# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 18:52:52 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: ~{N}-[[(5~{S})-3-(3-fluoranyl-4-thiomorpholin-4-yl-phenyl)-2-oxidanylidene-1,3-oxazolidin-5-yl]methyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NC[C@H]1CN(C(=O)O1)c2ccc(N3CCSCC3)c(F)c2
#
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
 9EN  9EN  ~{N}-[[(5~{S})-3-(3-fluoranyl-4-thiomorpholin-4-yl-phenyl)-2-oxidanylidene-1,3-oxazolidin-5-yl]methyl]ethanamide  ligand  44  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9EN
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
 9EN  C13  C  CR16  0  -0.476  -0.3251   0.9840   0.4649
 9EN  C15  C  CR6   0   0.131  -2.4545  -0.0252  -0.1876
 9EN  C17  C  CR16  0  -0.336  -0.3799  -0.6518  -1.2886
 9EN  C20  C  CH2   0  -0.564  -6.0691  -0.0609  -1.0357
 9EN  C22  C  CH2   0  -0.570  -5.6686  -0.3727   1.6280
 9EN  C01  C  CH3   0  -0.776   8.1625  -0.0593   0.6383
 9EN  C02  C  C     0   0.524   6.9456  -0.7275   0.0518
 9EN  O03  O  O     0  -0.504   7.0244  -1.5196  -0.8777
 9EN  C05  C  CH2   0  -0.312   4.5153  -0.9631   0.1997
 9EN  C06  C  CR15  0  -0.023   3.9309  -0.2481  -1.0101
 9EN  C07  C  CH2   0  -0.328   2.5124  -0.7111  -1.3279
 9EN  N08  N  NR5   0  -0.618   1.7378   0.3102  -0.6496
 9EN  C09  C  CR5   0   0.703   2.4984   1.4188  -0.4207
 9EN  O10  O  O     0  -0.469   2.1478   2.5007  -0.0242
 9EN  O11  O  O     0  -0.464   3.7741   1.1470  -0.7192
 9EN  C12  C  CR6   0   0.381   0.3491   0.2296  -0.4969
 9EN  C14  C  CR6   0   0.540  -1.6896   0.8535   0.5803
 9EN  C16  C  CR16  0  -0.304  -1.7515  -0.7798  -1.1221
 9EN  N18  N  NT    0  -0.490  -3.8440  -0.0850  -0.0029
 9EN  C19  C  CH2   0  -0.289  -4.6167  -0.4817  -1.1672
 9EN  S21  S  S2    0  -0.035  -6.8823  -0.8581   0.3734
 9EN  C23  C  CH2   0  -0.284  -4.2582  -0.7563   1.2263
 9EN  F24  F  F     0  -0.312  -2.3151   1.6144   1.4925
 9EN  H1   H  HCR6  0   0.291   0.1891   1.6755   1.1154
 9EN  H2   H  HCR6  0   0.281   0.1073  -1.2563  -2.0416
 9EN  H3   H  HCH2  0   0.266  -6.1446   1.0237  -0.9374
 9EN  H4   H  HCH2  0   0.283  -6.6205  -0.3598  -1.9274
 9EN  H5   H  HCH2  0   0.266  -5.7333   0.7023   1.8058
 9EN  H6   H  HCH2  0   0.283  -5.9461  -0.8864   2.5487
 9EN  H7   H  HCH3  0   0.266   8.7330   0.4204  -0.1560
 9EN  H8   H  HCH3  0   0.250   7.9309   0.6851   1.3977
 9EN  H9   H  HCH3  0   0.269   8.8051  -0.8173   1.0873
 9EN  H10  H  HNH1  0   0.407   5.7587   0.2745   1.3662
 9EN  H11  H  HCH2  0   0.269   4.6386  -2.0171  -0.0540
 9EN  H12  H  HCH2  0   0.271   3.8159  -0.9146   1.0366
 9EN  H13  H  HCR5  0   0.286   4.5970  -0.3361  -1.8668
