# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 11:26:02 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 4,4,4-trifluoro-1-(3-phenyl-1-oxa-2,8-diazaspiro[4.5]dec-2-en-8-yl)butan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)CCC(=O)N1CCC2(CC1)CC(=NO2)c3ccccc3
#
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
 69Y  69Y  4,4,4-trifluoro-1-(3-phenyl-1-oxa-2,8-diazaspiro[4.5]dec-2-en-8-yl)butan-1-one  ligand  43  24  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_69Y
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
 69Y  C1   C  CR5   0   0.204   3.6207  -0.0151   0.2915
 69Y  C2   C  CR6   0   0.068   5.0247   0.3078   0.0405
 69Y  C5   C  CR16  0  -0.259   7.6956   0.9600  -0.4529
 69Y  C6   C  CR16  0  -0.285   6.0552  -0.4941   0.5415
 69Y  C11  C  C     0   0.592  -2.6131  -0.9755  -0.5376
 69Y  C12  C  CH2   0  -0.638  -3.6118  -0.0460   0.1310
 69Y  C13  C  CH2   0  -0.634  -4.9172   0.0133  -0.6488
 69Y  C14  C  CT    0   1.002  -5.9193   0.9435  -0.0245
 69Y  C15  C  CH2   0  -0.321  -0.3701  -1.9283  -0.5463
 69Y  C16  C  CH2   0  -0.427   0.7737  -1.0223  -0.9832
 69Y  O1   O  O     0  -0.501  -2.8962  -1.5493  -1.5811
 69Y  F2   F  F     0  -0.312  -7.0649   0.9763  -0.7232
 69Y  F1   F  F     0  -0.316  -6.2454   0.5892   1.2294
 69Y  F    F  F     0  -0.316  -5.4758   2.2101   0.0427
 69Y  N1   N  NT    0  -0.460  -1.4229  -1.1432   0.0772
 69Y  C10  C  CH2   0  -0.333  -0.9696  -0.4096   1.2461
 69Y  C9   C  CH2   0  -0.437   0.1605   0.5440   0.8742
 69Y  C    C  CR5   0   0.196   1.3023  -0.1757   0.1718
 69Y  C8   C  CH2   0  -0.582   2.4494   0.7363  -0.2586
 69Y  N    N  N     0  -0.117   3.2809  -0.9806   1.0502
 69Y  O    O  O     0  -0.416   1.9249  -1.0715   1.1327
 69Y  C7   C  CR16  0  -0.238   7.3772  -0.1695   0.2951
 69Y  C4   C  CR16  0  -0.236   6.6800   1.7607  -0.9537
 69Y  C3   C  CR16  0  -0.322   5.3521   1.4360  -0.7105
 69Y  H1   H  HCR6  0   0.262   8.7307   1.2115  -0.6431
 69Y  H2   H  HCR6  0   0.257   5.8181  -1.3761   1.1220
 69Y  H3   H  HCH2  0   0.290  -3.7911  -0.3853   1.1541
 69Y  H4   H  HCH2  0   0.285  -3.1743   0.9528   0.2109
 69Y  H5   H  HCH2  0   0.283  -4.7400   0.3521  -1.6704
 69Y  H6   H  HCH2  0   0.283  -5.3733  -0.9754  -0.7153
 69Y  H7   H  HCH2  0   0.269  -0.7748  -2.4656  -1.3989
 69Y  H8   H  HCH2  0   0.250  -0.0150  -2.6757   0.1686
 69Y  H9   H  HCH2  0   0.255   1.5822  -1.6201  -1.4128
 69Y  H10  H  HCH2  0   0.244   0.4207  -0.3542  -1.7737
 69Y  H11  H  HCH2  0   0.281  -1.7836   0.1428   1.7056
 69Y  H12  H  HCH2  0   0.258  -0.6277  -1.1282   1.9961
 69Y  H13  H  HCH2  0   0.251  -0.2241   1.3206   0.2068
 69Y  H14  H  HCH2  0   0.258   0.5307   1.0464   1.7709
 69Y  H15  H  HCH2  0   0.290   2.3882   1.7376   0.1790
 69Y  H16  H  HCH2  0   0.286   2.4980   0.8606  -1.3418
 69Y  H17  H  HCR6  0   0.262   8.1648  -0.8014   0.6845
 69Y  H18  H  HCR6  0   0.262   6.9174   2.6415  -1.5357
 69Y  H19  H  HCR6  0   0.263   4.5706   2.0706  -1.1085

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
 69Y  C4   C3   aromatic  1.388  0.020  1.388
 69Y  C4   C5   aromatic  1.387  0.020  1.387
 69Y  F1   C14  single    1.343  0.020  1.343
 69Y  C3   C2   aromatic  1.394  0.020  1.394
 69Y  C8   C    single    1.527  0.020  1.527
 69Y  C8   C1   single    1.496  0.020  1.496
 69Y  C5   C7   aromatic  1.392  0.020  1.392
