# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 06:51:39 2021
#   Inital geometry file: a 146 line input string
#   Ligand name: (1S)-1-carboxy-4-({(1R)-1-carboxy-2-[(S)-{4-[(2S)-2-carboxy-2-(trimethylammonio)ethyl]-1H-imidazol-2-yl}sulfinyl]ethyl}amino)-4-oxobutan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)[C@@H](Cc1c[nH]c(n1)[S@@](=O)C[C@H](NC(=O)CC[C@H]([NH3+])C(O)=O)C(O)=O)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
 4NK  4NK  (1S)-1-carboxy-4-({(1R)-1-carboxy-2-[(S)-{4-[(2S)-2-carboxy-2-(trimethylammonio)ethyl]-1H-imidazol-2-yl}sulfinyl]ethyl}amino)-4-oxobutan-1-aminium  ligand  60  31  .  2021-08-04  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_4NK
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
 4NK  OXT  O  OH1   0  -0.579   2.6875   3.9608  -49.0749
 4NK  C    C  C     0   0.601   4.0019   3.9517  -49.1195
 4NK  O    O  O     0  -0.411   4.6870   2.9874  -49.3241
 4NK  CA   C  CH1   0  -0.259   4.6123   5.3273  -48.8945
 4NK  N    N  NT3   1  -0.786   3.5627   6.3509  -48.6390
 4NK  CB   C  CH2   0  -0.461   5.6226   5.3008  -47.7510
 4NK  CAN  C  CH2   0  -0.616   6.4392   6.5767  -47.6052
 4NK  CAU  C  C     0   0.585   7.4215   6.7917  -48.7384
 4NK  OAE  O  O     0  -0.470   7.9700   5.8585  -49.3024
 4NK  NAS  N  NH1   0  -0.634   7.6574   8.0850  -49.0380
 4NK  CBB  C  CH1   0  -0.230   8.6388   8.5083  -49.9951
 4NK  CAW  C  C     0   0.590   9.9020   9.0695  -49.3672
 4NK  OAK  O  O     0  -0.435  10.6880   9.7226  -50.0079
 4NK  OAG  O  OH1   0  -0.569  10.0596   8.7294  -48.1071
 4NK  CAQ  C  CH2   0  -0.602   8.0079   9.4837  -50.9859
 4NK  SBD  S  S3    0   0.776   9.0722  10.1767  -52.3087
 4NK  OAI  O  O     0  -0.761   8.0840  10.6325  -53.3472
 4NK  CAZ  C  CR5   0   0.209   9.7174   8.6083  -52.8469
 4NK  NAR  N  N     0  -0.412   8.9921   7.5566  -53.1200
 4NK  NAT  N  NR15  0  -0.571  11.0314   8.3506  -52.9739
 4NK  CAM  C  CR15  0  -0.099  11.1560   7.0466  -53.3361
 4NK  CAY  C  CR5   0   0.178   9.8735   6.5679  -53.4233
 4NK  CAP  C  CH2   0  -0.583   9.3995   5.1790  -53.6897
 4NK  CBC  C  CH1   0  -0.201   8.2590   4.8609  -52.7177
 4NK  CAX  C  C     0   0.562   6.9820   5.5833  -53.1709
 4NK  OAL  O  O     0  -0.400   6.6127   5.6035  -54.3143
 4NK  OAH  O  OH1   0  -0.570   6.3430   6.1540  -52.1686
 4NK  NBE  N  NT    1  -0.404   8.0037   3.3712  -52.5565
 4NK  CAB  C  CH3   0  -0.556   9.2035   2.7387  -51.9253
 4NK  CAC  C  CH3   0  -0.561   7.7301   2.6802  -53.8495
 4NK  CAA  C  CH3   0  -0.565   6.8549   3.1525  -51.6253
 4NK  H1   H  HOH1  0   0.505   2.3244   3.0757  -49.2405
 4NK  HA   H  HCH1  0   0.340   5.0931   5.6178  -49.8318
