# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 06:04:15 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (6S)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(2-hydroxyphenyl)-6-phenyl-5,6-dihydro-2H-pyran-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(Sc2ccccc2Cl)C(=O)O[C@@](C1)(c3ccccc3)c4ccccc4O
#
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
 D3S  D3S  (6S)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(2-hydroxyphenyl)-6-phenyl-5,6-dihydro-2H-pyran-2-one  ligand  46  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D3S
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
 D3S  C4   C   CR16  0  -0.274   5.3154  -2.6073   0.1127
 D3S  C14  C   CR6   0  -0.016  -3.1698  -1.0367  -0.1391
 D3S  C5   C   CR16  0  -0.233   3.9568  -2.8369   0.2777
 D3S  C6   C   CR16  0  -0.244   3.0604  -1.7797   0.2667
 D3S  C7   C   CR6   0  -0.029   3.5088  -0.4758   0.0884
 D3S  C9   C   C     0  -0.527   0.8415   0.2312   0.1138
 D3S  C10  C   C     0   0.526   0.1550   0.1646   1.2822
 D3S  C12  C   CH2   0  -0.597  -1.2257  -0.3933   1.3045
 D3S  C13  C   CT    0   0.134  -1.9123  -0.1847  -0.0439
 D3S  C3   C   CR16  0  -0.200   5.7783  -1.3119  -0.0592
 D3S  C2   C   CR6   0  -0.062   4.8758  -0.2611  -0.0704
 D3S  S8   S   S2    0   0.100   2.4396   0.9379   0.0551
 D3S  O11  O   OH1   0  -0.555   0.6247   0.5297   2.4494
 D3S  C15  C   CR16  0  -0.301  -3.2657  -2.1114  -1.0173
 D3S  C16  C   CR16  0  -0.266  -4.4176  -2.8824  -1.1007
 D3S  C17  C   CR16  0  -0.250  -5.5020  -2.5824  -0.2926
 D3S  C18  C   CR16  0  -0.376  -5.4281  -1.5212   0.5948
 D3S  C19  C   CR6   0   0.349  -4.2719  -0.7511   0.6784
 D3S  O20  O   OH1   0  -0.623  -4.1762   0.2786   1.5401
 D3S  C21  C   CR6   0   0.152  -2.2281   1.2724  -0.3725
 D3S  C22  C   CR16  0  -0.303  -2.0355   2.3174   0.5218
 D3S  C23  C   CR16  0  -0.242  -2.3191   3.6266   0.1528
 D3S  C24  C   CR16  0  -0.266  -2.8066   3.9060  -1.1146
 D3S  C25  C   CR16  0  -0.244  -3.0118   2.8656  -2.0121
 D3S  C26  C   CR16  0  -0.276  -2.7247   1.5608  -1.6427
 D3S  O27  O   O2    0  -0.469  -1.0341  -0.6644  -1.0743
 D3S  C28  C   C     0   0.588   0.2509  -0.2820  -1.1145
 D3S  O29  O   O     0  -0.422   0.8602  -0.4303  -2.1435
 D3S  H1   H   HCR6  0   0.271   6.0177  -3.4293   0.1194
 D3S  H2   H   HCR6  0   0.269   3.5874  -3.8438   0.4180
 D3S  H3   H   HCR6  0   0.265   2.0055  -1.9736   0.4063
 D3S  H4   H   HCH2  0   0.329  -1.1543  -1.4672   1.5076
 D3S  H5   H   HCH2  0   0.319  -1.8002   0.0393   2.1214
 D3S  H6   H   HCR6  0   0.285   6.8346  -1.1159  -0.1841
 D3S  H7   H   HOH1  0   0.488   1.5351   0.8656   2.3624
 D3S  H8   H   HCR6  0   0.262  -2.4323  -2.3602  -1.6576
 D3S  H9   H   HCR6  0   0.255  -4.4600  -3.7103  -1.7952
 D3S  H10  H   HCR6  0   0.262  -6.4083  -3.1714  -0.3463
 D3S  H11  H   HCR6  0   0.272  -6.2730  -1.2850   1.2326
 D3S  H12  H   HOH1  0   0.478  -4.9887   0.3648   2.0521
 D3S  H13  H   HCR6  0   0.253  -1.6758   2.1368   1.5259
