# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:40:05 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: (2S,3R,6R,7R)-3-[(acetyloxy)methyl]-7-({(6S)-6-[(ammonioacetyl)amino]-6-carboxylatohexanoyl}amino)-8-oxo-5-thia-1-azabicyclo[4.2.0]octane-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)OC[C@@H]1CS[C@@H]2[C@H](NC(=O)CCCC[C@H](NC(=O)C[NH3+])C([O-])=O)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
 H2A  H2A  (2S,3R,6R,7R)-3-[(acetyloxy)methyl]-7-({(6S)-6-[(ammonioacetyl)amino]-6-carboxylatohexanoyl}amino)-8-oxo-5-thia-1-azabicyclo[4.2.0]octane-2-carboxylate  ligand  60  33  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H2A
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
 H2A  S1    S  S2     0   0.002   3.8815  -1.3380   4.0166
 H2A  C2    C  CH2    0  -0.580   4.0687  -1.0925   2.2204
 H2A  C3    C  CH1    0  -0.289   2.8857  -1.5913   1.3905
 H2A  C3'   C  CH2    0  -0.145   2.6353  -3.0825   1.5163
 H2A  C4    C  CH1    0  -0.279   1.5980  -0.8220   1.7283
 H2A  C4'   C  C      0   0.446   1.6209   0.6405   1.1902
 H2A  O4A   O  OC    -1  -0.592   2.0020   0.7612   0.0135
 H2A  O4B   O  O      0  -0.579   1.2385   1.5269   1.9680
 H2A  N5    N  N      0  -0.395   1.3779  -0.8599   3.1471
 H2A  C6    C  C      0  -0.173   2.3053  -0.4487   4.1736
 H2A  C7    C  C      0  -0.261   1.3222  -1.0648   5.2055
 H2A  C8    C  C      0   0.541   0.5689  -1.5665   3.9623
 H2A  O9    O  O      0  -0.444  -0.3586  -2.3149   3.7582
 H2A  N10   N  NH1    0  -0.627   1.7929  -2.0334   6.1315
 H2A  C11   C  C      0   0.526   1.3488  -2.1167   7.4108
 H2A  O12   O  O      0  -0.479   0.5926  -1.2912   7.8943
 H2A  C13   C  CH2    0  -0.562   1.8760  -3.3003   8.1913
 H2A  C14   C  CH2    0  -0.463   1.7306  -4.6494   7.4844
 H2A  C15   C  CH2    0  -0.437   0.3141  -4.9366   7.0027
 H2A  C16   C  CH2    0  -0.415   0.1559  -6.3682   6.5040
 H2A  C17   C  CH1    0  -0.224  -1.1333  -6.6061   5.7129
 H2A  C18   C  C      0   0.423  -2.3720  -6.2056   6.5479
 H2A  O19   O  O      0  -0.601  -2.5541  -6.8707   7.5817
 H2A  O20   O  OC    -1  -0.596  -3.0576  -5.2531   6.1276
 H2A  N21   N  NH1    0  -0.623  -1.1403  -5.8691   4.4659
 H2A  C22   C  C      0   0.549  -0.4919  -6.2490   3.3721
 H2A  O23   O  O      0  -0.496   0.2325  -7.2308   3.2797
 H2A  C24   C  CH2    0  -0.451  -0.7269  -5.3551   2.1625
 H2A  N25   N  NT3    1  -0.811   0.0578  -5.8568   1.0199
 H2A  O1    O  O2     0  -0.436   3.8466  -3.7728   1.2030
 H2A  C1    C  C      0   0.611   3.8436  -5.0927   1.2073
 H2A  O2    O  O      0  -0.472   2.8513  -5.7582   1.4147
 H2A  C26   C  CH3    0  -0.769   5.1982  -5.6616   0.9283