 4NK  H2   H  HNT3  0   0.483   3.9710   7.2825  -48.5535
 4NK  H3   H  HNT3  0   0.489   2.8784   6.4152  -49.3943
 4NK  HB2  H  HCH2  0   0.295   5.0970   5.0993  -46.8153
 4NK  HB1  H  HCH2  0   0.294   6.2942   4.4612  -47.9195
 4NK  HAO  H  HCH2  0   0.325   7.0306   6.4913  -46.6892
 4NK  HAN  H  HCH2  0   0.264   5.8127   7.4591  -47.4517
 4NK  HAS  H  HNH1  0   0.416   7.1909   8.7979  -48.4980
 4NK  HBB  H  HCH1  0   0.323   8.9550   7.6132  -50.5374
 4NK  H4   H  HOH1  0   0.492  10.8995   9.0751  -47.7660
 4NK  HAQ  H  HCH2  0   0.317   7.5957  10.3575  -50.4772
 4NK  HB4  H  HCH2  0   0.318   7.2053   8.9771  -51.5234
 4NK  HAT  H  HNR5  0   0.436  11.7922   8.9932  -52.8082
 4NK  HAM  H  HCR5  0   0.305  12.1130   6.5769  -53.4871
 4NK  HB3  H  HCH2  0   0.302  10.2398   4.4999  -53.5576
 4NK  HAP  H  HCH2  0   0.294   9.0619   5.0674  -54.7219
 4NK  HBC  H  HCH1  0   0.347   8.5151   5.2052  -51.7145
 4NK  H7   H  HOH1  0   0.492   5.5520   6.6103  -52.4970
 4NK  HAF  H  HCH3  0   0.303  10.0426   2.7485  -52.6118
 4NK  HAE  H  HCH3  0   0.299   9.4564   3.2761  -51.0153
 4NK  HAD  H  HCH3  0   0.307   8.9571   1.7089  -51.6854
 4NK  HAI  H  HCH3  0   0.305   8.5775   2.8031  -54.5162
 4NK  HAH  H  HCH3  0   0.303   7.5908   1.6230  -53.6423
 4NK  HAG  H  HCH3  0   0.303   6.8314   3.0784  -54.3080
 4NK  HAA  H  HCH3  0   0.295   7.0506   3.6778  -50.6947
 4NK  HAC  H  HCH3  0   0.298   5.9299   3.4988  -52.0761
 4NK  HAB  H  HCH3  0   0.305   6.7692   2.0872  -51.4339
 4NK  H6   H  HNT3  0   0.481   3.0447   6.1802  -47.7747

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
 4NK  CAA  NBE  single    1.495  0.020  1.495
 4NK  OAL  CAX  double    1.202  0.020  1.202
 4NK  OAH  CAX  single    1.319  0.020  1.319
 4NK  CAC  NBE  single    1.491  0.020  1.491
 4NK  CAX  CBC  single    1.536  0.020  1.536
 4NK  NBE  CBC  single    1.520  0.020  1.520
 4NK  NBE  CAB  single    1.496  0.020  1.496
 4NK  CBC  CAP  single    1.532  0.020  1.532
 4NK  CAP  CAY  single    1.492  0.020  1.492
 4NK  CAY  NAR  aromatic  1.359  0.020  1.359
 4NK  CAY  CAM  aromatic  1.372  0.020  1.372
 4NK  NAR  CAZ  aromatic  1.306  0.020  1.306
 4NK  CAM  NAT  aromatic  1.359  0.020  1.359
 4NK  OAI  SBD  double    1.504  0.020  1.504
 4NK  CAZ  NAT  aromatic  1.345  0.020  1.345
 4NK  CAZ  SBD  single    1.779  0.020  1.779
 4NK  SBD  CAQ  single    1.834  0.020  1.834
 4NK  CAQ  CBB  single    1.527  0.020  1.527
 4NK  OAK  CAW  double    1.206  0.020  1.206
 4NK  CAW  OAG  single    1.315  0.020  1.315
 4NK  CAW  CBB  single    1.518  0.020  1.518
 4NK  CBB  NAS  single    1.435  0.020  1.435
