# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 14:57:45 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2R,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-3-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]2SC=C(COC(N)=O)[C@@H](N2C1=O)C(O)=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
 KEF  KEF  '(2R,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-3-ene-2-carboxylic acid'  ligand  44  29  .  2021-08-12  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KEF
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
 KEF  C14   C  CR5    0   0.373   3.9222   1.9790   0.7211
 KEF  O15   O  O      0  -0.410   2.9759   2.0719   1.6808
 KEF  C16   C  CR15   0   0.008   2.9450   3.3495   2.0987
 KEF  C17   C  CR15   0  -0.328   3.8609   4.0868   1.4229
 KEF  C19   C  CR15   0  -0.346   4.5017   3.1941   0.5206
 KEF  C18   C  CH3    0  -0.388   5.9542  -0.8827  -2.2937
 KEF  N16   N  N      0  -0.095   4.9588   0.5152  -0.7964
 KEF  C4'   C  C      0   0.446  -3.1279  -2.4782   1.1757
 KEF  C11   C  C      0   0.494   3.2722  -0.4594   0.6989
 KEF  C13   C  C      0  -0.011   4.1005   0.6718   0.1302
 KEF  C2    C  C1     0  -0.465  -2.0870   0.7928   0.4036
 KEF  C3    C  C      0   0.089  -2.8280  -0.2416   0.0003
 KEF  C4    C  CH1    0  -0.291  -2.3634  -1.6768   0.0741
 KEF  C6    C  C      0  -0.178  -0.2027  -0.9892   1.2618
 KEF  C7    C  C      0  -0.271   1.0872  -1.5178   0.5673
 KEF  C8    C  C      0   0.539   0.1106  -2.0777  -0.4795
 KEF  N10   N  NH1    0  -0.608   2.0703  -0.5972   0.1123
 KEF  N5    N  N      0  -0.411  -0.9479  -1.7122   0.2717
 KEF  O4A   O  OC    -1  -0.587  -4.3592  -2.5278   1.0170
 KEF  O4B   O  O      0  -0.573  -2.4450  -2.9769   2.0799
 KEF  O12   O  O      0  -0.444   3.6868  -1.1366   1.6166
 KEF  S1    S  S2     0   0.081  -0.4685   0.7983   1.0858
 KEF  O3'   O  O2     0  -0.484  -4.3296   1.3015  -1.0242
 KEF  C31   C  C      0   0.723  -5.5248   1.6814  -1.4913
 KEF  O31   O  O      0  -0.517  -6.4753   0.9348  -1.6028
 KEF  N31   N  NH2    0  -0.831  -5.5113   2.9782  -1.8439
 KEF  H16   H  HCR5   0   0.287   2.2329   3.5888   2.8713
 KEF  H17   H  HCR5   0   0.274   4.0571   5.1385   1.5513
 KEF  H19   H  HCR5   0   0.273   5.2863   3.4213  -0.1826
 KEF  H183  H  HCH3   0   0.228   5.6977  -0.2485  -3.1442
 KEF  H182  H  HCH3   0   0.245   5.9267  -1.9245  -2.6045
 KEF  H181  H  HCH3   0   0.228   6.9602  -0.6377  -1.9486
 KEF  H3'2  H  HCH2   0   0.254  -4.9662  -0.2816   0.1530
 KEF  H3'1  H  HCH2   0   0.236  -4.3357  -0.7337  -1.4246
 KEF  H2    H  H      0   0.290  -2.4561   1.8058   0.3059
 KEF  H4    H  HCH1   0   0.286  -2.5703  -2.1560  -0.8886
