# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 07:56:13 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (3R)-3-benzyl-4-oxo-4-[(2-oxo-2-phenylethyl)sulfanyl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H](Cc1ccccc1)C(=O)SCC(=O)c2ccccc2
#
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
 K1U  K1U  '(3R)-3-benzyl-4-oxo-4-[(2-oxo-2-phenylethyl)sulfanyl]butanoic acid'  ligand  42  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K1U
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
 K1U  O1   O  OH1   0  -0.589  -2.4629  -3.2154  -0.5690
 K1U  C8   C  C     0   0.560  -1.9284  -2.1294  -0.0290
 K1U  O2   O  O     0  -0.432  -1.3127  -2.1353   1.0078
 K1U  C24  C  CH2   0  -0.605  -2.1616  -0.9055  -0.8709
 K1U  C9   C  CH1   0  -0.361  -1.8672   0.3995  -0.1349
 K1U  C1   C  CH2   0  -0.505  -2.8663   0.7078   0.9901
 K1U  C2   C  CR6   0   0.120  -4.2861   0.7331   0.4957
 K1U  C3   C  CR16  0  -0.303  -4.7453   1.7905  -0.2885
 K1U  C4   C  CR16  0  -0.239  -6.0471   1.8079  -0.7678
 K1U  C5   C  CR16  0  -0.271  -6.9151   0.7644  -0.4684
 K1U  C6   C  CR16  0  -0.238  -6.4708  -0.2919   0.3143
 K1U  C7   C  CR16  0  -0.312  -5.1652  -0.3056   0.7901
 K1U  C10  C  C     0   0.299  -0.4385   0.4842   0.3751
 K1U  O3   O  O     0  -0.385  -0.1317   0.9088   1.4574
 K1U  S1   S  S2    0   0.035   0.7737  -0.0046  -0.8295
 K1U  C11  C  CH2   0  -0.703   2.2797   0.3205   0.1127
 K1U  C12  C  C     0   0.387   3.4738  -0.0483  -0.7343
 K1U  O4   O  O     0  -0.381   3.3254  -0.4923  -1.8513
 K1U  C13  C  CR6   0  -0.002   4.8220   0.1480  -0.1452
 K1U  C14  C  CR16  0  -0.288   4.9991   0.6846   1.1305
 K1U  C15  C  CR16  0  -0.237   6.2743   0.8562   1.6469
 K1U  C16  C  CR16  0  -0.244   7.3823   0.4903   0.8950
 K1U  C17  C  CR16  0  -0.241   7.2148  -0.0462  -0.3767
 K1U  C18  C  CR16  0  -0.257   5.9427  -0.2162  -0.8949
 K1U  H1   H  HOH1  0   0.483  -2.2750  -3.9886  -0.0155
 K1U  H2   H  HCH2  0   0.311  -1.5498  -0.9982  -1.7738
 K1U  H3   H  HCH2  0   0.308  -3.1903  -0.8969  -1.2369
 K1U  H4   H  HCH1  0   0.315  -1.9468   1.1960  -0.8859
 K1U  H5   H  HCH2  0   0.260  -2.7677  -0.0254   1.7921
 K1U  H6   H  HCH2  0   0.268  -2.6144   1.6785   1.4201
 K1U  H7   H  HCR6  0   0.249  -4.0774   2.6119  -0.5235
 K1U  H8   H  HCR6  0   0.255  -6.3868   2.6395  -1.3721
 K1U  H9   H  HCR6  0   0.255  -7.9312   0.7770  -0.8410
 K1U  H10  H  HCR6  0   0.255  -7.1408  -1.1065   0.5579
 K1U  H11  H  HCR6  0   0.249  -4.8285  -1.1332   1.4046
 K1U  H12  H  HCH2  0   0.321   2.3278   1.3732   0.3974
 K1U  H13  H  HCH2  0   0.322   2.2812  -0.2682   1.0325
 K1U  H14  H  HCR6  0   0.269   4.1494   0.9756   1.7345
 K1U  H15  H  HCR6  0   0.269   6.4025   1.2758   2.6356
 K1U  H16  H  HCR6  0   0.270   8.3772   0.6234   1.2991
 K1U  H17  H  HCR6  0   0.267   8.0786  -0.3302  -0.9629
 K1U  H18  H  HCR6  0   0.267   5.8175  -0.6339  -1.8850

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
 K1U  O2   C8   double    1.206  0.020  1.206
 K1U  C8   O1   single    1.325  0.020  1.325
 K1U  C8   C24  single    1.504  0.020  1.504
 K1U  C24  C9   single    1.527  0.020  1.527
 K1U  C9   C1   single    1.536  0.020  1.536
 K1U  C9   C10  single    1.519  0.020  1.519
 K1U  C1   C2   single    1.504  0.020  1.504
 K1U  C10  O3   double    1.202  0.020  1.202
 K1U  C10  S1   single    1.777  0.020  1.777
 K1U  C3   C2   aromatic  1.394  0.020  1.394
