# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 12:08:38 2020
#   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  48  25  .  2021-08-14  2021-08-14  
;
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   0.587   1.6836   0.6618  -0.0361
 M9F  OAV   O  O      0  -0.521   1.6237   1.2762   1.0183
 M9F  O     O  O      0  -0.550   8.6951  -0.7623  -0.2187
 M9F  CAT   C  CH2    0  -0.627   2.9693   0.0769  -0.5814
 M9F  C     C  C      0   0.385   7.7112  -1.3922   0.2076
 M9F  CA    C  CH1    0  -0.173   6.5447  -0.5918   0.8256
 M9F  CB    C  CH2    0  -0.416   5.3665  -0.5825  -0.1536
 M9F  CAS   C  CH2    0  -0.425   4.0996   0.0244   0.4338
 M9F  N     N  NH2    0  -0.814   6.8729   0.7681   1.2263
 M9F  NAC   N  NH1    0  -0.699   0.6080   0.4614  -0.8241
 M9F  CAD   C  CH1    0  -0.151  -0.7093   0.9458  -0.5261
 M9F  CAG   C  C      0   0.565  -1.7301  -0.1034  -0.9755
 M9F  OAH   O  O      0  -0.542  -1.4386  -0.9458  -1.8131
 M9F  CAE   C  CH2    0  -0.533  -1.0334   2.2659  -1.2358
 M9F  SAF   S  S2     0  -0.252   0.1530   3.5591  -0.7413
 M9F  CAN   C  CH3    0  -0.758  -7.0749   0.9582   1.4521
 M9F  SAM   S  S2     0  -0.036  -5.4827   0.1119   1.3543
 M9F  CAK   C  CH1    0  -0.374  -5.3673  -0.2591  -0.4370
 M9F  CAO   C  CH3    0  -0.636  -5.5935   0.9661  -1.3060
 M9F  CAJ   C  CH1    0  -0.218  -4.0059  -0.9125  -0.6867
 M9F  CAP   C  C      0   0.383  -3.8531  -2.2365   0.1135
 M9F  OAR   O  OC    -1  -0.735  -4.7103  -3.0995  -0.1570
 M9F  OAQ   O  O      0  -0.399  -2.9212  -2.3125   0.9282
 M9F  NAI   N  NH1    0  -0.594  -2.9420   0.0317  -0.4352
 M9F  HAT1  H  HCH2   0   0.283   2.7683  -0.9196  -0.9859
 M9F  HAT2  H  HCH2   0   0.325   3.2710   0.6868  -1.4409
 M9F  HA    H  HCH1   0   0.172   6.2174  -1.1297   1.7234
 M9F  HB1C  H  HCH2   0   0.148   5.6562  -0.0305  -1.0567
 M9F  HB2C  H  HCH2   0   0.278   5.1696  -1.6095  -0.4721
 M9F  HAS1  H  HCH2   0   0.231   4.3155   1.0280   0.8001
 M9F  HAS2  H  HCH2   0   0.268   3.7922  -0.5643   1.3039
 M9F  HN1   H  HNH2   0   0.344   7.5677   0.7321   1.9626
 M9F  HN2   H  HNH2   0   0.309   7.3483   1.2158   0.4503
 M9F  HAC   H  HNH1   0   0.377   0.7099  -0.0836  -1.6665
 M9F  HAD   H  HCH1   0   0.298  -0.7927   1.0913   0.5542
 M9F  HAE1  H  HCH2   0   0.250  -0.9858   2.1263  -2.3166
 M9F  HAE2  H  HCH2   0   0.275  -2.0419   2.5859  -0.9749
 M9F  HAF   H  HSH1   0   0.218  -0.3738   4.5297  -1.4971
 M9F  HAN1  H  HCH3   0   0.288  -7.0408   1.9512   1.0090
 M9F  HAN2  H  HCH3   0   0.259  -7.8582   0.3724   0.9733
