
#######################################################
#                                                     #
#                        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   15 (  116),  selected   15 , name T0356TS212_1_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS212_1_2-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    -       -      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      K      23           -
LGA    -       -      R      24           -
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    G     333      L      43          4.824
LGA    V     334      R      44          2.362
LGA    A     335      A      45           #
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    L     336      D     327          1.662
LGA    N     337      E     328          1.292
LGA    E     338      P     329          1.270
LGA    V     339      A     330          1.330
LGA    F     340      V     331          1.224
LGA    V     341      L     332          1.100
LGA    P     342      G     333          0.826
LGA    I     343      V     334          0.232
LGA    L     344      A     335          0.473
LGA    Q     345      L     336          0.972
LGA    K     346      N     337          1.288
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    Q     347      F     340          1.265
LGA    -       -      V     341           -
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15  124    5.0     14    1.78     0.00     10.121     0.743

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.909039 * X  +  -0.389643 * Y  +  -0.147741 * Z  + 126.053230
  Y_new =  -0.029522 * X  +  -0.293432 * Y  +   0.955524 * Z  +  27.921534
  Z_new =  -0.415665 * X  +   0.872970 * Y  +   0.255238 * Z  +  72.469139 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.286345   -1.855247  [ DEG:    73.7022   -106.2978 ]
  Theta =   0.428674    2.712919  [ DEG:    24.5612    155.4388 ]
  Phi   =  -3.109128    0.032464  [ DEG:  -178.1399      1.8601 ]
 
# 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: T0356TS212_1_2-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS212_1_2-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15  124   5.0   14   1.78    0.00  10.121
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS212_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0356
PARENT 1oi2_A
ATOM      1  N   GLY   333      48.765  68.795  87.532  1.00 12.64       1SG   2
ATOM      2  CA  GLY   333      50.238  68.669  87.612  1.00 12.64       1SG   3
ATOM      3  C   GLY   333      50.859  69.225  86.379  1.00 12.64       1SG   4
ATOM      4  O   GLY   333      50.278  69.170  85.295  1.00 12.64       1SG   5
ATOM      5  N   VAL   334      52.080  69.768  86.517  1.00 37.17       1SG   6
ATOM      6  CA  VAL   334      52.752  70.349  85.395  1.00 37.17       1SG   7
ATOM      7  CB  VAL   334      53.987  71.110  85.771  1.00 37.17       1SG   8
ATOM      8  CG1 VAL   334      54.648  71.658  84.495  1.00 37.17       1SG   9
ATOM      9  CG2 VAL   334      53.579  72.194  86.780  1.00 37.17       1SG  10
ATOM     10  C   VAL   334      53.145  69.237  84.482  1.00 37.17       1SG  11
ATOM     11  O   VAL   334      53.295  68.091  84.903  1.00 37.17       1SG  12
ATOM     12  N   ALA   335      53.285  69.556  83.185  1.00 28.32       1SG  13
ATOM     13  CA  ALA   335      53.653  68.567  82.221  1.00 28.32       1SG  14
ATOM     14  CB  ALA   335      53.633  69.084  80.772  1.00 28.32       1SG  15
ATOM     15  C   ALA   335      55.044  68.127  82.531  1.00 28.32       1SG  16
ATOM     16  O   ALA   335      55.813  68.838  83.175  1.00 28.32       1SG  17
ATOM     17  N   LEU   336      55.374  66.903  82.085  1.00125.21       1SG  18
ATOM     18  CA  LEU   336      56.663  66.317  82.297  1.00125.21       1SG  19
ATOM     19  CB  LEU   336      56.713  64.821  81.943  1.00125.21       1SG  20