 4NK  OAE  CAU  double    1.221  0.020  1.221
 4NK  NAS  CAU  single    1.348  0.020  1.348
 4NK  CAU  CAN  single    1.515  0.020  1.515
 4NK  O    C    double    1.200  0.020  1.200
 4NK  C    OXT  single    1.315  0.020  1.315
 4NK  C    CA   single    1.522  0.020  1.522
 4NK  CA   CB   single    1.526  0.020  1.526
 4NK  CA   N    single    1.488  0.020  1.488
 4NK  CB   CAN  single    1.522  0.020  1.522
 4NK  OXT  H1   single    0.850  0.020  0.980
 4NK  CA   HA   single    0.970  0.020  1.090
 4NK  N    H2   single    0.890  0.020  1.040
 4NK  N    H3   single    0.890  0.020  1.040
 4NK  CB   HB2  single    0.970  0.020  1.090
 4NK  CB   HB1  single    0.970  0.020  1.090
 4NK  CAN  HAO  single    0.970  0.020  1.090
 4NK  CAN  HAN  single    0.970  0.020  1.090
 4NK  NAS  HAS  single    0.860  0.020  1.020
 4NK  CBB  HBB  single    0.970  0.020  1.090
 4NK  OAG  H4   single    0.850  0.020  0.980
 4NK  CAQ  HAQ  single    0.970  0.020  1.090
 4NK  CAQ  HB4  single    0.970  0.020  1.090
 4NK  NAT  HAT  single    0.860  0.020  1.020
 4NK  CAM  HAM  single    0.930  0.020  1.080
 4NK  CAP  HB3  single    0.970  0.020  1.090
 4NK  CAP  HAP  single    0.970  0.020  1.090
 4NK  CBC  HBC  single    0.970  0.020  1.090
 4NK  OAH  H7   single    0.850  0.020  0.980
 4NK  CAB  HAF  single    0.970  0.020  1.090
 4NK  CAB  HAE  single    0.970  0.020  1.090
 4NK  CAB  HAD  single    0.970  0.020  1.090
 4NK  CAC  HAI  single    0.970  0.020  1.090
 4NK  CAC  HAH  single    0.970  0.020  1.090
 4NK  CAC  HAG  single    0.970  0.020  1.090
 4NK  CAA  HAA  single    0.970  0.020  1.090
 4NK  CAA  HAC  single    0.970  0.020  1.090
 4NK  CAA  HAB  single    0.970  0.020  1.090
 4NK  N    H6   single    0.890  0.020  1.040

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
 4NK  H1   OXT  C    111.21  3.000
 4NK  CA   C    O    121.50  3.000
 4NK  CA   C    OXT  112.93  3.000
 4NK  O    C    OXT  125.57  3.000
 4NK  HA   CA   CB   110.86  3.000
 4NK  HA   CA   N    105.95  3.000
 4NK  CB   CA   N    110.50  3.000
 4NK  HA   CA   C    106.86  3.000
 4NK  N    CA   C    111.36  3.000
 4NK  CB   CA   C    111.14  3.000
 4NK  H6   N    H3   107.24  3.000
 4NK  H6   N    H2   106.52  3.000
 4NK  H3   N    H2   105.81  3.000
 4NK  H6   N    CA   112.82  3.000
 4NK  H3   N    CA   112.89  3.000
 4NK  H2   N    CA   111.11  3.000
 4NK  HB1  CB   HB2  106.70  3.000
 4NK  HB1  CB   CAN  109.30  3.000
 4NK  HB2  CB   CAN  109.32  3.000
 4NK  HB1  CB   CA   107.81  3.000
 4NK  HB2  CB   CA   109.06  3.000
 4NK  CAN  CB   CA   114.36  3.000
 4NK  HAN  CAN  HAO  104.80  3.000
 4NK  HAN  CAN  CAU  111.23  3.000
