   ILE    42      29.830  11.919   8.374  1.00  0.00              
ATOM     54  CA  ILE    42      30.990  12.767   8.558  1.00  0.00              
ATOM     55  C   ILE    42      32.193  12.121   7.852  1.00  0.00              
ATOM     56  O   ILE    42      32.949  12.783   7.143  1.00  0.00              
ATOM     57  N   THR    43      32.358  10.822   8.071  1.00  0.00              
ATOM     58  CA  THR    43      33.496  10.143   7.452  1.00  0.00              
ATOM     59  C   THR    43      33.389  10.184   5.936  1.00  0.00              
ATOM     60  O   THR    43      34.331  10.383   5.273  1.00  0.00              
ATOM     61  N   GLN    44      32.179   9.958   5.406  1.00  0.00              
ATOM     62  CA  GLN    44      31.984   9.967   3.959  1.00  0.00              
ATOM     63  C   GLN    44      32.350  11.380   3.388  1.00  0.00              
ATOM     64  O   GLN    44      33.106  11.460   2.416  1.00  0.00              
ATOM     65  N   ILE    47      31.841  12.410   4.051  1.00  0.00              
ATOM     66  CA  ILE    47      32.127  13.799   3.602  1.00  0.00              
ATOM     67  C   ILE    47      33.591  14.097   3.740  1.00  0.00              
ATOM     68  O   ILE    47      34.198  14.726   2.853  1.00  0.00              
ATOM     69  N   LEU    48      34.220  13.660   4.837  1.00  0.00              
ATOM     70  CA  LEU    48      35.634  13.922   5.067  1.00  0.00              
ATOM     71  C   LEU    48      36.438  13.321   3.967  1.00  0.00              
ATOM     72  O   LEU    48      37.490  13.841   3.593  1.00  0.00              
ATOM     73  N   SER    49      35.990  12.196   3.420  1.00  0.00              
ATOM     74  CA  SER    49      36.740  11.482   2.433  1.00  0.00              
ATOM     75  C   SER    49      36.692  12.080   1.062  1.00  0.00              
ATOM     76  O   SER    49      37.411  11.599   0.211  1.00  0.00              
ATOM     77  N   GLN    50      35.924  13.153   0.858  1.00  0.00              
ATOM     78  CA  GLN    50      35.739  13.758  -0.474  1.00  0.00              
ATOM     79  C   GLN    50      36.895  14.529  -0.899  1.00  0.00              
ATOM     80  O   GLN    50      37.159  14.615  -2.083  1.00  0.00              
ATOM     81  N   PHE    51      37.628  15.129   0.026  1.00  0.00              
ATOM     82  CA  PHE    51      38.814  15.915  -0.332  1.00  0.00              
ATOM     83  C   PHE    51      39.628  16.221   0.892  1.00  0.00              
ATOM     84  O   PHE    51      39.156  16.079   2.001  1.00  0.00              
ATOM     85  N   PRO    52      40.870  16.709   0.700  1.00  0.00              
ATOM     86  CA  PRO    52      41.717  17.039   1.807  1.00  0.00              
ATOM     87  C   PRO    52      41.109  18.225   2.586  1.00  0.00              
ATOM     88  O   PRO    52      41.218  18.225   3.821  1.00  0.00              
ATOM     89  N   GLU    53      40.479  19.164   1.871  1.00  0.00              
ATOM     90  CA  GLU    53      39.847  20.310   2.552  1.00  0.00              
ATOM     91  C   GLU    53      38.686  19.820   3.416  1.00  0.00              
ATOM     92  O   GLU    53      38.523  20.292   4.496  1.00  0.00              
ATOM     93  N   ILE    54      37.846  18.947   2.861  1.00  0.00              
ATOM     94  CA  ILE    54      36.720  18.397   3.602  1.00  0.00              
ATOM     95  C   ILE    54      37.195  17.592   4.775  1.00  0.00              
ATOM     96  O   ILE    54      36.640  17.631   5.805  1.00  0.00              
ATOM     97  N   ASP    55      38.307  16.886   4.613  1.00  0.00              
ATOM     98  CA  ASP    55      38.796  16.092   5.730  1.00  0.00              
ATOM     99  C   ASP    55      39.300  16.951   6.823  1.00  0.00              
ATOM    100  O   ASP    55      39.006  16.752   7.948  1.00  0.00              
ATOM    101  N   LEU    56      39.983  18.022   6.463  1.00  0.00              
ATOM    102  CA  LEU    56      40.470  19.001   7.434  1.00  0.00              
ATOM    103  C   LEU    56      39.352  19.643   8.200  1.00  0.00              
ATOM    104  O   LEU    56      39.328  19.747   9.406  1.00  0.00              
END
