# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 19:56:53 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (6S)-6-cyclopentyl-6-{2-[3-fluoro-4-(1-methylethoxy)phenyl]ethyl}-4-hydroxy-5,6-dihydro-2H-pyran-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Oc1ccc(CC[C@]2(CC(=CC(=O)O2)O)C3CCCC3)cc1F
#
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
 PFI  PFI  (6S)-6-cyclopentyl-6-{2-[3-fluoro-4-(1-methylethoxy)phenyl]ethyl}-4-hydroxy-5,6-dihydro-2H-pyran-2-one  ligand  53  26  .  2022-07-22  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_PFI
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
 PFI  F26   F  F     0  -0.315   3.9548  -1.5490  -1.7950
 PFI  C23   C  CR6   0   0.462   3.3335  -1.1246  -0.6819
 PFI  C22   C  CR6   0   0.236   4.1037  -0.4852   0.2926
 PFI  O24   O  O2    0  -0.481   5.4156  -0.3669   0.0307
 PFI  C25   C  CH1   0  -0.003   6.2433   0.4563   0.8609
 PFI  C2    C  CH3   0  -0.665   7.6731   0.0769   0.5308
 PFI  C1    C  CH3   0  -0.681   5.9712   1.9298   0.6081
 PFI  C21   C  CR16  0  -0.356   3.4442  -0.0583   1.4390
 PFI  C20   C  CR16  0  -0.319   2.0756  -0.2652   1.5869
 PFI  C19   C  CR6   0   0.129   1.3238  -0.9017   0.6107
 PFI  C18   C  CR16  0  -0.459   1.9832  -1.3358  -0.5404
 PFI  C12   C  CH2   0  -0.515  -0.1621  -1.0796   0.7552
 PFI  C11   C  CH2   0  -0.465  -0.9152  -0.0006  -0.0289
 PFI  C5    C  CT    0   0.215  -2.4405  -0.1228  -0.0248
 PFI  C6    C  CH2   0  -0.562  -2.8747  -1.3402  -0.8427
 PFI  C17   C  CH1   0  -0.252  -3.1327   1.1485  -0.5487
 PFI  C13   C  CH2   0  -0.423  -2.9576   2.4169   0.2893
 PFI  C16   C  CH2   0  -0.455  -2.7117   1.6027  -1.9525
 PFI  C15   C  CH2   0  -0.439  -3.1852   3.0672  -2.0536
 PFI  C14   C  CH2   0  -0.452  -3.5416   3.5011  -0.6167
 PFI  O4    O  O2    0  -0.475  -2.8159  -0.2930   1.3572
 PFI  C3    C  C     0   0.538  -4.0066  -0.7946   1.7058
 PFI  O10   O  O     0  -0.468  -4.3543  -0.6750   2.8607
 PFI  C8    C  C1    0  -0.579  -4.7912  -1.4796   0.6982
 PFI  C7    C  C     0   0.451  -4.2640  -1.7549  -0.5081
 PFI  O9    O  OH1   0  -0.585  -4.8751  -2.4315  -1.4696
 PFI  H25   H  HCH1  0   0.231   6.0563   0.2188   1.9139
 PFI  H21A  H  HCH3  0   0.235   8.3596   0.6489   1.1540
 PFI  H22   H  HCH3  0   0.241   7.8558  -0.9812   0.7183
 PFI  H23   H  HCH3  0   0.230   7.9069   0.2917  -0.5132
 PFI  H11   H  HCH3  0   0.243   4.9391   2.2070   0.8227
 PFI  H12   H  HCH3  0   0.240   6.6104   2.5372   1.2488
 PFI  H13   H  HCH3  0   0.233   6.1866   2.1894  -0.4296
 PFI  H21   H  HCR6  0   0.285   3.9810   0.4387   2.2352
 PFI  H20   H  HCR6  0   0.253   1.5932   0.0859   2.4906
 PFI  H18   H  HCR6  0   0.269   1.4431  -1.8394  -1.3341
 PFI  H121  H  HCH2  0   0.246  -0.4441  -2.0766   0.4075
 PFI  H122  H  HCH2  0   0.255  -0.4304  -1.0309   1.8113
 PFI  H111  H  HCH2  0   0.259  -0.6200   0.9761   0.3610
 PFI  H112  H  HCH2  0   0.249  -0.5835  -0.0234  -1.0691
 PFI  H61   H  HCH2  0   0.290  -2.7936  -1.1090  -1.9058
 PFI  H62   H  HCH2  0   0.298  -2.2159  -2.1969  -0.6678
