# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:22:40 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (2~{S})-4-fluoranyl-2-(1~{H}-imidazol-5-yl)-1-propan-2-yl-2,3-dihydroindole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)N1[C@@H](Cc2c(F)cccc12)c3[nH]cnc3
#
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
 E39  E39  (2~{S})-4-fluoranyl-2-(1~{H}-imidazol-5-yl)-1-propan-2-yl-2,3-dihydroindole  ligand  34  18  .  2022-07-24  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_E39
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
 E39  C4   C  CH3   0  -0.650   1.2615  -3.2075   0.0078
 E39  C3   C  CH3   0  -0.697  -1.1962  -3.3570   0.3749
 E39  C2   C  CH1   0  -0.090  -0.0934  -2.6144  -0.3590
 E39  C1   C  CR16  0  -0.443  -3.1268   1.5737   0.6564
 E39  C10  C  CR56  0  -0.199  -1.2008   0.7831  -0.5596
 E39  C11  C  CR15  0   0.077   3.8363   1.1947   0.1606
 E39  C12  C  CR56  0   0.411  -1.1673  -0.3784   0.2208
 E39  C13  C  CR16  0  -0.323  -2.1070  -0.5572   1.2357
 E39  C14  C  CR16  0  -0.254  -3.0784   0.4196   1.4272
 E39  C5   C  CR15  0  -0.218   0.7857  -0.3894  -1.0119
 E39  C6   C  CH2   0  -0.471  -0.1046   0.7421  -1.5761
 E39  C7   C  CR5   0   0.346   1.9478   0.1478  -0.2398
 E39  C8   C  CR15  0  -0.248   2.2420   0.1369   1.0950
 E39  C9   C  CR6   0   0.489  -2.1678   1.7289  -0.3319
 E39  F1   F  F     0  -0.314  -2.1860   2.8332  -1.1007
 E39  N1   N  NR5   0  -0.523  -0.0770  -1.1675  -0.1193
 E39  N2   N  NR15  0  -0.614   2.9811   0.8310  -0.8183
 E39  N3   N  N     0  -0.446   3.4204   0.7924   1.3326
 E39  H1   H  HCH3  0   0.229   1.2845  -4.2699  -0.2375
 E39  H2   H  HCH3  0   0.235   2.0816  -2.7277  -0.5264
 E39  H3   H  HCH3  0   0.223   1.4476  -3.0977   1.0772
 E39  H4   H  HCH3  0   0.228  -1.0823  -3.2878   1.4574
 E39  H5   H  HCH3  0   0.244  -2.1925  -3.0117   0.1041
 E39  H6   H  HCH3  0   0.249  -1.1322  -4.4119   0.1080
 E39  H7   H  HCH1  0   0.221  -0.2577  -2.7779  -1.4344
 E39  H8   H  HCR6  0   0.268  -3.8764   2.3351   0.8253
 E39  H10  H  HCR6  0   0.261  -2.0816  -1.4170   1.8872
 E39  H11  H  HCR6  0   0.261  -3.8074   0.2859   2.2158
 E39  H12  H  HCR5  0   0.275   1.1486  -1.0207  -1.8290
 E39  H13  H  HCH2  0   0.270  -0.4936   0.4851  -2.5650
 E39  H14  H  HCH2  0   0.266   0.4385   1.6819  -1.6737
 E39  H15  H  HCR5  0   0.246   1.6655  -0.3125   1.8880
 E39  H16  H  HNR5  0   0.417   3.0985   1.0222  -1.8011
 E39  H9   H  HCR5  0   0.274   4.7420   1.7456  -0.0419

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
 E39  F1   C9   single    1.346  0.020  1.346
 E39  C9   C1   aromatic  1.386  0.020  1.386
 E39  C9   C10  aromatic  1.372  0.020  1.372
 E39  C6   C10  single    1.496  0.020  1.496
 E39  C6   C5   single    1.546  0.020  1.546
 E39  C1   C14  aromatic  1.389  0.020  1.389
