# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 03:34:53 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2S,4S,5R,6R)-4-hydroxy-3,3-dimethyl-7-oxo-6-[(phenylacetyl)amino]-4lambda~4~-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)[C@@H](N2[C@@H]([C@H](NC(=O)Cc3ccccc3)C2=O)[SH]1O)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
 SOX  SOX  '(2S,4S,5R,6R)-4-hydroxy-3,3-dimethyl-7-oxo-6-[(phenylacetyl)amino]-4lambda~4~-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid'  ligand  44  24  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SOX
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
 SOX  O8    O  O     0  -0.403  -2.8133   1.5852   2.5799
 SOX  C7    C  C     0   0.511  -1.9196   1.4718   3.3683
 SOX  N4    N  N     0  -0.439  -0.6429   0.9565   3.2138
 SOX  C3    C  CH1   0  -0.145  -0.2445  -0.2182   2.4866
 SOX  C11   C  C     0   0.554   0.6099   0.1310   1.2782
 SOX  O13   O  O     0  -0.407   1.0964   1.2110   1.0901
 SOX  O12   O  OH1   0  -0.579   0.7310  -0.9102   0.4736
 SOX  C2    C  CT    0  -0.271   0.5187  -1.1639   3.4802
 SOX  C10   C  CH3   0  -0.676   2.0267  -0.9449   3.4917
 SOX  C9    C  CH3   0  -0.638   0.1548  -2.6234   3.2684
 SOX  S1    S  SH1   0   0.272  -0.1605  -0.6387   5.1497
 SOX  C5    C  C     0  -0.193  -0.3080   1.0953   4.6059
 SOX  C6    C  C     0  -0.229  -1.6961   1.7455   4.8620
 SOX  N14   N  NH1   0  -0.563  -2.6283   1.0379   5.6792
 SOX  C15   C  C     0   0.439  -2.1299   0.7011   6.8532
 SOX  O16   O  O     0  -0.568  -0.9564   0.9143   7.2350
 SOX  C17   C  CH2   0  -0.619  -3.0655  -0.0753   7.7683
 SOX  C18   C  CR6   0   0.136  -2.4184  -1.3556   8.2179
 SOX  C19   C  CR16  0  -0.290  -2.4644  -2.4885   7.4080
 SOX  C20   C  CR16  0  -0.244  -1.8266  -3.6613   7.7891
 SOX  C21   C  CR16  0  -0.274  -1.1319  -3.7193   8.9907
 SOX  C22   C  CR16  0  -0.246  -1.0815  -2.5959   9.8059
 SOX  C23   C  CR16  0  -0.307  -1.7174  -1.4236   9.4181
 SOX  O5    O  OH1   0  -0.892  -2.9987  -1.2780   4.0928
 SOX  H3    H  HCH1  0   0.332  -1.1430  -0.7343   2.1366
 SOX  H12   H  HOH1  0   0.495   1.2970  -0.6941  -0.2841
 SOX  H101  H  HCH3  0   0.273   2.3072   0.0969   3.6516
 SOX  H102  H  HCH3  0   0.281   2.4913  -1.5480   4.2709
 SOX  H103  H  HCH3  0   0.279   2.4597  -1.2716   2.5458
 SOX  H9C1  H  HCH3  0   0.262   0.6609  -3.2604   3.9930
 SOX  H9C2  H  HCH3  0   0.272  -0.9197  -2.7748   3.3534
 SOX  H9C3  H  HCH3  0   0.271   0.4739  -2.9387   2.2752
 SOX  HS    H  HSH1  0   0.341   1.0003  -0.5775   5.8178
 SOX  H5    H  H     0   0.345   0.6013   1.6355   4.8583
 SOX  H6    H  H     0   0.293  -1.5893   2.8092   5.1078
