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sample_linker doesn't add atoms totally in the broken site #23

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BLEACH366 opened this issue May 16, 2024 · 2 comments
Open

sample_linker doesn't add atoms totally in the broken site #23

BLEACH366 opened this issue May 16, 2024 · 2 comments

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@BLEACH366
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Hi. I use sample_linker.py to generate linker, but the added atoms don't build a new connection between fragments.
My molecular is like this:
ligand

and its index is like this:
ligand2

so I use this command to generate linker:

python -u sample_linker.py --ckpt 500.pt --pdb_path 9AX6_ligand_pocket10.pdb --mol_file 9AX6_ligand.sdf --mask 1 2 3 43 51 57 --num_atom 6 --num_samples 50 --sampling_type generalized -build_method reconstruct

but I get generated molecular like this(the atoms that I want to link are labeled):
ligand3

its 3D view is like this:
ligand4

Could you offer me some help? Thank.

my 9AX6_ligand_pocket10.pdb is like this:

TITLE     9AX6_ligand_pocket10
REMARK   4      COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006
REMARK 888
REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
ATOM      1  N   ASP A  12      27.818 -14.945  -5.534  1.00 31.44           N1+
ATOM      2  CA  ASP A  12      26.823 -15.970  -5.303  1.00 30.78           C  
ATOM      3  C   ASP A  12      26.159 -15.774  -3.935  1.00 28.50           C  
ATOM      4  O   ASP A  12      26.821 -15.471  -2.933  1.00 31.55           O  
ATOM      5  CB  ASP A  12      27.422 -17.369  -5.430  1.00 35.38           C  
ATOM      6  CG  ASP A  12      28.541 -17.599  -4.503  1.00 47.47           C  
ATOM      7  OD1 ASP A  12      29.611 -16.977  -4.725  1.00 51.81           O  
ATOM      8  OD2 ASP A  12      28.370 -18.402  -3.546  1.00 52.89           O1-
ATOM      9  N   GLU A  31      14.633 -20.649  -0.016  1.00 46.76           N1+
ATOM     10  CA  GLU A  31      15.583 -21.719  -0.265  1.00 39.69           C  
ATOM     11  C   GLU A  31      16.629 -21.238  -1.256  1.00 38.63           C  
ATOM     12  O   GLU A  31      16.432 -20.258  -1.981  1.00 38.02           O  
ATOM     13  CB  GLU A  31      14.867 -22.968  -0.784  1.00 35.05           C  
ATOM     14  CG  GLU A  31      13.847 -23.490   0.235  1.00 45.90           C  
ATOM     15  CD  GLU A  31      12.965 -24.624  -0.268  1.00 47.81           C  
ATOM     16  OE1 GLU A  31      12.742 -24.728  -1.490  1.00 50.00           O  
ATOM     17  OE2 GLU A  31      12.473 -25.404   0.576  1.00 51.86           O1-
ATOM     18  N   TYR A  32      17.752 -21.932  -1.276  1.00 33.96           N  
ATOM     19  CA  TYR A  32      18.862 -21.558  -2.158  1.00 32.43           C  
ATOM     20  C   TYR A  32      18.876 -22.470  -3.384  1.00 27.54           C  
ATOM     21  O   TYR A  32      19.167 -23.666  -3.268  1.00 31.25           O  
ATOM     22  CB  TYR A  32      20.185 -21.650  -1.394  1.00 34.50           C  
ATOM     23  CG  TYR A  32      21.353 -21.198  -2.256  1.00 38.29           C  
ATOM     24  CD1 TYR A  32      21.172 -20.234  -3.219  1.00 38.20           C  
ATOM     25  CD2 TYR A  32      22.618 -21.782  -2.121  1.00 45.63           C  
ATOM     26  CE1 TYR A  32      22.208 -19.805  -4.021  1.00 38.48           C  
ATOM     27  CE2 TYR A  32      23.673 -21.375  -2.932  1.00 47.40           C  
ATOM     28  CZ  TYR A  32      23.460 -20.367  -3.871  1.00 39.91           C  
ATOM     29  OH  TYR A  32      24.495 -19.934  -4.700  1.00 44.55           O  
ATOM     30  N   ASP A  33      18.547 -21.906  -4.547  1.00 27.99           N  
ATOM     31  CA  ASP A  33      18.501 -22.600  -5.828  1.00 33.59           C  
ATOM     32  C   ASP A  33      19.536 -21.881  -6.689  1.00 27.38           C  
ATOM     33  O   ASP A  33      19.201 -20.901  -7.366  1.00 25.61           O  
ATOM     34  CB  ASP A  33      17.096 -22.528  -6.441  1.00 32.37           C  
ATOM     35  CG  ASP A  33      16.956 -23.367  -7.719  1.00 41.66           C  
ATOM     36  OD1 ASP A  33      17.891 -24.145  -8.010  1.00 38.49           O  
ATOM     37  OD2 ASP A  33      15.908 -23.259  -8.411  1.00 38.24           O1-
ATOM     38  N   PRO A  34      20.818 -22.268  -6.611  1.00 26.61           N  
ATOM     39  CA  PRO A  34      21.860 -21.508  -7.337  1.00 27.86           C  
ATOM     40  C   PRO A  34      21.549 -21.461  -8.821  1.00 27.40           C  
ATOM     41  O   PRO A  34      21.136 -22.456  -9.412  1.00 30.87           O  
ATOM     42  CB  PRO A  34      23.161 -22.283  -7.051  1.00 30.32           C  
ATOM     43  CG  PRO A  34      22.765 -23.592  -6.447  1.00 33.72           C  
ATOM     44  CD  PRO A  34      21.372 -23.389  -5.836  1.00 33.65           C  
ATOM     45  N   THR A  35      21.748 -20.287  -9.415  1.00 23.44           N1+
ATOM     46  CA  THR A  35      21.320 -20.036 -10.805  1.00 21.25           C  
ATOM     47  C   THR A  35      22.354 -20.532 -11.808  1.00 28.44           C  
ATOM     48  O   THR A  35      23.569 -20.441 -11.570  1.00 23.25           O  
ATOM     49  CB  THR A  35      21.105 -18.547 -10.982  1.00 19.86           C  
ATOM     50  OG1 THR A  35      20.095 -18.150 -10.040  1.00 21.78           O  
ATOM     51  CG2 THR A  35      20.632 -18.159 -12.432  1.00 22.55           C  
ATOM     52  N   ILE A  36      21.863 -21.093 -12.914  1.00 22.23           N  
ATOM     53  CA  ILE A  36      22.705 -21.315 -14.093  1.00 22.54           C  
ATOM     54  C   ILE A  36      22.540 -20.053 -14.929  1.00 25.61           C  
ATOM     55  O   ILE A  36      23.463 -19.234 -15.071  1.00 24.52           O  
ATOM     56  CB  ILE A  36      22.292 -22.564 -14.899  1.00 23.20           C  
ATOM     57  CG1 ILE A  36      22.232 -23.825 -14.043  1.00 25.92           C  
ATOM     58  CG2 ILE A  36      23.233 -22.814 -16.130  1.00 23.76           C  
ATOM     59  CD1 ILE A  36      23.534 -24.332 -13.457  1.00 26.39           C  
ATOM     60  N   GLU A  37      21.356 -19.889 -15.502  1.00 20.32           N  
ATOM     61  CA  GLU A  37      21.029 -18.619 -16.141  1.00 22.54           C  
ATOM     62  C   GLU A  37      19.517 -18.613 -16.356  1.00 23.03           C  
ATOM     63  O   GLU A  37      18.975 -19.629 -16.788  1.00 28.28           O  
ATOM     64  CB  GLU A  37      21.755 -18.491 -17.482  1.00 25.18           C  