 D3S  H14  H   HCR6  0   0.259  -2.1601   4.4270   0.8635
 D3S  H15  H   HCR6  0   0.259  -3.0277   4.9254  -1.4023
 D3S  H16  H   HCR6  0   0.258  -3.3980   3.0707  -3.0020
 D3S  H17  H   HCR6  0   0.258  -2.8944   0.7631  -2.3556
 D3S  CL1  CL  CL    0  -0.115   5.4615   1.3561  -0.2793

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
 D3S  C3   C4   aromatic  1.386  0.020  1.386
 D3S  C3   C2   aromatic  1.385  0.020  1.385
 D3S  C4   C5   aromatic  1.388  0.020  1.388
 D3S  CL1  C2   single    1.733  0.020  1.733
 D3S  O11  C10  single    1.310  0.020  1.310
 D3S  C2   C7   aromatic  1.393  0.020  1.393
 D3S  C5   C6   aromatic  1.386  0.020  1.386
 D3S  C7   C6   aromatic  1.390  0.020  1.390
 D3S  C7   S8   single    1.773  0.020  1.773
 D3S  C23  C22  aromatic  1.389  0.020  1.389
 D3S  C23  C24  aromatic  1.386  0.020  1.386
 D3S  S8   C9   single    1.748  0.020  1.748
 D3S  C10  C9   double    1.357  0.020  1.357
 D3S  C10  C12  single    1.489  0.020  1.489
 D3S  C22  C21  aromatic  1.389  0.020  1.389
 D3S  C24  C25  aromatic  1.389  0.020  1.389
 D3S  C9   C28  single    1.456  0.020  1.456
 D3S  C12  C13  single    1.528  0.020  1.528
 D3S  C21  C26  aromatic  1.394  0.020  1.394
 D3S  C21  C13  single    1.527  0.020  1.527
 D3S  C25  C26  aromatic  1.386  0.020  1.386
 D3S  C13  O27  single    1.436  0.020  1.436
 D3S  C13  C14  single    1.522  0.020  1.522
 D3S  C28  O29  double    1.205  0.020  1.205
 D3S  C28  O27  single    1.341  0.020  1.341
 D3S  C14  C15  aromatic  1.391  0.020  1.391
 D3S  C14  C19  aromatic  1.402  0.020  1.402
 D3S  C15  C16  aromatic  1.389  0.020  1.389
 D3S  O20  C19  single    1.346  0.020  1.346
 D3S  C19  C18  aromatic  1.392  0.020  1.392
 D3S  C16  C17  aromatic  1.385  0.020  1.385
 D3S  C18  C17  aromatic  1.385  0.020  1.385
 D3S  C4   H1   single    0.930  0.020  1.080
 D3S  C5   H2   single    0.930  0.020  1.080
 D3S  C6   H3   single    0.930  0.020  1.080
 D3S  C12  H4   single    0.970  0.020  1.090
 D3S  C12  H5   single    0.970  0.020  1.090
 D3S  C3   H6   single    0.930  0.020  1.080
 D3S  O11  H7   single    0.850  0.020  0.980
 D3S  C15  H8   single    0.930  0.020  1.080
 D3S  C16  H9   single    0.930  0.020  1.080
 D3S  C17  H10  single    0.930  0.020  1.080
 D3S  C18  H11  single    0.930  0.020  1.080
 D3S  O20  H12  single    0.850  0.020  0.980
 D3S  C22  H13  single    0.930  0.020  1.080
 D3S  C23  H14  single    0.930  0.020  1.080
 D3S  C24  H15  single    0.930  0.020  1.080
 D3S  C25  H16  single    0.930  0.020  1.080
 D3S  C26  H17  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
 D3S  H1   C4   C3   119.62  3.000
 D3S  H1   C4   C5   120.62  3.000
 D3S  C3   C4   C5   119.75  3.000
 D3S  C19  C14  C15  118.13  3.000
 D3S  C19  C14  C13  119.94  3.000
 D3S  C15  C14  C13  121.93  3.000
 D3S  H2   C5   C6   119.35  3.000
 D3S  H2   C5   C4   120.25  3.000
 D3S  C6   C5   C4   120.40  3.000
 D3S  H3   C6   C7   119.96  3.000
 D3S  H3   C6   C5   119.53  3.000