 SOX  H14   H  HNH1  0   0.448  -3.0827  -0.5285   4.7171
 SOX  H171  H  HCH2  0   0.248  -4.0064  -0.2743   7.2546
 SOX  H172  H  HCH2  0   0.260  -3.2958   0.5497   8.6361
 SOX  H19   H  HCR6  0   0.243  -2.9950  -2.4496   6.4638
 SOX  H20   H  HCR6  0   0.248  -1.8739  -4.5316   7.1467
 SOX  H21   H  HCR6  0   0.249  -0.6359  -4.6336   9.2910
 SOX  H22   H  HCR6  0   0.249  -0.5440  -2.6315  10.7453
 SOX  H23   H  HCR6  0   0.241  -1.6741  -0.5516  10.0594
 SOX  HO5   H  HOH1  0   0.438  -3.5947  -1.0631   3.3703

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
 SOX  O8   C7    double    1.197  0.020  1.197
 SOX  C7   N4    single    1.385  0.020  1.385
 SOX  C7   C6    single    1.535  0.020  1.535
 SOX  N4   C3    single    1.438  0.020  1.438
 SOX  N4   C5    single    1.439  0.020  1.439
 SOX  C3   C11   single    1.521  0.020  1.521
 SOX  C3   C2    single    1.570  0.020  1.570
 SOX  C3   H3    single    0.970  0.020  1.090
 SOX  C11  O13   double    1.199  0.020  1.199
 SOX  C11  O12   single    1.321  0.020  1.321
 SOX  O12  H12   single    0.850  0.020  0.980
 SOX  C2   C10   single    1.524  0.020  1.524
 SOX  C2   C9    single    1.519  0.020  1.519
 SOX  C2   S1    single    1.877  0.020  1.877
 SOX  C10  H101  single    0.970  0.020  1.090
 SOX  C10  H102  single    0.970  0.020  1.090
 SOX  C10  H103  single    0.970  0.020  1.090
 SOX  C9   H9C1  single    0.970  0.020  1.090
 SOX  C9   H9C2  single    0.970  0.020  1.090
 SOX  C9   H9C3  single    0.970  0.020  1.090
 SOX  S1   C5    single    1.823  0.020  1.823
 SOX  S1   O5    single    3.095  0.020  3.095
 SOX  S1   HS    single    1.200  0.020  1.300
 SOX  C5   C6    single    1.554  0.020  1.554
 SOX  C5   H5    single    0.970  0.020  1.090
 SOX  C6   N14   single    1.427  0.020  1.427
 SOX  C6   H6    single    0.970  0.020  1.090
 SOX  N14  C15   single    1.319  0.020  1.319
 SOX  N14  H14   single    0.890  0.020  1.040
 SOX  C15  O16   double    1.252  0.020  1.252
 SOX  C15  C17   single    1.522  0.020  1.522
 SOX  C17  C18   single    1.503  0.020  1.503
 SOX  C17  H171  single    0.970  0.020  1.090
 SOX  C17  H172  single    0.970  0.020  1.090
 SOX  C18  C19   aromatic  1.393  0.020  1.393
 SOX  C18  C23   aromatic  1.392  0.020  1.392
 SOX  C19  C20   aromatic  1.388  0.020  1.388
 SOX  C19  H19   single    0.930  0.020  1.080
 SOX  C20  C21   aromatic  1.389  0.020  1.389
 SOX  C20  H20   single    0.930  0.020  1.080
 SOX  C21  C22   aromatic  1.389  0.020  1.389
 SOX  C21  H21   single    0.930  0.020  1.080
 SOX  C22  C23   aromatic  1.389  0.020  1.389
 SOX  C22  H22   single    0.930  0.020  1.080
 SOX  C23  H23   single    0.930  0.020  1.080
