# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:16:00 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: (6R,7R)-7-{[(2R)-2-hydroxy-2-phenylacetyl]amino}-3-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nnnc1SCC2=C(N3[C@H](SC2)[C@H](NC(=O)[C@H](O)c4ccccc4)C3=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
 SMX  SMX  '(6R,7R)-7-{[(2R)-2-hydroxy-2-phenylacetyl]amino}-3-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid'  ligand  48  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SMX
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
 SMX  C    C  C      0   0.529   1.1450   2.5543   0.6102
 SMX  N    N  NH1    0  -0.627   3.3800   1.5643   0.1003
 SMX  O    O  O      0  -0.406   1.1786   3.2945   1.5537
 SMX  CA   C  C      0  -0.263   2.1632   2.0778  -0.4339
 SMX  CB   C  C      0  -0.200   1.0554   1.0769  -0.8514
 SMX  NBD  N  N      0  -0.491   0.1799   1.7377   0.0920
 SMX  NBE  N  NR5    0  -0.316  -6.1413  -1.6672  -1.0085
 SMX  NAN  N  N      0  -0.135  -6.4873  -2.6119   0.8222
 SMX  NAO  N  N      0  -0.348  -5.3102  -1.9948   0.9423
 SMX  NAP  N  N      0  -0.080  -6.9952  -2.4245  -0.3273
 SMX  CAA  C  CH3    0  -0.532  -6.3856  -1.2372  -2.3662
 SMX  OAB  O  O      0  -0.575  -1.9327   3.3872   0.7329
 SMX  OAC  O  O      0  -0.469   4.5329   1.6364  -1.8445
 SMX  OAE  O  OC    -1  -0.576  -2.4405   1.9496   2.3665
 SMX  OAF  O  OH1    0  -0.659   6.7241   0.5857  -0.8087
 SMX  CAG  C  CR16   0  -0.260   4.0693  -3.4123   0.6967
 SMX  CAH  C  CR16   0  -0.235   4.2151  -2.5296   1.7565
 SMX  CAI  C  CR16   0  -0.234   4.4456  -3.0215  -0.5830
 SMX  CAJ  C  CR16   0  -0.314   4.7319  -1.2593   1.5357
 SMX  CAK  C  CR16   0  -0.284   4.9573  -1.7525  -0.8032
 SMX  CAL  C  CH2    0  -0.624  -2.6655  -0.5963   0.7694
 SMX  CAM  C  CH2    0  -0.614  -0.4570  -1.0131  -0.3799
 SMX  SAR  S  S2     0   0.083  -3.7536  -0.4374  -0.7021
 SMX  SAS  S  S2     0   0.064   1.3230  -0.6358  -0.3567
 SMX  CAT  C  C      0   0.380  -1.8844   2.2922   1.3109
 SMX  CAU  C  C      0   0.513   4.4529   1.3181  -0.6707
 SMX  CAV  C  C      0  -0.003  -1.3332  -0.0408   0.3727
 SMX  CAX  C  C      0   0.194  -1.0170   1.2459   0.5999
 SMX  CAY  C  CR6    0   0.102   5.0976  -0.8602   0.2563
 SMX  CAZ  C  CR5    0   0.376  -5.1000  -1.4043  -0.2123
 SMX  CBA  C  CH1    0  -0.131   5.5926   0.5492   0.0032
 SMX  H1   H  HNH1   0   0.416   3.3776   1.2153   1.0472
 SMX  H2   H  H      0   0.334   2.3615   2.8162  -1.2111
 SMX  H3   H  H      0   0.313   0.7116   1.1414  -1.8844
 SMX  H4   H  HCH3   0   0.280  -6.5448  -0.1614  -2.3992
 SMX  H5   H  HCH3   0   0.277  -5.5385  -1.5009  -2.9958
 SMX  H6   H  HCH3   0   0.290  -7.2724  -1.7453  -2.7298
 SMX  H10  H  HCR6   0   0.255   4.3370  -3.7083  -1.4123
 SMX  H11  H  HCR6   0   0.257   4.8538  -0.5775   2.3701
 SMX  H12  H  HCR6   0   0.253   5.2398  -1.4573  -1.8064
 SMX  H13  H  HCH2   0   0.323  -3.1104  -0.0512   1.5950
