# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 09:35:23 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (2S,5R,6R,7R)-6-{[(2R)-2-carboxy-2-phenylacetyl]amino}-7-hydroxy-3,3-dimethyl-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)S[C@@H]2[C@H](NC(=O)[C@H](C(O)=O)c3ccccc3)[C@@H](O)N2[C@H]1C(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
 0JM  0JM  '(2S,5R,6R,7R)-6-{[(2R)-2-carboxy-2-phenylacetyl]amino}-7-hydroxy-3,3-dimethyl-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid'  ligand  44  26  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0JM
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
 0JM  O5   O  OC    -1  -0.611  -5.5952  -1.5377  -0.3011
 0JM  C16  C  C      0   0.404  -4.8431  -0.5741  -0.5596
 0JM  O1   O  O      0  -0.593  -5.1505   0.4831  -1.1313
 0JM  C13  C  CR15   0  -0.123  -3.3710  -0.7644  -0.1266
 0JM  C12  C  CR5    0  -0.238  -2.6295  -1.7439  -1.0833
 0JM  C14  C  CH3    0  -0.628  -2.9998  -1.5360  -2.5501
 0JM  C15  C  CH3    0  -0.634  -2.8378  -3.1973  -0.6854
 0JM  S1   S  S2     0  -0.016  -0.8504  -1.3152  -0.8485
 0JM  N2   N  NR5    0  -0.413  -2.6017   0.4660  -0.0426
 0JM  C11  C  CR15   0  -0.218  -1.3199   0.4399  -0.7269
 0JM  C10  C  CH1    0   0.229  -1.9784   0.8124   1.2190
 0JM  O4   O  OH1    0  -0.652  -2.6692   1.8065   1.9013
 0JM  C9   C  CH1    0  -0.148  -0.6936   1.1946   0.4581
 0JM  N1   N  NH1    0  -0.639   0.5526   0.7578   0.9942
 0JM  C8   C  C      0   0.587   1.7192   1.4115   0.8135
 0JM  O6   O  O      0  -0.492   1.8009   2.4529   0.1815
 0JM  C7   C  CH1    0  -0.668   2.9343   0.7512   1.4330
 0JM  C17  C  C      0   0.462   3.3982   1.6005   2.6576
 0JM  O2   O  OC    -1  -0.580   4.6083   1.5872   2.9255
 0JM  O3   O  O      0  -0.593   2.4841   2.1728   3.2774
 0JM  C1   C  C      0   0.192   3.9851   0.5109   0.3875
 0JM  C6   C  C1     0  -0.313   4.1946  -0.7735  -0.1059
 0JM  C2   C  C1     0  -0.286   4.7436   1.5553  -0.1421
 0JM  C3   C  C1     0  -0.251   5.6821   1.3153  -1.1340
 0JM  C4   C  C1     0  -0.274   5.8843   0.0267  -1.6170
 0JM  C5   C  C1     0  -0.244   5.1366  -1.0198  -1.0985
 0JM  H2   H  HCR5   0   0.227  -3.3758  -1.2328   0.8664
 0JM  H3   H  HCH3   0   0.238  -2.8868  -0.4980  -2.8630
 0JM  H4   H  HCH3   0   0.234  -2.3686  -2.1515  -3.1908
 0JM  H5   H  HCH3   0   0.233  -4.0361  -1.8278  -2.7280
 0JM  H6   H  HCH3   0   0.243  -3.8927  -3.4539  -0.7767
 0JM  H7   H  HCH3   0   0.230  -2.2681  -3.8699  -1.3279
 0JM  H8   H  HCH3   0   0.232  -2.5346  -3.3725   0.3474
 0JM  H10  H  HCR5   0   0.270  -1.2860   0.9200  -1.7070
 0JM  H11  H  HCH1   0   0.195  -1.8172  -0.0606   1.8722
 0JM  H12  H  HOH1   0   0.456  -2.4337   1.7644   2.8331
 0JM  H13  H  HCH1   0   0.283  -0.6517   2.2635   0.2549
 0JM  H14  H  HNH1   0   0.395   0.5682  -0.1278   1.4742
 0JM  H15  H  HCH1   0   0.275   2.6438  -0.2229   1.8452
 0JM  H17  H  H      0   0.244   3.6115  -1.5967   0.2914
 0JM  H18  H  H      0   0.238   4.6029   2.5643   0.2203
 0JM  H19  H  H      0   0.248   6.2653   2.1370  -1.5305
 0JM  H20  H  H      0   0.250   6.6202  -0.1553  -2.3898
 0JM  H21  H  H      0   0.249   5.2822  -2.0282  -1.4644

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
 0JM  O3   C17  deloc     1.244  0.020  1.244
 0JM  O2   C17  deloc     1.239  0.020  1.239
 0JM  C17  C7   single    1.561  0.020  1.561
 0JM  C7   C8   single    1.515  0.020  1.515
