# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 21:42:13 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: (5~{S})-5-[(1~{R})-1-(4-fluoranyl-1~{H}-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC1=NC(=O)[C@@H](O1)[C@H](C)c2c[nH]c3cccc(F)c23
#
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
 JE3  JE3  "(5S)-5-[(1R)-1-(4-fluoranyl-1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4-one"
  ligand  34  20  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JE3
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
 JE3  N    N  NH1   0  -0.637  14.0519  50.9225  20.4554
 JE3  O1   O  O     0  -0.447  12.4137  49.2673  16.5459
 JE3  C10  C  CR16  0  -0.270  19.2872  50.8261  13.8069
 JE3  C11  C  CR16  0  -0.435  17.9244  50.7215  13.4802
 JE3  C12  C  CR6   0   0.469  17.0640  50.1183  14.3628
 JE3  C13  C  CR56  0  -0.215  17.5029  49.6080  15.5833
 JE3  C    C  CH3   0  -0.688  15.1940  47.5150  17.8940
 JE3  O    O  O     0  -0.455  15.0480  50.4203  18.4922
 JE3  C1   C  CH1   0  -0.364  15.4310  48.6270  16.8756
 JE3  C2   C  CR15  0  -0.123  14.6585  49.9033  17.2172
 JE3  C3   C  CR5   0   0.757  13.9385  50.4739  19.2252
 JE3  C4   C  CH3   0  -0.516  12.9196  51.0295  21.3509
 JE3  C5   C  CR5   0   0.411  13.1569  49.7009  17.4002
 JE3  C6   C  CR5   0   0.088  16.8866  48.9382  16.6926
 JE3  C7   C  CR15  0  -0.086  17.8971  48.6924  17.5790
 JE3  C8   C  CR56  0   0.381  18.8810  49.7303  15.8702
 JE3  C9   C  CR16  0  -0.310  19.7855  50.3353  14.9954
 JE3  N1   N  N     0  -0.534  12.8208  50.0799  18.6643
 JE3  N2   N  NR15  0  -0.690  19.0824  49.1620  17.0901
 JE3  H1   H  HNH1  0   0.422  14.9643  51.1960  20.7859
 JE3  H2   H  HCR6  0   0.259  19.9561  51.3038  13.1036
 JE3  H3   H  HCR6  0   0.267  17.5536  51.1112  12.5413
 JE3  H4   H  HCH3  0   0.248  14.1383  47.2510  17.9572
 JE3  H5   H  HCH3  0   0.252  15.7342  46.6167  17.5975
 JE3  H6   H  HCH3  0   0.235  15.5320  47.7881  18.8941
 JE3  H7   H  HCH1  0   0.266  15.0192  48.2961  15.9179
 JE3  H8   H  HCR5  0   0.305  14.8470  50.6752  16.4662
 JE3  H9   H  HCH3  0   0.264  13.2750  51.4213  22.2985
 JE3  H10  H  HCH3  0   0.252  12.1650  51.7073  20.9545
 JE3  H11  H  HCH3  0   0.252  12.4604  50.0576  21.5256
 JE3  H12  H  HCR5  0   0.285  17.8630  48.2079  18.5420
 JE3  H13  H  HCR6  0   0.262  20.8361  50.4164  15.2411
 JE3  H14  H  HNR5  0   0.412  19.9703  49.0832  17.5581
 JE3  F    F  F     0  -0.315  15.7585  50.0136  14.0490

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
 JE3  C11  C10  aromatic  1.405  0.020  1.405
 JE3  C11  C12  aromatic  1.372  0.020  1.372
 JE3  C10  C9   aromatic  1.379  0.020  1.379
 JE3  F    C12  single    1.347  0.020  1.347
 JE3  C12  C13  aromatic  1.394  0.020  1.394
 JE3  C9   C8   aromatic  1.396  0.020  1.396
 JE3  C13  C8   aromatic  1.413  0.020  1.413
 JE3  C13  C6   aromatic  1.435  0.020  1.435
 JE3  C8   N2   aromatic  1.361  0.020  1.361
 JE3  C6   C1   single    1.500  0.020  1.500
 JE3  C6   C7   aromatic  1.367  0.020  1.367
 JE3  C1   C    single    1.526  0.020  1.526
 JE3  C1   C2   single    1.530  0.020  1.530
 JE3  O1   C5   double    1.213  0.020  1.213
 JE3  N2   C7   aromatic  1.365  0.020  1.365
 JE3  C2   C5   single    1.526  0.020  1.526
