# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 01:19:12 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: 2-cyclobutyl-7-(5-fluoranylpyridin-3-yl)-5,7-diazaspiro[3.4]octane-6,8-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cncc(c1)N2C(=O)N[C@@]3(C[C@H](C3)C4CCC4)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
 U9H  U9H  "2-cyclobutyl-7-(5-fluoropyridin-3-yl)-5,7-diazaspiro[3.4]octane-6,8-dione"
  ligand  37  21  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U9H
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
 U9H  C4   C  C     0  -0.228  -3.5216   0.7421  12.4908
 U9H  C14  C  CR6   0   0.438  -0.4427  -2.2472  19.2337
 U9H  C5   C  C     0  -0.254  -3.0943  -0.1283  11.3324
 U9H  C6   C  C     0  -0.436  -4.2744  -0.5708  10.4371
 U9H  C11  C  CR6   0   0.265  -0.8774  -1.0391  17.2572
 U9H  C7   C  C     0  -0.449  -3.9404   0.5893   9.4778
 U9H  C8   C  C     0  -0.436  -2.5508   0.6878  10.1380
 U9H  C9   C  C     0  -0.446  -2.3736   1.3053  13.3545
 U9H  C10  C  CR5   0   0.559  -1.9388  -0.5631  15.0770
 U9H  C12  C  CR16  0  -0.076   0.4555  -1.2338  16.9106
 U9H  C13  C  CR16  0  -0.199   0.8667  -2.4156  18.8211
 U9H  N1   N  NR15  0  -0.706  -3.1708   1.2262  15.7791
 U9H  N2   N  NR5   0  -0.688  -1.7298  -0.3086  16.4124
 U9H  C3   C  C     0  -0.444  -4.0777  -0.0026  13.7243
 U9H  N3   N  N     0  -0.380   1.2964  -1.9159  17.6715
 U9H  C1   C  CR5   0   0.694  -2.4850   0.8007  16.8502
 U9H  C2   C  C     0   0.083  -2.8876   0.5002  14.5755
 U9H  O2   O  O     0  -0.408  -1.4514  -1.4630  14.4419
 U9H  C15  C  CR16  0  -0.314  -1.3491  -1.5659  18.4505
 U9H  H1   H  H     0   0.245  -4.1958   1.5264  12.1364
 U9H  H2   H  H     0   0.222  -2.4458  -0.9312  11.6959
 U9H  H3   H  H     0   0.226  -5.2669  -0.5817  10.8928
 U9H  H4   H  H     0   0.229  -4.0970  -1.5443   9.9784
 U9H  H5   H  H     0   0.225  -4.5535   1.4709   9.6679
 U9H  H6   H  H     0   0.228  -3.9717   0.3783   8.4088
 U9H  H7   H  H     0   0.229  -1.7925   0.1389   9.5784
 U9H  H8   H  H     0   0.226  -2.1605   1.6847  10.3546
 U9H  H9   H  H     0   0.257  -1.3660   1.0469  13.0238
 U9H  H10  H  H     0   0.266  -2.4132   2.3807  13.5253
 U9H  H11  H  HCR6  0   0.285   0.8511  -0.8177  15.9917
 U9H  H12  H  HCR6  0   0.290   1.5760  -2.9596  19.4351
 U9H  H13  H  HNR5  0   0.416  -3.7553   2.0472  15.8110
 U9H  H14  H  H     0   0.265  -5.0332   0.3695  14.0922
 U9H  H15  H  H     0   0.256  -4.1459  -1.0875  13.6288
 U9H  H16  H  HCR6  0   0.312  -2.3797  -1.4560  18.7602
 U9H  O1   O  O     0  -0.457  -2.4755   1.2336  17.9774
 U9H  F1   F  F     0  -0.296  -0.8343  -2.7563  20.4045

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
 U9H  C7   C8   single    1.542  0.020  1.542
 U9H  C7   C6   single    1.542  0.020  1.542
 U9H  C8   C5   single    1.545  0.020  1.545
 U9H  C6   C5   single    1.546  0.020  1.546
 U9H  C5   C4   single    1.511  0.020  1.511
