# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:16:19 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (6R)-3-[(2-chlorophenyl)sulfanyl]-6-{6-[(4-fluorophenyl)amino]pyridin-2-yl}-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)n4
#
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
 D4A  D4A  (6R)-3-[(2-chlorophenyl)sulfanyl]-6-{6-[(4-fluorophenyl)amino]pyridin-2-yl}-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one  ligand  53  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_D4A
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
 D4A  C4    C   CR16  0  -0.288  -5.7503  -0.7337   0.2011
 D4A  C14   C   CR15  0  -0.556  -0.5179   3.9413  -1.4965
 D4A  C5    C   CR16  0  -0.294  -4.9136  -2.4276  -1.2832
 D4A  C6    C   CR16  0  -0.407  -6.9371  -1.4367   0.3392
 D4A  C11   C   CR16  0  -0.392  -2.9758  -0.1298   1.5805
 D4A  C7    C   CR16  0  -0.404  -6.1078  -3.1232  -1.1744
 D4A  C8    C   CR16  0  -0.245   4.9781  -0.3277  -0.2392
 D4A  C9    C   CR16  0  -0.200   6.6576  -2.3813   0.5839
 D4A  C10   C   CR16  0  -0.367  -1.0018   1.1859   1.9834
 D4A  C12   C   CR15  0  -0.198  -0.3581   4.3984   0.7672
 D4A  C13   C   CR15  0  -0.461  -0.8374   5.5839   0.3084
 D4A  C3    C   CR16  0  -0.141  -2.0971   0.4687   2.4564
 D4A  C1    C   CR16  0  -0.232   6.3416  -0.2533  -0.4780
 D4A  C2    C   CR16  0  -0.274   7.1842  -1.2765  -0.0674
 D4A  C15   C   CR5   0   0.200  -0.1671   3.4447  -0.2775
 D4A  C16   C   CR6   0   0.322  -4.7195  -1.2301  -0.5963
 D4A  C17   C   CR6   0   0.514  -7.0980  -2.6211  -0.3530
 D4A  C18   C   CR6   0  -0.029   4.4360  -1.4270   0.4168
 D4A  C19   C   CR6   0  -0.062   5.2942  -2.4475   0.8195
 D4A  C20   C   CR6   0   0.276  -0.8383   1.2511   0.6096
 D4A  C21   C   CR6   0   0.471  -2.7324   0.0184   0.2063
 D4A  C22   C   C     0  -0.530   2.0282  -0.0791   0.2772
 D4A  C23   C   C     0   0.532   1.4351   0.0634  -0.9364
 D4A  C24   C   C     0   0.582   2.1103   1.0486   1.1972
 D4A  C25   C   CH2   0  -0.576   0.8002   1.3586  -1.2996
 D4A  C26   C   CT    0   0.078   0.3071   2.0382  -0.0309
 D4A  N27   N   N     0  -0.467  -1.6794   0.6935  -0.2464
 D4A  N28   N   NH1   0  -0.759  -3.5205  -0.5313  -0.7660
 D4A  O30   O   O2    0  -0.463   1.3860   2.1438   0.9024
 D4A  O31   O   OH1   0  -0.552   1.3974  -0.8593  -1.8642
 D4A  F32   F   F     0  -0.317  -8.2502  -3.3008  -0.2263
 D4A  S33   S   S2    0   0.237  -1.0719   5.5565  -1.3888
 D4A  S34   S   S2    0   0.101   2.7076  -1.6142   0.7652
 D4A  CL35  CL  CL    0  -0.115   4.6403  -3.8342   1.6272
 D4A  H1    H   HCR6  0   0.287  -5.6411   0.2152   0.7092
 D4A  H2    H   HCR5  0   0.301  -0.4847   3.4487  -2.4560
 D4A  H3    H   HCR6  0   0.278  -4.1228  -2.8232  -1.9077
 D4A  H4    H   HCR6  0   0.284  -7.7323  -1.0514   0.9638
 D4A  H5    H   HCR6  0   0.284  -3.8111  -0.7049   1.9518
