# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 23:15:32 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (6R)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(3-hydroxyphenyl)-6-(thiophen-3-yl)-5,6-dihydropyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(Sc2ccccc2Cl)C(=O)N[C@@](C1)(c3cscc3)c4cccc(O)c4
#
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
 6EY  6EY  (6R)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(3-hydroxyphenyl)-6-(thiophen-3-yl)-5,6-dihydropyridin-2(1H)-one  ligand  44  28  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6EY
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
 6EY  C4   C   C     0  -0.485  -0.7891  -1.4061  -0.2425
 6EY  C6   C   CR6   0  -0.037  -3.1574  -0.0630   0.2325
 6EY  C11  C   CR6   0  -0.065  -4.5251   0.0538   0.4713
 6EY  C7   C   CR16  0  -0.240  -2.3764   1.0856   0.2935
 6EY  C8   C   CR16  0  -0.232  -2.9492   2.3114   0.5949
 6EY  C9   C   CR16  0  -0.275  -4.3125   2.4114   0.8326
 6EY  C10  C   CR16  0  -0.200  -5.1057   1.2758   0.7690
 6EY  C13  C   C     0   0.548   0.0238  -1.6396   0.9612
 6EY  C3   C   CH2   0  -0.583   1.2887  -1.0718  -1.5434
 6EY  C2   C   C     0   0.531  -0.1961  -1.1642  -1.4367
 6EY  S5   S   S2    0   0.087  -2.5168  -1.6701  -0.1593
 6EY  CL   CL  CL    0  -0.117  -5.5249  -1.3593   0.3883
 6EY  N14  N   NH1   0  -0.650   1.3474  -1.3626   0.8303
 6EY  C15  C   CT    0  -0.084   1.8725  -0.5279  -0.2424
 6EY  C16  C   CR5   0   0.230   1.4474   0.9240  -0.0429
 6EY  C17  C   CR15  0  -0.538   1.3261   1.8447  -1.0427
 6EY  S18  S   S2    0   0.228   0.8556   3.3796  -0.4471
 6EY  C19  C   CR15  0  -0.457   0.8170   2.8063   1.1646
 6EY  C20  C   CR15  0  -0.218   1.1497   1.4895   1.2329
 6EY  C21  C   CR6   0   0.223   3.3968  -0.5992  -0.2091
 6EY  C22  C   CR16  0  -0.363   4.1472  -1.0093  -1.3023
 6EY  C23  C   CR16  0  -0.221   5.5357  -1.0399  -1.2162
 6EY  C24  C   CR16  0  -0.347   6.1898  -0.6739  -0.0559
 6EY  C25  C   CR6   0   0.384   5.4404  -0.2599   1.0446
 6EY  O26  O   OH1   0  -0.630   6.1071   0.0940   2.1593
 6EY  C27  C   CR16  0  -0.453   4.0539  -0.2189   0.9608
 6EY  O28  O   O     0  -0.467  -0.4479  -2.0870   1.9945
 6EY  H1   H   HCR6  0   0.275  -1.3123   1.0232   0.1096
 6EY  H2   H   HCR6  0   0.259  -2.3198   3.1903   0.6385
 6EY  H3   H   HCR6  0   0.270  -4.7624   3.3664   1.0668
 6EY  H4   H   HCR6  0   0.284  -6.1706   1.3367   0.9479
 6EY  H5   H   HCH2  0   0.316   1.6720  -2.0790  -1.7377
 6EY  H6   H   HCH2  0   0.297   1.5626  -0.4570  -2.3996
 6EY  H7   H   HOH1  0   0.483  -1.7866  -1.1840  -2.4529
 6EY  H8   H   HNH1  0   0.406   1.9125  -1.4939   1.6570
 6EY  H9   H   HCR5  0   0.297   1.4989   1.7188  -2.1008
 6EY  H10  H   HCR5  0   0.300   0.5426   3.4627   1.9758
 6EY  H11  H   HCR5  0   0.269   1.1627   0.9381   2.1625
 6EY  H12  H   HCR6  0   0.261   3.6813  -1.3071  -2.2303
