# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:54:52 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: (6R,7R)-7-({(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-[(carboxymethoxy)imino]acetyl}amino)-3-ethenyl-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: Nc1scc(n1)C(=N/OCC(O)=O)/C(=O)N[C@H]2[C@H]3SCC(=C(N3C2=O)C(O)=O)C=C
#
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
 C04  C04  '(6R,7R)-7-({(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-[(carboxymethoxy)imino]acetyl}amino)-3-ethenyl-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid'  ligand  43  30  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C04
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
 C04  C1    C  C2     0  -0.562  -6.7083  -0.9124  -0.5956
 C04  N1    N  N      0  -0.492  -2.5233   1.5155  -0.2357
 C04  O1    O  O      0  -0.407  -1.2885   2.4699   1.5311
 C04  S1    S  S2     0   0.186   1.6353  -4.5589   0.0147
 C04  C2    C  C1     0  -0.197  -5.9443   0.0828  -0.1353
 C04  N2    N  NH1    0  -0.646   0.5340   0.4911  -0.1419
 C04  O2    O  O      0  -0.449   2.0804   1.0398  -1.7100
 C04  S2    S  S2     0   0.048  -2.0481  -0.9804  -1.0288
 C04  C3    C  C      0   0.015  -4.5089   0.2395  -0.3546
 C04  N3    N  N      0  -0.070   3.8428  -0.5746   0.0949
 C04  O3    O  O2     0  -0.374   4.3330   0.6592  -0.0984
 C04  C4    C  C      0   0.172  -3.8536   1.3262   0.1128
 C04  N4    N  N      0  -0.481   0.8007  -2.1960   0.5409
 C04  O4    O  OC    -1  -0.624   7.4688   2.2232   0.4234
 C04  C5    C  C      0  -0.195  -1.7734   0.7906  -1.2358
 C04  N5    N  NH2    0  -0.817  -0.7279  -3.8601   1.1395
 C04  O5    O  O      0  -0.590   5.4880   3.0250  -0.2344
 C04  C6    C  C      0  -0.276  -0.4802   1.3730  -0.6049
 C04  O6    O  OC    -1  -0.585  -5.1354   2.1453   1.9369
 C04  C7    C  C      0   0.540  -1.4261   1.9340   0.4664
 C04  O7    O  O      0  -0.577  -4.1457   3.5976   0.5560
 C04  C9    C  C      0   0.011   2.6096  -0.7207  -0.1894
 C04  C10   C  CH2    0  -0.280   5.7021   0.7061   0.2920
 C04  C11   C  C      0   0.366   6.2592   2.1293   0.1384
 C04  C12   C  CR5    0   0.353   2.0494  -2.0684  -0.0078
 C04  C13   C  CR15   0  -0.541   2.6658  -3.2229  -0.3569
 C04  C14   C  CR5    0   0.293   0.4376  -3.4396   0.6098
 C04  C15   C  CH2    0  -0.657  -3.8518  -0.8267  -1.1994
 C04  C16   C  C      0   0.373  -4.4409   2.4620   0.9584
 C04  H1    H  H      0   0.238  -6.3342  -1.7420  -1.1813
 C04  H1A   H  H      0   0.244  -7.7696  -0.9214  -0.3872
 C04  H2    H  H      0   0.249  -6.4247   0.8582   0.4449
 C04  HN2   H  HNH1   0   0.425   0.2816  -0.2443   0.5131
 C04  H5    H  H      0   0.312  -1.9930   1.0983  -2.2590
 C04  HN5   H  HNH2   0   0.408  -1.0653  -4.7817   0.9181
 C04  HN5A  H  HNH2   0   0.401  -1.4463  -3.1584   1.2314
 C04  H6    H  H      0   0.330  -0.0441   2.1516  -1.2307
 C04  H10   H  HCH2   0   0.226   5.8062   0.3869   1.3350
 C04  H10A  H  HCH2   0   0.226   6.2893   0.0133  -0.3200
 C04  H13   H  HCR5   0   0.305   3.6256  -3.3640  -0.8259
 C04  H15   H  HCH2   0   0.293  -4.1028  -0.6926  -2.2547
 C04  H15A  H  HCH2   0   0.292  -4.2333  -1.8075  -0.9120
 C04  C8    C  C      0   0.513   1.7264   0.3660  -0.7639

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
 C04  C1   C2    double    1.336  0.020  1.336
 C04  C1   H1    single    0.930  0.020  1.080
 C04  C1   H1A   single    0.930  0.020  1.080
 C04  N1   C5    single    1.445  0.020  1.445
 C04  N1   C7    single    1.368  0.020  1.368
 C04  S1   C14   aromatic  1.744  0.020  1.744
 C04  C2   C3    single    1.460  0.020  1.460
