
#######################################################
#                                                     #
#                        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 (  106),  selected   15 , name T0347TS401_1-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347TS401_1-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D     134           -
LGA    -       -      P     135           -
LGA    -       -      F     136           -
LGA    -       -      R     137           -
LGA    -       -      S     138           -
LGA    -       -      L     139           -
LGA    -       -      A     140           -
LGA    -       -      G     141           -
LGA    -       -      A     142           -
LGA    -       -      L     143           -
LGA    -       -      R     144           -
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    -       -      Y     149           -
LGA    -       -      A     150           -
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    -       -      S     157           -
LGA    -       -      E     158           -
LGA    -       -      F     159           -
LGA    -       -      G     160           -
LGA    -       -      W     161           -
LGA    -       -      A     162           -
LGA    -       -      D     163           -
LGA    -       -      F     164           -
LGA    -       -      L     165           -
LGA    -       -      R     166           -
LGA    -       -      R     167           -
LGA    -       -      R     168           -
LGA    -       -      I     169           -
LGA    -       -      D     170           -
LGA    -       -      R     171           -
LGA    -       -      D     172           -
LGA    -       -      L     173           -
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    -       -      F     178           -
LGA    D     134      D     179          0.532
LGA    P     135      D     180          0.996
LGA    F     136      A     181          0.675
LGA    R     137      L     182          0.455
LGA    S     138      A     183          0.415
LGA    L     139      E     184          0.585
LGA    A     140      A     185          0.735
LGA    G     141      M     186          0.777
LGA    A     142      K     187          0.594
LGA    L     143      L     188          0.822
LGA    R     144      A     189          0.943
LGA    M     145      K     190          0.560
LGA    A     146      S     191          0.658
LGA    G     147      R     192          1.156
LGA    -       -      E     193           -
LGA    G     148      A     194          3.328
LGA    -       -      R     195           -
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    -       -      C     201           -
LGA    -       -      G     202           -
LGA    -       -      V     203           -
LGA    -       -      E     204           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15   71    5.0     15    1.12    20.00     20.812     1.234

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.933762 * X  +   0.343484 * Y  +  -0.100535 * Z  +   4.588297
  Y_new =  -0.198384 * X  +   0.262950 * Y  +  -0.944193 * Z  +  75.525032
  Z_new =  -0.297880 * X  +   0.901596 * Y  +   0.313674 * Z  + -28.317337 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.235985   -1.905608  [ DEG:    70.8167   -109.1833 ]
  Theta =   0.302471    2.839122  [ DEG:    17.3303    162.6697 ]
  Phi   =  -0.209344    2.932248  [ DEG:   -11.9945    168.0054 ]
 
# 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: T0347TS401_1-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS401_1-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15   71   5.0   15   1.12   20.00  20.812
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS401_1-D2
PFRMAT TS
TARGET T0347
MODEL  1 REFINED
PARENT 5nul
ATOM   1032  N   ASP   134      15.951  66.274  -8.176  1.00103.04       1SG1033
ATOM   1033  CA  ASP   134      17.033  65.464  -7.690  1.00103.04       1SG1034
ATOM   1034  CB  ASP   134      18.227  65.506  -8.663  1.00103.04       1SG1035
ATOM   1035  CG  ASP   134      19.282  64.488  -8.263  1.00103.04       1SG1036
