# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 12:38:47 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (6R)-3-[(2-chlorophenyl)sulfanyl]-6-{3-[(4-fluorophenyl)amino]phenyl}-4-hydroxy-6-(thiophen-3-yl)-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)(c3cscc3)c4cccc(Nc5ccc(F)cc5)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
 D0Y  D0Y  (6R)-3-[(2-chlorophenyl)sulfanyl]-6-{3-[(4-fluorophenyl)amino]phenyl}-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one  ligand  54  35  .  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_D0Y
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
 D0Y  C4    C   C     0  -0.526  -2.6073   0.3053  -0.2241
 D0Y  C6    C   CR6   0  -0.032  -4.5748  -1.5958   0.1397
 D0Y  C11   C   CR6   0  -0.061  -5.8336  -2.0616   0.5112
 D0Y  C7    C   CR16  0  -0.244  -3.5925  -2.5272  -0.1777
 D0Y  C8    C   CR16  0  -0.232  -3.8648  -3.8851  -0.1179
 D0Y  C9    C   CR16  0  -0.274  -5.1232  -4.3336   0.2578
 D0Y  C10   C   CR16  0  -0.200  -6.1142  -3.4167   0.5724
 D0Y  C13   C   C     0   0.587  -1.6702   0.1634   0.8830
 D0Y  C3    C   CH2   0  -0.583  -0.7015   0.7146  -1.7301
 D0Y  C2    C   C     0   0.527  -2.1600   0.5558  -1.4805
 D0Y  S5    S   S2    0   0.099  -4.3208   0.1592   0.0962
 D0Y  CL12  CL  CL    0  -0.114  -7.0781  -0.9216   0.9024
 D0Y  O14   O   O2    0  -0.469  -0.3791   0.4491   0.6511
 D0Y  C15   C   CT    0   0.117  -0.0022   1.2448  -0.4810
 D0Y  C16   C   CR5   0   0.185  -0.3612   2.6775  -0.1700
 D0Y  C17   C   CR15  0  -0.549  -1.0184   3.5386  -0.9961
 D0Y  S18   S   S2    0   0.236  -1.2010   5.0855  -0.2877
 D0Y  C19   C   CR15  0  -0.461  -0.3904   4.5911   1.1388
 D0Y  C20   C   CR15  0  -0.185   0.0026   3.2931   1.0654
 D0Y  C21   C   CR6   0   0.094   1.4999   1.0844  -0.6530
 D0Y  C22   C   CR16  0  -0.416   2.1506  -0.0470  -0.1872
 D0Y  C23   C   CR6   0   0.403   3.5196  -0.2398  -0.4161
 D0Y  N24   N   NH1   0  -0.805   4.0918  -1.4035   0.0579
 D0Y  C25   C   CR6   0   0.353   5.4390  -1.7168   0.1863
 D0Y  C26   C   CR16  0  -0.309   6.4083  -0.7676   0.5204
 D0Y  C27   C   CR16  0  -0.403   7.7381  -1.1337   0.6653
 D0Y  C28   C   CR6   0   0.500   8.0955  -2.4572   0.5031
 D0Y  F29   F   F     0  -0.321   9.3858  -2.8128   0.6470
 D0Y  C30   C   CR16  0  -0.398   7.1579  -3.4252   0.2023
 D0Y  C31   C   CR16  0  -0.328   5.8353  -3.0485   0.0345
 D0Y  C32   C   CR16  0  -0.341   4.2216   0.7258  -1.1424
 D0Y  C33   C   CR16  0  -0.235   3.5635   1.8581  -1.5950
 D0Y  C34   C   CR16  0  -0.311   2.2125   2.0533  -1.3546
 D0Y  O35   O   O     0  -0.423  -1.9793  -0.2353   1.9774
 D0Y  H1    H   HCR6  0   0.266  -2.6094  -2.1955  -0.4825
 D0Y  H2    H   HCR6  0   0.269  -3.0860  -4.5932  -0.3680
 D0Y  H3    H   HCR6  0   0.271  -5.3387  -5.3922   0.3064
 D0Y  H4    H   HCR6  0   0.285  -7.1004  -3.7492   0.8665
 D0Y  H5    H   HCH2  0   0.332  -0.2888  -0.2635  -1.9982