 K1U  C3   C4   aromatic  1.387  0.020  1.387
 K1U  C2   C7   aromatic  1.392  0.020  1.392
 K1U  S1   C11  single    1.806  0.020  1.806
 K1U  C11  C12  single    1.510  0.020  1.510
 K1U  C4   C5   aromatic  1.390  0.020  1.390
 K1U  C7   C6   aromatic  1.390  0.020  1.390
 K1U  C12  O4   double    1.211  0.020  1.211
 K1U  C12  C13  single    1.484  0.020  1.484
 K1U  C5   C6   aromatic  1.388  0.020  1.388
 K1U  C13  C18  aromatic  1.397  0.020  1.397
 K1U  C13  C14  aromatic  1.395  0.020  1.395
 K1U  C18  C17  aromatic  1.384  0.020  1.384
 K1U  C14  C15  aromatic  1.386  0.020  1.386
 K1U  C17  C16  aromatic  1.390  0.020  1.390
 K1U  C15  C16  aromatic  1.388  0.020  1.388
 K1U  O1   H1   single    0.850  0.020  0.980
 K1U  C24  H2   single    0.970  0.020  1.090
 K1U  C24  H3   single    0.970  0.020  1.090
 K1U  C9   H4   single    0.970  0.020  1.090
 K1U  C1   H5   single    0.970  0.020  1.090
 K1U  C1   H6   single    0.970  0.020  1.090
 K1U  C3   H7   single    0.930  0.020  1.080
 K1U  C4   H8   single    0.930  0.020  1.080
 K1U  C5   H9   single    0.930  0.020  1.080
 K1U  C6   H10  single    0.930  0.020  1.080
 K1U  C7   H11  single    0.930  0.020  1.080
 K1U  C11  H12  single    0.970  0.020  1.090
 K1U  C11  H13  single    0.970  0.020  1.090
 K1U  C14  H14  single    0.930  0.020  1.080
 K1U  C15  H15  single    0.930  0.020  1.080
 K1U  C16  H16  single    0.930  0.020  1.080
 K1U  C17  H17  single    0.930  0.020  1.080
 K1U  C18  H18  single    0.930  0.020  1.080

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
 K1U  H1   O1   C8   110.04  3.000
 K1U  C24  C8   O2   124.37  3.000
 K1U  C24  C8   O1   112.10  3.000
 K1U  O2   C8   O1   123.52  3.000
 K1U  H3   C24  H2   104.52  3.000
 K1U  H3   C24  C9   109.66  3.000
 K1U  H2   C24  C9   111.24  3.000
 K1U  H3   C24  C8   109.89  3.000
 K1U  H2   C24  C8   107.83  3.000
 K1U  C9   C24  C8   113.32  3.000
 K1U  H4   C9   C10  104.92  3.000
 K1U  H4   C9   C1   107.96  3.000
 K1U  C10  C9   C1   110.77  3.000
 K1U  H4   C9   C24  106.05  3.000
 K1U  C10  C9   C24  113.00  3.000
 K1U  C1   C9   C24  113.53  3.000
 K1U  H6   C1   H5   106.70  3.000
 K1U  H6   C1   C2   109.43  3.000
 K1U  H5   C1   C2   109.77  3.000
 K1U  H6   C1   C9   108.48  3.000
 K1U  H5   C1   C9   110.17  3.000
 K1U  C2   C1   C9   112.13  3.000
 K1U  C7   C2   C3   118.48  3.000
 K1U  C7   C2   C1   120.94  3.000
 K1U  C3   C2   C1   120.58  3.000
 K1U  H7   C3   C4   119.57  3.000
 K1U  H7   C3   C2   119.57  3.000
 K1U  C4   C3   C2   120.86  3.000
 K1U  H8   C4   C5   120.06  3.000
 K1U  H8   C4   C3   119.80  3.000
 K1U  C5   C4   C3   120.14  3.000
 K1U  H9   C5   C6   120.24  3.000
 K1U  H9   C5   C4   120.22  3.000
 K1U  C6   C5   C4   119.54  3.000
 K1U  H10  C6   C7   119.80  3.000
 K1U  H10  C6   C5   120.10  3.000
 K1U  C7   C6   C5   120.09  3.000
 K1U  H11  C7   C6   119.56  3.000
 K1U  H11  C7   C2   119.55  3.000
 K1U  C6   C7   C2   120.90  3.000
 K1U  S1   C10  O3   122.22  3.000
 K1U  S1   C10  C9   113.48  3.000
 K1U  O3   C10  C9   124.18  3.000
 K1U  C11  S1   C10   99.53  3.000
 K1U  H13  C11  H12  107.46  3.000
 K1U  H13  C11  C12  109.86  3.000
 K1U  H12  C11  C12  110.31  3.000
 K1U  H13  C11  S1   110.09  3.000
 K1U  H12  C11  S1   110.27  3.000
 K1U  C12  C11  S1   108.84  3.000
 K1U  C13  C12  O4   121.72  3.000
 K1U  C13  C12  C11  117.61  3.000
 K1U  O4   C12  C11  120.67  3.000
