# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 23:07:10 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (2S,5R,6R)-6-[(2,6-dimethoxyphenyl)carbonylamino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(OC)c1C(=O)N[C@H]2[C@H]3SC(C)(C)[C@@H](N3C2=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
 MII  MII  '(2S,5R,6R)-6-[(2,6-dimethoxyphenyl)carbonylamino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid'  ligand  46  26  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MII
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
 MII  C     C  C     0   0.520  -1.7611  -1.6534   0.1819
 MII  N     N  NH1   0  -0.611   0.6565  -0.9907   0.3384
 MII  O     O  O     0  -0.396  -1.9065  -2.6787  -0.4214
 MII  CA    C  C     0  -0.235  -0.6219  -0.9801   0.9548
 MII  CB    C  C     0  -0.210  -1.5130   0.2852   0.8449
 MII  CAA   C  CH3   0  -0.437   4.5781  -3.8143   0.5408
 MII  CAB   C  CH3   0  -0.434   2.3167   2.8385  -0.8396
 MII  CAC   C  CH3   0  -0.636  -3.1153   1.7475  -2.4496
 MII  CAD   C  CH3   0  -0.645  -3.6348   2.4897  -0.1098
 MII  OAE   O  O     0  -0.417  -5.2614  -0.2256   0.9591
 MII  OAF   O  O     0  -0.456   1.8439  -0.7453   2.2490
 MII  OAH   O  OH1   0  -0.583  -5.7393   0.1702  -1.1898
 MII  CAI   C  CR16  0  -0.227   5.2518  -0.1298  -1.3604
 MII  CAJ   C  CR16  0  -0.409   5.0833  -1.3673  -0.7573
 MII  CAK   C  CR16  0  -0.406   4.3282   0.8943  -1.2179
 MII  SAO   S  S2    0   0.081  -1.1635   1.3653  -0.5641
 MII  CAP   C  C     0   0.547  -4.9147  -0.0429  -0.1760
 MII  CAQ   C  C     0   0.528   1.7974  -0.7780   1.0344
 MII  CAS   C  CR6   0   0.413   3.9471  -1.5866   0.0202
 MII  CAT   C  CR6   0   0.424   3.1935   0.6663  -0.4417
 MII  CAU   C  CR6   0  -0.312   3.0014  -0.5735   0.1694
 MII  CAW   C  CR15  0  -0.150  -3.4715  -0.0274  -0.6430
 MII  NAX   N  N     0  -0.418  -2.5886  -0.5695   0.3580
 MII  CAY   C  CR5   0  -0.260  -2.9641   1.4219  -0.9710
 MII  HN    H  HNH1  0   0.414   0.7011  -0.9339  -0.6676
 MII  HA    H  H     0   0.335  -0.5497  -1.3325   1.9840
 MII  HB    H  H     0   0.307  -1.7184   0.8312   1.7638
 MII  HAA   H  HCH3  0   0.263   4.1634  -4.6282   1.1297
 MII  HAAA  H  HCH3  0   0.232   4.6916  -4.1498  -0.4927
 MII  HAAB  H  HCH3  0   0.232   5.5605  -3.5544   0.9415
 MII  HAB   H  HCH3  0   0.234   3.2067   3.3883  -0.5245
 MII  HABA  H  HCH3  0   0.231   2.3189   2.7498  -1.9284
 MII  HABB  H  HCH3  0   0.258   1.4318   3.3906  -0.5342
 MII  HAC   H  HCH3  0   0.252  -2.6907   2.7265  -2.6722
 MII  HACA  H  HCH3  0   0.251  -2.6169   1.0071  -3.0749
 MII  HACB  H  HCH3  0   0.253  -4.1692   1.7780  -2.7269
 MII  HAD   H  HCH3  0   0.245  -4.6965   2.5803  -0.3498
 MII  HADA  H  HCH3  0   0.254  -3.5428   2.2883   0.9580
 MII  HADB  H  HCH3  0   0.261  -3.1778   3.4587  -0.3053