ATOM     20  CG  LEU   336      58.094  64.170  82.166  1.00125.21       1SG  21
ATOM     21  CD1 LEU   336      58.503  64.196  83.647  1.00125.21       1SG  22
ATOM     22  CD2 LEU   336      58.142  62.760  81.555  1.00125.21       1SG  23
ATOM     23  C   LEU   336      57.642  67.015  81.414  1.00125.21       1SG  24
ATOM     24  O   LEU   336      57.279  67.634  80.418  1.00125.21       1SG  25
ATOM     25  N   ASN   337      58.933  66.922  81.785  1.00 74.25       1SG  26
ATOM     26  CA  ASN   337      59.998  67.552  81.064  1.00 74.25       1SG  27
ATOM     27  CB  ASN   337      61.372  67.296  81.705  1.00 74.25       1SG  28
ATOM     28  CG  ASN   337      61.618  65.793  81.686  1.00 74.25       1SG  29
ATOM     29  OD1 ASN   337      60.784  65.006  82.132  1.00 74.25       1SG  30
ATOM     30  ND2 ASN   337      62.793  65.376  81.145  1.00 74.25       1SG  31
ATOM     31  C   ASN   337      60.027  66.981  79.689  1.00 74.25       1SG  32
ATOM     32  O   ASN   337      60.295  67.690  78.720  1.00 74.25       1SG  33
ATOM     33  N   GLU   338      59.741  65.674  79.572  1.00105.16       1SG  34
ATOM     34  CA  GLU   338      59.760  65.031  78.295  1.00105.16       1SG  35
ATOM     35  CB  GLU   338      59.364  63.549  78.381  1.00105.16       1SG  36
ATOM     36  CG  GLU   338      59.320  62.854  77.022  1.00105.16       1SG  37
ATOM     37  CD  GLU   338      60.748  62.577  76.580  1.00105.16       1SG  38
ATOM     38  OE1 GLU   338      61.688  62.953  77.327  1.00105.16       1SG  39
ATOM     39  OE2 GLU   338      60.915  61.982  75.480  1.00105.16       1SG  40
ATOM     40  C   GLU   338      58.755  65.701  77.417  1.00105.16       1SG  41
ATOM     41  O   GLU   338      59.012  65.938  76.241  1.00105.16       1SG  42
ATOM     42  N   VAL   339      57.572  66.038  77.956  1.00 28.09       1SG  43
ATOM     43  CA  VAL   339      56.583  66.639  77.111  1.00 28.09       1SG  44
ATOM     44  CB  VAL   339      55.318  66.973  77.846  1.00 28.09       1SG  45
ATOM     45  CG1 VAL   339      54.386  67.728  76.885  1.00 28.09       1SG  46
ATOM     46  CG2 VAL   339      54.716  65.679  78.419  1.00 28.09       1SG  47
ATOM     47  C   VAL   339      57.131  67.927  76.591  1.00 28.09       1SG  48
ATOM     48  O   VAL   339      57.044  68.214  75.398  1.00 28.09       1SG  49
ATOM     49  N   PHE   340      57.734  68.733  77.483  1.00 53.20       1SG  50
ATOM     50  CA  PHE   340      58.236  70.018  77.096  1.00 53.20       1SG  51
ATOM     51  CB  PHE   340      58.863  70.813  78.255  1.00 53.20       1SG  52
ATOM     52  CG  PHE   340      57.779  71.329  79.136  1.00 53.20       1SG  53
ATOM     53  CD1 PHE   340      57.217  70.534  80.107  1.00 53.20       1SG  54
ATOM     54  CD2 PHE   340      57.338  72.626  78.992  1.00 53.20       1SG  55
ATOM     55  CE1 PHE   340      56.217  71.023  80.915  1.00 53.20       1SG  56
ATOM     56  CE2 PHE   340      56.339  73.122  79.796  1.00 53.20       1SG  57
ATOM     57  CZ  PHE   340      55.777  72.318  80.759  1.00 53.20       1SG  58
ATOM     58  C   PHE   340      59.313  69.875  76.066  1.00 53.20       1SG  59
ATOM     59  O   PHE   340      59.275  70.551  75.039  1.00 53.20       1SG  60
ATOM     60  N   VAL   341      60.304  68.990  76.293  1.00131.36       1SG  61
ATOM     61  CA  VAL   341      61.378  68.979  75.342  1.00131.36       1SG  62
ATOM     62  CB  VAL   341      62.588  68.194  75.802  1.00131.36       1SG  63
ATOM     63  CG1 VAL   341      63.367  69.114  76.756  1.00131.36       1SG  64
ATOM     64  CG2 VAL   341      62.154  66.943  76.586  1.00131.36       1SG  65
ATOM     65  C   VAL   341      60.919  68.653  73.942  1.00131.36       1SG  66
ATOM     66  O   VAL   341      61.166  69.481  73.066  1.00131.36       1SG  67
ATOM     67  N   PRO   342      60.257  67.573  73.611  1.00111.84       1SG  68
ATOM     68  CA  PRO   342      59.834  67.501  72.241  1.00111.84       1SG  69
