# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 08:09:53 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: (5S)-5-(3-{4-[(2-chloro-4-fluorophenoxy)methyl]piperidin-1-yl}-3-oxopropyl)pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(OCC2CCN(CC2)C(=O)CC[C@@H]3CCC(=O)N3)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
 XP7  XP7  (5S)-5-(3-{4-[(2-chloro-4-fluorophenoxy)methyl]piperidin-1-yl}-3-oxopropyl)pyrrolidin-2-one  ligand  50  26  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XP7
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
 XP7  C4    C   CR6   0   0.466  28.4632  116.5686  280.0497
 XP7  C5    C   CR6   0   0.504  30.8390  117.7407  279.2224
 XP7  C6    C   CR6   0  -0.146  29.6726  116.2892  280.6965
 XP7  C7    C   CR5   0   0.512  15.7463  116.6301  281.9574
 XP7  C8    C   C     0   0.581  21.5610  114.9291  282.5791
 XP7  C10   C   CH2   0  -0.475  17.8016  116.6025  280.7233
 XP7  C13   C   CH2   0  -0.314  22.7592  114.3555  280.4696
 XP7  C15   C   CH1   0  -0.296  25.1330  115.1757  280.5111
 XP7  C17   C   CH2   0  -0.628  20.2816  115.0845  281.7759
 XP7  C1    C   CR16  0  -0.373  28.4804  117.4681  278.9880
 XP7  C2    C   CR16  0  -0.394  29.6681  118.0554  278.5688
 XP7  C3    C   CR16  0  -0.364  30.8622  116.8637  280.2904
 XP7  C9    C   CH2   0  -0.589  16.3322  116.9941  280.6075
 XP7  C11   C   CH2   0  -0.420  23.7670  115.3104  279.8416
 XP7  C12   C   CH2   0  -0.416  24.9872  115.3661  282.0193
 XP7  C14   C   CH2   0  -0.312  23.9471  114.4089  282.5856
 XP7  C16   C   CR15  0  -0.007  17.8134  115.5005  281.7912
 XP7  C18   C   CH2   0  -0.159  26.1205  116.1414  279.8858
 XP7  C19   C   CH2   0  -0.430  19.0793  115.4507  282.6328
 XP7  N20   N   NR15  0  -0.642  16.6438  115.8423  282.5792
 XP7  N21   N   NT    0  -0.458  22.6735  114.5620  281.9040
 XP7  O23   O   O     0  -0.498  21.5690  115.1256  283.7879
 XP7  O24   O   O2    0  -0.462  27.3785  115.9364  280.5098
 XP7  F25   F   F     0  -0.315  31.9954  118.2933  278.8217
 XP7  CL26  CL  CL    0  -0.100  29.6702  115.1916  282.0289
 XP7  H1    H   HCH2  0   0.255  18.2337  116.2674  279.7822
 XP7  H2    H   HCH2  0   0.244  18.3899  117.4545  281.0746
 XP7  H3    H   HCH2  0   0.274  21.7871  114.4795  280.0033
 XP7  H4    H   HCH2  0   0.241  23.0733  113.3226  280.2834
 XP7  H5    H   HCH1  0   0.236  25.4961  114.1563  280.3254
 XP7  H6    H   HCH2  0   0.268  20.0730  114.1541  281.2382
 XP7  H7    H   HCH2  0   0.277  20.4352  115.8445  281.0038
 XP7  H8    H   HCR6  0   0.298  27.5672  117.7233  278.4681
 XP7  H9    H   HCR6  0   0.287  29.6678  118.7493  277.7387
 XP7  H10   H   HCR6  0   0.299  31.7898  116.6310  280.7963
 XP7  H11   H   HCH2  0   0.270  16.1669  118.0448  280.3719
 XP7  H12   H   HCH2  0   0.270  15.8142  116.4050  279.8450
 XP7  H13   H   HCH2  0   0.244  23.8407  115.0925  278.7733
 XP7  H14   H   HCH2  0   0.229  23.4018  116.3380  279.9383
 XP7  H15   H   HCH2  0   0.243  25.9362  115.1919  282.5291
