# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:40:35 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: 1'-[2-[4-(trifluoromethyl)phenyl]ethyl]spiro[1~{H}-3,1-benzoxazine-4,4'-piperidine]-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1ccc(CCN2CCC3(CC2)OC(=O)Nc4ccccc34)cc1
#
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
 R6Q  R6Q  1'-[2-[4-(trifluoromethyl)phenyl]ethyl]spiro[1~{H}-3,1-benzoxazine-4,4'-piperidine]-2-one  ligand  49  28  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_R6Q
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
 R6Q  C12   C  CH2   0  -0.280   3.7186  1.8216  -22.5765
 R6Q  C01   C  CR16  0  -0.339   0.4639  4.1766  -25.0505
 R6Q  C02   C  CR16  0  -0.255  -0.5672  4.2312  -25.9795
 R6Q  C03   C  CR16  0  -0.261  -1.6368  3.3532  -25.8736
 R6Q  C04   C  CR16  0  -0.318  -1.6839  2.4297  -24.8408
 R6Q  C05   C  CR66  0   0.351  -0.6462  2.3844  -23.9181
 R6Q  C06   C  CR66  0   0.106   0.4378  3.2526  -24.0161
 R6Q  C08   C  CR6   0   0.645   0.0639  1.6324  -21.7347
 R6Q  C10   C  CR6   0   0.130   1.5504  3.0539  -23.0208
 R6Q  C11   C  CH2   0  -0.443   2.5483  2.0121  -23.5287
 R6Q  C14   C  CH2   0  -0.291   3.4814  4.0502  -21.7322
 R6Q  C15   C  CH2   0  -0.444   2.3059  4.3249  -22.6602
 R6Q  C17   C  CH2   0  -0.536   6.5413  4.0565  -21.5170
 R6Q  C18   C  CR6   0   0.136   7.7681  3.7491  -20.7087
 R6Q  C19   C  CR16  0  -0.296   8.9221  3.2604  -21.3115
 R6Q  C20   C  CR16  0  -0.269  10.0411  2.9304  -20.5594
 R6Q  C21   C  CR6   0  -0.211  10.0153  3.0845  -19.1806
 R6Q  C22   C  CR16  0  -0.252   8.8678  3.5736  -18.5617
 R6Q  C23   C  CR16  0  -0.292   7.7598  3.9010  -19.3222
 R6Q  C24   C  CT    0   1.048  11.1972  2.7447  -18.3322
 R6Q  F25   F  F     0  -0.316  11.6798  3.8226  -17.6935
 R6Q  F26   F  F     0  -0.316  10.8840  1.8534  -17.3788
 R6Q  F27   F  F     0  -0.303  12.2088  2.2244  -19.0332
 R6Q  N07   N  NR16  0  -0.755  -0.6597  1.4664  -22.8717
 R6Q  N13   N  NT    0  -0.427   4.3941  3.0803  -22.3125
 R6Q  O09   O  O     0  -0.475   0.9819  2.5948  -21.7702
 R6Q  O28   O  O     0  -0.476  -0.1113  0.9906  -20.7256
 R6Q  H121  H  HCH2  0   0.202   3.3771  1.3329  -21.6488
 R6Q  H122  H  HCH2  0   0.245   4.4303  1.1358  -23.0420
 R6Q  H011  H  HCR6  0   0.258   1.2985  4.8577  -25.1518
 R6Q  H021  H  HCR6  0   0.259  -0.5302  4.9534  -26.7835
 R6Q  H031  H  HCR6  0   0.263  -2.4443  3.3884  -26.5927
 R6Q  H041  H  HCR6  0   0.273  -2.5222  1.7502  -24.7491
 R6Q  H112  H  HCH2  0   0.255   2.0563  1.0523  -23.7067
 R6Q  H111  H  HCH2  0   0.252   2.9215  2.3554  -24.4969
 R6Q  H142  H  HCH2  0   0.203   3.1204  3.7268  -20.7417
 R6Q  H141  H  HCH2  0   0.249   4.0059  4.9936  -21.5744
 R6Q  H152  H  HCH2  0   0.248   2.6871  4.7802  -23.5757
 R6Q  H151  H  HCH2  0   0.259   1.6289  5.0467  -22.1984
 R6Q  H162  H  HCH2  0   0.201   5.3096  2.6312  -20.4511
 R6Q  H161  H  HCH2  0   0.240   6.1017  1.9976  -21.8865
 R6Q  H172  H  HCH2  0   0.249   6.8133  4.2725  -22.5521
 R6Q  H171  H  HCH2  0   0.256   6.0616  4.9521  -21.1170
 R6Q  H191  H  HCR6  0   0.259   8.9551  3.1351  -22.3868
