# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 09:06:41 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (6R,7R)-3-[(acetyloxy)methyl]-7-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: CC(=O)OCC1=C(N2[C@H](SC1)[C@H](N)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
 4KR  4KR  '(6R,7R)-3-[(acetyloxy)methyl]-7-amino-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid'  ligand  30  18  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4KR
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
 4KR  C     C  CH3   0  -0.772   5.0864  -1.3407   0.8438
 4KR  C1    C  C     0   0.581   4.3089  -0.3649   0.0132
 4KR  S1    S  S2    0   0.041  -1.1310  -2.0222  -1.0392
 4KR  C2    C  CH2   0  -0.631   0.5591  -1.5365  -0.5856
 4KR  O2    O  O     0  -0.454   4.7938   0.3888  -0.7928
 4KR  C3    C  C     0   0.041   0.7452  -0.0697  -0.2881
 4KR  O3    O  O2    0  -0.452   3.0009  -0.4350   0.2483
 4KR  C4    C  C     0   0.218  -0.2523   0.7013   0.1718
 4KR  N5    N  N     0  -0.513  -1.5074   0.1702   0.4405
 4KR  C6    C  C     0  -0.198  -1.8667  -1.2330   0.4065
 4KR  C7    C  C     0  -0.248  -3.3458  -0.8025   0.2259
 4KR  C8    C  C     0   0.510  -2.7665   0.6174   0.0966
 4KR  O9    O  O     0  -0.407  -3.1571   1.7008  -0.2388
 4KR  C10   C  C     0   0.478  -0.1601   2.1508   0.5300
 4KR  C13   C  CH2   0  -0.247   2.1429   0.4175  -0.5222
 4KR  N14   N  NH2   0  -0.784  -4.0908  -1.3817  -0.8424
 4KR  H     H  HCH3  0   0.264   4.5383  -1.6776   1.7196
 4KR  HA    H  HCH3  0   0.281   5.3216  -2.2148   0.2329
 4KR  HB    H  HCH3  0   0.271   6.0296  -0.8945   1.1510
 4KR  H2A   H  HCH2  0   0.308   1.1845  -1.8181  -1.4350
 4KR  HO4   H  HOH1  0   0.495   0.5338   3.7948  -0.0924
 4KR  H6    H  H     0   0.314  -1.6111  -1.7741   1.3175
 4KR  H7    H  H     0   0.318  -3.8944  -0.9231   1.1619
 4KR  H13   H  HCH2  0   0.265   2.3795   0.3285  -1.5863
 4KR  H13A  H  HCH2  0   0.267   2.3041   1.4514  -0.2280
 4KR  HN14  H  HNH2  0   0.375  -5.0756  -1.1819  -0.7420
 4KR  HN1A  H  HNH2  0   0.362  -3.8008  -1.0396  -1.7485
 4KR  H2    H  HCH2  0   0.309   0.8899  -2.1446   0.2589
 4KR  O4    O  OH1   0  -0.578   0.4595   2.8725  -0.3856
 4KR  O5    O  O     0  -0.414  -0.6313   2.5886   1.5461

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
 4KR  C1   C     single  1.499  0.020  1.499
 4KR  C    H     single  0.970  0.020  1.090
 4KR  C    HA    single  0.970  0.020  1.090
 4KR  C    HB    single  0.970  0.020  1.090
 4KR  O2   C1    double  1.205  0.020  1.205
 4KR  C1   O3    single  1.331  0.020  1.331
 4KR  C2   S1    single  1.816  0.020  1.816
 4KR  S1   C6    single  1.804  0.020  1.804
 4KR  C3   C2    single  1.508  0.020  1.508
 4KR  C2   H2    single  0.970  0.020  1.090
 4KR  C2   H2A   single  0.970  0.020  1.090
 4KR  C13  C3    single  1.499  0.020  1.499
 4KR  C3   C4    double  1.342  0.020  1.342
 4KR  C13  O3    single  1.434  0.020  1.434
 4KR  C10  C4    single  1.496  0.020  1.496
 4KR  C4   N5    single  1.389  0.020  1.389
 4KR  C10  O4    single  1.320  0.020  1.320
 4KR  O4   HO4   single  0.850  0.020  0.980
 4KR  N5   C8    single  1.380  0.020  1.380
 4KR  N5   C6    single  1.449  0.020  1.449
 4KR  O5   C10   double  1.203  0.020  1.203
 4KR  C6   C7    single  1.551  0.020  1.551
 4KR  C6   H6    single  0.970  0.020  1.090
 4KR  C8   C7    single  1.539  0.020  1.539
 4KR  N14  C7    single  1.425  0.020  1.425