 D3S  C7   C6   C5   120.51  3.000
 D3S  S8   C7   C2   117.83  3.000
 D3S  S8   C7   C6   123.76  3.000
 D3S  C2   C7   C6   118.41  3.000
 D3S  C28  C9   S8   119.00  3.000
 D3S  C28  C9   C10  120.25  3.000
 D3S  S8   C9   C10  120.75  3.000
 D3S  O11  C10  C12  115.05  3.000
 D3S  C12  C10  C9   120.03  3.000
 D3S  O11  C10  C9   124.90  3.000
 D3S  H5   C12  H4   106.56  3.000
 D3S  H5   C12  C13  111.78  3.000
 D3S  H4   C12  C13  109.08  3.000
 D3S  H5   C12  C10  110.59  3.000
 D3S  H4   C12  C10  108.04  3.000
 D3S  C13  C12  C10  110.63  3.000
 D3S  O27  C13  C21  106.91  3.000
 D3S  O27  C13  C12  108.23  3.000
 D3S  C21  C13  C12  114.41  3.000
 D3S  O27  C13  C14  105.86  3.000
 D3S  C21  C13  C14  110.48  3.000
 D3S  C12  C13  C14  110.50  3.000
 D3S  H6   C3   C2   119.87  3.000
 D3S  H6   C3   C4   120.65  3.000
 D3S  C2   C3   C4   119.49  3.000
 D3S  CL1  C2   C3   119.26  3.000
 D3S  CL1  C2   C7   119.30  3.000
 D3S  C3   C2   C7   121.44  3.000
 D3S  C9   S8   C7   103.20  3.000
 D3S  H7   O11  C10  110.58  3.000
 D3S  H8   C15  C16  118.46  3.000
 D3S  H8   C15  C14  119.94  3.000
 D3S  C16  C15  C14  121.60  3.000
 D3S  H9   C16  C17  120.64  3.000
 D3S  H9   C16  C15  119.74  3.000
 D3S  C17  C16  C15  119.61  3.000
 D3S  H10  C17  C18  119.56  3.000
 D3S  H10  C17  C16  120.58  3.000
 D3S  C18  C17  C16  119.85  3.000
 D3S  H11  C18  C19  119.43  3.000
 D3S  H11  C18  C17  120.13  3.000
 D3S  C19  C18  C17  120.44  3.000
 D3S  O20  C19  C18  121.38  3.000
 D3S  C18  C19  C14  120.37  3.000
 D3S  O20  C19  C14  118.25  3.000
 D3S  H12  O20  C19  110.39  3.000
 D3S  C26  C21  C22  118.72  3.000
 D3S  C26  C21  C13  117.86  3.000
 D3S  C22  C21  C13  123.43  3.000
 D3S  H13  C22  C23  118.15  3.000
 D3S  H13  C22  C21  121.21  3.000
 D3S  C23  C22  C21  120.64  3.000
 D3S  H14  C23  C24  120.20  3.000
 D3S  H14  C23  C22  119.50  3.000
 D3S  C24  C23  C22  120.30  3.000
 D3S  H15  C24  C25  120.24  3.000
 D3S  H15  C24  C23  120.32  3.000
 D3S  C25  C24  C23  119.45  3.000
 D3S  H16  C25  C26  119.74  3.000
 D3S  H16  C25  C24  120.11  3.000
 D3S  C26  C25  C24  120.15  3.000
 D3S  H17  C26  C25  119.04  3.000
 D3S  H17  C26  C21  120.21  3.000
 D3S  C25  C26  C21  120.75  3.000
 D3S  C28  O27  C13  120.80  3.000
 D3S  O29  C28  O27  118.36  3.000
 D3S  O27  C28  C9   117.63  3.000
 D3S  O29  C28  C9   123.95  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
 D3S  CONST_01  C7   C2   C3   C4     0.00   0.0  0
 D3S  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 D3S  CONST_03  C17  C16  C15  C14    0.00   0.0  0
 D3S  CONST_04  C17  C18  C19  C14    0.00   0.0  0
 D3S  CONST_05  C2   C3   C4   C5     0.00   0.0  0
 D3S  CONST_06  C2   C7   C6   C5     0.00   0.0  0
 D3S  CONST_07  C3   C4   C5   C6     0.00   0.0  0
 D3S  CONST_08  C3   C2   C7   C6     0.00   0.0  0
 D3S  CONST_09  C18  C19  C14  C15    0.00   0.0  0
 D3S  CONST_10  C18  C17  C16  C15    0.00   0.0  0
 D3S  CONST_11  C19  C14  C15  C16    0.00   0.0  0
