# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 16:22:03 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: (5S)-5-(2,4-difluorophenyl)-5-methyl-3-(phenylamino)-1,3-oxazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(OC(=O)N(Nc2ccccc2)C1=O)c3ccc(F)cc3F
#
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
 FDN  FDN  (5S)-5-(2,4-difluorophenyl)-5-methyl-3-(phenylamino)-1,3-oxazolidine-2,4-dione  ligand  35  23  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_FDN
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
 FDN  F13  F  F     0  -0.296  -2.0697  -2.2059   0.6713
 FDN  C13  C  CR6   0   0.566  -2.7226  -1.1188   0.2477
 FDN  C12  C  CR16  0  -0.548  -3.9790  -1.3138  -0.2899
 FDN  C11  C  CR6   0   0.546  -4.6700  -0.2025  -0.7280
 FDN  F11  F  F     0  -0.303  -5.8876  -0.3719  -1.2513
 FDN  C10  C  CR16  0  -0.406  -4.1407   1.0681  -0.6395
 FDN  C9   C  CR16  0  -0.263  -2.8747   1.2209  -0.0963
 FDN  C8   C  CR6   0  -0.112  -2.1320   0.1352   0.3622
 FDN  C5   C  CR5   0   0.018  -0.7479   0.3164   0.9549
 FDN  C7   C  CH3   0  -0.643  -0.5870  -0.2268   2.3692
 FDN  O4   O  O     0  -0.457  -0.4437   1.7186   0.9967
 FDN  C3   C  CR5   0   0.722   0.6428   2.0187   0.2883
 FDN  O3   O  O     0  -0.406   1.1050   3.1118   0.1871
 FDN  N2   N  NR5   0  -0.421   1.1165   0.8489  -0.2819
 FDN  C6   C  CR5   0   0.576   0.3278  -0.2354   0.0220
 FDN  O6   O  O     0  -0.370   0.4899  -1.3556  -0.3657
 FDN  N1   N  NH1   0  -0.545   2.2094   0.8287  -1.0885
 FDN  C21  C  CR6   0   0.344   3.3532   0.1706  -0.6186
 FDN  C22  C  CR16  0  -0.307   3.6101   0.0170   0.7413
 FDN  C23  C  CR16  0  -0.248   4.7849  -0.5955   1.1554
 FDN  C24  C  CR16  0  -0.276   5.7152  -1.0516   0.2328
 FDN  C25  C  CR16  0  -0.246   5.4555  -0.8901  -1.1226
 FDN  C26  C  CR16  0  -0.331   4.2839  -0.2873  -1.5502
 FDN  H12  H  HCR6  0   0.310  -4.3987  -2.3086  -0.3632
 FDN  H10  H  HCR6  0   0.292  -4.6993   1.9279  -0.9829
 FDN  H9   H  HCR6  0   0.288  -2.4739   2.2211  -0.0282
 FDN  H71  H  HCH3  0   0.274  -1.3214   0.2400   3.0240
 FDN  H72  H  HCH3  0   0.267  -0.7256  -1.3026   2.4050
 FDN  H73  H  HCH3  0   0.259   0.4100  -0.0030   2.7506
 FDN  HN1  H  HNH1  0   0.412   1.9717   0.6620  -2.0569
 FDN  H22  H  HCR6  0   0.256   2.9104   0.3704   1.4880
 FDN  H23  H  HCR6  0   0.261   4.9706  -0.7107   2.2154
 FDN  H24  H  HCR6  0   0.255   6.6285  -1.5267   0.5640
 FDN  H25  H  HCR6  0   0.260   6.1674  -1.2409  -1.8587
 FDN  H26  H  HCR6  0   0.269   4.0878  -0.1732  -2.6097

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
 FDN  F13  C13  single    1.337  0.020  1.337
 FDN  C13  C12  aromatic  1.380  0.020  1.380
 FDN  C13  C8   aromatic  1.391  0.020  1.391
 FDN  C12  C11  aromatic  1.380  0.020  1.380
 FDN  C12  H12  single    0.930  0.020  1.080
 FDN  C11  F11  single    1.336  0.020  1.336
 FDN  C11  C10  aromatic  1.379  0.020  1.379
 FDN  C10  C9   aromatic  1.386  0.020  1.386
 FDN  C10  H10  single    0.930  0.020  1.080
 FDN  C9   C8   aromatic  1.393  0.020  1.393
 FDN  C9   H9   single    0.930  0.020  1.080
 FDN  C8   C5   single    1.516  0.020  1.516