 SMX  H14  H  HCH2   0   0.301  -2.5957  -1.6533   1.0226
 SMX  H15  H  HCH2   0   0.295  -0.7858  -1.1155  -1.4177
 SMX  H16  H  HCH2   0   0.297  -0.5491  -2.0034   0.0706
 SMX  H17  H  HOH1   0   0.451   6.4459   0.9107  -1.6774
 SMX  H18  H  HCH1   0   0.281   5.8156   1.0245   0.9669
 SMX  H8   H  HCR6   0   0.256   3.6690  -4.4035   0.8663
 SMX  H9   H  HCR6   0   0.257   3.9341  -2.8299   2.7575

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
 SMX  CAG  CAH  aromatic  1.387  0.020  1.387
 SMX  CAG  CAI  aromatic  1.390  0.020  1.390
 SMX  CAH  CAJ  aromatic  1.389  0.020  1.389
 SMX  CAI  CAK  aromatic  1.386  0.020  1.386
 SMX  CAJ  CAY  aromatic  1.389  0.020  1.389
 SMX  CAK  CAY  aromatic  1.392  0.020  1.392
 SMX  CAY  CBA  single    1.515  0.020  1.515
 SMX  CBA  OAF  single    1.393  0.020  1.393
 SMX  CBA  CAU  single    1.531  0.020  1.531
 SMX  OAC  CAU  double    1.219  0.020  1.219
 SMX  CAU  N    single    1.344  0.020  1.344
 SMX  N    CA   single    1.425  0.020  1.425
 SMX  CA   C    single    1.534  0.020  1.534
 SMX  CA   CB   single    1.550  0.020  1.550
 SMX  O    C    double    1.200  0.020  1.200
 SMX  C    NBD  single    1.366  0.020  1.366
 SMX  CB   SAS  single    1.803  0.020  1.803
 SMX  CB   NBD  single    1.447  0.020  1.447
 SMX  SAS  CAM  single    1.820  0.020  1.820
 SMX  NBD  CAX  single    1.390  0.020  1.390
 SMX  CAX  CAT  single    1.534  0.020  1.534
 SMX  CAX  CAV  double    1.344  0.020  1.344
 SMX  CAM  CAV  single    1.510  0.020  1.510
 SMX  OAB  CAT  deloc     1.239  0.020  1.239
 SMX  NAN  NAO  aromatic  1.334  0.020  1.334
 SMX  NAN  NAP  aromatic  1.271  0.020  1.271
 SMX  CAT  OAE  deloc     1.241  0.020  1.241
 SMX  CAV  CAL  single    1.497  0.020  1.497
 SMX  NAO  CAZ  aromatic  1.314  0.020  1.314
 SMX  NAP  NBE  aromatic  1.329  0.020  1.329
 SMX  CAZ  NBE  aromatic  1.337  0.020  1.337
 SMX  CAZ  SAR  single    1.728  0.020  1.728
 SMX  CAL  SAR  single    1.837  0.020  1.837
 SMX  NBE  CAA  single    1.445  0.020  1.445
 SMX  N    H1   single    0.860  0.020  1.020
 SMX  CA   H2   single    0.970  0.020  1.090
 SMX  CB   H3   single    0.970  0.020  1.090
 SMX  CAA  H4   single    0.970  0.020  1.090
 SMX  CAA  H5   single    0.970  0.020  1.090
 SMX  CAA  H6   single    0.970  0.020  1.090
 SMX  CAG  H8   single    0.930  0.020  1.080
 SMX  CAH  H9   single    0.930  0.020  1.080
 SMX  CAI  H10  single    0.930  0.020  1.080
 SMX  CAJ  H11  single    0.930  0.020  1.080
 SMX  CAK  H12  single    0.930  0.020  1.080
 SMX  CAL  H13  single    0.970  0.020  1.090
 SMX  CAL  H14  single    0.970  0.020  1.090
 SMX  CAM  H15  single    0.970  0.020  1.090
 SMX  CAM  H16  single    0.970  0.020  1.090
 SMX  OAF  H17  single    0.850  0.020  0.980
 SMX  CBA  H18  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
 SMX  NBD  C    CA    91.44  3.000
 SMX  NBD  C    O    133.38  3.000
 SMX  CA   C    O    135.09  3.000
