# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 07:17:54 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2S,5R,6R)-6-{[(2S)-2-amino-2-phenylacetyl]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](NC(=O)[C@@H](N)c3ccccc3)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
 PN1  PN1  '(2S,5R,6R)-6-{[(2S)-2-amino-2-phenylacetyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid'  ligand  42  24  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_PN1
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
 PN1  C8    C  CR16   0  -0.238  -2.0396   1.5787  -3.7066
 PN1  C5    C  CR6    0   0.134   0.0882   0.4346  -3.6616
 PN1  C6    C  CT     0  -0.242  -0.3042   1.2322   2.9665
 PN1  N1    N  NH1    0  -0.628   1.3017  -0.1242  -1.0229
 PN1  N3    N  N      0  -0.409   0.1618  -0.8856   1.9202
 PN1  C4    C  CH1    0  -0.323   1.5772   0.4286  -3.3554
 PN1  C3    C  C      0   0.565   1.8309  -0.5355  -2.1956
 PN1  C7    C  CR16   0  -0.327  -0.6776   1.5715  -3.4287
 PN1  C9    C  CR16   0  -0.266  -2.6480   0.4447  -4.2238
 PN1  C10   C  CR16   0  -0.237  -1.8884  -0.6956  -4.4618
 PN1  C11   C  CR16   0  -0.293  -0.5305  -0.6998  -4.1837
 PN1  C12   C  CH1    0  -0.145  -0.8282  -0.2197   2.7432
 PN1  C13   C  C      0  -0.199   1.3470  -0.1436   1.5195
 PN1  C14   C  C      0  -0.240   1.3150  -0.8987   0.1693
 PN1  C15   C  C      0   0.516  -0.0441  -1.4115   0.6777
 PN1  N2    N  NH2    0  -0.769   2.4470   0.0960  -4.4607
 PN1  O3    O  O      0  -0.468   2.4375  -1.5816  -2.3313
 PN1  O4    O  O      0  -0.419  -0.9847  -1.9796   0.1895
 PN1  S1    S  S2     0   0.025   0.7839   1.5783   1.5027
 PN1  H8    H  HCR6   0   0.258  -2.6219   2.4720  -3.5209
 PN1  H1    H  HNH1   0   0.393   0.7297   0.7089  -1.0203
 PN1  H4    H  HCH1   0   0.285   1.8482   1.4324  -3.0110
 PN1  H1C1  H  HCH3   0   0.244   0.9860   2.3669   4.2735
 PN1  H1C2  H  HCH3   0   0.241  -0.0743   1.2451   5.1180
 PN1  H1C3  H  HCH3   0   0.243   1.3509   0.6407   4.2726
 PN1  H7    H  HCR6   0   0.259  -0.2075   2.4638  -3.0306
 PN1  H9    H  HCR6   0   0.257  -3.7079   0.4474  -4.4424
 PN1  H10   H  HCR6   0   0.257  -2.3567  -1.5842  -4.8646
 PN1  H11   H  HCR6   0   0.251   0.0459  -1.5986  -4.3728
 PN1  H12   H  HCH1   0   0.258  -1.7543  -0.1615   2.1614
 PN1  H13   H  H      0   0.297   2.2298  -0.2827   2.1423
 PN1  H14   H  H      0   0.323   2.0759  -1.6758   0.1029
 PN1  H161  H  HCH3   0   0.239  -1.0619   3.2600   3.0771
 PN1  H162  H  HCH3   0   0.241  -2.0277   2.1859   2.0549
 PN1  H163  H  HCH3   0   0.249  -2.1014   2.0405   3.8131
 PN1  H2N1  H  HNH2   0   0.350   2.2712  -0.8468  -4.7846
 PN1  H2N2  H  HNH2   0   0.358   2.2376   0.7094  -5.2377
 PN1  C1    C  CH3    0  -0.633   0.5438   1.3722   4.2279
 PN1  C2    C  C      0   0.416  -1.1354  -0.9370   4.0787
 PN1  O1    O  O      0  -0.586  -0.3315  -1.8004   4.4590
 PN1  O2    O  OC    -1  -0.599  -2.1747  -0.5506   4.6470
 PN1  C16   C  CH3    0  -0.636  -1.4397   2.2425   2.9711

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
 PN1  C8   C7    aromatic  1.390  0.020  1.390
 PN1  C8   C9    aromatic  1.387  0.020  1.387
 PN1  C8   H8    single    0.930  0.020  1.080
 PN1  C5   C4    single    1.520  0.020  1.520
 PN1  C5   C7    aromatic  1.390  0.020  1.390
 PN1  C5   C11   aromatic  1.394  0.020  1.394
 PN1  C6   C1    single    1.526  0.020  1.526