 H2A  H21A  H  HCH2   0   0.303   4.9873  -1.6109   1.9483
 H2A  H22   H  HCH2   0   0.292   4.2382  -0.0317   2.0257
 H2A  H3    H  HCH1   0   0.284   3.1173  -1.3712   0.3459
 H2A  H3'1  H  HCH2   0   0.245   1.8482  -3.3686   0.8141
 H2A  H3'2  H  HCH2   0   0.225   2.3185  -3.3567   2.5257
 H2A  H4    H  HCH1   0   0.284   0.7456  -1.3241   1.2570
 H2A  H6    H  H      0   0.300   2.4683   0.6262   4.2330
 H2A  H7    H  H      0   0.324   0.7658  -0.2941   5.7376
 H2A  H10   H  HNH1   0   0.399   2.3871  -2.7691   5.7804
 H2A  H131  H  HCH2   0   0.278   2.9298  -3.1165   8.4220
 H2A  H132  H  HCH2   0   0.259   1.3418  -3.3234   9.1413
 H2A  H141  H  HCH2   0   0.247   2.0475  -5.4224   8.1890
 H2A  H142  H  HCH2   0   0.224   2.4243  -4.7264   6.6411
 H2A  H151  H  HCH2   0   0.224   0.0559  -4.2374   6.2015
 H2A  H152  H  HCH2   0   0.224  -0.3926  -4.7508   7.8171
 H2A  H161  H  HCH2   0   0.227   1.0070  -6.6394   5.8729
 H2A  H162  H  HCH2   0   0.228   0.1731  -7.0572   7.3511
 H2A  H17   H  HCH1   0   0.254  -1.2046  -7.6743   5.4857
 H2A  H21   H  HNH1   0   0.394  -1.7744  -5.0808   4.4417
 H2A  H241  H  HCH2   0   0.313  -0.4399  -4.3231   2.3610
 H2A  H242  H  HCH2   0   0.331  -1.7781  -5.3587   1.8774
 H2A  H251  H  HNT3   0   0.477   1.0789  -5.7741   1.1693
 H2A  H252  H  HNT3   0   0.475  -0.1799  -5.3515   0.1674
 H2A  H253  H  HNT3   0   0.465  -0.1356  -6.8425   0.8419
 H2A  H261  H  HCH3   0   0.278   5.9249  -5.2843   1.6479
 H2A  H262  H  HCH3   0   0.281   5.5356  -5.3568  -0.0630
 H2A  H263  H  HCH3   0   0.268   5.1734  -6.7460   0.9774

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
 H2A  S1   C2    single  1.823  0.020  1.823
 H2A  S1   C6    single  1.817  0.020  1.817
 H2A  C2   C3    single  1.529  0.020  1.529
 H2A  C2   H21A  single  0.970  0.020  1.090
 H2A  C2   H22   single  0.970  0.020  1.090
 H2A  C3   C3'   single  1.517  0.020  1.517
 H2A  C3   C4    single  1.538  0.020  1.538
 H2A  C3   H3    single  0.970  0.020  1.090
 H2A  C3'  O1    single  1.429  0.020  1.429
 H2A  C3'  H3'1  single  0.970  0.020  1.090
 H2A  C3'  H3'2  single  0.970  0.020  1.090
 H2A  C4   C4'   single  1.559  0.020  1.559
 H2A  C4   N5    single  1.436  0.020  1.436
 H2A  C4   H4    single  0.970  0.020  1.090
 H2A  C4'  O4A   deloc   1.243  0.020  1.243
 H2A  C4'  O4B   deloc   1.240  0.020  1.240
 H2A  N5   C6    single  1.443  0.020  1.443
 H2A  N5   C8    single  1.348  0.020  1.348
 H2A  C6   C7    single  1.553  0.020  1.553
 H2A  C6   H6    single  0.970  0.020  1.090
 H2A  C7   C8    single  1.538  0.020  1.538
 H2A  C7   N10   single  1.420  0.020  1.420
 H2A  C7   H7    single  0.970  0.020  1.090
 H2A  C8   O9    double  1.209  0.020  1.209