 U9H  C4   C9   single    1.543  0.020  1.543
 U9H  C4   C3   single    1.544  0.020  1.544
 U9H  C9   C2   single    1.550  0.020  1.550
 U9H  C3   C2   single    1.547  0.020  1.547
 U9H  C2   C10  single    1.511  0.020  1.511
 U9H  C2   N1   single    1.434  0.020  1.434
 U9H  O2   C10  double    1.204  0.020  1.204
 U9H  C10  N2   single    1.375  0.020  1.375
 U9H  N1   C1   single    1.341  0.020  1.341
 U9H  N2   C1   single    1.412  0.020  1.412
 U9H  N2   C11  single    1.405  0.020  1.405
 U9H  C1   O1   double    1.208  0.020  1.208
 U9H  C12  C11  aromatic  1.391  0.020  1.391
 U9H  C12  N3   aromatic  1.323  0.020  1.323
 U9H  C11  C15  aromatic  1.387  0.020  1.387
 U9H  N3   C13  aromatic  1.325  0.020  1.325
 U9H  C15  C14  aromatic  1.378  0.020  1.378
 U9H  C13  C14  aromatic  1.383  0.020  1.383
 U9H  C14  F1   single    1.335  0.020  1.335
 U9H  C4   H1   single    0.970  0.020  1.090
 U9H  C5   H2   single    0.970  0.020  1.090
 U9H  C6   H3   single    0.970  0.020  1.090
 U9H  C6   H4   single    0.970  0.020  1.090
 U9H  C7   H5   single    0.970  0.020  1.090
 U9H  C7   H6   single    0.970  0.020  1.090
 U9H  C8   H7   single    0.970  0.020  1.090
 U9H  C8   H8   single    0.970  0.020  1.090
 U9H  C9   H9   single    0.970  0.020  1.090
 U9H  C9   H10  single    0.970  0.020  1.090
 U9H  C12  H11  single    0.930  0.020  1.080
 U9H  C13  H12  single    0.930  0.020  1.080
 U9H  N1   H13  single    0.860  0.020  1.020
 U9H  C3   H14  single    0.970  0.020  1.090
 U9H  C3   H15  single    0.970  0.020  1.090
 U9H  C15  H16  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
 U9H  H1   C4   C3   112.51  3.000
 U9H  H1   C4   C9   112.23  3.000
 U9H  C3   C4   C9    89.82  3.000
 U9H  H1   C4   C5   109.83  3.000
 U9H  C3   C4   C5   115.88  3.000
 U9H  C9   C4   C5   115.41  3.000
 U9H  C15  C14  F1   119.59  3.000
 U9H  F1   C14  C13  119.52  3.000
 U9H  C15  C14  C13  120.88  3.000
 U9H  H2   C5   C8   115.84  3.000
 U9H  H2   C5   C6   115.77  3.000
 U9H  C8   C5   C6    88.40  3.000
 U9H  H2   C5   C4   109.61  3.000
 U9H  C6   C5   C4   113.14  3.000
 U9H  C8   C5   C4   112.82  3.000
 U9H  H4   C6   H3   108.32  3.000
 U9H  H4   C6   C7   112.00  3.000
 U9H  H3   C6   C7   117.64  3.000
 U9H  H4   C6   C5   112.02  3.000
 U9H  H3   C6   C5   117.06  3.000
 U9H  C7   C6   C5    88.83  3.000
 U9H  C15  C11  N2   120.56  3.000
 U9H  C15  C11  C12  119.15  3.000
 U9H  N2   C11  C12  120.28  3.000
 U9H  H6   C7   H5   108.13  3.000
 U9H  H6   C7   C8   117.27  3.000
 U9H  H5   C7   C8   112.36  3.000
 U9H  H6   C7   C6   117.28  3.000
 U9H  H5   C7   C6   112.21  3.000
 U9H  C8   C7   C6    88.68  3.000
 U9H  H8   C8   H7   108.22  3.000
 U9H  H8   C8   C7   117.74  3.000
 U9H  H7   C8   C7   112.01  3.000
 U9H  H8   C8   C5   117.03  3.000
 U9H  H7   C8   C5   112.04  3.000
 U9H  C7   C8   C5    88.86  3.000
 U9H  H10  C9   H9   108.35  3.000
