# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  8 20:08:19 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (4S)-1-[(2S)-2-methyl-3-sulfanylpropanoyl]-4-(phenylsulfanyl)-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CS)C(=O)N1C[C@H](C[C@H]1C(O)=O)Sc2ccccc2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 ZED  ZED  (4S)-1-[(2S)-2-methyl-3-sulfanylpropanoyl]-4-(phenylsulfanyl)-L-proline  ligand  39  21  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZED
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 ZED  CZ1   C  CR16   0  -0.270  -4.9333  -1.4248   0.6468
 ZED  CZ2   C  CR6    0  -0.092  -3.7849  -0.9468   0.0110
 ZED  CZ3   C  CR16   0  -0.260  -3.9073  -0.2976  -1.2151
 ZED  CZ4   C  CR16   0  -0.237  -5.1613  -0.1293  -1.7897
 ZED  CZ5   C  CR16   0  -0.272  -6.3009  -0.6058  -1.1594
 ZED  CZ6   C  CR16   0  -0.240  -6.1781  -1.2560   0.0629
 ZED  CZ7   C  CH1    0  -0.147   0.3618   1.6309  -0.3028
 ZED  CZ8   C  C      0   0.403   0.8277   2.7907   0.6052
 ZED  CZ9   C  CH2    0  -0.461  -1.0551   1.1922   0.0969
 ZED  CZA   C  CH1    0  -0.453  -1.0355  -0.3164  -0.1061
 ZED  CZB   C  CH2    0  -0.239   0.3653  -0.6962   0.3665
 ZED  CZC   C  CH3    0  -0.647   3.6703  -0.5387   1.5919
 ZED  CZD   C  CH1    0  -0.395   3.2931  -0.7488   0.1217
 ZED  CZF   C  CH2    0  -0.532   4.5116  -0.9039  -0.7822
 ZED  OZ1   O  OC    -1  -0.614   0.5406   3.9329   0.1965
 ZED  OZ2   O  O      0  -0.594   1.3706   2.4810   1.6783
 ZED  OZ3   O  O      0  -0.510   3.0197   1.4358  -0.8199
 ZED  NZ1   N  NT     0  -0.479   1.1502   0.4173  -0.1285
 ZED  SZ1   S  S2     0   0.065  -2.2577  -1.2524   0.8388
 ZED  SZ2   S  S2     0  -0.262   5.3987  -2.4380  -0.3396
 ZED  HZ1   H  HCR6   0   0.263  -4.8547  -1.9310   1.6017
 ZED  HZ3   H  HCR6   0   0.262  -3.0409   0.0852  -1.7367
 ZED  HZ4   H  HCR6   0   0.261  -5.2395   0.3820  -2.7405
 ZED  HZ5   H  HCR6   0   0.257  -7.2739  -0.4708  -1.6124
 ZED  HZ6   H  HCR6   0   0.261  -7.0573  -1.6320   0.5699
 ZED  HZ7   H  HCH1   0   0.239   0.3839   1.9422  -1.3505
 ZED  HZ91  H  HCH2   0   0.265  -1.8242   1.7001  -0.4815
 ZED  HZ92  H  HCH2   0   0.249  -1.2379   1.3998   1.1541
 ZED  H100  H  HCH1   0   0.302  -1.1252  -0.5773  -1.1630
 ZED  H111  H  HCH2   0   0.273   0.6832  -1.6490  -0.0523
 ZED  H112  H  HCH2   0   0.244   0.4081  -0.7691   1.4598
 ZED  H123  H  HCH3   0   0.241   4.1891  -1.4079   1.9951
 ZED  H133  H  HCH1   0   0.264   2.6968  -1.6608   0.0424
 ZED  H151  H  HCH2   0   0.278   4.2020  -0.9732  -1.8246
 ZED  H152  H  HCH2   0   0.268   5.1822  -0.0531  -0.6768
 ZED  HSZ2  H  HSH1   0   0.225   6.2909  -2.4097  -1.3350
 ZED  CZE   C  C      0   0.602   2.4765   0.4529  -0.3280
 ZED  H121  H  HCH3   0   0.232   4.3263   0.3263   1.6991
 ZED  H122  H  HCH3   0   0.246   2.7865  -0.3673   2.2059

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 ZED  CZ1  CZ2   aromatic  1.397  0.020  1.397
 ZED  CZ1  CZ6   aromatic  1.385  0.020  1.385
 ZED  CZ1  HZ1   single    0.930  0.020  1.080
 ZED  CZ2  CZ3   aromatic  1.393  0.020  1.393
