# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 15:23:18 2021
#   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  40  21  .  2021-08-25  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.231  70.8407  51.0344  21.6742
 ZED  CZ2   C  CR6   0  -0.129  69.5760  50.5343  21.9761
 ZED  CZ3   C  CR16  0  -0.237  69.4509  49.2818  22.5701
 ZED  CZ4   C  CR16  0  -0.246  70.5846  48.5327  22.8581
 ZED  CZ5   C  CR16  0  -0.253  71.8436  49.0285  22.5484
 ZED  CZ6   C  CR16  0  -0.245  71.9699  50.2784  21.9539
 ZED  CZ7   C  CH1   0  -0.207  66.0099  49.8671  19.7195
 ZED  CZ8   C  C     0   0.566  65.5687  49.5168  21.1331
 ZED  CZ9   C  CH2   0  -0.453  67.5244  49.8513  19.4972
 ZED  CZA   C  CH1   0  -0.415  67.9531  51.2675  19.8479
 ZED  CZB   C  CH2   0  -0.268  66.7922  52.1230  19.3461
 ZED  CZC   C  CH3   0  -0.641  62.6621  53.3812  19.0783
 ZED  CZD   C  CH1   0  -0.402  64.0717  52.9696  18.6746
 ZED  CZF   C  CH2   0  -0.539  64.3287  53.1442  17.1746
 ZED  OZ1   O  OH1   0  -0.596  65.9665  48.2924  21.4611
 ZED  OZ2   O  O     0  -0.426  64.9088  50.2216  21.8472
 ZED  OZ3   O  O     0  -0.490  63.4828  50.6900  19.1002
 ZED  NZ1   N  NT    0  -0.467  65.6426  51.2243  19.3868
 ZED  SZ1   S  S2    0   0.012  68.1319  51.5107  21.6540
 ZED  SZ2   S  S2    0  -0.251  63.3070  51.9994  16.1808
 ZED  HZ1   H  HCR6  0   0.268  70.9414  52.0141  21.2243
 ZED  HZ3   H  HCR6  0   0.264  68.4684  48.8920  22.8009
 ZED  HZ4   H  HCR6  0   0.263  70.4809  47.5605  23.3221
 ZED  HZ5   H  HCR6  0   0.263  72.7267  48.4438  22.7706
 ZED  HZ6   H  HCR6  0   0.264  72.9501  50.6703  21.7163
 ZED  HZ7   H  HCH1  0   0.312  65.5219  49.1534  19.0496
 ZED  HZ91  H  HCH2  0   0.280  67.7204  49.6705  18.4384
 ZED  HZ92  H  HCH2  0   0.283  68.0469  49.0807  20.0603
 ZED  H100  H  HCH1  0   0.316  68.8886  51.5559  19.3703
 ZED  H111  H  HCH2  0   0.274  67.0033  52.4492  18.3245
 ZED  H112  H  HCH2  0   0.275  66.6366  53.0170  19.9524
 ZED  H122  H  HCH3  0   0.235  62.4977  54.4258  18.8135
 ZED  H123  H  HCH3  0   0.240  62.5225  53.2882  20.1553
 ZED  H133  H  HCH1  0   0.283  64.7703  53.6467  19.1727
 ZED  H151  H  HCH2  0   0.280  65.3787  52.9747  16.9376
 ZED  H152  H  HCH2  0   0.288  64.0854  54.1680  16.8933
 ZED  HOZ1  H  HOH1  0   0.483  65.6483  48.0652  22.3477
 ZED  HSZ2  H  HSH1  0   0.220  63.5539  52.5742  14.9989
 ZED  CZE   C  C     0   0.594  64.3652  51.5357  19.0856
 ZED  H121  H  HCH3  0   0.234  61.8983  52.7840  18.5846

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  1.393  0.020  1.393
 ZED  CZ1  CZ6   aromatic  1.387  0.020  1.387
 ZED  CZ1  HZ1   single    0.930  0.020  1.080
 ZED  CZ2  CZ3   aromatic  1.392  0.020  1.392
 ZED  CZ2  SZ1   single    1.773  0.020  1.773
 ZED  CZ3  CZ4   aromatic  1.389  0.020  1.389
 ZED  CZ3  HZ3   single    0.930  0.020  1.080
 ZED  CZ4  CZ5   aromatic  1.388  0.020  1.388
 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    1.522  0.020  1.522
 ZED  CZ7  CZ9   single    1.531  0.020  1.531
 ZED  CZ7  NZ1   single    1.445  0.020  1.445
 ZED  CZ7  HZ7   single    0.970  0.020  1.090
 ZED  CZ8  OZ1   single    1.328  0.020  1.328
 ZED  CZ8  OZ2   double    1.201  0.020  1.201
 ZED  CZ9  CZA   single    1.521  0.020  1.521
 ZED  CZ9  HZ91  single    0.970  0.020  1.090
 ZED  CZ9  HZ92  single    0.970  0.020  1.090
 ZED  CZA  CZB   single    1.527  0.020  1.527
 ZED  CZA  SZ1   single    1.831  0.020  1.831
 ZED  CZA  H100  single    0.970  0.020  1.090
 ZED  CZB  NZ1   single    1.460  0.020  1.460