 R6Q  H201  H  HCR6  0   0.269  10.9208  2.5556  -21.0642
 R6Q  H221  H  HCR6  0   0.272   8.8281  3.7039  -17.4875
 R6Q  H231  H  HCR6  0   0.259   6.8743  4.2846  -18.8302
 R6Q  H071  H  HNR6  0   0.419  -1.4046  0.7866  -22.8334
 R6Q  C16   C  CH2   0  -0.253   5.5736  2.8713  -21.4956

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
 R6Q  C03  C02   aromatic  1.388  0.020  1.388
 R6Q  C03  C04   aromatic  1.386  0.020  1.386
 R6Q  C02  C01   aromatic  1.389  0.020  1.389
 R6Q  C04  C05   aromatic  1.389  0.020  1.389
 R6Q  C01  C06   aromatic  1.387  0.020  1.387
 R6Q  C05  C06   aromatic  1.392  0.020  1.392
 R6Q  C05  N07   single    1.392  0.020  1.392
 R6Q  C06  C10   single    1.506  0.020  1.506
 R6Q  C11  C10   single    1.529  0.020  1.529
 R6Q  C11  C12   single    1.521  0.020  1.521
 R6Q  N07  C08   single    1.358  0.020  1.358
 R6Q  C10  O09   single    1.448  0.020  1.448
 R6Q  C10  C15   single    1.522  0.020  1.522
 R6Q  C12  N13   single    1.453  0.020  1.453
 R6Q  N13  C16   single    1.450  0.020  1.450
 R6Q  N13  C14   single    1.453  0.020  1.453
 R6Q  C17  C16   single    1.530  0.020  1.530
 R6Q  C17  C18   single    1.501  0.020  1.501
 R6Q  C08  O09   single    1.330  0.020  1.330
 R6Q  C08  O28   double    1.209  0.020  1.209
 R6Q  C15  C14   single    1.523  0.020  1.523
 R6Q  C19  C18   aromatic  1.391  0.020  1.391
 R6Q  C19  C20   aromatic  1.388  0.020  1.388
 R6Q  C18  C23   aromatic  1.395  0.020  1.395
 R6Q  C20  C21   aromatic  1.388  0.020  1.388
 R6Q  C23  C22   aromatic  1.383  0.020  1.383
 R6Q  C21  C22   aromatic  1.393  0.020  1.393
 R6Q  C21  C24   single    1.494  0.020  1.494
 R6Q  F27  C24   single    1.336  0.020  1.336
 R6Q  F25  C24   single    1.343  0.020  1.343
 R6Q  C24  F26   single    1.342  0.020  1.342
 R6Q  C12  H121  single    0.970  0.020  1.090
 R6Q  C12  H122  single    0.970  0.020  1.090
 R6Q  C01  H011  single    0.930  0.020  1.080
 R6Q  C02  H021  single    0.930  0.020  1.080
 R6Q  C03  H031  single    0.930  0.020  1.080
 R6Q  C04  H041  single    0.930  0.020  1.080
 R6Q  C11  H112  single    0.970  0.020  1.090
 R6Q  C11  H111  single    0.970  0.020  1.090
 R6Q  C14  H142  single    0.970  0.020  1.090
 R6Q  C14  H141  single    0.970  0.020  1.090
 R6Q  C15  H152  single    0.970  0.020  1.090
 R6Q  C15  H151  single    0.970  0.020  1.090
 R6Q  C16  H162  single    0.970  0.020  1.090
 R6Q  C16  H161  single    0.970  0.020  1.090
 R6Q  C17  H172  single    0.970  0.020  1.090
 R6Q  C17  H171  single    0.970  0.020  1.090
 R6Q  C19  H191  single    0.930  0.020  1.080
 R6Q  C20  H201  single    0.930  0.020  1.080
 R6Q  C22  H221  single    0.930  0.020  1.080
 R6Q  C23  H231  single    0.930  0.020  1.080
 R6Q  N07  H071  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
 R6Q  H122  C12  H121  106.38  3.000
 R6Q  H122  C12  N13   108.56  3.000
 R6Q  H121  C12  N13   112.03  3.000
 R6Q  H122  C12  C11   108.25  3.000
 R6Q  H121  C12  C11   110.12  3.000
 R6Q  N13   C12  C11   111.29  3.000
 R6Q  H011  C01  C06   120.24  3.000
 R6Q  H011  C01  C02   119.03  3.000
 R6Q  C06   C01  C02   120.73  3.000
