# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 23:48:13 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  46  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  OH1   0  -0.588  -4.9519  -2.2182  -0.6717
 0JM  C16  C  C     0   0.539  -4.4609  -0.9861  -0.6135
 0JM  O1   O  O     0  -0.425  -5.1024   0.0004  -0.8583
 0JM  C13  C  CH1   0  -0.133  -2.9994  -0.9956  -0.2063
 0JM  C12  C  CT    0  -0.258  -2.0677  -1.4232  -1.3852
 0JM  C14  C  CH3   0  -0.639  -2.5070  -0.8419  -2.7267
 0JM  C15  C  CH3   0  -0.635  -1.9050  -2.9333  -1.4847
 0JM  S1   S  S2    0   0.039  -0.4522  -0.6971  -0.8877
 0JM  N2   N  N     0  -0.419  -2.5811   0.3029   0.2695
 0JM  C11  C  C     0  -0.226  -1.3233   0.7805  -0.2931
 0JM  C10  C  C     0   0.215  -2.0813   0.4194   1.6289
 0JM  O4   O  OH1   0  -0.645  -3.0040   0.9996   2.4811
 0JM  C9   C  C     0  -0.123  -0.9139   1.2764   1.1035
 0JM  N1   N  NH1   0  -0.644   0.3833   0.9393   1.6008
 0JM  C8   C  C     0   0.602   1.4930   1.4630   1.0625
 0JM  O6   O  O     0  -0.468   1.4666   2.2900   0.1687
 0JM  C7   C  CH1   0  -0.653   2.8059   0.9166   1.6102
 0JM  C17  C  C     0   0.600   3.5537   2.0336   2.3109
 0JM  O2   O  OH1   0  -0.579   4.8340   1.7499   2.4724
 0JM  O3   O  O     0  -0.426   3.0257   3.0329   2.7251
 0JM  C1   C  CR6   0   0.165   3.5675   0.2319   0.5019
 0JM  C6   C  CR16  0  -0.288   3.5583  -1.1560   0.4259
 0JM  C2   C  CR16  0  -0.284   4.2311   0.9604  -0.4826
 0JM  C3   C  CR16  0  -0.246   4.8847   0.3058  -1.5155
 0JM  C4   C  CR16  0  -0.264   4.8758  -1.0825  -1.5831
 0JM  C5   C  CR16  0  -0.242   4.2094  -1.8128  -0.6102
 0JM  H1   H  HOH1  0   0.485  -5.8774  -2.1946  -0.9589
 0JM  H2   H  HCH1  0   0.288  -2.8799  -1.7379   0.5923
 0JM  H3   H  HCH3  0   0.250  -2.6589   0.2369  -2.6875
 0JM  H4   H  HCH3  0   0.254  -1.7506  -1.0465  -3.4832
 0JM  H5   H  HCH3  0   0.240  -3.4384  -1.3011  -3.0654
 0JM  H6   H  HCH3  0   0.249  -2.8436  -3.4044  -1.7759
 0JM  H7   H  HCH3  0   0.247  -1.1649  -3.1871  -2.2441
 0JM  H8   H  HCH3  0   0.244  -1.5851  -3.3656  -0.5364
 0JM  H10  H  H     0   0.286  -1.4111   1.5313  -1.0786
 0JM  H11  H  H     0   0.214  -1.7216  -0.5392   2.0349
 0JM  H12  H  HOH1  0   0.462  -2.8093   0.7331   3.3849
 0JM  H13  H  H     0   0.293  -1.1167   2.3441   1.2077
 0JM  H14  H  HNH1  0   0.411   0.4581   0.2217   2.3039
 0JM  H15  H  HCH1  0   0.336   2.6093   0.1740   2.3928
 0JM  H16  H  HOH1  0   0.487   5.2729   2.4596   2.9665
 0JM  H17  H  HCR6  0   0.255   3.0399  -1.7303   1.1846
 0JM  H18  H  HCR6  0   0.251   4.2449   2.0426  -0.4495
 0JM  H19  H  HCR6  0   0.257   5.4019   0.8813  -2.2722
 0JM  H20  H  HCR6  0   0.257   5.3865  -1.5905  -2.3908
 0JM  H21  H  HCR6  0   0.257   4.1960  -2.8941  -0.6540

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  double    1.204  0.020  1.204
 0JM  O2   C17  single    1.321  0.020  1.321
 0JM  C17  C7   single    1.516  0.020  1.516
 0JM  C7   C8   single    1.524  0.020  1.524
 0JM  C7   C1   single    1.509  0.020  1.509
 0JM  O6   C8   double    1.218  0.020  1.218
 0JM  C8   N1   single    1.340  0.020  1.340
 0JM  C2   C1   aromatic  1.393  0.020  1.393
 0JM  C2   C3   aromatic  1.387  0.020  1.387
 0JM  N1   C9   single    1.430  0.020  1.430
 0JM  C1   C6   aromatic  1.390  0.020  1.390
 0JM  O4   C10  single    1.384  0.020  1.384
 0JM  C9   C10  single    1.541  0.020  1.541
 0JM  C9   C11  single    1.538  0.020  1.538
 0JM  C3   C4   aromatic  1.390  0.020  1.390
 0JM  C10  N2   single    1.453  0.020  1.453
 0JM  C6   C5   aromatic  1.389  0.020  1.389
 0JM  C11  N2   single    1.458  0.020  1.458
 0JM  C11  S1   single    1.815  0.020  1.815
 0JM  C4   C5   aromatic  1.387  0.020  1.387
 0JM  N2   C13  single    1.445  0.020  1.445
 0JM  S1   C12  single    1.840  0.020  1.840