 PN1  C6   C12   single    1.560  0.020  1.560
 PN1  C6   C16   single    1.520  0.020  1.520
 PN1  C6   S1    single    1.856  0.020  1.856
 PN1  N1   C3    single    1.351  0.020  1.351
 PN1  N1   C14   single    1.422  0.020  1.422
 PN1  N1   H1    single    0.860  0.020  1.020
 PN1  C2   C12   single    1.547  0.020  1.547
 PN1  C2   O1    deloc     1.240  0.020  1.240
 PN1  C2   O2    deloc     1.246  0.020  1.246
 PN1  N3   C12   single    1.449  0.020  1.449
 PN1  N3   C13   single    1.455  0.020  1.455
 PN1  N3   C15   single    1.365  0.020  1.365
 PN1  C4   C3    single    1.529  0.020  1.529
 PN1  C4   N2    single    1.445  0.020  1.445
 PN1  C4   H4    single    0.970  0.020  1.090
 PN1  C1   H1C1  single    0.970  0.020  1.090
 PN1  C1   H1C2  single    0.970  0.020  1.090
 PN1  C1   H1C3  single    0.970  0.020  1.090
 PN1  C3   O3    double    1.217  0.020  1.217
 PN1  C7   H7    single    0.930  0.020  1.080
 PN1  C9   C10   aromatic  1.391  0.020  1.391
 PN1  C9   H9    single    0.930  0.020  1.080
 PN1  C10  C11   aromatic  1.386  0.020  1.386
 PN1  C10  H10   single    0.930  0.020  1.080
 PN1  C11  H11   single    0.930  0.020  1.080
 PN1  C12  H12   single    0.970  0.020  1.090
 PN1  C13  C14   single    1.547  0.020  1.547
 PN1  C13  S1    single    1.812  0.020  1.812
 PN1  C13  H13   single    0.970  0.020  1.090
 PN1  C14  C15   single    1.539  0.020  1.539
 PN1  C14  H14   single    0.970  0.020  1.090
 PN1  C15  O4    double    1.202  0.020  1.202
 PN1  C16  H161  single    0.970  0.020  1.090
 PN1  C16  H162  single    0.970  0.020  1.090
 PN1  C16  H163  single    0.970  0.020  1.090
 PN1  N2   H2N1  single    0.890  0.020  1.040
 PN1  N2   H2N2  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
 PN1  H8    C8   C9    120.19  3.000
 PN1  H8    C8   C7    119.81  3.000
 PN1  C9    C8   C7    120.00  3.000
 PN1  C11   C5   C7    118.93  3.000
 PN1  C11   C5   C4    120.47  3.000
 PN1  C7    C5   C4    120.60  3.000
 PN1  S1    C6   C16   108.45  3.000
 PN1  S1    C6   C12   104.93  3.000
 PN1  C16   C6   C12   111.61  3.000
 PN1  S1    C6   C1    107.99  3.000
 PN1  C16   C6   C1    110.58  3.000
 PN1  C12   C6   C1    112.98  3.000
 PN1  H1    N1   C14   116.89  3.000
 PN1  H1    N1   C3    118.36  3.000
 PN1  C14   N1   C3    123.95  3.000
 PN1  C15   N3   C13    93.94  3.000
 PN1  C15   N3   C12   126.22  3.000
 PN1  C13   N3   C12   118.59  3.000
 PN1  H4    C4   N2    107.61  3.000
 PN1  H4    C4   C3    107.35  3.000
 PN1  N2    C4   C3    109.58  3.000
 PN1  H4    C4   C5    107.58  3.000
 PN1  N2    C4   C5    115.87  3.000
 PN1  C3    C4   C5    108.52  3.000
 PN1  O3    C3   C4    122.69  3.000
 PN1  O3    C3   N1    123.64  3.000
 PN1  C4    C3   N1    113.67  3.000
 PN1  H7    C7   C5    119.71  3.000
 PN1  H7    C7   C8    119.60  3.000
 PN1  C5    C7   C8    120.69  3.000
 PN1  H9    C9   C10   120.16  3.000
 PN1  H9    C9   C8    120.19  3.000
 PN1  C10   C9   C8    119.65  3.000
 PN1  H10   C10  C11   119.74  3.000
 PN1  H10   C10  C9    120.04  3.000
 PN1  C11   C10  C9    120.22  3.000
 PN1  H11   C11  C10   119.23  3.000
 PN1  H11   C11  C5    120.27  3.000
 PN1  C10   C11  C5    120.50  3.000
 PN1  H12   C12  N3    107.47  3.000
 PN1  H12   C12  C2    108.39  3.000
 PN1  N3    C12  C2    114.39  3.000
 PN1  H12   C12  C6    108.10  3.000
 PN1  N3    C12  C6    106.23  3.000
 PN1  C2    C12  C6    112.01  3.000