 K1U  C18  C13  C14  119.29  3.000
 K1U  C14  C13  C12  121.94  3.000
 K1U  C18  C13  C12  118.77  3.000
 K1U  H14  C14  C15  118.74  3.000
 K1U  H14  C14  C13  120.93  3.000
 K1U  C15  C14  C13  120.33  3.000
 K1U  H15  C15  C16  120.19  3.000
 K1U  H15  C15  C14  119.83  3.000
 K1U  C16  C15  C14  119.98  3.000
 K1U  H16  C16  C17  119.99  3.000
 K1U  H16  C16  C15  119.94  3.000
 K1U  C17  C16  C15  120.06  3.000
 K1U  H17  C17  C18  119.91  3.000
 K1U  H17  C17  C16  120.05  3.000
 K1U  C18  C17  C16  120.04  3.000
 K1U  H18  C18  C17  119.77  3.000
 K1U  H18  C18  C13  119.93  3.000
 K1U  C17  C18  C13  120.29  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
 K1U  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 K1U  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 K1U  CONST_03  C6   C7   C2   C3     0.00   0.0  0
 K1U  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 K1U  CONST_05  C7   C2   C3   C4     0.00   0.0  0
 K1U  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 K1U  CONST_07  C16  C17  C18  C13    0.00   0.0  0
 K1U  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 K1U  CONST_09  C17  C18  C13  C14    0.00   0.0  0
 K1U  CONST_10  C17  C16  C15  C14    0.00   0.0  0
 K1U  CONST_11  C18  C13  C14  C15    0.00   0.0  0
 K1U  CONST_12  C18  C17  C16  C15    0.00   0.0  0
 K1U  CONST_13  C4   C3   C2   C1   180.00   0.0  0
 K1U  CONST_14  C6   C7   C2   C1   180.00   0.0  0
 K1U  CONST_15  C17  C18  C13  C12  180.00   0.0  0
 K1U  CONST_16  C15  C14  C13  C12  180.00   0.0  0
 K1U  CONST_17  H8   C4   C3   C2   180.00   0.0  0
 K1U  CONST_18  H10  C6   C7   C2   180.00   0.0  0
 K1U  CONST_19  H11  C7   C2   C3   180.00   0.0  0
 K1U  CONST_20  H9   C5   C4   C3   180.00   0.0  0
 K1U  CONST_21  H7   C3   C4   C5   180.00   0.0  0
 K1U  CONST_22  H17  C17  C18  C13  180.00   0.0  0
 K1U  CONST_23  H15  C15  C14  C13  180.00   0.0  0
 K1U  CONST_24  H18  C18  C13  C14  180.00   0.0  0
 K1U  CONST_25  H16  C16  C15  C14  180.00   0.0  0
 K1U  CONST_26  H14  C14  C15  C16  180.00   0.0  0
 K1U  CONST_27  H1   O1   C8   O2     0.00   0.0  0
 K1U  Var_01    C3   C2   C1   C9   -72.69  30.0  2
 K1U  Var_02    C18  C13  C12  C11  178.43  30.0  2
 K1U  Var_03    C13  C12  C11  S1   179.78  30.0  3
 K1U  Var_04    C9   C24  C8   O1   165.98  30.0  3
 K1U  Var_05    C12  C11  S1   C10  179.36  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
 K1U  chir_01  C9  C24  C1  C10  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
 K1U  plan-1  C1   0.020
 K1U  plan-1  C2   0.020
 K1U  plan-1  C3   0.020
 K1U  plan-1  C4   0.020
 K1U  plan-1  C5   0.020
 K1U  plan-1  C6   0.020
 K1U  plan-1  C7   0.020
 K1U  plan-1  H7   0.020
 K1U  plan-1  H8   0.020
 K1U  plan-1  H9   0.020
 K1U  plan-1  H10  0.020
 K1U  plan-1  H11  0.020
 K1U  plan-2  C12  0.020
 K1U  plan-2  C13  0.020
 K1U  plan-2  C14  0.020
 K1U  plan-2  C15  0.020
 K1U  plan-2  C16  0.020
 K1U  plan-2  C17  0.020
 K1U  plan-2  C18  0.020
 K1U  plan-2  H14  0.020
 K1U  plan-2  H15  0.020
 K1U  plan-2  H16  0.020
 K1U  plan-2  H17  0.020
 K1U  plan-2  H18  0.020
 K1U  plan-3  C11  0.020
 K1U  plan-3  C12  0.020
 K1U  plan-3  O4   0.020
 K1U  plan-3  C13  0.020
 K1U  plan-4  O1   0.020
 K1U  plan-4  C8   0.020
 K1U  plan-4  O2   0.020
 K1U  plan-4  C24  0.020
 K1U  plan-4  H1   0.020
 K1U  plan-5  C9   0.020
 K1U  plan-5  C10  0.020
 K1U  plan-5  O3   0.020
 K1U  plan-5  S1   0.020