 D4A  H6    H   HCR6  0   0.283  -6.2543  -4.0513  -1.7109
 D4A  H8    H   HCR6  0   0.285   7.3001  -3.1887   0.9084
 D4A  H9    H   HCR6  0   0.269  -0.3193   1.6605   2.6730
 D4A  H10   H   HCR5  0   0.268  -0.1475   4.2133   1.8105
 D4A  H11   H   HCR5  0   0.299  -1.0644   6.4709   0.8792
 D4A  H12   H   HCR6  0   0.273  -2.2586   0.3705   3.5220
 D4A  H13   H   HCR6  0   0.269   6.7435   0.6116  -0.9881
 D4A  H14   H   HCR6  0   0.271   8.2482  -1.2207  -0.2524
 D4A  H15   H   HCH2  0   0.321   1.5402   1.9881  -1.8045
 D4A  H16   H   HCH2  0   0.310  -0.0216   1.1907  -1.9929
 D4A  H17   H   HNH1  0   0.397  -3.1081  -0.5405  -1.6864
 D4A  H18   H   HOH1  0   0.488   1.8473  -1.6687  -1.5619
 D4A  O29   O   O     0  -0.418   2.8138   1.0730   2.1741
 D4A  H7    H   HCR6  0   0.265   4.3366   0.4768  -0.5728

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
 D4A  F32   C17  single    1.344  0.020  1.344
 D4A  C17   C7   aromatic  1.381  0.020  1.381
 D4A  C17   C6   aromatic  1.381  0.020  1.381
 D4A  C7    C5   aromatic  1.386  0.020  1.386
 D4A  C6    C4   aromatic  1.386  0.020  1.386
 D4A  C5    C16  aromatic  1.394  0.020  1.394
 D4A  C4    C16  aromatic  1.395  0.020  1.395
 D4A  C16   N28  single    1.398  0.020  1.398
 D4A  C9    C2   aromatic  1.386  0.020  1.386
 D4A  C9    C19  aromatic  1.385  0.020  1.385
 D4A  C2    C1   aromatic  1.388  0.020  1.388
 D4A  CL35  C19  single    1.733  0.020  1.733
 D4A  O31   C23  single    1.309  0.020  1.309
 D4A  C19   C18  aromatic  1.393  0.020  1.393
 D4A  C1    C8   aromatic  1.386  0.020  1.386
 D4A  N28   C21  single    1.367  0.020  1.367
 D4A  C18   C8   aromatic  1.390  0.020  1.390
 D4A  C18   S34  single    1.773  0.020  1.773
 D4A  S34   C22  single    1.748  0.020  1.748
 D4A  C23   C22  double    1.358  0.020  1.358
 D4A  C23   C25  single    1.487  0.020  1.487
 D4A  C21   N27  aromatic  1.330  0.020  1.330
 D4A  C21   C11  aromatic  1.403  0.020  1.403
 D4A  C22   C24  single    1.458  0.020  1.458
 D4A  N27   C20  aromatic  1.323  0.020  1.323
 D4A  C25   C26  single    1.521  0.020  1.521
 D4A  C11   C3   aromatic  1.377  0.020  1.377
 D4A  C20   C26  single    1.530  0.020  1.530
 D4A  C20   C10  aromatic  1.385  0.020  1.385
 D4A  C24   O29  double    1.204  0.020  1.204
 D4A  C24   O30  single    1.346  0.020  1.346
 D4A  C26   O30  single    1.430  0.020  1.430
 D4A  C26   C15  single    1.505  0.020  1.505
 D4A  C3    C10  aromatic  1.392  0.020  1.392
 D4A  C15   C14  aromatic  1.362  0.020  1.362
 D4A  C15   C12  aromatic  1.427  0.020  1.427
 D4A  C14   S33  aromatic  1.711  0.020  1.711
 D4A  C12   C13  aromatic  1.359  0.020  1.359
 D4A  S33   C13  aromatic  1.713  0.020  1.713
 D4A  C4    H1   single    0.930  0.020  1.080
 D4A  C14   H2   single    0.930  0.020  1.080
