# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 31 21:51:12 2020
#   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  57  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  OC     0  -0.567  -7.0459   2.8591  -1.8614
 4NK  C    C  C      0   0.473  -7.2661   2.8453  -0.6473
 4NK  O    O  O     -1  -0.594  -8.2745   3.2519  -0.0319
 4NK  CA   C  CH1    0  -0.252  -6.1291   2.2810   0.2515
 4NK  N    N  NT3    1  -0.806  -6.6958   2.1634   1.6257
 4NK  CB   C  CH2    0  -0.451  -5.5518   0.9660  -0.2381
 4NK  CAN  C  CH2    0  -0.602  -4.3909   0.4796   0.6169
 4NK  CAU  C  C      0   0.579  -3.7694  -0.8026   0.1032
 4NK  OAE  O  O      0  -0.495  -4.3573  -1.5591  -0.6539
 4NK  NAS  N  NH1    0  -0.628  -2.5159  -1.0242   0.5449
 4NK  CBB  C  CH1    0  -0.233  -1.8728  -2.3092   0.4400
 4NK  CAW  C  C      0   0.435  -2.2872  -3.2993   1.5718
 4NK  OAK  O  O      0  -0.579  -3.2302  -2.9543   2.2974
 4NK  OAG  O  OC    -1  -0.603  -1.6296  -4.3551   1.6127
 4NK  CAQ  C  CH2    0  -0.622  -0.3655  -2.1236   0.4148
 4NK  SBD  S  S3     0   0.783   0.0804  -1.0216  -0.9679
 4NK  OAI  O  O      0  -0.769  -0.2521  -1.7775  -2.2311
 4NK  CAZ  C  CR5    0   0.198   1.8410  -1.1708  -0.7864
 4NK  NAR  N  N      0  -0.418   2.5773  -0.4732   0.0334
 4NK  NAT  N  NR15   0  -0.559   2.5620  -2.0322  -1.5220
 4NK  CAM  C  CR15   0  -0.099   3.8623  -1.8809  -1.1416
 4NK  CAY  C  CR5    0   0.127   3.8558  -0.9111  -0.1736
 4NK  CAP  C  CH2    0  -0.579   5.0089  -0.3565   0.5898
 4NK  CBC  C  CH1    0  -0.184   5.2023   1.1616   0.5374
 4NK  CAX  C  C      0   0.417   6.1952   1.5373   1.6807
 4NK  OAL  O  O      0  -0.577   7.3994   1.2920   1.4908
 4NK  OAH  O  OC    -1  -0.568   5.6564   1.9851   2.7020
 4NK  NBE  N  NT     1  -0.388   5.6260   1.7046  -0.8290
 4NK  CAB  C  CH3    0  -0.548   4.4722   1.7086  -1.7766
 4NK  CAC  C  CH3    0  -0.554   6.0555   3.1253  -0.6622
 4NK  CAA  C  CH3    0  -0.554   6.7361   0.9340  -1.4570
 4NK  HA   H  HCH1   0   0.303  -5.3411   3.0355   0.3086
 4NK  H2   H  HNT3   0   0.464  -6.0976   2.5353   2.3591
 4NK  H3   H  HNT3   0   0.454  -7.5769   2.7102   1.5767
 4NK  HB2  H  HCH2   0   0.253  -6.3404   0.2104  -0.2802
 4NK  HB1  H  HCH2   0   0.267  -5.2161   1.1257  -1.2621
 4NK  HAO  H  HCH2   0   0.269  -3.6243   1.2561   0.6932
 4NK  HAN  H  HCH2   0   0.273  -4.7157   0.2783   1.6444
 4NK  HAS  H  HNH1   0   0.394  -2.1838  -0.4175   1.2802
 4NK  HBB  H  HCH1   0   0.272  -2.1776  -2.7587  -0.5085
 4NK  HAQ  H  HCH2   0   0.293   0.0086  -1.6487   1.3256
 4NK  HB4  H  HCH2   0   0.313   0.1436  -3.0751   0.2705
 4NK  HAT  H  HNR5   0   0.429   2.2044  -2.6629  -2.2247
 4NK  HAM  H  HCR5   0   0.300   4.6629  -2.4493  -1.5847
 4NK  HB3  H  HCH2   0   0.292   4.8500  -0.5784   1.6495
 4NK  HAP  H  HCH2   0   0.278   5.9270  -0.8774   0.3176
 4NK  HBC  H  HCH1   0   0.287   4.2487   1.6527   0.7356
 4NK  HAF  H  HCH3   0   0.290   3.6338   2.2348  -1.3293
 4NK  HAE  H  HCH3   0   0.291   4.7795   2.2165  -2.6873
 4NK  HAD  H  HCH3   0   0.296   4.1864   0.6930  -2.0205
 4NK  HAI  H  HCH3   0   0.296   6.9830   3.1641  -0.1026
 4NK  HAH  H  HCH3   0   0.289   6.2081   3.5639  -1.6448
