# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 10:31:22 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](C=O)[C@@H]1N=C([C@@H](S[C@@H]2CN[C@@H](C2)C(=O)N(C)C)[C@@H]1C)C(O)=O
#
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
 DWZ  DWZ  '(2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid'  ligand  52  26  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DWZ
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
 DWZ  CBE   C  CH3    0  -0.516   6.8731   0.9975  -1.6140
 DWZ  NBC   N  NT     0  -0.448   5.9771   0.0185  -1.0285
 DWZ  CBD   C  CH3    0  -0.528   5.7720  -1.1977  -1.7895
 DWZ  C     C  C      0   0.558   5.1920   0.4072   0.0022
 DWZ  O     O  O      0  -0.495   5.2919   1.5191   0.4996
 DWZ  CA    C  CH1    0  -0.253   4.1436  -0.5829   0.5013
 DWZ  CB    C  CH2    0  -0.458   2.9383  -0.6093  -0.4899
 DWZ  N     N  NH1    0  -0.569   3.6274  -0.1739   1.8021
 DWZ  CD    C  CH2    0  -0.288   2.3258   0.4271   1.5640
 DWZ  CG    C  CH1    0  -0.388   1.7317  -0.3934   0.4229
 DWZ  SAK   S  S2     0  -0.006   0.3920   0.4065  -0.4923
 DWZ  CAI   C  CR15   0  -0.460  -0.9332   0.6049   0.7601
 DWZ  CAH   C  CR15   0  -0.244  -2.0517   1.4536   0.1416
 DWZ  CAS   C  CH3    0  -0.686  -2.7651   2.2577   1.2215
 DWZ  CAL   C  CR5    0   0.142  -1.6512  -0.7034   0.9818
 DWZ  CAM   C  C      0   0.378  -1.1706  -1.7646   1.9641
 DWZ  OAT   O  O      0  -0.579  -0.3248  -1.3694   2.7897
 DWZ  OAU   O  OC    -1  -0.582  -1.6736  -2.8939   1.8649
 DWZ  NAJ   N  N      0  -0.340  -2.7129  -0.8410   0.2999
 DWZ  CAD   C  CR15   0  -0.120  -2.9097   0.3490  -0.5184
 DWZ  CAB   C  CH1    0  -0.391  -4.3788   0.6971  -0.7568
 DWZ  CAE   C  CH1    0   0.053  -5.0959  -0.1494  -1.8260
 DWZ  CAF   C  CH3    0  -0.704  -4.3847  -0.1752  -3.1692
 DWZ  OAG   O  OH1    0  -0.662  -5.2744  -1.4456  -1.2956
 DWZ  CAA   C  C1     0   0.193  -5.2151   0.6051   0.4988
 DWZ  OAC   O  O      0  -0.392  -6.2657   1.1833   0.6389
 DWZ  HBE   H  HCH3   0   0.235   6.3476   1.6970  -2.2694
 DWZ  HBEA  H  HCH3   0   0.249   7.3838   1.5692  -0.8435
 DWZ  HBEB  H  HCH3   0   0.239   7.6237   0.4785  -2.2059
 DWZ  HBD   H  HCH3   0   0.257   6.7240  -1.5257  -2.2032
 DWZ  HBDA  H  HCH3   0   0.256   5.4013  -2.0078  -1.1680
 DWZ  HBDB  H  HCH3   0   0.239   5.0732  -1.0540  -2.6172
 DWZ  HA    H  HCH1   0   0.280   4.5830  -1.5771   0.5987
 DWZ  HB    H  HCH2   0   0.250   3.0154   0.2002  -1.2224
 DWZ  HBA   H  HCH2   0   0.266   2.8822  -1.5431  -1.0473
 DWZ  HN    H  HNH1   0   0.354   3.5070  -1.0003   2.3722
 DWZ  HD    H  HCH2   0   0.252   1.7104   0.4016   2.4616
 DWZ  HDA   H  HCH2   0   0.221   2.4422   1.4695   1.2529
 DWZ  HG    H  HCH1   0   0.284   1.3880  -1.3503   0.8157