 SOX  O5   HO5   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
 SOX  C6    C7   N4     92.33  3.000
 SOX  C6    C7   O8    137.11  3.000
 SOX  N4    C7   O8    130.52  3.000
 SOX  C5    N4   C3    120.25  3.000
 SOX  C5    N4   C7     94.06  3.000
 SOX  C3    N4   C7    128.00  3.000
 SOX  H3    C3   C2    108.52  3.000
 SOX  H3    C3   C11   108.40  3.000
 SOX  C2    C3   C11   111.60  3.000
 SOX  H3    C3   N4    108.64  3.000
 SOX  C2    C3   N4    107.87  3.000
 SOX  C11   C3   N4    111.72  3.000
 SOX  O12   C11  O13   125.23  3.000
 SOX  O12   C11  C3    110.76  3.000
 SOX  O13   C11  C3    124.01  3.000
 SOX  H12   O12  C11   110.70  3.000
 SOX  S1    C2   C9    107.82  3.000
 SOX  S1    C2   C10   108.13  3.000
 SOX  C9    C2   C10   112.10  3.000
 SOX  S1    C2   C3    102.62  3.000
 SOX  C9    C2   C3    111.97  3.000
 SOX  C10   C2   C3    113.54  3.000
 SOX  H103  C10  H102  106.58  3.000
 SOX  H103  C10  H101  108.13  3.000
 SOX  H102  C10  H101  108.32  3.000
 SOX  H103  C10  C2    110.08  3.000
 SOX  H102  C10  C2    110.36  3.000
 SOX  H101  C10  C2    113.14  3.000
 SOX  H9C3  C9   H9C2  108.66  3.000
 SOX  H9C3  C9   H9C1  107.51  3.000
 SOX  H9C2  C9   H9C1  108.98  3.000
 SOX  H9C3  C9   C2    109.57  3.000
 SOX  H9C2  C9   C2    111.06  3.000
 SOX  H9C1  C9   C2    110.96  3.000
 SOX  HS    S1   O5    166.77  3.000
 SOX  HS    S1   C5    100.09  3.000
 SOX  O5    S1   C5     91.17  3.000
 SOX  HS    S1   C2     98.20  3.000
 SOX  O5    S1   C2     88.30  3.000
 SOX  C5    S1   C2     91.73  3.000
 SOX  H5    C5   C6    120.05  3.000
 SOX  H5    C5   S1    109.61  3.000
 SOX  C6    C5   S1    114.90  3.000
 SOX  H5    C5   N4    117.85  3.000
 SOX  C6    C5   N4     89.53  3.000
 SOX  S1    C5   N4    102.46  3.000
 SOX  H6    C6   N14   114.59  3.000
 SOX  H6    C6   C5    110.83  3.000
 SOX  N14   C6   C5    118.05  3.000
 SOX  H6    C6   C7    113.91  3.000
 SOX  N14   C6   C7    111.94  3.000
 SOX  C5    C6   C7     83.98  3.000
 SOX  H14   N14  C15   109.37  3.000
 SOX  H14   N14  C6    106.02  3.000
 SOX  C15   N14  C6    112.91  3.000
 SOX  C17   C15  O16   118.66  3.000
 SOX  C17   C15  N14   115.67  3.000
 SOX  O16   C15  N14   125.59  3.000
 SOX  H172  C17  H171  107.24  3.000
 SOX  H172  C17  C18   109.88  3.000
 SOX  H171  C17  C18   110.91  3.000
 SOX  H172  C17  C15   108.36  3.000
 SOX  H171  C17  C15   109.90  3.000
 SOX  C18   C17  C15   110.47  3.000
 SOX  C23   C18  C19   118.56  3.000
 SOX  C23   C18  C17   121.09  3.000
 SOX  C19   C18  C17   120.30  3.000
 SOX  H19   C19  C20   119.63  3.000
 SOX  H19   C19  C18   119.56  3.000
 SOX  C20   C19  C18   120.81  3.000
 SOX  H20   C20  C21   120.09  3.000
