# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 21:42:54 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (6R,7R)-7-{[(5R)-5-amino-5-carboxypentanoyl]amino}-3-methyl-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(N2[C@H](SC1)[C@H](NC(=O)CCC[C@@H](N)C(O)=O)C2=O)C(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
 P1C  P1C  '(6R,7R)-7-{[(5R)-5-amino-5-carboxypentanoyl]amino}-3-methyl-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid'  ligand  43  24  .  2022-07-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_P1C
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
 P1C  C1    C  C     0   0.522   0.3752   0.6445  -7.3519
 P1C  C2    C  CH1   0  -0.209  -0.2924  -0.1583  -6.2423
 P1C  C3    C  CH2   0  -0.434   0.2371   0.3180  -4.8826
 P1C  C4    C  CH2   0  -0.410  -0.2453  -0.5513  -3.7295
 P1C  C7    C  CH2   0  -0.594   0.2935  -0.0438  -2.3990
 P1C  C10   C  C     0   0.579  -0.0802  -0.9223  -1.2289
 P1C  N11   N  NH1   0  -0.649  -0.2576  -0.2574  -0.0588
 P1C  C12   C  C     0  -0.255  -0.5368  -0.9155   1.1669
 P1C  C13   C  C     0   0.529  -1.3282  -0.1107   2.2043
 P1C  N14   N  NH2   0  -0.776  -1.7334  -0.1014  -6.2769
 P1C  O15   O  O     0  -0.479  -0.1876  -2.1329  -1.3119
 P1C  C16   C  C     0  -0.201   0.5522  -0.9912   2.2731
 P1C  O18   O  O     0  -0.402  -2.3206   0.5621   2.1990
 P1C  O19   O  O     0  -0.440  -0.1815   1.4720  -8.0294
 P1C  O20   O  OH1   0  -0.594   1.6614   0.3397  -7.4853
 P1C  N29   N  N     0  -0.508  -0.4071  -0.3984   3.1768
 P1C  C30   C  C     0   0.188  -0.1176   0.2157   4.3982
 P1C  C31   C  C     0   0.487  -1.3213   0.3800   5.2561
 P1C  C32   C  C     0   0.080   1.1506   0.5115   4.7282
 P1C  C33   C  CH3   0  -0.718   1.6091   1.0178   6.0617
 P1C  C37   C  CH2   0  -0.631   2.3105   0.2768   3.7954
 P1C  O42   O  OH1   0  -0.582  -1.2800   1.4582   6.0192
 P1C  O43   O  O     0  -0.428  -2.2467  -0.3914   5.2232
 P1C  S     S  S2    0   0.048   1.9356   0.1413   2.0260
 P1C  H2    H  HCH1  0   0.267   0.0125  -1.2021  -6.3735
 P1C  H3C1  H  HCH2  0   0.232  -0.0716   1.3575  -4.7254
 P1C  H3C2  H  HCH2  0   0.243   1.3296   0.3194  -4.8959
 P1C  H4C1  H  HCH2  0   0.230   0.0814  -1.5809  -3.8919
 P1C  H4C2  H  HCH2  0   0.239  -1.3359  -0.5661  -3.7086
 P1C  H7C1  H  HCH2  0   0.259  -0.0344   0.9837  -2.2240
 P1C  H7C2  H  HCH2  0   0.277   1.3883  -0.0096  -2.4304
 P1C  H11   H  HNH1  0   0.412  -0.1495   0.7450  -0.0546
 P1C  H12   H  H     0   0.334  -0.9726  -1.8966   0.9754
 P1C  H141  H  HNH2  0   0.343  -2.0464   0.8613  -6.2382
 P1C  H142  H  HNH2  0   0.354  -2.0824  -0.4790  -7.1484
 P1C  H16   H  H     0   0.317   0.8943  -1.9821   2.5715
 P1C  H20   H  HOH1  0   0.481   2.0641   0.8827  -8.1797
 P1C  H331  H  HCH3  0   0.255   2.5344   0.5098   6.3390
 P1C  H332  H  HCH3  0   0.263   1.8432   2.0827   5.9981
 P1C  H333  H  HCH3  0   0.260   0.8971   0.8710   6.8663
 P1C  H371  H  HCH2  0   0.312   3.0052   1.1144   3.8878
 P1C  H372  H  HCH2  0   0.309   2.8553  -0.6117   4.1256
 P1C  H421  H  HOH1  0   0.491  -2.0694   1.4958   6.5815

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
 P1C  C1   C2    single  1.524  0.020  1.524
 P1C  C1   O19   double  1.206  0.020  1.206