ATOM     65  CG  GLU A  37      21.662 -17.099 -18.060  1.00 25.47           C  
ATOM     66  CD  GLU A  37      22.290 -17.057 -19.419  1.00 42.62           C  
ATOM     67  OE1 GLU A  37      21.584 -17.434 -20.361  1.00 41.81           O  
ATOM     68  OE2 GLU A  37      23.483 -16.719 -19.515  1.00 51.13           O1-
ATOM     69  N   ASP A  38      18.837 -17.533 -16.003  1.00 21.12           N1+
ATOM     70  CA  ASP A  38      17.398 -17.474 -16.266  1.00 22.38           C  
ATOM     71  C   ASP A  38      17.025 -16.114 -16.825  1.00 27.35           C  
ATOM     72  O   ASP A  38      17.645 -15.093 -16.517  1.00 24.16           O  
ATOM     73  CB  ASP A  38      16.556 -17.740 -14.990  1.00 20.76           C  
ATOM     74  CG  ASP A  38      16.698 -19.154 -14.487  1.00 26.21           C  
ATOM     75  OD1 ASP A  38      16.106 -20.100 -15.068  1.00 29.61           O  
ATOM     76  OD2 ASP A  38      17.435 -19.306 -13.486  1.00 30.66           O1-
ATOM     77  N   THR A  58      21.792 -13.839 -13.533  1.00 17.83           N  
ATOM     78  CA  THR A  58      23.037 -14.527 -13.904  1.00 21.76           C  
ATOM     79  C   THR A  58      23.588 -15.330 -12.733  1.00 23.14           C  
ATOM     80  O   THR A  58      23.161 -15.150 -11.594  1.00 24.73           O  
ATOM     81  CB  THR A  58      24.137 -13.558 -14.354  1.00 24.53           C  
ATOM     82  OG1 THR A  58      24.476 -12.697 -13.236  1.00 23.78           O  
ATOM     83  CG2 THR A  58      23.593 -12.701 -15.486  1.00 22.87           C  
ATOM     84  N   ALA A  59      24.500 -16.244 -13.048  1.00 19.79           N  
ATOM     85  CA  ALA A  59      25.171 -17.044 -12.015  1.00 23.52           C  
ATOM     86  C   ALA A  59      26.187 -16.236 -11.225  1.00 26.34           C  
ATOM     87  O   ALA A  59      26.979 -15.484 -11.783  1.00 26.94           O  
ATOM     88  CB  ALA A  59      25.878 -18.252 -12.616  1.00 25.79           C  
ATOM     89  N   GLY A  60      26.204 -16.451  -9.911  1.00 24.98           N  
ATOM     90  CA  GLY A  60      27.263 -15.901  -9.095  1.00 31.77           C  
ATOM     91  C   GLY A  60      28.515 -16.748  -8.967  1.00 31.44           C  
ATOM     92  O   GLY A  60      29.408 -16.368  -8.205  1.00 35.85           O  
ATOM     93  N   GLN A  61      28.646 -17.872  -9.681  1.00 31.26           N  
ATOM     94  CA  GLN A  61      29.825 -18.727  -9.501  1.00 35.34           C  
ATOM     95  C   GLN A  61      31.101 -18.038 -10.010  1.00 43.54           C  
ATOM     96  O   GLN A  61      31.219 -17.746 -11.200  1.00 38.79           O  
ATOM     97  CB  GLN A  61      29.632 -20.067 -10.222  1.00 39.41           C  
ATOM     98  CG  GLN A  61      28.350 -20.846  -9.864  1.00 33.81           C  
ATOM     99  CD  GLN A  61      28.267 -21.182  -8.359  1.00 42.17           C  
ATOM    100  OE1 GLN A  61      29.199 -21.739  -7.778  1.00 41.31           O  
ATOM    101  NE2 GLN A  61      27.151 -20.815  -7.734  1.00 41.87           N  
ATOM    102  N   GLU A  63      33.824 -19.436 -10.551  1.00 38.24           N  
ATOM    103  CA  GLU A  63      34.484 -20.376 -11.449  1.00 41.01           C  
ATOM    104  C   GLU A  63      34.282 -20.022 -12.915  1.00 35.20           C  
ATOM    105  O   GLU A  63      35.174 -20.282 -13.740  1.00 38.39           O  
ATOM    106  CB  GLU A  63      33.969 -21.797 -11.196  1.00 41.39           C  
ATOM    107  CG  GLU A  63      34.403 -22.816 -12.271  1.00 41.18           C  
ATOM    108  CD  GLU A  63      35.855 -23.261 -12.137  1.00 48.98           C  
ATOM    109  OE1 GLU A  63      36.353 -23.271 -10.994  1.00 56.88           O  
ATOM    110  OE2 GLU A  63      36.494 -23.632 -13.159  1.00 52.15           O1-
ATOM    111  N   TYR A  64      33.138 -19.429 -13.254  1.00 34.95           N  
ATOM    112  CA  TYR A  64      32.773 -19.136 -14.645  1.00 36.20           C  
ATOM    113  C   TYR A  64      32.846 -17.640 -14.943  1.00 38.83           C  
ATOM    114  O   TYR A  64      32.139 -17.138 -15.823  1.00 31.64           O  
ATOM    115  CB  TYR A  64      31.380 -19.710 -14.959  1.00 34.18           C  
ATOM    116  CG  TYR A  64      31.283 -21.165 -14.568  1.00 36.59           C  
ATOM    117  CD1 TYR A  64      32.012 -22.101 -15.250  1.00 31.38           C  
ATOM    118  CD2 TYR A  64      30.469 -21.596 -13.501  1.00 32.30           C  
ATOM    119  CE1 TYR A  64      32.016 -23.444 -14.899  1.00 33.38           C  
ATOM    120  CE2 TYR A  64      30.457 -22.946 -13.133  1.00 29.09           C  
ATOM    121  CZ  TYR A  64      31.181 -23.861 -13.843  1.00 31.16           C  
ATOM    122  OH  TYR A  64      31.250 -25.212 -13.560  1.00 33.42           O  
ATOM    123  N   SER A  65      33.718 -16.913 -14.215  1.00 38.52           N  
ATOM    124  CA  SER A  65      33.872 -15.470 -14.423  1.00 41.07           C  
ATOM    125  C   SER A  65      34.241 -15.140 -15.864  1.00 33.77           C  
ATOM    126  O   SER A  65      33.871 -14.078 -16.375  1.00 40.36           O  
ATOM    127  CB  SER A  65      34.953 -14.919 -13.480  1.00 38.73           C  
ATOM    128  OG  SER A  65      36.116 -15.706 -13.535  1.00 41.95           O  
ATOM    129  N   ALA A  66      34.915 -16.059 -16.533  1.00 36.04           N  
ATOM    130  CA  ALA A  66      35.378 -15.832 -17.900  1.00 41.85           C  
ATOM    131  C   ALA A  66      34.241 -15.844 -18.913  1.00 45.62           C  
ATOM    132  O   ALA A  66      34.433 -15.430 -20.059  1.00 52.92           O  
ATOM    133  CB  ALA A  66      36.418 -16.885 -18.281  1.00 47.40           C  
ATOM    134  N   MET A  67      33.082 -16.353 -18.548  1.00 36.94           N  
ATOM    135  CA  MET A  67      31.977 -16.505 -19.477  1.00 40.67           C  
ATOM    136  C   MET A  67      30.942 -15.401 -19.351  1.00 40.98           C  
ATOM    137  O   MET A  67      29.859 -15.505 -19.942  1.00 38.32           O  
ATOM    138  CB  MET A  67      31.328 -17.866 -19.265  1.00 41.03           C  
ATOM    139  CG  MET A  67      32.345 -18.965 -19.510  1.00 47.85           C  
ATOM    140  SD  MET A  67      31.614 -20.553 -19.176  1.00 46.91           S  
ATOM    141  CE  MET A  67      30.200 -20.437 -20.310  1.00 38.99           C  
ATOM    142  N   ARG A  68      31.235 -14.357 -18.573  1.00 36.22           N  
ATOM    143  CA  ARG A  68      30.286 -13.264 -18.427  1.00 38.65           C  