 FDN  C5   C7   single    1.524  0.020  1.524
 FDN  C5   O4   single    1.435  0.020  1.435
 FDN  C5   C6   single    1.527  0.020  1.527
 FDN  C7   H71  single    0.970  0.020  1.090
 FDN  C7   H72  single    0.970  0.020  1.090
 FDN  C7   H73  single    0.970  0.020  1.090
 FDN  O4   C3   single    1.331  0.020  1.331
 FDN  C3   O3   double    1.191  0.020  1.191
 FDN  C3   N2   single    1.385  0.020  1.385
 FDN  N2   C6   single    1.375  0.020  1.375
 FDN  N2   N1   single    1.358  0.020  1.358
 FDN  C6   O6   double    1.196  0.020  1.196
 FDN  N1   C21  single    1.401  0.020  1.401
 FDN  N1   HN1  single    0.890  0.020  1.040
 FDN  C21  C22  aromatic  1.392  0.020  1.392
 FDN  C21  C26  aromatic  1.394  0.020  1.394
 FDN  C22  C23  aromatic  1.388  0.020  1.388
 FDN  C22  H22  single    0.930  0.020  1.080
 FDN  C23  C24  aromatic  1.387  0.020  1.387
 FDN  C23  H23  single    0.930  0.020  1.080
 FDN  C24  C25  aromatic  1.390  0.020  1.390
 FDN  C24  H24  single    0.930  0.020  1.080
 FDN  C25  C26  aromatic  1.385  0.020  1.385
 FDN  C25  H25  single    0.930  0.020  1.080
 FDN  C26  H26  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
 FDN  C8   C13  C12  123.09  3.000
 FDN  C8   C13  F13  119.98  3.000
 FDN  C12  C13  F13  116.94  3.000
 FDN  H12  C12  C11  121.64  3.000
 FDN  H12  C12  C13  120.61  3.000
 FDN  C11  C12  C13  117.75  3.000
 FDN  C10  C11  F11  119.45  3.000
 FDN  C10  C11  C12  121.96  3.000
 FDN  F11  C11  C12  118.59  3.000
 FDN  H10  C10  C9   120.58  3.000
 FDN  H10  C10  C11  120.92  3.000
 FDN  C9   C10  C11  118.50  3.000
 FDN  H9   C9   C8   120.22  3.000
 FDN  H9   C9   C10  117.77  3.000
 FDN  C8   C9   C10  122.01  3.000
 FDN  C5   C8   C9   121.48  3.000
 FDN  C5   C8   C13  121.83  3.000
 FDN  C9   C8   C13  116.69  3.000
 FDN  C6   C5   O4   102.79  3.000
 FDN  C6   C5   C7   111.34  3.000
 FDN  O4   C5   C7   107.39  3.000
 FDN  C6   C5   C8   111.16  3.000
 FDN  O4   C5   C8   108.75  3.000
 FDN  C7   C5   C8   114.63  3.000
 FDN  H73  C7   H72  107.98  3.000
 FDN  H73  C7   H71  108.56  3.000
 FDN  H72  C7   H71  108.59  3.000
 FDN  H73  C7   C5   110.37  3.000
 FDN  H72  C7   C5   111.75  3.000
 FDN  H71  C7   C5   109.52  3.000
 FDN  C3   O4   C5   112.19  3.000
 FDN  N2   C3   O3   127.41  3.000
 FDN  N2   C3   O4   107.93  3.000
 FDN  O3   C3   O4   124.67  3.000
 FDN  N1   N2   C6   125.53  3.000
 FDN  N1   N2   C3   122.16  3.000
 FDN  C6   N2   C3   112.27  3.000
 FDN  O6   C6   N2   126.09  3.000
 FDN  O6   C6   C5   129.17  3.000
 FDN  N2   C6   C5   104.73  3.000
 FDN  HN1  N1   C21  115.84  3.000
 FDN  HN1  N1   N2   112.46  3.000
 FDN  C21  N1   N2   117.69  3.000
 FDN  C26  C21  C22  119.55  3.000
 FDN  C26  C21  N1   118.37  3.000
 FDN  C22  C21  N1   122.01  3.000
 FDN  H22  C22  C23  119.03  3.000
 FDN  H22  C22  C21  121.22  3.000
 FDN  C23  C22  C21  119.75  3.000
 FDN  H23  C23  C24  120.09  3.000
 FDN  H23  C23  C22  118.97  3.000
 FDN  C24  C23  C22  120.94  3.000
 FDN  H24  C24  C25  120.51  3.000
 FDN  H24  C24  C23  120.47  3.000
 FDN  C25  C24  C23  119.03  3.000
 FDN  H25  C25  C26  119.17  3.000
