# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:28:55 2021
#   Inital geometry file: a 82 line input string
#   Ligand name: (1-methylpiperidin-4-yl) 3-fluoranylbenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC(CC1)OC(=O)c2cccc(F)c2
#
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
 S2V  S2V  '(1-methylpiperidin-4-yl) 3-fluoranylbenzoate'  ligand  33  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S2V
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
 S2V  N1   N  NT    0  -0.392  5.3144  14.6656  -3.9245
 S2V  C4   C  CH1   0   0.051  5.3024  17.5013  -3.2004
 S2V  C5   C  CH2   0  -0.482  4.0045  16.7238  -3.3534
 S2V  C6   C  CH2   0  -0.330  4.2264  15.5448  -4.3096
 S2V  C8   C  CR6   0  -0.077  4.5480  20.5956  -1.3222
 S2V  C10  C  CR16  0  -0.226  4.9879  21.1659   0.9727
 S2V  C13  C  CR16  0  -0.425  3.9291  21.8292  -1.5104
 S2V  C1   C  CH3   0  -0.528  5.0059  13.8311  -2.7814
 S2V  C11  C  CR16  0  -0.397  4.3708  22.3963   0.7992
 S2V  C12  C  CR6   0   0.551  3.8530  22.7009  -0.4457
 S2V  C2   C  CH2   0  -0.332  6.5449  15.4209  -3.7695
 S2V  C3   C  CH2   0  -0.473  6.4372  16.5854  -2.7781
 S2V  C9   C  CR16  0  -0.280  5.0793  20.2641  -0.0776
 S2V  F1   F  F     0  -0.312  3.2522  23.8865  -0.6253
 S2V  O1   O  O2    0  -0.473  5.1810  18.5208  -2.1880
 S2V  O2   O  O     0  -0.445  4.1815  19.9581  -3.5812
 S2V  H2   H  HCH1  0   0.237  5.5611  17.9759  -4.1526
 S2V  H3   H  HCH2  0   0.250  3.2106  17.3596  -3.7498
 S2V  H4   H  HCH2  0   0.236  3.6759  16.3636  -2.3743
 S2V  H5   H  HCH2  0   0.234  4.4388  15.9353  -5.3108
 S2V  H6   H  HCH2  0   0.245  3.3067  14.9619  -4.3920
 S2V  H7   H  HCR6  0   0.278  5.4004  20.9088   1.9386
 S2V  H8   H  HCR6  0   0.285  3.5117  22.1049  -2.4697
 S2V  H9   H  HCH3  0   0.234  4.0918  13.2683  -2.9757
 S2V  H10  H  HCH3  0   0.233  5.8093  13.1084  -2.6281
 S2V  H11  H  HCH3  0   0.200  4.8636  14.3687  -1.8342
 S2V  H12  H  HCR6  0   0.290  4.2921  23.1029   1.6149
 S2V  H13  H  HCH2  0   0.234  6.8278  15.8148  -4.7518
 S2V  H14  H  HCH2  0   0.246  7.3455  14.7451  -3.4623
 S2V  H15  H  HCH2  0   0.235  6.2579  16.2069  -1.7674
 S2V  H16  H  HCH2  0   0.249  7.3816  17.1344  -2.7546
 S2V  H17  H  HCR6  0   0.269  5.5633  19.3115   0.0828
 S2V  C7   C  C     0   0.615  4.6093  19.6717  -2.4889

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
 S2V  O2   C7   double    1.208  0.020  1.208
 S2V  C2   C3   single    1.533  0.020  1.533
 S2V  C2   N1   single    1.452  0.020  1.452
 S2V  C6   N1   single    1.451  0.020  1.451
 S2V  C6   C5   single    1.534  0.020  1.534
 S2V  C4   C3   single    1.518  0.020  1.518
 S2V  C4   C5   single    1.521  0.020  1.521
 S2V  C4   O1   single    1.442  0.020  1.442
 S2V  N1   C1   single    1.448  0.020  1.448
 S2V  C7   O1   single    1.320  0.020  1.320
 S2V  C7   C8   single    1.489  0.020  1.489
 S2V  C8   C13  aromatic  1.393  0.020  1.393
 S2V  C8   C9   aromatic  1.393  0.020  1.393
 S2V  C13  C12  aromatic  1.378  0.020  1.378
 S2V  C9   C10  aromatic  1.387  0.020  1.387
 S2V  C12  F1   single    1.341  0.020  1.341
 S2V  C12  C11  aromatic  1.382  0.020  1.382
 S2V  C10  C11  aromatic  1.387  0.020  1.387
 S2V  C4   H2   single    0.970  0.020  1.090
 S2V  C5   H3   single    0.970  0.020  1.090
 S2V  C5   H4   single    0.970  0.020  1.090
 S2V  C6   H5   single    0.970  0.020  1.090
 S2V  C6   H6   single    0.970  0.020  1.090
 S2V  C10  H7   single    0.930  0.020  1.080
 S2V  C13  H8   single    0.930  0.020  1.080
 S2V  C1   H9   single    0.970  0.020  1.090
 S2V  C1   H10  single    0.970  0.020  1.090
 S2V  C1   H11  single    0.970  0.020  1.090
 S2V  C11  H12  single    0.930  0.020  1.080
 S2V  C2   H13  single    0.970  0.020  1.090
 S2V  C2   H14  single    0.970  0.020  1.090
 S2V  C3   H15  single    0.970  0.020  1.090
 S2V  C3   H16  single    0.970  0.020  1.090
