
#######################################################
#                                                     #
#                        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 T0356TS213_1_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS213_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    G     333      R      41          2.320
LGA    V     334      T      42          3.982
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      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    A     335      P     326          3.646
LGA    L     336      D     327          1.205
LGA    N     337      E     328          1.132
LGA    E     338      P     329          1.071
LGA    V     339      A     330          0.904
LGA    F     340      V     331          1.252
LGA    V     341      L     332          0.680
LGA    P     342      G     333          0.744
LGA    I     343      V     334          0.948
LGA    L     344      A     335          0.714
LGA    Q     345      L     336          0.834
LGA    K     346      N     337          0.831
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    Q     347      F     340          3.113
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     15    1.90     0.00     11.177     0.749

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.704041 * X  +  -0.700780 * Y  +  -0.115036 * Z  + 117.264580
  Y_new =   0.226104 * X  +  -0.374753 * Y  +   0.899131 * Z  +  18.078739
  Z_new =  -0.673204 * X  +   0.607015 * Y  +   0.422290 * Z  +  83.800056 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.962973   -2.178619  [ DEG:    55.1743   -124.8257 ]
  Theta =   0.738533    2.403060  [ DEG:    42.3148    137.6852 ]
  Phi   =   2.830845   -0.310748  [ DEG:   162.1955    -17.8045 ]
 
# 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: T0356TS213_1_2-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS213_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   15   1.90    0.00  11.177
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS213_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0356
PARENT 1oi2_A 2iu4_A
ATOM      1  N   GLY   333      49.035  67.403  87.687  1.00 10.94       1SG   2
ATOM      2  CA  GLY   333      50.443  67.734  88.000  1.00 10.94       1SG   3
ATOM      3  C   GLY   333      51.052  68.525  86.892  1.00 10.94       1SG   4
ATOM      4  O   GLY   333      50.376  68.909  85.939  1.00 10.94       1SG   5
ATOM      5  N   VAL   334      52.366  68.793  87.004  1.00 93.00       1SG   6
ATOM      6  CA  VAL   334      53.060  69.537  85.998  1.00 93.00       1SG   7
ATOM      7  CB  VAL   334      54.367  70.113  86.460  1.00 93.00       1SG   8
ATOM      8  CG1 VAL   334      54.093  71.124  87.585  1.00 93.00       1SG   9
ATOM      9  CG2 VAL   334      55.293  68.955  86.867  1.00 93.00       1SG  10
ATOM     10  C   VAL   334      53.349  68.600  84.876  1.00 93.00       1SG  11
ATOM     11  O   VAL   334      53.408  67.387  85.066  1.00 93.00       1SG  12
ATOM     12  N   ALA   335      53.507  69.153  83.659  1.00 28.75       1SG  13
ATOM     13  CA  ALA   335      53.778  68.339  82.514  1.00 28.75       1SG  14
ATOM     14  CB  ALA   335      53.780  69.123  81.189  1.00 28.75       1SG  15
ATOM     15  C   ALA   335      55.132  67.738  82.695  1.00 28.75       1SG  16
ATOM     16  O   ALA   335      55.970  68.257  83.431  1.00 28.75       1SG  17
ATOM     17  N   LEU   336      55.354  66.590  82.028  1.00 40.20       1SG  18
ATOM     18  CA  LEU   336      56.586  65.865  82.121  1.00 40.20       1SG  19
ATOM     19  CB  LEU   336      56.487  64.467  81.486  1.00 40.20       1SG  20
ATOM     20  CG  LEU   336      55.406  63.590  82.145  1.00 40.20       1SG  21
ATOM     21  CD1 LEU   336      55.390  62.171  81.555  1.00 40.20       1SG  22