 P1C  C1   O20   single  1.329  0.020  1.329
 P1C  C2   C3    single  1.535  0.020  1.535
 P1C  C2   N14   single  1.443  0.020  1.443
 P1C  C2   H2    single  0.970  0.020  1.090
 P1C  C3   C4    single  1.523  0.020  1.523
 P1C  C3   H3C1  single  0.970  0.020  1.090
 P1C  C3   H3C2  single  0.970  0.020  1.090
 P1C  C4   C7    single  1.522  0.020  1.522
 P1C  C4   H4C1  single  0.970  0.020  1.090
 P1C  C4   H4C2  single  0.970  0.020  1.090
 P1C  C7   C10   single  1.510  0.020  1.510
 P1C  C7   H7C1  single  0.970  0.020  1.090
 P1C  C7   H7C2  single  0.970  0.020  1.090
 P1C  C10  N11   single  1.357  0.020  1.357
 P1C  C10  O15   double  1.218  0.020  1.218
 P1C  N11  C12   single  1.419  0.020  1.419
 P1C  N11  H11   single  0.860  0.020  1.020
 P1C  C12  C13   single  1.533  0.020  1.533
 P1C  C12  C16   single  1.554  0.020  1.554
 P1C  C12  H12   single  0.970  0.020  1.090
 P1C  C13  O18   double  1.199  0.020  1.199
 P1C  C13  N29   single  1.370  0.020  1.370
 P1C  N14  H141  single  0.890  0.020  1.040
 P1C  N14  H142  single  0.890  0.020  1.040
 P1C  C16  N29   single  1.445  0.020  1.445
 P1C  C16  S     single  1.805  0.020  1.805
 P1C  C16  H16   single  0.970  0.020  1.090
 P1C  O20  H20   single  0.850  0.020  0.980
 P1C  N29  C30   single  1.397  0.020  1.397
 P1C  C30  C31   single  1.487  0.020  1.487
 P1C  C30  C32   double  1.343  0.020  1.343
 P1C  C31  O42   single  1.322  0.020  1.322
 P1C  C31  O43   double  1.205  0.020  1.205
 P1C  C32  C33   single  1.498  0.020  1.498
 P1C  C32  C37   single  1.507  0.020  1.507
 P1C  C33  H331  single  0.970  0.020  1.090
 P1C  C33  H332  single  0.970  0.020  1.090
 P1C  C33  H333  single  0.970  0.020  1.090
 P1C  C37  S     single  1.814  0.020  1.814
 P1C  C37  H371  single  0.970  0.020  1.090
 P1C  C37  H372  single  0.970  0.020  1.090
 P1C  O42  H421  single  0.850  0.020  0.980

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
 P1C  O20   C1   O19   123.24  3.000
 P1C  O20   C1   C2    112.11  3.000
 P1C  O19   C1   C2    124.65  3.000
 P1C  H2    C2   N14   108.23  3.000
 P1C  H2    C2   C3    107.80  3.000
 P1C  N14   C2   C3    110.71  3.000
 P1C  H2    C2   C1    107.03  3.000
 P1C  N14   C2   C1    113.54  3.000
 P1C  C3    C2   C1    109.30  3.000
 P1C  H3C2  C3   H3C1  106.40  3.000
 P1C  H3C2  C3   C4    109.07  3.000
 P1C  H3C1  C3   C4    110.10  3.000
 P1C  H3C2  C3   C2    109.55  3.000
 P1C  H3C1  C3   C2    108.92  3.000
 P1C  C4    C3   C2    112.61  3.000
 P1C  H4C2  C4   H4C1  106.80  3.000
 P1C  H4C2  C4   C7    109.98  3.000
 P1C  H4C1  C4   C7    109.77  3.000
 P1C  H4C2  C4   C3    109.81  3.000
 P1C  H4C1  C4   C3    109.31  3.000
 P1C  C7    C4   C3    111.06  3.000
 P1C  H7C2  C7   H7C1  105.96  3.000
 P1C  H7C2  C7   C10   106.72  3.000
 P1C  H7C1  C7   C10   110.41  3.000
 P1C  H7C2  C7   C4    109.81  3.000
 P1C  H7C1  C7   C4    110.32  3.000
 P1C  C10   C7   C4    113.31  3.000
 P1C  O15   C10  N11   122.27  3.000
 P1C  O15   C10  C7    123.17  3.000
 P1C  N11   C10  C7    114.54  3.000
 P1C  H11   N11  C12   118.60  3.000
 P1C  H11   N11  C10   118.46  3.000
 P1C  C12   N11  C10   122.90  3.000
 P1C  H12   C12  C16   111.17  3.000
 P1C  H12   C12  C13   112.64  3.000
 P1C  C16   C12  C13    84.59  3.000