 C04  C2   H2    single    0.930  0.020  1.080
 C04  N2   C8    single    1.351  0.020  1.351
 C04  N2   HN2   single    0.890  0.020  1.040
 C04  O2   C8    double    1.214  0.020  1.214
 C04  C3   C15   single    1.511  0.020  1.511
 C04  C3   C4    double    1.352  0.020  1.352
 C04  O3   N3    single    1.342  0.020  1.342
 C04  O3   C10   single    1.424  0.020  1.424
 C04  C4   N1    single    1.388  0.020  1.388
 C04  N4   C14   aromatic  1.297  0.020  1.297
 C04  C5   S2    single    1.804  0.020  1.804
 C04  C5   C6    single    1.552  0.020  1.552
 C04  C5   H5    single    0.970  0.020  1.090
 C04  N5   HN5   single    0.890  0.020  1.040
 C04  N5   HN5A  single    0.890  0.020  1.040
 C04  O5   C11   deloc     1.239  0.020  1.239
 C04  C6   N2    single    1.422  0.020  1.422
 C04  C6   H6    single    0.970  0.020  1.090
 C04  C7   O1    double    1.200  0.020  1.200
 C04  C7   C6    single    1.535  0.020  1.535
 C04  O7   C16   deloc     1.240  0.020  1.240
 C04  C8   C9    single    1.514  0.020  1.514
 C04  C9   N3    double    1.274  0.020  1.274
 C04  C9   C12   single    1.471  0.020  1.471
 C04  C10  C11   single    1.536  0.020  1.536
 C04  C10  H10   single    0.970  0.020  1.090
 C04  C10  H10A  single    0.970  0.020  1.090
 C04  C11  O4    deloc     1.246  0.020  1.246
 C04  C12  N4    aromatic  1.370  0.020  1.370
 C04  C13  S1    aromatic  1.728  0.020  1.728
 C04  C13  C12   aromatic  1.355  0.020  1.355
 C04  C13  H13   single    0.930  0.020  1.080
 C04  C14  N5    single    1.347  0.020  1.347
 C04  C15  S2    single    1.818  0.020  1.818
 C04  C15  H15   single    0.970  0.020  1.090
 C04  C15  H15A  single    0.970  0.020  1.090
 C04  C16  C4    single    1.533  0.020  1.533
 C04  C16  O6    deloc     1.241  0.020  1.241

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
 C04  H1A   C1   H1   115.92  3.000
 C04  H1A   C1   C2   120.05  3.000
 C04  H1    C1   C2   124.03  3.000
 C04  C7    N1   C5    95.30  3.000
 C04  C7    N1   C4   132.95  3.000
 C04  C5    N1   C4   127.06  3.000
 C04  C14   S1   C13   89.24  3.000
 C04  H2    C2   C3   116.13  3.000
 C04  H2    C2   C1   117.71  3.000
 C04  C3    C2   C1   126.16  3.000
 C04  HN2   N2   C8   116.68  3.000
 C04  HN2   N2   C6   118.78  3.000
 C04  C8    N2   C6   122.50  3.000
 C04  C15   S2   C5    93.28  3.000
 C04  C15   C3   C4   123.35  3.000
 C04  C4    C3   C2   120.70  3.000
 C04  C15   C3   C2   115.83  3.000
 C04  C9    N3   O3   115.28  3.000
 C04  C10   O3   N3   110.00  3.000
 C04  C16   C4   C3   126.90  3.000
 C04  C16   C4   N1   113.86  3.000
 C04  C3    C4   N1   119.16  3.000
 C04  C14   N4   C12  111.45  3.000
 C04  H5    C5   C6   116.30  3.000
 C04  H5    C5   S2   110.72  3.000
 C04  C6    C5   S2   116.65  3.000
 C04  H5    C5   N1   113.78  3.000
 C04  C6    C5   N1    87.87  3.000
 C04  S2    C5   N1   109.51  3.000
 C04  HN5A  N5   HN5  114.74  3.000
 C04  HN5A  N5   C14  115.78  3.000
 C04  HN5   N5   C14  119.30  3.000
 C04  H6    C6   C7   112.71  3.000
 C04  C7    C6   C5    84.69  3.000
 C04  H6    C6   C5   111.59  3.000
 C04  C7    C6   N2   116.04  3.000
 C04  H6    C6   N2   110.16  3.000
 C04  C5    C6   N2   119.60  3.000
 C04  C6    C7   O1   135.37  3.000
 C04  C6    C7   N1    91.39  3.000
 C04  O1    C7   N1   133.15  3.000
 C04  C12   C9   C8   118.85  3.000
 C04  C12   C9   N3   116.51  3.000
 C04  C8    C9   N3   124.56  3.000
 C04  H10A  C10  H10  107.26  3.000
 C04  H10A  C10  C11  109.62  3.000
 C04  H10   C10  C11  109.31  3.000
 C04  H10A  C10  O3   109.96  3.000
 C04  H10   C10  O3   110.04  3.000
