# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 10:09:05 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: (6R,7R)-3-[(carbamoyloxy)methyl]-7-{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}-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: CO/N=C(C(=O)N[C@H]1[C@H]2SCC(=C(N2C1=O)C(O)=O)COC(N)=O)/c3occc3
#
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
 KOV  KOV  '(6R,7R)-3-[(carbamoyloxy)methyl]-7-{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid'  ligand  44  29  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KOV
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
 KOV  S     S  S2     0   0.044   0.3948   1.2247  -0.3049
 KOV  C1    C  CH3    0  -0.388  -6.4307  -1.6720   0.6228
 KOV  N1    N  N      0  -0.094  -5.1985   0.2361   0.4546
 KOV  O1    O  O2     0  -0.389  -5.2663  -1.0661   0.0859
 KOV  C2    C  C      0  -0.009  -4.1610   0.8154  -0.0017
 KOV  N2    N  NH1    0  -0.616  -2.1518  -0.4702  -0.2529
 KOV  O2    O  O      0  -0.408  -2.8053   2.7502  -0.2076
 KOV  C3    C  CR5    0   0.375  -3.9301   2.2083   0.3067
 KOV  N3    N  N      0  -0.491   0.9223  -1.3882  -0.4559
 KOV  O3    O  O      0  -0.443  -3.2779   0.1670  -2.1137
 KOV  C4    C  CR15   0  -0.347  -4.6031   3.1397   1.0366
 KOV  N4    N  NH2    0  -0.832   6.8069   1.6054  -1.1724
 KOV  C5    C  CR15   0  -0.327  -3.8297   4.3304   0.9592
 KOV  O5    O  O2     0  -0.482   4.9820   0.6266  -0.4042
 KOV  C6    C  CR15   0   0.007  -2.7518   4.0326   0.1918
 KOV  O6    O  O      0  -0.523   6.7182   0.9429   0.9965
 KOV  C7    C  C      0   0.497  -3.1592   0.1320  -0.9064
 KOV  O7    O  OC    -1  -0.581   3.4042  -2.6998   1.6059
 KOV  C8    C  C      0  -0.260  -1.0829  -1.1188  -0.9380
 KOV  O8    O  O      0  -0.579   2.5182  -3.6112  -0.2324
 KOV  C9    C  C      0  -0.195   0.2348  -0.3421  -1.1822
 KOV  C10   C  C      0   0.527  -0.2154  -2.0352  -0.0657
 KOV  C11   C  C      0   0.163   2.2016  -1.3214   0.0937
 KOV  C12   C  C      0  -0.007   2.8244  -0.1330   0.1370
 KOV  C13   C  CH2    0  -0.624   2.2132   1.1616  -0.3459
 KOV  C14   C  CH2    0  -0.225   4.2204   0.0261   0.6535
 KOV  C15   C  C      0   0.724   6.2145   1.0501  -0.1040
 KOV  C16   C  C      0   0.378   2.7660  -2.6738   0.5407
 KOV  H1    H  HCH3   0   0.245  -6.4000  -2.7120   0.3065
 KOV  H1A   H  HCH3   0   0.228  -6.4376  -1.6283   1.7132
 KOV  H1B   H  HCH3   0   0.228  -7.3389  -1.2062   0.2361
 KOV  HN2   H  HNH1   0   0.426  -2.1212  -0.4144   0.7542
 KOV  H4    H  HCR5   0   0.273  -5.5313   2.9941   1.5643
 KOV  HN4   H  HNH2   0   0.407   7.7505   1.9416  -1.0969
 KOV  HN4A  H  HNH2   0   0.405   6.3611   1.6417  -2.0727
 KOV  H5    H  HCR5   0   0.273  -4.0472   5.2818   1.4160
 KOV  H6    H  HCR5   0   0.287  -1.9040   4.6087  -0.1406
 KOV  H8    H  H      0   0.335  -1.4429  -1.6040  -1.8459
 KOV  H9    H  H      0   0.313   0.5544  -0.2434  -2.2200
 KOV  H13   H  HCH2   0   0.296   2.5464   1.3997  -1.3581
 KOV  H13A  H  HCH2   0   0.295   2.5448   1.9824   0.2937
 KOV  H14   H  HCH2   0   0.258   4.6600  -0.9228   0.9466
 KOV  H14A  H  HCH2   0   0.241   4.2164   0.6862   1.5262
 KOV  O4    O  O      0  -0.407  -0.4370  -2.9243   0.7089

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
 KOV  S    C9    single    1.803  0.020  1.803
 KOV  C1   O1    single    1.418  0.020  1.418
 KOV  C1   H1    single    0.970  0.020  1.090
 KOV  C1   H1A   single    0.970  0.020  1.090
 KOV  C1   H1B   single    0.970  0.020  1.090
 KOV  N1   O1    single    1.355  0.020  1.355