ATOM    144  C   ARG A  68      30.310 -12.311 -19.609  1.00 34.36           C  
ATOM    145  O   ARG A  68      29.347 -11.542 -19.797  1.00 31.79           O  
ATOM    146  CB  ARG A  68      30.572 -12.482 -17.151  1.00 31.59           C  
ATOM    147  CG  ARG A  68      30.490 -13.344 -15.922  1.00 36.28           C  
ATOM    148  CD  ARG A  68      30.760 -12.550 -14.677  1.00 34.04           C  
ATOM    149  NE  ARG A  68      31.091 -13.423 -13.555  1.00 40.26           N  
ATOM    150  CZ  ARG A  68      31.986 -13.155 -12.612  1.00 40.60           C  
ATOM    151  NH1 ARG A  68      32.825 -12.121 -12.703  1.00 40.26           N  
ATOM    152  NH2 ARG A  68      32.045 -13.943 -11.536  1.00 44.34           N1+
ATOM    153  N   TYR A  71      27.105 -12.011 -22.092  1.00 34.41           N  
ATOM    154  CA  TYR A  71      25.879 -11.348 -21.653  1.00 28.61           C  
ATOM    155  C   TYR A  71      26.137  -9.895 -21.256  1.00 25.39           C  
ATOM    156  O   TYR A  71      25.222  -9.069 -21.332  1.00 27.97           O  
ATOM    157  CB  TYR A  71      25.180 -12.150 -20.542  1.00 26.00           C  
ATOM    158  CG  TYR A  71      25.826 -12.192 -19.171  1.00 28.41           C  
ATOM    159  CD1 TYR A  71      25.999 -11.029 -18.422  1.00 26.71           C  
ATOM    160  CD2 TYR A  71      26.218 -13.411 -18.609  1.00 32.32           C  
ATOM    161  CE1 TYR A  71      26.556 -11.066 -17.118  1.00 30.15           C  
ATOM    162  CE2 TYR A  71      26.761 -13.463 -17.305  1.00 31.65           C  
ATOM    163  CZ  TYR A  71      26.925 -12.286 -16.575  1.00 29.74           C  
ATOM    164  OH  TYR A  71      27.451 -12.325 -15.281  1.00 32.36           O  
TER     165      TYR A  71
ATOM    166  N   HIS D  54      16.401 -33.143 -12.082  1.00 20.78           N  
ATOM    167  CA  HIS D  54      15.907 -31.778 -12.191  1.00 23.62           C  
ATOM    168  C   HIS D  54      16.717 -30.899 -13.123  1.00 23.48           C  
ATOM    169  O   HIS D  54      16.202 -29.858 -13.584  1.00 25.51           O  
ATOM    170  CB  HIS D  54      15.823 -31.104 -10.832  1.00 25.81           C  
ATOM    171  CG  HIS D  54      17.139 -30.924 -10.141  1.00 25.88           C  
ATOM    172  ND1 HIS D  54      17.784 -31.944  -9.470  1.00 22.99           N  
ATOM    173  CD2 HIS D  54      17.923 -29.830 -10.012  1.00 20.88           C  
ATOM    174  CE1 HIS D  54      18.920 -31.486  -8.963  1.00 22.72           C  
ATOM    175  NE2 HIS D  54      18.994 -30.195  -9.224  1.00 23.14           N  
ATOM    176  N   ARG D  55      17.953 -31.279 -13.416  1.00 22.87           N1+
ATOM    177  CA  ARG D  55      18.809 -30.443 -14.236  1.00 23.55           C  
ATOM    178  C   ARG D  55      19.506 -31.310 -15.268  1.00 22.07           C  
ATOM    179  O   ARG D  55      20.330 -32.160 -14.921  1.00 23.40           O  
ATOM    180  CB  ARG D  55      19.820 -29.717 -13.357  1.00 23.73           C  
ATOM    181  CG  ARG D  55      20.783 -28.870 -14.127  1.00 22.69           C  
ATOM    182  CD  ARG D  55      21.753 -28.166 -13.175  1.00 20.89           C  
ATOM    183  NE  ARG D  55      21.022 -27.113 -12.482  1.00 25.58           N  
ATOM    184  CZ  ARG D  55      21.399 -26.668 -11.302  1.00 27.51           C  
ATOM    185  NH1 ARG D  55      22.470 -27.170 -10.697  1.00 26.07           N  
ATOM    186  NH2 ARG D  55      20.708 -25.689 -10.726  1.00 27.90           N1+
ATOM    187  N   ILE D  56      19.217 -31.088 -16.556  1.00 19.09           N  
ATOM    188  CA  ILE D  56      19.877 -31.846 -17.603  1.00 18.60           C  
ATOM    189  C   ILE D  56      20.417 -30.868 -18.622  1.00 21.97           C  
ATOM    190  O   ILE D  56      19.648 -30.117 -19.215  1.00 21.24           O  
ATOM    191  CB  ILE D  56      18.907 -32.820 -18.297  1.00 22.61           C  
ATOM    192  CG1 ILE D  56      18.390 -33.820 -17.283  1.00 24.58           C  
ATOM    193  CG2 ILE D  56      19.594 -33.516 -19.519  1.00 22.13           C  
ATOM    194  CD1 ILE D  56      17.412 -34.791 -17.813  1.00 26.63           C  
ATOM    195  N   ILE D  57      21.732 -30.860 -18.810  1.00 21.57           N  
ATOM    196  CA  ILE D  57      22.325 -29.908 -19.742  1.00 21.77           C  
ATOM    197  C   ILE D  57      23.080 -30.713 -20.780  1.00 21.35           C  
ATOM    198  O   ILE D  57      24.142 -31.294 -20.492  1.00 21.46           O  
ATOM    199  CB  ILE D  57      23.240 -28.903 -19.042  1.00 22.99           C  
ATOM    200  CG1 ILE D  57      22.409 -28.172 -17.982  1.00 23.13           C  
ATOM    201  CG2 ILE D  57      23.777 -27.913 -20.104  1.00 24.35           C  
ATOM    202  CD1 ILE D  57      23.236 -27.149 -17.147  1.00 22.29           C  
ATOM    203  N   PRO D  58      22.571 -30.743 -21.999  1.00 22.36           N  
ATOM    204  CA  PRO D  58      23.220 -31.540 -23.041  1.00 23.84           C  
ATOM    205  C   PRO D  58      24.647 -31.087 -23.276  1.00 22.58           C  
ATOM    206  O   PRO D  58      24.947 -29.892 -23.363  1.00 23.59           O  
ATOM    207  CB  PRO D  58      22.338 -31.284 -24.281  1.00 22.47           C  
ATOM    208  CG  PRO D  58      20.954 -30.922 -23.694  1.00 25.39           C  
ATOM    209  CD  PRO D  58      21.312 -30.109 -22.463  1.00 25.16           C  
ATOM    210  N   GLY D  59      25.540 -32.070 -23.420  1.00 24.08           N  
ATOM    211  CA  GLY D  59      26.926 -31.786 -23.578  1.00 23.91           C  
ATOM    212  C   GLY D  59      27.715 -31.787 -22.273  1.00 24.90           C  
ATOM    213  O   GLY D  59      28.945 -31.709 -22.319  1.00 23.48           O  
ATOM    214  N   PHE D  60      27.026 -31.883 -21.123  1.00 21.44           N  
ATOM    215  CA  PHE D  60      27.677 -31.727 -19.834  1.00 21.18           C  
ATOM    216  C   PHE D  60      27.261 -32.802 -18.855  1.00 21.73           C  
ATOM    217  O   PHE D  60      28.100 -33.652 -18.507  1.00 21.00           O  
ATOM    218  CB  PHE D  60      27.453 -30.325 -19.225  1.00 20.58           C  
ATOM    219  CG  PHE D  60      28.152 -29.232 -20.036  1.00 22.70           C  
ATOM    220  CD1 PHE D  60      29.480 -28.955 -19.864  1.00 20.95           C  
ATOM    221  CD2 PHE D  60      27.449 -28.562 -21.010  1.00 22.46           C  
ATOM    222  CE1 PHE D  60      30.153 -27.967 -20.665  1.00 25.83           C  
ATOM    223  CE2 PHE D  60      28.099 -27.597 -21.834  1.00 27.37           C  
ATOM    224  CZ  PHE D  60      29.426 -27.288 -21.606  1.00 26.34           C  