 U9H  H10  C9   C2   112.15  3.000
 U9H  H9   C9   C2   114.94  3.000
 U9H  H10  C9   C4   114.89  3.000
 U9H  H9   C9   C4   115.52  3.000
 U9H  C2   C9   C4    90.26  3.000
 U9H  O2   C10  C2   127.22  3.000
 U9H  O2   C10  N2   126.07  3.000
 U9H  C2   C10  N2   106.71  3.000
 U9H  H11  C12  N3   116.97  3.000
 U9H  H11  C12  C11  120.50  3.000
 U9H  N3   C12  C11  122.53  3.000
 U9H  H12  C13  N3   117.92  3.000
 U9H  H12  C13  C14  120.75  3.000
 U9H  N3   C13  C14  121.32  3.000
 U9H  H13  N1   C2   123.60  3.000
 U9H  H13  N1   C1   121.97  3.000
 U9H  C2   N1   C1   114.12  3.000
 U9H  C1   N2   C10  111.42  3.000
 U9H  C1   N2   C11  123.14  3.000
 U9H  C10  N2   C11  125.44  3.000
 U9H  H15  C3   H14  108.32  3.000
 U9H  H15  C3   C2   114.79  3.000
 U9H  H14  C3   C2   112.20  3.000
 U9H  H15  C3   C4   115.59  3.000
 U9H  H14  C3   C4   114.89  3.000
 U9H  C2   C3   C4    90.33  3.000
 U9H  C13  N3   C12  119.15  3.000
 U9H  O1   C1   N2   124.55  3.000
 U9H  O1   C1   N1   129.48  3.000
 U9H  N2   C1   N1   105.98  3.000
 U9H  C3   C2   N1   118.33  3.000
 U9H  N1   C2   C10  101.64  3.000
 U9H  C3   C2   C10  115.91  3.000
 U9H  N1   C2   C9   117.62  3.000
 U9H  C10  C2   C9   114.75  3.000
 U9H  C3   C2   C9    89.46  3.000
 U9H  H16  C15  C11  122.12  3.000
 U9H  H16  C15  C14  120.94  3.000
 U9H  C11  C15  C14  116.94  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
 U9H  CONST_01  C12  C11  C15  C14     0.00   0.0  0
 U9H  CONST_02  C12  N3   C13  C14     0.00   0.0  0
 U9H  CONST_03  C13  N3   C12  C11     0.00   0.0  0
 U9H  CONST_04  C13  C14  C15  C11     0.00   0.0  0
 U9H  CONST_05  C15  C11  C12  N3      0.00   0.0  0
 U9H  CONST_06  C15  C14  C13  N3      0.00   0.0  0
 U9H  CONST_07  N2   C11  C15  C14   180.00   0.0  0
 U9H  CONST_08  N3   C12  C11  N2    180.00   0.0  0
 U9H  CONST_09  C2   C10  N2   C11   180.00   0.0  0
 U9H  CONST_10  N1   C1   N2   C11   180.00   0.0  0
 U9H  CONST_11  C1   N1   C2   C10     0.00   0.0  0
 U9H  CONST_12  N1   C1   N2   C10     0.00   0.0  0
 U9H  CONST_13  N2   C10  C2   N1      0.00   0.0  0
 U9H  CONST_14  C2   N1   C1   N2      0.00   0.0  0
 U9H  CONST_15  C2   C10  N2   C1      0.00   0.0  0
 U9H  CONST_16  F1   C14  C15  C11   180.00   0.0  0
 U9H  CONST_17  F1   C14  C13  N3    180.00   0.0  0
 U9H  CONST_18  O2   C10  N2   C11     0.00   0.0  0
 U9H  CONST_19  O1   C1   N2   C11     0.00   0.0  0
 U9H  CONST_20  O1   C1   N2   C10   180.00   0.0  0
 U9H  CONST_21  C2   N1   C1   O1    180.00   0.0  0
 U9H  CONST_22  O2   C10  N2   C1    180.00   0.0  0
 U9H  CONST_23  H16  C15  C11  C12   180.00   0.0  0
 U9H  CONST_24  H12  C13  N3   C12   180.00   0.0  0
 U9H  CONST_25  H11  C12  N3   C13   180.00   0.0  0
 U9H  CONST_26  H16  C15  C14  C13   180.00   0.0  0
 U9H  CONST_27  H11  C12  C11  N2      0.00   0.0  0
 U9H  CONST_28  H16  C15  C11  N2      0.00   0.0  0