 H2A  N10  C11   single  1.357  0.020  1.357
 H2A  N10  H10   single  0.860  0.020  1.020
 H2A  C11  O12   double  1.219  0.020  1.219
 H2A  C11  C13   single  1.513  0.020  1.513
 H2A  C13  C14   single  1.530  0.020  1.530
 H2A  C13  H131  single  0.970  0.020  1.090
 H2A  C13  H132  single  0.970  0.020  1.090
 H2A  C14  C15   single  1.523  0.020  1.523
 H2A  C14  H141  single  0.970  0.020  1.090
 H2A  C14  H142  single  0.970  0.020  1.090
 H2A  C15  C16   single  1.524  0.020  1.524
 H2A  C15  H151  single  0.970  0.020  1.090
 H2A  C15  H152  single  0.970  0.020  1.090
 H2A  C16  C17   single  1.531  0.020  1.531
 H2A  C16  H161  single  0.970  0.020  1.090
 H2A  C16  H162  single  0.970  0.020  1.090
 H2A  C17  C18   single  1.547  0.020  1.547
 H2A  C17  N21   single  1.449  0.020  1.449
 H2A  C17  H17   single  0.970  0.020  1.090
 H2A  C18  O19   deloc   1.243  0.020  1.243
 H2A  C18  O20   deloc   1.247  0.020  1.247
 H2A  N21  C22   single  1.327  0.020  1.327
 H2A  N21  H21   single  0.860  0.020  1.020
 H2A  C22  O23   double  1.224  0.020  1.224
 H2A  C22  C24   single  1.522  0.020  1.522
 H2A  C24  N25   single  1.474  0.020  1.474
 H2A  C24  H241  single  0.970  0.020  1.090
 H2A  C24  H242  single  0.970  0.020  1.090
 H2A  N25  H251  single  0.890  0.020  1.040
 H2A  N25  H252  single  0.890  0.020  1.040
 H2A  N25  H253  single  0.890  0.020  1.040
 H2A  O1   C1    single  1.320  0.020  1.320
 H2A  C1   O2    double  1.213  0.020  1.213
 H2A  C1   C26   single  1.495  0.020  1.495
 H2A  C26  H261  single  0.970  0.020  1.090
 H2A  C26  H262  single  0.970  0.020  1.090
 H2A  C26  H263  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
 H2A  C6    S1   C2     96.22  3.000
 H2A  H22   C2   H21A  106.68  3.000
 H2A  H22   C2   C3    109.90  3.000
 H2A  H21A  C2   C3    111.20  3.000
 H2A  H22   C2   S1    108.82  3.000
 H2A  H21A  C2   S1    105.59  3.000
 H2A  C3    C2   S1    114.30  3.000
 H2A  H3    C3   C4    106.67  3.000
 H2A  H3    C3   C3'   108.20  3.000
 H2A  C4    C3   C3'   109.59  3.000
 H2A  H3    C3   C2    106.81  3.000
 H2A  C4    C3   C2    111.44  3.000
 H2A  C3'   C3   C2    113.79  3.000
 H2A  H3'2  C3'  H3'1  108.60  3.000
 H2A  H3'2  C3'  O1    109.09  3.000
 H2A  H3'1  C3'  O1    110.07  3.000
 H2A  H3'2  C3'  C3    111.78  3.000
 H2A  H3'1  C3'  C3    108.84  3.000
 H2A  O1    C3'  C3    108.46  3.000
 H2A  H4    C4   N5    107.07  3.000
 H2A  H4    C4   C4'   107.03  3.000
 H2A  N5    C4   C4'   111.60  3.000
 H2A  H4    C4   C3    109.13  3.000
 H2A  N5    C4   C3    109.40  3.000
 H2A  C4'   C4   C3    112.42  3.000
 H2A  O4B   C4'  O4A   128.26  3.000
 H2A  O4B   C4'  C4    116.73  3.000