ATOM   1036  OD1 ASP   134      19.050  63.717  -7.293  1.00103.04       1SG1037
ATOM   1037  OD2 ASP   134      20.344  64.468  -8.938  1.00103.04       1SG1038
ATOM   1038  C   ASP   134      17.529  65.983  -6.368  1.00103.04       1SG1039
ATOM   1039  O   ASP   134      17.966  65.191  -5.536  1.00103.04       1SG1040
ATOM   1040  N   PRO   135      17.493  67.256  -6.103  1.00131.03       1SG1041
ATOM   1041  CA  PRO   135      18.049  67.691  -4.854  1.00131.03       1SG1042
ATOM   1042  CD  PRO   135      17.796  68.230  -7.132  1.00131.03       1SG1043
ATOM   1043  CB  PRO   135      18.081  69.203  -4.904  1.00131.03       1SG1044
ATOM   1044  CG  PRO   135      18.390  69.431  -6.380  1.00131.03       1SG1045
ATOM   1045  C   PRO   135      17.508  67.137  -3.591  1.00131.03       1SG1046
ATOM   1046  O   PRO   135      18.241  67.183  -2.606  1.00131.03       1SG1047
ATOM   1047  N   PHE   136      16.268  66.631  -3.556  1.00 85.47       1SG1048
ATOM   1048  CA  PHE   136      15.839  66.081  -2.309  1.00 85.47       1SG1049
ATOM   1049  CB  PHE   136      14.428  65.486  -2.350  1.00 85.47       1SG1050
ATOM   1050  CG  PHE   136      14.245  64.811  -1.036  1.00 85.47       1SG1051
ATOM   1051  CD1 PHE   136      13.867  65.520   0.081  1.00 85.47       1SG1052
ATOM   1052  CD2 PHE   136      14.464  63.457  -0.924  1.00 85.47       1SG1053
ATOM   1053  CE1 PHE   136      13.706  64.883   1.289  1.00 85.47       1SG1054
ATOM   1054  CE2 PHE   136      14.305  62.818   0.281  1.00 85.47       1SG1055
ATOM   1055  CZ  PHE   136      13.926  63.532   1.390  1.00 85.47       1SG1056
ATOM   1056  C   PHE   136      16.774  64.961  -1.998  1.00 85.47       1SG1057
ATOM   1057  O   PHE   136      17.231  64.811  -0.868  1.00 85.47       1SG1058
ATOM   1058  N   ARG   137      17.098  64.158  -3.023  1.00117.99       1SG1059
ATOM   1059  CA  ARG   137      17.968  63.034  -2.862  1.00117.99       1SG1060
ATOM   1060  CB  ARG   137      18.024  62.166  -4.128  1.00117.99       1SG1061
ATOM   1061  CG  ARG   137      16.628  61.623  -4.443  1.00117.99       1SG1062
ATOM   1062  CD  ARG   137      16.484  60.878  -5.767  1.00117.99       1SG1063
ATOM   1063  NE  ARG   137      15.052  60.474  -5.857  1.00117.99       1SG1064
ATOM   1064  CZ  ARG   137      14.469  60.214  -7.063  1.00117.99       1SG1065
ATOM   1065  NH1 ARG   137      15.208  60.265  -8.209  1.00117.99       1SG1066
ATOM   1066  NH2 ARG   137      13.140  59.907  -7.122  1.00117.99       1SG1067
ATOM   1067  C   ARG   137      19.335  63.523  -2.490  1.00117.99       1SG1068
ATOM   1068  O   ARG   137      20.046  62.867  -1.731  1.00117.99       1SG1069
ATOM   1069  N   SER   138      19.745  64.688  -3.027  1.00 76.81       1SG1070
ATOM   1070  CA  SER   138      21.037  65.237  -2.719  1.00 76.81       1SG1071
ATOM   1071  CB  SER   138      21.298  66.564  -3.453  1.00 76.81       1SG1072
ATOM   1072  OG  SER   138      22.581  67.067  -3.112  1.00 76.81       1SG1073
ATOM   1073  C   SER   138      21.097  65.513  -1.246  1.00 76.81       1SG1074
ATOM   1074  O   SER   138      22.060  65.157  -0.568  1.00 76.81       1SG1075
ATOM   1075  N   LEU   139      20.047  66.157  -0.707  1.00 93.07       1SG1076
ATOM   1076  CA  LEU   139      19.980  66.454   0.695  1.00 93.07       1SG1077
ATOM   1077  CB  LEU   139      18.699  67.229   1.061  1.00 93.07       1SG1078
ATOM   1078  CG  LEU   139      18.741  68.745   0.778  1.00 93.07       1SG1079
ATOM   1079  CD2 LEU   139      17.531  69.458   1.411  1.00 93.07       1SG1080
ATOM   1080  CD1 LEU   139      18.895  69.056  -0.717  1.00 93.07       1SG1081
ATOM   1081  C   LEU   139      19.963  65.159   1.450  1.00 93.07       1SG1082
ATOM   1082  O   LEU   139      20.657  64.997   2.450  1.00 93.07       1SG1083
ATOM   1083  N   ALA   140      19.195  64.174   0.960  1.00 36.31       1SG1084
ATOM   1084  CA  ALA   140      19.050  62.927   1.657  1.00 36.31       1SG1085
ATOM   1085  CB  ALA   140      18.129  61.939   0.918  1.00 36.31       1SG1086
ATOM   1086  C   ALA   140      20.389  62.273   1.797  1.00 36.31       1SG1087
