
#######################################################
#                                                     #
#                        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   10 (   77),  selected   10 , name T0378TS401_2-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS401_2-D1.T0378_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    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      K       8           -
LGA    -       -      F       9           -
LGA    -       -      L      10           -
LGA    -       -      R      11           -
LGA    -       -      S      12           -
LGA    -       -      L      13           -
LGA    -       -      R      14           -
LGA    -       -      E      15           -
LGA    -       -      R      16           -
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    -       -      R      41           -
LGA    -       -      C      42           -
LGA    T      80      R      43          2.988
LGA    P      81      M      44          1.756
LGA    Q      82      L      45          2.865
LGA    P      83      V      46          3.777
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    L      84      E      62          3.383
LGA    M      85      V      63          3.697
LGA    A      86      V      64          3.593
LGA    V      87      -       -           -
LGA    F      88      E      65          2.530
LGA    D      89      L      66          2.836
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   10   89    5.0      9    3.11     0.00      6.776     0.281

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.729766 * X  +  -0.557925 * Y  +  -0.395172 * Z  +  -9.167775
  Y_new =  -0.455687 * X  +   0.033977 * Y  +  -0.889491 * Z  +  53.610687
  Z_new =   0.509696 * X  +   0.829196 * Y  +  -0.229444 * Z  +  35.197742 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.840748   -1.300844  [ DEG:   105.4671    -74.5329 ]
  Theta =  -0.534831   -2.606761  [ DEG:   -30.6436   -149.3564 ]
  Phi   =  -0.558189    2.583404  [ DEG:   -31.9819    148.0181 ]
 
# 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: T0378TS401_2-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS401_2-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10   89   5.0    9   3.11    0.00   6.776
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS401_2-D1
PFRMAT TS
TARGET T0378
MODEL  2 REFINED
PARENT 1v2x_A
ATOM      1  N   THR    80       4.164  20.393  55.620  1.00114.65       1SG   2
ATOM      2  CA  THR    80       2.775  20.903  55.579  1.00114.65       1SG   3
ATOM      3  CB  THR    80       1.990  20.401  56.759  1.00114.65       1SG   4
ATOM      4  OG1 THR    80       0.636  20.813  56.650  1.00114.65       1SG   5
ATOM      5  CG2 THR    80       2.605  20.924  58.067  1.00114.65       1SG   6
ATOM      6  C   THR    80       2.633  22.391  55.490  1.00114.65       1SG   7
ATOM      7  O   THR    80       1.547  22.843  55.144  1.00114.65       1SG   8
ATOM      8  N   PRO    81       3.599  23.219  55.786  1.00 95.24       1SG   9
ATOM      9  CA  PRO    81       3.330  24.609  55.560  1.00 95.24       1SG  10
ATOM     10  CD  PRO    81       4.458  23.036  56.948  1.00 95.24       1SG  11
ATOM     11  CB  PRO    81       4.428  25.374  56.290  1.00 95.24       1SG  12
ATOM     12  CG  PRO    81       4.777  24.447  57.468  1.00 95.24       1SG  13
ATOM     13  C   PRO    81       3.211  24.916  54.103  1.00 95.24       1SG  14
ATOM     14  O   PRO    81       2.501  25.859  53.751  1.00 95.24       1SG  15
ATOM     15  N   GLN    82       3.910  24.159  53.235  1.00 99.31       1SG  16
ATOM     16  CA  GLN    82       3.833  24.464  51.838  1.00 99.31       1SG  17
ATOM     17  CB  GLN    82       4.863  23.682  50.996  1.00 99.31       1SG  18
ATOM     18  CG  GLN    82       6.313  23.970  51.393  1.00 99.31       1SG  19
ATOM     19  CD  GLN    82       7.217  23.022  50.617  1.00 99.31       1SG  20
ATOM     20  OE1 GLN    82       7.440  23.189  49.420  1.00 99.31       1SG  21
ATOM     21  NE2 GLN    82       7.753  21.993  51.327  1.00 99.31       1SG  22
ATOM     22  C   GLN    82       2.448  24.157  51.353  1.00 99.31       1SG  23
ATOM     23  O   GLN    82       1.847  24.975  50.659  1.00 99.31       1SG  24
ATOM     24  N   PRO    83       1.902  23.008  51.665  1.00 84.37       1SG  25