 KOV  C2   N1    double    1.273  0.020  1.273
 KOV  C2   C7    single    1.513  0.020  1.513
 KOV  N2   C7    single    1.343  0.020  1.343
 KOV  N2   C8    single    1.426  0.020  1.426
 KOV  N2   HN2   single    0.860  0.020  1.020
 KOV  O2   C3    aromatic  1.350  0.020  1.350
 KOV  C3   C2    single    1.445  0.020  1.445
 KOV  N3   C10   single    1.366  0.020  1.366
 KOV  N3   C9    single    1.447  0.020  1.447
 KOV  C4   C3    aromatic  1.361  0.020  1.361
 KOV  C4   H4    single    0.930  0.020  1.080
 KOV  N4   HN4   single    0.860  0.020  1.020
 KOV  N4   HN4A  single    0.860  0.020  1.020
 KOV  O4   C10   double    1.200  0.020  1.200
 KOV  C5   C4    aromatic  1.422  0.020  1.422
 KOV  C5   C6    aromatic  1.356  0.020  1.356
 KOV  C5   H5    single    0.930  0.020  1.080
 KOV  C6   O2    aromatic  1.344  0.020  1.344
 KOV  C6   H6    single    0.930  0.020  1.080
 KOV  O6   C15   double    1.215  0.020  1.215
 KOV  C7   O3    double    1.214  0.020  1.214
 KOV  C8   H8    single    0.970  0.020  1.090
 KOV  O8   C16   deloc     1.240  0.020  1.240
 KOV  C9   C8    single    1.549  0.020  1.549
 KOV  C9   H9    single    0.970  0.020  1.090
 KOV  C10  C8    single    1.534  0.020  1.534
 KOV  C11  N3    single    1.394  0.020  1.394
 KOV  C12  C11   double    1.342  0.020  1.342
 KOV  C12  C13   single    1.511  0.020  1.511
 KOV  C13  S     single    1.820  0.020  1.820
 KOV  C13  H13   single    0.970  0.020  1.090
 KOV  C13  H13A  single    0.970  0.020  1.090
 KOV  C14  O5    single    1.435  0.020  1.435
 KOV  C14  C12   single    1.497  0.020  1.497
 KOV  C14  H14   single    0.970  0.020  1.090
 KOV  C14  H14A  single    0.970  0.020  1.090
 KOV  C15  N4    single    1.342  0.020  1.342
 KOV  C15  O5    single    1.337  0.020  1.337
 KOV  C16  O7    deloc     1.242  0.020  1.242
 KOV  C16  C11   single    1.532  0.020  1.532

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
 KOV  C13   S    C9    92.73  3.000
 KOV  H1B   C1   H1A  109.37  3.000
 KOV  H1B   C1   H1   109.19  3.000
 KOV  H1A   C1   H1   109.21  3.000
 KOV  H1B   C1   O1   111.51  3.000
 KOV  H1A   C1   O1   111.49  3.000
 KOV  H1    C1   O1   105.98  3.000
 KOV  C2    N1   O1   112.37  3.000
 KOV  N1    O1   C1   110.40  3.000
 KOV  C7    C2   C3   117.20  3.000
 KOV  C3    C2   N1   119.50  3.000
 KOV  C7    C2   N1   123.26  3.000
 KOV  HN2   N2   C8   118.82  3.000
 KOV  HN2   N2   C7   118.91  3.000
 KOV  C8    N2   C7   122.17  3.000
 KOV  C6    O2   C3   107.63  3.000
 KOV  C4    C3   O2   109.96  3.000
 KOV  C4    C3   C2   134.02  3.000
 KOV  O2    C3   C2   116.02  3.000
 KOV  C11   N3   C10  132.41  3.000
 KOV  C11   N3   C9   126.82  3.000
 KOV  C10   N3   C9    95.17  3.000
 KOV  H4    C4   C5   127.47  3.000
 KOV  C5    C4   C3   105.95  3.000
 KOV  H4    C4   C3   126.58  3.000
 KOV  HN4A  N4   HN4  118.15  3.000
 KOV  HN4A  N4   C15  122.16  3.000
 KOV  HN4   N4   C15  119.55  3.000
 KOV  H5    C5   C6   126.45  3.000
 KOV  H5    C5   C4   127.33  3.000
 KOV  C6    C5   C4   106.21  3.000
 KOV  C15   O5   C14  117.14  3.000
 KOV  H6    C6   C5   133.03  3.000
 KOV  H6    C6   O2   116.73  3.000
 KOV  C5    C6   O2   110.24  3.000
 KOV  O3    C7   N2   124.76  3.000
 KOV  O3    C7   C2   121.14  3.000
 KOV  N2    C7   C2   114.09  3.000
 KOV  H8    C8   C10  113.22  3.000
 KOV  C10   C8   C9    84.73  3.000
 KOV  H8    C8   C9   111.88  3.000
 KOV  C10   C8   N2   114.99  3.000
 KOV  C9    C8   N2   119.05  3.000
 KOV  H8    C8   N2   110.79  3.000
 KOV  H9    C9   C8   116.41  3.000
 KOV  H9    C9   N3   113.82  3.000