 SMX  H1   N    CAU  118.47  3.000
 SMX  H1   N    CA   118.33  3.000
 SMX  CAU  N    CA   122.19  3.000
 SMX  H2   CA   CB   112.04  3.000
 SMX  H2   CA   N    110.86  3.000
 SMX  CB   CA   N    118.60  3.000
 SMX  H2   CA   C    113.30  3.000
 SMX  CB   CA   C     84.81  3.000
 SMX  N    CA   C    115.06  3.000
 SMX  H3   CB   SAS  111.28  3.000
 SMX  H3   CB   NBD  113.57  3.000
 SMX  SAS  CB   NBD  110.17  3.000
 SMX  H3   CB   CA   116.25  3.000
 SMX  NBD  CB   CA    87.82  3.000
 SMX  SAS  CB   CA   115.68  3.000
 SMX  CAX  NBD  CB   126.70  3.000
 SMX  CAX  NBD  C    132.93  3.000
 SMX  CB   NBD  C     95.33  3.000
 SMX  CAZ  NBE  CAA  129.25  3.000
 SMX  CAA  NBE  NAP  122.85  3.000
 SMX  CAZ  NBE  NAP  107.89  3.000
 SMX  NAP  NAN  NAO  111.46  3.000
 SMX  CAZ  NAO  NAN  105.66  3.000
 SMX  NAN  NAP  NBE  106.91  3.000
 SMX  H6   CAA  H5   109.21  3.000
 SMX  H6   CAA  H4   109.48  3.000
 SMX  H5   CAA  H4   109.64  3.000
 SMX  H6   CAA  NBE  108.28  3.000
 SMX  H5   CAA  NBE  109.88  3.000
 SMX  H4   CAA  NBE  110.33  3.000
 SMX  H17  OAF  CBA  107.35  3.000
 SMX  H8   CAG  CAI  120.13  3.000
 SMX  H8   CAG  CAH  120.13  3.000
 SMX  CAI  CAG  CAH  119.75  3.000
 SMX  H9   CAH  CAJ  119.82  3.000
 SMX  H9   CAH  CAG  120.20  3.000
 SMX  CAJ  CAH  CAG  119.98  3.000
 SMX  H10  CAI  CAK  119.76  3.000
 SMX  H10  CAI  CAG  120.00  3.000
 SMX  CAK  CAI  CAG  120.24  3.000
 SMX  H11  CAJ  CAY  119.89  3.000
 SMX  H11  CAJ  CAH  119.64  3.000
 SMX  CAY  CAJ  CAH  120.47  3.000
 SMX  H12  CAK  CAY  120.25  3.000
 SMX  H12  CAK  CAI  119.54  3.000
 SMX  CAY  CAK  CAI  120.21  3.000
 SMX  H14  CAL  H13  109.70  3.000
 SMX  H14  CAL  CAV  111.39  3.000
 SMX  H13  CAL  CAV  112.35  3.000
 SMX  H14  CAL  SAR  107.94  3.000
 SMX  H13  CAL  SAR  108.86  3.000
 SMX  CAV  CAL  SAR  106.43  3.000
 SMX  H16  CAM  H15  106.34  3.000
 SMX  H16  CAM  CAV  109.24  3.000
 SMX  H15  CAM  CAV  111.04  3.000
 SMX  H16  CAM  SAS  105.38  3.000
 SMX  H15  CAM  SAS  109.00  3.000
 SMX  CAV  CAM  SAS  115.33  3.000
 SMX  CAZ  SAR  CAL  100.72  3.000
 SMX  CAM  SAS  CB    92.77  3.000
 SMX  CAX  CAT  OAE  117.34  3.000
 SMX  OAE  CAT  OAB  128.54  3.000
 SMX  CAX  CAT  OAB  114.12  3.000
 SMX  CBA  CAU  OAC  120.40  3.000
 SMX  OAC  CAU  N    123.86  3.000
 SMX  CBA  CAU  N    115.71  3.000
 SMX  CAX  CAV  CAM  124.35  3.000
 SMX  CAM  CAV  CAL  114.18  3.000
 SMX  CAX  CAV  CAL  121.31  3.000
 SMX  CAV  CAX  CAT  126.75  3.000
 SMX  CAV  CAX  NBD  118.64  3.000
 SMX  CAT  CAX  NBD  114.52  3.000
 SMX  CBA  CAY  CAK  120.13  3.000
 SMX  CBA  CAY  CAJ  120.47  3.000
 SMX  CAK  CAY  CAJ  119.35  3.000
 SMX  SAR  CAZ  NAO  128.69  3.000
 SMX  SAR  CAZ  NBE  123.23  3.000
 SMX  NAO  CAZ  NBE  108.08  3.000
 SMX  H18  CBA  CAY  108.82  3.000
 SMX  H18  CBA  CAU  108.68  3.000
 SMX  CAY  CBA  CAU  107.31  3.000
 SMX  H18  CBA  OAF  109.59  3.000
 SMX  CAU  CBA  OAF  109.57  3.000
 SMX  CAY  CBA  OAF  112.77  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