 4NK  HAG  H  HCH3   0   0.291   5.2748   3.6730  -0.1400
 4NK  HAA  H  HCH3   0   0.278   6.3844  -0.0595  -1.7190
 4NK  HAC  H  HCH3   0   0.286   7.0362   1.4515  -2.3645
 4NK  HAB  H  HCH3   0   0.301   7.5640   0.8718  -0.7615
 4NK  H6   H  HNT3   0   0.458  -6.9416   1.2076   1.8788

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    1.490  0.020  1.490
 4NK  OAL  CAX  deloc     1.243  0.020  1.243
 4NK  OAH  CAX  deloc     1.239  0.020  1.239
 4NK  CAC  NBE  single    1.494  0.020  1.494
 4NK  CAX  CBC  single    1.560  0.020  1.560
 4NK  NBE  CBC  single    1.530  0.020  1.530
 4NK  NBE  CAB  single    1.493  0.020  1.493
 4NK  CBC  CAP  single    1.531  0.020  1.531
 4NK  CAP  CAY  single    1.490  0.020  1.490
 4NK  CAY  NAR  aromatic  1.367  0.020  1.367
 4NK  CAY  CAM  aromatic  1.370  0.020  1.370
 4NK  NAR  CAZ  aromatic  1.304  0.020  1.304
 4NK  CAM  NAT  aromatic  1.363  0.020  1.363
 4NK  OAI  SBD  double    1.509  0.020  1.509
 4NK  CAZ  NAT  aromatic  1.343  0.020  1.343
 4NK  CAZ  SBD  single    1.776  0.020  1.776
 4NK  SBD  CAQ  single    1.824  0.020  1.824
 4NK  CAQ  CBB  single    1.519  0.020  1.519
 4NK  OAK  CAW  deloc     1.239  0.020  1.239
 4NK  CAW  OAG  deloc     1.244  0.020  1.244
 4NK  CAW  CBB  single    1.560  0.020  1.560
 4NK  CBB  NAS  single    1.441  0.020  1.441
 4NK  OAE  CAU  double    1.221  0.020  1.221
 4NK  NAS  CAU  single    1.347  0.020  1.347
 4NK  CAU  CAN  single    1.515  0.020  1.515
 4NK  O    C    deloc     1.249  0.020  1.249
 4NK  C    OXT  deloc     1.234  0.020  1.234
 4NK  C    CA   single    1.555  0.020  1.555
 4NK  CA   CB   single    1.517  0.020  1.517
 4NK  CA   N    single    1.491  0.020  1.491
 4NK  CB   CAN  single    1.522  0.020  1.522
 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    0.890  0.020  1.040
 4NK  CBB  HBB  single    0.970  0.020  1.090
 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  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  CA   C    O    115.06  3.000
 4NK  CA   C    OXT  116.24  3.000
 4NK  O    C    OXT  128.68  3.000
 4NK  HA   CA   CB   109.94  3.000
 4NK  HA   CA   N    106.29  3.000
 4NK  CB   CA   N    111.94  3.000
 4NK  HA   CA   C    107.87  3.000
 4NK  N    CA   C    106.46  3.000
 4NK  CB   CA   C    113.96  3.000
 4NK  H6   N    H3   107.53  3.000
 4NK  H6   N    H2   107.81  3.000
 4NK  H3   N    H2   109.92  3.000
 4NK  H6   N    CA   113.24  3.000
 4NK  H3   N    CA   103.74  3.000
 4NK  H2   N    CA   114.34  3.000
 4NK  HB1  CB   HB2  106.71  3.000
 4NK  HB1  CB   CAN  109.87  3.000
 4NK  HB2  CB   CAN  110.56  3.000
 4NK  HB1  CB   CA   107.07  3.000
 4NK  HB2  CB   CA   109.70  3.000
 4NK  CAN  CB   CA   112.70  3.000
 4NK  HAN  CAN  HAO  105.82  3.000
 4NK  HAN  CAN  CAU  106.50  3.000
 4NK  HAO  CAN  CAU  109.70  3.000
 4NK  HAN  CAN  CB   111.06  3.000
 4NK  HAO  CAN  CB   110.30  3.000
 4NK  CAU  CAN  CB   113.14  3.000
 4NK  NAS  CAU  OAE  123.32  3.000
 4NK  NAS  CAU  CAN  114.19  3.000
 4NK  OAE  CAU  CAN  122.49  3.000
 4NK  HAS  NAS  CBB  116.25  3.000
 4NK  HAS  NAS  CAU  116.49  3.000
 4NK  CBB  NAS  CAU  122.55  3.000
 4NK  HBB  CBB  CAQ  108.22  3.000
