# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 11:17:42 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: N-(1-benzylpiperidin-4-yl)-4-sulfanylbutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCCCC(=O)NC1CCN(CC1)Cc2ccccc2
#
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
 F1H  F1H  N-(1-benzylpiperidin-4-yl)-4-sulfanylbutanamide  ligand  44  20  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F1H
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
 F1H  C16   C  CR16  0  -0.284  -4.5874  -0.4372   1.0897
 F1H  C17   C  CR16  0  -0.241  -5.4114  -1.4157   1.6266
 F1H  C20   C  CR16  0  -0.315  -5.6661  -0.6931  -1.0334
 F1H  C15   C  CR6   0   0.082  -4.7067  -0.0630  -0.2475
 F1H  C12   C  CH2   0  -0.282  -1.7670   2.2214  -0.5818
 F1H  C13   C  CH2   0  -0.446  -0.4014   2.2079   0.0890
 F1H  C14   C  CH2   0  -0.311  -3.8439   1.0339  -0.8194
 F1H  C10   C  CH2   0  -0.283  -1.7542  -0.1574  -0.8451
 F1H  C9    C  CH2   0  -0.427  -0.3917  -0.2729  -0.1810
 F1H  C7    C  CH2   0  -0.553   6.3791  -0.1666   1.1875
 F1H  C5    C  CH2   0  -0.582   3.9995   0.4712   0.7511
 F1H  C6    C  CH2   0  -0.413   5.2449  -0.1832   0.1741
 F1H  C1    C  CH1   0  -0.067   0.4153   1.0082  -0.3752
 F1H  O4    O  O     0  -0.501   2.9054   0.0765  -1.3588
 F1H  S8    S  S2    0  -0.257   7.8344  -0.9958   0.4640
 F1H  N2    N  NH1   0  -0.645   1.6848   0.9651   0.3204
 F1H  N11   N  NT    0  -0.415  -2.4839   0.9863  -0.3303
 F1H  C18   C  CR16  0  -0.272  -6.3721  -2.0353   0.8352
 F1H  C19   C  CR16  0  -0.242  -6.4974  -1.6698  -0.4978
 F1H  H16   H  HCR6  0   0.244  -3.8331   0.0362   1.7058
 F1H  H17   H  HCR6  0   0.251  -5.3036  -1.6973   2.6665
 F1H  H20   H  HCR6  0   0.246  -5.7648  -0.4198  -2.0780
 F1H  H12   H  HCH2  0   0.241  -2.3541   3.0549  -0.1896
 F1H  H12A  H  HCH2  0   0.190  -1.6381   2.4058  -1.6632
 F1H  H13   H  HCH2  0   0.244   0.1253   3.1364  -0.1412
 F1H  H13A  H  HCH2  0   0.224  -0.5365   2.1660   1.1749
 F1H  H14   H  HCH2  0   0.210  -3.8979   1.0016  -1.9209
 F1H  H14A  H  HCH2  0   0.251  -4.2703   1.9985  -0.5256
 F1H  H10   H  HCH2  0   0.192  -1.6277  -0.0886  -1.9411
 F1H  H10A  H  HCH2  0   0.243  -2.3304  -1.0646  -0.6543
 F1H  H9    H  HCH2  0   0.219  -0.5258  -0.4592   0.8887
 F1H  H9A   H  HCH2  0   0.238   0.1495  -1.1250  -0.5979
 F1H  H7    H  HCH2  0   0.265   6.6460   0.8574   1.4491
 F1H  H7A   H  HCH2  0   0.263   6.0841  -0.6848   2.1006
 F1H  H5    H  HCH2  0   0.265   3.7012  -0.0356   1.6741
 F1H  H5A   H  HCH2  0   0.271   4.2145   1.5060   1.0364
 F1H  H6    H  HCH2  0   0.240   5.5568   0.3381  -0.7326
 F1H  H6A   H  HCH2  0   0.239   5.0245  -1.2144  -0.1107
 F1H  H1    H  HCH1  0   0.237   0.6275   1.1285  -1.4410
 F1H  HS8   H  HSH1  0   0.222   8.6960  -0.7517   1.4572
 F1H  HN2   H  HNH1  0   0.394   1.6804   1.2081   1.2991
 F1H  H18   H  HCR6  0   0.252  -7.0140  -2.7992   1.2550
 F1H  H19   H  HCR6  0   0.252  -7.2374  -2.1494  -1.1257
 F1H  C3    C  C     0   0.560   2.8209   0.4739  -0.2052

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
 F1H  C16  C17   aromatic  1.387  0.020  1.387
 F1H  C16  C15   aromatic  1.394  0.020  1.394
 F1H  C17  C18   aromatic  1.390  0.020  1.390
 F1H  C20  C15   aromatic  1.391  0.020  1.391
 F1H  C20  C19   aromatic  1.390  0.020  1.390
 F1H  C15  C14   single    1.508  0.020  1.508