 PFI  H17   H  HCH1  0   0.241  -4.2107   0.9453  -0.5853
 PFI  H131  H  HCH2  0   0.238  -3.4572   2.3675   1.2573
 PFI  H132  H  HCH2  0   0.222  -1.8991   2.6183   0.4766
 PFI  H161  H  HCH2  0   0.234  -1.6262   1.5546  -2.0591
 PFI  H162  H  HCH2  0   0.240  -3.1361   0.9791  -2.7407
 PFI  H151  H  HCH2  0   0.230  -4.0493   3.1578  -2.7124
 PFI  H152  H  HCH2  0   0.230  -2.4020   3.6958  -2.4785
 PFI  H141  H  HCH2  0   0.225  -4.6262   3.5346  -0.4922
 PFI  H142  H  HCH2  0   0.232  -3.1645   4.4946  -0.3720
 PFI  H8    H  H     0   0.282  -5.7845  -1.8060   0.9797
 PFI  HO9   H  HOH1  0   0.486  -5.7509  -2.7273  -1.1853

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
 PFI  F26  C23   single    1.344  0.020  1.344
 PFI  C23  C22   aromatic  1.397  0.020  1.397
 PFI  C23  C18   aromatic  1.374  0.020  1.374
 PFI  C22  O24   single    1.343  0.020  1.343
 PFI  C22  C21   aromatic  1.390  0.020  1.390
 PFI  O24  C25   single    1.432  0.020  1.432
 PFI  C25  C2    single    1.516  0.020  1.516
 PFI  C25  C1    single    1.520  0.020  1.520
 PFI  C25  H25   single    0.970  0.020  1.090
 PFI  C2   H21A  single    0.970  0.020  1.090
 PFI  C2   H22   single    0.970  0.020  1.090
 PFI  C2   H23   single    0.970  0.020  1.090
 PFI  C1   H11   single    0.970  0.020  1.090
 PFI  C1   H12   single    0.970  0.020  1.090
 PFI  C1   H13   single    0.970  0.020  1.090
 PFI  C21  C20   aromatic  1.392  0.020  1.392
 PFI  C21  H21   single    0.930  0.020  1.080
 PFI  C20  C19   aromatic  1.387  0.020  1.387
 PFI  C20  H20   single    0.930  0.020  1.080
 PFI  C19  C18   aromatic  1.396  0.020  1.396
 PFI  C19  C12   single    1.504  0.020  1.504
 PFI  C18  H18   single    0.930  0.020  1.080
 PFI  C12  C11   single    1.532  0.020  1.532
 PFI  C12  H121  single    0.970  0.020  1.090
 PFI  C12  H122  single    0.970  0.020  1.090
 PFI  C11  C5    single    1.530  0.020  1.530
 PFI  C11  H111  single    0.970  0.020  1.090
 PFI  C11  H112  single    0.970  0.020  1.090
 PFI  C5   C6    single    1.530  0.020  1.530
 PFI  C5   C17   single    1.539  0.020  1.539
 PFI  C5   O4    single    1.442  0.020  1.442
 PFI  C6   C7    single    1.488  0.020  1.488
 PFI  C6   H61   single    0.970  0.020  1.090
 PFI  C6   H62   single    0.970  0.020  1.090
 PFI  C17  C13   single    1.530  0.020  1.530
 PFI  C17  C16   single    1.534  0.020  1.534
 PFI  C17  H17   single    0.970  0.020  1.090
 PFI  C13  C14   single    1.529  0.020  1.529
 PFI  C13  H131  single    0.970  0.020  1.090
 PFI  C13  H132  single    0.970  0.020  1.090
 PFI  C16  C15   single    1.543  0.020  1.543
 PFI  C16  H161  single    0.970  0.020  1.090
 PFI  C16  H162  single    0.970  0.020  1.090
 PFI  C15  C14   single    1.543  0.020  1.543
 PFI  C15  H151  single    0.970  0.020  1.090
 PFI  C15  H152  single    0.970  0.020  1.090
 PFI  C14  H141  single    0.970  0.020  1.090
 PFI  C14  H142  single    0.970  0.020  1.090
 PFI  O4   C3    single    1.338  0.020  1.338
 PFI  C3   O10   double    1.212  0.020  1.212
 PFI  C3   C8    single    1.449  0.020  1.449