 DWZ  HAI   H  HCR5   0   0.292  -0.5031   1.0345   1.6644
 DWZ  HAH   H  HCR5   0   0.256  -1.6721   2.1477  -0.6120
 DWZ  HAS   H  HCH3   0   0.255  -2.0731   2.9664   1.6779
 DWZ  HASA  H  HCH3   0   0.242  -3.5925   2.8403   0.8139
 DWZ  HASB  H  HCH3   0   0.228  -3.1525   1.6271   2.0249
 DWZ  HAD   H  HCR5   0   0.267  -2.4614   0.1335  -1.4960
 DWZ  HAB   H  HCH1   0   0.285  -4.4297   1.7300  -1.1169
 DWZ  HAE   H  HCH1   0   0.218  -6.0711   0.3338  -1.9809
 DWZ  HAF   H  HCH3   0   0.232  -4.1735   0.8347  -3.5235
 DWZ  HAFA  H  HCH3   0   0.233  -3.4458  -0.7281  -3.1258
 DWZ  HAFB  H  HCH3   0   0.244  -5.0174  -0.6587  -3.9160
 DWZ  HOAG  H  HOH1   0   0.452  -5.8319  -1.9431  -1.9026
 DWZ  HAA   H  H      0   0.198  -4.8309  -0.0587   1.2912

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
 DWZ  CBE  HBE   single  0.970  0.020  1.090
 DWZ  CBE  HBEA  single  0.970  0.020  1.090
 DWZ  CBE  HBEB  single  0.970  0.020  1.090
 DWZ  NBC  CBE   single  1.451  0.020  1.451
 DWZ  CBD  NBC   single  1.449  0.020  1.449
 DWZ  CBD  HBD   single  0.970  0.020  1.090
 DWZ  CBD  HBDA  single  0.970  0.020  1.090
 DWZ  CBD  HBDB  single  0.970  0.020  1.090
 DWZ  C    NBC   single  1.353  0.020  1.353
 DWZ  C    CA    single  1.526  0.020  1.526
 DWZ  O    C     double  1.222  0.020  1.222
 DWZ  CA   N     single  1.458  0.020  1.458
 DWZ  CA   HA    single  0.970  0.020  1.090
 DWZ  CB   CA    single  1.561  0.020  1.561
 DWZ  CB   CG    single  1.528  0.020  1.528
 DWZ  CB   HB    single  0.970  0.020  1.090
 DWZ  CB   HBA   single  0.970  0.020  1.090
 DWZ  N    HN    single  0.890  0.020  1.040
 DWZ  CD   N     single  1.453  0.020  1.453
 DWZ  CD   HD    single  0.970  0.020  1.090
 DWZ  CD   HDA   single  0.970  0.020  1.090
 DWZ  CG   CD    single  1.526  0.020  1.526
 DWZ  CG   HG    single  0.970  0.020  1.090
 DWZ  SAK  CG    single  1.809  0.020  1.809
 DWZ  SAK  CAI   single  1.834  0.020  1.834
 DWZ  CAI  HAI   single  0.970  0.020  1.090
 DWZ  CAH  CAI   single  1.534  0.020  1.534
 DWZ  CAH  CAS   single  1.524  0.020  1.524
 DWZ  CAH  HAH   single  0.970  0.020  1.090
 DWZ  CAS  HAS   single  0.970  0.020  1.090
 DWZ  CAS  HASA  single  0.970  0.020  1.090
 DWZ  CAS  HASB  single  0.970  0.020  1.090
 DWZ  CAL  CAI   single  1.509  0.020  1.509
 DWZ  CAL  CAM   single  1.524  0.020  1.524
 DWZ  CAM  OAU   deloc   1.240  0.020  1.240
 DWZ  OAT  CAM   deloc   1.246  0.020  1.246
 DWZ  NAJ  CAL   double  1.269  0.020  1.269
 DWZ  NAJ  CAD   single  1.458  0.020  1.458
 DWZ  CAD  CAH   single  1.547  0.020  1.547
 DWZ  CAD  CAB   single  1.528  0.020  1.528
 DWZ  CAD  HAD   single  0.970  0.020  1.090
 DWZ  CAB  HAB   single  0.970  0.020  1.090
