# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:53:54 2021
#   Inital geometry file: a 73 line input string
#   Ligand name: (2~{R})-1-[3-sulfanyl-2-(sulfanylmethyl)propanoyl]pyrrolidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1CCCN1C(=O)C(CS)CS
#
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
 EEL  EEL  '(2~{R})-1-[3-sulfanyl-2-(sulfanylmethyl)propanoyl]pyrrolidine-2-carboxylic acid'  ligand  30  15  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EEL
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
 EEL  C4   C  CH2   0  -0.474  15.0328  13.7025   0.6035
 EEL  C5   C  C     0   0.610  13.2436  12.5773   3.5776
 EEL  C6   C  CH1   0  -0.379  14.2283  12.0352   4.6004
 EEL  C7   C  CH2   0  -0.549  13.8234  12.4340   6.0110
 EEL  C8   C  CH2   0  -0.543  14.3463  10.5156   4.4416
 EEL  C9   C  C     0   0.549  12.0765  14.5716   1.6020
 EEL  N1   N  NR5   0  -0.479  13.7106  12.8712   2.3530
 EEL  C3   C  CH2   0  -0.492  13.6542  13.3442   0.0605
 EEL  C1   C  CH2   0  -0.277  15.1052  12.9397   1.9211
 EEL  C2   C  CR15  0  -0.184  12.7740  13.2559   1.3172
 EEL  O1   O  O     0  -0.491  12.0512  12.6689   3.8385
 EEL  S1   S  S2    0  -0.229  13.8568  14.2338   6.2666
 EEL  S2   S  S2    0  -0.249  12.7273   9.6891   4.6391
 EEL  O2   O  O     0  -0.448  10.9801  14.8370   1.1755
 EEL  O3   O  OH1   0  -0.577  12.8178  15.4103   2.3057
 EEL  H1   H  HCH2  0   0.262  15.8353  13.4166  -0.0745
 EEL  H2   H  HCH2  0   0.250  15.1160  14.7754   0.7797
 EEL  H3   H  HCH1  0   0.287  15.2321  12.4252   4.4152
 EEL  H4   H  HCH2  0   0.284  12.8060  12.1225   6.2382
 EEL  H5   H  HCH2  0   0.286  14.4809  11.9572   6.7374
 EEL  H6   H  HCH2  0   0.292  15.0316  10.1346   5.1980
 EEL  H7   H  HCH2  0   0.286  14.7580  10.2683   3.4633
 EEL  H8   H  HCH2  0   0.271  13.2749  14.0522  -0.6755
 EEL  H9   H  HCH2  0   0.266  13.6765  12.3617  -0.4134
 EEL  H10  H  HCH2  0   0.249  15.5158  11.9376   1.7716
 EEL  H11  H  HCH2  0   0.261  15.7241  13.4537   2.6557
 EEL  H12  H  HCR5  0   0.298  11.9929  12.5038   1.1943
 EEL  H13  H  HSH1  0   0.217  15.1872  14.3774   6.2831
 EEL  H14  H  HSH1  0   0.222  13.2149   8.4505   4.7664
 EEL  H15  H  HOH1  0   0.482  12.3441  16.2465   2.4303

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
 EEL  C3  C4   single  1.524  0.020  1.524
 EEL  C3  C2   single  1.537  0.020  1.537
 EEL  C4  C1   single  1.524  0.020  1.524
 EEL  O2  C9   double  1.206  0.020  1.206
 EEL  C2  C9   single  1.516  0.020  1.516
 EEL  C2  N1   single  1.449  0.020  1.449
 EEL  C9  O3   single  1.322  0.020  1.322
 EEL  C1  N1   single  1.462  0.020  1.462
 EEL  N1  C5   single  1.343  0.020  1.343
 EEL  C5  O1   double  1.224  0.020  1.224
 EEL  C5  C6   single  1.520  0.020  1.520
 EEL  C8  S2   single  1.828  0.020  1.828
 EEL  C8  C6   single  1.532  0.020  1.532
 EEL  C6  C7   single  1.521  0.020  1.521
 EEL  C7  S1   single  1.818  0.020  1.818
 EEL  C4  H1   single  0.970  0.020  1.090
 EEL  C4  H2   single  0.970  0.020  1.090
 EEL  C6  H3   single  0.970  0.020  1.090
 EEL  C7  H4   single  0.970  0.020  1.090
 EEL  C7  H5   single  0.970  0.020  1.090
 EEL  C8  H6   single  0.970  0.020  1.090
 EEL  C8  H7   single  0.970  0.020  1.090
 EEL  C3  H8   single  0.970  0.020  1.090
 EEL  C3  H9   single  0.970  0.020  1.090
 EEL  C1  H10  single  0.970  0.020  1.090
 EEL  C1  H11  single  0.970  0.020  1.090
 EEL  C2  H12  single  0.970  0.020  1.090
 EEL  S1  H13  single  1.200  0.020  1.300
 EEL  S2  H14  single  1.200  0.020  1.300
 EEL  O3  H15  single  0.850  0.020  0.980