 D4A  C5    H3   single    0.930  0.020  1.080
 D4A  C6    H4   single    0.930  0.020  1.080
 D4A  C11   H5   single    0.930  0.020  1.080
 D4A  C7    H6   single    0.930  0.020  1.080
 D4A  C8    H7   single    0.930  0.020  1.080
 D4A  C9    H8   single    0.930  0.020  1.080
 D4A  C10   H9   single    0.930  0.020  1.080
 D4A  C12   H10  single    0.930  0.020  1.080
 D4A  C13   H11  single    0.930  0.020  1.080
 D4A  C3    H12  single    0.930  0.020  1.080
 D4A  C1    H13  single    0.930  0.020  1.080
 D4A  C2    H14  single    0.930  0.020  1.080
 D4A  C25   H15  single    0.970  0.020  1.090
 D4A  C25   H16  single    0.970  0.020  1.090
 D4A  N28   H17  single    0.860  0.020  1.020
 D4A  O31   H18  single    0.850  0.020  0.980

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
 D4A  H1    C4   C16  120.40  3.000
 D4A  H1    C4   C6   118.97  3.000
 D4A  C16   C4   C6   120.62  3.000
 D4A  H2    C14  S33  119.80  3.000
 D4A  H2    C14  C15  128.41  3.000
 D4A  S33   C14  C15  111.79  3.000
 D4A  H3    C5   C16  119.76  3.000
 D4A  H3    C5   C7   119.42  3.000
 D4A  C16   C5   C7   120.82  3.000
 D4A  H4    C6   C17  120.60  3.000
 D4A  H4    C6   C4   120.41  3.000
 D4A  C17   C6   C4   118.98  3.000
 D4A  H5    C11  C21  121.80  3.000
 D4A  H5    C11  C3   120.41  3.000
 D4A  C21   C11  C3   117.78  3.000
 D4A  H6    C7   C17  120.65  3.000
 D4A  H6    C7   C5   120.53  3.000
 D4A  C17   C7   C5   118.81  3.000
 D4A  H7    C8   C18  120.16  3.000
 D4A  H7    C8   C1   119.36  3.000
 D4A  C18   C8   C1   120.48  3.000
 D4A  H8    C9   C19  119.87  3.000
 D4A  H8    C9   C2   120.67  3.000
 D4A  C19   C9   C2   119.46  3.000
 D4A  H9    C10  C20  122.55  3.000
 D4A  H9    C10  C3   120.44  3.000
 D4A  C20   C10  C3   117.01  3.000
 D4A  H10   C12  C15  124.49  3.000
 D4A  H10   C12  C13  122.99  3.000
 D4A  C15   C12  C13  112.53  3.000
 D4A  H11   C13  S33  120.56  3.000
 D4A  H11   C13  C12  127.80  3.000
 D4A  S33   C13  C12  111.64  3.000
 D4A  H12   C3   C10  119.92  3.000
 D4A  H12   C3   C11  119.44  3.000
 D4A  C10   C3   C11  120.65  3.000
 D4A  H13   C1   C2   120.24  3.000
 D4A  H13   C1   C8   119.32  3.000
 D4A  C2    C1   C8   120.44  3.000
 D4A  H14   C2   C1   120.58  3.000
 D4A  H14   C2   C9   119.68  3.000
 D4A  C1    C2   C9   119.73  3.000
 D4A  C26   C15  C12  123.15  3.000
 D4A  C12   C15  C14  112.14  3.000
 D4A  C26   C15  C14  124.65  3.000
 D4A  N28   C16  C5   119.27  3.000
 D4A  N28   C16  C4   121.70  3.000
 D4A  C5    C16  C4   118.98  3.000
 D4A  F32   C17  C7   119.14  3.000
 D4A  C7    C17  C6   121.76  3.000
 D4A  F32   C17  C6   119.10  3.000
 D4A  S34   C18  C19  117.80  3.000
 D4A  S34   C18  C8   123.80  3.000
 D4A  C19   C18  C8   118.40  3.000
 D4A  CL35  C19  C18  119.25  3.000
 D4A  C18   C19  C9   121.48  3.000
 D4A  CL35  C19  C9   119.27  3.000