ATOM    225  N   MET D  61      26.010 -32.765 -18.352  1.00 21.50           N  
ATOM    226  CA  MET D  61      25.700 -33.681 -17.266  1.00 19.84           C  
ATOM    227  C   MET D  61      24.195 -33.744 -17.048  1.00 20.80           C  
ATOM    228  O   MET D  61      23.434 -32.882 -17.528  1.00 21.41           O  
ATOM    229  CB  MET D  61      26.414 -33.265 -15.949  1.00 17.82           C  
ATOM    230  CG  MET D  61      25.505 -32.382 -15.112  1.00 29.58           C  
ATOM    231  SD  MET D  61      25.488 -30.688 -15.789  1.00 24.21           S  
ATOM    232  CE  MET D  61      24.043 -30.056 -14.898  1.00 27.84           C  
ATOM    233  N   CYS D  62      23.785 -34.804 -16.338  1.00 17.99           N  
ATOM    234  CA  CYS D  62      22.440 -35.024 -15.819  1.00 20.05           C  
ATOM    235  C   CYS D  62      22.530 -35.003 -14.300  1.00 20.25           C  
ATOM    236  O   CYS D  62      23.298 -35.795 -13.740  1.00 21.34           O  
ATOM    237  CB  CYS D  62      21.924 -36.413 -16.225  1.00 19.04           C  
ATOM    238  SG  CYS D  62      21.675 -36.424 -18.052  1.00 25.85           S  
ATOM    239  N   GLN D  63      21.726 -34.161 -13.641  1.00 18.60           N  
ATOM    240  CA  GLN D  63      21.807 -34.002 -12.186  1.00 17.93           C  
ATOM    241  C   GLN D  63      20.457 -34.311 -11.534  1.00 20.03           C  
ATOM    242  O   GLN D  63      19.392 -33.935 -12.068  1.00 20.98           O  
ATOM    243  CB  GLN D  63      22.240 -32.581 -11.860  1.00 18.96           C  
ATOM    244  CG  GLN D  63      22.447 -32.308 -10.308  1.00 20.73           C  
ATOM    245  CD  GLN D  63      22.931 -30.865 -10.043  1.00 22.29           C  
ATOM    246  OE1 GLN D  63      23.512 -30.223 -10.927  1.00 22.06           O  
ATOM    247  NE2 GLN D  63      22.675 -30.333  -8.827  1.00 20.51           N  
ATOM    248  N   GLY D  64      20.508 -34.957 -10.369  1.00 19.64           N  
ATOM    249  CA  GLY D  64      19.282 -35.376  -9.697  1.00 21.02           C  
ATOM    250  C   GLY D  64      19.564 -35.566  -8.220  1.00 22.67           C  
ATOM    251  O   GLY D  64      20.571 -35.092  -7.701  1.00 22.57           O  
ATOM    252  N   GLY D  65      18.618 -36.201  -7.529  1.00 19.88           N1+
ATOM    253  CA  GLY D  65      18.872 -36.629  -6.156  1.00 21.62           C  
ATOM    254  C   GLY D  65      18.201 -35.820  -5.068  1.00 24.29           C  
ATOM    255  O   GLY D  65      18.471 -36.090  -3.888  1.00 24.91           O  
ATOM    256  N   ASP D  66      17.379 -34.828  -5.402  1.00 24.00           N  
ATOM    257  CA  ASP D  66      16.669 -34.057  -4.373  1.00 23.51           C  
ATOM    258  C   ASP D  66      15.390 -34.804  -4.046  1.00 27.62           C  
ATOM    259  O   ASP D  66      14.353 -34.591  -4.664  1.00 26.08           O  
ATOM    260  CB  ASP D  66      16.351 -32.641  -4.835  1.00 26.78           C  
ATOM    261  CG  ASP D  66      15.597 -31.836  -3.769  1.00 28.52           C  
ATOM    262  OD1 ASP D  66      15.334 -32.384  -2.667  1.00 28.76           O  
ATOM    263  OD2 ASP D  66      15.276 -30.661  -4.007  1.00 28.30           O1-
ATOM    264  N   ARG D  69      12.961 -32.063  -1.105  1.00 33.64           N  
ATOM    265  CA  ARG D  69      12.144 -30.958  -1.566  1.00 33.43           C  
ATOM    266  C   ARG D  69      11.671 -31.088  -2.998  1.00 32.79           C  
ATOM    267  O   ARG D  69      10.730 -30.380  -3.365  1.00 36.85           O  
ATOM    268  CB  ARG D  69      12.923 -29.644  -1.437  1.00 33.57           C  
ATOM    269  CG  ARG D  69      13.298 -29.356  -0.002  1.00 37.02           C  
ATOM    270  CD  ARG D  69      14.207 -28.186   0.020  1.00 40.51           C  
ATOM    271  NE  ARG D  69      14.679 -27.854   1.353  1.00 44.85           N  
ATOM    272  CZ  ARG D  69      15.668 -27.000   1.565  1.00 49.91           C  
ATOM    273  NH1 ARG D  69      16.283 -26.389   0.549  1.00 36.00           N  
ATOM    274  NH2 ARG D  69      16.035 -26.734   2.818  1.00 56.07           N1+
ATOM    275  N   ASN D  71      12.791 -29.991  -5.726  1.00 29.43           N  
ATOM    276  CA  ASN D  71      12.912 -28.790  -6.533  1.00 32.25           C  
ATOM    277  C   ASN D  71      14.357 -28.446  -6.855  1.00 31.58           C  
ATOM    278  O   ASN D  71      14.619 -27.322  -7.306  1.00 36.05           O  
ATOM    279  CB  ASN D  71      12.212 -27.604  -5.860  1.00 31.90           C  
ATOM    280  CG  ASN D  71      12.816 -27.224  -4.532  1.00 32.06           C  
ATOM    281  OD1 ASN D  71      13.927 -27.643  -4.181  1.00 31.42           O  
ATOM    282  ND2 ASN D  71      12.086 -26.388  -3.783  1.00 36.48           N  
ATOM    283  N   GLY D  72      15.310 -29.360  -6.609  1.00 27.84           N  
ATOM    284  CA  GLY D  72      16.688 -29.094  -6.903  1.00 26.38           C  
ATOM    285  C   GLY D  72      17.442 -28.419  -5.800  1.00 30.81           C  
ATOM    286  O   GLY D  72      18.645 -28.232  -5.938  1.00 26.20           O  
ATOM    287  N   THR D  73      16.785 -28.046  -4.700  1.00 30.07           N  
ATOM    288  CA  THR D  73      17.517 -27.368  -3.648  1.00 28.72           C  
ATOM    289  C   THR D  73      17.820 -28.269  -2.450  1.00 31.17           C  
ATOM    290  O   THR D  73      18.575 -27.843  -1.565  1.00 30.81           O  
ATOM    291  CB  THR D  73      16.759 -26.131  -3.130  1.00 33.27           C  
ATOM    292  OG1 THR D  73      15.623 -26.537  -2.353  1.00 30.42           O  
ATOM    293  CG2 THR D  73      16.300 -25.186  -4.269  1.00 29.76           C  
ATOM    294  N   GLY D  74      17.261 -29.489  -2.404  1.00 29.27           N  
ATOM    295  CA  GLY D  74      17.298 -30.267  -1.160  1.00 30.09           C  
ATOM    296  C   GLY D  74      18.124 -31.537  -1.283  1.00 33.43           C  
ATOM    297  O   GLY D  74      19.122 -31.598  -2.034  1.00 26.58           O  
ATOM    298  N   GLY D  75      17.685 -32.571  -0.568  1.00 26.08           N  
ATOM    299  CA  GLY D  75      18.452 -33.783  -0.400  1.00 28.87           C  
ATOM    300  C   GLY D  75      19.145 -33.816   0.962  1.00 28.60           C  
ATOM    301  O   GLY D  75      19.374 -32.797   1.601  1.00 29.65           O  
ATOM    302  N   GLU D  81      22.436 -33.849   7.392  1.00 30.90           N  
ATOM    303  CA  GLU D  81      22.029 -33.123   6.186  1.00 32.66           C  