 MII  HOAH  H  HOH1  0   0.490  -6.6583   0.1882  -0.8811
 MII  HAI   H  HCR6  0   0.268   6.1343   0.0423  -1.9628
 MII  HAJ   H  HCR6  0   0.282   5.8308  -2.1343  -0.9012
 MII  HAK   H  HCR6  0   0.281   4.5027   1.8450  -1.7020
 MII  HAW   H  HCR5  0   0.315  -3.4016  -0.6410  -1.5469
 MII  OAM   O  O2    0  -0.464   3.6649  -2.7379   0.6491
 MII  OAN   O  O2    0  -0.465   2.2309   1.5738  -0.2104

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
 MII  C    O     double    1.198  0.020  1.198
 MII  C    CA    single    1.532  0.020  1.532
 MII  C    NAX   single    1.375  0.020  1.375
 MII  N    CA    single    1.419  0.020  1.419
 MII  N    CAQ   single    1.353  0.020  1.353
 MII  CA   CB    single    1.551  0.020  1.551
 MII  CB   SAO   single    1.809  0.020  1.809
 MII  CB   NAX   single    1.458  0.020  1.458
 MII  CAA  OAM   single    1.416  0.020  1.416
 MII  CAB  OAN   single    1.415  0.020  1.415
 MII  CAC  CAY   single    1.522  0.020  1.522
 MII  CAD  CAY   single    1.527  0.020  1.527
 MII  OAE  CAP   double    1.201  0.020  1.201
 MII  OAF  CAQ   double    1.216  0.020  1.216
 MII  OAH  CAP   single    1.324  0.020  1.324
 MII  CAI  CAJ   aromatic  1.387  0.020  1.387
 MII  CAI  CAK   aromatic  1.386  0.020  1.386
 MII  CAJ  CAS   aromatic  1.394  0.020  1.394
 MII  CAK  CAT   aromatic  1.394  0.020  1.394
 MII  OAM  CAS   single    1.342  0.020  1.342
 MII  OAN  CAT   single    1.343  0.020  1.343
 MII  SAO  CAY   single    1.847  0.020  1.847
 MII  CAP  CAW   single    1.517  0.020  1.517
 MII  CAQ  CAU   single    1.497  0.020  1.497
 MII  CAS  CAU   aromatic  1.394  0.020  1.394
 MII  CAT  CAU   aromatic  1.395  0.020  1.395
 MII  CAW  NAX   single    1.441  0.020  1.441
 MII  CAW  CAY   single    1.570  0.020  1.570
 MII  N    HN    single    0.860  0.020  1.020
 MII  CA   HA    single    0.970  0.020  1.090
 MII  CB   HB    single    0.970  0.020  1.090
 MII  CAA  HAA   single    0.970  0.020  1.090
 MII  CAA  HAAA  single    0.970  0.020  1.090
 MII  CAA  HAAB  single    0.970  0.020  1.090
 MII  CAB  HAB   single    0.970  0.020  1.090
 MII  CAB  HABA  single    0.970  0.020  1.090
 MII  CAB  HABB  single    0.970  0.020  1.090
 MII  CAC  HAC   single    0.970  0.020  1.090
 MII  CAC  HACA  single    0.970  0.020  1.090
 MII  CAC  HACB  single    0.970  0.020  1.090
 MII  CAD  HAD   single    0.970  0.020  1.090
 MII  CAD  HADA  single    0.970  0.020  1.090
 MII  CAD  HADB  single    0.970  0.020  1.090
 MII  OAH  HOAH  single    0.850  0.020  0.980
 MII  CAI  HAI   single    0.930  0.020  1.080
 MII  CAJ  HAJ   single    0.930  0.020  1.080
 MII  CAK  HAK   single    0.930  0.020  1.080
 MII  CAW  HAW   single    0.970  0.020  1.090

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
 MII  NAX   C    CA     92.09  3.000