 XP7  H16   H   HCH2  0   0.224  24.6863  116.3974  282.2319
 XP7  H17   H   HCH2  0   0.263  23.8079  114.5738  283.6499
 XP7  H18   H   HCH2  0   0.235  24.2908  113.3763  282.4565
 XP7  H19   H   HCR5  0   0.237  17.6681  114.5207  281.3165
 XP7  H20   H   HCH2  0   0.226  25.7897  117.1781  280.0269
 XP7  H21   H   HCH2  0   0.238  26.1932  115.9548  278.8081
 XP7  H22   H   HCH2  0   0.231  19.2260  116.4221  283.1109
 XP7  H23   H   HCH2  0   0.241  18.9528  114.7141  283.4297
 XP7  H24   H   HNR5  0   0.389  16.4200  115.3634  283.4390
 XP7  O22   O   O     0  -0.486  14.6594  116.9671  282.3947

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
 XP7  C2   C1    aromatic  1.390  0.020  1.390
 XP7  C2   C5    aromatic  1.377  0.020  1.377
 XP7  F25  C5    single    1.343  0.020  1.343
 XP7  C1   C4    aromatic  1.392  0.020  1.392
 XP7  C5   C3    aromatic  1.382  0.020  1.382
 XP7  C11  C13   single    1.524  0.020  1.524
 XP7  C11  C15   single    1.527  0.020  1.527
 XP7  C18  O24   single    1.419  0.020  1.419
 XP7  C18  C15   single    1.516  0.020  1.516
 XP7  C4   O24   single    1.337  0.020  1.337
 XP7  C4   C6    aromatic  1.400  0.020  1.400
 XP7  C3   C6    aromatic  1.382  0.020  1.382
 XP7  C13  N21   single    1.452  0.020  1.452
 XP7  C15  C12   single    1.527  0.020  1.527
 XP7  C6   CL26  single    1.726  0.020  1.726
 XP7  C9   C10   single    1.525  0.020  1.525
 XP7  C9   C7    single    1.516  0.020  1.516
 XP7  C10  C16   single    1.535  0.020  1.535
 XP7  C16  N20   single    1.451  0.020  1.451
 XP7  C16  C19   single    1.521  0.020  1.521
 XP7  C17  C19   single    1.521  0.020  1.521
 XP7  C17  C8    single    1.519  0.020  1.519
 XP7  N21  C8    single    1.352  0.020  1.352
 XP7  N21  C14   single    1.453  0.020  1.453
 XP7  C7   N20   single    1.346  0.020  1.346
 XP7  C7   O22   double    1.219  0.020  1.219
 XP7  C12  C14   single    1.523  0.020  1.523
 XP7  C8   O23   double    1.225  0.020  1.225
 XP7  C10  H1    single    0.970  0.020  1.090
 XP7  C10  H2    single    0.970  0.020  1.090
 XP7  C13  H3    single    0.970  0.020  1.090
 XP7  C13  H4    single    0.970  0.020  1.090
 XP7  C15  H5    single    0.970  0.020  1.090
 XP7  C17  H6    single    0.970  0.020  1.090
 XP7  C17  H7    single    0.970  0.020  1.090
 XP7  C1   H8    single    0.930  0.020  1.080
 XP7  C2   H9    single    0.930  0.020  1.080
 XP7  C3   H10   single    0.930  0.020  1.080
 XP7  C9   H11   single    0.970  0.020  1.090
 XP7  C9   H12   single    0.970  0.020  1.090
 XP7  C11  H13   single    0.970  0.020  1.090
 XP7  C11  H14   single    0.970  0.020  1.090
 XP7  C12  H15   single    0.970  0.020  1.090
 XP7  C12  H16   single    0.970  0.020  1.090
 XP7  C14  H17   single    0.970  0.020  1.090
 XP7  C14  H18   single    0.970  0.020  1.090
 XP7  C16  H19   single    0.970  0.020  1.090
 XP7  C18  H20   single    0.970  0.020  1.090
 XP7  C18  H21   single    0.970  0.020  1.090
 XP7  C19  H22   single    0.970  0.020  1.090
 XP7  C19  H23   single    0.970  0.020  1.090