 PN1  H13   C13  S1    112.25  3.000
 PN1  H13   C13  C14   116.96  3.000
 PN1  S1    C13  C14   116.70  3.000
 PN1  H13   C13  N3    115.96  3.000
 PN1  S1    C13  N3    103.54  3.000
 PN1  C14   C13  N3     88.54  3.000
 PN1  H14   C14  C15   113.53  3.000
 PN1  H14   C14  C13   112.76  3.000
 PN1  C15   C14  C13    83.84  3.000
 PN1  H14   C14  N1    110.12  3.000
 PN1  C15   C14  N1    116.76  3.000
 PN1  C13   C14  N1    117.78  3.000
 PN1  O4    C15  C14   135.57  3.000
 PN1  O4    C15  N3    132.04  3.000
 PN1  C14   C15  N3     92.24  3.000
 PN1  H2N2  N2   H2N1  106.43  3.000
 PN1  H2N2  N2   C4    108.86  3.000
 PN1  H2N1  N2   C4    110.76  3.000
 PN1  C13   S1   C6     89.87  3.000
 PN1  H1C3  C1   H1C2  107.92  3.000
 PN1  H1C3  C1   H1C1  108.08  3.000
 PN1  H1C2  C1   H1C1  107.59  3.000
 PN1  H1C3  C1   C6    112.56  3.000
 PN1  H1C2  C1   C6    110.41  3.000
 PN1  H1C1  C1   C6    110.11  3.000
 PN1  O2    C2   O1    128.11  3.000
 PN1  O2    C2   C12   114.56  3.000
 PN1  O1    C2   C12   117.33  3.000
 PN1  H163  C16  H162  108.20  3.000
 PN1  H163  C16  H161  107.95  3.000
 PN1  H162  C16  H161  108.48  3.000
 PN1  H163  C16  C6    109.44  3.000
 PN1  H162  C16  C6    111.46  3.000
 PN1  H161  C16  C6    111.20  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
 PN1  CONST_01  C11   C5   C7   C8      0.00   0.0  0
 PN1  CONST_02  C11   C10  C9   C8      0.00   0.0  0
 PN1  CONST_03  C9    C8   C7   C5      0.00   0.0  0
 PN1  CONST_04  C9    C10  C11  C5      0.00   0.0  0
 PN1  CONST_05  C10   C9   C8   C7      0.00   0.0  0
 PN1  CONST_06  C10   C11  C5   C7      0.00   0.0  0
 PN1  CONST_08  C14   C15  N3   C13     0.00   0.0  0
 PN1  CONST_09  C4    C5   C7   C8    180.00   0.0  0
 PN1  CONST_10  C10   C11  C5   C4    180.00   0.0  0
 PN1  CONST_12  O4    C15  N3   C13   180.00   0.0  0
 PN1  CONST_13  H10   C10  C9   C8    180.00   0.0  0
 PN1  CONST_14  H8    C8   C7   C5    180.00   0.0  0
 PN1  CONST_15  H9    C9   C8   C7    180.00   0.0  0
 PN1  CONST_16  H11   C11  C5   C7    180.00   0.0  0
 PN1  CONST_17  H7    C7   C8   C9    180.00   0.0  0
 PN1  CONST_18  C14   N1   C3   C4    180.00   0.0  0
 PN1  CONST_19  O3    C3   N1   C14     0.00   0.0  0
 PN1  CONST_20  H1    N1   C3   C4      0.00   0.0  0
 PN1  Var_01    C16   C6   S1   C13  -155.71  30.0  1
 PN1  Var_02    H1C1  C1   C6   C12   172.98  30.0  3
 PN1  Var_03    H161  C16  C6   C12  -177.13  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
 PN1  chir_01  C4   C5  C3   N2   negativ
 PN1  chir_02  C12  C6  C2   N3   positiv
 PN1  chir_03  C13  S1  N3   C14  negativ
 PN1  chir_04  C14  N1  C13  C15  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
 PN1  plan-1  C8   0.020
 PN1  plan-1  C5   0.020
 PN1  plan-1  C4   0.020
 PN1  plan-1  C7   0.020
 PN1  plan-1  C9   0.020
 PN1  plan-1  C10  0.020
 PN1  plan-1  C11  0.020
 PN1  plan-1  H8   0.020
 PN1  plan-1  H7   0.020
 PN1  plan-1  H9   0.020
 PN1  plan-1  H10  0.020
 PN1  plan-1  H11  0.020
 PN1  plan-2  N1   0.020
 PN1  plan-2  C4   0.020
 PN1  plan-2  C3   0.020
 PN1  plan-2  C14  0.020
 PN1  plan-2  O3   0.020
 PN1  plan-2  H1   0.020
 PN1  plan-3  N3   0.020
 PN1  plan-3  C12  0.020
 PN1  plan-3  C13  0.020
 PN1  plan-3  C14  0.020
 PN1  plan-3  C15  0.020
 PN1  plan-3  O4   0.020
 PN1  plan-4  C12  0.020
 PN1  plan-4  C2   0.020
 PN1  plan-4  O1   0.020
 PN1  plan-4  O2   0.020

