# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 16:45:51 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: (2S,5R,6R)-6-amino-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: CC1(C)S[C@@H]2[C@H](N)C(=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
 X1E  X1E  '(2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid'  ligand  25  14  .  2022-03-29  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X1E
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
 X1E  O13   O  OC    -1  -0.602   3.0916   1.0999  -0.3467
 X1E  C11   C  C      0   0.414   2.0183   1.1954   0.2804
 X1E  O12   O  O      0  -0.587   1.8001   1.8313   1.3220
 X1E  C3    C  CR15   0  -0.145   0.8412   0.4061  -0.3372
 X1E  C2    C  CR5    0  -0.239   1.0095  -1.1336  -0.1662
 X1E  C10   C  CH3    0  -0.633   1.6446  -1.5105   1.1699
 X1E  C9    C  CH3    0  -0.635   1.7834  -1.7497  -1.3205
 X1E  N4    N  N      0  -0.409  -0.4606   0.7322   0.2137
 X1E  C7    C  C      0   0.481  -1.5045   1.2916  -0.4694
 X1E  O8    O  O      0  -0.438  -1.5283   2.1226  -1.3433
 X1E  C6    C  C      0  -0.234  -2.5332   0.3764   0.2226
 X1E  N14   N  NH2    0  -0.784  -3.4746  -0.3755  -0.5456
 X1E  C5    C  C      0  -0.197  -1.2738  -0.3508   0.7464
 X1E  S1    S  S2     0   0.014  -0.7235  -1.7943  -0.1987
 X1E  H3    H  HCR5   0   0.252   0.8098   0.6262  -1.4098
 X1E  H101  H  HCH3   0   0.242   1.1329  -1.0518   2.0162
 X1E  H102  H  HCH3   0   0.240   1.6213  -2.5914   1.3049
 X1E  H103  H  HCH3   0   0.239   2.6886  -1.1952   1.1999
 X1E  H91C  H  HCH3   0   0.247   2.7950  -1.3461  -1.3347
 X1E  H92C  H  HCH3   0   0.235   1.8534  -2.8331  -1.2145
 X1E  H93C  H  HCH3   0   0.236   1.3137  -1.5270  -2.2792
 X1E  H5    H  H      0   0.285  -1.2015  -0.5156   1.8216
 X1E  H6    H  H      0   0.297  -3.0543   0.8895   1.0334
 X1E  H141  H  HNH2   0   0.366  -4.2951   0.1807  -0.7418
 X1E  H142  H  HNH2   0   0.354  -3.0859  -0.6636  -1.4337

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
 X1E  O13  C11   deloc   1.247  0.020  1.247
 X1E  C11  O12   deloc   1.240  0.020  1.240
 X1E  C11  C3    single  1.546  0.020  1.546
 X1E  C3   C2    single  1.558  0.020  1.558
 X1E  C3   N4    single  1.451  0.020  1.451
 X1E  C2   C10   single  1.527  0.020  1.527
 X1E  C2   C9    single  1.520  0.020  1.520
 X1E  C2   S1    single  1.855  0.020  1.855
 X1E  N4   C7    single  1.367  0.020  1.367
 X1E  N4   C5    single  1.455  0.020  1.455
 X1E  C7   O8    double  1.206  0.020  1.206
 X1E  C7   C6    single  1.541  0.020  1.541
 X1E  C6   N14   single  1.429  0.020  1.429
 X1E  C6   C5    single  1.546  0.020  1.546
 X1E  C5   S1    single  1.811  0.020  1.811
 X1E  C3   H3    single  0.970  0.020  1.090
 X1E  C10  H101  single  0.970  0.020  1.090
 X1E  C10  H102  single  0.970  0.020  1.090
 X1E  C10  H103  single  0.970  0.020  1.090
