# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 12:09:20 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: (2s,4R)-2-{4-[(2-chloro-4-fluorophenoxy)methyl]piperidine-1-carbonyl}-7-oxa-5-azaspiro[3.4]octan-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(OC[C@H]2CCN(CC2)C(=O)[C@H]3C[C@]4(COC(=O)N4)C3)c(Cl)c1
#
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
 XOV  XOV  (2s,4R)-2-{4-[(2-chloro-4-fluorophenoxy)methyl]piperidine-1-carbonyl}-7-oxa-5-azaspiro[3.4]octan-6-one  ligand  49  27  .  2022-03-29  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XOV
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
 XOV  C4    C   CR6   0   0.464  -34.0797  -10.1998  -53.6535
 XOV  C5    C   CR6   0   0.504  -35.5440   -8.9339  -55.6428
 XOV  C6    C   CR6   0  -0.147  -34.1127  -10.7015  -54.9591
 XOV  C7    C   CR5   0   0.663  -26.4037   -9.6387  -43.6150
 XOV  C8    C   C     0   0.573  -28.5436  -10.7329  -48.8216
 XOV  C10   C   CH2   0  -0.415  -30.7625  -11.1752  -51.4240
 XOV  C13   C   CH2   0  -0.319  -30.9145  -11.4438  -48.5442
 XOV  C15   C   CH2   0  -0.183  -28.3917   -9.1215  -44.5632
 XOV  C17   C   CH1   0  -0.295  -32.1277  -11.1795  -50.7362
 XOV  C1    C   CR16  0  -0.371  -34.8166   -9.0526  -53.3736
 XOV  C2    C   CR16  0  -0.393  -35.5494   -8.4150  -54.3670
 XOV  C3    C   CR16  0  -0.364  -34.8366  -10.0787  -55.9589
 XOV  C9    C   CH2   0  -0.418  -31.9940  -10.6785  -49.2983
 XOV  C11   C   C     0  -0.443  -28.5446  -11.0953  -46.2151
 XOV  C12   C   C     0  -0.423  -27.3113   -9.4754  -46.9020
 XOV  C14   C   CH2   0  -0.316  -29.7265  -11.9254  -50.5957
 XOV  C16   C   C     0  -0.442  -28.5914  -10.1380  -47.4322
 XOV  C18   C   C     0   0.144  -27.6512  -10.0629  -45.5182
 XOV  C19   C   CH2   0  -0.161  -33.1502  -10.3331  -51.4686
 XOV  N20   N   NR15  0  -0.690  -26.5964  -10.4919  -44.6458
 XOV  N21   N   NT    0  -0.449  -29.6490  -11.3792  -49.2516
 XOV  O23   O   O     0  -0.490  -27.5308  -10.6392  -49.5035
 XOV  O24   O   O     0  -0.466  -27.4160   -8.7540  -43.5881
 XOV  O25   O   O2    0  -0.462  -33.3333  -10.8716  -52.7690
 XOV  F26   F   F     0  -0.315  -36.2374   -8.3175  -56.6134
 XOV  CL27  CL  CL    0  -0.100  -33.2147  -12.1301  -55.3211
 XOV  H1    H   HCH2  0   0.224  -30.4275  -10.1427  -51.5710
 XOV  H2    H   HCH2  0   0.243  -30.8252  -11.6364  -52.4114
 XOV  H3    H   HCH2  0   0.245  -31.2030  -12.4960  -48.4492
 XOV  H4    H   HCH2  0   0.274  -30.8177  -11.0562  -47.5348
 XOV  H5    H   HCH2  0   0.260  -28.7691   -8.2223  -45.0476
 XOV  H6    H   HCH2  0   0.251  -29.2188   -9.6320  -44.0625
 XOV  H7    H   HCH1  0   0.239  -32.4955  -12.2128  -50.6990
 XOV  H8    H   HCR6  0   0.299  -34.8303   -8.6355  -52.3762
 XOV  H9    H   HCR6  0   0.287  -36.1153   -7.5223  -54.1366
 XOV  H10   H   HCR6  0   0.299  -34.8454  -10.4767  -56.9648
 XOV  H11   H   HCH2  0   0.229  -31.7435   -9.6124  -49.2943
 XOV  H12   H   HCH2  0   0.245  -32.9424  -10.7871  -48.7665
 XOV  H13   H   H     0   0.259  -29.4811  -11.3666  -45.7263