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
 EEL  H2   C4  H1   107.62  3.000
 EEL  H2   C4  C1   110.43  3.000
 EEL  H1   C4  C1   111.83  3.000
 EEL  H2   C4  C3   110.97  3.000
 EEL  H1   C4  C3   112.52  3.000
 EEL  C1   C4  C3   103.49  3.000
 EEL  O1   C5  N1   121.11  3.000
 EEL  O1   C5  C6   120.96  3.000
 EEL  N1   C5  C6   117.80  3.000
 EEL  H3   C6  C8   105.40  3.000
 EEL  H3   C6  C7   107.95  3.000
 EEL  C8   C6  C7   112.13  3.000
 EEL  H3   C6  C5   110.72  3.000
 EEL  C7   C6  C5   110.99  3.000
 EEL  C8   C6  C5   109.50  3.000
 EEL  H5   C7  H4   107.44  3.000
 EEL  H5   C7  S1   109.17  3.000
 EEL  H4   C7  S1   105.74  3.000
 EEL  H5   C7  C6   110.06  3.000
 EEL  H4   C7  C6   111.56  3.000
 EEL  S1   C7  C6   112.65  3.000
 EEL  H7   C8  H6   107.83  3.000
 EEL  H7   C8  S2   109.20  3.000
 EEL  H6   C8  S2   108.90  3.000
 EEL  H7   C8  C6   110.31  3.000
 EEL  H6   C8  C6   108.86  3.000
 EEL  S2   C8  C6   111.64  3.000
 EEL  O3   C9  O2   123.94  3.000
 EEL  O3   C9  C2   113.12  3.000
 EEL  O2   C9  C2   122.87  3.000
 EEL  C2   N1  C1   113.15  3.000
 EEL  C1   N1  C5   127.69  3.000
 EEL  C2   N1  C5   119.03  3.000
 EEL  H9   C3  H8   107.39  3.000
 EEL  H9   C3  C2   108.37  3.000
 EEL  H8   C3  C2   112.98  3.000
 EEL  H9   C3  C4   110.36  3.000
 EEL  H8   C3  C4   113.75  3.000
 EEL  C2   C3  C4   103.90  3.000
 EEL  H11  C1  H10  108.14  3.000
 EEL  H11  C1  N1   111.40  3.000
 EEL  H10  C1  N1   110.85  3.000
 EEL  H11  C1  C4   111.95  3.000
 EEL  H10  C1  C4   111.00  3.000
 EEL  N1   C1  C4   103.50  3.000
 EEL  H12  C2  C3   110.95  3.000
 EEL  H12  C2  N1   111.12  3.000
 EEL  C3   C2  N1   103.28  3.000
 EEL  H12  C2  C9   106.86  3.000
 EEL  N1   C2  C9   113.18  3.000
 EEL  C3   C2  C9   111.55  3.000
 EEL  H13  S1  C7    97.25  3.000
 EEL  H14  S2  C8    96.09  3.000
 EEL  H15  O3  C9   109.98  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
 EEL  CONST_01  C2   N1  C5  C6  180.00   0.0  0
 EEL  CONST_02  C1   N1  C5  C6    0.00   0.0  0
 EEL  CONST_03  O1   C5  N1  C1  180.00   0.0  0
 EEL  CONST_04  O1   C5  N1  C2    0.00   0.0  0
 EEL  CONST_05  H15  O3  C9  C2  180.00   0.0  0
 EEL  Var_01    C2   N1  C1  C4   12.25  30.0  1
 EEL  Var_02    C3   C4  C1  N1  -29.47  30.0  1
 EEL  Var_03    C2   C3  C4  C1   35.92  30.0  1
 EEL  Var_04    N1   C5  C6  C7  149.80  30.0  2
 EEL  Var_05    S2   C8  C6  C5  -58.11  30.0  3
 EEL  Var_06    S1   C7  C6  C5  -63.49  30.0  3

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
 EEL  chir_01  C2  C3  C9  N1  positiv

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
 EEL  plan-1  C5   0.020
 EEL  plan-1  C6   0.020
 EEL  plan-1  N1   0.020
 EEL  plan-1  C1   0.020
 EEL  plan-1  C2   0.020
 EEL  plan-1  O1   0.020
 EEL  plan-2  C9   0.020
 EEL  plan-2  C2   0.020
 EEL  plan-2  O2   0.020
 EEL  plan-2  O3   0.020
 EEL  plan-2  H15  0.020