 H2A  O4A   C4'  C4    115.00  3.000
 H2A  C8    N5   C6     96.02  3.000
 H2A  C8    N5   C4    134.67  3.000
 H2A  C6    N5   C4    126.63  3.000
 H2A  H6    C6   C7    116.76  3.000
 H2A  H6    C6   N5    114.60  3.000
 H2A  C7    C6   N5     87.30  3.000
 H2A  H6    C6   S1    110.98  3.000
 H2A  C7    C6   S1    114.37  3.000
 H2A  N5    C6   S1    110.89  3.000
 H2A  H7    C7   N10   109.47  3.000
 H2A  H7    C7   C8    112.06  3.000
 H2A  N10   C7   C8    117.84  3.000
 H2A  H7    C7   C6    111.55  3.000
 H2A  N10   C7   C6    119.61  3.000
 H2A  C8    C7   C6     84.39  3.000
 H2A  O9    C8   C7    135.57  3.000
 H2A  O9    C8   N5    133.04  3.000
 H2A  C7    C8   N5     91.37  3.000
 H2A  H10   N10  C11   118.44  3.000
 H2A  H10   N10  C7    117.76  3.000
 H2A  C11   N10  C7    123.24  3.000
 H2A  C13   C11  O12   122.76  3.000
 H2A  C13   C11  N10   114.87  3.000
 H2A  O12   C11  N10   122.36  3.000
 H2A  H132  C13  H131  106.96  3.000
 H2A  H132  C13  C14   109.72  3.000
 H2A  H131  C13  C14   109.70  3.000
 H2A  H132  C13  C11   107.18  3.000
 H2A  H131  C13  C11   108.24  3.000
 H2A  C14   C13  C11   114.73  3.000
 H2A  H142  C14  H141  105.26  3.000
 H2A  H142  C14  C15   109.41  3.000
 H2A  H141  C14  C15   109.89  3.000
 H2A  H142  C14  C13   110.96  3.000
 H2A  H141  C14  C13   107.35  3.000
 H2A  C15   C14  C13   113.62  3.000
 H2A  H152  C15  H151  106.51  3.000
 H2A  H152  C15  C16   109.63  3.000
 H2A  H151  C15  C16   109.64  3.000
 H2A  H152  C15  C14   109.46  3.000
 H2A  H151  C15  C14   109.30  3.000
 H2A  C16   C15  C14   112.15  3.000
 H2A  H162  C16  H161  106.20  3.000
 H2A  H162  C16  C17   108.42  3.000
 H2A  H161  C16  C17   108.57  3.000
 H2A  H162  C16  C15   109.71  3.000
 H2A  H161  C16  C15   109.93  3.000
 H2A  C17   C16  C15   113.73  3.000
 H2A  H17   C17  N21   108.51  3.000
 H2A  H17   C17  C18   108.22  3.000
 H2A  N21   C17  C18   109.22  3.000
 H2A  H17   C17  C16   108.29  3.000
 H2A  N21   C17  C16   111.70  3.000
 H2A  C18   C17  C16   110.81  3.000
 H2A  O20   C18  O19   127.51  3.000
 H2A  O20   C18  C17   117.15  3.000
 H2A  O19   C18  C17   115.33  3.000
 H2A  H21   N21  C22   120.63  3.000
 H2A  H21   N21  C17   114.83  3.000
 H2A  C22   N21  C17   124.16  3.000
 H2A  C24   C22  O23   120.17  3.000
 H2A  C24   C22  N21   114.29  3.000
 H2A  O23   C22  N21   125.54  3.000
 H2A  H242  C24  H241  107.77  3.000
 H2A  H242  C24  N25   108.04  3.000
 H2A  H241  C24  N25   108.87  3.000
 H2A  H242  C24  C22   110.80  3.000
 H2A  H241  C24  C22   111.77  3.000
 H2A  N25   C24  C22   109.50  3.000
 H2A  H253  N25  H252  106.79  3.000
 H2A  H253  N25  H251  106.82  3.000
 H2A  H252  N25  H251  108.12  3.000