 XOV  H14   H   H     0   0.264  -27.9885  -12.0049  -46.4500
 XOV  H15   H   H     0   0.253  -26.4188   -9.9454  -47.3160
 XOV  H16   H   H     0   0.253  -27.2184   -8.3924  -46.9862
 XOV  H17   H   HCH2  0   0.238  -30.0067  -12.9818  -50.5226
 XOV  H18   H   HCH2  0   0.264  -28.7478  -11.8796  -51.0645
 XOV  H19   H   H     0   0.297  -29.4388   -9.4522  -47.3429
 XOV  H20   H   HCH2  0   0.226  -32.7970   -9.2965  -51.5334
 XOV  H21   H   HCH2  0   0.239  -34.1008  -10.3309  -50.9222
 XOV  H22   H   HNR5  0   0.405  -25.8513  -11.0964  -44.9559
 XOV  O22   O   O     0  -0.480  -25.5084   -9.6178  -42.8075

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
 XOV  F26   C5   single    1.343  0.020  1.343
 XOV  C3    C5   aromatic  1.382  0.020  1.382
 XOV  C3    C6   aromatic  1.383  0.020  1.383
 XOV  C5    C2   aromatic  1.377  0.020  1.377
 XOV  CL27  C6   single    1.726  0.020  1.726
 XOV  C6    C4   aromatic  1.399  0.020  1.399
 XOV  C2    C1   aromatic  1.389  0.020  1.389
 XOV  C4    C1   aromatic  1.392  0.020  1.392
 XOV  C4    O25  single    1.338  0.020  1.338
 XOV  O25   C19  single    1.419  0.020  1.419
 XOV  C10   C14  single    1.524  0.020  1.524
 XOV  C10   C17  single    1.529  0.020  1.529
 XOV  C19   C17  single    1.516  0.020  1.516
 XOV  C14   N21  single    1.453  0.020  1.453
 XOV  C17   C9   single    1.528  0.020  1.528
 XOV  O23   C8   double    1.224  0.020  1.224
 XOV  N21   C8   single    1.351  0.020  1.351
 XOV  N21   C13  single    1.451  0.020  1.451
 XOV  C9    C13  single    1.523  0.020  1.523
 XOV  C8    C16  single    1.512  0.020  1.512
 XOV  C16   C12  single    1.536  0.020  1.536
 XOV  C16   C11  single    1.549  0.020  1.549
 XOV  C12   C18  single    1.541  0.020  1.541
 XOV  C11   C18  single    1.533  0.020  1.533
 XOV  C18   C15  single    1.532  0.020  1.532
 XOV  C18   N20  single    1.434  0.020  1.434
 XOV  C15   O24  single    1.428  0.020  1.428
 XOV  N20   C7   single    1.352  0.020  1.352
 XOV  O24   C7   single    1.345  0.020  1.345
 XOV  C7    O22  double    1.206  0.020  1.206
 XOV  C10   H1   single    0.970  0.020  1.090
 XOV  C10   H2   single    0.970  0.020  1.090
 XOV  C13   H3   single    0.970  0.020  1.090
 XOV  C13   H4   single    0.970  0.020  1.090
 XOV  C15   H5   single    0.970  0.020  1.090
 XOV  C15   H6   single    0.970  0.020  1.090
 XOV  C17   H7   single    0.970  0.020  1.090
 XOV  C1    H8   single    0.930  0.020  1.080
 XOV  C2    H9   single    0.930  0.020  1.080
 XOV  C3    H10  single    0.930  0.020  1.080
 XOV  C9    H11  single    0.970  0.020  1.090
 XOV  C9    H12  single    0.970  0.020  1.090
 XOV  C11   H13  single    0.970  0.020  1.090
 XOV  C11   H14  single    0.970  0.020  1.090
 XOV  C12   H15  single    0.970  0.020  1.090
 XOV  C12   H16  single    0.970  0.020  1.090
 XOV  C14   H17  single    0.970  0.020  1.090
 XOV  C14   H18  single    0.970  0.020  1.090
 XOV  C16   H19  single    0.970  0.020  1.090
 XOV  C19   H20  single    0.970  0.020  1.090
 XOV  C19   H21  single    0.970  0.020  1.090
 XOV  N20   H22  single    0.890  0.020  1.040