 PFI  C8   C7    double    1.345  0.020  1.345
 PFI  C8   H8    single    0.930  0.020  1.080
 PFI  C7   O9    single    1.325  0.020  1.325
 PFI  O9   HO9   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
 PFI  C18   C23  C22   122.70  3.000
 PFI  C18   C23  F26   119.42  3.000
 PFI  C22   C23  F26   117.88  3.000
 PFI  C21   C22  O24   126.68  3.000
 PFI  C21   C22  C23   117.03  3.000
 PFI  O24   C22  C23   116.28  3.000
 PFI  C25   O24  C22   120.13  3.000
 PFI  H25   C25  C1    109.85  3.000
 PFI  H25   C25  C2    108.43  3.000
 PFI  C1    C25  C2    112.05  3.000
 PFI  H25   C25  O24   109.51  3.000
 PFI  C1    C25  O24   110.94  3.000
 PFI  C2    C25  O24   105.96  3.000
 PFI  H23   C2   H22   108.64  3.000
 PFI  H23   C2   H21A  108.00  3.000
 PFI  H22   C2   H21A  107.79  3.000
 PFI  H23   C2   C25   111.17  3.000
 PFI  H22   C2   C25   111.33  3.000
 PFI  H21A  C2   C25   109.79  3.000
 PFI  H13   C1   H12   108.10  3.000
 PFI  H13   C1   H11   108.28  3.000
 PFI  H12   C1   H11   107.32  3.000
 PFI  H13   C1   C25   110.70  3.000
 PFI  H12   C1   C25   109.73  3.000
 PFI  H11   C1   C25   112.54  3.000
 PFI  H21   C21  C20   118.57  3.000
 PFI  H21   C21  C22   120.87  3.000
 PFI  C20   C21  C22   120.56  3.000
 PFI  H20   C20  C19   119.65  3.000
 PFI  H20   C20  C21   118.58  3.000
 PFI  C19   C20  C21   121.77  3.000
 PFI  C12   C19  C18   120.62  3.000
 PFI  C12   C19  C20   121.49  3.000
 PFI  C18   C19  C20   117.85  3.000
 PFI  H18   C18  C19   120.86  3.000
 PFI  H18   C18  C23   119.05  3.000
 PFI  C19   C18  C23   120.09  3.000
 PFI  H122  C12  H121  106.58  3.000
 PFI  H122  C12  C11   110.08  3.000
 PFI  H121  C12  C11   110.66  3.000
 PFI  H122  C12  C19   109.33  3.000
 PFI  H121  C12  C19   109.41  3.000
 PFI  C11   C12  C19   110.69  3.000
 PFI  H112  C11  H111  106.05  3.000
 PFI  H112  C11  C5    107.68  3.000
 PFI  H111  C11  C5    109.87  3.000
 PFI  H112  C11  C12   108.88  3.000
 PFI  H111  C11  C12   108.32  3.000
 PFI  C5    C11  C12   115.62  3.000
 PFI  O4    C5   C17   107.85  3.000
 PFI  O4    C5   C6    110.15  3.000
 PFI  C17   C5   C6    110.35  3.000
 PFI  O4    C5   C11   105.75  3.000
 PFI  C17   C5   C11   112.42  3.000
 PFI  C6    C5   C11   110.19  3.000
 PFI  H62   C6   H61   106.06  3.000
 PFI  H62   C6   C7    107.93  3.000
 PFI  H61   C6   C7    110.34  3.000
 PFI  H62   C6   C5    111.51  3.000
 PFI  H61   C6   C5    109.35  3.000
 PFI  C7    C6   C5    111.51  3.000
 PFI  H17   C17  C16   107.09  3.000
 PFI  H17   C17  C13   106.51  3.000
 PFI  C16   C17  C13   102.96  3.000
 PFI  H17   C17  C5    107.46  3.000
 PFI  C16   C17  C5    115.62  3.000
 PFI  C13   C17  C5    116.53  3.000
 PFI  H132  C13  H131  107.44  3.000
 PFI  H132  C13  C14   109.91  3.000
 PFI  H131  C13  C14   112.53  3.000
 PFI  H132  C13  C17   110.93  3.000
 PFI  H131  C13  C17   113.34  3.000
 PFI  C14   C13  C17   102.68  3.000
 PFI  H162  C16  H161  106.92  3.000
 PFI  H162  C16  C15   112.08  3.000
 PFI  H161  C16  C15   109.91  3.000
 PFI  H162  C16  C17   112.65  3.000