 6EY  H13  H   HCR6  0   0.263   6.1133  -1.3594  -2.0738
 6EY  H14  H   HCR6  0   0.268   7.2704  -0.7023   0.0056
 6EY  H15  H   HOH1  0   0.476   5.4914   0.3534   2.8541
 6EY  H16  H   HCR6  0   0.272   3.4923   0.1317   1.8210
 6EY  O1   O   OH1   0  -0.562  -0.8329  -1.0322  -2.5795

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
 6EY  C10  C9   aromatic  1.387  0.020  1.387
 6EY  C10  C11  aromatic  1.385  0.020  1.385
 6EY  C9   C8   aromatic  1.387  0.020  1.387
 6EY  CL   C11  single    1.733  0.020  1.733
 6EY  C11  C6   aromatic  1.393  0.020  1.393
 6EY  O1   C2   single    1.315  0.020  1.315
 6EY  C8   C7   aromatic  1.386  0.020  1.386
 6EY  C6   C7   aromatic  1.390  0.020  1.390
 6EY  C6   S5   single    1.774  0.020  1.774
 6EY  S5   C4   single    1.750  0.020  1.750
 6EY  C2   C4   double    1.355  0.020  1.355
 6EY  C2   C3   single    1.491  0.020  1.491
 6EY  S18  C17  aromatic  1.712  0.020  1.712
 6EY  S18  C19  aromatic  1.711  0.020  1.711
 6EY  C17  C16  aromatic  1.365  0.020  1.365
 6EY  C4   C13  single    1.471  0.020  1.471
 6EY  C3   C15  single    1.526  0.020  1.526
 6EY  C16  C15  single    1.526  0.020  1.526
 6EY  C16  C20  aromatic  1.427  0.020  1.427
 6EY  C19  C20  aromatic  1.360  0.020  1.360
 6EY  C15  N14  single    1.457  0.020  1.457
 6EY  C15  C21  single    1.526  0.020  1.526
 6EY  C13  O28  double    1.221  0.020  1.221
 6EY  C13  N14  single    1.359  0.020  1.359
 6EY  C21  C22  aromatic  1.388  0.020  1.388
 6EY  C21  C27  aromatic  1.395  0.020  1.395
 6EY  C22  C23  aromatic  1.392  0.020  1.392
 6EY  C27  C25  aromatic  1.390  0.020  1.390
 6EY  C23  C24  aromatic  1.381  0.020  1.381
 6EY  C25  C24  aromatic  1.394  0.020  1.394
 6EY  C25  O26  single    1.346  0.020  1.346
 6EY  C7   H1   single    0.930  0.020  1.080
 6EY  C8   H2   single    0.930  0.020  1.080
 6EY  C9   H3   single    0.930  0.020  1.080
 6EY  C10  H4   single    0.930  0.020  1.080
 6EY  C3   H5   single    0.970  0.020  1.090
 6EY  C3   H6   single    0.970  0.020  1.090
 6EY  O1   H7   single    0.850  0.020  0.980
 6EY  N14  H8   single    0.890  0.020  1.040
 6EY  C17  H9   single    0.930  0.020  1.080
 6EY  C19  H10  single    0.930  0.020  1.080
 6EY  C20  H11  single    0.930  0.020  1.080
 6EY  C22  H12  single    0.930  0.020  1.080
 6EY  C23  H13  single    0.930  0.020  1.080
 6EY  C24  H14  single    0.930  0.020  1.080
 6EY  O26  H15  single    0.850  0.020  0.980
 6EY  C27  H16  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
 6EY  S5   C4   C2   120.06  3.000
 6EY  C2   C4   C13  120.50  3.000
 6EY  S5   C4   C13  118.86  3.000
 6EY  S5   C6   C7   123.73  3.000
 6EY  S5   C6   C11  117.93  3.000
 6EY  C7   C6   C11  118.33  3.000
 6EY  CL   C11  C10  119.20  3.000
 6EY  CL   C11  C6   119.32  3.000
 6EY  C10  C11  C6   121.48  3.000
 6EY  H1   C7   C8   119.63  3.000
