
#######################################################
#                                                     #
#                        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   12 (  106),  selected   12 , name T0372TS022_2_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372TS022_2_1-D2.T0372_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R     118           -
LGA    -       -      A     119           -
LGA    -       -      Y     120           -
LGA    -       -      A     121           -
LGA    -       -      D     122           -
LGA    -       -      Y     123           -
LGA    -       -      I     124           -
LGA    -       -      Y     125           -
LGA    -       -      L     126           -
LGA    -       -      R     127           -
LGA    -       -      S     128           -
LGA    -       -      D     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      T     132           -
LGA    -       -      L     133           -
LGA    -       -      K     134           -
LGA    -       -      G     135           -
LGA    -       -      K     136           -
LGA    -       -      K     137           -
LGA    -       -      F     138           -
LGA    -       -      Q     139           -
LGA    -       -      A     140           -
LGA    R     118      K     141          2.385
LGA    A     119      R     142          2.531
LGA    Y     120      N     143          2.236
LGA    A     121      H     144          1.588
LGA    D     122      I     145          1.537
LGA    -       -      N     146           -
LGA    -       -      R     147           -
LGA    Y     123      F     148          2.335
LGA    -       -      R     149           -
LGA    -       -      N     150           -
LGA    -       -      T     151           -
LGA    -       -      Y     152           -
LGA    -       -      P     153           -
LGA    -       -      D     154           -
LGA    -       -      Y     155           -
LGA    -       -      E     156           -
LGA    -       -      Y     157           -
LGA    -       -      T     158           -
LGA    -       -      P     159           -
LGA    -       -      I     160           -
LGA    -       -      T     161           -
LGA    -       -      P     162           -
LGA    -       -      D     163           -
LGA    -       -      R     164           -
LGA    -       -      I     165           -
LGA    -       -      Q     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      L     169           -
LGA    -       -      D     170           -
LGA    -       -      L     171           -
LGA    -       -      E     172           -
LGA    -       -      A     173           -
LGA    -       -      E     174           -
LGA    -       -      W     175           -
LGA    -       -      C     176           -
LGA    -       -      K     177           -
LGA    -       -      V     178           -
LGA    -       -      N     179           -
LGA    -       -      N     180           -
LGA    -       -      C     181           -
LGA    -       -      D     182           -
LGA    -       -      Q     183           -
LGA    -       -      Q     184           -
LGA    -       -      E     185           -
LGA    -       -      G     186           -
LGA    -       -      T     187           -
LGA    -       -      G     188           -
LGA    -       -      N     189           -
LGA    -       -      E     190           -
LGA    -       -      R     191           -
LGA    -       -      R     192           -
LGA    -       -      A     193           -
LGA    -       -      L     194           -
LGA    -       -      I     195           -
LGA    -       -      Y     196           -
LGA    -       -      A     197           -
LGA    -       -      L     198           -
LGA    -       -      H     199           -
LGA    -       -      N     200           -