 0JM  C7   C1   single    1.502  0.020  1.502
 0JM  O6   C8   double    1.221  0.020  1.221
 0JM  C8   N1   single    1.349  0.020  1.349
 0JM  C2   C1   aromatic  1.395  0.020  1.395
 0JM  C2   C3   aromatic  1.387  0.020  1.387
 0JM  N1   C9   single    1.425  0.020  1.425
 0JM  C1   C6   aromatic  1.392  0.020  1.392
 0JM  O4   C10  single    1.390  0.020  1.390
 0JM  C9   C10  single    1.541  0.020  1.541
 0JM  C9   C11  single    1.538  0.020  1.538
 0JM  C3   C4   aromatic  1.391  0.020  1.391
 0JM  C10  N2   single    1.449  0.020  1.449
 0JM  C6   C5   aromatic  1.390  0.020  1.390
 0JM  C11  N2   single    1.453  0.020  1.453
 0JM  C11  S1   single    1.821  0.020  1.821
 0JM  C4   C5   aromatic  1.387  0.020  1.387
 0JM  N2   C13  single    1.454  0.020  1.454
 0JM  S1   C12  single    1.845  0.020  1.845
 0JM  C13  C12  single    1.557  0.020  1.557
 0JM  C13  C16  single    1.546  0.020  1.546
 0JM  O1   C16  deloc     1.241  0.020  1.241
 0JM  C12  C15  single    1.521  0.020  1.521
 0JM  C12  C14  single    1.527  0.020  1.527
 0JM  C16  O5   deloc     1.249  0.020  1.249
 0JM  C13  H2   single    0.970  0.020  1.090
 0JM  C14  H3   single    0.970  0.020  1.090
 0JM  C14  H4   single    0.970  0.020  1.090
 0JM  C14  H5   single    0.970  0.020  1.090
 0JM  C15  H6   single    0.970  0.020  1.090
 0JM  C15  H7   single    0.970  0.020  1.090
 0JM  C15  H8   single    0.970  0.020  1.090
 0JM  C11  H10  single    0.970  0.020  1.090
 0JM  C10  H11  single    0.970  0.020  1.090
 0JM  O4   H12  single    0.850  0.020  0.980
 0JM  C9   H13  single    0.970  0.020  1.090
 0JM  N1   H14  single    0.860  0.020  1.020
 0JM  C7   H15  single    0.970  0.020  1.090
 0JM  C6   H17  single    0.930  0.020  1.080
 0JM  C2   H18  single    0.930  0.020  1.080
 0JM  C3   H19  single    0.930  0.020  1.080
 0JM  C4   H20  single    0.930  0.020  1.080
 0JM  C5   H21  single    0.930  0.020  1.080

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
 0JM  C13  C16  O1   118.02  3.000
 0JM  O1   C16  O5   127.12  3.000
 0JM  C13  C16  O5   114.85  3.000
 0JM  H2   C13  N2   108.13  3.000
 0JM  H2   C13  C12  106.82  3.000
 0JM  N2   C13  C12  108.42  3.000
 0JM  H2   C13  C16  107.55  3.000
 0JM  C12  C13  C16  111.02  3.000
 0JM  N2   C13  C16  114.58  3.000
 0JM  S1   C12  C15  108.71  3.000
 0JM  C15  C12  C14  110.37  3.000
 0JM  S1   C12  C14  108.93  3.000
 0JM  C14  C12  C13  112.89  3.000
 0JM  C15  C12  C13  112.03  3.000
 0JM  S1   C12  C13  103.58  3.000
 0JM  H5   C14  H4   107.65  3.000
 0JM  H5   C14  H3   107.83  3.000
 0JM  H4   C14  H3   108.00  3.000
 0JM  H5   C14  C12  110.52  3.000
 0JM  H4   C14  C12  110.33  3.000
 0JM  H3   C14  C12  112.35  3.000
 0JM  H8   C15  H7   108.28  3.000
 0JM  H8   C15  H6   108.10  3.000
 0JM  H7   C15  H6   108.13  3.000
 0JM  H8   C15  C12  111.29  3.000
 0JM  H7   C15  C12  111.32  3.000
 0JM  H6   C15  C12  109.61  3.000
 0JM  C11  S1   C12   89.08  3.000
 0JM  C10  N2   C11   92.00  3.000
 0JM  C11  N2   C13  115.11  3.000
 0JM  C10  N2   C13  118.70  3.000
 0JM  H10  C11  C9   117.59  3.000
 0JM  H10  C11  N2   116.24  3.000
 0JM  C9   C11  N2    89.29  3.000
 0JM  H10  C11  S1   110.85  3.000
 0JM  N2   C11  S1   106.03  3.000
 0JM  C9   C11  S1   114.80  3.000
 0JM  H11  C10  C9   111.53  3.000
 0JM  H11  C10  O4   110.39  3.000
 0JM  C9   C10  O4   118.65  3.000
 0JM  H11  C10  N2   112.92  3.000
