# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 22:17:59 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  29  18  .  2021-08-04  2021-08-04  
;
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  -0.773   5.0747  -1.2375   0.8216
 4KR  C1    C  C      0   0.578   4.2604  -0.2621   0.0224
 4KR  S1    S  S2     0   0.019  -1.2007  -2.0679  -1.0494
 4KR  C2    C  CH2    0  -0.623   0.4971  -1.5591  -0.6430
 4KR  O2    O  O      0  -0.464   4.7345   0.5965  -0.6817
 4KR  C3    C  C      0  -0.007   0.6788  -0.0916  -0.3336
 4KR  O3    O  O2     0  -0.453   2.9567  -0.4511   0.1666
 4KR  C4    C  C      0   0.156  -0.2974   0.7019   0.1383
 4KR  N5    N  N      0  -0.494  -1.5529   0.1537   0.3886
 4KR  C6    C  C      0  -0.193  -1.9030  -1.2489   0.3986
 4KR  C7    C  C      0  -0.255  -3.3893  -0.8339   0.2660
 4KR  C8    C  C      0   0.505  -2.8219   0.5865   0.0943
 4KR  O9    O  O      0  -0.424  -3.2559   1.6519  -0.2548
 4KR  C10   C  C      0   0.381  -0.1812   2.1883   0.4905
 4KR  C13   C  CH2    0  -0.245   2.0693   0.3997  -0.5863
 4KR  N14   N  NH2    0  -0.785  -4.1644  -1.4336  -0.7738
 4KR  H     H  HCH3   0   0.259   4.4671  -1.8874   1.4450
 4KR  HA    H  HCH3   0   0.276   5.6589  -1.8550   0.1385
 4KR  HB    H  HCH3   0   0.273   5.7818  -0.6950   1.4482
 4KR  H6    H  H      0   0.301  -1.6101  -1.7712   1.3105
 4KR  H7    H  H      0   0.306  -3.9072  -0.9511   1.2198
 4KR  H13   H  HCH2   0   0.245   2.3081   0.3127  -1.6511
 4KR  H13A  H  HCH2   0   0.265   2.2043   1.4366  -0.2934
 4KR  HN14  H  HNH2   0   0.371  -5.1419  -1.2021  -0.6640
 4KR  HN1A  H  HNH2   0   0.358  -3.8834  -1.1124  -1.6908
 4KR  H2    H  HCH2   0   0.293   0.8565  -2.1789   0.1814
 4KR  O4    O  OC    -1  -0.584   0.5032   2.9019  -0.2630
 4KR  O5    O  O      0  -0.580  -0.7933   2.5234   1.5155
 4KR  H2A   H  HCH2   0   0.293   1.0965  -1.8270  -1.5161

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  1.501  0.020  1.501
 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  1.207  0.020  1.207
 4KR  C1   O3    single  1.325  0.020  1.325
 4KR  C2   S1    single  1.818  0.020  1.818
 4KR  S1   C6    single  1.806  0.020  1.806
 4KR  C3   C2    single  1.511  0.020  1.511
 4KR  C2   H2    single  0.970  0.020  1.090
 4KR  C2   H2A   single  0.970  0.020  1.090
 4KR  C13  C3    single  1.496  0.020  1.496
 4KR  C3   C4    double  1.344  0.020  1.344
 4KR  C13  O3    single  1.442  0.020  1.442
 4KR  C10  C4    single  1.532  0.020  1.532
 4KR  C4   N5    single  1.393  0.020  1.393
 4KR  C10  O4    deloc   1.243  0.020  1.243
 4KR  N5   C8    single  1.373  0.020  1.373
 4KR  N5   C6    single  1.446  0.020  1.446
 4KR  O5   C10   deloc   1.240  0.020  1.240
 4KR  C6   C7    single  1.549  0.020  1.549
 4KR  C6   H6    single  0.970  0.020  1.090
 4KR  C8   C7    single  1.539  0.020  1.539
 4KR  N14  C7    single  1.429  0.020  1.429
 4KR  C7   H7    single  0.970  0.020  1.090
 4KR  O9   C8    double  1.202  0.020  1.202
 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    107.13  3.000
 4KR  HB    C    H     109.32  3.000
 4KR  HA    C    H     108.68  3.000
 4KR  HB    C    C1    109.55  3.000
 4KR  HA    C    C1    108.97  3.000
 4KR  H     C    C1    113.01  3.000
 4KR  O3    C1   O2    123.44  3.000
 4KR  O3    C1   C     112.53  3.000
 4KR  O2    C1   C     124.03  3.000
 4KR  C6    S1   C2     93.27  3.000
 4KR  H2A   C2   H2    106.47  3.000
 4KR  H2A   C2   C3    109.63  3.000
 4KR  H2    C2   C3    110.91  3.000
 4KR  H2A   C2   S1    105.37  3.000
 4KR  H2    C2   S1    108.49  3.000
 4KR  C3    C2   S1    115.46  3.000
 4KR  C13   C3   C4    122.73  3.000
 4KR  C4    C3   C2    123.93  3.000
 4KR  C13   C3   C2    113.34  3.000
 4KR  C13   O3   C1    117.69  3.000
 4KR  C10   C4   N5    114.14  3.000
 4KR  N5    C4   C3    119.06  3.000
 4KR  C10   C4   C3    126.77  3.000
 4KR  C8    N5   C6     94.79  3.000
 4KR  C6    N5   C4    126.97  3.000
 4KR  C8    N5   C4    132.13  3.000
 4KR  H6    C6   C7    117.23  3.000
 4KR  H6    C6   N5    113.91  3.000
 4KR  C7    C6   N5     88.38  3.000
 4KR  H6    C6   S1    110.41  3.000
 4KR  C7    C6   S1    115.22  3.000
 4KR  N5    C6   S1    109.89  3.000
 4KR  H7    C7   N14   109.48  3.000
 4KR  H7    C7   C8    111.81  3.000
 4KR  N14   C7   C8    120.41  3.000
 4KR  H7    C7   C6    110.59  3.000
 4KR  N14   C7   C6    118.06  3.000
 4KR  C8    C7   C6     84.44  3.000
 4KR  O9    C8   C7    135.81  3.000
 4KR  O9    C8   N5    132.49  3.000
 4KR  C7    C8   N5     91.49  3.000
 4KR  O5    C10  O4    128.14  3.000
 4KR  O5    C10  C4    114.51  3.000
 4KR  O4    C10  C4    117.35  3.000
 4KR  H13A  C13  H13   108.13  3.000
 4KR  H13A  C13  O3    110.25  3.000
 4KR  H13   C13  O3    109.08  3.000
 4KR  H13A  C13  C3    112.55  3.000
 4KR  H13   C13  C3    109.93  3.000
 4KR  O3    C13  C3    106.86  3.000
 4KR  HN1A  N14  HN14  107.13  3.000
 4KR  HN1A  N14  C7    112.08  3.000
 4KR  HN14  N14  C7    110.45  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_03  O9  C8   N5  C4     0.00   0.0  0
 4KR  CONST_04  O9  C8   N5  C6   180.00   0.0  0
 4KR  Var_01    C4  C3   C2  S1    25.77  30.0  1
 4KR  Var_02    N5  C4   C3  C2     1.29  30.0  1
 4KR  Var_03    C8  N5   C4  C3  -134.80  30.0  1
 4KR  Var_04    O3  C13  C3  C2   -54.75  30.0  2
 4KR  Var_05    O4  C10  C4  C3    39.52  30.0  2
 4KR  Var_06    C3  C13  O3  C1   175.38  30.0  1
 4KR  Var_07    H   C    C1  O2   175.99  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  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

