# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 20:35:43 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  41  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_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   0.384   0.4998   0.6345  -7.3468
 P1C  C2    C  CH1    0  -0.213  -0.2230  -0.1726  -6.2382
 P1C  C3    C  CH2    0  -0.421   0.2844   0.2749  -4.8656
 P1C  C4    C  CH2    0  -0.406  -0.2118  -0.5890  -3.7140
 P1C  C7    C  CH2    0  -0.590   0.3142  -0.0878  -2.3753
 P1C  C10   C  C      0   0.574  -0.0554  -0.9737  -1.2095
 P1C  N11   N  NH1    0  -0.646  -0.3014  -0.3120  -0.0514
 P1C  C12   C  C      0  -0.261  -0.5637  -0.9747   1.1781
 P1C  C13   C  C      0   0.523  -1.3721  -0.1804   2.2128
 P1C  N14   N  NH2    0  -0.785  -1.6767  -0.1211  -6.2706
 P1C  O15   O  O      0  -0.484  -0.1032  -2.1896  -1.2868
 P1C  C16   C  C      0  -0.195   0.5280  -1.0090   2.2807
 P1C  O18   O  O      0  -0.421  -2.3944   0.4517   2.1887
 P1C  O19   O  O      0  -0.608  -0.1885   1.4001  -8.0501
 P1C  O20   O  OC    -1  -0.625   1.7329   0.4538  -7.4367
 P1C  N29   N  N      0  -0.485  -0.4318  -0.4043   3.1735
 P1C  C30   C  C      0   0.136  -0.1607   0.2149   4.3994
 P1C  C31   C  C      0   0.374  -1.3824   0.4062   5.2952
 P1C  C32   C  C      0   0.032   1.1108   0.5143   4.7058
 P1C  C33   C  CH3    0  -0.710   1.5525   1.0571   6.0324
 P1C  C37   C  CH2    0  -0.621   2.2839   0.2722   3.7866
 P1C  O42   O  OC    -1  -0.588  -1.4259   1.4375   5.9875
 P1C  O43   O  O      0  -0.589  -2.2197  -0.5099   5.2384
 P1C  S     S  S2     0   0.025   1.9142   0.1153   2.0144
 P1C  H2    H  HCH1   0   0.208   0.0689  -1.2230  -6.3646
 P1C  H3C1  H  HCH2   0   0.206  -0.0114   1.3188  -4.6990
 P1C  H3C2  H  HCH2   0   0.220   1.3767   0.2657  -4.8771
 P1C  H4C1  H  HCH2   0   0.218   0.1103  -1.6212  -3.8725
 P1C  H4C2  H  HCH2   0   0.228  -1.3032  -0.6008  -3.7048
 P1C  H7C1  H  HCH2   0   0.253  -0.0212   0.9371  -2.1974
 P1C  H7C2  H  HCH2   0   0.270   1.4090  -0.0452  -2.4026
 P1C  H11   H  HNH1   0   0.409  -0.2242   0.6930  -0.0487
 P1C  H12   H  H      0   0.323  -0.9716  -1.9679   0.9887
 P1C  H141  H  HNH2   0   0.322  -1.9573   0.8538  -6.2749
 P1C  H142  H  HNH2   0   0.333  -1.9945  -0.4750  -7.1651
 P1C  H16   H  H      0   0.305   0.8761  -1.9917   2.6010
 P1C  H331  H  HCH3   0   0.231   2.4290   0.5065   6.3829
 P1C  H332  H  HCH3   0   0.239   1.8595   2.1017   5.9369
 P1C  H333  H  HCH3   0   0.254   0.7841   1.0012   6.7948
 P1C  H371  H  HCH2   0   0.294   2.9753   1.1143   3.8643
 P1C  H372  H  HCH2   0   0.290   2.8375  -0.6101   4.1198

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  1.550  0.020  1.550
 P1C  C1   O19   deloc   1.247  0.020  1.247
 P1C  C1   O20   deloc   1.250  0.020  1.250
 P1C  C2   C3    single  1.530  0.020  1.530
 P1C  C2   N14   single  1.455  0.020  1.455
 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  1.523  0.020  1.523
 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  1.356  0.020  1.356
 P1C  C10  O15   double  1.219  0.020  1.219
 P1C  N11  C12   single  1.421  0.020  1.421
 P1C  N11  H11   single  0.860  0.020  1.020
 P1C  C12  C13   single  1.535  0.020  1.535
 P1C  C12  C16   single  1.552  0.020  1.552
 P1C  C12  H12   single  0.970  0.020  1.090
 P1C  C13  O18   double  1.202  0.020  1.202
 P1C  C13  N29   single  1.363  0.020  1.363
 P1C  N14  H141  single  0.890  0.020  1.040
 P1C  N14  H142  single  0.890  0.020  1.040
 P1C  C16  N29   single  1.444  0.020  1.444
 P1C  C16  S     single  1.805  0.020  1.805
 P1C  C16  H16   single  0.970  0.020  1.090
 P1C  N29  C30   single  1.400  0.020  1.400
 P1C  C30  C31   single  1.527  0.020  1.527
 P1C  C30  C32   double  1.342  0.020  1.342
 P1C  C31  O42   deloc   1.243  0.020  1.243
 P1C  C31  O43   deloc   1.242  0.020  1.242
 P1C  C32  C33   single  1.500  0.020  1.500