 0JM  C13  C12  single    1.562  0.020  1.562
 0JM  C13  C16  single    1.517  0.020  1.517
 0JM  O1   C16  double    1.202  0.020  1.202
 0JM  C12  C15  single    1.522  0.020  1.522
 0JM  C12  C14  single    1.527  0.020  1.527
 0JM  C16  O5   single    1.328  0.020  1.328
 0JM  O5   H1   single    0.850  0.020  0.980
 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  O2   H16  single    0.850  0.020  0.980
 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  H1   O5   C16  110.09  3.000
 0JM  C13  C16  O1   125.03  3.000
 0JM  O1   C16  O5   123.73  3.000
 0JM  C13  C16  O5   111.24  3.000
 0JM  H2   C13  N2   109.69  3.000
 0JM  H2   C13  C12  107.41  3.000
 0JM  N2   C13  C12  108.78  3.000
 0JM  H2   C13  C16  107.73  3.000
 0JM  C12  C13  C16  111.94  3.000
 0JM  N2   C13  C16  111.20  3.000
 0JM  S1   C12  C15  108.38  3.000
 0JM  C15  C12  C14  110.56  3.000
 0JM  S1   C12  C14  109.88  3.000
 0JM  C14  C12  C13  112.78  3.000
 0JM  C15  C12  C13  112.62  3.000
 0JM  S1   C12  C13  102.22  3.000
 0JM  H5   C14  H4   107.32  3.000
 0JM  H5   C14  H3   107.96  3.000
 0JM  H4   C14  H3   107.91  3.000
 0JM  H5   C14  C12  110.96  3.000
 0JM  H4   C14  C12  109.82  3.000
 0JM  H3   C14  C12  112.67  3.000
 0JM  H8   C15  H7   108.32  3.000
 0JM  H8   C15  H6   108.29  3.000
 0JM  H7   C15  H6   107.33  3.000
 0JM  H8   C15  C12  111.59  3.000
 0JM  H7   C15  C12  110.43  3.000
 0JM  H6   C15  C12  110.74  3.000
 0JM  C11  S1   C12   89.34  3.000
 0JM  C10  N2   C11   92.18  3.000
 0JM  C11  N2   C13  114.65  3.000
 0JM  C10  N2   C13  118.67  3.000
 0JM  H10  C11  C9   117.00  3.000
 0JM  H10  C11  N2   115.73  3.000
 0JM  C9   C11  N2    89.13  3.000
 0JM  H10  C11  S1   111.30  3.000
 0JM  N2   C11  S1   105.88  3.000
 0JM  C9   C11  S1   115.61  3.000
 0JM  H11  C10  C9   111.25  3.000
 0JM  H11  C10  O4   110.84  3.000
 0JM  C9   C10  O4   118.83  3.000
 0JM  H11  C10  N2   112.80  3.000
 0JM  C9   C10  N2    89.21  3.000
 0JM  O4   C10  N2   112.36  3.000
 0JM  H12  O4   C10  109.12  3.000
 0JM  H13  C9   N1   111.46  3.000
 0JM  H13  C9   C10  111.76  3.000
 0JM  N1   C9   C10  115.97  3.000
 0JM  H13  C9   C11  110.65  3.000
 0JM  C10  C9   C11   85.91  3.000
 0JM  N1   C9   C11  118.79  3.000
 0JM  H14  N1   C8   119.82  3.000
 0JM  H14  N1   C9   118.56  3.000
 0JM  C8   N1   C9   121.30  3.000
 0JM  C7   C8   O6   121.73  3.000
 0JM  O6   C8   N1   122.83  3.000
 0JM  C7   C8   N1   115.40  3.000
 0JM  H15  C7   C1   107.90  3.000
 0JM  H15  C7   C17  104.92  3.000
 0JM  C1   C7   C17  115.14  3.000
 0JM  H15  C7   C8   110.18  3.000
 0JM  C1   C7   C8   109.48  3.000
 0JM  C17  C7   C8   109.08  3.000
 0JM  O3   C17  O2   124.15  3.000
 0JM  O2   C17  C7   112.10  3.000
 0JM  O3   C17  C7   123.67  3.000
 0JM  H16  O2   C17  110.10  3.000
 0JM  C2   C1   C6   119.13  3.000
 0JM  C6   C1   C7   119.33  3.000
 0JM  C2   C1   C7   121.48  3.000
 0JM  H17  C6   C5   119.73  3.000
 0JM  H17  C6   C1   119.61  3.000
 0JM  C5   C6   C1   120.65  3.000
 0JM  H18  C2   C3   119.25  3.000
 0JM  H18  C2   C1   120.48  3.000
 0JM  C3   C2   C1   120.27  3.000
 0JM  H19  C3   C4   120.01  3.000
 0JM  H19  C3   C2   119.67  3.000
 0JM  C4   C3   C2   120.32  3.000
 0JM  H20  C4   C5   120.21  3.000
 0JM  H20  C4   C3   120.14  3.000
 0JM  C5   C4   C3   119.66  3.000
 0JM  H21  C5   C4   120.24  3.000
 0JM  H21  C5   C6   119.79  3.000
 0JM  C4   C5   C6   119.97  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  H1   O5   C16  C13  180.00   0.0  0
 0JM  CONST_17  H14  N1   C8   O6   180.00   0.0  0
 0JM  CONST_18  H16  O2   C17  C7   180.00   0.0  0
 0JM  Var_01    H6   C15  C12  C13   67.53  30.0  3
 0JM  Var_02    H3   C14  C12  C13   51.44  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-3  H1   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
 0JM  plan-4  H16  0.020