 E39  C10  C12  aromatic  1.400  0.020  1.400
 E39  N3   C8   aromatic  1.369  0.020  1.369
 E39  N3   C11  aromatic  1.307  0.020  1.307
 E39  C8   C7   aromatic  1.367  0.020  1.367
 E39  C11  N2   aromatic  1.350  0.020  1.350
 E39  C7   N2   aromatic  1.367  0.020  1.367
 E39  C7   C5   single    1.495  0.020  1.495
 E39  C5   N1   single    1.465  0.020  1.465
 E39  C14  C13  aromatic  1.391  0.020  1.391
 E39  C12  C13  aromatic  1.395  0.020  1.395
 E39  C12  N1   single    1.388  0.020  1.388
 E39  N1   C2   single    1.467  0.020  1.467
 E39  C2   C3   single    1.519  0.020  1.519
 E39  C2   C4   single    1.524  0.020  1.524
 E39  C4   H1   single    0.970  0.020  1.090
 E39  C4   H2   single    0.970  0.020  1.090
 E39  C4   H3   single    0.970  0.020  1.090
 E39  C3   H4   single    0.970  0.020  1.090
 E39  C3   H5   single    0.970  0.020  1.090
 E39  C3   H6   single    0.970  0.020  1.090
 E39  C2   H7   single    0.970  0.020  1.090
 E39  C1   H8   single    0.930  0.020  1.080
 E39  C11  H9   single    0.930  0.020  1.080
 E39  C13  H10  single    0.930  0.020  1.080
 E39  C14  H11  single    0.930  0.020  1.080
 E39  C5   H12  single    0.970  0.020  1.090
 E39  C6   H13  single    0.970  0.020  1.090
 E39  C6   H14  single    0.970  0.020  1.090
 E39  C8   H15  single    0.930  0.020  1.080
 E39  N2   H16  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
 E39  H3   C4   H2   107.92  3.000
 E39  H3   C4   H1   108.36  3.000
 E39  H2   C4   H1   107.62  3.000
 E39  H3   C4   C2   110.39  3.000
 E39  H2   C4   C2   112.31  3.000
 E39  H1   C4   C2   110.11  3.000
 E39  H6   C3   H5   107.45  3.000
 E39  H6   C3   H4   107.36  3.000
 E39  H5   C3   H4   108.80  3.000
 E39  H6   C3   C2   108.19  3.000
 E39  H5   C3   C2   112.91  3.000
 E39  H4   C3   C2   111.89  3.000
 E39  H7   C2   N1   107.94  3.000
 E39  H7   C2   C3   106.94  3.000
 E39  N1   C2   C3   114.30  3.000
 E39  H7   C2   C4   108.07  3.000
 E39  C3   C2   C4   109.81  3.000
 E39  N1   C2   C4   109.55  3.000
 E39  H8   C1   C9   120.80  3.000
 E39  H8   C1   C14  121.50  3.000
 E39  C9   C1   C14  117.70  3.000
 E39  C9   C10  C6   130.42  3.000
 E39  C6   C10  C12  109.80  3.000
 E39  C9   C10  C12  119.77  3.000
 E39  H9   C11  N3   126.33  3.000
 E39  H9   C11  N2   122.22  3.000
 E39  N3   C11  N2   111.45  3.000
 E39  N1   C12  C13  129.39  3.000
 E39  N1   C12  C10  110.73  3.000
 E39  C13  C12  C10  119.73  3.000
 E39  H10  C13  C14  119.53  3.000
 E39  H10  C13  C12  121.71  3.000
 E39  C14  C13  C12  118.73  3.000
 E39  H11  C14  C13  118.95  3.000
 E39  H11  C14  C1   118.93  3.000
 E39  C13  C14  C1   122.11  3.000
 E39  H12  C5   N1   110.11  3.000
 E39  H12  C5   C7   109.57  3.000
 E39  N1   C5   C7   109.50  3.000
 E39  H12  C5   C6   109.91  3.000
 E39  N1   C5   C6   105.78  3.000
 E39  C7   C5   C6   111.90  3.000