 KOV  C8    C9   N3    87.86  3.000
 KOV  H9    C9   S    111.01  3.000
 KOV  C8    C9   S    115.76  3.000
 KOV  N3    C9   S    109.99  3.000
 KOV  C8    C10  O4   134.86  3.000
 KOV  C8    C10  N3    91.47  3.000
 KOV  O4    C10  N3   133.58  3.000
 KOV  C16   C11  C12  126.95  3.000
 KOV  C16   C11  N3   114.26  3.000
 KOV  C12   C11  N3   118.74  3.000
 KOV  C14   C12  C13  113.36  3.000
 KOV  C14   C12  C11  122.54  3.000
 KOV  C13   C12  C11  124.09  3.000
 KOV  H13A  C13  H13  106.64  3.000
 KOV  H13A  C13  C12  109.51  3.000
 KOV  H13   C13  C12  111.09  3.000
 KOV  H13A  C13  S    105.31  3.000
 KOV  H13   C13  S    108.55  3.000
 KOV  C12   C13  S    115.26  3.000
 KOV  H14A  C14  H14  108.26  3.000
 KOV  H14A  C14  C12  109.62  3.000
 KOV  H14   C14  C12  112.19  3.000
 KOV  H14A  C14  O5   109.72  3.000
 KOV  H14   C14  O5   110.47  3.000
 KOV  C12   C14  O5   106.57  3.000
 KOV  O6    C15  O5   123.88  3.000
 KOV  O5    C15  N4   111.04  3.000
 KOV  O6    C15  N4   125.08  3.000
 KOV  C11   C16  O8   114.32  3.000
 KOV  C11   C16  O7   117.25  3.000
 KOV  O8    C16  O7   128.43  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
 KOV  CONST_01  C5   C4   C3   O2     0.00   0.0  0
 KOV  CONST_02  C4   C5   C6   O2     0.00   0.0  0
 KOV  CONST_03  C5   C6   O2   C3     0.00   0.0  0
 KOV  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 KOV  CONST_05  C6   O2   C3   C4     0.00   0.0  0
 KOV  CONST_06  C9   N3   C10  C8     0.00   0.0  0
 KOV  CONST_08  C6   O2   C3   C2   180.00   0.0  0
 KOV  CONST_09  C5   C4   C3   C2   180.00   0.0  0
 KOV  CONST_10  C9   N3   C10  O4   180.00   0.0  0
 KOV  CONST_12  H4   C4   C3   O2   180.00   0.0  0
 KOV  CONST_13  H5   C5   C6   O2   180.00   0.0  0
 KOV  CONST_14  H6   C6   O2   C3   180.00   0.0  0
 KOV  CONST_15  C8   N2   C7   C2   180.00   0.0  0
 KOV  CONST_16  C8   N2   C7   O3     0.00   0.0  0
 KOV  CONST_17  C3   C2   N1   O1   180.00   0.0  0
 KOV  CONST_18  C7   C2   N1   O1     0.00   0.0  0
 KOV  CONST_19  HN2  N2   C7   C2     0.00   0.0  0
 KOV  Var_01    C11  C12  C13  S     26.32  30.0  1
 KOV  Var_02    C13  C12  C11  N3     1.53  30.0  1
 KOV  Var_03    C12  C13  S    C9   -50.59  30.0  1
 KOV  Var_04    C12  C11  N3   C9     9.90  30.0  1
 KOV  Var_05    O2   C3   C2   N1   179.68  30.0  2
 KOV  Var_06    O8   C16  C11  N3    40.21  30.0  2
 KOV  Var_07    C3   C2   C7   N2    91.55  30.0  2
 KOV  Var_08    H1   C1   O1   N1  -178.60  30.0  3
 KOV  Var_09    HN4  N4   C15  O5  -178.08  30.0  2

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
 KOV  chir_01  C8  N2  C9  C10  negativ
 KOV  chir_02  C9  S   N3  C8   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
 KOV  plan-1  C2   0.020
 KOV  plan-1  O2   0.020
 KOV  plan-1  C3   0.020
 KOV  plan-1  C4   0.020
 KOV  plan-1  C5   0.020
 KOV  plan-1  C6   0.020
 KOV  plan-1  H4   0.020
 KOV  plan-1  H5   0.020
 KOV  plan-1  H6   0.020
 KOV  plan-2  C2   0.020
 KOV  plan-2  N2   0.020
 KOV  plan-2  O3   0.020
 KOV  plan-2  C7   0.020
 KOV  plan-2  C8   0.020
 KOV  plan-2  HN2  0.020
 KOV  plan-3  N3   0.020
 KOV  plan-3  C8   0.020
 KOV  plan-3  C9   0.020
 KOV  plan-3  C10  0.020
 KOV  plan-3  C11  0.020
 KOV  plan-3  O4   0.020
 KOV  plan-4  O7   0.020
 KOV  plan-4  O8   0.020
 KOV  plan-4  C11  0.020
 KOV  plan-4  C16  0.020
 KOV  plan-5  N1   0.020
 KOV  plan-5  O1   0.020
 KOV  plan-5  C2   0.020
 KOV  plan-5  C3   0.020
 KOV  plan-5  C7   0.020
 KOV  plan-6  N4   0.020
 KOV  plan-6  O5   0.020
 KOV  plan-6  O6   0.020
 KOV  plan-6  C15  0.020