LGA    -       -      F     201           -
LGA    -       -      E     202           -
LGA    -       -      A     203           -
LGA    -       -      L     204           -
LGA    -       -      G     205           -
LGA    -       -      L     206           -
LGA    -       -      T     207           -
LGA    -       -      G     208           -
LGA    -       -      G     209           -
LGA    -       -      I     210           -
LGA    -       -      L     211           -
LGA    -       -      H     212           -
LGA    -       -      V     213           -
LGA    -       -      N     214           -
LGA    -       -      G     215           -
LGA    -       -      K     216           -
LGA    -       -      I     217           -
LGA    -       -      V     218           -
LGA    -       -      A     219           -
LGA    -       -      F     220           -
LGA    -       -      T     221           -
LGA    -       -      F     222           -
LGA    -       -      G     223           -
LGA    -       -      M     224           -
LGA    -       -      P     225           -
LGA    -       -      I     226           -
LGA    -       -      N     227           -
LGA    -       -      H     228           -
LGA    -       -      E     229           -
LGA    -       -      T     230           -
LGA    -       -      F     231           -
LGA    -       -      G     232           -
LGA    -       -      V     233           -
LGA    -       -      H     234           -
LGA    -       -      V     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      A     238           -
LGA    -       -      D     239           -
LGA    -       -      T     240           -
LGA    -       -      S     241           -
LGA    -       -      I     242           -
LGA    -       -      D     243           -
LGA    I     124      G     244          1.250
LGA    Y     125      A     245          2.895
LGA    -       -      Y     246           -
LGA    -       -      A     247           -
LGA    L     126      M     248          1.208
LGA    R     127      I     249          1.053
LGA    -       -      N     250           -
LGA    -       -      Y     251           -
LGA    S     128      E     252          1.578
LGA    D     129      F     253          1.734
LGA    -       -      A     254           -
LGA    -       -      N     255           -
LGA    -       -      R     256           -
LGA    -       -      I     257           -
LGA    -       -      P     258           -
LGA    -       -      E     259           -
LGA    -       -      Q     260           -
LGA    -       -      Y     261           -
LGA    -       -      I     262           -
LGA    -       -      Y     263           -
LGA    -       -      I     264           -
LGA    -       -      N     265           -
LGA    -       -      R     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      D     269           -
LGA    -       -      L     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      E     273           -
LGA    -       -      G     274           -
LGA    -       -      L     275           -
LGA    -       -      R     276           -
LGA    -       -      K     277           -
LGA    -       -      A     278           -
LGA    -       -      K     279           -
LGA    -       -      L     280           -
LGA    -       -      S     281           -
LGA    -       -      Y     282           -
LGA    -       -      Q     283           -
LGA    -       -      P     284           -
LGA    -       -      V     285           -
LGA    -       -      T     286           -
LGA    -       -      I     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   12  172    5.0     12    1.95     0.00      6.367     0.587

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.445954 * X  +   0.769272 * Y  +   0.457544 * Z  +  37.071514
  Y_new =   0.164369 * X  +  -0.432110 * Y  +   0.886715 * Z  +  28.179996