 XP7  N20  H24   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
 XP7  O24   C4   C1   125.32  3.000
 XP7  O24   C4   C6   116.58  3.000
 XP7  C1    C4   C6   118.09  3.000
 XP7  F25   C5   C3   118.51  3.000
 XP7  C3    C5   C2   121.73  3.000
 XP7  F25   C5   C2   119.76  3.000
 XP7  CL26  C6   C3   119.49  3.000
 XP7  CL26  C6   C4   118.85  3.000
 XP7  C3    C6   C4   121.67  3.000
 XP7  O22   C7   N20  126.18  3.000
 XP7  O22   C7   C9   126.70  3.000
 XP7  N20   C7   C9   107.11  3.000
 XP7  O23   C8   N21  122.07  3.000
 XP7  O23   C8   C17  120.74  3.000
 XP7  N21   C8   C17  117.19  3.000
 XP7  H2    C10  H1   107.71  3.000
 XP7  H2    C10  C16  109.38  3.000
 XP7  H1    C10  C16  112.18  3.000
 XP7  H2    C10  C9   110.04  3.000
 XP7  H1    C10  C9   113.32  3.000
 XP7  C16   C10  C9   104.16  3.000
 XP7  H4    C13  H3   106.94  3.000
 XP7  H4    C13  N21  108.60  3.000
 XP7  H3    C13  N21  110.82  3.000
 XP7  H4    C13  C11  109.34  3.000
 XP7  H3    C13  C11  110.11  3.000
 XP7  N21   C13  C11  110.93  3.000
 XP7  H5    C15  C18  107.83  3.000
 XP7  H5    C15  C12  108.32  3.000
 XP7  C18   C15  C12  112.96  3.000
 XP7  H5    C15  C11  107.67  3.000
 XP7  C12   C15  C11  109.67  3.000
 XP7  C18   C15  C11  110.22  3.000
 XP7  H7    C17  H6   105.69  3.000
 XP7  H7    C17  C19  109.96  3.000
 XP7  H6    C17  C19  109.31  3.000
 XP7  H7    C17  C8   109.02  3.000
 XP7  H6    C17  C8   109.47  3.000
 XP7  C19   C17  C8   113.11  3.000
 XP7  H8    C1   C2   118.49  3.000
 XP7  H8    C1   C4   120.59  3.000
 XP7  C2    C1   C4   120.92  3.000
 XP7  H9    C2   C1   120.14  3.000
 XP7  H9    C2   C5   120.72  3.000
 XP7  C1    C2   C5   119.13  3.000
 XP7  H10   C3   C6   120.74  3.000
 XP7  H10   C3   C5   120.81  3.000
 XP7  C6    C3   C5   118.45  3.000
 XP7  H12   C9   H11  107.27  3.000
 XP7  H12   C9   C10  111.76  3.000
 XP7  H11   C9   C10  114.22  3.000
 XP7  H12   C9   C7   107.96  3.000
 XP7  H11   C9   C7   111.44  3.000
 XP7  C10   C9   C7   104.07  3.000
 XP7  H14   C11  H13  107.22  3.000
 XP7  H14   C11  C15  110.02  3.000
 XP7  H13   C11  C15  110.53  3.000
 XP7  H14   C11  C13  109.34  3.000
 XP7  H13   C11  C13  108.82  3.000
 XP7  C15   C11  C13  110.83  3.000
 XP7  H16   C12  H15  107.37  3.000
 XP7  H16   C12  C14  109.39  3.000
 XP7  H15   C12  C14  108.66  3.000
 XP7  H16   C12  C15  109.60  3.000
 XP7  H15   C12  C15  111.01  3.000
 XP7  C14   C12  C15  110.74  3.000
 XP7  H18   C14  H17  107.38  3.000
 XP7  H18   C14  N21  108.60  3.000
 XP7  H17   C14  N21  109.36  3.000
 XP7  H18   C14  C12  109.52  3.000
 XP7  H17   C14  C12  110.89  3.000
 XP7  N21   C14  C12  110.98  3.000
 XP7  H19   C16  N20  109.76  3.000
 XP7  H19   C16  C19  108.67  3.000
 XP7  N20   C16  C19  112.21  3.000
 XP7  H19   C16  C10  109.80  3.000
 XP7  C19   C16  C10  114.52  3.000
 XP7  N20   C16  C10  101.69  3.000
 XP7  H21   C18  H20  107.89  3.000
 XP7  H21   C18  O24  110.42  3.000
 XP7  H20   C18  O24  110.32  3.000
 XP7  H21   C18  C15  109.89  3.000
 XP7  H20   C18  C15  110.63  3.000
