# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 10:12:52 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (2S,5R,6R)-3,3-dimethyl-7-oxo-6-[(phenylacetyl)amino]-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)Cc3ccccc3)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
 PNN  PNN  '(2S,5R,6R)-3,3-dimethyl-7-oxo-6-[(phenylacetyl)amino]-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid'  ligand  40  23  .  2021-08-19  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PNN
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
 PNN  O8    O  O      0  -0.421  -2.3958   0.8241   1.0134
 PNN  C7    C  C      0   0.510  -1.4497   0.0900   1.1291
 PNN  N4    N  N      0  -0.408  -0.7559  -0.3425   2.2213
 PNN  C3    C  CH1    0  -0.146  -0.4578   0.4394   3.4057
 PNN  C11   C  C      0   0.416  -1.0855  -0.1038   4.7107
 PNN  O13   O  OC    -1  -0.600  -1.0544   0.6928   5.6686
 PNN  O12   O  O      0  -0.585  -1.5446  -1.2547   4.6889
 PNN  C2    C  CT     0  -0.240   1.0978   0.5222   3.4904
 PNN  C10   C  CH3    0  -0.634   1.7092  -0.6114   4.3095
 PNN  C9    C  CH3    0  -0.636   1.5553   1.8726   4.0179
 PNN  S1    S  S2     0   0.029   1.6728   0.3512   1.7337
 PNN  C5    C  C      0  -0.200   0.3563  -0.8517   1.4322
 PNN  C6    C  C      0  -0.238  -0.5032  -0.6355   0.1615
 PNN  N14   N  NH1    0  -0.639   0.0100   0.1295  -0.9191
 PNN  C15   C  C      0   0.574   0.2120  -0.3726  -2.1593
 PNN  O16   O  O      0  -0.469  -0.0741  -1.5135  -2.4716
 PNN  C17   C  CH2    0  -0.695   0.8591   0.6016  -3.1275
 PNN  C18   C  C      0   0.147   0.4234   0.3612  -4.5427
 PNN  C19   C  C1     0  -0.293  -0.6931   1.0170  -5.0545
 PNN  C20   C  C1     0  -0.242  -1.1184   0.7840  -6.3554
 PNN  C21   C  C1     0  -0.269  -0.4289  -0.1115  -7.1628
 PNN  C22   C  C1     0  -0.244   0.6863  -0.7697  -6.6607
 PNN  C23   C  C1     0  -0.304   1.1072  -0.5349  -5.3584
 PNN  HC3   H  HCH1   0   0.257  -0.8409   1.4517   3.2375
 PNN  H101  H  HCH3   0   0.243   2.7956  -0.5863   4.2307
 PNN  H102  H  HCH3   0   0.241   1.4510  -0.5009   5.3636
 PNN  H103  H  HCH3   0   0.243   1.3687  -1.5938   3.9820
 PNN  HC91  H  HCH3   0   0.238   2.6435   1.9396   4.0440
 PNN  HC92  H  HCH3   0   0.239   1.1740   2.6888   3.4035
 PNN  HC93  H  HCH3   0   0.248   1.1833   2.0091   5.0328
 PNN  HC5   H  H      0   0.294   0.6646  -1.8736   1.6502
 PNN  HC6   H  H      0   0.323  -0.9148  -1.5720  -0.2142
 PNN  H14   H  HNH1   0   0.408   0.2935   1.0791  -0.7329
 PNN  H171  H  HCH2   0   0.283   0.6532   1.6315  -2.8294
 PNN  H172  H  HCH2   0   0.303   1.9408   0.4648  -3.0328
 PNN  H19   H  H      0   0.251  -1.2330   1.7184  -4.4295
 PNN  H20   H  H      0   0.255  -1.9872   1.3036  -6.7389
 PNN  H21   H  H      0   0.255  -0.7556  -0.2920  -8.1788
 PNN  H22   H  H      0   0.255   1.2300  -1.4676  -7.2843
 PNN  H23   H  H      0   0.250   1.9822  -1.0479  -4.9775

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
 PNN  O8   C7    double    1.203  0.020  1.203
 PNN  C7   N4    single    1.364  0.020  1.364
 PNN  C7   C6    single    1.536  0.020  1.536
 PNN  N4   C3    single    1.450  0.020  1.450
 PNN  N4   C5    single    1.456  0.020  1.456
 PNN  C3   C11   single    1.547  0.020  1.547
 PNN  C3   C2    single    1.560  0.020  1.560