 KEF  H6    H  H      0   0.305  -0.3731  -1.3074   2.2882
 KEF  H7    H  H      0   0.331   1.5585  -2.3060   1.1538
 KEF  H10   H  HNH1   0   0.421   1.8146   0.0562  -0.6132
 KEF  HN31  H  HNH2   0   0.405  -4.7470   3.5808  -1.5903
 KEF  HN32  H  HNH2   0   0.407  -6.3780   3.4181  -2.1000
 KEF  O17   O  O2     0  -0.389   5.0020  -0.7614  -1.2495
 KEF  C3'   C  CH2    0  -0.161  -4.1996  -0.0446  -0.5857
 KEF  O9    O  O      0  -0.437   0.2141  -2.6277  -1.5474

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
 KEF  C14  O15   aromatic  1.351  0.020  1.351
 KEF  C14  C19   aromatic  1.361  0.020  1.361
 KEF  C14  C13   single    1.446  0.020  1.446
 KEF  O15  C16   aromatic  1.345  0.020  1.345
 KEF  C16  C17   aromatic  1.356  0.020  1.356
 KEF  C16  H16   single    0.930  0.020  1.080
 KEF  C17  C19   aromatic  1.422  0.020  1.422
 KEF  C17  H17   single    0.930  0.020  1.080
 KEF  C19  H19   single    0.930  0.020  1.080
 KEF  C18  O17   single    1.418  0.020  1.418
 KEF  C18  H183  single    0.970  0.020  1.090
 KEF  C18  H182  single    0.970  0.020  1.090
 KEF  C18  H181  single    0.970  0.020  1.090
 KEF  O17  N16   single    1.355  0.020  1.355
 KEF  N16  C13   double    1.273  0.020  1.273
 KEF  C4'  C4    single    1.562  0.020  1.562
 KEF  C4'  O4A   deloc     1.242  0.020  1.242
 KEF  C4'  O4B   deloc     1.238  0.020  1.238
 KEF  C3'  C3    single    1.504  0.020  1.504
 KEF  C3'  O3'   single    1.422  0.020  1.422
 KEF  C3'  H3'2  single    0.970  0.020  1.090
 KEF  C3'  H3'1  single    0.970  0.020  1.090
 KEF  C11  C13   single    1.513  0.020  1.513
 KEF  C11  N10   single    1.344  0.020  1.344
 KEF  C11  O12   double    1.214  0.020  1.214
 KEF  C2   C3    double    1.335  0.020  1.335
 KEF  C2   S1    single    1.756  0.020  1.756
 KEF  C2   H2    single    0.930  0.020  1.080
 KEF  C3   C4    single    1.510  0.020  1.510
 KEF  C4   N5    single    1.430  0.020  1.430
 KEF  C4   H4    single    0.970  0.020  1.090
 KEF  C6   C7    single    1.557  0.020  1.557
 KEF  C6   N5    single    1.435  0.020  1.435
 KEF  C6   S1    single    1.816  0.020  1.816
 KEF  C6   H6    single    0.970  0.020  1.090
 KEF  C7   C8    single    1.537  0.020  1.537
 KEF  C7   N10   single    1.422  0.020  1.422
 KEF  C7   H7    single    0.970  0.020  1.090
 KEF  C8   N5    single    1.348  0.020  1.348
 KEF  C8   O9    double    1.206  0.020  1.206
 KEF  N10  H10   single    0.860  0.020  1.020
 KEF  O3'  C31   single    1.338  0.020  1.338
 KEF  C31  O31   double    1.214  0.020  1.214
 KEF  C31  N31   single    1.344  0.020  1.344
 KEF  N31  HN31  single    0.860  0.020  1.020
 KEF  N31  HN32  single    0.860  0.020  1.020