ATOM   1087  O   ALA   140      20.700  61.703   2.842  1.00 36.31       1SG1088
ATOM   1088  N   GLY   141      21.226  62.345   0.748  1.00 29.89       1SG1089
ATOM   1089  CA  GLY   141      22.509  61.705   0.802  1.00 29.89       1SG1090
ATOM   1090  C   GLY   141      23.256  62.314   1.937  1.00 29.89       1SG1091
ATOM   1091  O   GLY   141      23.981  61.644   2.672  1.00 29.89       1SG1092
ATOM   1092  N   ALA   142      23.083  63.630   2.096  1.00 52.17       1SG1093
ATOM   1093  CA  ALA   142      23.731  64.359   3.134  1.00 52.17       1SG1094
ATOM   1094  CB  ALA   142      23.244  65.790   3.159  1.00 52.17       1SG1095
ATOM   1095  C   ALA   142      23.294  63.790   4.443  1.00 52.17       1SG1096
ATOM   1096  O   ALA   142      24.112  63.582   5.338  1.00 52.17       1SG1097
ATOM   1097  N   LEU   143      21.984  63.505   4.582  1.00108.49       1SG1098
ATOM   1098  CA  LEU   143      21.495  63.004   5.836  1.00108.49       1SG1099
ATOM   1099  CB  LEU   143      20.024  62.505   5.815  1.00108.49       1SG1100
ATOM   1100  CG  LEU   143      18.847  63.504   5.699  1.00108.49       1SG1101
ATOM   1101  CD2 LEU   143      18.749  64.167   4.316  1.00108.49       1SG1102
ATOM   1102  CD1 LEU   143      18.796  64.466   6.899  1.00108.49       1SG1103
ATOM   1103  C   LEU   143      22.238  61.742   6.138  1.00108.49       1SG1104
ATOM   1104  O   LEU   143      22.758  61.561   7.238  1.00108.49       1SG1105
ATOM   1105  N   ARG   144      22.319  60.847   5.135  1.00130.55       1SG1106
ATOM   1106  CA  ARG   144      22.884  59.546   5.337  1.00130.55       1SG1107
ATOM   1107  CB  ARG   144      22.812  58.672   4.073  1.00130.55       1SG1108
ATOM   1108  CG  ARG   144      23.295  57.238   4.293  1.00130.55       1SG1109
ATOM   1109  CD  ARG   144      23.137  56.339   3.065  1.00130.55       1SG1110
ATOM   1110  NE  ARG   144      21.676  56.160   2.822  1.00130.55       1SG1111
ATOM   1111  CZ  ARG   144      21.246  55.539   1.686  1.00130.55       1SG1112
ATOM   1112  NH1 ARG   144      22.155  55.072   0.780  1.00130.55       1SG1113
ATOM   1113  NH2 ARG   144      19.908  55.388   1.458  1.00130.55       1SG1114
ATOM   1114  C   ARG   144      24.318  59.666   5.730  1.00130.55       1SG1115
ATOM   1115  O   ARG   144      24.762  59.023   6.680  1.00130.55       1SG1116
ATOM   1116  N   MET   145      25.087  60.514   5.029  1.00142.29       1SG1117
ATOM   1117  CA  MET   145      26.473  60.611   5.377  1.00142.29       1SG1118
ATOM   1118  CB  MET   145      27.281  61.545   4.465  1.00142.29       1SG1119
ATOM   1119  CG  MET   145      28.711  61.751   4.970  1.00142.29       1SG1120
ATOM   1120  SD  MET   145      29.709  60.233   5.070  1.00142.29       1SG1121
ATOM   1121  CE  MET   145      29.714  59.907   3.287  1.00142.29       1SG1122
ATOM   1122  C   MET   145      26.575  61.117   6.769  1.00142.29       1SG1123
ATOM   1123  O   MET   145      27.379  60.621   7.557  1.00142.29       1SG1124
ATOM   1124  N   ALA   146      25.744  62.117   7.118  1.00235.02       1SG1125
ATOM   1125  CA  ALA   146      25.796  62.621   8.454  1.00235.02       1SG1126
ATOM   1126  CB  ALA   146      24.770  63.732   8.733  1.00235.02       1SG1127
ATOM   1127  C   ALA   146      25.466  61.464   9.327  1.00235.02       1SG1128
ATOM   1128  O   ALA   146      24.554  60.692   9.043  1.00235.02       1SG1129
ATOM   1129  N   GLY   147      26.215  61.300  10.423  1.00198.39       1SG1130
ATOM   1130  CA  GLY   147      25.946  60.159  11.235  1.00198.39       1SG1131
ATOM   1131  C   GLY   147      26.294  58.986  10.387  1.00198.39       1SG1132
ATOM   1132  O   GLY   147      27.285  59.008   9.659  1.00198.39       1SG1133
ATOM   1133  N   GLY   148      25.472  57.924  10.456  1.00 38.09       1SG1134
ATOM   1134  CA  GLY   148      25.730  56.767   9.655  1.00 38.09       1SG1135
ATOM   1135  C   GLY   148      26.721  55.892  10.407  1.00 38.09       1SG1136
ATOM   1136  O   GLY   148      27.195  56.315  11.494  1.00 38.09       1SG1137
ATOM   1137  OXT GLY   148      27.017  54.779   9.894  1.00 38.09       1SG1138
TER
END