ATOM     69  CD  PRO   342      60.722  66.264  74.041  1.00111.84       1SG  70
ATOM     70  CB  PRO   342      59.486  66.042  71.969  1.00111.84       1SG  71
ATOM     71  CG  PRO   342      60.467  65.290  72.878  1.00111.84       1SG  72
ATOM     72  C   PRO   342      58.773  68.471  71.846  1.00111.84       1SG  73
ATOM     73  O   PRO   342      58.727  68.837  70.674  1.00111.84       1SG  74
ATOM     74  N   ILE   343      57.904  68.909  72.773  1.00119.82       1SG  75
ATOM     75  CA  ILE   343      56.874  69.797  72.328  1.00119.82       1SG  76
ATOM     76  CB  ILE   343      55.853  70.108  73.394  1.00119.82       1SG  77
ATOM     77  CG2 ILE   343      56.548  70.795  74.579  1.00119.82       1SG  78
ATOM     78  CG1 ILE   343      54.688  70.918  72.799  1.00119.82       1SG  79
ATOM     79  CD1 ILE   343      53.825  70.123  71.822  1.00119.82       1SG  80
ATOM     80  C   ILE   343      57.507  71.069  71.859  1.00119.82       1SG  81
ATOM     81  O   ILE   343      57.197  71.565  70.777  1.00119.82       1SG  82
ATOM     82  N   LEU   344      58.437  71.623  72.659  1.00125.00       1SG  83
ATOM     83  CA  LEU   344      59.056  72.858  72.295  1.00125.00       1SG  84
ATOM     84  CB  LEU   344      59.915  73.497  73.400  1.00125.00       1SG  85
ATOM     85  CG  LEU   344      59.108  74.134  74.549  1.00125.00       1SG  86
ATOM     86  CD1 LEU   344      58.277  73.092  75.312  1.00125.00       1SG  87
ATOM     87  CD2 LEU   344      60.020  74.961  75.468  1.00125.00       1SG  88
ATOM     88  C   LEU   344      59.916  72.666  71.101  1.00125.00       1SG  89
ATOM     89  O   LEU   344      59.998  73.559  70.264  1.00125.00       1SG  90
ATOM     90  N   GLN   345      60.611  71.517  70.991  1.00281.08       1SG  91
ATOM     91  CA  GLN   345      61.465  71.390  69.851  1.00281.08       1SG  92
ATOM     92  CB  GLN   345      62.953  71.261  70.230  1.00281.08       1SG  93
ATOM     93  CG  GLN   345      63.287  69.987  71.011  1.00281.08       1SG  94
ATOM     94  CD  GLN   345      64.772  69.998  71.348  1.00281.08       1SG  95
ATOM     95  OE1 GLN   345      65.312  69.032  71.884  1.00281.08       1SG  96
ATOM     96  NE2 GLN   345      65.449  71.136  71.039  1.00281.08       1SG  97
ATOM     97  C   GLN   345      61.090  70.172  69.077  1.00281.08       1SG  98
ATOM     98  O   GLN   345      61.145  69.051  69.577  1.00281.08       1SG  99
ATOM     99  N   LYS   346      60.666  70.368  67.819  1.00239.55       1SG 100
ATOM    100  CA  LYS   346      60.422  69.239  66.975  1.00239.55       1SG 101
ATOM    101  CB  LYS   346      58.969  68.725  66.951  1.00239.55       1SG 102
ATOM    102  CG  LYS   346      58.634  67.809  68.132  1.00239.55       1SG 103
ATOM    103  CD  LYS   346      57.147  67.464  68.261  1.00239.55       1SG 104
ATOM    104  CE  LYS   346      56.837  66.538  69.441  1.00239.55       1SG 105
ATOM    105  NZ  LYS   346      55.387  66.244  69.495  1.00239.55       1SG 106
ATOM    106  C   LYS   346      60.773  69.650  65.592  1.00239.55       1SG 107
ATOM    107  O   LYS   346      60.256  70.638  65.074  1.00239.55       1SG 108
ATOM    108  N   GLN   347      61.694  68.900  64.963  1.00282.07       1SG 109
ATOM    109  CA  GLN   347      62.031  69.204  63.611  1.00282.07       1SG 110
ATOM    110  CB  GLN   347      63.538  69.445  63.391  1.00282.07       1SG 111
ATOM    111  CG  GLN   347      64.423  68.218  63.624  1.00282.07       1SG 112
ATOM    112  CD  GLN   347      64.615  67.517  62.286  1.00282.07       1SG 113
ATOM    113  OE1 GLN   347      64.389  68.103  61.229  1.00282.07       1SG 114
ATOM    114  NE2 GLN   347      65.053  66.230  62.331  1.00282.07       1SG 115
ATOM    115  C   GLN   347      61.603  68.012  62.828  1.00282.07       1SG 116
ATOM    116  O   GLN   347      62.060  66.897  63.069  1.00282.07       1SG 117
TER
END