 ZED  CZB  H111  single    0.970  0.020  1.090
 ZED  CZB  H112  single    0.970  0.020  1.090
 ZED  CZC  CZD   single    1.523  0.020  1.523
 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    1.520  0.020  1.520
 ZED  CZD  CZF   single    1.532  0.020  1.532
 ZED  CZD  H133  single    0.970  0.020  1.090
 ZED  CZE  OZ3   double    1.222  0.020  1.222
 ZED  CZE  NZ1   single    1.349  0.020  1.349
 ZED  CZF  SZ2   single    1.828  0.020  1.828
 ZED  CZF  H151  single    0.970  0.020  1.090
 ZED  CZF  H152  single    0.970  0.020  1.090
 ZED  OZ1  HOZ1  single    0.850  0.020  0.980
 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   120.07  3.000
 ZED  HZ1   CZ1  CZ2   119.96  3.000
 ZED  CZ6   CZ1  CZ2   119.97  3.000
 ZED  SZ1   CZ2  CZ3   120.00  3.000
 ZED  SZ1   CZ2  CZ1   120.16  3.000
 ZED  CZ3   CZ2  CZ1   119.81  3.000
 ZED  HZ3   CZ3  CZ4   120.18  3.000
 ZED  HZ3   CZ3  CZ2   119.79  3.000
 ZED  CZ4   CZ3  CZ2   120.03  3.000
 ZED  HZ4   CZ4  CZ5   120.23  3.000
 ZED  HZ4   CZ4  CZ3   119.68  3.000
 ZED  CZ5   CZ4  CZ3   120.09  3.000
 ZED  HZ5   CZ5  CZ6   119.97  3.000
 ZED  HZ5   CZ5  CZ4   120.09  3.000
 ZED  CZ6   CZ5  CZ4   119.94  3.000
 ZED  HZ6   CZ6  CZ5   120.13  3.000
 ZED  HZ6   CZ6  CZ1   119.71  3.000
 ZED  CZ5   CZ6  CZ1   120.15  3.000
 ZED  HZ7   CZ7  NZ1   111.01  3.000
 ZED  HZ7   CZ7  CZ9   110.23  3.000
 ZED  NZ1   CZ7  CZ9   103.17  3.000
 ZED  HZ7   CZ7  CZ8   106.82  3.000
 ZED  NZ1   CZ7  CZ8   110.88  3.000
 ZED  CZ9   CZ7  CZ8   114.79  3.000
 ZED  OZ2   CZ8  OZ1   123.96  3.000
 ZED  OZ2   CZ8  CZ7   125.21  3.000
 ZED  OZ1   CZ8  CZ7   110.77  3.000
 ZED  HZ92  CZ9  HZ91  107.36  3.000
 ZED  HZ92  CZ9  CZA   113.88  3.000
 ZED  HZ91  CZ9  CZA   109.10  3.000
 ZED  HZ92  CZ9  CZ7   114.03  3.000
 ZED  HZ91  CZ9  CZ7   108.67  3.000
 ZED  CZA   CZ9  CZ7   103.64  3.000
 ZED  H100  CZA  SZ1   108.27  3.000
 ZED  H100  CZA  CZB   111.14  3.000
 ZED  SZ1   CZA  CZB   108.90  3.000
 ZED  H100  CZA  CZ9   112.81  3.000
 ZED  SZ1   CZA  CZ9   112.25  3.000
 ZED  CZB   CZA  CZ9   103.40  3.000
 ZED  H112  CZB  H111  107.60  3.000
 ZED  H112  CZB  NZ1   112.12  3.000
 ZED  H111  CZB  NZ1   111.22  3.000
 ZED  H112  CZB  CZA   112.63  3.000
 ZED  H111  CZB  CZA   109.12  3.000
 ZED  NZ1   CZB  CZA   104.16  3.000
 ZED  H123  CZC  H122  107.60  3.000
 ZED  H123  CZC  H121  108.15  3.000
 ZED  H122  CZC  H121  108.05  3.000
 ZED  H123  CZC  CZD   110.94  3.000
 ZED  H122  CZC  CZD   109.52  3.000
 ZED  H121  CZC  CZD   112.40  3.000
 ZED  H133  CZD  CZF   105.57  3.000
 ZED  H133  CZD  CZE   109.74  3.000
 ZED  CZF   CZD  CZE   109.86  3.000
 ZED  H133  CZD  CZC   107.66  3.000
 ZED  CZF   CZD  CZC   112.58  3.000
 ZED  CZE   CZD  CZC   111.22  3.000
 ZED  H152  CZF  H151  107.77  3.000
 ZED  H152  CZF  SZ2   108.87  3.000
 ZED  H151  CZF  SZ2   108.84  3.000
 ZED  H152  CZF  CZD   108.81  3.000
 ZED  H151  CZF  CZD   110.91  3.000
 ZED  SZ2   CZF  CZD   111.55  3.000
 ZED  HOZ1  OZ1  CZ8   110.10  3.000
 ZED  CZE   NZ1  CZB   126.69  3.000
 ZED  CZE   NZ1  CZ7   120.60  3.000
 ZED  CZB   NZ1  CZ7   112.61  3.000
 ZED  CZA   SZ1  CZ2   100.70  3.000
 ZED  HSZ2  SZ2  CZF    96.20  3.000
 ZED  NZ1   CZE  OZ3   121.42  3.000
 ZED  NZ1   CZE  CZD   117.45  3.000
 ZED  OZ3   CZE  CZD   121.09  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  CONST_18  HOZ1  OZ1  CZ8  CZ7  180.00   0.0  0
 ZED  Var_01    CZA   CZB  NZ1  CZ7   -6.49  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
 ZED  plan-3  HOZ1  0.020

