# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 06:23:35 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: (2S)-2-amino-6-[[(2R)-1-[[(2S)-1-hydroxy-3-methylsulfanyl-1-oxo-butan-2-yl]amino]-1-oxo-3-sulfanyl-propan-2-yl]amino]-6-oxo-hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@@H](C)[C@@H](NC(=O)[C@H](CS)NC(=O)CCC[C@H](N)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
 M9F  M9F  '(2S)-2-amino-6-[[(2R)-1-[[(2S)-1-hydroxy-3-methylsulfanyl-1-oxo-butan-2-yl]amino]-1-oxo-3-sulfanyl-propan-2-yl]amino]-6-oxo-hexanoic acid'  ligand  50  25  .  2021-08-14  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M9F
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
 M9F  CAU   C  C     0   0.554  11.9277  40.7520  5.7593
 M9F  OAV   O  O     0  -0.497  11.2073  40.4791  6.7091
 M9F  O     O  O     0  -0.455  17.6913  37.6313  4.6806
 M9F  CAT   C  CH2   0  -0.569  13.4244  40.5628  5.7938
 M9F  C     C  C     0   0.526  17.1758  37.2660  5.7100
 M9F  CA    C  CH1   0  -0.209  15.6783  37.3895  5.9827
 M9F  CB    C  CH2   0  -0.433  15.2876  38.8700  5.9039
 M9F  CAS   C  CH2   0  -0.413  13.7804  39.0812  5.9181
 M9F  N     N  NH2   0  -0.780  15.1850  36.7953  7.2012
 M9F  NAC   N  NH1   0  -0.619  11.4291  41.2304  4.6036
 M9F  CAD   C  CH1   0  -0.215  10.0160  41.2909  4.3744
 M9F  CAG   C  C     0   0.572   9.3974  39.8889  4.3698
 M9F  OAH   O  O     0  -0.463  10.0401  38.9028  4.0651
 M9F  CAE   C  CH2   0  -0.565   9.7188  41.9911  3.0508
 M9F  SAF   S  S2    0  -0.241  10.4562  41.0766  1.6499
 M9F  CAN   C  CH3   0  -0.764   3.9724  39.5123  2.2419
 M9F  SAM   S  S2    0  -0.040   5.2697  40.0857  3.3594
 M9F  CAK   C  CH1   0  -0.345   6.3935  38.6451  3.3318
 M9F  CAO   C  CH3   0  -0.642   7.2319  38.5898  2.0677
 M9F  CAJ   C  CH1   0  -0.223   7.2610  38.7036  4.6022
 M9F  CAP   C  C     0   0.563   6.4134  38.6216  5.8628
 M9F  OAR   O  OH1   0  -0.583   5.6974  37.5108  5.8902
 M9F  OAQ   O  O     0  -0.425   6.4056  39.4543  6.7313
 M9F  NAI   N  NH1   0  -0.633   8.0826  39.8808  4.6566
 M9F  HAT1  H  HCH2  0   0.249  13.8938  40.9862  4.9026
 M9F  HAT2  H  HCH2  0   0.263  13.8191  41.1101  6.6538
 M9F  HA    H  HCH1  0   0.273  15.1984  36.8784  5.1400
 M9F  HB1C  H  HCH2  0   0.242  15.7037  39.3007  4.9907
 M9F  HB2C  H  HCH2  0   0.234  15.7445  39.4094  6.7415
 M9F  HAS1  H  HCH2  0   0.238  13.3535  38.6750  6.8351
 M9F  HAS2  H  HCH2  0   0.228  13.3304  38.5285  5.0871
 M9F  HN1   H  HNH2  0   0.356  15.3931  35.8063  7.2360
 M9F  HN2   H  HNH2  0   0.345  15.6247  37.2162  8.0099
 M9F  HXT   H  HOH1  0   0.480  18.7972  36.6679  6.4685