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
 KEF  C13   C14  C19   133.99  3.000
 KEF  C13   C14  O15   116.04  3.000
 KEF  C19   C14  O15   109.97  3.000
 KEF  C16   O15  C14   107.59  3.000
 KEF  H16   C16  C17   133.06  3.000
 KEF  H16   C16  O15   116.68  3.000
 KEF  C17   C16  O15   110.26  3.000
 KEF  H17   C17  C19   127.33  3.000
 KEF  H17   C17  C16   126.46  3.000
 KEF  C19   C17  C16   106.21  3.000
 KEF  H19   C19  C17   127.57  3.000
 KEF  H19   C19  C14   126.46  3.000
 KEF  C17   C19  C14   105.97  3.000
 KEF  H181  C18  H182  109.19  3.000
 KEF  H181  C18  H183  109.42  3.000
 KEF  H182  C18  H183  109.15  3.000
 KEF  H181  C18  O17   111.52  3.000
 KEF  H182  C18  O17   105.98  3.000
 KEF  H183  C18  O17   111.48  3.000
 KEF  C13   N16  O17   112.39  3.000
 KEF  O4B   C4'  O4A   128.60  3.000
 KEF  O4B   C4'  C4    116.85  3.000
 KEF  O4A   C4'  C4    114.54  3.000
 KEF  O12   C11  N10   125.33  3.000
 KEF  O12   C11  C13   120.95  3.000
 KEF  N10   C11  C13   113.71  3.000
 KEF  C11   C13  N16   123.42  3.000
 KEF  C11   C13  C14   117.06  3.000
 KEF  N16   C13  C14   119.48  3.000
 KEF  H2    C2   S1    110.26  3.000
 KEF  H2    C2   C3    120.57  3.000
 KEF  S1    C2   C3    129.15  3.000
 KEF  C4    C3   C2    123.43  3.000
 KEF  C4    C3   C3'   115.08  3.000
 KEF  C2    C3   C3'   121.49  3.000
 KEF  H4    C4   N5    107.32  3.000
 KEF  H4    C4   C3    108.35  3.000
 KEF  N5    C4   C3    109.56  3.000
 KEF  H4    C4   C4'   107.64  3.000
 KEF  N5    C4   C4'   111.99  3.000
 KEF  C3    C4   C4'   111.80  3.000
 KEF  H6    C6   S1    110.88  3.000
 KEF  H6    C6   N5    114.98  3.000
 KEF  S1    C6   N5    110.68  3.000
 KEF  H6    C6   C7    116.82  3.000
 KEF  S1    C6   C7    114.34  3.000
 KEF  N5    C6   C7     87.22  3.000
 KEF  H7    C7   N10   109.97  3.000
 KEF  H7    C7   C8    112.21  3.000
 KEF  N10   C7   C8    117.21  3.000
 KEF  H7    C7   C6    111.33  3.000
 KEF  N10   C7   C6    119.71  3.000
 KEF  C8    C7   C6     84.32  3.000
 KEF  O9    C8   N5    133.19  3.000
 KEF  O9    C8   C7    135.62  3.000
 KEF  N5    C8   C7     91.19  3.000
 KEF  H10   N10  C7    118.30  3.000
 KEF  H10   N10  C11   118.28  3.000
 KEF  C7    N10  C11   123.02  3.000
 KEF  C8    N5   C6     96.50  3.000
 KEF  C8    N5   C4    134.99  3.000
 KEF  C6    N5   C4    126.67  3.000
 KEF  C6    S1   C2     99.76  3.000
 KEF  C31   O3'  C3'   117.26  3.000
 KEF  N31   C31  O31   125.25  3.000
 KEF  N31   C31  O3'   110.88  3.000
 KEF  O31   C31  O3'   123.84  3.000
 KEF  HN32  N31  HN31  117.21  3.000
 KEF  HN32  N31  C31   118.72  3.000
 KEF  HN31  N31  C31   121.31  3.000
 KEF  N16   O17  C18   110.37  3.000