 69Y  F2   C14  single    1.342  0.020  1.342
 69Y  C16  C    single    1.526  0.020  1.526
 69Y  C16  C15  single    1.523  0.020  1.523
 69Y  C14  C13  single    1.503  0.020  1.503
 69Y  C14  F    single    1.344  0.020  1.344
 69Y  C13  C12  single    1.522  0.020  1.522
 69Y  C12  C11  single    1.519  0.020  1.519
 69Y  C2   C1   single    1.462  0.020  1.462
 69Y  C2   C6   aromatic  1.399  0.020  1.399
 69Y  C    C9   single    1.522  0.020  1.522
 69Y  C    O    single    1.454  0.020  1.454
 69Y  C11  O1   double    1.224  0.020  1.224
 69Y  C11  N1   single    1.350  0.020  1.350
 69Y  C9   C10  single    1.525  0.020  1.525
 69Y  C15  N1   single    1.454  0.020  1.454
 69Y  C1   N    double    1.274  0.020  1.274
 69Y  N1   C10  single    1.453  0.020  1.453
 69Y  C7   C6   aromatic  1.383  0.020  1.383
 69Y  O    N    single    1.362  0.020  1.362
 69Y  C5   H1   single    0.930  0.020  1.080
 69Y  C6   H2   single    0.930  0.020  1.080
 69Y  C12  H3   single    0.970  0.020  1.090
 69Y  C12  H4   single    0.970  0.020  1.090
 69Y  C13  H5   single    0.970  0.020  1.090
 69Y  C13  H6   single    0.970  0.020  1.090
 69Y  C15  H7   single    0.970  0.020  1.090
 69Y  C15  H8   single    0.970  0.020  1.090
 69Y  C16  H9   single    0.970  0.020  1.090
 69Y  C16  H10  single    0.970  0.020  1.090
 69Y  C10  H11  single    0.970  0.020  1.090
 69Y  C10  H12  single    0.970  0.020  1.090
 69Y  C9   H13  single    0.970  0.020  1.090
 69Y  C9   H14  single    0.970  0.020  1.090
 69Y  C8   H15  single    0.970  0.020  1.090
 69Y  C8   H16  single    0.970  0.020  1.090
 69Y  C7   H17  single    0.930  0.020  1.080
 69Y  C4   H18  single    0.930  0.020  1.080
 69Y  C3   H19  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
 69Y  N    C1   C8   113.00  3.000
 69Y  N    C1   C2   121.71  3.000
 69Y  C8   C1   C2   125.28  3.000
 69Y  C3   C2   C6   118.94  3.000
 69Y  C6   C2   C1   121.28  3.000
 69Y  C3   C2   C1   119.78  3.000
 69Y  H1   C5   C4   120.19  3.000
 69Y  H1   C5   C7   120.13  3.000
 69Y  C4   C5   C7   119.68  3.000
 69Y  H2   C6   C7   119.74  3.000
 69Y  H2   C6   C2   119.88  3.000
 69Y  C7   C6   C2   120.38  3.000
 69Y  N1   C11  O1   122.27  3.000
 69Y  N1   C11  C12  117.07  3.000
 69Y  O1   C11  C12  120.66  3.000
 69Y  H4   C12  H3   106.32  3.000
 69Y  H4   C12  C13  110.19  3.000
 69Y  H3   C12  C13  110.55  3.000
 69Y  H4   C12  C11  109.15  3.000
 69Y  H3   C12  C11  109.27  3.000
 69Y  C13  C12  C11  111.23  3.000
 69Y  H6   C13  H5   107.00  3.000
 69Y  H6   C13  C14  107.91  3.000
 69Y  H5   C13  C14  107.76  3.000
 69Y  H6   C13  C12  110.77  3.000
 69Y  H5   C13  C12  110.65  3.000
 69Y  C14  C13  C12  112.53  3.000
 69Y  F    C14  F1   106.39  3.000
 69Y  F    C14  F2   106.54  3.000
 69Y  F1   C14  F2   106.57  3.000
 69Y  F    C14  C13  112.59  3.000
 69Y  F2   C14  C13  111.59  3.000
 69Y  F1   C14  C13  112.73  3.000
 69Y  H8   C15  H7   107.23  3.000
 69Y  H8   C15  N1   108.89  3.000
 69Y  H7   C15  N1   109.51  3.000
 69Y  H8   C15  C16  110.50  3.000
 69Y  H7   C15  C16  110.42  3.000
 69Y  N1   C15  C16  110.22  3.000
 69Y  H10  C16  H9   106.78  3.000
 69Y  H10  C16  C    108.65  3.000
 69Y  H9   C16  C    110.15  3.000
 69Y  H10  C16  C15  109.17  3.000
 69Y  H9   C16  C15  110.04  3.000
 69Y  C    C16  C15  111.89  3.000
 69Y  C10  N1   C15  113.07  3.000
