# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:40:36 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](SCc1ccccc1)[C@@H](CC(O)=O)Cc2ccccc2
#
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
 K2U  K2U  '(3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid'  ligand  41  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_K2U
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
 K2U  O22  O  OC    -1  -0.629  -1.0834  -2.9569  -1.2933
 K2U  C1   C  C      0   0.425  -1.1429  -2.0795  -0.4072
 K2U  O21  O  O      0  -0.595  -1.1333  -2.2824   0.8242
 K2U  C2   C  CH2    0  -0.595  -1.2544  -0.6340  -0.9252
 K2U  C3   C  CH1    0  -0.269  -1.2070   0.5150   0.0816
 K2U  C4   C  CH2    0  -0.478  -2.4195   0.5405   1.0343
 K2U  C5   C  CR6    0   0.121  -3.7325   0.5376   0.3057
 K2U  C6   C  CR16   0  -0.305  -4.4857  -0.6289   0.1905
 K2U  C7   C  CR16   0  -0.241  -5.6880  -0.6381  -0.5051
 K2U  C8   C  CR16   0  -0.276  -6.1557   0.5241  -1.1044
 K2U  C9   C  CR16   0  -0.241  -5.4126   1.6937  -0.9999
 K2U  C10  C  CR16   0  -0.311  -4.2139   1.6976  -0.2997
 K2U  C11  C  CH1    0  -0.059   0.0821   0.5522   0.9109
 K2U  O12  O  OH1    0  -0.641   0.1583   1.6685   1.7483
 K2U  S13  S  S2     0  -0.047   1.5354   0.4778  -0.2104
 K2U  C14  C  CH2    0  -0.607   2.8744   0.5039   1.0253
 K2U  C15  C  CR6    0   0.111   4.1725   0.2474   0.3210
 K2U  C16  C  CR16   0  -0.292   4.9455   1.3056  -0.1493
 K2U  C17  C  CR16   0  -0.241   6.1406   1.0684  -0.8160
 K2U  C18  C  CR16   0  -0.268   6.5749  -0.2339  -1.0242
 K2U  C19  C  CR16   0  -0.242   5.8069  -1.2964  -0.5635
 K2U  C20  C  CR16   0  -0.288   4.6120  -1.0560   0.0997
 K2U  H2   H  HCH2   0   0.237  -0.4784  -0.4886  -1.6824
 K2U  H3   H  HCH2   0   0.246  -2.1912  -0.5591  -1.4875
 K2U  H4   H  HCH1   0   0.228  -1.2342   1.4442  -0.5069
 K2U  H5   H  HCH2   0   0.246  -2.3633  -0.3248   1.6932
 K2U  H6   H  HCH2   0   0.237  -2.3605   1.4329   1.6602
 K2U  H7   H  HCR6   0   0.243  -4.1177  -1.5411   0.6461
 K2U  H8   H  HCR6   0   0.250  -6.2591  -1.5548  -0.5814
 K2U  H9   H  HCR6   0   0.250  -7.0918   0.5191  -1.6481
 K2U  H10  H  HCR6   0   0.250  -5.7693   2.6055  -1.4622
 K2U  H11  H  HCR6   0   0.241  -3.6441   2.6170  -0.2198
 K2U  H12  H  HCH1   0   0.269   0.1282  -0.3243   1.5568
 K2U  H13  H  HOH1   0   0.446   0.0673   2.4624   1.2080
 K2U  H14  H  HCH2   0   0.278   2.8886   1.4687   1.5310
 K2U  H15  H  HCH2   0   0.278   2.6792  -0.2701   1.7696
 K2U  H16  H  HCR6   0   0.252   4.6126   2.3241   0.0125
 K2U  H17  H  HCR6   0   0.255   6.7338   1.9020  -1.1697
 K2U  H18  H  HCR6   0   0.255   7.5073  -0.4215  -1.5409
 K2U  H19  H  HCR6   0   0.256   6.1403  -2.3143  -0.7195
 K2U  H20  H  HCR6   0   0.251   4.0163  -1.8888   0.4552

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
 K2U  C18  C17  aromatic  1.389  0.020  1.389
 K2U  C18  C19  aromatic  1.390  0.020  1.390
 K2U  C17  C16  aromatic  1.389  0.020  1.389
 K2U  C19  C20  aromatic  1.388  0.020  1.388
 K2U  C16  C15  aromatic  1.392  0.020  1.392
 K2U  C20  C15  aromatic  1.393  0.020  1.393
 K2U  C15  C14  single    1.499  0.020  1.499
 K2U  C9   C8   aromatic  1.390  0.020  1.390
 K2U  C9   C10  aromatic  1.388  0.020  1.388