 ZED  CZ2  SZ1   single    1.764  0.020  1.764
 ZED  CZ3  CZ4   aromatic  1.390  0.020  1.390
 ZED  CZ3  HZ3   single    0.930  0.020  1.080
 ZED  CZ4  CZ5   aromatic  1.387  0.020  1.387
 ZED  CZ4  HZ4   single    0.930  0.020  1.080
 ZED  CZ5  CZ6   aromatic  1.390  0.020  1.390
 ZED  CZ5  HZ5   single    0.930  0.020  1.080
 ZED  CZ6  HZ6   single    0.930  0.020  1.080
 ZED  CZ7  CZ8   single    1.545  0.020  1.545
 ZED  CZ7  CZ9   single    1.536  0.020  1.536
 ZED  CZ7  NZ1   single    1.458  0.020  1.458
 ZED  CZ7  HZ7   single    0.970  0.020  1.090
 ZED  CZ8  OZ1   deloc     1.247  0.020  1.247
 ZED  CZ8  OZ2   deloc     1.242  0.020  1.242
 ZED  CZ9  CZA   single    1.522  0.020  1.522
 ZED  CZ9  HZ91  single    0.970  0.020  1.090
 ZED  CZ9  HZ92  single    0.970  0.020  1.090
 ZED  CZA  CZB   single    1.526  0.020  1.526
 ZED  CZA  SZ1   single    1.806  0.020  1.806
 ZED  CZA  H100  single    0.970  0.020  1.090
 ZED  CZB  NZ1   single    1.450  0.020  1.450
 ZED  CZB  H111  single    0.970  0.020  1.090
 ZED  CZB  H112  single    0.970  0.020  1.090
 ZED  CZC  CZD   single    1.532  0.020  1.532
 ZED  CZC  H121  single    0.970  0.020  1.090
 ZED  CZC  H122  single    0.970  0.020  1.090
 ZED  CZC  H123  single    0.970  0.020  1.090
 ZED  CZD  CZE   single    1.521  0.020  1.521
 ZED  CZD  CZF   single    1.525  0.020  1.525
 ZED  CZD  H133  single    0.970  0.020  1.090
 ZED  CZE  OZ3   double    1.226  0.020  1.226
 ZED  CZE  NZ1   single    1.342  0.020  1.342
 ZED  CZF  SZ2   single    1.827  0.020  1.827
 ZED  CZF  H151  single    0.970  0.020  1.090
 ZED  CZF  H152  single    0.970  0.020  1.090
 ZED  SZ2  HSZ2  single    1.200  0.020  1.300

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 ZED  HZ1   CZ1  CZ6   119.57  3.000
 ZED  HZ1   CZ1  CZ2   120.09  3.000
 ZED  CZ6   CZ1  CZ2   120.34  3.000
 ZED  SZ1   CZ2  CZ3   124.75  3.000
 ZED  SZ1   CZ2  CZ1   116.03  3.000
 ZED  CZ3   CZ2  CZ1   119.21  3.000
 ZED  HZ3   CZ3  CZ4   118.73  3.000
 ZED  HZ3   CZ3  CZ2   121.28  3.000
 ZED  CZ4   CZ3  CZ2   119.99  3.000
 ZED  HZ4   CZ4  CZ5   120.14  3.000
 ZED  HZ4   CZ4  CZ3   119.06  3.000
 ZED  CZ5   CZ4  CZ3   120.80  3.000
 ZED  HZ5   CZ5  CZ6   120.40  3.000
 ZED  HZ5   CZ5  CZ4   120.40  3.000
 ZED  CZ6   CZ5  CZ4   119.20  3.000
 ZED  HZ6   CZ6  CZ5   120.19  3.000
 ZED  HZ6   CZ6  CZ1   119.35  3.000
 ZED  CZ5   CZ6  CZ1   120.47  3.000
 ZED  HZ7   CZ7  NZ1   109.93  3.000
 ZED  HZ7   CZ7  CZ9   110.44  3.000
 ZED  NZ1   CZ7  CZ9   103.30  3.000
 ZED  HZ7   CZ7  CZ8   110.08  3.000
 ZED  NZ1   CZ7  CZ8   113.06  3.000
 ZED  CZ9   CZ7  CZ8   109.85  3.000
 ZED  OZ2   CZ8  OZ1   127.77  3.000
 ZED  OZ2   CZ8  CZ7   116.90  3.000
 ZED  OZ1   CZ8  CZ7   115.20  3.000
 ZED  HZ92  CZ9  HZ91  107.90  3.000
 ZED  HZ92  CZ9  CZA   108.62  3.000
 ZED  HZ91  CZ9  CZA   113.63  3.000
 ZED  HZ92  CZ9  CZ7   110.60  3.000
 ZED  HZ91  CZ9  CZ7   112.35  3.000
 ZED  CZA   CZ9  CZ7   103.67  3.000
 ZED  H100  CZA  SZ1   109.08  3.000
 ZED  H100  CZA  CZB   108.39  3.000