ATOM    304  C   GLU D  81      23.173 -33.075   5.168  1.00 34.24           C  
ATOM    305  O   GLU D  81      22.985 -33.331   3.959  1.00 32.89           O  
ATOM    306  CB  GLU D  81      21.571 -31.717   6.529  1.00 33.52           C  
ATOM    307  CG  GLU D  81      21.130 -30.999   5.238  1.00 39.45           C  
ATOM    308  CD  GLU D  81      20.710 -29.540   5.429  1.00 51.28           C  
ATOM    309  OE1 GLU D  81      21.412 -28.780   6.153  1.00 51.36           O  
ATOM    310  OE2 GLU D  81      19.662 -29.172   4.848  1.00 48.33           O1-
ATOM    311  N   LYS D  82      24.371 -32.772   5.627  1.00 25.94           N  
ATOM    312  CA  LYS D  82      25.532 -32.787   4.741  1.00 28.76           C  
ATOM    313  C   LYS D  82      26.716 -33.539   5.354  1.00 29.52           C  
ATOM    314  O   LYS D  82      26.760 -33.814   6.564  1.00 29.92           O  
ATOM    315  CB  LYS D  82      25.945 -31.355   4.388  1.00 37.08           C  
ATOM    316  CG  LYS D  82      24.858 -30.581   3.590  1.00 37.89           C  
ATOM    317  CD  LYS D  82      25.135 -29.069   3.508  1.00 42.19           C  
ATOM    318  CE  LYS D  82      25.048 -28.425   4.921  1.00 52.21           C  
ATOM    319  NZ  LYS D  82      25.044 -26.907   4.968  1.00 56.05           N1+
ATOM    320  N   HIS D  92      36.989 -36.239 -13.129  1.00 26.62           N  
ATOM    321  CA  HIS D  92      35.857 -36.235 -14.068  1.00 22.77           C  
ATOM    322  C   HIS D  92      36.417 -36.438 -15.470  1.00 27.22           C  
ATOM    323  O   HIS D  92      36.614 -35.482 -16.225  1.00 29.08           O  
ATOM    324  CB  HIS D  92      35.101 -34.920 -13.983  1.00 23.40           C  
ATOM    325  CG  HIS D  92      34.564 -34.640 -12.607  1.00 21.55           C  
ATOM    326  ND1 HIS D  92      35.326 -34.035 -11.634  1.00 21.35           N  
ATOM    327  CD2 HIS D  92      33.344 -34.876 -12.053  1.00 23.79           C  
ATOM    328  CE1 HIS D  92      34.614 -33.949 -10.511  1.00 23.26           C  
ATOM    329  NE2 HIS D  92      33.397 -34.422 -10.748  1.00 21.15           N  
ATOM    330  N   SER D  99      29.276 -38.356  -9.713  1.00 20.88           N  
ATOM    331  CA  SER D  99      30.030 -37.445  -8.840  1.00 21.60           C  
ATOM    332  C   SER D  99      29.021 -36.677  -7.990  1.00 20.60           C  
ATOM    333  O   SER D  99      27.864 -36.594  -8.349  1.00 19.14           O  
ATOM    334  CB  SER D  99      30.924 -36.519  -9.697  1.00 21.31           C  
ATOM    335  OG  SER D  99      31.593 -35.566  -8.892  1.00 20.77           O  
ATOM    336  N   MET D 100      29.440 -36.195  -6.809  1.00 17.71           N  
ATOM    337  CA  MET D 100      28.504 -35.517  -5.907  1.00 18.19           C  
ATOM    338  C   MET D 100      28.296 -34.053  -6.275  1.00 20.00           C  
ATOM    339  O   MET D 100      29.270 -33.304  -6.494  1.00 22.17           O  
ATOM    340  CB  MET D 100      29.017 -35.576  -4.445  1.00 19.98           C  
ATOM    341  CG  MET D 100      29.015 -36.966  -3.899  1.00 23.96           C  
ATOM    342  SD  MET D 100      27.364 -37.692  -3.824  1.00 22.94           S  
ATOM    343  CE  MET D 100      26.484 -36.739  -2.556  1.00 23.05           C  
ATOM    344  N   ALA D 101      27.025 -33.635  -6.301  1.00 18.14           N  
ATOM    345  CA  ALA D 101      26.744 -32.205  -6.341  1.00 19.63           C  
ATOM    346  C   ALA D 101      27.036 -31.558  -4.983  1.00 20.05           C  
ATOM    347  O   ALA D 101      27.057 -32.229  -3.944  1.00 24.94           O  
ATOM    348  CB  ALA D 101      25.257 -31.980  -6.717  1.00 21.25           C  
ATOM    349  N   ASN D 102      27.264 -30.245  -4.979  1.00 21.75           N  
ATOM    350  CA  ASN D 102      27.441 -29.569  -3.690  1.00 23.55           C  
ATOM    351  C   ASN D 102      27.217 -28.064  -3.834  1.00 24.76           C  
ATOM    352  O   ASN D 102      27.029 -27.533  -4.929  1.00 24.81           O  
ATOM    353  CB  ASN D 102      28.830 -29.875  -3.085  1.00 23.88           C  
ATOM    354  CG  ASN D 102      29.972 -29.349  -3.929  1.00 24.18           C  
ATOM    355  OD1 ASN D 102      30.028 -28.157  -4.227  1.00 25.31           O  
ATOM    356  ND2 ASN D 102      30.924 -30.219  -4.264  1.00 22.33           N  
ATOM    357  N   ALA D 103      27.257 -27.375  -2.697  1.00 23.99           N  
ATOM    358  CA  ALA D 103      27.165 -25.923  -2.634  1.00 27.45           C  
ATOM    359  C   ALA D 103      28.421 -25.332  -2.012  1.00 25.64           C  
ATOM    360  O   ALA D 103      28.358 -24.367  -1.244  1.00 31.22           O  
ATOM    361  CB  ALA D 103      25.948 -25.469  -1.823  1.00 34.59           C  
ATOM    362  N   GLY D 104      29.577 -25.876  -2.376  1.00 26.84           N  
ATOM    363  CA  GLY D 104      30.833 -25.464  -1.802  1.00 31.98           C  
ATOM    364  C   GLY D 104      31.489 -26.591  -1.024  1.00 27.39           C  
ATOM    365  O   GLY D 104      30.990 -27.710  -0.954  1.00 25.82           O  
ATOM    366  N   THR D 107      29.847 -29.946   1.598  1.00 26.85           N  
ATOM    367  CA  THR D 107      28.391 -29.790   1.633  1.00 29.63           C  
ATOM    368  C   THR D 107      27.709 -30.902   0.835  1.00 28.19           C  
ATOM    369  O   THR D 107      26.687 -30.672   0.196  1.00 31.67           O  
ATOM    370  CB  THR D 107      27.944 -28.413   1.109  1.00 24.62           C  
ATOM    371  OG1 THR D 107      28.418 -28.233  -0.227  1.00 26.44           O  
ATOM    372  CG2 THR D 107      28.369 -27.201   2.040  1.00 25.59           C  
ATOM    373  N   ASN D 108      28.248 -32.110   0.861  1.00 24.99           N  
ATOM    374  CA  ASN D 108      27.638 -33.216   0.137  1.00 21.99           C  
ATOM    375  C   ASN D 108      26.365 -33.666   0.830  1.00 29.16           C  
ATOM    376  O   ASN D 108      26.360 -33.818   2.048  1.00 28.31           O  
ATOM    377  CB  ASN D 108      28.594 -34.382   0.085  1.00 25.24           C  
ATOM    378  CG  ASN D 108      29.888 -34.050  -0.618  1.00 28.30           C  
ATOM    379  OD1 ASN D 108      29.897 -33.939  -1.826  1.00 25.25           O  
ATOM    380  ND2 ASN D 108      30.991 -33.874   0.141  1.00 22.10           N  
ATOM    381  N   GLY D 109      25.292 -33.898   0.038  1.00 24.69           N  
ATOM    382  CA  GLY D 109      24.039 -34.378   0.596  1.00 23.53           C  
ATOM    383  C   GLY D 109      23.600 -35.653  -0.070  1.00 26.41           C  