 DWZ  CAE  CAB   single  1.541  0.020  1.541
 DWZ  CAE  CAF   single  1.520  0.020  1.520
 DWZ  CAE  HAE   single  0.970  0.020  1.090
 DWZ  CAF  HAF   single  0.970  0.020  1.090
 DWZ  CAF  HAFA  single  0.970  0.020  1.090
 DWZ  CAF  HAFB  single  0.970  0.020  1.090
 DWZ  OAG  CAE   single  1.412  0.020  1.412
 DWZ  OAG  HOAG  single  0.850  0.020  0.980
 DWZ  CAA  CAB   single  1.511  0.020  1.511
 DWZ  CAA  OAC   double  1.207  0.020  1.207
 DWZ  CAA  HAA   single  0.930  0.020  1.080

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
 DWZ  HBEB  CBE  HBEA  108.21  3.000
 DWZ  HBEB  CBE  HBE   108.11  3.000
 DWZ  HBEA  CBE  HBE   108.32  3.000
 DWZ  HBEB  CBE  NBC   108.90  3.000
 DWZ  HBEA  CBE  NBC   111.05  3.000
 DWZ  HBE   CBE  NBC   112.14  3.000
 DWZ  C     NBC  CBD   124.00  3.000
 DWZ  C     NBC  CBE   118.17  3.000
 DWZ  CBD   NBC  CBE   116.22  3.000
 DWZ  HBDB  CBD  HBDA  108.25  3.000
 DWZ  HBDB  CBD  HBD   108.13  3.000
 DWZ  HBDA  CBD  HBD   106.93  3.000
 DWZ  HBDB  CBD  NBC   112.20  3.000
 DWZ  HBDA  CBD  NBC   111.94  3.000
 DWZ  HBD   CBD  NBC   109.19  3.000
 DWZ  CA    C    O     120.89  3.000
 DWZ  O     C    NBC   121.61  3.000
 DWZ  CA    C    NBC   117.48  3.000
 DWZ  HA    CA   N     108.57  3.000
 DWZ  HA    CA   CB    110.62  3.000
 DWZ  N     CA   CB    107.33  3.000
 DWZ  CB    CA   C     109.50  3.000
 DWZ  HA    CA   C     110.10  3.000
 DWZ  N     CA   C     110.67  3.000
 DWZ  HBA   CB   HB    107.17  3.000
 DWZ  HBA   CB   CG    112.72  3.000
 DWZ  HB    CB   CG    110.54  3.000
 DWZ  HBA   CB   CA    112.30  3.000
 DWZ  HB    CB   CA    110.99  3.000
 DWZ  CG    CB   CA    103.18  3.000
 DWZ  HN    N    CD    108.89  3.000
 DWZ  CD    N    CA    106.67  3.000
 DWZ  HN    N    CA    108.42  3.000
 DWZ  HDA   CD   HD    108.48  3.000
 DWZ  HDA   CD   CG    109.94  3.000
 DWZ  HD    CD   CG    112.58  3.000
 DWZ  CG    CD   N     104.41  3.000
 DWZ  HDA   CD   N     110.21  3.000
 DWZ  HD    CD   N     111.19  3.000
 DWZ  HG    CG   SAK   109.69  3.000
 DWZ  SAK   CG   CD    115.40  3.000
 DWZ  HG    CG   CD    108.99  3.000
 DWZ  SAK   CG   CB    110.18  3.000
 DWZ  HG    CG   CB    109.89  3.000
 DWZ  CD    CG   CB    102.43  3.000
 DWZ  CAI   SAK  CG    103.74  3.000
 DWZ  HAI   CAI  CAL   114.07  3.000
 DWZ  CAL   CAI  CAH   101.07  3.000
 DWZ  HAI   CAI  CAH   113.84  3.000
 DWZ  CAL   CAI  SAK   110.51  3.000
 DWZ  CAH   CAI  SAK   108.14  3.000
 DWZ  HAI   CAI  SAK   108.91  3.000
 DWZ  HAH   CAH  CAD   110.61  3.000
 DWZ  CAD   CAH  CAS   114.81  3.000
 DWZ  HAH   CAH  CAS   108.44  3.000
 DWZ  CAD   CAH  CAI   100.45  3.000
 DWZ  HAH   CAH  CAI   112.10  3.000
 DWZ  CAS   CAH  CAI   110.34  3.000