 D0Y  H6    H   HCH2  0   0.314  -0.5192   1.3694  -2.5828
 D0Y  H7    H   HOH1  0   0.487  -3.8542   0.4960  -2.3068
 D0Y  H8    H   HCR5  0   0.297  -1.4023   3.3620  -1.9892
 D0Y  H9    H   HCR5  0   0.299  -0.2444   5.2835   1.9531
 D0Y  H10   H   HCR5  0   0.272   0.5344   2.7886   1.8598
 D0Y  H11   H   HCR6  0   0.266   1.6080  -0.8055   0.3629
 D0Y  H12   H   HNH1  0   0.401   3.4503  -2.1566   0.2484
 D0Y  H13   H   HCR6  0   0.285   6.1334   0.2642   0.6910
 D0Y  H14   H   HCR6  0   0.281   8.4828  -0.3907   0.9199
 D0Y  H15   H   HCR6  0   0.280   7.4512  -4.4604   0.0853
 D0Y  H16   H   HCR6  0   0.274   5.0986  -3.8017  -0.2166
 D0Y  H17   H   HCR6  0   0.276   5.2689   0.5947  -1.3751
 D0Y  H18   H   HCR6  0   0.259   4.1189   2.5997  -2.1543
 D0Y  H19   H   HCR6  0   0.256   1.7234   2.9494  -1.7119
 D0Y  O1    O   OH1   0  -0.553  -2.9197   0.6358  -2.5446

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
 D0Y  C10   C9   aromatic  1.386  0.020  1.386
 D0Y  C10   C11  aromatic  1.385  0.020  1.385
 D0Y  C9    C8   aromatic  1.388  0.020  1.388
 D0Y  CL12  C11  single    1.733  0.020  1.733
 D0Y  C11   C6   aromatic  1.393  0.020  1.393
 D0Y  O1    C2   single    1.310  0.020  1.310
 D0Y  C8    C7   aromatic  1.386  0.020  1.386
 D0Y  C6    C7   aromatic  1.390  0.020  1.390
 D0Y  C6    S5   single    1.774  0.020  1.774
 D0Y  S5    C4   single    1.749  0.020  1.749
 D0Y  C2    C4   double    1.357  0.020  1.357
 D0Y  C2    C3   single    1.488  0.020  1.488
 D0Y  S18   C17  aromatic  1.711  0.020  1.711
 D0Y  S18   C19  aromatic  1.714  0.020  1.714
 D0Y  C4    C13  single    1.457  0.020  1.457
 D0Y  C17   C16  aromatic  1.362  0.020  1.362
 D0Y  C3    C15  single    1.527  0.020  1.527
 D0Y  C16   C15  single    1.509  0.020  1.509
 D0Y  C16   C20  aromatic  1.427  0.020  1.427
 D0Y  C19   C20  aromatic  1.358  0.020  1.358
 D0Y  C13   O35  double    1.205  0.020  1.205
 D0Y  C13   O14  single    1.342  0.020  1.342
 D0Y  C15   O14  single    1.434  0.020  1.434
 D0Y  C15   C21  single    1.520  0.020  1.520
 D0Y  F29   C28  single    1.346  0.020  1.346
 D0Y  C21   C22  aromatic  1.386  0.020  1.386
 D0Y  C21   C34  aromatic  1.392  0.020  1.392
 D0Y  C28   C27  aromatic  1.380  0.020  1.380
 D0Y  C28   C30  aromatic  1.381  0.020  1.381
 D0Y  C27   C26  aromatic  1.387  0.020  1.387
 D0Y  C22   C23  aromatic  1.401  0.020  1.401
 D0Y  C30   C31  aromatic  1.385  0.020  1.385
 D0Y  C26   C25  aromatic  1.397  0.020  1.397
 D0Y  C34   C33  aromatic  1.386  0.020  1.386
 D0Y  C25   C31  aromatic  1.398  0.020  1.398
 D0Y  C25   N24  single    1.389  0.020  1.389
 D0Y  C23   N24  single    1.381  0.020  1.381
 D0Y  C23   C32  aromatic  1.397  0.020  1.397
 D0Y  C33   C32  aromatic  1.386  0.020  1.386
 D0Y  C7    H1   single    0.930  0.020  1.080
 D0Y  C8    H2   single    0.930  0.020  1.080
 D0Y  C9    H3   single    0.930  0.020  1.080