 PNN  C3   HC3   single    0.970  0.020  1.090
 PNN  C11  O13   deloc     1.246  0.020  1.246
 PNN  C11  O12   deloc     1.239  0.020  1.239
 PNN  C2   C10   single    1.526  0.020  1.526
 PNN  C2   C9    single    1.520  0.020  1.520
 PNN  C2   S1    single    1.856  0.020  1.856
 PNN  C10  H101  single    0.970  0.020  1.090
 PNN  C10  H102  single    0.970  0.020  1.090
 PNN  C10  H103  single    0.970  0.020  1.090
 PNN  C9   HC91  single    0.970  0.020  1.090
 PNN  C9   HC92  single    0.970  0.020  1.090
 PNN  C9   HC93  single    0.970  0.020  1.090
 PNN  S1   C5    single    1.809  0.020  1.809
 PNN  C5   C6    single    1.549  0.020  1.549
 PNN  C5   HC5   single    0.970  0.020  1.090
 PNN  C6   N14   single    1.420  0.020  1.420
 PNN  C6   HC6   single    0.970  0.020  1.090
 PNN  N14  C15   single    1.353  0.020  1.353
 PNN  N14  H14   single    0.860  0.020  1.020
 PNN  C15  O16   double    1.217  0.020  1.217
 PNN  C15  C17   single    1.518  0.020  1.518
 PNN  C17  C18   single    1.500  0.020  1.500
 PNN  C17  H171  single    0.970  0.020  1.090
 PNN  C17  H172  single    0.970  0.020  1.090
 PNN  C18  C19   aromatic  1.392  0.020  1.392
 PNN  C18  C23   aromatic  1.391  0.020  1.391
 PNN  C19  C20   aromatic  1.388  0.020  1.388
 PNN  C19  H19   single    0.930  0.020  1.080
 PNN  C20  C21   aromatic  1.389  0.020  1.389
 PNN  C20  H20   single    0.930  0.020  1.080
 PNN  C21  C22   aromatic  1.389  0.020  1.389
 PNN  C21  H21   single    0.930  0.020  1.080
 PNN  C22  C23   aromatic  1.389  0.020  1.389
 PNN  C22  H22   single    0.930  0.020  1.080
 PNN  C23  H23   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
 PNN  C6    C7   N4     92.37  3.000
 PNN  C6    C7   O8    135.42  3.000
 PNN  N4    C7   O8    132.09  3.000
 PNN  C5    N4   C3    118.31  3.000
 PNN  C5    N4   C7     93.75  3.000
 PNN  C3    N4   C7    125.98  3.000
 PNN  HC3   C3   C2    107.94  3.000
 PNN  HC3   C3   C11   108.20  3.000
 PNN  C2    C3   C11   112.18  3.000
 PNN  HC3   C3   N4    107.51  3.000
 PNN  C2    C3   N4    106.14  3.000
 PNN  C11   C3   N4    114.60  3.000
 PNN  O12   C11  O13   128.05  3.000
 PNN  O12   C11  C3    117.50  3.000
 PNN  O13   C11  C3    114.45  3.000
 PNN  S1    C2   C9    108.48  3.000
 PNN  S1    C2   C10   108.38  3.000
 PNN  C9    C2   C10   110.67  3.000
 PNN  S1    C2   C3    104.63  3.000
 PNN  C9    C2   C3    111.47  3.000
 PNN  C10   C2   C3    112.90  3.000
 PNN  H103  C10  H102  107.92  3.000
 PNN  H103  C10  H101  108.09  3.000
 PNN  H102  C10  H101  107.67  3.000
 PNN  H103  C10  C2    112.52  3.000
 PNN  H102  C10  C2    110.39  3.000
 PNN  H101  C10  C2    110.09  3.000
 PNN  HC93  C9   HC92  108.16  3.000
 PNN  HC93  C9   HC91  108.11  3.000
 PNN  HC92  C9   HC91  108.44  3.000
 PNN  HC93  C9   C2    109.38  3.000
 PNN  HC92  C9   C2    111.36  3.000
 PNN  HC91  C9   C2    111.29  3.000
 PNN  C5    S1   C2     89.63  3.000
 PNN  HC5   C5   C6    116.88  3.000
 PNN  HC5   C5   S1    112.61  3.000
 PNN  C6    C5   S1    116.60  3.000
 PNN  HC5   C5   N4    115.84  3.000
 PNN  C6    C5   N4     88.39  3.000
 PNN  S1    C5   N4    103.48  3.000
 PNN  HC6   C6   N14   109.70  3.000
 PNN  HC6   C6   C5    111.86  3.000
 PNN  N14   C6   C5    119.92  3.000
 PNN  HC6   C6   C7    112.98  3.000