 U9H  CONST_29  H11  C12  C11  C15   180.00   0.0  0
 U9H  CONST_30  H12  C13  C14  C15   180.00   0.0  0
 U9H  CONST_31  H13  N1   C2   C10   180.00   0.0  0
 U9H  CONST_32  H13  N1   C1   N2    180.00   0.0  0
 U9H  CONST_33  H13  N1   C1   O1      0.00   0.0  0
 U9H  Var_01    C3   C2   C9   C4     -2.75  30.0  3
 U9H  Var_02    C10  C2   C9   C4    115.73  30.0  3
 U9H  Var_03    N1   C2   C9   C4   -124.79  30.0  3
 U9H  Var_04    C10  C2   C3   C4   -114.70  30.0  3
 U9H  Var_05    N1   C2   C3   C4    124.19  30.0  3
 U9H  Var_06    C6   C7   C8   C5    -17.20  30.0  1
 U9H  Var_07    N2   C10  C2   C9    124.91  30.0  1
 U9H  Var_08    C1   N1   C2   C9   -122.52  30.0  1
 U9H  Var_09    C12  C11  N2   C10    53.89  30.0  2
 U9H  Var_10    C15  C11  N2   C10  -126.62  30.0  2
 U9H  Var_11    C1   N2   C11  C12  -125.93  30.0  2
 U9H  Var_12    C3   C2   C10  N2   -132.82  30.0  1
 U9H  Var_13    C1   N1   C2   C3    131.82  30.0  1
 U9H  Var_14    C15  C11  N2   C1     53.56  30.0  2
 U9H  Var_15    O2   C10  C2   C9    -55.00  30.0  1
 U9H  Var_16    O2   C10  C2   C3     47.26  30.0  1
 U9H  Var_17    H5   C7   C8   C5     96.34  30.0  1
 U9H  Var_18    H6   C7   C8   C5   -137.46  30.0  1
 U9H  Var_19    H5   C7   C6   C5    -96.49  30.0  1
 U9H  Var_20    H6   C7   C6   C5    137.45  30.0  1
 U9H  Var_21    H7   C8   C7   C6     96.18  30.0  1
 U9H  Var_22    H8   C8   C7   C6   -137.40  30.0  1
 U9H  Var_23    H3   C6   C7   C8    137.39  30.0  1
 U9H  Var_24    H4   C6   C7   C8    -96.15  30.0  1
 U9H  Var_25    H14  C3   C2   C9   -114.44  30.0  3
 U9H  Var_26    H15  C3   C2   C9    121.33  30.0  3
 U9H  Var_27    H13  N1   C2   C9     51.22  30.0  1
 U9H  Var_28    H9   C9   C2   C10    -2.78  30.0  3
 U9H  Var_29    H10  C9   C2   C10  -127.12  30.0  3
 U9H  Var_30    H14  C3   C2   C10   128.12  30.0  3
 U9H  Var_31    H15  C3   C2   C10     3.89  30.0  3
 U9H  Var_32    H9   C9   C2   N1    116.70  30.0  3
 U9H  Var_33    H10  C9   C2   N1     -7.64  30.0  3
 U9H  Var_34    H14  C3   C2   N1      7.00  30.0  3
 U9H  Var_35    H15  C3   C2   N1   -117.23  30.0  3
 U9H  Var_36    H9   C9   C2   C3   -121.26  30.0  3
 U9H  Var_37    H10  C9   C2   C3    114.40  30.0  3
 U9H  Var_38    H13  N1   C2   C3    -54.44  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
 U9H  chir_01  C4  C5  C9  C3  positiv
 U9H  chir_02  C5  C8  C6  C4  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
 U9H  plan-1  C11  0.020
 U9H  plan-1  C10  0.020
 U9H  plan-1  N1   0.020
 U9H  plan-1  N2   0.020
 U9H  plan-1  C1   0.020
 U9H  plan-1  C2   0.020
 U9H  plan-1  O2   0.020
 U9H  plan-1  H13  0.020
 U9H  plan-1  O1   0.020
 U9H  plan-2  C14  0.020
 U9H  plan-2  C11  0.020
 U9H  plan-2  C12  0.020
 U9H  plan-2  C13  0.020
 U9H  plan-2  N2   0.020
 U9H  plan-2  N3   0.020
 U9H  plan-2  C15  0.020
 U9H  plan-2  H11  0.020
 U9H  plan-2  H12  0.020
 U9H  plan-2  H16  0.020
 U9H  plan-2  F1   0.020

