# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 19:40:03 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: (3~{S})-3'-(5-fluoranylpyridin-3-yl)spiro[1,2-dihydroindene-3,5'-imidazolidine]-2',4'-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cncc(c1)N2C(=O)N[C@]3(CCc4ccccc34)C2=O
#
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
 TU8  TU8  "(3~{S})-3'-(5-fluoranylpyridin-3-yl)spiro[1,2-dihydroindene-3,5'-imidazolidine]-2',4'-dione"
  ligand  34  22  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TU8
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
 TU8  N1   N  NR15  0  -0.688   9.3568  -0.4892  22.5749
 TU8  N3   N  N     0  -0.381   7.4925   1.1158  17.4928
 TU8  C4   C  CH2   0  -0.497  11.4314   2.1834  24.1361
 TU8  C5   C  CR56  0   0.098  12.3556   1.3553  23.2895
 TU8  C6   C  CR16  0  -0.322  13.7420   1.3503  23.2536
 TU8  C7   C  CR16  0  -0.248  14.3895   0.4862  22.3777
 TU8  C8   C  CR16  0  -0.259  13.6628  -0.3622  21.5469
 TU8  C10  C  CR56  0   0.164  11.6400   0.5052  22.4587
 TU8  C13  C  CR16  0  -0.060   8.1798   0.7837  18.5746
 TU8  C15  C  CR6   0   0.436   5.9575   2.2684  18.8752
 TU8  C1   C  CR5   0   0.692   8.4218  -0.4585  21.6097
 TU8  C11  C  CR5   0   0.568   9.5741   1.5324  21.5183
 TU8  C12  C  CR6   0   0.239   7.7950   1.1694  19.8511
 TU8  C14  C  CR16  0  -0.190   6.3966   1.8475  17.6324
 TU8  C16  C  CR16  0  -0.296   6.6532   1.9356  20.0184
 TU8  C2   C  C     0  -0.061  10.1563   0.7026  22.6574
 TU8  C3   C  CH2   0  -0.450  10.0886   1.4525  24.0060
 TU8  C9   C  CR16  0  -0.311  12.2734  -0.3568  21.5801
 TU8  N2   N  NR5   0  -0.680   8.5705   0.7834  20.9634
 TU8  O1   O  O     0  -0.452   7.5996  -1.2879  21.3072
 TU8  O2   O  O     0  -0.396   9.9219   2.6295  21.1693
 TU8  H1   H  HNR5  0   0.414   9.4315  -1.2514  23.2307
 TU8  H2   H  HCH2  0   0.260  11.7605   2.2584  25.1731
 TU8  H3   H  HCH2  0   0.260  11.3664   3.2025  23.7479
 TU8  H4   H  HCR6  0   0.252  14.3153   2.0014  23.9022
 TU8  H5   H  HCR6  0   0.257  15.4714   0.4678  22.3454
 TU8  H6   H  HCR6  0   0.257  14.1833  -1.0318  20.8747
 TU8  H7   H  HCR6  0   0.286   9.0740   0.1864  18.4357
 TU8  H8   H  HCR6  0   0.294   5.8461   2.1127  16.7365
 TU8  H9   H  HCR6  0   0.312   6.3223   2.2529  20.9993
 TU8  H10  H  HCH2  0   0.266   9.2219   2.1089  24.0808
 TU8  H11  H  HCH2  0   0.272   9.9983   0.7007  24.7927
 TU8  H12  H  HCR6  0   0.256  11.7045  -1.0203  20.9398
 TU8  F1   F  F     0  -0.295   4.8463   3.0022  18.9620

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
 TU8  N3   C14  aromatic  1.325  0.020  1.325
 TU8  N3   C13  aromatic  1.324  0.020  1.324