ATOM     22  CD2 LEU   336      55.532  63.607  83.676  1.00 40.20       1SG  23
ATOM     23  C   LEU   336      57.640  66.636  81.391  1.00 40.20       1SG  24
ATOM     24  O   LEU   336      57.348  67.363  80.443  1.00 40.20       1SG  25
ATOM     25  N   ASN   337      58.905  66.499  81.842  1.00 72.56       1SG  26
ATOM     26  CA  ASN   337      60.004  67.206  81.245  1.00 72.56       1SG  27
ATOM     27  CB  ASN   337      61.342  66.960  81.968  1.00 72.56       1SG  28
ATOM     28  CG  ASN   337      61.691  65.480  81.874  1.00 72.56       1SG  29
ATOM     29  OD1 ASN   337      60.921  64.615  82.284  1.00 72.56       1SG  30
ATOM     30  ND2 ASN   337      62.894  65.176  81.315  1.00 72.56       1SG  31
ATOM     31  C   ASN   337      60.151  66.753  79.831  1.00 72.56       1SG  32
ATOM     32  O   ASN   337      60.378  67.564  78.934  1.00 72.56       1SG  33
ATOM     33  N   GLU   338      60.025  65.437  79.588  1.00 85.06       1SG  34
ATOM     34  CA  GLU   338      60.164  64.968  78.245  1.00 85.06       1SG  35
ATOM     35  CB  GLU   338      60.198  63.437  78.095  1.00 85.06       1SG  36
ATOM     36  CG  GLU   338      58.926  62.705  78.510  1.00 85.06       1SG  37
ATOM     37  CD  GLU   338      59.138  61.239  78.154  1.00 85.06       1SG  38
ATOM     38  OE1 GLU   338      60.249  60.904  77.663  1.00 85.06       1SG  39
ATOM     39  OE2 GLU   338      58.192  60.433  78.366  1.00 85.06       1SG  40
ATOM     40  C   GLU   338      59.027  65.513  77.451  1.00 85.06       1SG  41
ATOM     41  O   GLU   338      59.163  65.799  76.269  1.00 85.06       1SG  42
ATOM     42  N   VAL   339      57.843  65.667  78.056  1.00 29.29       1SG  43
ATOM     43  CA  VAL   339      56.784  66.231  77.274  1.00 29.29       1SG  44
ATOM     44  CB  VAL   339      55.499  66.328  78.042  1.00 29.29       1SG  45
ATOM     45  CG1 VAL   339      54.451  67.047  77.177  1.00 29.29       1SG  46
ATOM     46  CG2 VAL   339      55.088  64.911  78.476  1.00 29.29       1SG  47
ATOM     47  C   VAL   339      57.202  67.620  76.902  1.00 29.29       1SG  48
ATOM     48  O   VAL   339      57.025  68.062  75.767  1.00 29.29       1SG  49
ATOM     49  N   PHE   340      57.800  68.329  77.875  1.00101.85       1SG  50
ATOM     50  CA  PHE   340      58.190  69.705  77.768  1.00101.85       1SG  51
ATOM     51  CB  PHE   340      58.798  70.193  79.099  1.00101.85       1SG  52
ATOM     52  CG  PHE   340      59.071  71.657  79.052  1.00101.85       1SG  53
ATOM     53  CD1 PHE   340      58.046  72.560  79.211  1.00101.85       1SG  54
ATOM     54  CD2 PHE   340      60.354  72.127  78.881  1.00101.85       1SG  55
ATOM     55  CE1 PHE   340      58.292  73.911  79.179  1.00101.85       1SG  56
ATOM     56  CE2 PHE   340      60.605  73.479  78.848  1.00101.85       1SG  57
ATOM     57  CZ  PHE   340      59.572  74.374  78.995  1.00101.85       1SG  58
ATOM     58  C   PHE   340      59.215  69.882  76.687  1.00101.85       1SG  59
ATOM     59  O   PHE   340      59.083  70.772  75.847  1.00101.85       1SG  60
ATOM     60  N   VAL   341      60.267  69.039  76.664  1.00 59.70       1SG  61
ATOM     61  CA  VAL   341      61.307  69.283  75.708  1.00 59.70       1SG  62
ATOM     62  CB  VAL   341      62.537  68.447  75.936  1.00 59.70       1SG  63
ATOM     63  CG1 VAL   341      63.550  68.756  74.822  1.00 59.70       1SG  64
ATOM     64  CG2 VAL   341      63.057  68.719  77.357  1.00 59.70       1SG  65
ATOM     65  C   VAL   341      60.801  69.135  74.296  1.00 59.70       1SG  66
ATOM     66  O   VAL   341      60.971  70.063  73.506  1.00 59.70       1SG  67
ATOM     67  N   PRO   342      60.173  68.050  73.914  1.00115.35       1SG  68
ATOM     68  CA  PRO   342      59.660  68.035  72.576  1.00115.35       1SG  69
ATOM     69  CD  PRO   342      60.766  66.752  74.202  1.00115.35       1SG  70