 D0Y  C10   H4   single    0.930  0.020  1.080
 D0Y  C3    H5   single    0.970  0.020  1.090
 D0Y  C3    H6   single    0.970  0.020  1.090
 D0Y  O1    H7   single    0.850  0.020  0.980
 D0Y  C17   H8   single    0.930  0.020  1.080
 D0Y  C19   H9   single    0.930  0.020  1.080
 D0Y  C20   H10  single    0.930  0.020  1.080
 D0Y  C22   H11  single    0.930  0.020  1.080
 D0Y  N24   H12  single    0.860  0.020  1.020
 D0Y  C26   H13  single    0.930  0.020  1.080
 D0Y  C27   H14  single    0.930  0.020  1.080
 D0Y  C30   H15  single    0.930  0.020  1.080
 D0Y  C31   H16  single    0.930  0.020  1.080
 D0Y  C32   H17  single    0.930  0.020  1.080
 D0Y  C33   H18  single    0.930  0.020  1.080
 D0Y  C34   H19  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
 D0Y  S5    C4   C2   120.52  3.000
 D0Y  C2    C4   C13  120.62  3.000
 D0Y  S5    C4   C13  118.86  3.000
 D0Y  S5    C6   C7   123.78  3.000
 D0Y  S5    C6   C11  117.83  3.000
 D0Y  C7    C6   C11  118.39  3.000
 D0Y  CL12  C11  C10  119.22  3.000
 D0Y  CL12  C11  C6   119.30  3.000
 D0Y  C10   C11  C6   121.47  3.000
 D0Y  H1    C7   C8   119.41  3.000
 D0Y  H1    C7   C6   120.08  3.000
 D0Y  C8    C7   C6   120.51  3.000
 D0Y  H2    C8   C9   120.25  3.000
 D0Y  H2    C8   C7   119.33  3.000
 D0Y  C9    C8   C7   120.42  3.000
 D0Y  H3    C9   C10  119.66  3.000
 D0Y  H3    C9   C8   120.61  3.000
 D0Y  C10   C9   C8   119.73  3.000
 D0Y  H4    C10  C9   120.68  3.000
 D0Y  H4    C10  C11  119.84  3.000
 D0Y  C9    C10  C11  119.48  3.000
 D0Y  O35   C13  O14  118.29  3.000
 D0Y  O14   C13  C4   117.80  3.000
 D0Y  O35   C13  C4   123.86  3.000
 D0Y  H6    C3   H5   106.38  3.000
 D0Y  H6    C3   C15  110.77  3.000
 D0Y  H5    C3   C15  109.76  3.000
 D0Y  H6    C3   C2   111.04  3.000
 D0Y  H5    C3   C2   108.37  3.000
 D0Y  C15   C3   C2   110.41  3.000
 D0Y  O1    C2   C3   115.19  3.000
 D0Y  C3    C2   C4   119.87  3.000
 D0Y  O1    C2   C4   124.91  3.000
 D0Y  C6    S5   C4   103.14  3.000
 D0Y  C15   O14  C13  120.47  3.000
 D0Y  C21   C15  C16  111.00  3.000
 D0Y  C21   C15  O14  106.88  3.000
 D0Y  C16   C15  O14  107.55  3.000
 D0Y  C21   C15  C3   108.87  3.000
 D0Y  O14   C15  C3   109.44  3.000
 D0Y  C16   C15  C3   112.92  3.000
 D0Y  C20   C16  C17  112.04  3.000
 D0Y  C20   C16  C15  121.81  3.000
 D0Y  C17   C16  C15  126.14  3.000
 D0Y  H8    C17  S18  119.40  3.000
 D0Y  H8    C17  C16  128.77  3.000
 D0Y  S18   C17  C16  111.83  3.000
 D0Y  C19   S18  C17   91.91  3.000
 D0Y  H9    C19  C20  127.95  3.000
 D0Y  H9    C19  S18  120.48  3.000
 D0Y  C20   C19  S18  111.57  3.000
 D0Y  H10   C20  C19  123.28  3.000
 D0Y  H10   C20  C16  124.07  3.000
 D0Y  C19   C20  C16  112.65  3.000
 D0Y  C34   C21  C22  119.81  3.000
 D0Y  C34   C21  C15  119.29  3.000
 D0Y  C22   C21  C15  120.80  3.000
 D0Y  H11   C22  C23  118.44  3.000
 D0Y  H11   C22  C21  120.49  3.000
 D0Y  C23   C22  C21  121.07  3.000