 S2V  C9   H17  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
 S2V  C2   N1   C1   113.32  3.000
 S2V  C1   N1   C6   113.51  3.000
 S2V  C2   N1   C6   110.40  3.000
 S2V  H2   C4   O1   108.90  3.000
 S2V  H2   C4   C3   109.07  3.000
 S2V  O1   C4   C3   107.11  3.000
 S2V  H2   C4   C5   109.62  3.000
 S2V  O1   C4   C5   111.12  3.000
 S2V  C3   C4   C5   110.95  3.000
 S2V  H4   C5   H3   107.36  3.000
 S2V  H4   C5   C6   110.38  3.000
 S2V  H3   C5   C6   109.06  3.000
 S2V  H4   C5   C4   109.55  3.000
 S2V  H3   C5   C4   111.07  3.000
 S2V  C6   C5   C4   109.41  3.000
 S2V  H6   C6   H5   106.53  3.000
 S2V  H6   C6   C5   109.61  3.000
 S2V  H5   C6   C5   108.89  3.000
 S2V  H6   C6   N1   109.16  3.000
 S2V  H5   C6   N1   108.25  3.000
 S2V  C5   C6   N1   114.12  3.000
 S2V  C9   C8   C13  120.06  3.000
 S2V  C9   C8   C7   122.44  3.000
 S2V  C13  C8   C7   117.50  3.000
 S2V  H7   C10  C9   119.77  3.000
 S2V  H7   C10  C11  119.49  3.000
 S2V  C9   C10  C11  120.74  3.000
 S2V  H8   C13  C12  120.17  3.000
 S2V  H8   C13  C8   121.13  3.000
 S2V  C12  C13  C8   118.71  3.000
 S2V  H11  C1   H10  107.36  3.000
 S2V  H11  C1   H9   107.31  3.000
 S2V  H10  C1   H9   107.47  3.000
 S2V  H11  C1   N1   115.22  3.000
 S2V  H10  C1   N1   109.60  3.000
 S2V  H9   C1   N1   109.58  3.000
 S2V  H12  C11  C12  120.52  3.000
 S2V  H12  C11  C10  121.15  3.000
 S2V  C12  C11  C10  118.33  3.000
 S2V  F1   C12  C11  118.90  3.000
 S2V  C11  C12  C13  122.39  3.000
 S2V  F1   C12  C13  118.71  3.000
 S2V  H14  C2   H13  106.59  3.000
 S2V  H14  C2   C3   109.86  3.000
 S2V  H13  C2   C3   108.96  3.000
 S2V  H14  C2   N1   109.23  3.000
 S2V  H13  C2   N1   108.07  3.000
 S2V  C3   C2   N1   113.87  3.000
 S2V  H16  C3   H15  107.20  3.000
 S2V  H16  C3   C2   109.56  3.000
 S2V  H15  C3   C2   110.25  3.000
 S2V  H16  C3   C4   110.42  3.000
 S2V  H15  C3   C4   110.07  3.000
 S2V  C2   C3   C4   109.32  3.000
 S2V  H17  C9   C10  119.35  3.000
 S2V  H17  C9   C8   120.88  3.000
 S2V  C10  C9   C8   119.77  3.000
 S2V  C7   O1   C4   119.54  3.000
 S2V  O2   C7   O1   124.51  3.000
 S2V  O1   C7   C8   112.34  3.000
 S2V  O2   C7   C8   123.15  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
 S2V  CONST_01  C11  C12  C13  C8     0.00   0.0  0
 S2V  CONST_02  C11  C10  C9   C8     0.00   0.0  0
 S2V  CONST_03  C13  C8   C9   C10    0.00   0.0  0
 S2V  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 S2V  CONST_05  C9   C8   C13  C12    0.00   0.0  0
 S2V  CONST_06  C9   C10  C11  C12    0.00   0.0  0
 S2V  CONST_07  C12  C13  C8   C7   180.00   0.0  0
 S2V  CONST_08  C10  C9   C8   C7   180.00   0.0  0
 S2V  CONST_09  F1   C12  C13  C8   180.00   0.0  0
 S2V  CONST_10  F1   C12  C11  C10  180.00   0.0  0
 S2V  CONST_11  H7   C10  C9   C8   180.00   0.0  0
 S2V  CONST_12  H17  C9   C8   C13  180.00   0.0  0
 S2V  CONST_13  H12  C11  C12  C13  180.00   0.0  0
 S2V  CONST_14  H8   C13  C12  C11  180.00   0.0  0
 S2V  Var_01    C4   C3   C2   N1   -55.95  30.0  1
 S2V  Var_02    C4   C5   C6   N1    55.08  30.0  1
 S2V  Var_03    C2   N1   C6   C5   -55.36  30.0  1
 S2V  Var_04    C3   C2   N1   C6    55.75  30.0  1
 S2V  Var_05    C8   C7   O1   C4   179.02  30.0  2
 S2V  Var_06    O2   C7   C8   C13    1.91  30.0  3
 S2V  Var_07    H9   C1   N1   C6    54.90  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
 S2V  chir_01  C4  C3  C5  O1  negativ

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
 S2V  plan-1  C8   0.020
 S2V  plan-1  C10  0.020
 S2V  plan-1  C13  0.020
 S2V  plan-1  C11  0.020
 S2V  plan-1  C12  0.020
 S2V  plan-1  C9   0.020
 S2V  plan-1  F1   0.020
 S2V  plan-1  H7   0.020
 S2V  plan-1  H8   0.020
 S2V  plan-1  H12  0.020
 S2V  plan-1  H17  0.020
 S2V  plan-1  C7   0.020
 S2V  plan-2  C8   0.020
 S2V  plan-2  O1   0.020
 S2V  plan-2  O2   0.020
 S2V  plan-2  C7   0.020