 D3S  CONST_12  C19  C18  C17  C16    0.00   0.0  0
 D3S  CONST_13  C24  C23  C22  C21    0.00   0.0  0
 D3S  CONST_14  C24  C25  C26  C21    0.00   0.0  0
 D3S  CONST_15  C25  C24  C23  C22    0.00   0.0  0
 D3S  CONST_16  C25  C26  C21  C22    0.00   0.0  0
 D3S  CONST_17  C26  C21  C22  C23    0.00   0.0  0
 D3S  CONST_18  C26  C25  C24  C23    0.00   0.0  0
 D3S  CONST_19  C23  C22  C21  C13  180.00   0.0  0
 D3S  CONST_20  C25  C26  C21  C13  180.00   0.0  0
 D3S  CONST_21  C16  C15  C14  C13  180.00   0.0  0
 D3S  CONST_22  C18  C19  C14  C13  180.00   0.0  0
 D3S  CONST_23  CL1  C2   C3   C4   180.00   0.0  0
 D3S  CONST_24  S8   C7   C6   C5   180.00   0.0  0
 D3S  CONST_25  CL1  C2   C7   C6   180.00   0.0  0
 D3S  CONST_26  O20  C19  C14  C13    0.00   0.0  0
 D3S  CONST_27  S8   C7   C2   C3   180.00   0.0  0
 D3S  CONST_28  O20  C19  C14  C15  180.00   0.0  0
 D3S  CONST_29  O20  C19  C18  C17  180.00   0.0  0
 D3S  CONST_30  H3   C6   C5   C4   180.00   0.0  0
 D3S  CONST_31  H9   C16  C15  C14  180.00   0.0  0
 D3S  CONST_32  H11  C18  C19  C14  180.00   0.0  0
 D3S  CONST_33  H6   C3   C4   C5   180.00   0.0  0
 D3S  CONST_34  H1   C4   C5   C6   180.00   0.0  0
 D3S  CONST_35  H2   C5   C6   C7   180.00   0.0  0
 D3S  CONST_36  H13  C22  C21  C13    0.00   0.0  0
 D3S  CONST_37  H17  C26  C21  C13    0.00   0.0  0
 D3S  CONST_38  H8   C15  C14  C13    0.00   0.0  0
 D3S  CONST_39  H10  C17  C16  C15  180.00   0.0  0
 D3S  CONST_40  H14  C23  C22  C21  180.00   0.0  0
 D3S  CONST_41  H16  C25  C26  C21  180.00   0.0  0
 D3S  CONST_42  H15  C24  C23  C22  180.00   0.0  0
 D3S  Var_01    C13  C12  C10  C9   -27.96  30.0  1
 D3S  Var_02    O27  C28  C9   C10    7.84  30.0  1
 D3S  Var_03    C28  C9   C10  C12   -2.04  30.0  1
 D3S  Var_04    C10  C9   S8   C7    99.16  30.0  3
 D3S  Var_05    C2   C7   S8   C9   174.24  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
 D3S  chir_01  C13  C21  O27  C14  positiv

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
 D3S  plan-1  C14  0.020
 D3S  plan-1  C13  0.020
 D3S  plan-1  C15  0.020
 D3S  plan-1  C16  0.020
 D3S  plan-1  C17  0.020
 D3S  plan-1  C18  0.020
 D3S  plan-1  C19  0.020
 D3S  plan-1  O20  0.020
 D3S  plan-1  H8   0.020
 D3S  plan-1  H9   0.020
 D3S  plan-1  H10  0.020
 D3S  plan-1  H11  0.020
 D3S  plan-2  C9   0.020
 D3S  plan-2  O27  0.020
 D3S  plan-2  C28  0.020
 D3S  plan-2  O29  0.020
 D3S  plan-3  C4   0.020
 D3S  plan-3  C5   0.020
 D3S  plan-3  C6   0.020
 D3S  plan-3  C7   0.020
 D3S  plan-3  C3   0.020
 D3S  plan-3  C2   0.020
 D3S  plan-3  S8   0.020
 D3S  plan-3  H1   0.020
 D3S  plan-3  H2   0.020
 D3S  plan-3  H3   0.020
 D3S  plan-3  H6   0.020
 D3S  plan-3  CL1  0.020
 D3S  plan-4  C13  0.020
 D3S  plan-4  C21  0.020
 D3S  plan-4  C22  0.020
 D3S  plan-4  C23  0.020
 D3S  plan-4  C24  0.020
 D3S  plan-4  C25  0.020
 D3S  plan-4  C26  0.020
 D3S  plan-4  H13  0.020
 D3S  plan-4  H14  0.020
 D3S  plan-4  H15  0.020
 D3S  plan-4  H16  0.020
 D3S  plan-4  H17  0.020