 PNN  N14   C6   C7    116.60  3.000
 PNN  C5    C6   C7     83.75  3.000
 PNN  H14   N14  C15   118.47  3.000
 PNN  H14   N14  C6    117.94  3.000
 PNN  C15   N14  C6    123.47  3.000
 PNN  C17   C15  O16   122.55  3.000
 PNN  C17   C15  N14   114.20  3.000
 PNN  O16   C15  N14   123.23  3.000
 PNN  H172  C17  H171  106.30  3.000
 PNN  H172  C17  C18   110.40  3.000
 PNN  H171  C17  C18   110.74  3.000
 PNN  H172  C17  C15   106.61  3.000
 PNN  H171  C17  C15   110.54  3.000
 PNN  C18   C17  C15   112.02  3.000
 PNN  C23   C18  C19   118.81  3.000
 PNN  C23   C18  C17   120.90  3.000
 PNN  C19   C18  C17   120.27  3.000
 PNN  H19   C19  C20   119.77  3.000
 PNN  H19   C19  C18   119.50  3.000
 PNN  C20   C19  C18   120.73  3.000
 PNN  H20   C20  C21   120.13  3.000
 PNN  H20   C20  C19   119.81  3.000
 PNN  C21   C20  C19   120.05  3.000
 PNN  H21   C21  C22   120.18  3.000
 PNN  H21   C21  C20   120.22  3.000
 PNN  C22   C21  C20   119.60  3.000
 PNN  H22   C22  C23   119.81  3.000
 PNN  H22   C22  C21   120.04  3.000
 PNN  C23   C22  C21   120.15  3.000
 PNN  H23   C23  C22   119.63  3.000
 PNN  H23   C23  C18   119.72  3.000
 PNN  C22   C23  C18   120.65  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
 PNN  CONST_01  C21   C20  C19  C18     0.00   0.0  0
 PNN  CONST_02  C21   C22  C23  C18     0.00   0.0  0
 PNN  CONST_03  C22   C23  C18  C19     0.00   0.0  0
 PNN  CONST_04  C22   C21  C20  C19     0.00   0.0  0
 PNN  CONST_05  C23   C18  C19  C20     0.00   0.0  0
 PNN  CONST_06  C23   C22  C21  C20     0.00   0.0  0
 PNN  CONST_08  C6    C7   N4   C5      0.00   0.0  0
 PNN  CONST_09  C20   C19  C18  C17   180.00   0.0  0
 PNN  CONST_10  C22   C23  C18  C17   180.00   0.0  0
 PNN  CONST_12  C5    N4   C7   O8    180.00   0.0  0
 PNN  CONST_13  H20   C20  C19  C18   180.00   0.0  0
 PNN  CONST_14  H22   C22  C23  C18   180.00   0.0  0
 PNN  CONST_15  H23   C23  C18  C19   180.00   0.0  0
 PNN  CONST_16  H21   C21  C20  C19   180.00   0.0  0
 PNN  CONST_17  H19   C19  C20  C21   180.00   0.0  0
 PNN  CONST_18  O16   C15  N14  C6      0.00   0.0  0
 PNN  CONST_19  C17   C15  N14  C6    180.00   0.0  0
 PNN  CONST_20  H14   N14  C15  O16   180.00   0.0  0
 PNN  Var_01    C19   C18  C17  C15    90.42  30.0  2
 PNN  Var_02    H101  C10  C2   C3    172.58  30.0  3
 PNN  Var_03    HC91  C9   C2   C3   -178.07  30.0  3
 PNN  Var_04    C18   C17  C15  N14  -149.30  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
 PNN  chir_01  C3  N4   C11  C2  negativ
 PNN  chir_02  C5  S1   N4   C6  negativ
 PNN  chir_03  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
 PNN  plan-1  C17  0.020
 PNN  plan-1  C18  0.020
 PNN  plan-1  C19  0.020
 PNN  plan-1  C20  0.020
 PNN  plan-1  C21  0.020
 PNN  plan-1  C22  0.020
 PNN  plan-1  C23  0.020
 PNN  plan-1  H19  0.020
 PNN  plan-1  H20  0.020
 PNN  plan-1  H21  0.020
 PNN  plan-1  H22  0.020
 PNN  plan-1  H23  0.020
 PNN  plan-2  C6   0.020
 PNN  plan-2  N14  0.020
 PNN  plan-2  C15  0.020
 PNN  plan-2  O16  0.020
 PNN  plan-2  C17  0.020
 PNN  plan-2  H14  0.020
 PNN  plan-3  O8   0.020
 PNN  plan-3  C7   0.020
 PNN  plan-3  N4   0.020
 PNN  plan-3  C3   0.020
 PNN  plan-3  C5   0.020
 PNN  plan-3  C6   0.020
 PNN  plan-4  C3   0.020
 PNN  plan-4  C11  0.020
 PNN  plan-4  O13  0.020
 PNN  plan-4  O12  0.020