 SOX  H20   C20  C19   119.74  3.000
 SOX  C21   C20  C19   120.17  3.000
 SOX  H21   C21  C22   120.24  3.000
 SOX  H21   C21  C20   120.29  3.000
 SOX  C22   C21  C20   119.47  3.000
 SOX  H22   C22  C23   119.82  3.000
 SOX  H22   C22  C21   120.03  3.000
 SOX  C23   C22  C21   120.15  3.000
 SOX  H23   C23  C22   119.73  3.000
 SOX  H23   C23  C18   119.43  3.000
 SOX  C22   C23  C18   120.84  3.000
 SOX  HO5   O5   S1    141.19  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
 SOX  CONST_01  C21   C20  C19  C18     0.00   0.0  0
 SOX  CONST_02  C21   C22  C23  C18     0.00   0.0  0
 SOX  CONST_03  C22   C23  C18  C19     0.00   0.0  0
 SOX  CONST_04  C22   C21  C20  C19     0.00   0.0  0
 SOX  CONST_05  C23   C18  C19  C20     0.00   0.0  0
 SOX  CONST_06  C23   C22  C21  C20     0.00   0.0  0
 SOX  CONST_08  C6    C7   N4   C5      0.00   0.0  0
 SOX  CONST_09  C20   C19  C18  C17   180.00   0.0  0
 SOX  CONST_10  C22   C23  C18  C17   180.00   0.0  0
 SOX  CONST_12  C5    N4   C7   O8    180.00   0.0  0
 SOX  CONST_13  H20   C20  C19  C18   180.00   0.0  0
 SOX  CONST_14  H22   C22  C23  C18   180.00   0.0  0
 SOX  CONST_15  H23   C23  C18  C19   180.00   0.0  0
 SOX  CONST_16  H21   C21  C20  C19   180.00   0.0  0
 SOX  CONST_17  H19   C19  C20  C21   180.00   0.0  0
 SOX  CONST_18  O16   C15  N14  C6      0.00   0.0  0
 SOX  CONST_19  C17   C15  N14  C6    180.00   0.0  0
 SOX  CONST_20  H12   O12  C11  C3    180.00   0.0  0
 SOX  Var_01    C19   C18  C17  C15   -83.55  30.0  2
 SOX  Var_02    H101  C10  C2   C3     52.39  30.0  3
 SOX  Var_03    H9C1  C9   C2   C3   -177.60  30.0  3
 SOX  Var_04    C18   C17  C15  N14   125.86  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
 SOX  chir_01  C3  N4   C11  C2  negativ
 SOX  chir_02  S1  O5   C2   C5  negativ
 SOX  chir_03  C5  S1   N4   C6  negativ
 SOX  chir_04  C6  N14  C5   C7  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
 SOX  plan-1  C17  0.020
 SOX  plan-1  C18  0.020
 SOX  plan-1  C19  0.020
 SOX  plan-1  C20  0.020
 SOX  plan-1  C21  0.020
 SOX  plan-1  C22  0.020
 SOX  plan-1  C23  0.020
 SOX  plan-1  H19  0.020
 SOX  plan-1  H20  0.020
 SOX  plan-1  H21  0.020
 SOX  plan-1  H22  0.020
 SOX  plan-1  H23  0.020
 SOX  plan-2  C6   0.020
 SOX  plan-2  N14  0.020
 SOX  plan-2  C15  0.020
 SOX  plan-2  O16  0.020
 SOX  plan-2  C17  0.020
 SOX  plan-2  H14  0.020
 SOX  plan-3  O8   0.020
 SOX  plan-3  C7   0.020
 SOX  plan-3  N4   0.020
 SOX  plan-3  C3   0.020
 SOX  plan-3  C5   0.020
 SOX  plan-3  C6   0.020
 SOX  plan-4  C3   0.020
 SOX  plan-4  C11  0.020
 SOX  plan-4  O13  0.020
 SOX  plan-4  O12  0.020
 SOX  plan-4  H12  0.020