 D0Y  C32   C23  N24  123.55  3.000
 D0Y  C32   C23  C22  118.73  3.000
 D0Y  N24   C23  C22  117.69  3.000
 D0Y  H12   N24  C25  115.56  3.000
 D0Y  H12   N24  C23  115.53  3.000
 D0Y  C25   N24  C23  128.59  3.000
 D0Y  C31   C25  C26  118.46  3.000
 D0Y  C31   C25  N24  118.68  3.000
 D0Y  C26   C25  N24  122.80  3.000
 D0Y  H13   C26  C27  118.63  3.000
 D0Y  H13   C26  C25  120.64  3.000
 D0Y  C27   C26  C25  120.72  3.000
 D0Y  H14   C27  C28  120.51  3.000
 D0Y  H14   C27  C26  120.20  3.000
 D0Y  C28   C27  C26  119.28  3.000
 D0Y  C30   C28  F29  119.27  3.000
 D0Y  C30   C28  C27  121.46  3.000
 D0Y  F29   C28  C27  119.27  3.000
 D0Y  H15   C30  C31  120.38  3.000
 D0Y  H15   C30  C28  120.67  3.000
 D0Y  C31   C30  C28  118.94  3.000
 D0Y  H16   C31  C30  119.23  3.000
 D0Y  H16   C31  C25  119.66  3.000
 D0Y  C30   C31  C25  121.11  3.000
 D0Y  H17   C32  C33  119.28  3.000
 D0Y  H17   C32  C23  120.99  3.000
 D0Y  C33   C32  C23  119.72  3.000
 D0Y  H18   C33  C34  119.57  3.000
 D0Y  H18   C33  C32  119.01  3.000
 D0Y  C34   C33  C32  121.42  3.000
 D0Y  H19   C34  C33  120.01  3.000
 D0Y  H19   C34  C21  120.76  3.000
 D0Y  C33   C34  C21  119.23  3.000
 D0Y  H7    O1   C2   110.44  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
 D0Y  CONST_01  C9    C10  C11  C6      0.00   0.0  0
 D0Y  CONST_02  C9    C8   C7   C6      0.00   0.0  0
 D0Y  CONST_03  C8    C9   C10  C11     0.00   0.0  0
 D0Y  CONST_04  C8    C7   C6   C11     0.00   0.0  0
 D0Y  CONST_05  C10   C9   C8   C7      0.00   0.0  0
 D0Y  CONST_06  C10   C11  C6   C7      0.00   0.0  0
 D0Y  CONST_07  C19   S18  C17  C16     0.00   0.0  0
 D0Y  CONST_08  S18   C19  C20  C16     0.00   0.0  0
 D0Y  CONST_09  C20   C19  S18  C17     0.00   0.0  0
 D0Y  CONST_10  C19   C20  C16  C17     0.00   0.0  0
 D0Y  CONST_11  C20   C16  C17  S18     0.00   0.0  0
 D0Y  CONST_12  C32   C23  C22  C21     0.00   0.0  0
 D0Y  CONST_13  C32   C33  C34  C21     0.00   0.0  0
 D0Y  CONST_14  C33   C34  C21  C22     0.00   0.0  0
 D0Y  CONST_15  C33   C32  C23  C22     0.00   0.0  0
 D0Y  CONST_16  C34   C21  C22  C23     0.00   0.0  0
 D0Y  CONST_17  C34   C33  C32  C23     0.00   0.0  0
 D0Y  CONST_18  C28   C27  C26  C25     0.00   0.0  0
 D0Y  CONST_19  C28   C30  C31  C25     0.00   0.0  0
 D0Y  CONST_20  C30   C28  C27  C26     0.00   0.0  0
 D0Y  CONST_21  C30   C31  C25  C26     0.00   0.0  0
 D0Y  CONST_22  C31   C30  C28  C27     0.00   0.0  0
 D0Y  CONST_23  C31   C25  C26  C27     0.00   0.0  0
 D0Y  CONST_24  S18   C17  C16  C15   180.00   0.0  0
 D0Y  CONST_25  C19   C20  C16  C15   180.00   0.0  0
 D0Y  CONST_26  C23   C22  C21  C15   180.00   0.0  0
 D0Y  CONST_27  C33   C34  C21  C15   180.00   0.0  0
 D0Y  CONST_28  CL12  C11  C6   C7    180.00   0.0  0
 D0Y  CONST_29  S5    C6   C7   C8    180.00   0.0  0
 D0Y  CONST_30  CL12  C11  C10  C9    180.00   0.0  0
 D0Y  CONST_31  S5    C6   C11  C10   180.00   0.0  0