 0JM  C9   C10  N2    89.31  3.000
 0JM  O4   C10  N2   112.62  3.000
 0JM  H12  O4   C10  108.81  3.000
 0JM  H13  C9   N1   109.72  3.000
 0JM  H13  C9   C10  111.57  3.000
 0JM  N1   C9   C10  117.85  3.000
 0JM  H13  C9   C11  110.71  3.000
 0JM  C10  C9   C11   85.37  3.000
 0JM  N1   C9   C11  119.69  3.000
 0JM  H14  N1   C8   118.44  3.000
 0JM  H14  N1   C9   117.53  3.000
 0JM  C8   N1   C9   123.86  3.000
 0JM  C7   C8   O6   121.98  3.000
 0JM  O6   C8   N1   122.71  3.000
 0JM  C7   C8   N1   115.30  3.000
 0JM  H15  C7   C1   107.75  3.000
 0JM  H15  C7   C17  105.49  3.000
 0JM  C1   C7   C17  115.17  3.000
 0JM  H15  C7   C8   109.16  3.000
 0JM  C1   C7   C8   110.25  3.000
 0JM  C17  C7   C8   108.78  3.000
 0JM  O3   C17  O2   127.93  3.000
 0JM  O2   C17  C7   117.00  3.000
 0JM  O3   C17  C7   115.02  3.000
 0JM  C2   C1   C6   118.32  3.000
 0JM  C6   C1   C7   119.99  3.000
 0JM  C2   C1   C7   121.66  3.000
 0JM  H17  C6   C5   119.43  3.000
 0JM  H17  C6   C1   119.34  3.000
 0JM  C5   C6   C1   121.23  3.000
 0JM  H18  C2   C3   119.30  3.000
 0JM  H18  C2   C1   120.04  3.000
 0JM  C3   C2   C1   120.66  3.000
 0JM  H19  C3   C4   119.84  3.000
 0JM  H19  C3   C2   119.68  3.000
 0JM  C4   C3   C2   120.48  3.000
 0JM  H20  C4   C5   120.44  3.000
 0JM  H20  C4   C3   120.16  3.000
 0JM  C5   C4   C3   119.40  3.000
 0JM  H21  C5   C4   120.26  3.000
 0JM  H21  C5   C6   119.83  3.000
 0JM  C4   C5   C6   119.91  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
 0JM  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 0JM  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 0JM  CONST_03  C3   C2   C1   C6     0.00   0.0  0
 0JM  CONST_04  C3   C4   C5   C6     0.00   0.0  0
 0JM  CONST_05  C5   C6   C1   C2     0.00   0.0  0
 0JM  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 0JM  CONST_07  C3   C2   C1   C7   180.00   0.0  0
 0JM  CONST_08  C5   C6   C1   C7   180.00   0.0  0
 0JM  CONST_09  H19  C3   C2   C1   180.00   0.0  0
 0JM  CONST_10  H21  C5   C6   C1   180.00   0.0  0
 0JM  CONST_11  H18  C2   C1   C6   180.00   0.0  0
 0JM  CONST_12  H20  C4   C5   C6   180.00   0.0  0
 0JM  CONST_13  H17  C6   C1   C2   180.00   0.0  0
 0JM  CONST_14  C7   C8   N1   C9   180.00   0.0  0
 0JM  CONST_15  O6   C8   N1   C9     0.00   0.0  0
 0JM  CONST_16  H14  N1   C8   O6   180.00   0.0  0
 0JM  Var_01    H6   C15  C12  C13   63.67  30.0  3
 0JM  Var_02    H3   C14  C12  C13   52.28  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
 0JM  chir_01  C13  N2   C12  C16  positiv
 0JM  chir_02  C11  S1   N2   C9   negativ
 0JM  chir_03  C10  O4   N2   C9   negativ
 0JM  chir_04  C9   N1   C10  C11  positiv
 0JM  chir_05  C7   C17  C8   C1   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
 0JM  plan-1  C7   0.020
 0JM  plan-1  C1   0.020
 0JM  plan-1  C6   0.020
 0JM  plan-1  C2   0.020
 0JM  plan-1  C3   0.020
 0JM  plan-1  C4   0.020
 0JM  plan-1  C5   0.020
 0JM  plan-1  H17  0.020
 0JM  plan-1  H18  0.020
 0JM  plan-1  H19  0.020
 0JM  plan-1  H20  0.020
 0JM  plan-1  H21  0.020
 0JM  plan-2  C9   0.020
 0JM  plan-2  N1   0.020
 0JM  plan-2  C8   0.020
 0JM  plan-2  O6   0.020
 0JM  plan-2  C7   0.020
 0JM  plan-2  H14  0.020
 0JM  plan-3  O5   0.020
 0JM  plan-3  C16  0.020
 0JM  plan-3  O1   0.020
 0JM  plan-3  C13  0.020
 0JM  plan-4  C7   0.020
 0JM  plan-4  C17  0.020
 0JM  plan-4  O2   0.020
 0JM  plan-4  O3   0.020