 4NK  HAO  CAN  CAU  106.67  3.000
 4NK  HAN  CAN  CB   112.51  3.000
 4NK  HAO  CAN  CB   107.76  3.000
 4NK  CAU  CAN  CB   113.28  3.000
 4NK  NAS  CAU  OAE  123.51  3.000
 4NK  NAS  CAU  CAN  114.57  3.000
 4NK  OAE  CAU  CAN  121.91  3.000
 4NK  HAS  NAS  CBB  117.71  3.000
 4NK  HAS  NAS  CAU  118.56  3.000
 4NK  CBB  NAS  CAU  123.43  3.000
 4NK  HBB  CBB  CAQ  108.71  3.000
 4NK  HBB  CBB  CAW  105.49  3.000
 4NK  CAQ  CBB  CAW  112.09  3.000
 4NK  HBB  CBB  NAS  106.68  3.000
 4NK  CAW  CBB  NAS  113.72  3.000
 4NK  CAQ  CBB  NAS  109.80  3.000
 4NK  OAG  CAW  OAK  124.82  3.000
 4NK  OAG  CAW  CBB  113.61  3.000
 4NK  OAK  CAW  CBB  121.51  3.000
 4NK  H4   OAG  CAW  110.40  3.000
 4NK  HB4  CAQ  HAQ  108.88  3.000
 4NK  HB4  CAQ  SBD  104.31  3.000
 4NK  HAQ  CAQ  SBD  104.64  3.000
 4NK  HB4  CAQ  CBB  109.10  3.000
 4NK  HAQ  CAQ  CBB  111.40  3.000
 4NK  SBD  CAQ  CBB  118.01  3.000
 4NK  CAZ  SBD  OAI  107.25  3.000
 4NK  CAZ  SBD  CAQ   95.48  3.000
 4NK  OAI  SBD  CAQ  103.37  3.000
 4NK  NAT  CAZ  NAR  111.61  3.000
 4NK  NAT  CAZ  SBD  123.49  3.000
 4NK  NAR  CAZ  SBD  124.86  3.000
 4NK  CAY  NAR  CAZ  105.80  3.000
 4NK  HAT  NAT  CAM  125.83  3.000
 4NK  HAT  NAT  CAZ  126.78  3.000
 4NK  CAM  NAT  CAZ  107.37  3.000
 4NK  HAM  CAM  CAY  132.06  3.000
 4NK  HAM  CAM  NAT  122.51  3.000
 4NK  CAY  CAM  NAT  105.43  3.000
 4NK  CAP  CAY  CAM  129.31  3.000
 4NK  CAM  CAY  NAR  109.78  3.000
 4NK  CAP  CAY  NAR  120.75  3.000
 4NK  HAP  CAP  HB3  106.84  3.000
 4NK  HAP  CAP  CBC  110.39  3.000
 4NK  HB3  CAP  CBC  111.60  3.000
 4NK  HAP  CAP  CAY  111.25  3.000
 4NK  HB3  CAP  CAY  108.30  3.000
 4NK  CBC  CAP  CAY  108.46  3.000
 4NK  HBC  CBC  NBE  104.55  3.000
 4NK  HBC  CBC  CAX  108.55  3.000
 4NK  NBE  CBC  CAX  110.65  3.000
 4NK  HBC  CBC  CAP  110.07  3.000
 4NK  NBE  CBC  CAP  113.32  3.000
 4NK  CAX  CBC  CAP  109.52  3.000
 4NK  OAH  CAX  OAL  124.55  3.000
 4NK  OAH  CAX  CBC  112.48  3.000
 4NK  OAL  CAX  CBC  122.97  3.000
 4NK  H7   OAH  CAX  109.96  3.000
 4NK  CAA  NBE  CAC  109.35  3.000
 4NK  CAC  NBE  CAB  108.49  3.000
 4NK  CAA  NBE  CAB  106.96  3.000
 4NK  CAB  NBE  CBC  108.93  3.000
 4NK  CAC  NBE  CBC  113.14  3.000
 4NK  CAA  NBE  CBC  109.78  3.000
 4NK  HAD  CAB  HAE  109.68  3.000
 4NK  HAD  CAB  HAF  108.91  3.000
 4NK  HAE  CAB  HAF  110.22  3.000
 4NK  HAD  CAB  NBE  108.19  3.000
 4NK  HAE  CAB  NBE  109.33  3.000
 4NK  HAF  CAB  NBE  110.47  3.000
 4NK  HAG  CAC  HAH  109.37  3.000
 4NK  HAG  CAC  HAI  110.22  3.000
 4NK  HAH  CAC  HAI  109.12  3.000
 4NK  HAG  CAC  NBE  110.39  3.000
 4NK  HAH  CAC  NBE  108.00  3.000
 4NK  HAI  CAC  NBE  109.69  3.000