 D0Y  CONST_32  N24   C23  C22  C21   180.00   0.0  0
 D0Y  CONST_33  C27   C26  C25  N24   180.00   0.0  0
 D0Y  CONST_34  C30   C31  C25  N24   180.00   0.0  0
 D0Y  CONST_35  C33   C32  C23  N24   180.00   0.0  0
 D0Y  CONST_36  F29   C28  C27  C26   180.00   0.0  0
 D0Y  CONST_37  C31   C30  C28  F29   180.00   0.0  0
 D0Y  CONST_38  H4    C10  C11  C6    180.00   0.0  0
 D0Y  CONST_39  H2    C8   C7   C6    180.00   0.0  0
 D0Y  CONST_40  H3    C9   C10  C11   180.00   0.0  0
 D0Y  CONST_41  H1    C7   C6   C11   180.00   0.0  0
 D0Y  CONST_42  H8    C17  C16  C15     0.00   0.0  0
 D0Y  CONST_43  H10   C20  C16  C15     0.00   0.0  0
 D0Y  CONST_44  H11   C22  C21  C15     0.00   0.0  0
 D0Y  CONST_45  H19   C34  C21  C15     0.00   0.0  0
 D0Y  CONST_46  H9    C19  C20  C16   180.00   0.0  0
 D0Y  CONST_47  H18   C33  C34  C21   180.00   0.0  0
 D0Y  CONST_48  H17   C32  C23  C22   180.00   0.0  0
 D0Y  CONST_49  H14   C27  C26  C25   180.00   0.0  0
 D0Y  CONST_50  H15   C30  C31  C25   180.00   0.0  0
 D0Y  CONST_51  H16   C31  C25  C26   180.00   0.0  0
 D0Y  CONST_52  H13   C26  C27  C28   180.00   0.0  0
 D0Y  Var_01    C15   C3   C2   C4    -28.21  30.0  1
 D0Y  Var_02    C3    C2   C4   C13    -1.23  30.0  1
 D0Y  Var_03    O14   C13  C4   C2      7.99  30.0  1
 D0Y  Var_04    C11   C6   S5   C4    173.72  30.0  2
 D0Y  Var_05    C2    C4   S5   C6     99.40  30.0  3
 D0Y  Var_06    C25   N24  C23  C22  -166.70  30.0  2
 D0Y  Var_07    C26   C25  N24  C23    34.59  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
 D0Y  chir_01  C15  C16  O14  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
 D0Y  plan-1  C15   0.020
 D0Y  plan-1  C16   0.020
 D0Y  plan-1  C17   0.020
 D0Y  plan-1  S18   0.020
 D0Y  plan-1  C19   0.020
 D0Y  plan-1  C20   0.020
 D0Y  plan-1  H8    0.020
 D0Y  plan-1  H9    0.020
 D0Y  plan-1  H10   0.020
 D0Y  plan-2  C6    0.020
 D0Y  plan-2  C11   0.020
 D0Y  plan-2  C7    0.020
 D0Y  plan-2  C8    0.020
 D0Y  plan-2  C9    0.020
 D0Y  plan-2  C10   0.020
 D0Y  plan-2  S5    0.020
 D0Y  plan-2  CL12  0.020
 D0Y  plan-2  H1    0.020
 D0Y  plan-2  H2    0.020
 D0Y  plan-2  H3    0.020
 D0Y  plan-2  H4    0.020
 D0Y  plan-3  C4    0.020
 D0Y  plan-3  C13   0.020
 D0Y  plan-3  O14   0.020
 D0Y  plan-3  O35   0.020
 D0Y  plan-4  C15   0.020
 D0Y  plan-4  C21   0.020
 D0Y  plan-4  C22   0.020
 D0Y  plan-4  C23   0.020
 D0Y  plan-4  N24   0.020
 D0Y  plan-4  C32   0.020
 D0Y  plan-4  C33   0.020
 D0Y  plan-4  C34   0.020
 D0Y  plan-4  H11   0.020
 D0Y  plan-4  H17   0.020
 D0Y  plan-4  H18   0.020
 D0Y  plan-4  H19   0.020
 D0Y  plan-5  N24   0.020
 D0Y  plan-5  C25   0.020
 D0Y  plan-5  C26   0.020
 D0Y  plan-5  C27   0.020
 D0Y  plan-5  C28   0.020
 D0Y  plan-5  F29   0.020
 D0Y  plan-5  C30   0.020
 D0Y  plan-5  C31   0.020
 D0Y  plan-5  H13   0.020
 D0Y  plan-5  H14   0.020
 D0Y  plan-5  H15   0.020
 D0Y  plan-5  H16   0.020