 TU8  C14  C15  aromatic  1.384  0.020  1.384
 TU8  C13  C12  aromatic  1.388  0.020  1.388
 TU8  C15  F1   single    1.334  0.020  1.334
 TU8  C15  C16  aromatic  1.379  0.020  1.379
 TU8  C12  C16  aromatic  1.385  0.020  1.385
 TU8  C12  N2   single    1.410  0.020  1.410
 TU8  O2   C11  double    1.203  0.020  1.203
 TU8  N2   C11  single    1.370  0.020  1.370
 TU8  N2   C1   single    1.408  0.020  1.408
 TU8  C11  C2   single    1.525  0.020  1.525
 TU8  O1   C1   double    1.206  0.020  1.206
 TU8  C1   N1   single    1.344  0.020  1.344
 TU8  C9   C8   aromatic  1.390  0.020  1.390
 TU8  C9   C10  aromatic  1.384  0.020  1.384
 TU8  C8   C7   aromatic  1.392  0.020  1.392
 TU8  C10  C2   single    1.510  0.020  1.510
 TU8  C10  C5   aromatic  1.387  0.020  1.387
 TU8  C7   C6   aromatic  1.390  0.020  1.390
 TU8  N1   C2   single    1.437  0.020  1.437
 TU8  C2   C3   single    1.545  0.020  1.545
 TU8  C5   C6   aromatic  1.387  0.020  1.387
 TU8  C5   C4   single    1.502  0.020  1.502
 TU8  C4   C3   single    1.534  0.020  1.534
 TU8  N1   H1   single    0.860  0.020  1.020
 TU8  C4   H2   single    0.970  0.020  1.090
 TU8  C4   H3   single    0.970  0.020  1.090
 TU8  C6   H4   single    0.930  0.020  1.080
 TU8  C7   H5   single    0.930  0.020  1.080
 TU8  C8   H6   single    0.930  0.020  1.080
 TU8  C13  H7   single    0.930  0.020  1.080
 TU8  C14  H8   single    0.930  0.020  1.080
 TU8  C16  H9   single    0.930  0.020  1.080
 TU8  C3   H10  single    0.970  0.020  1.090
 TU8  C3   H11  single    0.970  0.020  1.090
 TU8  C9   H12  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
 TU8  H1   N1   C2   123.25  3.000
 TU8  H1   N1   C1   122.40  3.000
 TU8  C2   N1   C1   114.15  3.000
 TU8  C14  N3   C13  118.80  3.000
 TU8  H3   C4   H2   106.96  3.000
 TU8  H3   C4   C3   111.23  3.000
 TU8  H2   C4   C3   112.18  3.000
 TU8  H3   C4   C5   110.53  3.000
 TU8  H2   C4   C5   112.84  3.000
 TU8  C3   C4   C5   103.18  3.000
 TU8  C10  C5   C6   119.86  3.000
 TU8  C6   C5   C4   129.16  3.000
 TU8  C10  C5   C4   110.97  3.000
 TU8  H4   C6   C7   120.29  3.000
 TU8  H4   C6   C5   120.76  3.000
 TU8  C7   C6   C5   118.95  3.000
 TU8  H5   C7   C8   119.57  3.000
 TU8  H5   C7   C6   119.66  3.000
 TU8  C8   C7   C6   120.77  3.000
 TU8  H6   C8   C9   119.88  3.000
 TU8  H6   C8   C7   119.78  3.000
 TU8  C9   C8   C7   120.34  3.000
 TU8  C9   C10  C2   127.92  3.000
 TU8  C2   C10  C5   110.36  3.000
 TU8  C9   C10  C5   121.71  3.000
 TU8  H7   C13  C12  119.97  3.000
 TU8  H7   C13  N3   117.49  3.000
 TU8  C12  C13  N3   122.54  3.000
 TU8  F1   C15  C16  119.93  3.000
 TU8  C16  C15  C14  120.74  3.000
 TU8  F1   C15  C14  119.33  3.000