 K2U  C8   C7   aromatic  1.389  0.020  1.389
 K2U  C14  S13  single    1.822  0.020  1.822
 K2U  C10  C5   aromatic  1.394  0.020  1.394
 K2U  C7   C6   aromatic  1.389  0.020  1.389
 K2U  S13  C11  single    1.837  0.020  1.837
 K2U  C5   C6   aromatic  1.393  0.020  1.393
 K2U  C5   C4   single    1.502  0.020  1.502
 K2U  O12  C11  single    1.397  0.020  1.397
 K2U  C11  C3   single    1.533  0.020  1.533
 K2U  C4   C3   single    1.542  0.020  1.542
 K2U  C3   C2   single    1.528  0.020  1.528
 K2U  C2   C1   single    1.540  0.020  1.540
 K2U  O21  C1   deloc     1.248  0.020  1.248
 K2U  C1   O22  deloc     1.248  0.020  1.248
 K2U  C2   H2   single    0.970  0.020  1.090
 K2U  C2   H3   single    0.970  0.020  1.090
 K2U  C3   H4   single    0.970  0.020  1.090
 K2U  C4   H5   single    0.970  0.020  1.090
 K2U  C4   H6   single    0.970  0.020  1.090
 K2U  C6   H7   single    0.930  0.020  1.080
 K2U  C7   H8   single    0.930  0.020  1.080
 K2U  C8   H9   single    0.930  0.020  1.080
 K2U  C9   H10  single    0.930  0.020  1.080
 K2U  C10  H11  single    0.930  0.020  1.080
 K2U  C11  H12  single    0.970  0.020  1.090
 K2U  O12  H13  single    0.850  0.020  0.980
 K2U  C14  H14  single    0.970  0.020  1.090
 K2U  C14  H15  single    0.970  0.020  1.090
 K2U  C16  H16  single    0.930  0.020  1.080
 K2U  C17  H17  single    0.930  0.020  1.080
 K2U  C18  H18  single    0.930  0.020  1.080
 K2U  C19  H19  single    0.930  0.020  1.080
 K2U  C20  H20  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
 K2U  C2   C1   O21  119.03  3.000
 K2U  O21  C1   O22  125.86  3.000
 K2U  C2   C1   O22  115.12  3.000
 K2U  H3   C2   H2   104.03  3.000
 K2U  H3   C2   C3   108.27  3.000
 K2U  H2   C2   C3   109.51  3.000
 K2U  H3   C2   C1   107.39  3.000
 K2U  H2   C2   C1   107.84  3.000
 K2U  C3   C2   C1   118.81  3.000
 K2U  H4   C3   C11  106.84  3.000
 K2U  H4   C3   C4   107.28  3.000
 K2U  C11  C3   C4   109.06  3.000
 K2U  H4   C3   C2   106.37  3.000
 K2U  C4   C3   C2   113.26  3.000
 K2U  C11  C3   C2   113.62  3.000
 K2U  H6   C4   H5   107.45  3.000
 K2U  H6   C4   C5   109.09  3.000
 K2U  H5   C4   C5   109.70  3.000
 K2U  H6   C4   C3   108.98  3.000
 K2U  H5   C4   C3   108.67  3.000
 K2U  C5   C4   C3   112.81  3.000
 K2U  C10  C5   C6   118.29  3.000
 K2U  C6   C5   C4   120.96  3.000
 K2U  C10  C5   C4   120.73  3.000
 K2U  H7   C6   C7   119.92  3.000
 K2U  H7   C6   C5   119.09  3.000
 K2U  C7   C6   C5   120.99  3.000
 K2U  H8   C7   C8   120.03  3.000
 K2U  H8   C7   C6   119.83  3.000
 K2U  C8   C7   C6   120.14  3.000
 K2U  H9   C8   C9   120.27  3.000
 K2U  H9   C8   C7   120.27  3.000
 K2U  C9   C8   C7   119.46  3.000
 K2U  H10  C9   C10  119.83  3.000
 K2U  H10  C9   C8   120.03  3.000
 K2U  C10  C9   C8   120.14  3.000
 K2U  H11  C10  C9   119.55  3.000
 K2U  H11  C10  C5   119.47  3.000
 K2U  C9   C10  C5   120.99  3.000
 K2U  H12  C11  S13  107.20  3.000
 K2U  H12  C11  O12  106.56  3.000
 K2U  S13  C11  O12  110.79  3.000
 K2U  H12  C11  C3   109.67  3.000
 K2U  O12  C11  C3   112.91  3.000
 K2U  S13  C11  C3   109.51  3.000
 K2U  H13  O12  C11  108.46  3.000
 K2U  C14  S13  C11   99.60  3.000
 K2U  H15  C14  H14  108.28  3.000
 K2U  H15  C14  C15  110.73  3.000
 K2U  H14  C14  C15  111.00  3.000