 X1E  C9   H91C  single  0.970  0.020  1.090
 X1E  C9   H92C  single  0.970  0.020  1.090
 X1E  C9   H93C  single  0.970  0.020  1.090
 X1E  C5   H5    single  0.970  0.020  1.090
 X1E  C6   H6    single  0.970  0.020  1.090
 X1E  N14  H141  single  0.890  0.020  1.040
 X1E  N14  H142  single  0.890  0.020  1.040

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
 X1E  C3    C11  O12   117.62  3.000
 X1E  C3    C11  O13   114.54  3.000
 X1E  O12   C11  O13   127.84  3.000
 X1E  H3    C3   N4    107.51  3.000
 X1E  H3    C3   C2    108.00  3.000
 X1E  N4    C3   C2    106.10  3.000
 X1E  H3    C3   C11   108.09  3.000
 X1E  N4    C3   C11   114.63  3.000
 X1E  C2    C3   C11   112.24  3.000
 X1E  S1    C2   C9    108.54  3.000
 X1E  S1    C2   C10   108.42  3.000
 X1E  C9    C2   C10   110.65  3.000
 X1E  S1    C2   C3    104.43  3.000
 X1E  C9    C2   C3    111.85  3.000
 X1E  C10   C2   C3    112.64  3.000
 X1E  H103  C10  H102  107.68  3.000
 X1E  H103  C10  H101  107.83  3.000
 X1E  H102  C10  H101  108.13  3.000
 X1E  H103  C10  C2    110.54  3.000
 X1E  H102  C10  C2    110.15  3.000
 X1E  H101  C10  C2    112.35  3.000
 X1E  H93C  C9   H92C  108.42  3.000
 X1E  H93C  C9   H91C  108.23  3.000
 X1E  H92C  C9   H91C  108.04  3.000
 X1E  H93C  C9   C2    111.44  3.000
 X1E  H92C  C9   C2    111.18  3.000
 X1E  H91C  C9   C2    109.42  3.000
 X1E  C5    N4   C7     93.48  3.000
 X1E  C5    N4   C3    118.24  3.000
 X1E  C7    N4   C3    125.97  3.000
 X1E  C6    C7   O8    136.16  3.000
 X1E  C6    C7   N4     92.42  3.000
 X1E  O8    C7   N4    131.23  3.000
 X1E  H6    C6   C5    111.00  3.000
 X1E  H6    C6   N14   109.39  3.000
 X1E  C5    C6   N14   118.12  3.000
 X1E  H6    C6   C7    111.90  3.000
 X1E  C5    C6   C7     83.56  3.000
 X1E  N14   C6   C7    120.72  3.000
 X1E  H142  N14  H141  107.36  3.000
 X1E  H142  N14  C6    111.64  3.000
 X1E  H141  N14  C6    110.47  3.000
 X1E  H5    C5   S1    111.97  3.000
 X1E  H5    C5   C6    117.35  3.000
 X1E  S1    C5   C6    116.47  3.000
 X1E  H5    C5   N4    115.88  3.000
 X1E  S1    C5   N4    103.43  3.000
 X1E  C6    C5   N4     88.91  3.000
 X1E  C5    S1   C2     89.48  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
 X1E  CONST_02  C5    N4   C7  C6    0.00   0.0  0
 X1E  CONST_04  C5    N4   C7  O8  180.00   0.0  0
 X1E  Var_01    H101  C10  C2  C3   51.82  30.0  3
 X1E  Var_02    H91C  C9   C2  C3   63.47  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
 X1E  chir_01  C3  C11  C2  N4  negativ
 X1E  chir_02  C6  N14  C5  C7  negativ
 X1E  chir_03  C5  S1   N4  C6  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
 X1E  plan-1  C3   0.020
 X1E  plan-1  N4   0.020
 X1E  plan-1  C7   0.020
 X1E  plan-1  O8   0.020
 X1E  plan-1  C6   0.020
 X1E  plan-1  C5   0.020
 X1E  plan-2  O13  0.020
 X1E  plan-2  C11  0.020
 X1E  plan-2  O12  0.020
 X1E  plan-2  C3   0.020