 P1C  H12   C12  N11   110.13  3.000
 P1C  C16   C12  N11   119.97  3.000
 P1C  C13   C12  N11   116.27  3.000
 P1C  N29   C13  O18   132.65  3.000
 P1C  N29   C13  C12    91.32  3.000
 P1C  O18   C13  C12   135.96  3.000
 P1C  H142  N14  H141  106.31  3.000
 P1C  H142  N14  C2    110.52  3.000
 P1C  H141  N14  C2    110.19  3.000
 P1C  H16   C16  S     111.55  3.000
 P1C  H16   C16  N29   114.21  3.000
 P1C  S     C16  N29   109.70  3.000
 P1C  H16   C16  C12   117.33  3.000
 P1C  S     C16  C12   114.15  3.000
 P1C  N29   C16  C12    87.71  3.000
 P1C  H20   O20  C1    110.22  3.000
 P1C  C30   N29  C16   126.11  3.000
 P1C  C30   N29  C13   131.87  3.000
 P1C  C16   N29  C13    95.08  3.000
 P1C  C32   C30  C31   126.73  3.000
 P1C  C32   C30  N29   120.47  3.000
 P1C  C31   C30  N29   112.65  3.000
 P1C  O43   C31  O42   124.19  3.000
 P1C  O43   C31  C30   122.34  3.000
 P1C  O42   C31  C30   113.45  3.000
 P1C  C37   C32  C33   111.60  3.000
 P1C  C37   C32  C30   122.70  3.000
 P1C  C33   C32  C30   125.58  3.000
 P1C  H333  C33  H332  108.42  3.000
 P1C  H333  C33  H331  107.76  3.000
 P1C  H332  C33  H331  106.67  3.000
 P1C  H333  C33  C32   114.44  3.000
 P1C  H332  C33  C32   110.08  3.000
 P1C  H331  C33  C32   109.17  3.000
 P1C  H372  C37  H371  106.31  3.000
 P1C  H372  C37  S     109.69  3.000
 P1C  H371  C37  S     105.75  3.000
 P1C  H372  C37  C32   108.85  3.000
 P1C  H371  C37  C32   108.52  3.000
 P1C  S     C37  C32   117.16  3.000
 P1C  H421  O42  C31   109.93  3.000
 P1C  C37   S    C16    94.12  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
 P1C  CONST_01  C16   N29  C13  C12     0.00   0.0  0
 P1C  CONST_03  O18   C13  N29  C16   180.00   0.0  0
 P1C  CONST_05  C12   N11  C10  C7    180.00   0.0  0
 P1C  CONST_06  O15   C10  N11  C12     0.00   0.0  0
 P1C  CONST_07  H421  O42  C31  C30   180.00   0.0  0
 P1C  CONST_08  H11   N11  C10  C7      0.00   0.0  0
 P1C  CONST_09  H20   O20  C1   C2    180.00   0.0  0
 P1C  Var_01    C32   C30  N29  C13  -131.39  30.0  1
 P1C  Var_02    C32   C37  S    C16   -46.60  30.0  1
 P1C  Var_03    C37   C32  C30  N29     3.39  30.0  1
 P1C  Var_04    S     C37  C32  C30    21.25  30.0  1
 P1C  Var_05    O42   C31  C30  N29  -147.80  30.0  2
 P1C  Var_06    H331  C33  C32  C30   137.82  30.0  3
 P1C  Var_07    C7    C4   C3   C2   -179.69  30.0  3
 P1C  Var_08    C10   C7   C4   C3   -176.23  30.0  3
 P1C  Var_09    N11   C10  C7   C4   -147.67  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
 P1C  chir_01  C2   C1   C3   N14  negativ
 P1C  chir_02  C12  N11  C13  C16  positiv
 P1C  chir_03  C16  S    N29  C12  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
 P1C  plan-1  C7    0.020
 P1C  plan-1  C10   0.020
 P1C  plan-1  N11   0.020
 P1C  plan-1  C12   0.020
 P1C  plan-1  O15   0.020
 P1C  plan-1  H11   0.020
 P1C  plan-2  C12   0.020
 P1C  plan-2  C13   0.020
 P1C  plan-2  C16   0.020
 P1C  plan-2  O18   0.020
 P1C  plan-2  N29   0.020
 P1C  plan-2  C30   0.020
 P1C  plan-3  C1    0.020
 P1C  plan-3  C2    0.020
 P1C  plan-3  O19   0.020
 P1C  plan-3  O20   0.020
 P1C  plan-3  H20   0.020
 P1C  plan-4  C30   0.020
 P1C  plan-4  C31   0.020
 P1C  plan-4  O42   0.020
 P1C  plan-4  O43   0.020
 P1C  plan-4  H421  0.020