 SMX  CONST_01  NAO  NAN  NAP  NBE     0.00   0.0  0
 SMX  CONST_02  NAN  NAO  CAZ  NBE     0.00   0.0  0
 SMX  CONST_03  CAZ  NBE  NAP  NAN     0.00   0.0  0
 SMX  CONST_04  NAP  NBE  CAZ  NAO     0.00   0.0  0
 SMX  CONST_05  CAZ  NAO  NAN  NAP     0.00   0.0  0
 SMX  CONST_06  CAY  CAJ  CAH  CAG     0.00   0.0  0
 SMX  CONST_07  CAY  CAK  CAI  CAG     0.00   0.0  0
 SMX  CONST_08  CAK  CAI  CAG  CAH     0.00   0.0  0
 SMX  CONST_09  CAK  CAY  CAJ  CAH     0.00   0.0  0
 SMX  CONST_10  CAJ  CAH  CAG  CAI     0.00   0.0  0
 SMX  CONST_11  CAJ  CAY  CAK  CAI     0.00   0.0  0
 SMX  CONST_12  CB   NBD  C    CA      0.00   0.0  0
 SMX  CONST_14  SAR  CAZ  NAO  NAN   180.00   0.0  0
 SMX  CONST_15  CAA  NBE  NAP  NAN   180.00   0.0  0
 SMX  CONST_16  CAA  NBE  CAZ  NAO   180.00   0.0  0
 SMX  CONST_17  SAR  CAZ  NBE  NAP   180.00   0.0  0
 SMX  CONST_18  CBA  CAY  CAJ  CAH   180.00   0.0  0
 SMX  CONST_19  CBA  CAY  CAK  CAI   180.00   0.0  0
 SMX  CONST_20  CB   NBD  C    O     180.00   0.0  0
 SMX  CONST_22  H11  CAJ  CAH  CAG   180.00   0.0  0
 SMX  CONST_23  H12  CAK  CAI  CAG   180.00   0.0  0
 SMX  CONST_24  H10  CAI  CAG  CAH   180.00   0.0  0
 SMX  CONST_25  H9   CAH  CAG  CAI   180.00   0.0  0
 SMX  CONST_26  H8   CAG  CAH  CAJ   180.00   0.0  0
 SMX  CONST_27  CBA  CAU  N    CA    180.00   0.0  0
 SMX  CONST_28  OAC  CAU  N    CA      0.00   0.0  0
 SMX  CONST_29  H1   N    CAU  OAC   180.00   0.0  0
 SMX  Var_01    CAV  CAX  NBD  C    -137.77  30.0  1
 SMX  Var_02    CAV  CAM  SAS  CB    -49.87  30.0  1
 SMX  Var_03    CAM  CAV  CAX  NBD     1.37  30.0  1
 SMX  Var_04    CAX  CAV  CAM  SAS    25.78  30.0  1
 SMX  Var_05    OAB  CAT  CAX  NBD    41.81  30.0  2
 SMX  Var_06    SAR  CAL  CAV  CAM   -82.40  30.0  3
 SMX  Var_07    H4   CAA  NBE  NAP   112.10  30.0  2

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
 SMX  chir_01  CA   N    C    CB   positiv
 SMX  chir_02  CB   SAS  NBD  CA   negativ
 SMX  chir_03  CBA  OAF  CAY  CAU  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
 SMX  plan-1  NBE  0.020
 SMX  plan-1  NAN  0.020
 SMX  plan-1  NAO  0.020
 SMX  plan-1  NAP  0.020
 SMX  plan-1  CAA  0.020
 SMX  plan-1  SAR  0.020
 SMX  plan-1  CAZ  0.020
 SMX  plan-2  CAG  0.020
 SMX  plan-2  CAH  0.020
 SMX  plan-2  CAI  0.020
 SMX  plan-2  CAJ  0.020
 SMX  plan-2  CAK  0.020
 SMX  plan-2  CAY  0.020
 SMX  plan-2  CBA  0.020
 SMX  plan-2  H10  0.020
 SMX  plan-2  H11  0.020
 SMX  plan-2  H12  0.020
 SMX  plan-2  H8   0.020
 SMX  plan-2  H9   0.020
 SMX  plan-3  N    0.020
 SMX  plan-3  CA   0.020
 SMX  plan-3  OAC  0.020
 SMX  plan-3  CAU  0.020
 SMX  plan-3  CBA  0.020
 SMX  plan-3  H1   0.020
 SMX  plan-4  C    0.020
 SMX  plan-4  O    0.020
 SMX  plan-4  CA   0.020
 SMX  plan-4  CB   0.020
 SMX  plan-4  NBD  0.020
 SMX  plan-4  CAX  0.020
 SMX  plan-5  OAB  0.020
 SMX  plan-5  OAE  0.020
 SMX  plan-5  CAT  0.020
 SMX  plan-5  CAX  0.020