 JE3  C2   O    single    1.430  0.020  1.430
 JE3  C5   N1   single    1.362  0.020  1.362
 JE3  O    C3   single    1.331  0.020  1.331
 JE3  N1   C3   double    1.311  0.020  1.311
 JE3  C3   N    single    1.314  0.020  1.314
 JE3  N    C4   single    1.448  0.020  1.448
 JE3  N    H1   single    0.860  0.020  1.020
 JE3  C10  H2   single    0.930  0.020  1.080
 JE3  C11  H3   single    0.930  0.020  1.080
 JE3  C    H4   single    0.970  0.020  1.090
 JE3  C    H5   single    0.970  0.020  1.090
 JE3  C    H6   single    0.970  0.020  1.090
 JE3  C1   H7   single    0.970  0.020  1.090
 JE3  C2   H8   single    0.970  0.020  1.090
 JE3  C4   H9   single    0.970  0.020  1.090
 JE3  C4   H10  single    0.970  0.020  1.090
 JE3  C4   H11  single    0.970  0.020  1.090
 JE3  C7   H12  single    0.930  0.020  1.080
 JE3  C9   H13  single    0.930  0.020  1.080
 JE3  N2   H14  single    0.860  0.020  1.020

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
 JE3  H1   N    C4   119.02  3.000
 JE3  H1   N    C3   118.52  3.000
 JE3  C4   N    C3   122.46  3.000
 JE3  H2   C10  C9   119.61  3.000
 JE3  H2   C10  C11  118.77  3.000
 JE3  C9   C10  C11  121.62  3.000
 JE3  H3   C11  C12  120.10  3.000
 JE3  H3   C11  C10  120.48  3.000
 JE3  C12  C11  C10  119.42  3.000
 JE3  F    C12  C13  118.74  3.000
 JE3  C13  C12  C11  121.78  3.000
 JE3  F    C12  C11  119.48  3.000
 JE3  C8   C13  C6   107.60  3.000
 JE3  C6   C13  C12  135.44  3.000
 JE3  C8   C13  C12  116.95  3.000
 JE3  H6   C    H5   107.60  3.000
 JE3  H6   C    H4   107.92  3.000
 JE3  H5   C    H4   107.23  3.000
 JE3  H6   C    C1   112.42  3.000
 JE3  H5   C    C1   110.01  3.000
 JE3  H4   C    C1   111.44  3.000
 JE3  C3   O    C2   106.18  3.000
 JE3  H7   C1   C6   108.75  3.000
 JE3  H7   C1   C2   104.93  3.000
 JE3  C6   C1   C2   110.12  3.000
 JE3  H7   C1   C    107.78  3.000
 JE3  C2   C1   C    112.35  3.000
 JE3  C6   C1   C    112.54  3.000
 JE3  H8   C2   C5   110.22  3.000
 JE3  H8   C2   C1   110.39  3.000
 JE3  C5   C2   C1   114.38  3.000
 JE3  H8   C2   O    108.07  3.000
 JE3  C5   C2   O    102.07  3.000
 JE3  C1   C2   O    111.29  3.000
 JE3  N1   C3   O    117.58  3.000
 JE3  N1   C3   N    125.21  3.000
 JE3  O    C3   N    117.22  3.000
 JE3  H11  C4   H10  108.77  3.000
 JE3  H11  C4   H9   108.68  3.000
 JE3  H10  C4   H9   108.67  3.000
 JE3  H11  C4   N    111.29  3.000
 JE3  H10  C4   N    111.27  3.000
 JE3  H9   C4   N    108.10  3.000
 JE3  N1   C5   C2   108.49  3.000
 JE3  N1   C5   O1   127.03  3.000
 JE3  C2   C5   O1   124.47  3.000
 JE3  C7   C6   C1   126.96  3.000
 JE3  C7   C6   C13  105.53  3.000
 JE3  C1   C6   C13  127.45  3.000
 JE3  H12  C7   N2   120.11  3.000
 JE3  H12  C7   C6   129.53  3.000
 JE3  N2   C7   C6   110.35  3.000
 JE3  N2   C8   C9   130.30  3.000
 JE3  N2   C8   C13  106.88  3.000
 JE3  C9   C8   C13  122.83  3.000
 JE3  H13  C9   C8   121.28  3.000
 JE3  H13  C9   C10  121.33  3.000
 JE3  C8   C9   C10  117.40  3.000
 JE3  C5   N1   C3   105.69  3.000
 JE3  H14  N2   C8   125.45  3.000
 JE3  H14  N2   C7   124.91  3.000
 JE3  C8   N2   C7   109.64  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
 JE3  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 JE3  CONST_02  C13  C8   C9   C10    0.00   0.0  0