ATOM    384  O   GLY D 109      24.172 -36.727   0.163  1.00 22.67           O  
ATOM    385  N   SER D 110      22.596 -35.539  -0.956  1.00 22.43           N  
ATOM    386  CA  SER D 110      22.216 -36.654  -1.799  1.00 23.10           C  
ATOM    387  C   SER D 110      22.275 -36.313  -3.277  1.00 21.88           C  
ATOM    388  O   SER D 110      22.334 -37.235  -4.097  1.00 20.69           O  
ATOM    389  CB  SER D 110      20.797 -37.139  -1.464  1.00 23.01           C  
ATOM    390  OG  SER D 110      19.903 -36.072  -1.574  1.00 23.84           O  
ATOM    391  N   GLN D 111      22.313 -35.038  -3.631  1.00 21.79           N  
ATOM    392  CA  GLN D 111      22.335 -34.701  -5.064  1.00 19.24           C  
ATOM    393  C   GLN D 111      23.649 -35.144  -5.703  1.00 20.37           C  
ATOM    394  O   GLN D 111      24.733 -35.070  -5.102  1.00 20.95           O  
ATOM    395  CB  GLN D 111      22.121 -33.215  -5.278  1.00 18.36           C  
ATOM    396  CG  GLN D 111      20.638 -32.716  -4.983  1.00 20.29           C  
ATOM    397  CD  GLN D 111      20.436 -31.287  -5.499  1.00 23.24           C  
ATOM    398  OE1 GLN D 111      20.843 -30.966  -6.646  1.00 23.26           O  
ATOM    399  NE2 GLN D 111      19.805 -30.429  -4.692  1.00 23.03           N  
ATOM    400  N   PHE D 112      23.536 -35.564  -6.956  1.00 20.61           N  
ATOM    401  CA  PHE D 112      24.637 -36.168  -7.677  1.00 20.44           C  
ATOM    402  C   PHE D 112      24.488 -35.776  -9.138  1.00 19.27           C  
ATOM    403  O   PHE D 112      23.439 -35.298  -9.569  1.00 18.78           O  
ATOM    404  CB  PHE D 112      24.608 -37.689  -7.574  1.00 19.84           C  
ATOM    405  CG  PHE D 112      23.344 -38.290  -8.190  1.00 20.55           C  
ATOM    406  CD1 PHE D 112      22.185 -38.373  -7.428  1.00 20.73           C  
ATOM    407  CD2 PHE D 112      23.292 -38.645  -9.539  1.00 25.38           C  
ATOM    408  CE1 PHE D 112      20.972 -38.882  -7.956  1.00 21.59           C  
ATOM    409  CE2 PHE D 112      22.100 -39.118 -10.085  1.00 25.71           C  
ATOM    410  CZ  PHE D 112      20.941 -39.213  -9.329  1.00 22.34           C  
ATOM    411  N   PHE D 113      25.531 -36.050  -9.896  1.00 18.26           N  
ATOM    412  CA  PHE D 113      25.406 -35.834 -11.331  1.00 18.52           C  
ATOM    413  C   PHE D 113      26.170 -36.915 -12.062  1.00 20.84           C  
ATOM    414  O   PHE D 113      27.106 -37.506 -11.532  1.00 21.21           O  
ATOM    415  CB  PHE D 113      25.848 -34.421 -11.719  1.00 17.84           C  
ATOM    416  CG  PHE D 113      27.301 -34.112 -11.467  1.00 18.31           C  
ATOM    417  CD1 PHE D 113      27.766 -33.839 -10.189  1.00 21.81           C  
ATOM    418  CD2 PHE D 113      28.204 -34.065 -12.503  1.00 19.25           C  
ATOM    419  CE1 PHE D 113      29.118 -33.494  -9.967  1.00 25.02           C  
ATOM    420  CE2 PHE D 113      29.548 -33.722 -12.332  1.00 19.48           C  
ATOM    421  CZ  PHE D 113      30.024 -33.458 -11.054  1.00 19.26           C  
ATOM    422  N   ILE D 114      25.708 -37.194 -13.280  1.00 18.17           N  
ATOM    423  CA  ILE D 114      26.327 -38.142 -14.202  1.00 19.41           C  
ATOM    424  C   ILE D 114      26.866 -37.322 -15.358  1.00 22.46           C  
ATOM    425  O   ILE D 114      26.081 -36.657 -16.049  1.00 19.83           O  
ATOM    426  CB  ILE D 114      25.300 -39.177 -14.696  1.00 19.64           C  
ATOM    427  CG1 ILE D 114      24.540 -39.830 -13.521  1.00 24.97           C  
ATOM    428  CG2 ILE D 114      25.974 -40.263 -15.560  1.00 21.23           C  
ATOM    429  CD1 ILE D 114      23.225 -40.554 -13.941  1.00 20.75           C  
ATOM    430  N   CYS D 115      28.184 -37.376 -15.583  1.00 21.48           N  
ATOM    431  CA  CYS D 115      28.780 -36.653 -16.700  1.00 21.56           C  
ATOM    432  C   CYS D 115      28.354 -37.275 -18.029  1.00 22.78           C  
ATOM    433  O   CYS D 115      28.264 -38.499 -18.167  1.00 22.03           O  
ATOM    434  CB  CYS D 115      30.282 -36.711 -16.666  1.00 19.76           C  
ATOM    435  SG  CYS D 115      30.909 -35.921 -15.118  1.00 24.18           S  
ATOM    436  N   THR D 116      28.123 -36.428 -19.021  1.00 20.81           N  
ATOM    437  CA  THR D 116      27.992 -36.945 -20.387  1.00 22.59           C  
ATOM    438  C   THR D 116      29.125 -36.471 -21.268  1.00 23.38           C  
ATOM    439  O   THR D 116      29.075 -36.655 -22.500  1.00 25.84           O  
ATOM    440  CB  THR D 116      26.653 -36.531 -20.995  1.00 23.31           C  
ATOM    441  OG1 THR D 116      26.565 -35.101 -20.939  1.00 24.07           O  
ATOM    442  CG2 THR D 116      25.481 -37.172 -20.200  1.00 23.15           C  
ATOM    443  N   ALA D 117      30.168 -35.931 -20.664  1.00 21.43           N  
ATOM    444  CA  ALA D 117      31.390 -35.481 -21.337  1.00 24.06           C  
ATOM    445  C   ALA D 117      32.448 -35.358 -20.249  1.00 26.97           C  
ATOM    446  O   ALA D 117      32.117 -35.391 -19.071  1.00 26.44           O  
ATOM    447  CB  ALA D 117      31.187 -34.134 -22.008  1.00 26.37           C  
ATOM    448  N   LYS D 118      33.698 -35.151 -20.645  1.00 25.83           N  
ATOM    449  CA  LYS D 118      34.728 -34.775 -19.670  1.00 25.51           C  
ATOM    450  C   LYS D 118      34.487 -33.370 -19.098  1.00 24.98           C  
ATOM    451  O   LYS D 118      34.290 -32.397 -19.842  1.00 25.11           O  
ATOM    452  CB  LYS D 118      36.104 -34.846 -20.351  1.00 23.48           C  
ATOM    453  CG  LYS D 118      37.291 -34.462 -19.519  1.00 28.28           C  
ATOM    454  CD  LYS D 118      38.573 -34.666 -20.371  1.00 31.65           C  
ATOM    455  CE  LYS D 118      39.801 -34.266 -19.571  1.00 38.13           C  
ATOM    456  NZ  LYS D 118      41.081 -34.299 -20.356  1.00 48.56           N1+
ATOM    457  N   THR D 119      34.510 -33.248 -17.769  1.00 25.47           N  
ATOM    458  CA  THR D 119      34.285 -31.957 -17.101  1.00 25.51           C  
ATOM    459  C   THR D 119      35.419 -31.714 -16.102  1.00 25.80           C  
ATOM    460  O   THR D 119      35.180 -31.635 -14.881  1.00 24.44           O  
ATOM    461  CB  THR D 119      32.914 -31.904 -16.394  1.00 23.51           C  
ATOM    462  OG1 THR D 119      32.858 -32.940 -15.417  1.00 24.53           O  
ATOM    463  CG2 THR D 119      31.800 -32.123 -17.420  1.00 25.18           C  