 9EN  H14  H  HCH2  0   0.282   2.3142  -0.7210  -2.4024
 9EN  H15  H  HCH2  0   0.284   2.3002  -1.7032  -0.9274
 9EN  H16  H  HCR6  0   0.279  -2.2798  -1.4870  -1.7483
 9EN  H17  H  HCH2  0   0.218  -4.5745  -1.5652  -1.3494
 9EN  H18  H  HCH2  0   0.261  -4.1979   0.0153  -2.0450
 9EN  H19  H  HCH2  0   0.262  -3.5847  -0.4735   2.0350
 9EN  H20  H  HCH2  0   0.224  -4.1894  -1.8485   1.1182
 9EN  N04  N  NH1   0  -0.623   5.7726  -0.4106   0.6302

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
 9EN  S21  C22  single    1.812  0.020  1.812
 9EN  S21  C20  single    1.812  0.020  1.812
 9EN  C22  C23  single    1.516  0.020  1.516
 9EN  C23  N18  single    1.461  0.020  1.461
 9EN  F24  C14  single    1.342  0.020  1.342
 9EN  C20  C19  single    1.518  0.020  1.518
 9EN  C19  N18  single    1.453  0.020  1.453
 9EN  N18  C15  single    1.403  0.020  1.403
 9EN  C14  C15  aromatic  1.395  0.020  1.395
 9EN  C14  C13  aromatic  1.376  0.020  1.376
 9EN  C15  C16  aromatic  1.392  0.020  1.392
 9EN  O10  C09  double    1.204  0.020  1.204
 9EN  C13  C12  aromatic  1.396  0.020  1.396
 9EN  C16  C17  aromatic  1.388  0.020  1.388
 9EN  C09  N08  single    1.364  0.020  1.364
 9EN  C09  O11  single    1.338  0.020  1.338
 9EN  C12  C17  aromatic  1.391  0.020  1.391
 9EN  C12  N08  single    1.399  0.020  1.399
 9EN  N08  C07  single    1.450  0.020  1.450
 9EN  O11  C06  single    1.434  0.020  1.434
 9EN  C07  C06  single    1.526  0.020  1.526
 9EN  C06  C05  single    1.522  0.020  1.522
 9EN  N04  C05  single    1.439  0.020  1.439
 9EN  N04  C02  single    1.346  0.020  1.346
 9EN  C02  C01  single    1.507  0.020  1.507
 9EN  C02  O03  double    1.224  0.020  1.224
 9EN  C13  H1   single    0.930  0.020  1.080
 9EN  C17  H2   single    0.930  0.020  1.080
 9EN  C20  H3   single    0.970  0.020  1.090
 9EN  C20  H4   single    0.970  0.020  1.090
 9EN  C22  H5   single    0.970  0.020  1.090
 9EN  C22  H6   single    0.970  0.020  1.090
 9EN  C01  H7   single    0.970  0.020  1.090
 9EN  C01  H8   single    0.970  0.020  1.090
 9EN  C01  H9   single    0.970  0.020  1.090
 9EN  N04  H10  single    0.860  0.020  1.020
 9EN  C05  H11  single    0.970  0.020  1.090
 9EN  C05  H12  single    0.970  0.020  1.090
 9EN  C06  H13  single    0.970  0.020  1.090
 9EN  C07  H14  single    0.970  0.020  1.090
 9EN  C07  H15  single    0.970  0.020  1.090
 9EN  C16  H16  single    0.930  0.020  1.080
 9EN  C19  H17  single    0.970  0.020  1.090
 9EN  C19  H18  single    0.970  0.020  1.090
 9EN  C23  H19  single    0.970  0.020  1.090
 9EN  C23  H20  single    0.970  0.020  1.090

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