 M9F  HAN3  H  HCH3   0   0.279  -7.3172   1.0591   2.5086
 M9F  HAK   H  HCH1   0   0.301  -6.1237  -1.0131  -0.6611
 M9F  HAO1  H  HCH3   0   0.225  -6.6033   1.3581  -1.1913
 M9F  HAO2  H  HCH3   0   0.222  -4.8930   1.7681  -1.0741
 M9F  HAO3  H  HCH3   0   0.203  -5.4656   0.6995  -2.3575
 M9F  HAJ   H  HCH1   0   0.299  -3.9794  -1.1676  -1.7499
 M9F  HAI   H  HNH1   0   0.372  -3.0536   0.6668   0.3412
 M9F  OXT   O  OC    -1  -0.693   7.5563  -2.6355   0.1701

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  1.833  0.020  1.833
 M9F  CAK  CAO   single  1.519  0.020  1.519
 M9F  CAK  CAJ   single  1.531  0.020  1.531
 M9F  CAJ  CAP   single  1.555  0.020  1.555
 M9F  CAJ  NAI   single  1.444  0.020  1.444
 M9F  CAP  OAR   deloc   1.246  0.020  1.246
 M9F  CAP  OAQ   deloc   1.240  0.020  1.240
 M9F  NAI  CAG   single  1.334  0.020  1.334
 M9F  CAG  OAH   double  1.223  0.020  1.223
 M9F  CAG  CAD   single  1.531  0.020  1.531
 M9F  CAD  CAE   single  1.533  0.020  1.533
 M9F  CAD  NAC   single  1.435  0.020  1.435
 M9F  CAE  SAF   single  1.823  0.020  1.823
 M9F  NAC  CAU   single  1.348  0.020  1.348
 M9F  CAU  OAV   double  1.222  0.020  1.222
 M9F  CAU  CAT   single  1.514  0.020  1.514
 M9F  CAT  CAS   single  1.520  0.020  1.520
 M9F  CAS  CB    single  1.523  0.020  1.523
 M9F  CB   CA    single  1.532  0.020  1.532
 M9F  CA   C     single  1.544  0.020  1.544
 M9F  CA   N     single  1.455  0.020  1.455
 M9F  C    O     deloc   1.244  0.020  1.244
 M9F  C    OXT   deloc   1.254  0.020  1.254
 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  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

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   114.17  3.000
 M9F  CAT   CAU  OAV   123.14  3.000
 M9F  NAC   CAU  OAV   122.68  3.000
 M9F  HAT2  CAT  HAT1  105.51  3.000
 M9F  HAT2  CAT  CAS   109.77  3.000
 M9F  HAT1  CAT  CAS   110.61  3.000
 M9F  HAT2  CAT  CAU   107.52  3.000
 M9F  HAT1  CAT  CAU   109.21  3.000
 M9F  CAS   CAT  CAU   113.84  3.000
 M9F  OXT   C    CA    115.65  3.000
 M9F  OXT   C    O     126.15  3.000
 M9F  CA    C    O     118.19  3.000
 M9F  HA    CA   N     107.48  3.000
 M9F  HA    CA   CB    107.26  3.000
 M9F  N     CA   CB    110.11  3.000
 M9F  HA    CA   C     107.39  3.000
 M9F  N     CA   C     115.11  3.000
 M9F  CB    CA   C     109.17  3.000
 M9F  HB2C  CB   HB1C  106.28  3.000
 M9F  HB2C  CB   CAS   109.70  3.000
 M9F  HB1C  CB   CAS   109.67  3.000
 M9F  HB2C  CB   CA    108.60  3.000
 M9F  HB1C  CB   CA    109.02  3.000
 M9F  CAS   CB   CA    113.31  3.000