 DWZ  HASB  CAS  HASA  108.31  3.000
 DWZ  HASB  CAS  HAS   107.00  3.000
 DWZ  HASA  CAS  HAS   106.89  3.000
 DWZ  HASB  CAS  CAH   112.50  3.000
 DWZ  HASA  CAS  CAH   111.85  3.000
 DWZ  HAS   CAS  CAH   110.02  3.000
 DWZ  NAJ   CAL  CAM   122.31  3.000
 DWZ  NAJ   CAL  CAI   114.40  3.000
 DWZ  CAM   CAL  CAI   123.27  3.000
 DWZ  OAU   CAM  OAT   128.09  3.000
 DWZ  OAT   CAM  CAL   114.85  3.000
 DWZ  OAU   CAM  CAL   117.04  3.000
 DWZ  CAD   NAJ  CAL   109.03  3.000
 DWZ  HAD   CAD  CAB   107.37  3.000
 DWZ  HAD   CAD  NAJ   106.54  3.000
 DWZ  CAB   CAD  NAJ   113.78  3.000
 DWZ  HAD   CAD  CAH   107.09  3.000
 DWZ  CAB   CAD  CAH   115.92  3.000
 DWZ  NAJ   CAD  CAH   105.58  3.000
 DWZ  HAB   CAB  CAA   107.75  3.000
 DWZ  CAA   CAB  CAE   106.59  3.000
 DWZ  HAB   CAB  CAE   105.56  3.000
 DWZ  CAA   CAB  CAD   112.85  3.000
 DWZ  CAE   CAB  CAD   115.49  3.000
 DWZ  HAB   CAB  CAD   108.11  3.000
 DWZ  HAE   CAE  OAG   110.14  3.000
 DWZ  OAG   CAE  CAF   112.06  3.000
 DWZ  HAE   CAE  CAF   107.34  3.000
 DWZ  OAG   CAE  CAB   107.61  3.000
 DWZ  HAE   CAE  CAB   105.61  3.000
 DWZ  CAF   CAE  CAB   113.88  3.000
 DWZ  HAFB  CAF  HAFA  107.56  3.000
 DWZ  HAFB  CAF  HAF   107.46  3.000
 DWZ  HAFA  CAF  HAF   108.40  3.000
 DWZ  HAFB  CAF  CAE   109.93  3.000
 DWZ  HAFA  CAF  CAE   112.10  3.000
 DWZ  HAF   CAF  CAE   111.22  3.000
 DWZ  HOAG  OAG  CAE   108.11  3.000
 DWZ  HAA   CAA  OAC   120.54  3.000
 DWZ  HAA   CAA  CAB   116.16  3.000
 DWZ  OAC   CAA  CAB   123.28  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
 DWZ  CONST_01  CA   C    NBC  CBE   180.00   0.0  0
 DWZ  CONST_02  CA   C    NBC  CBD     0.00   0.0  0
 DWZ  CONST_03  O    C    NBC  CBE     0.00   0.0  0
 DWZ  CONST_04  O    C    NBC  CBD   180.00   0.0  0
 DWZ  Var_01    CG   CD   N    CA     35.90  30.0  1
 DWZ  Var_02    OAU  CAM  CAL  CAI  -165.64  30.0  2
 DWZ  Var_03    HBD  CBD  NBC  CBE    41.41  30.0  3
 DWZ  Var_04    HBE  CBE  NBC  CBD    89.15  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
 DWZ  chir_01  CA   C    N    CB   negativ
 DWZ  chir_02  CG   SAK  CD   CB   positiv
 DWZ  chir_03  CAI  SAK  CAH  CAL  negativ
 DWZ  chir_04  CAH  CAI  CAS  CAD  positiv
 DWZ  chir_05  CAD  NAJ  CAH  CAB  positiv
 DWZ  chir_06  CAB  CAD  CAE  CAA  negativ
 DWZ  chir_07  CAE  OAG  CAB  CAF  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
 DWZ  plan-1  CBE  0.020
 DWZ  plan-1  NBC  0.020
 DWZ  plan-1  CBD  0.020
 DWZ  plan-1  C    0.020
 DWZ  plan-1  O    0.020
 DWZ  plan-1  CA   0.020
 DWZ  plan-2  CAL  0.020
 DWZ  plan-2  CAM  0.020
 DWZ  plan-2  OAT  0.020
 DWZ  plan-2  OAU  0.020
 DWZ  plan-3  CAB  0.020
 DWZ  plan-3  CAA  0.020
 DWZ  plan-3  OAC  0.020
 DWZ  plan-3  HAA  0.020