 R6Q  H021  C02  C03   120.37  3.000
 R6Q  H021  C02  C01   119.88  3.000
 R6Q  C03   C02  C01   119.75  3.000
 R6Q  H031  C03  C04   119.44  3.000
 R6Q  H031  C03  C02   120.26  3.000
 R6Q  C04   C03  C02   120.30  3.000
 R6Q  H041  C04  C05   120.09  3.000
 R6Q  H041  C04  C03   120.49  3.000
 R6Q  C05   C04  C03   119.42  3.000
 R6Q  N07   C05  C06   118.14  3.000
 R6Q  N07   C05  C04   120.89  3.000
 R6Q  C06   C05  C04   120.96  3.000
 R6Q  C10   C06  C05   116.51  3.000
 R6Q  C10   C06  C01   124.52  3.000
 R6Q  C05   C06  C01   118.85  3.000
 R6Q  O28   C08  O09   120.42  3.000
 R6Q  O28   C08  N07   123.84  3.000
 R6Q  O09   C08  N07   115.71  3.000
 R6Q  O09   C10  C15   104.77  3.000
 R6Q  C15   C10  C11   108.88  3.000
 R6Q  O09   C10  C11   109.08  3.000
 R6Q  C15   C10  C06   114.40  3.000
 R6Q  O09   C10  C06   108.81  3.000
 R6Q  C11   C10  C06   110.64  3.000
 R6Q  H111  C11  H112  106.57  3.000
 R6Q  H111  C11  C10   107.64  3.000
 R6Q  H112  C11  C10   111.00  3.000
 R6Q  H111  C11  C12   109.35  3.000
 R6Q  H112  C11  C12   109.77  3.000
 R6Q  C10   C11  C12   112.31  3.000
 R6Q  H141  C14  H142  106.32  3.000
 R6Q  H141  C14  N13   109.46  3.000
 R6Q  H142  C14  N13   111.63  3.000
 R6Q  H141  C14  C15   107.65  3.000
 R6Q  H142  C14  C15   110.34  3.000
 R6Q  N13   C14  C15   111.23  3.000
 R6Q  H151  C15  H152  107.20  3.000
 R6Q  H151  C15  C14   109.89  3.000
 R6Q  H152  C15  C14   108.48  3.000
 R6Q  H151  C15  C10   110.14  3.000
 R6Q  H152  C15  C10   108.84  3.000
 R6Q  C14   C15  C10   112.14  3.000
 R6Q  H171  C17  H172  107.13  3.000
 R6Q  H171  C17  C18   109.25  3.000
 R6Q  H172  C17  C18   110.33  3.000
 R6Q  H171  C17  C16   110.63  3.000
 R6Q  H172  C17  C16   108.91  3.000
 R6Q  C18   C17  C16   110.53  3.000
 R6Q  C23   C18  C19   118.30  3.000
 R6Q  C23   C18  C17   120.54  3.000
 R6Q  C19   C18  C17   121.12  3.000
 R6Q  H191  C19  C20   119.07  3.000
 R6Q  H191  C19  C18   119.75  3.000
 R6Q  C20   C19  C18   121.18  3.000
 R6Q  H201  C20  C21   121.16  3.000
 R6Q  H201  C20  C19   119.04  3.000
 R6Q  C21   C20  C19   119.80  3.000
 R6Q  C24   C21  C22   118.64  3.000
 R6Q  C24   C21  C20   121.63  3.000
 R6Q  C22   C21  C20   119.73  3.000
 R6Q  H221  C22  C23   119.19  3.000
 R6Q  H221  C22  C21   120.89  3.000
 R6Q  C23   C22  C21   119.93  3.000
 R6Q  H231  C23  C22   119.27  3.000
 R6Q  H231  C23  C18   119.66  3.000
 R6Q  C22   C23  C18   121.07  3.000
 R6Q  F27   C24  F26   106.90  3.000
 R6Q  F26   C24  F25   106.21  3.000
 R6Q  F27   C24  F25   106.86  3.000
 R6Q  F26   C24  C21   111.70  3.000
 R6Q  F25   C24  C21   111.83  3.000
 R6Q  F27   C24  C21   112.92  3.000
 R6Q  H071  N07  C08   116.36  3.000
 R6Q  H071  N07  C05   118.68  3.000
 R6Q  C08   N07  C05   122.93  3.000
 R6Q  C16   N13  C14   112.47  3.000
 R6Q  C14   N13  C12   111.03  3.000
 R6Q  C16   N13  C12   110.84  3.000
 R6Q  C10   O09  C08   121.54  3.000
 R6Q  H161  C16  H162  106.26  3.000
 R6Q  H161  C16  N13   107.86  3.000
 R6Q  H162  C16  N13   111.72  3.000
 R6Q  H161  C16  C17   107.97  3.000
 R6Q  H162  C16  C17   109.45  3.000
 R6Q  N13   C16  C17   113.26  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