 C04  C11   C10  O3   110.59  3.000
 C04  C10   C11  O5   118.29  3.000
 C04  C10   C11  O4   113.51  3.000
 C04  O5    C11  O4   128.19  3.000
 C04  C13   C12  C9   125.16  3.000
 C04  C13   C12  N4   116.02  3.000
 C04  C9    C12  N4   118.82  3.000
 C04  H13   C13  C12  128.99  3.000
 C04  H13   C13  S1   121.58  3.000
 C04  C12   C13  S1   109.40  3.000
 C04  N5    C14  N4   124.19  3.000
 C04  N5    C14  S1   121.86  3.000
 C04  N4    C14  S1   113.89  3.000
 C04  H15A  C15  H15  106.52  3.000
 C04  H15A  C15  C3   109.58  3.000
 C04  H15   C15  C3   110.70  3.000
 C04  H15A  C15  S2   104.25  3.000
 C04  H15   C15  S2   109.19  3.000
 C04  C3    C15  S2   116.02  3.000
 C04  O7    C16  O6   128.51  3.000
 C04  O6    C16  C4   117.40  3.000
 C04  O7    C16  C4   114.09  3.000
 C04  C9    C8   O2   121.60  3.000
 C04  C9    C8   N2   114.01  3.000
 C04  O2    C8   N2   124.39  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
 C04  CONST_01  C12  N4   C14  S1      0.00   0.0  0
 C04  CONST_02  N4   C12  C13  S1      0.00   0.0  0
 C04  CONST_03  C13  S1   C14  N4      0.00   0.0  0
 C04  CONST_04  C14  S1   C13  C12     0.00   0.0  0
 C04  CONST_05  C14  N4   C12  C13     0.00   0.0  0
 C04  CONST_07  C6   C7   N1   C5      0.00   0.0  0
 C04  CONST_08  C9   C12  C13  S1    180.00   0.0  0
 C04  CONST_09  C13  S1   C14  N5    180.00   0.0  0
 C04  CONST_10  C12  N4   C14  N5    180.00   0.0  0
 C04  CONST_11  C14  N4   C12  C9    180.00   0.0  0
 C04  CONST_12  C5   N1   C7   O1    180.00   0.0  0
 C04  CONST_13  C4   N1   C7   O1      0.00   0.0  0
 C04  CONST_14  H13  C13  C12  N4    180.00   0.0  0
 C04  CONST_17  C6   N2   C8   O2      0.00   0.0  0
 C04  CONST_18  C9   C8   N2   C6    180.00   0.0  0
 C04  CONST_19  H1   C1   C2   C3      0.00   0.0  0
 C04  CONST_20  H1A  C1   C2   C3    180.00   0.0  0
 C04  CONST_21  HN2  N2   C8   O2    180.00   0.0  0
 C04  Var_01    C15  C3   C4   N1      2.69  30.0  1
 C04  Var_02    C4   C3   C15  S2     23.91  30.0  1
 C04  Var_03    C5   N1   C4   C3     10.82  30.0  1
 C04  Var_04    O7   C16  C4   N1     44.10  30.0  2
 C04  Var_05    N4   C12  C9   N3    138.64  30.0  2
 C04  Var_06    C12  C9   N3   O3    179.06   0.0  2
 C04  Var_07    C11  C10  O3   N3   -177.35  30.0  3
 C04  Var_08    O5   C11  C10  O3      2.58  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
 C04  chir_01  C5  N1  S2  C6  positiv
 C04  chir_02  C6  N2  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
 C04  plan-1  S1    0.020
 C04  plan-1  N4    0.020
 C04  plan-1  N5    0.020
 C04  plan-1  C9    0.020
 C04  plan-1  C12   0.020
 C04  plan-1  C13   0.020
 C04  plan-1  C14   0.020
 C04  plan-1  H13   0.020
 C04  plan-2  C1    0.020
 C04  plan-2  C2    0.020
 C04  plan-2  C3    0.020
 C04  plan-2  H1    0.020
 C04  plan-2  H1A   0.020
 C04  plan-2  H2    0.020
 C04  plan-3  N3    0.020
 C04  plan-3  O3    0.020
 C04  plan-3  C9    0.020
 C04  plan-3  C12   0.020
 C04  plan-3  C8    0.020
 C04  plan-4  N2    0.020
 C04  plan-4  O2    0.020
 C04  plan-4  C6    0.020
 C04  plan-4  C9    0.020
 C04  plan-4  HN2   0.020
 C04  plan-4  C8    0.020
 C04  plan-5  N5    0.020
 C04  plan-5  C14   0.020
 C04  plan-5  HN5   0.020
 C04  plan-5  HN5A  0.020
 C04  plan-6  N1    0.020
 C04  plan-6  O1    0.020
 C04  plan-6  C4    0.020
 C04  plan-6  C5    0.020
 C04  plan-6  C6    0.020
 C04  plan-6  C7    0.020
 C04  plan-7  O4    0.020
 C04  plan-7  O5    0.020
 C04  plan-7  C10   0.020
 C04  plan-7  C11   0.020
 C04  plan-8  C4    0.020
 C04  plan-8  O6    0.020
 C04  plan-8  O7    0.020
 C04  plan-8  C16   0.020