 D4A  N27   C20  C26  114.94  3.000
 D4A  C26   C20  C10  121.85  3.000
 D4A  N27   C20  C10  123.15  3.000
 D4A  N28   C21  N27  114.73  3.000
 D4A  N27   C21  C11  121.61  3.000
 D4A  N28   C21  C11  123.64  3.000
 D4A  S34   C22  C24  118.77  3.000
 D4A  C24   C22  C23  120.48  3.000
 D4A  S34   C22  C23  120.75  3.000
 D4A  O31   C23  C25  115.37  3.000
 D4A  C25   C23  C22  119.73  3.000
 D4A  O31   C23  C22  124.88  3.000
 D4A  O30   C24  O29  118.41  3.000
 D4A  O30   C24  C22  117.46  3.000
 D4A  O29   C24  C22  124.10  3.000
 D4A  H16   C25  H15  107.77  3.000
 D4A  H16   C25  C26  110.82  3.000
 D4A  H15   C25  C26  110.29  3.000
 D4A  H16   C25  C23  110.09  3.000
 D4A  H15   C25  C23  108.95  3.000
 D4A  C26   C25  C23  108.89  3.000
 D4A  O30   C26  C25  109.43  3.000
 D4A  O30   C26  C20  109.24  3.000
 D4A  C25   C26  C20  111.22  3.000
 D4A  O30   C26  C15  106.00  3.000
 D4A  C20   C26  C15  108.27  3.000
 D4A  C25   C26  C15  112.52  3.000
 D4A  C21   N27  C20  119.79  3.000
 D4A  H17   N28  C21  114.64  3.000
 D4A  H17   N28  C16  117.18  3.000
 D4A  C21   N28  C16  127.52  3.000
 D4A  C26   O30  C24  119.26  3.000
 D4A  H18   O31  C23  110.63  3.000
 D4A  C13   S33  C14   91.90  3.000
 D4A  C22   S34  C18  103.37  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
 D4A  CONST_01  C7    C17  C6   C4     0.00   0.0  0
 D4A  CONST_02  C7    C5   C16  C4     0.00   0.0  0
 D4A  CONST_03  C13   C12  C15  C14    0.00   0.0  0
 D4A  CONST_04  C12   C13  S33  C14    0.00   0.0  0
 D4A  CONST_05  C6    C17  C7   C5     0.00   0.0  0
 D4A  CONST_06  C6    C4   C16  C5     0.00   0.0  0
 D4A  CONST_07  C20   N27  C21  C11    0.00   0.0  0
 D4A  CONST_08  C20   C10  C3   C11    0.00   0.0  0
 D4A  CONST_09  C9    C2   C1   C8     0.00   0.0  0
 D4A  CONST_10  C9    C19  C18  C8     0.00   0.0  0
 D4A  CONST_11  C21   N27  C20  C10    0.00   0.0  0
 D4A  CONST_12  C21   C11  C3   C10    0.00   0.0  0
 D4A  CONST_13  S33   C14  C15  C12    0.00   0.0  0
 D4A  CONST_14  C15   C14  S33  C13    0.00   0.0  0
 D4A  CONST_15  N27   C21  C11  C3     0.00   0.0  0
 D4A  CONST_16  N27   C20  C10  C3     0.00   0.0  0
 D4A  CONST_17  C19   C9   C2   C1     0.00   0.0  0
 D4A  CONST_18  C19   C18  C8   C1     0.00   0.0  0
 D4A  CONST_19  C18   C19  C9   C2     0.00   0.0  0
 D4A  CONST_20  C18   C8   C1   C2     0.00   0.0  0
 D4A  CONST_21  S33   C13  C12  C15    0.00   0.0  0
 D4A  CONST_22  C17   C7   C5   C16    0.00   0.0  0
 D4A  CONST_23  C17   C6   C4   C16    0.00   0.0  0
 D4A  CONST_24  C26   C15  C12  C13  180.00   0.0  0
 D4A  CONST_25  C26   C20  C10  C3   180.00   0.0  0
 D4A  CONST_26  C26   C20  N27  C21  180.00   0.0  0
 D4A  CONST_27  S33   C14  C15  C26  180.00   0.0  0
 D4A  CONST_28  F32   C17  C6   C4   180.00   0.0  0
 D4A  CONST_29  F32   C17  C7   C5   180.00   0.0  0