 PFI  H161  C16  C17   110.43  3.000
 PFI  C15   C16  C17   104.88  3.000
 PFI  H152  C15  H151  106.61  3.000
 PFI  H152  C15  C14   111.52  3.000
 PFI  H151  C15  C14   110.87  3.000
 PFI  H152  C15  C16   110.63  3.000
 PFI  H151  C15  C16   111.21  3.000
 PFI  C14   C15  C16   106.07  3.000
 PFI  H142  C14  H141  106.85  3.000
 PFI  H142  C14  C15   112.67  3.000
 PFI  H141  C14  C15   110.13  3.000
 PFI  H142  C14  C13   112.40  3.000
 PFI  H141  C14  C13   109.48  3.000
 PFI  C15   C14  C13   105.32  3.000
 PFI  C3    O4   C5    121.70  3.000
 PFI  C8    C3   O10   123.63  3.000
 PFI  C8    C3   O4    118.54  3.000
 PFI  O10   C3   O4    117.81  3.000
 PFI  H8    C8   C7    122.08  3.000
 PFI  H8    C8   C3    117.28  3.000
 PFI  C7    C8   C3    120.54  3.000
 PFI  O9    C7   C8    125.07  3.000
 PFI  O9    C7   C6    114.19  3.000
 PFI  C8    C7   C6    120.71  3.000
 PFI  HO9   O9   C7    111.13  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
 PFI  CONST_01  C20   C21  C22  C23     0.00   0.0  0
 PFI  CONST_02  C20   C19  C18  C23     0.00   0.0  0
 PFI  CONST_03  C19   C18  C23  C22     0.00   0.0  0
 PFI  CONST_04  C19   C20  C21  C22     0.00   0.0  0
 PFI  CONST_05  C18   C23  C22  C21     0.00   0.0  0
 PFI  CONST_06  C18   C19  C20  C21     0.00   0.0  0
 PFI  CONST_07  C21   C22  C23  F26   180.00   0.0  0
 PFI  CONST_08  C19   C18  C23  F26   180.00   0.0  0
 PFI  CONST_09  C12   C19  C18  C23   180.00   0.0  0
 PFI  CONST_10  C18   C23  C22  O24   180.00   0.0  0
 PFI  CONST_11  C20   C21  C22  O24   180.00   0.0  0
 PFI  CONST_12  C12   C19  C20  C21   180.00   0.0  0
 PFI  CONST_13  H21   C21  C22  C23   180.00   0.0  0
 PFI  CONST_14  H18   C18  C23  C22   180.00   0.0  0
 PFI  CONST_15  H20   C20  C21  C22   180.00   0.0  0
 PFI  Var_01    C8    C7   C6   C5    -26.08  30.0  1
 PFI  Var_02    C8    C3   O4   C5     15.39  30.0  1
 PFI  Var_03    C3    C8   C7   C6     -1.16  30.0  1
 PFI  Var_04    C15   C14  C13  C17   -34.57  30.0  1
 PFI  Var_05    C14   C15  C16  C17    13.40  30.0  1
 PFI  Var_06    C16   C15  C14  C13    13.11  30.0  1
 PFI  Var_07    C7    C8   C3   O4      8.42  30.0  1
 PFI  Var_08    C21   C22  O24  C25   -11.24  30.0  3
 PFI  Var_09    C11   C12  C19  C20    98.58  30.0  2
 PFI  Var_10    C5    C11  C12  C19   176.65  30.0  3
 PFI  Var_11    C2    C25  O24  C22   165.18  30.0  3
 PFI  Var_12    H21A  C2   C25  O24  -178.28  30.0  3
 PFI  Var_13    H11   C1   C25  O24    60.57  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
 PFI  chir_01  C5   C6   C17  O4  negativ
 PFI  chir_02  C17  C16  C13  C5  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
 PFI  plan-1  F26  0.020
 PFI  plan-1  C23  0.020
 PFI  plan-1  C22  0.020
 PFI  plan-1  O24  0.020
 PFI  plan-1  C21  0.020
 PFI  plan-1  C20  0.020
 PFI  plan-1  C19  0.020
 PFI  plan-1  C18  0.020
 PFI  plan-1  C12  0.020
 PFI  plan-1  H21  0.020
 PFI  plan-1  H20  0.020
 PFI  plan-1  H18  0.020
 PFI  plan-2  O4   0.020
 PFI  plan-2  C3   0.020
 PFI  plan-2  O10  0.020
 PFI  plan-2  C8   0.020