 ZED  SZ1   CZA  CZB   109.27  3.000
 ZED  H100  CZA  CZ9   111.38  3.000
 ZED  SZ1   CZA  CZ9   115.79  3.000
 ZED  CZB   CZA  CZ9   102.54  3.000
 ZED  H112  CZB  H111  108.31  3.000
 ZED  H112  CZB  NZ1   111.74  3.000
 ZED  H111  CZB  NZ1   112.52  3.000
 ZED  H112  CZB  CZA   111.17  3.000
 ZED  H111  CZB  CZA   111.52  3.000
 ZED  NZ1   CZB  CZA   101.54  3.000
 ZED  H123  CZC  H122  107.65  3.000
 ZED  H123  CZC  H121  108.06  3.000
 ZED  H122  CZC  H121  107.92  3.000
 ZED  H123  CZC  CZD   111.28  3.000
 ZED  H122  CZC  CZD   111.25  3.000
 ZED  H121  CZC  CZD   110.55  3.000
 ZED  H133  CZD  CZF   107.94  3.000
 ZED  H133  CZD  CZE   110.18  3.000
 ZED  CZF   CZD  CZE   109.52  3.000
 ZED  H133  CZD  CZC   108.57  3.000
 ZED  CZF   CZD  CZC   112.70  3.000
 ZED  CZE   CZD  CZC   107.91  3.000
 ZED  H152  CZF  H151  108.51  3.000
 ZED  H152  CZF  SZ2   109.50  3.000
 ZED  H151  CZF  SZ2   108.45  3.000
 ZED  H152  CZF  CZD   110.81  3.000
 ZED  H151  CZF  CZD   110.27  3.000
 ZED  SZ2   CZF  CZD   109.26  3.000
 ZED  CZE   NZ1  CZB   127.33  3.000
 ZED  CZE   NZ1  CZ7   119.66  3.000
 ZED  CZB   NZ1  CZ7   112.80  3.000
 ZED  CZA   SZ1  CZ2   104.51  3.000
 ZED  HSZ2  SZ2  CZF    97.23  3.000
 ZED  NZ1   CZE  OZ3   121.26  3.000
 ZED  NZ1   CZE  CZD   117.77  3.000
 ZED  OZ3   CZE  CZD   120.94  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 ZED  CONST_01  CZ4  CZ3  CZ2  CZ1    0.00   0.0  0
 ZED  CONST_02  CZ4  CZ5  CZ6  CZ1    0.00   0.0  0
 ZED  CONST_03  CZ5  CZ6  CZ1  CZ2    0.00   0.0  0
 ZED  CONST_04  CZ5  CZ4  CZ3  CZ2    0.00   0.0  0
 ZED  CONST_05  CZ6  CZ1  CZ2  CZ3    0.00   0.0  0
 ZED  CONST_06  CZ6  CZ5  CZ4  CZ3    0.00   0.0  0
 ZED  CONST_07  SZ1  CZ2  CZ3  CZ4  180.00   0.0  0
 ZED  CONST_08  SZ1  CZ2  CZ1  CZ6  180.00   0.0  0
 ZED  CONST_09  HZ3  CZ3  CZ2  CZ1  180.00   0.0  0
 ZED  CONST_10  HZ5  CZ5  CZ6  CZ1  180.00   0.0  0
 ZED  CONST_11  HZ6  CZ6  CZ1  CZ2  180.00   0.0  0
 ZED  CONST_12  HZ4  CZ4  CZ3  CZ2  180.00   0.0  0
 ZED  CONST_13  HZ1  CZ1  CZ2  CZ3  180.00   0.0  0
 ZED  CONST_14  CZD  CZE  NZ1  CZ7  180.00   0.0  0
 ZED  CONST_15  OZ3  CZE  NZ1  CZ7    0.00   0.0  0
 ZED  CONST_16  CZD  CZE  NZ1  CZB    0.00   0.0  0
 ZED  CONST_17  OZ3  CZE  NZ1  CZB  180.00   0.0  0
 ZED  Var_01    CZA  CZB  NZ1  CZ7   25.07  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 ZED  chir_01  CZ7  CZ8  CZ9  NZ1  positiv
 ZED  chir_02  CZA  SZ1  CZ9  CZB  negativ
 ZED  chir_03  CZD  CZC  CZE  CZF  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 ZED  plan-1  CZ1  0.020
 ZED  plan-1  CZ2  0.020
 ZED  plan-1  CZ3  0.020
 ZED  plan-1  CZ4  0.020
 ZED  plan-1  CZ5  0.020
 ZED  plan-1  CZ6  0.020
 ZED  plan-1  SZ1  0.020
 ZED  plan-1  HZ1  0.020
 ZED  plan-1  HZ3  0.020
 ZED  plan-1  HZ4  0.020
 ZED  plan-1  HZ5  0.020
 ZED  plan-1  HZ6  0.020
 ZED  plan-2  CZ7  0.020
 ZED  plan-2  CZB  0.020
 ZED  plan-2  CZD  0.020
 ZED  plan-2  OZ3  0.020
 ZED  plan-2  NZ1  0.020
 ZED  plan-2  CZE  0.020
 ZED  plan-3  CZ7  0.020
 ZED  plan-3  CZ8  0.020
 ZED  plan-3  OZ1  0.020
 ZED  plan-3  OZ2  0.020