 P1C  C32  C37   single  1.510  0.020  1.510
 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  1.817  0.020  1.817
 P1C  C37  H371  single  0.970  0.020  1.090
 P1C  C37  H372  single  0.970  0.020  1.090

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   126.37  3.000
 P1C  O20   C1   C2    115.87  3.000
 P1C  O19   C1   C2    117.76  3.000
 P1C  H2    C2   N14   107.29  3.000
 P1C  H2    C2   C3    107.16  3.000
 P1C  N14   C2   C3    109.93  3.000
 P1C  H2    C2   C1    106.97  3.000
 P1C  N14   C2   C1    115.56  3.000
 P1C  C3    C2   C1    109.55  3.000
 P1C  H3C2  C3   H3C1  106.20  3.000
 P1C  H3C2  C3   C4    109.21  3.000
 P1C  H3C1  C3   C4    109.69  3.000
 P1C  H3C2  C3   C2    108.64  3.000
 P1C  H3C1  C3   C2    108.96  3.000
 P1C  C4    C3   C2    113.85  3.000
 P1C  H4C2  C4   H4C1  106.60  3.000
 P1C  H4C2  C4   C7    109.96  3.000
 P1C  H4C1  C4   C7    109.67  3.000
 P1C  H4C2  C4   C3    109.77  3.000
 P1C  H4C1  C4   C3    109.28  3.000
 P1C  C7    C4   C3    111.44  3.000
 P1C  H7C2  C7   H7C1  105.91  3.000
 P1C  H7C2  C7   C10   106.65  3.000
 P1C  H7C1  C7   C10   110.45  3.000
 P1C  H7C2  C7   C4    109.62  3.000
 P1C  H7C1  C7   C4    110.22  3.000
 P1C  C10   C7   C4    113.64  3.000
 P1C  O15   C10  N11   122.25  3.000
 P1C  O15   C10  C7    123.07  3.000
 P1C  N11   C10  C7    114.67  3.000
 P1C  H11   N11  C12   118.47  3.000
 P1C  H11   N11  C10   118.35  3.000
 P1C  C12   N11  C10   123.00  3.000
 P1C  H12   C12  C16   111.50  3.000
 P1C  H12   C12  C13   113.05  3.000
 P1C  C16   C12  C13    84.43  3.000
 P1C  H12   C12  N11   110.09  3.000
 P1C  C16   C12  N11   119.68  3.000
 P1C  C13   C12  N11   116.05  3.000
 P1C  N29   C13  O18   133.41  3.000
 P1C  N29   C13  C12    91.53  3.000
 P1C  O18   C13  C12   134.96  3.000
 P1C  H142  N14  H141  104.20  3.000
 P1C  H142  N14  C2    108.71  3.000
 P1C  H141  N14  C2    108.09  3.000
 P1C  H16   C16  S     111.08  3.000
 P1C  H16   C16  N29   114.08  3.000
 P1C  S     C16  N29   109.94  3.000
 P1C  H16   C16  C12   116.94  3.000
 P1C  S     C16  C12   114.95  3.000
 P1C  N29   C16  C12    87.85  3.000
 P1C  C30   N29  C16   126.73  3.000
 P1C  C30   N29  C13   132.71  3.000
 P1C  C16   N29  C13    95.26  3.000
 P1C  C32   C30  C31   126.61  3.000
 P1C  C32   C30  N29   118.83  3.000
 P1C  C31   C30  N29   114.47  3.000
 P1C  O43   C31  O42   127.86  3.000
 P1C  O43   C31  C30   114.84  3.000
 P1C  O42   C31  C30   117.31  3.000
 P1C  C37   C32  C33   111.57  3.000
 P1C  C37   C32  C30   124.16  3.000
 P1C  C33   C32  C30   124.18  3.000
 P1C  H333  C33  H332  108.05  3.000
 P1C  H333  C33  H331  108.48  3.000
 P1C  H332  C33  H331  106.51  3.000
 P1C  H333  C33  C32   113.25  3.000
 P1C  H332  C33  C32   110.57  3.000
 P1C  H331  C33  C32   109.73  3.000
 P1C  H372  C37  H371  106.26  3.000
 P1C  H372  C37  S     109.30  3.000
 P1C  H371  C37  S     105.35  3.000
 P1C  H372  C37  C32   109.71  3.000
 P1C  H371  C37  C32   108.95  3.000
 P1C  S     C37  C32   116.71  3.000
 P1C  C37   S    C16    93.79  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_04  C30   N29  C13  O18     0.00   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  H11   N11  C10  C7      0.00   0.0  0
 P1C  Var_01    C32   C30  N29  C13  -134.49  30.0  1
 P1C  Var_02    C32   C37  S    C16   -46.24  30.0  1
 P1C  Var_03    C37   C32  C30  N29     2.33  30.0  1
 P1C  Var_04    S     C37  C32  C30    21.62  30.0  1
 P1C  Var_05    O42   C31  C30  N29  -144.45  30.0  2
 P1C  Var_06    H331  C33  C32  C30   133.02  30.0  3
 P1C  Var_07    C7    C4   C3   C2   -179.45  30.0  3
 P1C  Var_08    C10   C7   C4   C3   -175.31  30.0  3
 P1C  Var_09    N11   C10  C7   C4   -144.89  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-4  C30  0.020
 P1C  plan-4  C31  0.020
 P1C  plan-4  O42  0.020
 P1C  plan-4  O43  0.020