 F1H  C12  C13   single    1.522  0.020  1.522
 F1H  C12  N11   single    1.450  0.020  1.450
 F1H  C13  C1    single    1.524  0.020  1.524
 F1H  C14  N11   single    1.446  0.020  1.446
 F1H  C10  C9    single    1.520  0.020  1.520
 F1H  C10  N11   single    1.451  0.020  1.451
 F1H  C9   C1    single    1.526  0.020  1.526
 F1H  C7   C6    single    1.521  0.020  1.521
 F1H  C7   S8    single    1.825  0.020  1.825
 F1H  C5   C6    single    1.521  0.020  1.521
 F1H  C5   C3    single    1.518  0.020  1.518
 F1H  C3   O4    double    1.223  0.020  1.223
 F1H  C3   N2    single    1.345  0.020  1.345
 F1H  C1   N2    single    1.448  0.020  1.448
 F1H  C18  C19   aromatic  1.388  0.020  1.388
 F1H  C16  H16   single    0.930  0.020  1.080
 F1H  C17  H17   single    0.930  0.020  1.080
 F1H  C20  H20   single    0.930  0.020  1.080
 F1H  C12  H12   single    0.970  0.020  1.090
 F1H  C12  H12A  single    0.970  0.020  1.090
 F1H  C13  H13   single    0.970  0.020  1.090
 F1H  C13  H13A  single    0.970  0.020  1.090
 F1H  C14  H14   single    0.970  0.020  1.090
 F1H  C14  H14A  single    0.970  0.020  1.090
 F1H  C10  H10   single    0.970  0.020  1.090
 F1H  C10  H10A  single    0.970  0.020  1.090
 F1H  C9   H9    single    0.970  0.020  1.090
 F1H  C9   H9A   single    0.970  0.020  1.090
 F1H  C7   H7    single    0.970  0.020  1.090
 F1H  C7   H7A   single    0.970  0.020  1.090
 F1H  C5   H5    single    0.970  0.020  1.090
 F1H  C5   H5A   single    0.970  0.020  1.090
 F1H  C6   H6    single    0.970  0.020  1.090
 F1H  C6   H6A   single    0.970  0.020  1.090
 F1H  C1   H1    single    0.970  0.020  1.090
 F1H  S8   HS8   single    1.200  0.020  1.300
 F1H  N2   HN2   single    0.860  0.020  1.020
 F1H  C18  H18   single    0.930  0.020  1.080
 F1H  C19  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
 F1H  H16   C16  C15  119.22  3.000
 F1H  H16   C16  C17  120.12  3.000
 F1H  C15   C16  C17  120.66  3.000
 F1H  H17   C17  C18  119.98  3.000
 F1H  H17   C17  C16  119.73  3.000
 F1H  C18   C17  C16  120.29  3.000
 F1H  H20   C20  C19  119.60  3.000
 F1H  H20   C20  C15  119.53  3.000
 F1H  C19   C20  C15  120.87  3.000
 F1H  C14   C15  C20  120.64  3.000
 F1H  C14   C15  C16  120.68  3.000
 F1H  C20   C15  C16  118.65  3.000
 F1H  H12A  C12  H12  106.67  3.000
 F1H  H12A  C12  N11  111.69  3.000
 F1H  H12   C12  N11  108.78  3.000
 F1H  H12A  C12  C13  109.17  3.000
 F1H  H12   C12  C13  109.33  3.000
 F1H  N11   C12  C13  111.08  3.000
 F1H  H13A  C13  H13  107.52  3.000
 F1H  H13A  C13  C1   109.76  3.000
 F1H  H13   C13  C1   110.29  3.000
 F1H  H13A  C13  C12  109.07  3.000
 F1H  H13   C13  C12  109.41  3.000
 F1H  C1    C13  C12  110.71  3.000
 F1H  H14A  C14  H14  105.94  3.000
 F1H  H14A  C14  N11  107.73  3.000
 F1H  H14   C14  N11  112.51  3.000
 F1H  H14A  C14  C15  108.43  3.000
 F1H  H14   C14  C15  109.23  3.000
 F1H  N11   C14  C15  112.70  3.000
 F1H  H10A  C10  H10  106.59  3.000
 F1H  H10A  C10  N11  109.12  3.000
 F1H  H10   C10  N11  111.12  3.000
 F1H  H10A  C10  C9   109.49  3.000
 F1H  H10   C10  C9   109.59  3.000
 F1H  N11   C10  C9   110.83  3.000
 F1H  H9A   C9   H9   107.52  3.000
 F1H  H9A   C9   C1   110.14  3.000
 F1H  H9    C9   C1   109.40  3.000
 F1H  H9A   C9   C10  109.67  3.000
 F1H  H9    C9   C10  109.28  3.000
 F1H  C1    C9   C10  110.76  3.000
 F1H  H7A   C7   H7   108.16  3.000