 D4A  CONST_30  N28   C16  C4   C6   180.00   0.0  0
 D4A  CONST_31  N28   C16  C5   C7   180.00   0.0  0
 D4A  CONST_32  CL35  C19  C18  C8   180.00   0.0  0
 D4A  CONST_33  S34   C18  C19  C9   180.00   0.0  0
 D4A  CONST_34  N28   C21  C11  C3   180.00   0.0  0
 D4A  CONST_35  S34   C18  C8   C1   180.00   0.0  0
 D4A  CONST_36  CL35  C19  C9   C2   180.00   0.0  0
 D4A  CONST_37  N28   C21  N27  C20  180.00   0.0  0
 D4A  CONST_38  H3    C5   C16  C4   180.00   0.0  0
 D4A  CONST_39  H10   C12  C15  C14  180.00   0.0  0
 D4A  CONST_40  H11   C13  S33  C14  180.00   0.0  0
 D4A  CONST_41  H1    C4   C16  C5   180.00   0.0  0
 D4A  CONST_42  H6    C7   C17  C6   180.00   0.0  0
 D4A  CONST_43  H9    C10  C3   C11  180.00   0.0  0
 D4A  CONST_44  H4    C6   C17  C7   180.00   0.0  0
 D4A  CONST_45  H14   C2   C1   C8   180.00   0.0  0
 D4A  CONST_46  H13   C1   C2   C9   180.00   0.0  0
 D4A  CONST_47  H5    C11  C3   C10  180.00   0.0  0
 D4A  CONST_48  H2    C14  C15  C12  180.00   0.0  0
 D4A  CONST_49  H8    C9   C2   C1   180.00   0.0  0
 D4A  CONST_50  H7    C8   C1   C2   180.00   0.0  0
 D4A  CONST_51  H12   C3   C10  C20  180.00   0.0  0
 D4A  Var_01    C26   C25  C23  C22  -29.20  30.0  1
 D4A  Var_02    O30   C24  C22  C23   11.24  30.0  1
 D4A  Var_03    C25   C23  C22  C24   -3.31  30.0  1
 D4A  Var_04    C21   N28  C16  C4    48.89  30.0  2
 D4A  Var_05    C16   N28  C21  C11    4.97  30.0  2
 D4A  Var_06    C23   C22  S34  C18   98.31  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
 D4A  chir_01  C26  C20  O30  C15  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
 D4A  plan-1  C14   0.020
 D4A  plan-1  C12   0.020
 D4A  plan-1  C13   0.020
 D4A  plan-1  C15   0.020
 D4A  plan-1  C26   0.020
 D4A  plan-1  S33   0.020
 D4A  plan-1  H2    0.020
 D4A  plan-1  H10   0.020
 D4A  plan-1  H11   0.020
 D4A  plan-2  C8    0.020
 D4A  plan-2  C9    0.020
 D4A  plan-2  C1    0.020
 D4A  plan-2  C2    0.020
 D4A  plan-2  C18   0.020
 D4A  plan-2  C19   0.020
 D4A  plan-2  S34   0.020
 D4A  plan-2  CL35  0.020
 D4A  plan-2  H8    0.020
 D4A  plan-2  H13   0.020
 D4A  plan-2  H14   0.020
 D4A  plan-2  H7    0.020
 D4A  plan-3  C4    0.020
 D4A  plan-3  C5    0.020
 D4A  plan-3  C6    0.020
 D4A  plan-3  C7    0.020
 D4A  plan-3  C16   0.020
 D4A  plan-3  C17   0.020
 D4A  plan-3  N28   0.020
 D4A  plan-3  F32   0.020
 D4A  plan-3  H1    0.020
 D4A  plan-3  H3    0.020
 D4A  plan-3  H4    0.020
 D4A  plan-3  H6    0.020
 D4A  plan-4  C11   0.020
 D4A  plan-4  C10   0.020
 D4A  plan-4  C3    0.020
 D4A  plan-4  C20   0.020
 D4A  plan-4  C21   0.020
 D4A  plan-4  C26   0.020
 D4A  plan-4  N27   0.020
 D4A  plan-4  N28   0.020
 D4A  plan-4  H5    0.020
 D4A  plan-4  H9    0.020
 D4A  plan-4  H12   0.020
 D4A  plan-5  C22   0.020
 D4A  plan-5  C24   0.020
 D4A  plan-5  O30   0.020
 D4A  plan-5  O29   0.020