 6EY  H1   C7   C6   119.84  3.000
 6EY  C8   C7   C6   120.53  3.000
 6EY  H2   C8   C9   120.41  3.000
 6EY  H2   C8   C7   119.13  3.000
 6EY  C9   C8   C7   120.46  3.000
 6EY  H3   C9   C10  119.68  3.000
 6EY  H3   C9   C8   120.63  3.000
 6EY  C10  C9   C8   119.68  3.000
 6EY  H4   C10  C9   120.63  3.000
 6EY  H4   C10  C11  119.86  3.000
 6EY  C9   C10  C11  119.51  3.000
 6EY  O28  C13  N14  122.18  3.000
 6EY  N14  C13  C4   115.29  3.000
 6EY  O28  C13  C4   122.50  3.000
 6EY  H6   C3   H5   106.96  3.000
 6EY  H6   C3   C15  111.88  3.000
 6EY  H5   C3   C15  110.19  3.000
 6EY  H6   C3   C2   109.97  3.000
 6EY  H5   C3   C2   107.72  3.000
 6EY  C15  C3   C2   109.99  3.000
 6EY  O1   C2   C3   114.44  3.000
 6EY  C3   C2   C4   120.65  3.000
 6EY  O1   C2   C4   124.88  3.000
 6EY  C6   S5   C4   103.32  3.000
 6EY  H8   N14  C15  118.39  3.000
 6EY  H8   N14  C13  116.09  3.000
 6EY  C15  N14  C13  122.60  3.000
 6EY  C21  C15  C16  108.65  3.000
 6EY  C21  C15  N14  108.48  3.000
 6EY  C16  C15  N14  110.40  3.000
 6EY  C21  C15  C3   112.58  3.000
 6EY  N14  C15  C3   106.59  3.000
 6EY  C16  C15  C3   110.12  3.000
 6EY  C20  C16  C17  111.67  3.000
 6EY  C20  C16  C15  123.50  3.000
 6EY  C17  C16  C15  124.82  3.000
 6EY  H9   C17  S18  119.30  3.000
 6EY  H9   C17  C16  128.70  3.000
 6EY  S18  C17  C16  111.99  3.000
 6EY  C19  S18  C17   91.92  3.000
 6EY  H10  C19  C20  127.85  3.000
 6EY  H10  C19  S18  120.66  3.000
 6EY  C20  C19  S18  111.48  3.000
 6EY  H11  C20  C19  122.69  3.000
 6EY  H11  C20  C16  124.36  3.000
 6EY  C19  C20  C16  112.94  3.000
 6EY  C27  C21  C22  119.12  3.000
 6EY  C27  C21  C15  118.43  3.000
 6EY  C22  C21  C15  122.45  3.000
 6EY  H12  C22  C23  118.52  3.000
 6EY  H12  C22  C21  121.67  3.000
 6EY  C23  C22  C21  119.81  3.000
 6EY  H13  C23  C24  119.42  3.000
 6EY  H13  C23  C22  119.34  3.000
 6EY  C24  C23  C22  121.24  3.000
 6EY  H14  C24  C25  119.96  3.000
 6EY  H14  C24  C23  120.89  3.000
 6EY  C25  C24  C23  119.15  3.000
 6EY  C27  C25  O26  122.43  3.000
 6EY  O26  C25  C24  117.73  3.000
 6EY  C27  C25  C24  119.84  3.000
 6EY  H15  O26  C25  110.56  3.000
 6EY  H16  C27  C25  118.55  3.000
 6EY  H16  C27  C21  120.60  3.000
 6EY  C25  C27  C21  120.84  3.000
 6EY  H7   O1   C2   110.22  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
 6EY  CONST_01  C9   C10  C11  C6      0.00   0.0  0
 6EY  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 6EY  CONST_03  C8   C9   C10  C11     0.00   0.0  0
 6EY  CONST_04  C8   C7   C6   C11     0.00   0.0  0
 6EY  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 6EY  CONST_06  C10  C11  C6   C7      0.00   0.0  0
 6EY  CONST_07  C19  S18  C17  C16     0.00   0.0  0
 6EY  CONST_08  S18  C19  C20  C16     0.00   0.0  0
 6EY  CONST_09  C20  C19  S18  C17     0.00   0.0  0
 6EY  CONST_10  C19  C20  C16  C17     0.00   0.0  0