  Z_new =   0.879834 * X  +   0.470640 * Y  +   0.066257 * Z  + -38.569614 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.430936   -1.710657  [ DEG:    81.9866    -98.0134 ]
  Theta =  -1.075513   -2.066080  [ DEG:   -61.6224   -118.3776 ]
  Phi   =   2.788463   -0.353129  [ DEG:   159.7672    -20.2328 ]
 
# 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: T0372TS022_2_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_2_1-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   12  172   5.0   12   1.95    0.00   6.367
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_2_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT 1cm0_A
ATOM    953  N   ARG   118      23.665  39.854  35.354  1.00  0.00
ATOM    954  CA  ARG   118      24.864  40.078  36.103  1.00  0.00
ATOM    955  C   ARG   118      24.928  39.125  37.262  1.00  0.00
ATOM    956  O   ARG   118      25.989  38.593  37.580  1.00  0.00
ATOM    957  CB  ARG   118      24.900  41.510  36.640  1.00  0.00
ATOM    958  CG  ARG   118      25.124  42.568  35.573  1.00  0.00
ATOM    959  CD  ARG   118      25.070  43.968  36.164  1.00  0.00
ATOM    960  NE  ARG   118      25.278  44.998  35.148  1.00  0.00
ATOM    961  CZ  ARG   118      25.203  46.303  35.383  1.00  0.00
ATOM    962  NH1 ARG   118      25.407  47.168  34.399  1.00  0.00
ATOM    963  NH2 ARG   118      24.923  46.743  36.603  1.00  0.00
ATOM    964  N   ALA   119      23.781  38.862  37.919  1.00  0.00
ATOM    965  CA  ALA   119      23.798  38.058  39.113  1.00  0.00
ATOM    966  C   ALA   119      24.325  36.691  38.814  1.00  0.00
ATOM    967  O   ALA   119      25.149  36.161  39.557  1.00  0.00
ATOM    968  CB  ALA   119      22.393  37.921  39.679  1.00  0.00
ATOM    969  N   TYR   120      23.875  36.089  37.702  1.00  0.00
ATOM    970  CA  TYR   120      24.315  34.777  37.326  1.00  0.00
ATOM    971  C   TYR   120      25.781  34.855  37.042  1.00  0.00
ATOM    972  O   TYR   120      26.540  33.939  37.353  1.00  0.00
ATOM    973  CB  TYR   120      23.569  34.297  36.081  1.00  0.00
ATOM    974  CG  TYR   120      22.099  34.026  36.313  1.00  0.00
ATOM    975  CD1 TYR   120      21.594  33.901  37.601  1.00  0.00
ATOM    976  CD2 TYR   120      21.222  33.895  35.245  1.00  0.00
ATOM    977  CE1 TYR   120      20.254  33.653  37.824  1.00  0.00
ATOM    978  CE2 TYR   120      19.878  33.647  35.448  1.00  0.00
ATOM    979  CZ  TYR   120      19.398  33.527  36.751  1.00  0.00
ATOM    980  OH  TYR   120      18.062  33.279  36.970  1.00  0.00
ATOM    981  N   ALA   121      26.198  35.994  36.467  1.00  0.00
ATOM    982  CA  ALA   121      27.498  36.287  35.930  1.00  0.00
ATOM    983  C   ALA   121      28.614  36.168  36.929  1.00  0.00
ATOM    984  O   ALA   121      29.727  35.824  36.540  1.00  0.00
ATOM    985  CB  ALA   121      27.542  37.710  35.394  1.00  0.00
ATOM    986  N   ASP   122      28.367  36.425  38.228  1.00  0.00
ATOM    987  CA  ASP   122      29.420  36.518  39.209  1.00  0.00
ATOM    988  C   ASP   122      30.316  35.317  39.151  1.00  0.00
ATOM    989  O   ASP   122      31.525  35.437  39.336  1.00  0.00
ATOM    990  CB  ASP   122      28.832  36.607  40.619  1.00  0.00
ATOM    991  CG  ASP   122      28.192  37.952  40.900  1.00  0.00
ATOM    992  OD1 ASP   122      28.398  38.887  40.097  1.00  0.00
ATOM    993  OD2 ASP   122      27.485  38.072  41.922  1.00  0.00
ATOM    994  N   TYR   123      29.767  34.122  38.886  1.00  0.00
ATOM    995  CA  TYR   123      30.628  32.979  38.817  1.00  0.00
ATOM    996  C   TYR   123      31.615  33.155  37.706  1.00  0.00
ATOM    997  O   TYR   123      32.806  32.913  37.890  1.00  0.00
ATOM    998  CB  TYR   123      29.814  31.710  38.558  1.00  0.00
ATOM    999  CG  TYR   123      29.040  31.222  39.762  1.00  0.00
ATOM   1000  CD1 TYR   123      27.665  31.400  39.843  1.00  0.00