 4KR  C7   H7    single  0.970  0.020  1.090
 4KR  O9   C8    double  1.199  0.020  1.199
 4KR  C13  H13   single  0.970  0.020  1.090
 4KR  C13  H13A  single  0.970  0.020  1.090
 4KR  N14  HN14  single  0.890  0.020  1.040
 4KR  N14  HN1A  single  0.890  0.020  1.040

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
 4KR  HB    C    HA    107.44  3.000
 4KR  HB    C    H     109.69  3.000
 4KR  HA    C    H     108.14  3.000
 4KR  HB    C    C1    109.83  3.000
 4KR  HA    C    C1    108.83  3.000
 4KR  H     C    C1    112.75  3.000
 4KR  O3    C1   O2    123.12  3.000
 4KR  O3    C1   C     112.19  3.000
 4KR  O2    C1   C     124.68  3.000
 4KR  C6    S1   C2     93.58  3.000
 4KR  H2A   C2   H2    106.53  3.000
 4KR  H2A   C2   C3    109.48  3.000
 4KR  H2    C2   C3    110.59  3.000
 4KR  H2A   C2   S1    105.66  3.000
 4KR  H2    C2   S1    109.04  3.000
 4KR  C3    C2   S1    115.10  3.000
 4KR  C13   C3   C4    124.06  3.000
 4KR  C4    C3   C2    122.32  3.000
 4KR  C13   C3   C2    113.61  3.000
 4KR  C13   O3   C1    117.51  3.000
 4KR  C10   C4   N5    112.32  3.000
 4KR  N5    C4   C3    121.22  3.000
 4KR  C10   C4   C3    126.36  3.000
 4KR  C8    N5   C6     94.69  3.000
 4KR  C6    N5   C4    126.14  3.000
 4KR  C8    N5   C4    130.73  3.000
 4KR  H6    C6   C7    117.30  3.000
 4KR  H6    C6   N5    113.76  3.000
 4KR  C7    C6   N5     88.30  3.000
 4KR  H6    C6   S1    110.92  3.000
 4KR  C7    C6   S1    114.65  3.000
 4KR  N5    C6   S1    109.96  3.000
 4KR  H7    C7   N14   109.58  3.000
 4KR  H7    C7   C8    111.29  3.000
 4KR  N14   C7   C8    120.58  3.000
 4KR  H7    C7   C6    110.41  3.000
 4KR  N14   C7   C6    118.22  3.000
 4KR  C8    C7   C6     84.66  3.000
 4KR  O9    C8   C7    137.25  3.000
 4KR  O9    C8   N5    131.27  3.000
 4KR  C7    C8   N5     91.35  3.000
 4KR  O5    C10  O4    124.81  3.000
 4KR  O5    C10  C4    122.07  3.000
 4KR  O4    C10  C4    113.11  3.000
 4KR  H13A  C13  H13   107.98  3.000
 4KR  H13A  C13  O3    109.35  3.000
 4KR  H13   C13  O3    110.18  3.000
 4KR  H13A  C13  C3    113.91  3.000
 4KR  H13   C13  C3    109.11  3.000
 4KR  O3    C13  C3    106.31  3.000
 4KR  HN1A  N14  HN14  107.57  3.000
 4KR  HN1A  N14  C7    112.59  3.000
 4KR  HN14  N14  C7    110.78  3.000
 4KR  HO4   O4   C10   110.24  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
 4KR  CONST_02  C7   C8   N5   C6     0.00   0.0  0
 4KR  CONST_04  O9   C8   N5   C6   180.00   0.0  0
 4KR  CONST_05  HO4  O4   C10  C4   180.00   0.0  0
 4KR  Var_01    C4   C3   C2   S1    27.42  30.0  1
 4KR  Var_02    N5   C4   C3   C2     2.14  30.0  1
 4KR  Var_03    C8   N5   C4   C3  -132.87  30.0  1
 4KR  Var_04    O3   C13  C3   C2   -54.49  30.0  2
 4KR  Var_05    O4   C10  C4   C3    47.00  30.0  2
 4KR  Var_06    C3   C13  O3   C1   167.70  30.0  1
 4KR  Var_07    H    C    C1   O2   160.67  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
 4KR  chir_01  C6  S1   N5  C7  negativ
 4KR  chir_02  C7  N14  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
 4KR  plan-1  C4   0.020
 4KR  plan-1  N5   0.020
 4KR  plan-1  C6   0.020
 4KR  plan-1  C7   0.020
 4KR  plan-1  C8   0.020
 4KR  plan-1  O9   0.020
 4KR  plan-2  C4   0.020
 4KR  plan-2  C10  0.020
 4KR  plan-2  HO4  0.020
 4KR  plan-2  O4   0.020
 4KR  plan-2  O5   0.020
 4KR  plan-3  C    0.020
 4KR  plan-3  C1   0.020
 4KR  plan-3  O2   0.020
 4KR  plan-3  O3   0.020