 M9F  HAC   H  HNH1  0   0.400  12.0385  41.3147  3.8038
 M9F  HAD   H  HCH1  0   0.302   9.5419  41.8907  5.1575
 M9F  HAE1  H  HCH2  0   0.290   8.6418  42.0754  2.9147
 M9F  HAE2  H  HCH2  0   0.310  10.1385  42.9952  3.0765
 M9F  HAF   H  HSH1  0   0.235  10.5573  42.1210  0.8221
 M9F  HAN1  H  HCH3  0   0.266   3.5191  38.5918  2.6063
 M9F  HAN2  H  HCH3  0   0.280   3.2102  40.2883  2.2095
 M9F  HAN3  H  HCH3  0   0.264   4.3498  39.3592  1.2326
 M9F  HAK   H  HCH1  0   0.291   5.7709  37.7499  3.3880
 M9F  HAO1  H  HCH3  0   0.247   6.5944  38.5224  1.1868
 M9F  HAO2  H  HCH3  0   0.234   7.8617  39.4721  1.9558
 M9F  HAO3  H  HCH3  0   0.240   7.8758  37.7084  2.0759
 M9F  HAJ   H  HCH1  0   0.322   7.9212  37.8307  4.5887
 M9F  HAI   H  HNH1  0   0.406   7.6596  40.7360  4.9846
 M9F  HAR   H  HOH1  0   0.490   5.1571  37.4791  6.6945
 M9F  OXT   O  OH1   0  -0.584  17.8582  36.7167  6.7041

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
 M9F  CAN  SAM   single  1.806  0.020  1.806
 M9F  SAM  CAK   single  1.827  0.020  1.827
 M9F  CAK  CAO   single  1.518  0.020  1.518
 M9F  CAK  CAJ   single  1.539  0.020  1.539
 M9F  CAJ  CAP   single  1.521  0.020  1.521
 M9F  CAJ  NAI   single  1.437  0.020  1.437
 M9F  CAP  OAR   single  1.322  0.020  1.322
 M9F  CAP  OAQ   double  1.203  0.020  1.203
 M9F  NAI  CAG   single  1.346  0.020  1.346
 M9F  CAG  OAH   double  1.216  0.020  1.216
 M9F  CAG  CAD   single  1.532  0.020  1.532
 M9F  CAD  CAE   single  1.527  0.020  1.527
 M9F  CAD  NAC   single  1.433  0.020  1.433
 M9F  CAE  SAF   single  1.828  0.020  1.828
 M9F  NAC  CAU   single  1.346  0.020  1.346
 M9F  CAU  OAV   double  1.223  0.020  1.223
 M9F  CAU  CAT   single  1.509  0.020  1.509
 M9F  CAT  CAS   single  1.529  0.020  1.529
 M9F  CAS  CB    single  1.522  0.020  1.522
 M9F  CB   CA    single  1.533  0.020  1.533
 M9F  CA   C     single  1.527  0.020  1.527
 M9F  CA   N     single  1.443  0.020  1.443
 M9F  C    O     double  1.208  0.020  1.208
 M9F  C    OXT   single  1.325  0.020  1.325
 M9F  CAN  HAN1  single  0.970  0.020  1.090
 M9F  CAN  HAN2  single  0.970  0.020  1.090
 M9F  CAN  HAN3  single  0.970  0.020  1.090
 M9F  CAK  HAK   single  0.970  0.020  1.090
 M9F  CAO  HAO1  single  0.970  0.020  1.090
 M9F  CAO  HAO2  single  0.970  0.020  1.090
 M9F  CAO  HAO3  single  0.970  0.020  1.090
 M9F  CAJ  HAJ   single  0.970  0.020  1.090
 M9F  NAI  HAI   single  0.860  0.020  1.020
 M9F  OAR  HAR   single  0.850  0.020  0.980
 M9F  CAD  HAD   single  0.970  0.020  1.090
 M9F  CAE  HAE1  single  0.970  0.020  1.090
 M9F  CAE  HAE2  single  0.970  0.020  1.090