 9EN  H1   C13  C14  118.86  3.000
 9EN  H1   C13  C12  122.08  3.000
 9EN  C14  C13  C12  119.05  3.000
 9EN  N18  C15  C16  124.44  3.000
 9EN  C16  C15  C14  115.73  3.000
 9EN  N18  C15  C14  119.82  3.000
 9EN  H2   C17  C16  118.50  3.000
 9EN  H2   C17  C12  120.95  3.000
 9EN  C16  C17  C12  120.54  3.000
 9EN  H4   C20  H3   108.13  3.000
 9EN  H4   C20  S21  106.76  3.000
 9EN  H3   C20  S21  109.64  3.000
 9EN  H4   C20  C19  109.71  3.000
 9EN  H3   C20  C19  110.45  3.000
 9EN  S21  C20  C19  112.02  3.000
 9EN  H6   C22  H5   108.15  3.000
 9EN  H6   C22  C23  109.96  3.000
 9EN  H5   C22  C23  110.33  3.000
 9EN  H6   C22  S21  106.74  3.000
 9EN  H5   C22  S21  109.69  3.000
 9EN  C23  C22  S21  111.84  3.000
 9EN  H9   C01  H8   108.27  3.000
 9EN  H9   C01  H7   107.33  3.000
 9EN  H8   C01  H7   108.60  3.000
 9EN  H9   C01  C02  109.14  3.000
 9EN  H8   C01  C02  113.76  3.000
 9EN  H7   C01  C02  109.54  3.000
 9EN  N04  C02  O03  122.34  3.000
 9EN  O03  C02  C01  122.05  3.000
 9EN  N04  C02  C01  115.60  3.000
 9EN  H12  C05  H11  107.07  3.000
 9EN  H12  C05  C06  110.03  3.000
 9EN  H11  C05  C06  108.20  3.000
 9EN  H12  C05  N04  108.26  3.000
 9EN  H11  C05  N04  109.98  3.000
 9EN  C06  C05  N04  113.13  3.000
 9EN  H13  C06  O11  107.77  3.000
 9EN  H13  C06  C07  112.36  3.000
 9EN  O11  C06  C07  103.64  3.000
 9EN  H13  C06  C05  110.64  3.000
 9EN  C07  C06  C05  112.34  3.000
 9EN  O11  C06  C05  109.75  3.000
 9EN  H15  C07  H14  108.52  3.000
 9EN  H15  C07  N08  111.40  3.000
 9EN  H14  C07  N08  111.68  3.000
 9EN  H15  C07  C06  112.36  3.000
 9EN  H14  C07  C06  112.10  3.000
 9EN  N08  C07  C06  100.69  3.000
 9EN  C12  N08  C09  125.59  3.000
 9EN  C12  N08  C07  122.72  3.000
 9EN  C09  N08  C07  110.68  3.000
 9EN  O11  C09  O10  122.24  3.000
 9EN  O11  C09  N08  109.22  3.000
 9EN  O10  C09  N08  128.54  3.000
 9EN  C09  O11  C06  110.32  3.000
 9EN  N08  C12  C17  119.64  3.000
 9EN  N08  C12  C13  121.55  3.000
 9EN  C17  C12  C13  118.78  3.000
 9EN  F24  C14  C15  118.39  3.000
 9EN  C15  C14  C13  123.87  3.000
 9EN  F24  C14  C13  117.74  3.000
 9EN  H16  C16  C17  118.25  3.000
 9EN  H16  C16  C15  119.75  3.000
 9EN  C17  C16  C15  122.00  3.000
 9EN  C23  N18  C19  113.47  3.000
 9EN  C19  N18  C15  115.65  3.000
 9EN  C23  N18  C15  114.28  3.000
 9EN  H18  C19  H17  107.48  3.000
 9EN  H18  C19  N18  108.42  3.000
 9EN  H17  C19  N18  112.43  3.000
 9EN  H18  C19  C20  108.08  3.000
 9EN  H17  C19  C20  108.92  3.000
 9EN  N18  C19  C20  111.34  3.000
 9EN  C22  S21  C20   96.89  3.000
 9EN  H20  C23  H19  106.98  3.000
 9EN  H20  C23  N18  110.86  3.000