ATOM    464  N   GLU D 120      36.628 -31.544 -16.635  1.00 27.77           N  
ATOM    465  CA  GLU D 120      37.828 -31.508 -15.783  1.00 27.56           C  
ATOM    466  C   GLU D 120      37.882 -30.311 -14.857  1.00 27.55           C  
ATOM    467  O   GLU D 120      38.555 -30.403 -13.823  1.00 26.35           O  
ATOM    468  CB  GLU D 120      39.084 -31.530 -16.643  1.00 30.66           C  
ATOM    469  CG  GLU D 120      39.410 -30.217 -17.347  1.00 30.87           C  
ATOM    470  CD  GLU D 120      38.528 -29.970 -18.621  1.00 37.11           C  
ATOM    471  OE1 GLU D 120      37.664 -30.833 -19.035  1.00 34.51           O  
ATOM    472  OE2 GLU D 120      38.706 -28.872 -19.225  1.00 47.55           O1-
ATOM    473  N   TRP D 121      37.216 -29.194 -15.183  1.00 26.61           N  
ATOM    474  CA  TRP D 121      37.251 -28.059 -14.270  1.00 26.51           C  
ATOM    475  C   TRP D 121      36.530 -28.342 -12.952  1.00 27.57           C  
ATOM    476  O   TRP D 121      36.670 -27.553 -12.012  1.00 26.63           O  
ATOM    477  CB  TRP D 121      36.652 -26.784 -14.888  1.00 25.76           C  
ATOM    478  CG  TRP D 121      35.202 -26.912 -15.224  1.00 27.10           C  
ATOM    479  CD1 TRP D 121      34.094 -26.532 -14.450  1.00 27.46           C  
ATOM    480  CD2 TRP D 121      34.677 -27.541 -16.385  1.00 25.48           C  
ATOM    481  NE1 TRP D 121      32.940 -26.864 -15.126  1.00 28.62           N  
ATOM    482  CE2 TRP D 121      33.268 -27.487 -16.304  1.00 26.98           C  
ATOM    483  CE3 TRP D 121      35.270 -28.116 -17.524  1.00 27.46           C  
ATOM    484  CZ2 TRP D 121      32.439 -28.010 -17.308  1.00 27.14           C  
ATOM    485  CZ3 TRP D 121      34.442 -28.637 -18.525  1.00 31.36           C  
ATOM    486  CH2 TRP D 121      33.051 -28.562 -18.412  1.00 30.65           C  
ATOM    487  N   LEU D 122      35.767 -29.425 -12.856  1.00 25.33           N  
ATOM    488  CA  LEU D 122      35.152 -29.862 -11.597  1.00 23.98           C  
ATOM    489  C   LEU D 122      36.081 -30.719 -10.727  1.00 23.35           C  
ATOM    490  O   LEU D 122      35.751 -30.988  -9.571  1.00 24.58           O  
ATOM    491  CB  LEU D 122      33.850 -30.638 -11.877  1.00 23.68           C  
ATOM    492  CG  LEU D 122      32.828 -29.843 -12.700  1.00 24.73           C  
ATOM    493  CD1 LEU D 122      31.584 -30.708 -12.946  1.00 21.80           C  
ATOM    494  CD2 LEU D 122      32.465 -28.530 -11.949  1.00 25.03           C  
ATOM    495  N   LYS D 125      36.820 -30.305  -6.869  1.00 25.57           N  
ATOM    496  CA  LYS D 125      35.703 -29.580  -6.276  1.00 26.75           C  
ATOM    497  C   LYS D 125      34.500 -30.451  -5.990  1.00 25.29           C  
ATOM    498  O   LYS D 125      33.741 -30.144  -5.073  1.00 24.89           O  
ATOM    499  CB  LYS D 125      35.277 -28.443  -7.211  1.00 28.30           C  
ATOM    500  CG  LYS D 125      36.318 -27.332  -7.163  1.00 35.00           C  
ATOM    501  CD  LYS D 125      36.493 -26.626  -8.490  1.00 42.70           C  
ATOM    502  CE  LYS D 125      37.582 -25.564  -8.326  1.00 52.79           C  
ATOM    503  NZ  LYS D 125      37.893 -24.945  -9.633  1.00 53.52           N1+
ATOM    504  N   HIS D 126      34.303 -31.508  -6.760  1.00 20.67           N  
ATOM    505  CA  HIS D 126      33.239 -32.472  -6.559  1.00 19.39           C  
ATOM    506  C   HIS D 126      33.879 -33.839  -6.415  1.00 20.71           C  
ATOM    507  O   HIS D 126      34.773 -34.187  -7.186  1.00 22.34           O  
ATOM    508  CB  HIS D 126      32.235 -32.457  -7.778  1.00 19.32           C  
ATOM    509  CG  HIS D 126      31.564 -31.120  -7.978  1.00 20.73           C  
ATOM    510  ND1 HIS D 126      30.298 -30.848  -7.508  1.00 21.33           N  
ATOM    511  CD2 HIS D 126      32.017 -29.966  -8.534  1.00 19.48           C  
ATOM    512  CE1 HIS D 126      30.008 -29.575  -7.731  1.00 21.59           C  
ATOM    513  NE2 HIS D 126      31.039 -29.014  -8.346  1.00 20.27           N  
ATOM    514  N   SER D 147      18.207 -28.875 -21.602  1.00 22.59           N  
ATOM    515  CA  SER D 147      18.295 -27.571 -22.262  1.00 24.64           C  
ATOM    516  C   SER D 147      19.549 -26.875 -21.758  1.00 22.73           C  
ATOM    517  O   SER D 147      20.210 -27.346 -20.828  1.00 23.89           O  
ATOM    518  CB  SER D 147      17.053 -26.695 -21.983  1.00 25.24           C  
ATOM    519  OG  SER D 147      16.969 -26.445 -20.548  1.00 22.52           O  
ATOM    520  N   ARG D 148      19.829 -25.713 -22.357  1.00 25.96           N1+
ATOM    521  CA  ARG D 148      21.000 -24.908 -22.018  1.00 24.35           C  
ATOM    522  C   ARG D 148      21.118 -24.600 -20.516  1.00 24.87           C  
ATOM    523  O   ARG D 148      22.214 -24.709 -19.940  1.00 24.30           O  
ATOM    524  CB  ARG D 148      20.934 -23.608 -22.798  1.00 31.57           C  
ATOM    525  CG  ARG D 148      22.101 -22.687 -22.535  1.00 27.70           C  
ATOM    526  CD  ARG D 148      22.135 -21.554 -23.544  1.00 35.79           C  
ATOM    527  NE  ARG D 148      23.237 -20.645 -23.264  1.00 36.55           N  
ATOM    528  CZ  ARG D 148      23.143 -19.622 -22.436  1.00 34.71           C  
ATOM    529  NH1 ARG D 148      22.023 -19.379 -21.773  1.00 40.79           N  
ATOM    530  NH2 ARG D 148      24.191 -18.821 -22.275  1.00 35.93           N1+
ATOM    531  N   ASN D 149      20.023 -24.169 -19.864  1.00 27.33           N  
ATOM    532  CA  ASN D 149      20.090 -23.878 -18.429  1.00 22.56           C  
ATOM    533  C   ASN D 149      19.663 -25.052 -17.569  1.00 25.18           C  
ATOM    534  O   ASN D 149      19.642 -24.936 -16.335  1.00 25.69           O  
ATOM    535  CB  ASN D 149      19.285 -22.615 -18.046  1.00 28.00           C  
ATOM    536  CG  ASN D 149      17.771 -22.857 -17.927  1.00 30.52           C  
ATOM    537  OD1 ASN D 149      17.256 -23.895 -18.326  1.00 30.50           O  
ATOM    538  ND2 ASN D 149      17.053 -21.853 -17.415  1.00 29.28           N  
ATOM    539  N   GLY D 150      19.389 -26.194 -18.156  1.00 22.16           N  
ATOM    540  CA  GLY D 150      19.146 -27.366 -17.378  1.00 21.26           C  
ATOM    541  C   GLY D 150      17.687 -27.694 -17.163  1.00 25.23           C  
ATOM    542  O   GLY D 150      17.392 -28.829 -16.792  1.00 22.37           O  
TER     543      GLY D 150
END