 KEF  H3'1  C3'  H3'2  107.16  3.000
 KEF  H3'1  C3'  O3'   110.39  3.000
 KEF  H3'2  C3'  O3'   110.51  3.000
 KEF  H3'1  C3'  C3    109.24  3.000
 KEF  H3'2  C3'  C3    110.39  3.000
 KEF  O3'   C3'  C3    109.12  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
 KEF  CONST_01  C17   C16  O15  C14    0.00   0.0  0
 KEF  CONST_02  C16   C17  C19  C14    0.00   0.0  0
 KEF  CONST_03  C17   C19  C14  O15    0.00   0.0  0
 KEF  CONST_04  C19   C17  C16  O15    0.00   0.0  0
 KEF  CONST_05  C19   C14  O15  C16    0.00   0.0  0
 KEF  CONST_06  C7    C8   N5   C4   180.00   0.0  0
 KEF  CONST_07  C7    C8   N5   C6     0.00   0.0  0
 KEF  CONST_08  C13   C14  O15  C16  180.00   0.0  0
 KEF  CONST_09  C13   C14  C19  C17  180.00   0.0  0
 KEF  CONST_10  O9    C8   N5   C4     0.00   0.0  0
 KEF  CONST_11  O9    C8   N5   C6   180.00   0.0  0
 KEF  CONST_12  H16   C16  O15  C14  180.00   0.0  0
 KEF  CONST_13  H17   C17  C19  C14  180.00   0.0  0
 KEF  CONST_14  H19   C19  C14  O15  180.00   0.0  0
 KEF  CONST_15  C7    N10  C11  C13  180.00   0.0  0
 KEF  CONST_16  O12   C11  N10  C7     0.00   0.0  0
 KEF  CONST_17  O17   N16  C13  C14  180.00   0.0  0
 KEF  CONST_18  C11   C13  N16  O17    0.00   0.0  0
 KEF  CONST_19  H10   N10  C11  C13    0.00   0.0  0
 KEF  Var_01    S1    C2   C3   C4     0.18  30.0  1
 KEF  Var_02    N16   C13  C14  O15  178.80  30.0  2
 KEF  Var_03    O3'   C3'  C3   C2    19.21  30.0  1
 KEF  Var_04    N10   C11  C13  C14   88.44  30.0  3
 KEF  Var_05    O31   C31  O3'  C3'   -2.71  30.0  3
 KEF  Var_06    H183  C18  O17  N16  -61.08  30.0  3
 KEF  Var_07    HN31  N31  C31  O3'  -11.65  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
 KEF  chir_01  C4  C4'  C3  N5  negativ
 KEF  chir_02  C6  S1   N5  C7  negativ
 KEF  chir_03  C7  N10  C6  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
 KEF  plan-1  C14  0.020
 KEF  plan-1  O15  0.020
 KEF  plan-1  C16  0.020
 KEF  plan-1  C17  0.020
 KEF  plan-1  C19  0.020
 KEF  plan-1  C13  0.020
 KEF  plan-1  H16  0.020
 KEF  plan-1  H17  0.020
 KEF  plan-1  H19  0.020
 KEF  plan-2  O3'  0.020
 KEF  plan-2  C31  0.020
 KEF  plan-2  O31  0.020
 KEF  plan-2  N31  0.020
 KEF  plan-3  C11  0.020
 KEF  plan-3  C13  0.020
 KEF  plan-3  C7   0.020
 KEF  plan-3  N10  0.020
 KEF  plan-3  O12  0.020
 KEF  plan-3  H10  0.020
 KEF  plan-4  C4   0.020
 KEF  plan-4  C6   0.020
 KEF  plan-4  C7   0.020
 KEF  plan-4  C8   0.020
 KEF  plan-4  N5   0.020
 KEF  plan-4  O9   0.020
 KEF  plan-5  C4'  0.020
 KEF  plan-5  C4   0.020
 KEF  plan-5  O4A  0.020
 KEF  plan-5  O4B  0.020
 KEF  plan-6  C14  0.020
 KEF  plan-6  N16  0.020
 KEF  plan-6  C11  0.020
 KEF  plan-6  C13  0.020
 KEF  plan-6  O17  0.020