 R6Q  CONST_01  C04   C03  C02  C01     0.00   0.0  0
 R6Q  CONST_02  C04   C05  C06  C01     0.00   0.0  0
 R6Q  CONST_03  C05   C04  C03  C02     0.00   0.0  0
 R6Q  CONST_04  C05   C06  C01  C02     0.00   0.0  0
 R6Q  CONST_05  C06   C01  C02  C03     0.00   0.0  0
 R6Q  CONST_06  C06   C05  C04  C03     0.00   0.0  0
 R6Q  CONST_07  C21   C20  C19  C18     0.00   0.0  0
 R6Q  CONST_08  C21   C22  C23  C18     0.00   0.0  0
 R6Q  CONST_09  C22   C23  C18  C19     0.00   0.0  0
 R6Q  CONST_10  C22   C21  C20  C19     0.00   0.0  0
 R6Q  CONST_11  C23   C18  C19  C20     0.00   0.0  0
 R6Q  CONST_12  C23   C22  C21  C20     0.00   0.0  0
 R6Q  CONST_13  C10   C06  C01  C02   180.00   0.0  0
 R6Q  CONST_14  C10   C06  C05  C04   180.00   0.0  0
 R6Q  CONST_15  N07   C05  C06  C10     0.00   0.0  0
 R6Q  CONST_16  C20   C19  C18  C17   180.00   0.0  0
 R6Q  CONST_17  C22   C23  C18  C17   180.00   0.0  0
 R6Q  CONST_18  C24   C21  C20  C19   180.00   0.0  0
 R6Q  CONST_19  C24   C21  C22  C23   180.00   0.0  0
 R6Q  CONST_20  H031  C03  C02  C01   180.00   0.0  0
 R6Q  CONST_21  H041  C04  C03  C02   180.00   0.0  0
 R6Q  CONST_22  H011  C01  C02  C03   180.00   0.0  0
 R6Q  CONST_23  H021  C02  C03  C04   180.00   0.0  0
 R6Q  CONST_24  H201  C20  C19  C18   180.00   0.0  0
 R6Q  CONST_25  H221  C22  C23  C18   180.00   0.0  0
 R6Q  CONST_26  H231  C23  C18  C19   180.00   0.0  0
 R6Q  CONST_27  H191  C19  C20  C21   180.00   0.0  0
 R6Q  Var_01    C06   C10  C11  C12   177.74  30.0  3
 R6Q  Var_02    C15   C14  N13  C12   -59.37  30.0  1
 R6Q  Var_03    C11   C10  C06  C01   -89.56  30.0  1
 R6Q  Var_04    C08   N07  C05  C04  -158.69  30.0  1
 R6Q  Var_05    O09   C08  N07  C05   -12.06  30.0  1
 R6Q  Var_06    C14   C15  C10  C06  -175.79  30.0  3
 R6Q  Var_07    N13   C12  C11  C10   -55.77  30.0  1
 R6Q  Var_08    N07   C08  O09  C10   -23.92  30.0  1
 R6Q  Var_09    N13   C14  C15  C10    56.48  30.0  1
 R6Q  Var_10    C14   N13  C12  C11    59.05  30.0  1
 R6Q  Var_11    C17   C16  N13  C12   163.24  30.0  3
 R6Q  Var_12    C19   C18  C17  C16    95.54  30.0  2
 R6Q  Var_13    N13   C16  C17  C18  -177.20  30.0  3
 R6Q  Var_14    F27   C24  C21  C20    -3.47  30.0  2

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
 R6Q  plan-1  C17   0.020
 R6Q  plan-1  C18   0.020
 R6Q  plan-1  C19   0.020
 R6Q  plan-1  C20   0.020
 R6Q  plan-1  C21   0.020
 R6Q  plan-1  C22   0.020
 R6Q  plan-1  C23   0.020
 R6Q  plan-1  C24   0.020
 R6Q  plan-1  H191  0.020
 R6Q  plan-1  H201  0.020
 R6Q  plan-1  H221  0.020
 R6Q  plan-1  H231  0.020
 R6Q  plan-2  C01   0.020
 R6Q  plan-2  C02   0.020
 R6Q  plan-2  C03   0.020
 R6Q  plan-2  C04   0.020
 R6Q  plan-2  C05   0.020
 R6Q  plan-2  C06   0.020
 R6Q  plan-2  C10   0.020
 R6Q  plan-2  N07   0.020
 R6Q  plan-2  H011  0.020
 R6Q  plan-2  H021  0.020
 R6Q  plan-2  H031  0.020
 R6Q  plan-2  H041  0.020
 R6Q  plan-3  C05   0.020
 R6Q  plan-3  C08   0.020
 R6Q  plan-3  N07   0.020
 R6Q  plan-3  H071  0.020
 R6Q  plan-4  C08   0.020
 R6Q  plan-4  N07   0.020
 R6Q  plan-4  O09   0.020
 R6Q  plan-4  O28   0.020