 MII  NAX   C    O     131.75  3.000
 MII  CA    C    O     136.05  3.000
 MII  HN    N    CAQ   117.83  3.000
 MII  HN    N    CA    118.20  3.000
 MII  CAQ   N    CA    122.34  3.000
 MII  HA    CA   CB    111.62  3.000
 MII  HA    CA   N     110.36  3.000
 MII  CB    CA   N     119.52  3.000
 MII  HA    CA   C     112.54  3.000
 MII  CB    CA   C      84.01  3.000
 MII  N     CA   C     116.57  3.000
 MII  HB    CB   NAX   115.91  3.000
 MII  HB    CB   SAO   113.23  3.000
 MII  NAX   CB   SAO   103.44  3.000
 MII  HB    CB   CA    117.24  3.000
 MII  NAX   CB   CA     88.24  3.000
 MII  SAO   CB   CA    115.54  3.000
 MII  HAAB  CAA  HAAA  109.07  3.000
 MII  HAAB  CAA  HAA   108.82  3.000
 MII  HAAA  CAA  HAA   108.80  3.000
 MII  HAAB  CAA  OAM   111.79  3.000
 MII  HAAA  CAA  OAM   111.89  3.000
 MII  HAA   CAA  OAM   106.36  3.000
 MII  HABB  CAB  HABA  108.84  3.000
 MII  HABB  CAB  HAB   109.06  3.000
 MII  HABA  CAB  HAB   109.07  3.000
 MII  HABB  CAB  OAN   106.24  3.000
 MII  HABA  CAB  OAN   111.76  3.000
 MII  HAB   CAB  OAN   111.77  3.000
 MII  HACB  CAC  HACA  108.37  3.000
 MII  HACB  CAC  HAC   107.43  3.000
 MII  HACA  CAC  HAC   108.36  3.000
 MII  HACB  CAC  CAY   110.43  3.000
 MII  HACA  CAC  CAY   111.51  3.000
 MII  HAC   CAC  CAY   110.60  3.000
 MII  HADB  CAD  HADA  107.74  3.000
 MII  HADB  CAD  HAD   107.14  3.000
 MII  HADA  CAD  HAD   108.21  3.000
 MII  HADB  CAD  CAY   109.67  3.000
 MII  HADA  CAD  CAY   112.71  3.000
 MII  HAD   CAD  CAY   111.16  3.000
 MII  HOAH  OAH  CAP   110.46  3.000
 MII  HAI   CAI  CAK   118.88  3.000
 MII  HAI   CAI  CAJ   118.88  3.000
 MII  CAK   CAI  CAJ   122.24  3.000
 MII  HAJ   CAJ  CAS   121.76  3.000
 MII  HAJ   CAJ  CAI   119.43  3.000
 MII  CAS   CAJ  CAI   118.81  3.000
 MII  HAK   CAK  CAT   121.65  3.000
 MII  HAK   CAK  CAI   119.74  3.000
 MII  CAT   CAK  CAI   118.61  3.000
 MII  CAY   SAO  CB     90.09  3.000
 MII  CAW   CAP  OAH   110.80  3.000
 MII  CAW   CAP  OAE   124.56  3.000
 MII  OAH   CAP  OAE   124.64  3.000
 MII  CAU   CAQ  OAF   122.88  3.000
 MII  CAU   CAQ  N     113.73  3.000
 MII  OAF   CAQ  N     123.38  3.000
 MII  CAU   CAS  OAM   115.51  3.000
 MII  CAU   CAS  CAJ   119.89  3.000
 MII  OAM   CAS  CAJ   124.60  3.000
 MII  CAU   CAT  OAN   115.23  3.000
 MII  CAU   CAT  CAK   120.09  3.000
 MII  OAN   CAT  CAK   124.68  3.000
 MII  CAT   CAU  CAS   120.36  3.000
 MII  CAT   CAU  CAQ   119.03  3.000
 MII  CAS   CAU  CAQ   120.56  3.000
 MII  HAW   CAW  CAY   108.92  3.000
 MII  HAW   CAW  NAX   108.88  3.000
 MII  CAY   CAW  NAX   107.12  3.000
 MII  HAW   CAW  CAP   108.01  3.000
 MII  CAY   CAW  CAP   112.41  3.000
 MII  NAX   CAW  CAP   111.43  3.000
 MII  CAW   NAX  CB    117.63  3.000
 MII  CAW   NAX  C     125.21  3.000
 MII  CB    NAX  C      93.49  3.000