 4NK  HBB  CBB  CAW  107.13  3.000
 4NK  CAQ  CBB  CAW  110.69  3.000
 4NK  HBB  CBB  NAS  107.78  3.000
 4NK  CAW  CBB  NAS  113.25  3.000
 4NK  CAQ  CBB  NAS  109.58  3.000
 4NK  OAG  CAW  OAK  128.26  3.000
 4NK  OAG  CAW  CBB  114.96  3.000
 4NK  OAK  CAW  CBB  116.78  3.000
 4NK  HB4  CAQ  HAQ  109.27  3.000
 4NK  HB4  CAQ  SBD  108.25  3.000
 4NK  HAQ  CAQ  SBD  106.59  3.000
 4NK  HB4  CAQ  CBB  111.07  3.000
 4NK  HAQ  CAQ  CBB  112.26  3.000
 4NK  SBD  CAQ  CBB  109.21  3.000
 4NK  CAZ  SBD  OAI  105.18  3.000
 4NK  CAZ  SBD  CAQ   96.55  3.000
 4NK  OAI  SBD  CAQ  106.15  3.000
 4NK  NAT  CAZ  NAR  112.60  3.000
 4NK  NAT  CAZ  SBD  122.01  3.000
 4NK  NAR  CAZ  SBD  125.38  3.000
 4NK  CAY  NAR  CAZ  105.16  3.000
 4NK  HAT  NAT  CAM  126.97  3.000
 4NK  HAT  NAT  CAZ  126.28  3.000
 4NK  CAM  NAT  CAZ  106.75  3.000
 4NK  HAM  CAM  CAY  131.88  3.000
 4NK  HAM  CAM  NAT  122.38  3.000
 4NK  CAY  CAM  NAT  105.73  3.000
 4NK  CAP  CAY  CAM  128.44  3.000
 4NK  CAM  CAY  NAR  109.76  3.000
 4NK  CAP  CAY  NAR  121.80  3.000
 4NK  HAP  CAP  HB3  105.51  3.000
 4NK  HAP  CAP  CBC  111.03  3.000
 4NK  HB3  CAP  CBC  104.63  3.000
 4NK  HAP  CAP  CAY  110.24  3.000
 4NK  HB3  CAP  CAY  107.96  3.000
 4NK  CBC  CAP  CAY  116.69  3.000
 4NK  HBC  CBC  NBE  104.16  3.000
 4NK  HBC  CBC  CAX  108.35  3.000
 4NK  NBE  CBC  CAX  113.12  3.000
 4NK  HBC  CBC  CAP  109.25  3.000
 4NK  NBE  CBC  CAP  114.67  3.000
 4NK  CAX  CBC  CAP  107.10  3.000
 4NK  OAH  CAX  OAL  128.21  3.000
 4NK  OAH  CAX  CBC  114.48  3.000
 4NK  OAL  CAX  CBC  117.19  3.000
 4NK  CAA  NBE  CAC  108.95  3.000
 4NK  CAC  NBE  CAB  106.89  3.000
 4NK  CAA  NBE  CAB  108.03  3.000
 4NK  CAB  NBE  CBC  110.72  3.000
 4NK  CAC  NBE  CBC  108.51  3.000
 4NK  CAA  NBE  CBC  113.53  3.000
 4NK  HAD  CAB  HAE  108.91  3.000
 4NK  HAD  CAB  HAF  110.09  3.000
 4NK  HAE  CAB  HAF  109.68  3.000
 4NK  HAD  CAB  NBE  110.14  3.000
 4NK  HAE  CAB  NBE  108.33  3.000
 4NK  HAF  CAB  NBE  109.66  3.000
 4NK  HAG  CAC  HAH  109.37  3.000
 4NK  HAG  CAC  HAI  110.39  3.000
 4NK  HAH  CAC  HAI  109.40  3.000
 4NK  HAG  CAC  NBE  109.04  3.000
 4NK  HAH  CAC  NBE  108.87  3.000
 4NK  HAI  CAC  NBE  109.74  3.000
 4NK  HAB  CAA  HAC  110.64  3.000
 4NK  HAB  CAA  HAA  110.48  3.000
 4NK  HAC  CAA  HAA  108.88  3.000
 4NK  HAB  CAA  NBE  109.18  3.000
 4NK  HAC  CAA  NBE  108.15  3.000
 4NK  HAA  CAA  NBE  109.48  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_14  HAS  NAS  CAU  CAN     0.00   0.0  0
 4NK  Var_01    NAR  CAZ  SBD  CAQ   -84.23  30.0  2
 4NK  Var_02    CBC  CAP  CAY  NAR   -55.42  30.0  2
 4NK  Var_03    CAZ  SBD  CAQ  CBB  -174.71  30.0  1
 4NK  Var_04    CAU  CAN  CB   CA   -177.58  30.0  3
 4NK  Var_05    OAE  CAU  CAN  CB    -20.01  30.0  2
 4NK  Var_06    HAA  CAA  NBE  CBC    67.41  30.0  3
 4NK  Var_07    HAI  CAC  NBE  CBC    69.08  30.0  3
 4NK  Var_08    HAF  CAB  NBE  CBC    53.12  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-4  CBB  0.020
 4NK  plan-4  CAW  0.020
 4NK  plan-4  OAK  0.020
 4NK  plan-4  OAG  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-6  CAQ  0.020
 4NK  plan-6  SBD  0.020
 4NK  plan-6  OAI  0.020
 4NK  plan-6  CAZ  0.020