 TU8  O1   C1   N2   124.29  3.000
 TU8  O1   C1   N1   129.67  3.000
 TU8  N2   C1   N1   106.04  3.000
 TU8  O2   C11  N2   126.38  3.000
 TU8  N2   C11  C2   106.55  3.000
 TU8  O2   C11  C2   127.07  3.000
 TU8  N2   C12  C16  120.64  3.000
 TU8  N2   C12  C13  119.81  3.000
 TU8  C16  C12  C13  119.56  3.000
 TU8  H8   C14  C15  120.43  3.000
 TU8  H8   C14  N3   117.90  3.000
 TU8  C15  C14  N3   121.67  3.000
 TU8  H9   C16  C12  121.56  3.000
 TU8  H9   C16  C15  121.74  3.000
 TU8  C12  C16  C15  116.70  3.000
 TU8  C3   C2   C11  111.80  3.000
 TU8  C3   C2   C10  102.79  3.000
 TU8  C11  C2   C10  110.37  3.000
 TU8  C3   C2   N1   115.36  3.000
 TU8  C10  C2   N1   115.50  3.000
 TU8  C11  C2   N1   101.30  3.000
 TU8  H11  C3   H10  107.42  3.000
 TU8  H11  C3   C2   107.36  3.000
 TU8  H10  C3   C2   112.78  3.000
 TU8  H11  C3   C4   109.83  3.000
 TU8  H10  C3   C4   113.78  3.000
 TU8  C2   C3   C4   105.49  3.000
 TU8  H12  C9   C10  121.07  3.000
 TU8  H12  C9   C8   120.56  3.000
 TU8  C10  C9   C8   118.36  3.000
 TU8  C12  N2   C11  124.95  3.000
 TU8  C11  N2   C1   111.95  3.000
 TU8  C12  N2   C1   123.07  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
 TU8  CONST_01  C16  C15  C14  N3      0.00   0.0  0
 TU8  CONST_02  C16  C12  C13  N3      0.00   0.0  0
 TU8  CONST_03  C8   C9   C10  C5      0.00   0.0  0
 TU8  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 TU8  CONST_05  C9   C8   C7   C6      0.00   0.0  0
 TU8  CONST_06  C9   C10  C5   C6      0.00   0.0  0
 TU8  CONST_07  C10  C9   C8   C7      0.00   0.0  0
 TU8  CONST_08  C10  C5   C6   C7      0.00   0.0  0
 TU8  CONST_09  C15  C14  N3   C13     0.00   0.0  0
 TU8  CONST_10  C15  C16  C12  C13     0.00   0.0  0
 TU8  CONST_11  C14  N3   C13  C12     0.00   0.0  0
 TU8  CONST_12  C14  C15  C16  C12     0.00   0.0  0
 TU8  CONST_13  N2   C12  C13  N3    180.00   0.0  0
 TU8  CONST_14  N2   C12  C16  C15   180.00   0.0  0
 TU8  CONST_15  C12  N2   C1   N1    180.00   0.0  0
 TU8  CONST_16  C11  N2   C1   N1      0.00   0.0  0
 TU8  CONST_17  C2   C11  N2   C1      0.00   0.0  0
 TU8  CONST_18  C2   C11  N2   C12   180.00   0.0  0
 TU8  CONST_19  N2   C1   N1   C2      0.00   0.0  0
 TU8  CONST_20  F1   C15  C14  N3    180.00   0.0  0
 TU8  CONST_21  F1   C15  C16  C12   180.00   0.0  0
 TU8  CONST_22  O2   C11  N2   C1    180.00   0.0  0
 TU8  CONST_23  O1   C1   N2   C11   180.00   0.0  0
 TU8  CONST_24  O2   C11  N2   C12     0.00   0.0  0
 TU8  CONST_25  O1   C1   N2   C12     0.00   0.0  0
 TU8  CONST_26  O1   C1   N1   C2    180.00   0.0  0
 TU8  CONST_27  H4   C6   C5   C4      0.00   0.0  0
 TU8  CONST_28  H12  C9   C10  C5    180.00   0.0  0