 6EY  CONST_11  C20  C16  C17  S18     0.00   0.0  0
 6EY  CONST_12  C24  C23  C22  C21     0.00   0.0  0
 6EY  CONST_13  C24  C25  C27  C21     0.00   0.0  0
 6EY  CONST_14  C25  C27  C21  C22     0.00   0.0  0
 6EY  CONST_15  C25  C24  C23  C22     0.00   0.0  0
 6EY  CONST_16  C27  C21  C22  C23     0.00   0.0  0
 6EY  CONST_17  C27  C25  C24  C23     0.00   0.0  0
 6EY  CONST_18  S18  C17  C16  C15   180.00   0.0  0
 6EY  CONST_19  C19  C20  C16  C15   180.00   0.0  0
 6EY  CONST_20  C23  C22  C21  C15   180.00   0.0  0
 6EY  CONST_21  C25  C27  C21  C15   180.00   0.0  0
 6EY  CONST_23  CL   C11  C6   C7    180.00   0.0  0
 6EY  CONST_24  S5   C6   C7   C8    180.00   0.0  0
 6EY  CONST_25  CL   C11  C10  C9    180.00   0.0  0
 6EY  CONST_26  S5   C6   C11  C10   180.00   0.0  0
 6EY  CONST_27  O26  C25  C27  C21   180.00   0.0  0
 6EY  CONST_28  O26  C25  C24  C23   180.00   0.0  0
 6EY  CONST_30  H4   C10  C11  C6    180.00   0.0  0
 6EY  CONST_31  H2   C8   C7   C6    180.00   0.0  0
 6EY  CONST_32  H3   C9   C10  C11   180.00   0.0  0
 6EY  CONST_33  H1   C7   C6   C11   180.00   0.0  0
 6EY  CONST_34  H9   C17  C16  C15     0.00   0.0  0
 6EY  CONST_35  H11  C20  C16  C15     0.00   0.0  0
 6EY  CONST_36  H12  C22  C21  C15     0.00   0.0  0
 6EY  CONST_37  H16  C27  C21  C15     0.00   0.0  0
 6EY  CONST_38  H10  C19  C20  C16   180.00   0.0  0
 6EY  CONST_39  H13  C23  C22  C21   180.00   0.0  0
 6EY  CONST_40  H14  C24  C23  C22   180.00   0.0  0
 6EY  CONST_41  H8   N14  C13  C4    180.00   0.0  0
 6EY  Var_01    C15  C3   C2   C4    -30.79  30.0  1
 6EY  Var_02    C3   C2   C4   C13    -2.64  30.0  1
 6EY  Var_03    N14  C13  C4   C2     11.11  30.0  1
 6EY  Var_04    C11  C6   S5   C4   -175.28  30.0  2
 6EY  Var_05    C2   C4   S5   C6    -95.15  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
 6EY  chir_01  C15  C16  N14  C21  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
 6EY  plan-1  C15  0.020
 6EY  plan-1  C16  0.020
 6EY  plan-1  C17  0.020
 6EY  plan-1  S18  0.020
 6EY  plan-1  C19  0.020
 6EY  plan-1  C20  0.020
 6EY  plan-1  H9   0.020
 6EY  plan-1  H10  0.020
 6EY  plan-1  H11  0.020
 6EY  plan-2  C6   0.020
 6EY  plan-2  C11  0.020
 6EY  plan-2  C7   0.020
 6EY  plan-2  C8   0.020
 6EY  plan-2  C9   0.020
 6EY  plan-2  C10  0.020
 6EY  plan-2  S5   0.020
 6EY  plan-2  CL   0.020
 6EY  plan-2  H1   0.020
 6EY  plan-2  H2   0.020
 6EY  plan-2  H3   0.020
 6EY  plan-2  H4   0.020
 6EY  plan-3  C15  0.020
 6EY  plan-3  C21  0.020
 6EY  plan-3  C22  0.020
 6EY  plan-3  C23  0.020
 6EY  plan-3  C24  0.020
 6EY  plan-3  C25  0.020
 6EY  plan-3  O26  0.020
 6EY  plan-3  C27  0.020
 6EY  plan-3  H12  0.020
 6EY  plan-3  H13  0.020
 6EY  plan-3  H14  0.020
 6EY  plan-3  H16  0.020
 6EY  plan-4  C4   0.020
 6EY  plan-4  C13  0.020
 6EY  plan-4  N14  0.020
 6EY  plan-4  C15  0.020
 6EY  plan-4  O28  0.020
 6EY  plan-4  H8   0.020