 XP7  O24   C18  C15  107.70  3.000
 XP7  H23   C19  H22  107.20  3.000
 XP7  H23   C19  C16  109.22  3.000
 XP7  H22   C19  C16  108.95  3.000
 XP7  H23   C19  C17  109.89  3.000
 XP7  H22   C19  C17  110.76  3.000
 XP7  C16   C19  C17  110.73  3.000
 XP7  H24   N20  C16  121.98  3.000
 XP7  H24   N20  C7   121.55  3.000
 XP7  C16   N20  C7   115.11  3.000
 XP7  C14   N21  C13  113.39  3.000
 XP7  C14   N21  C8   121.04  3.000
 XP7  C13   N21  C8   125.49  3.000
 XP7  C18   O24  C4   119.96  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
 XP7  CONST_01  C5    C2   C1   C4      0.00   0.0  0
 XP7  CONST_02  C5    C3   C6   C4      0.00   0.0  0
 XP7  CONST_03  C2    C1   C4   C6      0.00   0.0  0
 XP7  CONST_04  C2    C5   C3   C6      0.00   0.0  0
 XP7  CONST_05  C3    C5   C2   C1      0.00   0.0  0
 XP7  CONST_06  C3    C6   C4   C1      0.00   0.0  0
 XP7  CONST_07  C16   N20  C7   C9      0.00   0.0  0
 XP7  CONST_08  CL26  C6   C3   C5    180.00   0.0  0
 XP7  CONST_09  F25   C5   C3   C6    180.00   0.0  0
 XP7  CONST_10  F25   C5   C2   C1    180.00   0.0  0
 XP7  CONST_11  CL26  C6   C4   C1    180.00   0.0  0
 XP7  CONST_12  O24   C4   C1   C2    180.00   0.0  0
 XP7  CONST_13  O24   C4   C6   C3    180.00   0.0  0
 XP7  CONST_14  O22   C7   N20  C16   180.00   0.0  0
 XP7  CONST_15  H9    C2   C1   C4    180.00   0.0  0
 XP7  CONST_16  H10   C3   C6   C4    180.00   0.0  0
 XP7  CONST_17  H8    C1   C2   C5    180.00   0.0  0
 XP7  CONST_18  H24   N20  C7   C9    180.00   0.0  0
 XP7  CONST_19  C17   C8   N21  C13     0.00   0.0  0
 XP7  CONST_20  O23   C8   N21  C13   180.00   0.0  0
 XP7  CONST_21  C14   N21  C8   C17   180.00   0.0  0
 XP7  CONST_22  O23   C8   N21  C14     0.00   0.0  0
 XP7  Var_01    C16   C10  C9   C7     25.54  30.0  1
 XP7  Var_02    N20   C7   C9   C10   -14.13  30.0  1
 XP7  Var_03    C12   C14  N21  C13    57.49  30.0  1
 XP7  Var_04    N21   C13  C11  C15    55.47  30.0  1
 XP7  Var_05    N21   C14  C12  C15   -55.59  30.0  1
 XP7  Var_06    C14   N21  C13  C11   -57.37  30.0  1
 XP7  Var_07    C15   C18  O24  C4    173.23  30.0  1
 XP7  Var_08    C16   C19  C17  C8   -176.18  30.0  3
 XP7  Var_09    N21   C8   C17  C19   177.95  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
 XP7  chir_01  C15  C11  C18  C12  negativ
 XP7  chir_02  C16  C10  N20  C19  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
 XP7  plan-1  C4    0.020
 XP7  plan-1  C5    0.020
 XP7  plan-1  C6    0.020
 XP7  plan-1  C1    0.020
 XP7  plan-1  C2    0.020
 XP7  plan-1  C3    0.020
 XP7  plan-1  O24   0.020
 XP7  plan-1  F25   0.020
 XP7  plan-1  CL26  0.020
 XP7  plan-1  H8    0.020
 XP7  plan-1  H9    0.020
 XP7  plan-1  H10   0.020
 XP7  plan-2  C8    0.020
 XP7  plan-2  C13   0.020
 XP7  plan-2  C17   0.020
 XP7  plan-2  C14   0.020
 XP7  plan-2  N21   0.020
 XP7  plan-2  O23   0.020
 XP7  plan-3  C7    0.020
 XP7  plan-3  C9    0.020
 XP7  plan-3  C16   0.020
 XP7  plan-3  N20   0.020
 XP7  plan-3  H24   0.020
 XP7  plan-3  O22   0.020