 TU8  CONST_29  H5   C7   C6   C5    180.00   0.0  0
 TU8  CONST_30  H6   C8   C7   C6    180.00   0.0  0
 TU8  CONST_31  H12  C9   C8   C7    180.00   0.0  0
 TU8  CONST_32  H4   C6   C7   C8    180.00   0.0  0
 TU8  CONST_33  H6   C8   C9   C10   180.00   0.0  0
 TU8  CONST_34  H4   C6   C5   C10   180.00   0.0  0
 TU8  CONST_35  H8   C14  N3   C13   180.00   0.0  0
 TU8  CONST_36  H9   C16  C12  C13   180.00   0.0  0
 TU8  CONST_37  H7   C13  N3   C14   180.00   0.0  0
 TU8  CONST_38  H9   C16  C15  C14   180.00   0.0  0
 TU8  CONST_39  H8   C14  C15  C16   180.00   0.0  0
 TU8  CONST_40  H7   C13  C12  C16   180.00   0.0  0
 TU8  CONST_41  H12  C9   C10  C2      0.00   0.0  0
 TU8  CONST_42  H5   C7   C8   C9    180.00   0.0  0
 TU8  CONST_43  H7   C13  C12  N2      0.00   0.0  0
 TU8  CONST_44  H9   C16  C12  N2      0.00   0.0  0
 TU8  CONST_45  H1   N1   C1   N2    180.00   0.0  0
 TU8  CONST_46  H1   N1   C1   O1      0.00   0.0  0
 TU8  Var_01    C2   C3   C4   C5    -25.41  30.0  1
 TU8  Var_02    C3   C4   C5   C6   -164.36  30.0  1
 TU8  Var_03    C3   C4   C5   C10    15.60  30.0  1
 TU8  Var_04    C11  N2   C12  C13    92.95  30.0  2
 TU8  Var_05    C1   N2   C12  C13   -84.88  30.0  2
 TU8  Var_06    C16  C12  N2   C1     95.36  30.0  2
 TU8  Var_07    C16  C12  N2   C11   -86.80  30.0  2
 TU8  Var_08    H10  C3   C4   C5   -149.55  30.0  1
 TU8  Var_09    H11  C3   C4   C5     90.00  30.0  1
 TU8  Var_10    H2   C4   C5   C6    -43.07  30.0  1
 TU8  Var_11    H3   C4   C5   C6     76.65  30.0  1
 TU8  Var_12    H2   C4   C5   C10   136.89  30.0  1
 TU8  Var_13    H3   C4   C5   C10  -103.39  30.0  1
 TU8  Var_14    H2   C4   C3   C2   -147.14  30.0  1
 TU8  Var_15    H3   C4   C3   C2     93.10  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
 TU8  chir_01  C2  C10  N1  C3  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
 TU8  plan-1  N3   0.020
 TU8  plan-1  C13  0.020
 TU8  plan-1  C15  0.020
 TU8  plan-1  C12  0.020
 TU8  plan-1  C14  0.020
 TU8  plan-1  C16  0.020
 TU8  plan-1  N2   0.020
 TU8  plan-1  H7   0.020
 TU8  plan-1  H8   0.020
 TU8  plan-1  H9   0.020
 TU8  plan-1  F1   0.020
 TU8  plan-2  C4   0.020
 TU8  plan-2  C5   0.020
 TU8  plan-2  C6   0.020
 TU8  plan-2  C7   0.020
 TU8  plan-2  C8   0.020
 TU8  plan-2  C10  0.020
 TU8  plan-2  C2   0.020
 TU8  plan-2  C9   0.020
 TU8  plan-2  H4   0.020
 TU8  plan-2  H5   0.020
 TU8  plan-2  H6   0.020
 TU8  plan-2  H12  0.020
 TU8  plan-3  N1   0.020
 TU8  plan-3  C1   0.020
 TU8  plan-3  C11  0.020
 TU8  plan-3  C12  0.020
 TU8  plan-3  C2   0.020
 TU8  plan-3  N2   0.020
 TU8  plan-3  O1   0.020
 TU8  plan-3  O2   0.020
 TU8  plan-3  H1   0.020