 F1H  H7A   C7   S8   109.38  3.000
 F1H  H7    C7   S8   109.07  3.000
 F1H  H7A   C7   C6   110.54  3.000
 F1H  H7    C7   C6   110.65  3.000
 F1H  S8    C7   C6   109.00  3.000
 F1H  H5A   C5   H5   105.75  3.000
 F1H  H5A   C5   C3   108.36  3.000
 F1H  H5    C5   C3   108.69  3.000
 F1H  H5A   C5   C6   110.18  3.000
 F1H  H5    C5   C6   110.12  3.000
 F1H  C3    C5   C6   113.43  3.000
 F1H  H6A   C6   H6   106.98  3.000
 F1H  H6A   C6   C5   109.88  3.000
 F1H  H6    C6   C5   110.11  3.000
 F1H  H6A   C6   C7   109.54  3.000
 F1H  H6    C6   C7   109.58  3.000
 F1H  C5    C6   C7   110.68  3.000
 F1H  H1    C1   N2   107.54  3.000
 F1H  H1    C1   C9   108.60  3.000
 F1H  N2    C1   C9   112.17  3.000
 F1H  H1    C1   C13  108.32  3.000
 F1H  N2    C1   C13  110.30  3.000
 F1H  C9    C1   C13  109.80  3.000
 F1H  HS8   S8   C7    97.84  3.000
 F1H  HN2   N2   C1   117.07  3.000
 F1H  HN2   N2   C3   118.10  3.000
 F1H  C1    N2   C3   124.32  3.000
 F1H  C10   N11  C14  112.26  3.000
 F1H  C10   N11  C12  111.17  3.000
 F1H  C14   N11  C12  112.23  3.000
 F1H  H18   C18  C19  120.31  3.000
 F1H  H18   C18  C17  120.23  3.000
 F1H  C19   C18  C17  119.46  3.000
 F1H  H19   C19  C18  120.15  3.000
 F1H  H19   C19  C20  119.78  3.000
 F1H  C18   C19  C20  120.07  3.000
 F1H  N2    C3   O4   123.07  3.000
 F1H  N2    C3   C5   114.24  3.000
 F1H  O4    C3   C5   122.69  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
 F1H  CONST_01  C19  C18  C17  C16     0.00   0.0  0
 F1H  CONST_02  C19  C20  C15  C16     0.00   0.0  0
 F1H  CONST_03  C20  C15  C16  C17     0.00   0.0  0
 F1H  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 F1H  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 F1H  CONST_06  C18  C19  C20  C15     0.00   0.0  0
 F1H  CONST_07  C14  C15  C16  C17   180.00   0.0  0
 F1H  CONST_08  C19  C20  C15  C14   180.00   0.0  0
 F1H  CONST_09  H18  C18  C17  C16   180.00   0.0  0
 F1H  CONST_10  H20  C20  C15  C16   180.00   0.0  0
 F1H  CONST_11  H19  C19  C18  C17   180.00   0.0  0
 F1H  CONST_12  H16  C16  C15  C20   180.00   0.0  0
 F1H  CONST_13  H17  C17  C16  C15   180.00   0.0  0
 F1H  CONST_14  C1   N2   C3   C5    180.00   0.0  0
 F1H  CONST_15  O4   C3   N2   C1      0.00   0.0  0
 F1H  CONST_16  HN2  N2   C3   C5      0.00   0.0  0
 F1H  Var_01    C9   C10  N11  C12    60.35  30.0  1
 F1H  Var_02    C10  N11  C12  C13   -60.24  30.0  1
 F1H  Var_03    N11  C12  C13  C1     56.63  30.0  1
 F1H  Var_04    N11  C10  C9   C1    -56.95  30.0  1
 F1H  Var_05    N11  C14  C15  C16    39.68  30.0  2
 F1H  Var_06    C12  N11  C14  C15  -164.29  30.0  3
 F1H  Var_07    C3   C5   C6   C7   -179.32  30.0  2
 F1H  Var_08    S8   C7   C6   C5    178.68  30.0  2
 F1H  Var_09    O4   C3   C5   C6     -5.14  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
 F1H  chir_01  C1  C13  C9  N2  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
 F1H  plan-1  C16  0.020
 F1H  plan-1  C17  0.020
 F1H  plan-1  C20  0.020
 F1H  plan-1  C15  0.020
 F1H  plan-1  C14  0.020
 F1H  plan-1  C18  0.020
 F1H  plan-1  C19  0.020
 F1H  plan-1  H16  0.020
 F1H  plan-1  H17  0.020
 F1H  plan-1  H20  0.020
 F1H  plan-1  H18  0.020
 F1H  plan-1  H19  0.020
 F1H  plan-2  C5   0.020
 F1H  plan-2  C1   0.020
 F1H  plan-2  O4   0.020
 F1H  plan-2  N2   0.020
 F1H  plan-2  HN2  0.020
 F1H  plan-2  C3   0.020