 E39  H14  C6   H13  107.40  3.000
 E39  H14  C6   C5   112.13  3.000
 E39  H13  C6   C5   111.27  3.000
 E39  H14  C6   C10  113.73  3.000
 E39  H13  C6   C10  111.13  3.000
 E39  C5   C6   C10  101.19  3.000
 E39  N2   C7   C8   104.74  3.000
 E39  N2   C7   C5   123.27  3.000
 E39  C8   C7   C5   131.97  3.000
 E39  H15  C8   N3   122.14  3.000
 E39  H15  C8   C7   127.32  3.000
 E39  N3   C8   C7   110.54  3.000
 E39  F1   C9   C10  118.72  3.000
 E39  C10  C9   C1   121.94  3.000
 E39  F1   C9   C1   119.34  3.000
 E39  C5   N1   C12  108.05  3.000
 E39  C12  N1   C2   126.30  3.000
 E39  C5   N1   C2   115.52  3.000
 E39  H16  N2   C7   126.53  3.000
 E39  H16  N2   C11  125.61  3.000
 E39  C7   N2   C11  107.86  3.000
 E39  C8   N3   C11  105.41  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
 E39  CONST_01  C12  C10  C9   C1      0.00   0.0  0
 E39  CONST_02  C12  C13  C14  C1      0.00   0.0  0
 E39  CONST_03  C14  C1   C9   C10     0.00   0.0  0
 E39  CONST_04  C14  C13  C12  C10     0.00   0.0  0
 E39  CONST_05  C7   C8   N3   C11     0.00   0.0  0
 E39  CONST_06  C8   C7   N2   C11     0.00   0.0  0
 E39  CONST_07  C9   C1   C14  C13     0.00   0.0  0
 E39  CONST_08  C9   C10  C12  C13     0.00   0.0  0
 E39  CONST_09  N3   C11  N2   C7      0.00   0.0  0
 E39  CONST_10  N2   C11  N3   C8      0.00   0.0  0
 E39  CONST_11  N3   C8   C7   N2      0.00   0.0  0
 E39  CONST_12  C5   C7   N2   C11   180.00   0.0  0
 E39  CONST_13  N3   C8   C7   C5    180.00   0.0  0
 E39  CONST_14  F1   C9   C10  C12   180.00   0.0  0
 E39  CONST_15  F1   C9   C1   C14   180.00   0.0  0
 E39  CONST_16  F1   C9   C10  C6      0.00   0.0  0
 E39  CONST_17  H10  C13  C14  C1    180.00   0.0  0
 E39  CONST_18  H8   C1   C9   C10   180.00   0.0  0
 E39  CONST_19  H15  C8   N3   C11   180.00   0.0  0
 E39  CONST_20  H11  C14  C13  C12   180.00   0.0  0
 E39  CONST_21  H16  N2   C7   C5      0.00   0.0  0
 E39  CONST_22  H9   C11  N2   C7    180.00   0.0  0
 E39  Var_01    C5   N1   C12  C10     9.92  30.0  1
 E39  Var_02    C5   C6   C10  C12   -15.35  30.0  1
 E39  Var_03    H4   C3   C2   N1    -63.34  30.0  3
 E39  Var_04    H1   C4   C2   N1   -175.74  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
 E39  chir_01  C5  C6  C7  N1  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
 E39  plan-1  C11  0.020
 E39  plan-1  C5   0.020
 E39  plan-1  C7   0.020
 E39  plan-1  C8   0.020
 E39  plan-1  N2   0.020
 E39  plan-1  N3   0.020
 E39  plan-1  H15  0.020
 E39  plan-1  H16  0.020
 E39  plan-1  H9   0.020
 E39  plan-2  C1   0.020
 E39  plan-2  C10  0.020
 E39  plan-2  C12  0.020
 E39  plan-2  C13  0.020
 E39  plan-2  C14  0.020
 E39  plan-2  C6   0.020
 E39  plan-2  C9   0.020
 E39  plan-2  F1   0.020
 E39  plan-2  N1   0.020
 E39  plan-2  H8   0.020
 E39  plan-2  H10  0.020
 E39  plan-2  H11  0.020