 MII  CAW   CAY  SAO   103.93  3.000
 MII  CAW   CAY  CAD   112.69  3.000
 MII  SAO   CAY  CAD   108.99  3.000
 MII  CAW   CAY  CAC   111.62  3.000
 MII  SAO   CAY  CAC   108.51  3.000
 MII  CAD   CAY  CAC   110.78  3.000
 MII  CAS   OAM  CAA   118.74  3.000
 MII  CAT   OAN  CAB   118.94  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
 MII  CONST_01  CAU   CAS  CAJ  CAI     0.00   0.0  0
 MII  CONST_02  CAU   CAT  CAK  CAI     0.00   0.0  0
 MII  CONST_03  CAT   CAK  CAI  CAJ     0.00   0.0  0
 MII  CONST_04  CAT   CAU  CAS  CAJ     0.00   0.0  0
 MII  CONST_05  CAS   CAJ  CAI  CAK     0.00   0.0  0
 MII  CONST_06  CAS   CAU  CAT  CAK     0.00   0.0  0
 MII  CONST_07  CB    NAX  C    CA      0.00   0.0  0
 MII  CONST_09  OAM   CAS  CAJ  CAI   180.00   0.0  0
 MII  CONST_10  OAN   CAT  CAK  CAI   180.00   0.0  0
 MII  CONST_11  CAQ   CAU  CAS  CAJ   180.00   0.0  0
 MII  CONST_12  CAQ   CAU  CAT  CAK   180.00   0.0  0
 MII  CONST_13  CAT   CAU  CAS  OAM   180.00   0.0  0
 MII  CONST_14  CAS   CAU  CAT  OAN   180.00   0.0  0
 MII  CONST_17  HAK   CAK  CAI  CAJ   180.00   0.0  0
 MII  CONST_18  HAJ   CAJ  CAI  CAK   180.00   0.0  0
 MII  CONST_19  HAI   CAI  CAJ  CAS   180.00   0.0  0
 MII  CONST_20  CAU   CAQ  N    CA    180.00   0.0  0
 MII  CONST_21  OAF   CAQ  N    CA      0.00   0.0  0
 MII  CONST_22  HN    N    CAQ  CAU     0.00   0.0  0
 MII  CONST_23  HOAH  OAH  CAP  CAW   180.00   0.0  0
 MII  Var_01    CAW   CAY  SAO  CB    -36.87  30.0  1
 MII  Var_02    CAS   CAU  CAQ  N    -104.55  30.0  2
 MII  Var_03    CAJ   CAS  OAM  CAA     0.70  30.0  2
 MII  Var_04    CAK   CAT  OAN  CAB     3.25  30.0  2
 MII  Var_05    HAC   CAC  CAY  SAO   -61.83  30.0  3
 MII  Var_06    HAD   CAD  CAY  SAO   177.80  30.0  3
 MII  Var_07    HAA   CAA  OAM  CAS   179.24  30.0  3
 MII  Var_08    HAB   CAB  OAN  CAT   -62.64  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
 MII  chir_01  CA   C    N    CB   negativ
 MII  chir_02  CB   SAO  NAX  CA   negativ
 MII  chir_03  CAW  NAX  CAP  CAY  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
 MII  plan-1  CAI   0.020
 MII  plan-1  CAJ   0.020
 MII  plan-1  CAK   0.020
 MII  plan-1  CAQ   0.020
 MII  plan-1  CAS   0.020
 MII  plan-1  CAT   0.020
 MII  plan-1  CAU   0.020
 MII  plan-1  HAI   0.020
 MII  plan-1  HAJ   0.020
 MII  plan-1  HAK   0.020
 MII  plan-1  OAM   0.020
 MII  plan-1  OAN   0.020
 MII  plan-2  N     0.020
 MII  plan-2  CA    0.020
 MII  plan-2  OAF   0.020
 MII  plan-2  CAQ   0.020
 MII  plan-2  CAU   0.020
 MII  plan-2  HN    0.020
 MII  plan-3  C     0.020
 MII  plan-3  O     0.020
 MII  plan-3  CA    0.020
 MII  plan-3  CB    0.020
 MII  plan-3  CAW   0.020
 MII  plan-3  NAX   0.020
 MII  plan-4  OAE   0.020
 MII  plan-4  OAH   0.020
 MII  plan-4  CAP   0.020
 MII  plan-4  CAW   0.020
 MII  plan-4  HOAH  0.020