 M9F  NAC  HAC   single  0.860  0.020  1.020
 M9F  SAF  HAF   single  1.200  0.020  1.300
 M9F  CAT  HAT1  single  0.970  0.020  1.090
 M9F  CAT  HAT2  single  0.970  0.020  1.090
 M9F  CAS  HAS1  single  0.970  0.020  1.090
 M9F  CAS  HAS2  single  0.970  0.020  1.090
 M9F  CB   HB1C  single  0.970  0.020  1.090
 M9F  CB   HB2C  single  0.970  0.020  1.090
 M9F  CA   HA    single  0.970  0.020  1.090
 M9F  N    HN1   single  0.890  0.020  1.040
 M9F  N    HN2   single  0.890  0.020  1.040
 M9F  OXT  HXT   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
 M9F  NAC   CAU  CAT   115.56  3.000
 M9F  CAT   CAU  OAV   122.58  3.000
 M9F  NAC   CAU  OAV   121.85  3.000
 M9F  HAT2  CAT  HAT1  107.01  3.000
 M9F  HAT2  CAT  CAS   109.71  3.000
 M9F  HAT1  CAT  CAS   109.99  3.000
 M9F  HAT2  CAT  CAU   108.26  3.000
 M9F  HAT1  CAT  CAU   111.03  3.000
 M9F  CAS   CAT  CAU   110.76  3.000
 M9F  OXT   C    CA    113.86  3.000
 M9F  OXT   C    O     123.03  3.000
 M9F  CA    C    O     123.11  3.000
 M9F  HA    CA   N     107.91  3.000
 M9F  HA    CA   CB    107.41  3.000
 M9F  N     CA   CB    110.73  3.000
 M9F  HA    CA   C     104.74  3.000
 M9F  N     CA   C     116.93  3.000
 M9F  CB    CA   C     108.59  3.000
 M9F  HB2C  CB   HB1C  106.63  3.000
 M9F  HB2C  CB   CAS   109.72  3.000
 M9F  HB1C  CB   CAS   109.29  3.000
 M9F  HB2C  CB   CA    109.25  3.000
 M9F  HB1C  CB   CA    109.07  3.000
 M9F  CAS   CB   CA    112.70  3.000
 M9F  HAS2  CAS  HAS1  106.83  3.000
 M9F  HAS2  CAS  CB    109.26  3.000
 M9F  HAS1  CAS  CB    110.11  3.000
 M9F  HAS2  CAS  CAT   109.38  3.000
 M9F  HAS1  CAS  CAT   109.77  3.000
 M9F  CB    CAS  CAT   111.37  3.000
 M9F  HN2   N    HN1   106.85  3.000
 M9F  HN2   N    CA    110.80  3.000
 M9F  HN1   N    CA    111.20  3.000
 M9F  HAC   NAC  CAD   117.73  3.000
 M9F  HAC   NAC  CAU   119.10  3.000
 M9F  CAD   NAC  CAU   121.17  3.000
 M9F  HAD   CAD  CAE   106.54  3.000
 M9F  HAD   CAD  CAG   109.19  3.000
 M9F  CAE   CAD  CAG   109.78  3.000
 M9F  HAD   CAD  NAC   109.63  3.000
 M9F  CAE   CAD  NAC   110.49  3.000
 M9F  CAG   CAD  NAC   111.09  3.000
 M9F  NAI   CAG  OAH   124.40  3.000
 M9F  OAH   CAG  CAD   121.96  3.000
 M9F  NAI   CAG  CAD   113.53  3.000
 M9F  HAE2  CAE  HAE1  108.23  3.000
 M9F  HAE2  CAE  SAF   108.91  3.000
 M9F  HAE1  CAE  SAF   109.99  3.000
 M9F  HAE2  CAE  CAD   109.12  3.000
 M9F  HAE1  CAE  CAD   109.66  3.000
 M9F  SAF   CAE  CAD   110.88  3.000
 M9F  HAF   SAF  CAE    96.56  3.000
 M9F  HAN3  CAN  HAN2  108.40  3.000
 M9F  HAN3  CAN  HAN1  109.62  3.000
 M9F  HAN2  CAN  HAN1  108.73  3.000