 M9F  HAS2  CAS  HAS1  106.48  3.000
 M9F  HAS2  CAS  CB    109.02  3.000
 M9F  HAS1  CAS  CB    109.38  3.000
 M9F  HAS2  CAS  CAT   109.92  3.000
 M9F  HAS1  CAS  CAT   109.87  3.000
 M9F  CB    CAS  CAT   112.01  3.000
 M9F  HN2   N    HN1   104.50  3.000
 M9F  HN2   N    CA    107.91  3.000
 M9F  HN1   N    CA    108.76  3.000
 M9F  HAC   NAC  CAD   116.67  3.000
 M9F  HAC   NAC  CAU   119.20  3.000
 M9F  CAD   NAC  CAU   124.11  3.000
 M9F  HAD   CAD  CAE   109.07  3.000
 M9F  HAD   CAD  CAG   109.29  3.000
 M9F  CAE   CAD  CAG   108.25  3.000
 M9F  HAD   CAD  NAC   108.68  3.000
 M9F  CAE   CAD  NAC   112.87  3.000
 M9F  CAG   CAD  NAC   108.64  3.000
 M9F  NAI   CAG  OAH   124.32  3.000
 M9F  OAH   CAG  CAD   120.93  3.000
 M9F  NAI   CAG  CAD   114.67  3.000
 M9F  HAE2  CAE  HAE1  108.37  3.000
 M9F  HAE2  CAE  SAF   109.20  3.000
 M9F  HAE1  CAE  SAF   109.33  3.000
 M9F  HAE2  CAE  CAD   109.73  3.000
 M9F  HAE1  CAE  CAD   109.83  3.000
 M9F  SAF   CAE  CAD   110.34  3.000
 M9F  HAF   SAF  CAE    96.03  3.000
 M9F  HAN3  CAN  HAN2  108.44  3.000
 M9F  HAN3  CAN  HAN1  108.52  3.000
 M9F  HAN2  CAN  HAN1  109.54  3.000
 M9F  HAN3  CAN  SAM   107.00  3.000
 M9F  HAN2  CAN  SAM   110.99  3.000
 M9F  HAN1  CAN  SAM   112.22  3.000
 M9F  CAK   SAM  CAN   101.73  3.000
 M9F  HAK   CAK  CAJ   106.74  3.000
 M9F  HAK   CAK  CAO   109.67  3.000
 M9F  CAJ   CAK  CAO   112.55  3.000
 M9F  HAK   CAK  SAM   107.27  3.000
 M9F  CAJ   CAK  SAM   107.57  3.000
 M9F  CAO   CAK  SAM   112.74  3.000
 M9F  HAO3  CAO  HAO2  108.01  3.000
 M9F  HAO3  CAO  HAO1  107.33  3.000
 M9F  HAO2  CAO  HAO1  107.98  3.000
 M9F  HAO3  CAO  CAK   109.66  3.000
 M9F  HAO2  CAO  CAK   112.09  3.000
 M9F  HAO1  CAO  CAK   111.60  3.000
 M9F  HAJ   CAJ  NAI   107.69  3.000
 M9F  HAJ   CAJ  CAP   107.42  3.000
 M9F  NAI   CAJ  CAP   113.25  3.000
 M9F  HAJ   CAJ  CAK   106.24  3.000
 M9F  NAI   CAJ  CAK   110.35  3.000
 M9F  CAP   CAJ  CAK   111.53  3.000
 M9F  OAQ   CAP  OAR   128.11  3.000
 M9F  OAQ   CAP  CAJ   117.65  3.000
 M9F  OAR   CAP  CAJ   114.24  3.000
 M9F  HAI   NAI  CAJ   117.63  3.000
 M9F  HAI   NAI  CAG   118.42  3.000
 M9F  CAJ   NAI  CAG   122.17  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  Var_01    CB    CAS  CAT  CAU  179.44  30.0  3
 M9F  Var_02    CAS   CAT  CAU  OAV   13.90  30.0  3
 M9F  Var_03    CA    CB   CAS  CAT  177.38  30.0  3
 M9F  Var_04    HAN1  CAN  SAM  CAK  -71.20  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  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