 K2U  H15  C14  S13  108.72  3.000
 K2U  H14  C14  S13  109.70  3.000
 K2U  C15  C14  S13  108.38  3.000
 K2U  C20  C15  C16  118.83  3.000
 K2U  C20  C15  C14  120.52  3.000
 K2U  C16  C15  C14  120.63  3.000
 K2U  H16  C16  C17  119.77  3.000
 K2U  H16  C16  C15  119.57  3.000
 K2U  C17  C16  C15  120.67  3.000
 K2U  H17  C17  C18  120.12  3.000
 K2U  H17  C17  C16  119.79  3.000
 K2U  C18  C17  C16  120.09  3.000
 K2U  H18  C18  C19  120.13  3.000
 K2U  H18  C18  C17  120.24  3.000
 K2U  C19  C18  C17  119.63  3.000
 K2U  H19  C19  C20  119.81  3.000
 K2U  H19  C19  C18  120.06  3.000
 K2U  C20  C19  C18  120.13  3.000
 K2U  H20  C20  C19  119.79  3.000
 K2U  H20  C20  C15  119.56  3.000
 K2U  C19  C20  C15  120.64  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
 K2U  CONST_01  C8   C9   C10  C5      0.00   0.0  0
 K2U  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 K2U  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 K2U  CONST_04  C9   C10  C5   C6      0.00   0.0  0
 K2U  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 K2U  CONST_06  C10  C5   C6   C7      0.00   0.0  0
 K2U  CONST_07  C18  C17  C16  C15     0.00   0.0  0
 K2U  CONST_08  C18  C19  C20  C15     0.00   0.0  0
 K2U  CONST_09  C19  C18  C17  C16     0.00   0.0  0
 K2U  CONST_10  C19  C20  C15  C16     0.00   0.0  0
 K2U  CONST_11  C20  C19  C18  C17     0.00   0.0  0
 K2U  CONST_12  C20  C15  C16  C17     0.00   0.0  0
 K2U  CONST_13  C9   C10  C5   C4    180.00   0.0  0
 K2U  CONST_14  C7   C6   C5   C4    180.00   0.0  0
 K2U  CONST_15  C17  C16  C15  C14   180.00   0.0  0
 K2U  CONST_16  C19  C20  C15  C14   180.00   0.0  0
 K2U  CONST_17  H10  C9   C10  C5    180.00   0.0  0
 K2U  CONST_18  H8   C7   C6   C5    180.00   0.0  0
 K2U  CONST_19  H9   C8   C7   C6    180.00   0.0  0
 K2U  CONST_20  H11  C10  C5   C6    180.00   0.0  0
 K2U  CONST_21  H7   C6   C7   C8    180.00   0.0  0
 K2U  CONST_22  H17  C17  C16  C15   180.00   0.0  0
 K2U  CONST_23  H19  C19  C20  C15   180.00   0.0  0
 K2U  CONST_24  H18  C18  C17  C16   180.00   0.0  0
 K2U  CONST_25  H20  C20  C15  C16   180.00   0.0  0
 K2U  CONST_26  H16  C16  C17  C18   180.00   0.0  0
 K2U  Var_01    C10  C5   C4   C3    -76.78  30.0  2
 K2U  Var_02    C16  C15  C14  S13    92.05  30.0  2
 K2U  Var_03    C15  C14  S13  C11   171.83  30.0  1
 K2U  Var_04    C3   C2   C1   O22  -174.60  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
 K2U  chir_01  C3   C11  C4   C2  positiv
 K2U  chir_02  C11  S13  O12  C3  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
 K2U  plan-1  C4   0.020
 K2U  plan-1  C5   0.020
 K2U  plan-1  C6   0.020
 K2U  plan-1  C7   0.020
 K2U  plan-1  C8   0.020
 K2U  plan-1  C9   0.020
 K2U  plan-1  C10  0.020
 K2U  plan-1  H7   0.020
 K2U  plan-1  H8   0.020
 K2U  plan-1  H9   0.020
 K2U  plan-1  H10  0.020
 K2U  plan-1  H11  0.020
 K2U  plan-2  C14  0.020
 K2U  plan-2  C15  0.020
 K2U  plan-2  C16  0.020
 K2U  plan-2  C17  0.020
 K2U  plan-2  C18  0.020
 K2U  plan-2  C19  0.020
 K2U  plan-2  C20  0.020
 K2U  plan-2  H16  0.020
 K2U  plan-2  H17  0.020
 K2U  plan-2  H18  0.020
 K2U  plan-2  H19  0.020
 K2U  plan-2  H20  0.020
 K2U  plan-3  O22  0.020
 K2U  plan-3  C1   0.020
 K2U  plan-3  O21  0.020
 K2U  plan-3  C2   0.020