 JE3  CONST_03  N2   C8   C9   C10  180.00   0.0  0
 JE3  CONST_04  C8   C9   C10  C11    0.00   0.0  0
 JE3  CONST_05  C8   C13  C12  C11    0.00   0.0  0
 JE3  CONST_06  C6   C13  C12  C11  180.00   0.0  0
 JE3  CONST_07  C9   C10  C11  C12    0.00   0.0  0
 JE3  CONST_08  C9   C8   C13  C12    0.00   0.0  0
 JE3  CONST_09  N2   C8   C13  C12  180.00   0.0  0
 JE3  CONST_10  C7   C6   C13  C12  180.00   0.0  0
 JE3  CONST_11  C7   N2   C8   C13    0.00   0.0  0
 JE3  CONST_12  N2   C7   C6   C13    0.00   0.0  0
 JE3  CONST_13  C9   C8   C13  C6   180.00   0.0  0
 JE3  CONST_14  N2   C8   C13  C6     0.00   0.0  0
 JE3  CONST_15  C8   N2   C7   C6     0.00   0.0  0
 JE3  CONST_16  C8   C13  C6   C7     0.00   0.0  0
 JE3  CONST_17  C9   C8   N2   C7   180.00   0.0  0
 JE3  CONST_18  C5   N1   C3   O      0.00   0.0  0
 JE3  CONST_19  F    C12  C11  C10  180.00   0.0  0
 JE3  CONST_20  C1   C6   C13  C12    0.00   0.0  0
 JE3  CONST_21  C8   C13  C6   C1   180.00   0.0  0
 JE3  CONST_22  N2   C7   C6   C1   180.00   0.0  0
 JE3  CONST_23  F    C12  C13  C6     0.00   0.0  0
 JE3  CONST_24  F    C12  C13  C8   180.00   0.0  0
 JE3  CONST_25  C5   N1   C3   N    180.00   0.0  0
 JE3  CONST_26  H13  C9   C10  C11  180.00   0.0  0
 JE3  CONST_27  H2   C10  C11  C12  180.00   0.0  0
 JE3  CONST_28  H3   C11  C12  C13  180.00   0.0  0
 JE3  CONST_29  H13  C9   C8   C13  180.00   0.0  0
 JE3  CONST_30  H14  N2   C8   C13  180.00   0.0  0
 JE3  CONST_31  H12  C7   C6   C13  180.00   0.0  0
 JE3  CONST_32  H14  N2   C7   C6   180.00   0.0  0
 JE3  CONST_33  H2   C10  C9   C8   180.00   0.0  0
 JE3  CONST_34  H12  C7   N2   C8   180.00   0.0  0
 JE3  CONST_35  H3   C11  C10  C9   180.00   0.0  0
 JE3  CONST_36  H14  N2   C8   C9     0.00   0.0  0
 JE3  CONST_37  H13  C9   C8   N2     0.00   0.0  0
 JE3  CONST_38  C4   N    C3   O    180.00   0.0  0
 JE3  CONST_39  N1   C3   N    C4     0.00   0.0  0
 JE3  CONST_40  H1   N    C3   O      0.00   0.0  0
 JE3  CONST_41  H1   N    C3   N1   180.00   0.0  0
 JE3  Var_01    C3   N1   C5   C2     0.07  30.0  1
 JE3  Var_02    N1   C3   O    C2    -0.29  30.0  1
 JE3  Var_03    C2   O    C3   N    179.90  30.0  1
 JE3  Var_04    C3   N1   C5   O1   179.75  30.0  1
 JE3  Var_05    H9   C4   N    C3   179.89  30.0  3
 JE3  Var_06    H10  C4   N    C3   -60.87  30.0  3
 JE3  Var_07    H11  C4   N    C3    60.62  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
 JE3  chir_01  C1  C6  C   C2  negativ
 JE3  chir_02  C2  O   C1  C5  negativ

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
 JE3  plan-1  C10  0.020
 JE3  plan-1  C11  0.020
 JE3  plan-1  C12  0.020
 JE3  plan-1  C13  0.020
 JE3  plan-1  C1   0.020
 JE3  plan-1  C6   0.020
 JE3  plan-1  C7   0.020
 JE3  plan-1  C8   0.020
 JE3  plan-1  C9   0.020
 JE3  plan-1  N2   0.020
 JE3  plan-1  H2   0.020
 JE3  plan-1  H3   0.020
 JE3  plan-1  H12  0.020
 JE3  plan-1  H13  0.020
 JE3  plan-1  H14  0.020
 JE3  plan-1  F    0.020
 JE3  plan-2  N    0.020
 JE3  plan-2  O    0.020
 JE3  plan-2  C3   0.020
 JE3  plan-2  C4   0.020
 JE3  plan-2  C5   0.020
 JE3  plan-2  N1   0.020
 JE3  plan-2  H1   0.020
 JE3  plan-3  O1   0.020
 JE3  plan-3  C2   0.020
 JE3  plan-3  C5   0.020
 JE3  plan-3  N1   0.020