 FDN  H25  C25  C24  120.18  3.000
 FDN  C26  C25  C24  120.65  3.000
 FDN  H26  C26  C25  120.05  3.000
 FDN  H26  C26  C21  119.87  3.000
 FDN  C25  C26  C21  120.08  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
 FDN  CONST_01  C10  C11  C12  C13    0.00   0.0  0
 FDN  CONST_02  C10  C9   C8   C13    0.00   0.0  0
 FDN  CONST_03  C9   C8   C13  C12    0.00   0.0  0
 FDN  CONST_04  C9   C10  C11  C12    0.00   0.0  0
 FDN  CONST_05  C8   C13  C12  C11    0.00   0.0  0
 FDN  CONST_06  C8   C9   C10  C11    0.00   0.0  0
 FDN  CONST_07  C24  C23  C22  C21    0.00   0.0  0
 FDN  CONST_08  C24  C25  C26  C21    0.00   0.0  0
 FDN  CONST_09  C25  C26  C21  C22    0.00   0.0  0
 FDN  CONST_10  C25  C24  C23  C22    0.00   0.0  0
 FDN  CONST_11  C26  C21  C22  C23    0.00   0.0  0
 FDN  CONST_12  C26  C25  C24  C23    0.00   0.0  0
 FDN  CONST_13  C5   C8   C13  C12  180.00   0.0  0
 FDN  CONST_14  C5   C8   C9   C10  180.00   0.0  0
 FDN  CONST_15  C3   N2   C6   C5     0.00   0.0  0
 FDN  CONST_16  C11  C12  C13  F13  180.00   0.0  0
 FDN  CONST_17  C9   C8   C13  F13  180.00   0.0  0
 FDN  CONST_18  C5   C8   C13  F13    0.00   0.0  0
 FDN  CONST_19  F11  C11  C12  C13  180.00   0.0  0
 FDN  CONST_20  C9   C10  C11  F11  180.00   0.0  0
 FDN  CONST_21  C23  C22  C21  N1   180.00   0.0  0
 FDN  CONST_22  C25  C26  C21  N1   180.00   0.0  0
 FDN  CONST_27  N1   N2   C6   C5   180.00   0.0  0
 FDN  CONST_28  O6   C6   N2   C3   180.00   0.0  0
 FDN  CONST_29  H9   C9   C8   C13  180.00   0.0  0
 FDN  CONST_30  H10  C10  C11  C12  180.00   0.0  0
 FDN  CONST_31  H12  C12  C11  C10  180.00   0.0  0
 FDN  CONST_32  H23  C23  C22  C21  180.00   0.0  0
 FDN  CONST_33  H25  C25  C26  C21  180.00   0.0  0
 FDN  CONST_34  H26  C26  C21  C22  180.00   0.0  0
 FDN  CONST_35  H24  C24  C23  C22  180.00   0.0  0
 FDN  CONST_36  H22  C22  C23  C24  180.00   0.0  0
 FDN  CONST_37  N1   N2   C6   O6     0.00   0.0  0
 FDN  Var_01    N2   C3   O4   C5     0.85  30.0  1
 FDN  Var_02    C6   N2   C3   O4     1.32  30.0  1

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
 FDN  chir_01  C5  C8  O4  C6  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
 FDN  plan-1  F13  0.020
 FDN  plan-1  C13  0.020
 FDN  plan-1  C12  0.020
 FDN  plan-1  C11  0.020
 FDN  plan-1  F11  0.020
 FDN  plan-1  C10  0.020
 FDN  plan-1  C9   0.020
 FDN  plan-1  C8   0.020
 FDN  plan-1  C5   0.020
 FDN  plan-1  H12  0.020
 FDN  plan-1  H10  0.020
 FDN  plan-1  H9   0.020
 FDN  plan-2  N1   0.020
 FDN  plan-2  C21  0.020
 FDN  plan-2  C22  0.020
 FDN  plan-2  C23  0.020
 FDN  plan-2  C24  0.020
 FDN  plan-2  C25  0.020
 FDN  plan-2  C26  0.020
 FDN  plan-2  H22  0.020
 FDN  plan-2  H23  0.020
 FDN  plan-2  H24  0.020
 FDN  plan-2  H25  0.020
 FDN  plan-2  H26  0.020
 FDN  plan-3  N2   0.020
 FDN  plan-3  N1   0.020
 FDN  plan-3  C21  0.020
 FDN  plan-3  HN1  0.020
 FDN  plan-4  C5   0.020
 FDN  plan-4  C3   0.020
 FDN  plan-4  N2   0.020
 FDN  plan-4  C6   0.020
 FDN  plan-4  O6   0.020
 FDN  plan-4  N1   0.020
 FDN  plan-5  O4   0.020
 FDN  plan-5  C3   0.020
 FDN  plan-5  O3   0.020
 FDN  plan-5  N2   0.020