ATOM   1001  CD2 TYR   123      29.687  30.586  40.813  1.00  0.00
ATOM   1002  CE1 TYR   123      26.949  30.957  40.939  1.00  0.00
ATOM   1003  CE2 TYR   123      28.987  30.137  41.917  1.00  0.00
ATOM   1004  CZ  TYR   123      27.608  30.328  41.972  1.00  0.00
ATOM   1005  OH  TYR   123      26.896  29.886  43.065  1.00  0.00
ATOM   1006  N   ILE   124      31.160  33.609  36.522  1.00  0.00
ATOM   1007  CA  ILE   124      32.067  33.736  35.417  1.00  0.00
ATOM   1008  C   ILE   124      33.043  34.824  35.730  1.00  0.00
ATOM   1009  O   ILE   124      32.708  35.817  36.375  1.00  0.00
ATOM   1010  CB  ILE   124      31.325  34.087  34.115  1.00  0.00
ATOM   1011  CG1 ILE   124      32.248  33.906  32.909  1.00  0.00
ATOM   1012  CG2 ILE   124      30.849  35.531  34.145  1.00  0.00
ATOM   1013  CD1 ILE   124      31.535  33.980  31.576  1.00  0.00
ATOM   1014  N   TYR   125      34.305  34.629  35.308  1.00  0.00
ATOM   1015  CA  TYR   125      35.345  35.574  35.581  1.00  0.00
ATOM   1016  C   TYR   125      35.144  36.735  34.658  1.00  0.00
ATOM   1017  O   TYR   125      34.862  36.553  33.476  1.00  0.00
ATOM   1018  CB  TYR   125      36.718  34.944  35.342  1.00  0.00
ATOM   1019  CG  TYR   125      37.120  33.931  36.390  1.00  0.00
ATOM   1020  CD1 TYR   125      36.924  32.573  36.179  1.00  0.00
ATOM   1021  CD2 TYR   125      37.692  34.338  37.589  1.00  0.00
ATOM   1022  CE1 TYR   125      37.287  31.640  37.132  1.00  0.00
ATOM   1023  CE2 TYR   125      38.062  33.419  38.553  1.00  0.00
ATOM   1024  CZ  TYR   125      37.855  32.061  38.314  1.00  0.00
ATOM   1025  OH  TYR   125      38.217  31.134  39.266  1.00  0.00
ATOM   1026  N   LEU   126      35.262  37.969  35.193  1.00  0.00
ATOM   1027  CA  LEU   126      35.011  39.150  34.417  1.00  0.00
ATOM   1028  C   LEU   126      36.257  39.592  33.723  1.00  0.00
ATOM   1029  O   LEU   126      37.352  39.566  34.283  1.00  0.00
ATOM   1030  CB  LEU   126      34.526  40.289  35.316  1.00  0.00
ATOM   1031  CG  LEU   126      33.217  40.049  36.069  1.00  0.00
ATOM   1032  CD1 LEU   126      32.896  41.224  36.980  1.00  0.00
ATOM   1033  CD2 LEU   126      32.062  39.873  35.095  1.00  0.00
ATOM   1034  N   ARG   127      36.098  39.974  32.440  1.00  0.00
ATOM   1035  CA  ARG   127      37.174  40.486  31.648  1.00  0.00
ATOM   1036  C   ARG   127      37.539  41.810  32.209  1.00  0.00
ATOM   1037  O   ARG   127      38.714  42.155  32.294  1.00  0.00
ATOM   1038  CB  ARG   127      36.742  40.633  30.188  1.00  0.00
ATOM   1039  CG  ARG   127      37.868  41.023  29.244  1.00  0.00
ATOM   1040  CD  ARG   127      37.376  41.123  27.809  1.00  0.00
ATOM   1041  NE  ARG   127      36.951  39.827  27.285  1.00  0.00
ATOM   1042  CZ  ARG   127      37.780  38.906  26.807  1.00  0.00
ATOM   1043  NH1 ARG   127      37.302  37.757  26.352  1.00  0.00
ATOM   1044  NH2 ARG   127      39.086  39.136  26.786  1.00  0.00
ATOM   1045  N   SER   128      36.512  42.591  32.589  1.00  0.00
ATOM   1046  CA  SER   128      36.728  43.900  33.119  1.00  0.00
ATOM   1047  C   SER   128      37.508  44.638  32.085  1.00  0.00
ATOM   1048  O   SER   128      38.259  45.561  32.398  1.00  0.00
ATOM   1049  CB  SER   128      37.507  43.824  34.433  1.00  0.00
ATOM   1050  OG  SER   128      36.800  43.070  35.402  1.00  0.00
ATOM   1051  N   ASP   129      37.333  44.255  30.806  1.00  0.00
ATOM   1052  CA  ASP   129      38.067  44.905  29.763  1.00  0.00
ATOM   1053  C   ASP   129      37.061  45.617  28.867  1.00  0.00
ATOM   1054  O   ASP   129      35.996  45.014  28.567  1.00  0.00
ATOM   1055  CB  ASP   129      38.858  43.881  28.947  1.00  0.00
ATOM   1056  CG  ASP   129      39.800  44.530  27.952  1.00  0.00
ATOM   1057  OD1 ASP   129      40.062  45.744  28.087  1.00  0.00
ATOM   1058  OD2 ASP   129      40.277  43.826  27.038  1.00  0.00
TER
END