my 9AX6_ligand.sdf is like this:

9AX6 - prepared
                    3D
 Schrodinger Suite 2023-1.
 58 65  0  0  1  0            999 V2000
   28.3844  -19.9822  -16.9516 C   0  0  0  0  0  0
   25.4875  -23.1282  -10.3767 C   0  0  0  0  0  0
   26.6231  -25.1373   -9.5539 C   0  0  0  0  0  0
   27.0774  -26.3440   -8.7962 C   0  0  0  0  0  0
   25.9002  -27.2877   -8.5200 C   0  0  1  0  0  0
   24.0159  -27.3295   -6.9669 C   0  0  0  0  0  0
   23.6260  -27.3350   -5.5384 C   0  0  1  0  0  0
   22.2136  -26.9332   -5.2349 C   0  0  0  0  0  0
   22.6105  -28.3560   -5.0875 C   0  0  2  0  0  0
   22.7302  -28.9715   -3.7061 C   0  0  0  0  0  0
   26.4011  -28.7121   -8.6592 C   0  0  0  0  0  0
   27.1938  -20.8727  -17.1865 C   0  0  0  0  0  0
   26.9841  -30.5855  -10.2154 C   0  0  0  0  0  0
   28.1612  -30.3901  -11.1775 C   0  0  0  0  0  0
   27.6242  -29.6822  -12.4192 C   0  0  0  0  0  0
   26.9452  -28.3531  -12.0392 C   0  0  1  0  0  0
   26.2446  -27.7417  -13.2238 C   0  0  0  0  0  0
   26.5159  -26.8475  -15.3904 C   0  0  0  0  0  0
   27.6814  -26.7622  -16.3833 C   0  0  0  0  0  0
   27.1205  -26.5878  -17.8111 C   0  0  0  0  0  0
   28.4957  -28.0626  -16.3198 C   0  0  0  0  0  0
   28.6716  -25.6155  -16.0578 C   0  0  0  0  0  0
   27.1061  -22.3303  -15.1609 C   0  0  0  0  0  0
   28.0818  -24.2308  -15.9768 C   0  0  0  0  0  0
   28.0024  -23.2906  -16.9926 C   0  0  0  0  0  0
   28.5591  -23.4314  -18.3454 C   0  0  0  0  0  0
   27.7605  -23.4466  -19.5145 C   0  0  0  0  0  0
   29.6483  -23.8015  -20.8236 C   0  0  0  0  0  0
   30.4866  -23.8279  -19.7158 C   0  0  0  0  0  0
   29.9292  -23.6180  -18.4608 C   0  0  0  0  0  0
   32.7261  -24.1703  -18.6646 C   0  0  0  0  0  0
   33.9399  -25.0305  -18.9399 C   0  0  0  0  0  0
   35.9557  -25.1857  -20.2516 C   0  0  0  0  0  0
   27.5019  -23.6353  -14.8090 C   0  0  0  0  0  0
   33.8114  -24.6412  -21.2564 C   0  0  0  0  0  0
   32.5912  -23.7524  -21.1059 C   0  0  0  0  0  0
   26.2552  -23.2967  -19.4666 C   0  0  2  0  0  0
   25.5955  -24.3169  -20.3667 C   0  0  0  0  0  0
   24.5312  -21.6612  -19.7429 C   0  0  0  0  0  0
   27.2985  -24.0817  -13.4994 C   0  0  0  0  0  0
   26.6978  -23.2245  -12.5771 C   0  0  0  0  0  0
   26.2813  -21.9491  -12.9679 C   0  0  0  0  0  0
   26.4929  -21.4701  -14.2480 C   0  0  0  0  0  0
   26.3970  -23.6762  -11.2180 C   0  0  0  0  0  0
   27.4033  -22.1404  -16.5001 N   0  0  0  0  0  0
   25.2963  -27.0507   -7.2139 N   0  0  0  0  0  0
   26.4230  -29.2568   -9.9167 N   0  0  0  0  0  0
   25.8976  -28.5247  -11.0191 N   0  0  0  0  0  0
   28.3073  -23.6612  -20.7263 N   0  0  0  0  0  0
   31.8745  -23.9780  -19.8437 N   0  0  0  0  0  0
   34.6700  -24.4971  -20.0880 N   0  3  0  0  0  0
   27.0659  -24.7992  -10.7270 N   0  0  0  0  0  0
   23.2086  -27.6271   -7.8415 O   0  0  0  0  0  0
   26.8514  -29.3438   -7.7040 O   0  0  0  0  0  0
   25.0266  -27.6650  -13.3279 O   0  0  0  0  0  0
   27.1221  -27.3203  -14.1412 O   0  0  0  0  0  0
   25.9127  -21.9870  -19.9232 O   0  0  0  0  0  0
   25.4453  -24.0392   -8.9265 S   0  0  0  0  0  0
  1 12  1  0  0  0
  2 44  2  0  0  0
  2 58  1  0  0  0
  3  4  1  0  0  0
  3 52  2  0  0  0
  3 58  1  0  0  0
  4  5  1  0  0  0
  5 11  1  0  0  0
  5 46  1  0  0  0
  6  7  1  0  0  0
  6 46  1  0  0  0
  6 53  2  0  0  0
  7  8  1  0  0  0
  7  9  1  0  0  0
  8  9  1  0  0  0
  9 10  1  0  0  0
 11 47  1  0  0  0
 11 54  2  0  0  0
 12 45  1  0  0  0
 13 14  1  0  0  0
 13 47  1  0  0  0
 14 15  1  0  0  0
 15 16  1  0  0  0
 16 17  1  0  0  0
 16 48  1  0  0  0
 17 55  2  0  0  0
 17 56  1  0  0  0
 18 19  1  0  0  0
 18 56  1  0  0  0
 19 20  1  0  0  0
 19 21  1  0  0  0
 19 22  1  0  0  0
 22 24  1  0  0  0
 23 34  2  0  0  0
 23 43  1  0  0  0
 23 45  1  0  0  0
 24 25  2  0  0  0
 24 34  1  0  0  0
 25 26  1  0  0  0
 25 45  1  0  0  0
 26 27  1  0  0  0
 26 30  2  0  0  0
 27 37  1  0  0  0
 27 49  2  0  0  0
 28 29  2  0  0  0
 28 49  1  0  0  0
 29 30  1  0  0  0
 29 50  1  0  0  0
 31 32  1  0  0  0
 31 50  1  0  0  0
 32 51  1  0  0  0
 33 51  1  0  0  0
 34 40  1  0  0  0
 35 36  1  0  0  0
 35 51  1  0  0  0
 36 50  1  0  0  0
 37 38  1  0  0  0
 37 57  1  0  0  0
 39 57  1  0  0  0
 40 41  2  0  0  0
 41 42  1  0  0  0
 41 44  1  0  0  0
 42 43  2  0  0  0
 44 52  1  0  0  0
 47 48  1  0  0  0
M  CHG  1  51   1
M  END
> <s_m_entry_id>
1

> <s_m_entry_name>
9AX6_ligand.1

> <s_m_Source_Path>
C:\Users\user\Desktop

> <s_m_Source_File>
9AX6_ligand.sdf

> <i_m_Source_File_Index>
1

$$$$
@Layne-Huang
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Owner

Hi,

Thanks for your interest. Could you pls send me your pdb file? I will test it.

@Layne-Huang
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Owner

Hi,

We have solved this issue by adding the constraint of the generated region. The new version will be pushed soon!

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@Layne-Huang @BLEACH366