 H2A  H253  N25  C24   111.30  3.000
 H2A  H252  N25  C24   110.82  3.000
 H2A  H251  N25  C24   112.71  3.000
 H2A  C1    O1   C3'   118.71  3.000
 H2A  C26   C1   O2    124.36  3.000
 H2A  C26   C1   O1    112.20  3.000
 H2A  O2    C1   O1    123.45  3.000
 H2A  H263  C26  H262  109.10  3.000
 H2A  H263  C26  H261  109.33  3.000
 H2A  H262  C26  H261  107.28  3.000
 H2A  H263  C26  C1    110.54  3.000
 H2A  H262  C26  C1    110.09  3.000
 H2A  H261  C26  C1    110.43  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
 H2A  CONST_01  C7    C8   N5   C4    180.00   0.0  0
 H2A  CONST_02  C7    C8   N5   C6      0.00   0.0  0
 H2A  CONST_03  O9    C8   N5   C4      0.00   0.0  0
 H2A  CONST_04  O9    C8   N5   C6    180.00   0.0  0
 H2A  CONST_05  O12   C11  N10  C7      0.00   0.0  0
 H2A  CONST_06  C13   C11  N10  C7    180.00   0.0  0
 H2A  CONST_07  O23   C22  N21  C17     0.00   0.0  0
 H2A  CONST_08  C24   C22  N21  C17   180.00   0.0  0
 H2A  CONST_09  H10   N10  C11  O12   180.00   0.0  0
 H2A  CONST_10  H21   N21  C22  O23   180.00   0.0  0
 H2A  Var_01    H21A  C2   S1   C6   -178.33  30.0  1
 H2A  Var_02    O2    C1   O1   C3'     2.87  30.0  3
 H2A  Var_03    C14   C13  C11  N10   -50.30  30.0  3
 H2A  Var_04    C15   C14  C13  C11   -52.43  30.0  3
 H2A  Var_05    C16   C15  C14  C13  -171.00  30.0  3
 H2A  Var_06    C17   C16  C15  C14  -166.30  30.0  3
 H2A  Var_07    N25   C24  C22  N21   178.99  30.0  3
 H2A  Var_08    H251  N25  C24  C22   -66.35  30.0  3
 H2A  Var_09    H261  C26  C1   O1     56.62  30.0  3
 H2A  Var_10    H3'1  C3'  O1   C1    -58.84  30.0  1

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
 H2A  chir_01  C3   C2   C3'  C4   negativ
 H2A  chir_02  C4   N5   C3   C4'  positiv
 H2A  chir_03  C6   S1   N5   C7   negativ
 H2A  chir_04  C7   N10  C6   C8   negativ
 H2A  chir_05  C17  C16  C18  N21  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
 H2A  plan-1  C7   0.020
 H2A  plan-1  N10  0.020
 H2A  plan-1  C11  0.020
 H2A  plan-1  O12  0.020
 H2A  plan-1  C13  0.020
 H2A  plan-1  H10  0.020
 H2A  plan-2  O1   0.020
 H2A  plan-2  C1   0.020
 H2A  plan-2  O2   0.020
 H2A  plan-2  C26  0.020
 H2A  plan-3  C17  0.020
 H2A  plan-3  N21  0.020
 H2A  plan-3  C22  0.020
 H2A  plan-3  O23  0.020
 H2A  plan-3  C24  0.020
 H2A  plan-3  H21  0.020
 H2A  plan-4  C4   0.020
 H2A  plan-4  N5   0.020
 H2A  plan-4  C6   0.020
 H2A  plan-4  C7   0.020
 H2A  plan-4  C8   0.020
 H2A  plan-4  O9   0.020
 H2A  plan-5  C4   0.020
 H2A  plan-5  C4'  0.020
 H2A  plan-5  O4A  0.020
 H2A  plan-5  O4B  0.020
 H2A  plan-6  C17  0.020
 H2A  plan-6  C18  0.020
 H2A  plan-6  O19  0.020
 H2A  plan-6  O20  0.020