 9EN  H19  C23  N18  109.27  3.000
 9EN  H20  C23  C22  109.61  3.000
 9EN  H19  C23  C22  108.22  3.000
 9EN  N18  C23  C22  111.75  3.000
 9EN  H10  N04  C05  117.93  3.000
 9EN  H10  N04  C02  119.15  3.000
 9EN  C05  N04  C02  122.86  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
 9EN  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 9EN  CONST_02  C16  C17  C12  C13     0.00   0.0  0
 9EN  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 9EN  CONST_04  C12  C17  C16  C15     0.00   0.0  0
 9EN  CONST_05  C14  C15  C16  C17     0.00   0.0  0
 9EN  CONST_06  C14  C13  C12  C17     0.00   0.0  0
 9EN  CONST_07  N18  C15  C14  C13   180.00   0.0  0
 9EN  CONST_08  N18  C15  C16  C17   180.00   0.0  0
 9EN  CONST_09  C14  C13  C12  N08   180.00   0.0  0
 9EN  CONST_10  C16  C17  C12  N08   180.00   0.0  0
 9EN  CONST_11  F24  C14  C13  C12   180.00   0.0  0
 9EN  CONST_12  F24  C14  C15  C16   180.00   0.0  0
 9EN  CONST_13  F24  C14  C15  N18     0.00   0.0  0
 9EN  CONST_14  H2   C17  C12  C13   180.00   0.0  0
 9EN  CONST_15  H1   C13  C14  C15   180.00   0.0  0
 9EN  CONST_16  H16  C16  C17  C12   180.00   0.0  0
 9EN  CONST_17  C05  N04  C02  C01   180.00   0.0  0
 9EN  CONST_18  C05  N04  C02  O03     0.00   0.0  0
 9EN  CONST_19  H10  N04  C02  C01     0.00   0.0  0
 9EN  Var_01    C09  N08  C12  C13   -31.62  30.0  2
 9EN  Var_02    C22  C23  N18  C15   159.53  30.0  1
 9EN  Var_03    C20  C19  N18  C15  -160.15  30.0  1
 9EN  Var_04    C23  C22  S21  C20   -52.81  30.0  1
 9EN  Var_05    C19  C20  S21  C22    53.17  30.0  1
 9EN  Var_06    N08  C09  O11  C06    -7.31  30.0  1
 9EN  Var_07    O11  C09  N08  C07    -8.89  30.0  1
 9EN  Var_08    S21  C22  C23  N18    61.79  30.0  1
 9EN  Var_09    S21  C20  C19  N18   -62.34  30.0  1
 9EN  Var_10    C06  C05  N04  C02   -81.85  30.0  3
 9EN  Var_11    H7   C01  C02  O03    53.07  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
 9EN  chir_01  C06  O11  C07  C05  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
 9EN  plan-1  C13  0.020
 9EN  plan-1  C15  0.020
 9EN  plan-1  C17  0.020
 9EN  plan-1  N08  0.020
 9EN  plan-1  C12  0.020
 9EN  plan-1  C14  0.020
 9EN  plan-1  C16  0.020
 9EN  plan-1  N18  0.020
 9EN  plan-1  F24  0.020
 9EN  plan-1  H1   0.020
 9EN  plan-1  H2   0.020
 9EN  plan-1  H16  0.020
 9EN  plan-2  C01  0.020
 9EN  plan-2  C02  0.020
 9EN  plan-2  O03  0.020
 9EN  plan-2  C05  0.020
 9EN  plan-2  H10  0.020
 9EN  plan-2  N04  0.020
 9EN  plan-3  C07  0.020
 9EN  plan-3  N08  0.020
 9EN  plan-3  C09  0.020
 9EN  plan-3  C12  0.020
 9EN  plan-4  N08  0.020
 9EN  plan-4  C09  0.020
 9EN  plan-4  O10  0.020
 9EN  plan-4  O11  0.020