 M9F  HAN3  CAN  SAM   111.68  3.000
 M9F  HAN2  CAN  SAM   107.17  3.000
 M9F  HAN1  CAN  SAM   111.13  3.000
 M9F  CAK   SAM  CAN   100.50  3.000
 M9F  HAK   CAK  CAJ   108.06  3.000
 M9F  HAK   CAK  CAO   109.14  3.000
 M9F  CAJ   CAK  CAO   112.17  3.000
 M9F  HAK   CAK  SAM   107.15  3.000
 M9F  CAJ   CAK  SAM   107.71  3.000
 M9F  CAO   CAK  SAM   112.39  3.000
 M9F  HAO3  CAO  HAO2  108.28  3.000
 M9F  HAO3  CAO  HAO1  107.54  3.000
 M9F  HAO2  CAO  HAO1  107.77  3.000
 M9F  HAO3  CAO  CAK   110.42  3.000
 M9F  HAO2  CAO  CAK   112.04  3.000
 M9F  HAO1  CAO  CAK   110.63  3.000
 M9F  HAJ   CAJ  NAI   108.00  3.000
 M9F  HAJ   CAJ  CAP   107.66  3.000
 M9F  NAI   CAJ  CAP   109.35  3.000
 M9F  HAJ   CAJ  CAK   107.43  3.000
 M9F  NAI   CAJ  CAK   112.62  3.000
 M9F  CAP   CAJ  CAK   111.58  3.000
 M9F  OAQ   CAP  OAR   124.27  3.000
 M9F  OAQ   CAP  CAJ   124.36  3.000
 M9F  OAR   CAP  CAJ   111.36  3.000
 M9F  HAR   OAR  CAP   110.28  3.000
 M9F  HAI   NAI  CAJ   117.85  3.000
 M9F  HAI   NAI  CAG   118.29  3.000
 M9F  CAJ   NAI  CAG   123.75  3.000
 M9F  HXT   OXT  C     109.71  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
 M9F  CONST_01  CAD   NAC  CAU  OAV     0.00   0.0  0
 M9F  CONST_02  CAD   NAC  CAU  CAT   180.00   0.0  0
 M9F  CONST_03  CAJ   NAI  CAG  CAD   180.00   0.0  0
 M9F  CONST_04  CAJ   NAI  CAG  OAH     0.00   0.0  0
 M9F  CONST_05  HAC   NAC  CAU  OAV   180.00   0.0  0
 M9F  CONST_06  HAI   NAI  CAG  CAD     0.00   0.0  0
 M9F  CONST_07  HXT   OXT  C    O       0.00   0.0  0
 M9F  CONST_08  HAR   OAR  CAP  CAJ   180.00   0.0  0
 M9F  Var_01    CB    CAS  CAT  CAU   177.96  30.0  3
 M9F  Var_02    CAS   CAT  CAU  OAV    64.99  30.0  3
 M9F  Var_03    CA    CB   CAS  CAT  -178.20  30.0  3
 M9F  Var_04    HAN1  CAN  SAM  CAK    59.10  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
 M9F  chir_01  CA   CB   C    N    negativ
 M9F  chir_02  CAD  NAC  CAG  CAE  positiv
 M9F  chir_03  CAK  SAM  CAJ  CAO  positiv
 M9F  chir_04  CAJ  NAI  CAK  CAP  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
 M9F  plan-1  CAU  0.020
 M9F  plan-1  OAV  0.020
 M9F  plan-1  CAT  0.020
 M9F  plan-1  NAC  0.020
 M9F  plan-1  CAD  0.020
 M9F  plan-1  HAC  0.020
 M9F  plan-2  CAD  0.020
 M9F  plan-2  CAG  0.020
 M9F  plan-2  OAH  0.020
 M9F  plan-2  CAJ  0.020
 M9F  plan-2  NAI  0.020
 M9F  plan-2  HAI  0.020
 M9F  plan-3  O    0.020
 M9F  plan-3  C    0.020
 M9F  plan-3  CA   0.020
 M9F  plan-3  HXT  0.020
 M9F  plan-3  OXT  0.020
 M9F  plan-4  CAJ  0.020
 M9F  plan-4  CAP  0.020
 M9F  plan-4  OAR  0.020
 M9F  plan-4  OAQ  0.020
 M9F  plan-4  HAR  0.020