ATOM     25  CA  PRO    83       0.553  22.736  51.261  1.00 84.37       1SG  26
ATOM     26  CD  PRO    83       2.671  21.783  51.818  1.00 84.37       1SG  27
ATOM     27  CB  PRO    83       0.387  21.213  51.283  1.00 84.37       1SG  28
ATOM     28  CG  PRO    83       1.614  20.697  52.055  1.00 84.37       1SG  29
ATOM     29  C   PRO    83      -0.431  23.458  52.112  1.00 84.37       1SG  30
ATOM     30  O   PRO    83      -1.539  23.709  51.653  1.00 84.37       1SG  31
ATOM     31  N   LEU    84      -0.086  23.773  53.365  1.00132.55       1SG  32
ATOM     32  CA  LEU    84      -1.037  24.407  54.223  1.00132.55       1SG  33
ATOM     33  CB  LEU    84      -0.551  24.532  55.675  1.00132.55       1SG  34
ATOM     34  CG  LEU    84      -1.603  25.144  56.617  1.00132.55       1SG  35
ATOM     35  CD2 LEU    84      -0.993  25.502  57.981  1.00132.55       1SG  36
ATOM     36  CD1 LEU    84      -2.831  24.227  56.739  1.00132.55       1SG  37
ATOM     37  C   LEU    84      -1.282  25.781  53.702  1.00132.55       1SG  38
ATOM     38  O   LEU    84      -2.423  26.223  53.608  1.00132.55       1SG  39
ATOM     39  N   MET    85      -0.192  26.513  53.399  1.00 45.94       1SG  40
ATOM     40  CA  MET    85      -0.315  27.834  52.861  1.00 45.94       1SG  41
ATOM     41  CB  MET    85       1.030  28.575  52.789  1.00 45.94       1SG  42
ATOM     42  CG  MET    85       1.631  28.904  54.155  1.00 45.94       1SG  43
ATOM     43  SD  MET    85       3.232  29.763  54.083  1.00 45.94       1SG  44
ATOM     44  CE  MET    85       2.566  31.305  53.392  1.00 45.94       1SG  45
ATOM     45  C   MET    85      -0.844  27.777  51.461  1.00 45.94       1SG  46
ATOM     46  O   MET    85      -1.803  28.463  51.116  1.00 45.94       1SG  47
ATOM     47  N   ALA    86      -0.232  26.918  50.620  1.00 41.13       1SG  48
ATOM     48  CA  ALA    86      -0.584  26.871  49.229  1.00 41.13       1SG  49
ATOM     49  CB  ALA    86       0.316  25.923  48.420  1.00 41.13       1SG  50
ATOM     50  C   ALA    86      -1.989  26.395  49.069  1.00 41.13       1SG  51
ATOM     51  O   ALA    86      -2.774  26.990  48.333  1.00 41.13       1SG  52
ATOM     52  N   VAL    87      -2.347  25.306  49.771  1.00 95.50       1SG  53
ATOM     53  CA  VAL    87      -3.663  24.762  49.628  1.00 95.50       1SG  54
ATOM     54  CB  VAL    87      -3.911  23.434  50.306  1.00 95.50       1SG  55
ATOM     55  CG1 VAL    87      -4.261  23.640  51.793  1.00 95.50       1SG  56
ATOM     56  CG2 VAL    87      -5.005  22.696  49.517  1.00 95.50       1SG  57
ATOM     57  C   VAL    87      -4.630  25.742  50.194  1.00 95.50       1SG  58
ATOM     58  O   VAL    87      -5.729  25.903  49.681  1.00 95.50       1SG  59
ATOM     59  N   PHE    88      -4.281  26.412  51.302  1.00 99.01       1SG  60
ATOM     60  CA  PHE    88      -5.243  27.334  51.821  1.00 99.01       1SG  61
ATOM     61  CB  PHE    88      -4.872  27.928  53.188  1.00 99.01       1SG  62
ATOM     62  CG  PHE    88      -5.873  29.002  53.435  1.00 99.01       1SG  63
ATOM     63  CD1 PHE    88      -7.158  28.694  53.819  1.00 99.01       1SG  64
ATOM     64  CD2 PHE    88      -5.523  30.323  53.281  1.00 99.01       1SG  65
ATOM     65  CE1 PHE    88      -8.078  29.691  54.044  1.00 99.01       1SG  66
ATOM     66  CE2 PHE    88      -6.439  31.323  53.505  1.00 99.01       1SG  67
ATOM     67  CZ  PHE    88      -7.720  31.008  53.889  1.00 99.01       1SG  68
ATOM     68  C   PHE    88      -5.408  28.480  50.877  1.00 99.01       1SG  69
ATOM     69  O   PHE    88      -6.526  28.885  50.567  1.00 99.01       1SG  70
ATOM     70  N   ASP    89      -4.281  29.014  50.376  1.00 90.33       1SG  71
ATOM     71  CA  ASP    89      -4.305  30.210  49.590  1.00 90.33       1SG  72
ATOM     72  CB  ASP    89      -2.892  30.637  49.156  1.00 90.33       1SG  73
ATOM     73  CG  ASP    89      -2.966  32.045  48.588  1.00 90.33       1SG  74
ATOM     74  OD1 ASP    89      -3.684  32.889  49.188  1.00 90.33       1SG  75
ATOM     75  OD2 ASP    89      -2.288  32.303  47.558  1.00 90.33       1SG  76
ATOM     76  C   ASP    89      -5.114  30.027  48.348  1.00 90.33       1SG  77
ATOM     77  O   ASP    89      -5.989  30.844  48.062  1.00 90.33       1SG  78
TER
END