 69Y  C10  N1   C11  125.37  3.000
 69Y  C15  N1   C11  120.67  3.000
 69Y  H12  C10  H11  106.17  3.000
 69Y  H12  C10  C9   110.27  3.000
 69Y  H11  C10  C9   109.92  3.000
 69Y  H12  C10  N1   108.52  3.000
 69Y  H11  C10  N1   111.32  3.000
 69Y  C9   C10  N1   110.54  3.000
 69Y  H14  C9   H13  107.07  3.000
 69Y  H14  C9   C    110.01  3.000
 69Y  H13  C9   C    108.54  3.000
 69Y  H14  C9   C10  109.79  3.000
 69Y  H13  C9   C10  109.40  3.000
 69Y  C    C9   C10  111.90  3.000
 69Y  O    C    C8   103.44  3.000
 69Y  O    C    C9   107.92  3.000
 69Y  C8   C    C9   114.28  3.000
 69Y  O    C    C16  107.86  3.000
 69Y  C9   C    C16  110.60  3.000
 69Y  C8   C    C16  112.21  3.000
 69Y  H16  C8   H15  107.17  3.000
 69Y  H16  C8   C    112.41  3.000
 69Y  H15  C8   C    113.05  3.000
 69Y  H16  C8   C1   112.78  3.000
 69Y  H15  C8   C1   110.86  3.000
 69Y  C    C8   C1   100.63  3.000
 69Y  O    N    C1   110.63  3.000
 69Y  N    O    C    110.21  3.000
 69Y  H17  C7   C6   119.63  3.000
 69Y  H17  C7   C5   120.05  3.000
 69Y  C6   C7   C5   120.32  3.000
 69Y  H18  C4   C3   119.64  3.000
 69Y  H18  C4   C5   120.23  3.000
 69Y  C3   C4   C5   120.13  3.000
 69Y  H19  C3   C4   119.26  3.000
 69Y  H19  C3   C2   120.19  3.000
 69Y  C4   C3   C2   120.55  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
 69Y  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 69Y  CONST_02  C5   C7   C6   C2      0.00   0.0  0
 69Y  CONST_03  C4   C3   C2   C6      0.00   0.0  0
 69Y  CONST_04  C4   C5   C7   C6      0.00   0.0  0
 69Y  CONST_05  C3   C4   C5   C7      0.00   0.0  0
 69Y  CONST_06  C3   C2   C6   C7      0.00   0.0  0
 69Y  CONST_07  C4   C3   C2   C1    180.00   0.0  0
 69Y  CONST_08  C7   C6   C2   C1    180.00   0.0  0
 69Y  CONST_09  H19  C3   C2   C1      0.00   0.0  0
 69Y  CONST_10  H2   C6   C2   C1      0.00   0.0  0
 69Y  CONST_11  H18  C4   C3   C2    180.00   0.0  0
 69Y  CONST_12  H17  C7   C6   C2    180.00   0.0  0
 69Y  CONST_13  H1   C5   C7   C6    180.00   0.0  0
 69Y  CONST_14  C15  N1   C11  C12   180.00   0.0  0
 69Y  CONST_15  C10  N1   C11  C12     0.00   0.0  0
 69Y  CONST_16  O1   C11  N1   C15     0.00   0.0  0
 69Y  CONST_17  C10  N1   C11  O1    180.00   0.0  0
 69Y  Var_01    C16  C    C8   C1   -102.76  30.0  3
 69Y  Var_02    C    C8   C1   C2    172.11  30.0  1
 69Y  Var_03    C8   C1   C2   C6   -176.62  30.0  2
 69Y  Var_04    C8   C    C16  C15  -179.97  30.0  1
 69Y  Var_05    C9   C10  N1   C15    59.20  30.0  1
 69Y  Var_06    C10  C9   C    C16    50.69  30.0  1
 69Y  Var_07    C10  N1   C15  C16   -59.41  30.0  1
 69Y  Var_08    C    C16  C15  N1     54.78  30.0  1
 69Y  Var_09    C    C9   C10  N1    -54.29  30.0  1
 69Y  Var_10    N1   C11  C12  C13  -178.30  30.0  3
 69Y  Var_11    C14  C13  C12  C11  -179.05  30.0  1
 69Y  Var_12    F1   C14  C13  C12   -59.81  30.0  3

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
 69Y  plan-1  C11  0.020
 69Y  plan-1  C12  0.020
 69Y  plan-1  C15  0.020
 69Y  plan-1  O1   0.020
 69Y  plan-1  N1   0.020
 69Y  plan-1  C10  0.020
 69Y  plan-2  C1   0.020
 69Y  plan-2  C2   0.020
 69Y  plan-2  C5   0.020
 69Y  plan-2  C6   0.020
 69Y  plan-2  C7   0.020
 69Y  plan-2  C4   0.020
 69Y  plan-2  C3   0.020
 69Y  plan-2  H1   0.020
 69Y  plan-2  H2   0.020
 69Y  plan-2  H17  0.020
 69Y  plan-2  H18  0.020
 69Y  plan-2  H19  0.020