 4NK  HAB  CAA  HAC  108.60  3.000
 4NK  HAB  CAA  HAA  109.73  3.000
 4NK  HAC  CAA  HAA  110.79  3.000
 4NK  HAB  CAA  NBE  108.30  3.000
 4NK  HAC  CAA  NBE  110.46  3.000
 4NK  HAA  CAA  NBE  108.93  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
 4NK  CONST_01  CAM  CAY  NAR  CAZ    0.00   0.0  0
 4NK  CONST_02  CAY  CAM  NAT  CAZ    0.00   0.0  0
 4NK  CONST_03  NAT  CAM  CAY  NAR    0.00   0.0  0
 4NK  CONST_04  CAM  NAT  CAZ  NAR    0.00   0.0  0
 4NK  CONST_05  CAY  NAR  CAZ  NAT    0.00   0.0  0
 4NK  CONST_06  CAY  NAR  CAZ  SBD  180.00   0.0  0
 4NK  CONST_07  CAM  NAT  CAZ  SBD  180.00   0.0  0
 4NK  CONST_08  CAP  CAY  NAR  CAZ  180.00   0.0  0
 4NK  CONST_09  CAP  CAY  CAM  NAT  180.00   0.0  0
 4NK  CONST_10  HAM  CAM  NAT  CAZ  180.00   0.0  0
 4NK  CONST_11  HAT  NAT  CAZ  NAR  180.00   0.0  0
 4NK  CONST_12  CBB  NAS  CAU  CAN  180.00   0.0  0
 4NK  CONST_13  CBB  NAS  CAU  OAE    0.00   0.0  0
 4NK  CONST_14  HAS  NAS  CAU  CAN    0.00   0.0  0
 4NK  CONST_15  H1   OXT  C    O      0.00   0.0  0
 4NK  CONST_16  H4   OAG  CAW  CBB  180.00   0.0  0
 4NK  CONST_17  H7   OAH  CAX  CBC  180.00   0.0  0
 4NK  Var_01    NAR  CAZ  SBD  CAQ   49.52  30.0  1
 4NK  Var_02    CBC  CAP  CAY  NAR  -38.80  30.0  1
 4NK  Var_03    CAZ  SBD  CAQ  CBB   50.28  30.0  1
 4NK  Var_04    CAU  CAN  CB   CA   -69.23  30.0  3
 4NK  Var_05    OAE  CAU  CAN  CB   -33.14  30.0  1
 4NK  Var_06    HAA  CAA  NBE  CBC  -54.01  30.0  3
 4NK  Var_07    HAI  CAC  NBE  CBC   59.48  30.0  3
 4NK  Var_08    HAF  CAB  NBE  CBC  -68.87  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
 4NK  chir_01  CA   C    CB   N    positiv
 4NK  chir_02  CBB  NAS  CAQ  CAW  negativ
 4NK  chir_04  CBC  CAX  NBE  CAP  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
 4NK  plan-1  SBD  0.020
 4NK  plan-1  CAZ  0.020
 4NK  plan-1  NAR  0.020
 4NK  plan-1  NAT  0.020
 4NK  plan-1  CAM  0.020
 4NK  plan-1  CAY  0.020
 4NK  plan-1  CAP  0.020
 4NK  plan-1  HAT  0.020
 4NK  plan-1  HAM  0.020
 4NK  plan-2  CAN  0.020
 4NK  plan-2  CAU  0.020
 4NK  plan-2  OAE  0.020
 4NK  plan-2  NAS  0.020
 4NK  plan-2  CBB  0.020
 4NK  plan-2  HAS  0.020
 4NK  plan-3  OXT  0.020
 4NK  plan-3  C    0.020
 4NK  plan-3  O    0.020
 4NK  plan-3  CA   0.020
 4NK  plan-3  H1   0.020
 4NK  plan-4  CBB  0.020
 4NK  plan-4  CAW  0.020
 4NK  plan-4  OAK  0.020
 4NK  plan-4  OAG  0.020
 4NK  plan-4  H4   0.020
 4NK  plan-5  CBC  0.020
 4NK  plan-5  CAX  0.020
 4NK  plan-5  OAL  0.020
 4NK  plan-5  OAH  0.020
 4NK  plan-5  H7   0.020
 4NK  plan-6  CAQ  0.020
 4NK  plan-6  SBD  0.020
 4NK  plan-6  OAI  0.020
 4NK  plan-6  CAZ  0.020