ATOM     70  CB  PRO   342      59.322  66.583  72.262  1.00115.35       1SG  71
ATOM     71  CG  PRO   342      60.417  65.825  73.026  1.00115.35       1SG  72
ATOM     72  C   PRO   342      58.572  69.001  72.268  1.00115.35       1SG  73
ATOM     73  O   PRO   342      58.364  69.253  71.087  1.00115.35       1SG  74
ATOM     74  N   ILE   343      57.821  69.535  73.244  1.00 92.71       1SG  75
ATOM     75  CA  ILE   343      56.859  70.478  72.760  1.00 92.71       1SG  76
ATOM     76  CB  ILE   343      55.898  70.995  73.800  1.00 92.71       1SG  77
ATOM     77  CG2 ILE   343      55.048  69.810  74.289  1.00 92.71       1SG  78
ATOM     78  CG1 ILE   343      56.623  71.762  74.917  1.00 92.71       1SG  79
ATOM     79  CD1 ILE   343      55.686  72.614  75.773  1.00 92.71       1SG  80
ATOM     80  C   ILE   343      57.626  71.637  72.212  1.00 92.71       1SG  81
ATOM     81  O   ILE   343      57.353  72.121  71.115  1.00 92.71       1SG  82
ATOM     82  N   LEU   344      58.639  72.095  72.967  1.00 68.01       1SG  83
ATOM     83  CA  LEU   344      59.386  73.236  72.539  1.00 68.01       1SG  84
ATOM     84  CB  LEU   344      60.340  73.743  73.631  1.00 68.01       1SG  85
ATOM     85  CG  LEU   344      59.603  74.091  74.941  1.00 68.01       1SG  86
ATOM     86  CD1 LEU   344      60.550  74.748  75.954  1.00 68.01       1SG  87
ATOM     87  CD2 LEU   344      58.337  74.923  74.678  1.00 68.01       1SG  88
ATOM     88  C   LEU   344      60.184  72.926  71.301  1.00 68.01       1SG  89
ATOM     89  O   LEU   344      60.184  73.715  70.360  1.00 68.01       1SG  90
ATOM     90  N   GLN   345      60.920  71.794  71.286  1.00170.67       1SG  91
ATOM     91  CA  GLN   345      61.764  71.417  70.174  1.00170.67       1SG  92
ATOM     92  CB  GLN   345      62.813  70.361  70.558  1.00170.67       1SG  93
ATOM     93  CG  GLN   345      63.700  69.914  69.392  1.00170.67       1SG  94
ATOM     94  CD  GLN   345      64.531  71.095  68.912  1.00170.67       1SG  95
ATOM     95  OE1 GLN   345      64.027  72.210  68.783  1.00170.67       1SG  96
ATOM     96  NE2 GLN   345      65.839  70.848  68.634  1.00170.67       1SG  97
ATOM     97  C   GLN   345      61.029  70.876  68.975  1.00170.67       1SG  98
ATOM     98  O   GLN   345      61.340  71.245  67.844  1.00170.67       1SG  99
ATOM     99  N   LYS   346      60.017  70.018  69.226  1.00306.70       1SG 100
ATOM    100  CA  LYS   346      59.284  69.158  68.320  1.00306.70       1SG 101
ATOM    101  CB  LYS   346      57.748  69.236  68.426  1.00306.70       1SG 102
ATOM    102  CG  LYS   346      57.029  68.058  67.765  1.00306.70       1SG 103
ATOM    103  CD  LYS   346      55.552  67.946  68.153  1.00306.70       1SG 104
ATOM    104  CE  LYS   346      55.322  67.676  69.644  1.00306.70       1SG 105
ATOM    105  NZ  LYS   346      55.793  66.318  70.001  1.00306.70       1SG 106
ATOM    106  C   LYS   346      59.659  69.318  66.885  1.00306.70       1SG 107
ATOM    107  O   LYS   346      59.525  70.387  66.291  1.00306.70       1SG 108
ATOM    108  N   GLN   347      60.166  68.209  66.305  1.00326.90       1SG 109
ATOM    109  CA  GLN   347      60.532  68.140  64.924  1.00326.90       1SG 110
ATOM    110  CB  GLN   347      62.029  68.347  64.649  1.00326.90       1SG 111
ATOM    111  CG  GLN   347      62.370  68.159  63.168  1.00326.90       1SG 112
ATOM    112  CD  GLN   347      63.882  68.057  63.021  1.00326.90       1SG 113
ATOM    113  OE1 GLN   347      64.407  67.013  62.637  1.00326.90       1SG 114
ATOM    114  NE2 GLN   347      64.603  69.167  63.335  1.00326.90       1SG 115
ATOM    115  C   GLN   347      60.254  66.744  64.470  1.00326.90       1SG 116
ATOM    116  O   GLN   347      60.342  65.797  65.251  1.00326.90       1SG 117
TER
END