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
 XOV  O25   C4   C1   125.18  3.000
 XOV  O25   C4   C6   116.74  3.000
 XOV  C1    C4   C6   118.08  3.000
 XOV  F26   C5   C3   118.63  3.000
 XOV  C3    C5   C2   121.72  3.000
 XOV  F26   C5   C2   119.65  3.000
 XOV  CL27  C6   C3   119.58  3.000
 XOV  CL27  C6   C4   118.71  3.000
 XOV  C3    C6   C4   121.71  3.000
 XOV  O24   C7   O22  122.28  3.000
 XOV  O22   C7   N20  128.86  3.000
 XOV  O24   C7   N20  108.86  3.000
 XOV  O23   C8   N21  122.42  3.000
 XOV  N21   C8   C16  117.06  3.000
 XOV  O23   C8   C16  120.51  3.000
 XOV  H2    C10  H1   107.12  3.000
 XOV  H2    C10  C14  108.83  3.000
 XOV  H1    C10  C14  109.21  3.000
 XOV  H2    C10  C17  110.77  3.000
 XOV  H1    C10  C17  109.64  3.000
 XOV  C14   C10  C17  111.17  3.000
 XOV  H4    C13  H3   106.61  3.000
 XOV  H4    C13  N21  111.07  3.000
 XOV  H3    C13  N21  108.35  3.000
 XOV  H4    C13  C9   110.13  3.000
 XOV  H3    C13  C9   109.81  3.000
 XOV  N21   C13  C9   110.75  3.000
 XOV  H6    C15  H5   109.09  3.000
 XOV  H6    C15  O24  108.93  3.000
 XOV  H5    C15  O24  109.16  3.000
 XOV  H6    C15  C18  111.36  3.000
 XOV  H5    C15  C18  113.43  3.000
 XOV  O24   C15  C18  104.70  3.000
 XOV  H7    C17  C19  108.42  3.000
 XOV  H7    C17  C9   107.82  3.000
 XOV  C19   C17  C9   109.30  3.000
 XOV  H7    C17  C10  108.50  3.000
 XOV  C9    C17  C10  110.14  3.000
 XOV  C19   C17  C10  112.54  3.000
 XOV  H8    C1   C2   118.42  3.000
 XOV  H8    C1   C4   120.67  3.000
 XOV  C2    C1   C4   120.91  3.000
 XOV  H9    C2   C1   120.15  3.000
 XOV  H9    C2   C5   120.68  3.000
 XOV  C1    C2   C5   119.17  3.000
 XOV  H10   C3   C6   120.73  3.000
 XOV  H10   C3   C5   120.87  3.000
 XOV  C6    C3   C5   118.40  3.000
 XOV  H12   C9   H11  107.06  3.000
 XOV  H12   C9   C17  110.45  3.000
 XOV  H11   C9   C17  110.03  3.000
 XOV  H12   C9   C13  108.92  3.000
 XOV  H11   C9   C13  108.98  3.000
 XOV  C17   C9   C13  111.29  3.000
 XOV  H14   C11  H13  109.05  3.000
 XOV  H14   C11  C18  111.23  3.000
 XOV  H13   C11  C18  117.66  3.000
 XOV  H14   C11  C16  111.17  3.000
 XOV  H13   C11  C16  118.68  3.000
 XOV  C18   C11  C16   87.63  3.000
 XOV  H16   C12  H15  109.21  3.000
 XOV  H16   C12  C18  117.82  3.000
 XOV  H15   C12  C18  110.93  3.000
 XOV  H16   C12  C16  118.22  3.000
 XOV  H15   C12  C16  111.42  3.000
 XOV  C18   C12  C16   87.81  3.000
 XOV  H18   C14  H17  107.46  3.000
 XOV  H18   C14  N21  109.59  3.000
 XOV  H17   C14  N21  108.33  3.000
 XOV  H18   C14  C10  110.93  3.000
 XOV  H17   C14  C10  109.70  3.000
 XOV  N21   C14  C10  110.73  3.000
 XOV  H19   C16  C12  110.31  3.000
 XOV  H19   C16  C11  110.29  3.000
 XOV  C12   C16  C11   88.29  3.000
 XOV  H19   C16  C8   110.25  3.000
 XOV  C11   C16  C8   118.54  3.000
 XOV  C12   C16  C8   117.42  3.000
 XOV  N20   C18  C12  119.86  3.000
 XOV  N20   C18  C11  120.24  3.000
 XOV  C12   C18  C11   88.68  3.000
 XOV  N20   C18  C15   99.21  3.000
 XOV  C11   C18  C15  114.55  3.000
 XOV  C12   C18  C15  115.60  3.000
 XOV  H21   C19  H20  107.86  3.000
 XOV  H21   C19  O25  110.21  3.000
 XOV  H20   C19  O25  110.24  3.000
 XOV  H21   C19  C17  110.19  3.000
 XOV  H20   C19  C17  109.81  3.000
 XOV  O25   C19  C17  108.53  3.000
 XOV  H22   N20  C18  122.39  3.000
 XOV  H22   N20  C7   120.49  3.000
 XOV  C18   N20  C7   112.32  3.000
 XOV  C14   N21  C13  112.81  3.000
 XOV  C13   N21  C8   125.43  3.000
 XOV  C14   N21  C8   121.20  3.000
 XOV  C15   O24  C7   109.36  3.000
 XOV  C19   O25  C4   119.14  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
 XOV  CONST_01  C5    C3   C6   C4      0.00   0.0  0
 XOV  CONST_02  C5    C2   C1   C4      0.00   0.0  0
 XOV  CONST_03  C2    C5   C3   C6      0.00   0.0  0
 XOV  CONST_04  C2    C1   C4   C6      0.00   0.0  0
 XOV  CONST_05  C3    C5   C2   C1      0.00   0.0  0
 XOV  CONST_06  C3    C6   C4   C1      0.00   0.0  0
 XOV  CONST_07  CL27  C6   C3   C5    180.00   0.0  0
 XOV  CONST_08  F26   C5   C3   C6    180.00   0.0  0
 XOV  CONST_09  F26   C5   C2   C1    180.00   0.0  0
 XOV  CONST_10  CL27  C6   C4   C1    180.00   0.0  0
 XOV  CONST_11  O25   C4   C1   C2    180.00   0.0  0
 XOV  CONST_12  O25   C4   C6   C3    180.00   0.0  0
 XOV  CONST_13  C16   C8   N21  C13     0.00   0.0  0
 XOV  CONST_14  C16   C8   N21  C14   180.00   0.0  0
 XOV  CONST_15  H10   C3   C6   C4    180.00   0.0  0
 XOV  CONST_16  H9    C2   C1   C4    180.00   0.0  0
 XOV  CONST_17  H8    C1   C2   C5    180.00   0.0  0
 XOV  CONST_18  O23   C8   N21  C13   180.00   0.0  0
 XOV  CONST_19  O23   C8   N21  C14     0.00   0.0  0
 XOV  Var_01    C12   C18  N20  C7    106.18  30.0  1
 XOV  Var_02    C18   C15  O24  C7    -18.63  30.0  1
 XOV  Var_03    C13   N21  C14  C10    59.07  30.0  1
 XOV  Var_04    C16   C12  C18  C15   -95.98  30.0  3
 XOV  Var_05    C16   C11  C18  C15    97.12  30.0  3
 XOV  Var_06    N20   C7   O24  C15     6.05  30.0  1
 XOV  Var_07    N21   C14  C10  C17   -55.39  30.0  1
 XOV  Var_08    N21   C13  C9   C17    55.27  30.0  1
 XOV  Var_09    C14   N21  C13  C9    -58.97  30.0  1
 XOV  Var_10    O24   C15  C18  C11   152.01  30.0  1
 XOV  Var_11    O24   C7   N20  C18    10.46  30.0  1
 XOV  Var_12    C17   C19  O25  C4   -172.50  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
 XOV  chir_01  C17  C10  C19  C9   positiv
 XOV  chir_02  C16  C8   C12  C11  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
 XOV  plan-1  C8    0.020
 XOV  plan-1  C13   0.020
 XOV  plan-1  C14   0.020
 XOV  plan-1  C16   0.020
 XOV  plan-1  N21   0.020
 XOV  plan-1  O23   0.020
 XOV  plan-2  C7    0.020
 XOV  plan-2  C18   0.020
 XOV  plan-2  N20   0.020
 XOV  plan-2  H22   0.020
 XOV  plan-3  C4    0.020
 XOV  plan-3  C5    0.020
 XOV  plan-3  C6    0.020
 XOV  plan-3  C1    0.020
 XOV  plan-3  C2    0.020
 XOV  plan-3  C3    0.020
 XOV  plan-3  O25   0.020
 XOV  plan-3  F26   0.020
 XOV  plan-3  CL27  0.020
 XOV  plan-3  H8    0.020
 XOV  plan-3  H9    0.020
 XOV  plan-3  H10   0.020
 XOV  plan-4  C7    0.020
 XOV  plan-4  N20   0.020
 XOV  plan-4  O24   0.020
 XOV  plan-4  O22   0.020

