# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 02:58:58 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N-{[(3R)-1-benzylpiperidin-3-yl]methyl}naphthalene-2-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=[S](=O)(NC[C@@H]1CCCN(C1)Cc2ccccc2)c3ccc4ccccc4c3
#
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
 5HH  5HH  N-{[(3R)-1-benzylpiperidin-3-yl]methyl}naphthalene-2-sulfonamide  ligand  54  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5HH
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
 5HH  C2   C  CR16  0  -0.248   5.7929  -3.5138  -0.3347
 5HH  C3   C  CR16  0  -0.254   5.5292  -3.2645   1.0284
 5HH  C4   C  CR16  0  -0.242  -6.9455  -2.4487   0.3296
 5HH  C5   C  CR16  0  -0.241  -7.3268  -1.1141  -1.6279
 5HH  C6   C  CR16  0  -0.306   5.4102  -2.6142  -1.2927
 5HH  C7   C  CR16  0  -0.303   4.8862  -2.1184   1.4086
 5HH  C10  C  CR16  0  -0.315  -6.0175  -0.6512  -1.5601
 5HH  C11  C  CR16  0  -0.243   3.6983   0.6784  -1.5262
 5HH  C12  C  CR16  0  -0.292   3.8123   0.0190   0.8072
 5HH  C14  C  CR66  0   0.128   4.4784  -1.1722   0.4402
 5HH  C16  C  CR6   0  -0.208   3.4388   0.9128  -0.1575
 5HH  C18  C  C     0  -0.413  -1.8581   2.2850   0.9286
 5HH  C19  C  C     0  -0.317  -3.9349   0.9397   1.3494
 5HH  C20  C  C     0  -0.301  -1.8658  -0.2157   1.0016
 5HH  C21  C  CR16  0  -0.289  -1.2001   1.0195   0.3832
 5HH  C13  C  CR66  0   0.125   4.7448  -1.4216  -0.9306
 5HH  C8   C  CR16  0  -0.301   4.3378  -0.4688  -1.8959
 5HH  S1   S  S     0   1.376   2.5493   2.3768   0.2945
 5HH  O1   O  OS    0  -0.654   2.6706   2.5506   1.7324
 5HH  O2   O  OS    0  -0.658   2.9534   3.4454  -0.6046
 5HH  N2   N  NC1   0  -0.728   0.9662   2.0783  -0.0303
 5HH  C23  C  CH2   0  -0.262   0.2979   0.9706   0.6480
 5HH  C17  C  C     0  -0.448  -3.3725   2.2267   0.7505
 5HH  N1   N  NR6   0  -0.405  -3.3052  -0.2661   0.8319
 5HH  C22  C  CH2   0  -0.337  -3.7261  -0.6124  -0.5122
 5HH  C15  C  CR6   0   0.099  -5.1583  -1.0841  -0.5558
 5HH  C9   C  CR16  0  -0.284  -5.6391  -1.9866   0.3914
 5HH  C1   C  CR16  0  -0.272  -7.7951  -2.0148  -0.6823
 5HH  H1   H  HCR6  0   0.267   6.3016  -4.4247  -0.6214
 5HH  H2   H  HCR6  0   0.266   5.8388  -3.9856   1.7733
 5HH  H4   H  HCR6  0   0.252  -7.9814  -0.7627  -2.4154
 5HH  H5   H  HCR6  0   0.264   5.6127  -2.8078  -2.3387
 5HH  H6   H  HCR6  0   0.265   4.6827  -1.9226   2.4541
 5HH  H7   H  HCR6  0   0.245  -5.6612   0.0576  -2.2992
 5HH  H8   H  HCR6  0   0.282   3.4034   1.4000  -2.2763
 5HH  H9   H  HCR6  0   0.285   3.6098   0.2069   1.8539
 5HH  H10  H  H     0   0.211  -1.6215   2.3768   1.9959
 5HH  H11  H  H     0   0.237  -1.4485   3.1730   0.4429
 5HH  H12  H  H     0   0.226  -3.7866   0.9578   2.4348
 5HH  H13  H  H     0   0.241  -5.0128   0.8759   1.1859
 5HH  H14  H  H     0   0.240  -1.4290  -1.1277   0.5846
 5HH  H15  H  H     0   0.229  -1.6511  -0.2299   2.0777
 5HH  H16  H  HCR6  0   0.238  -1.3519   0.9819  -0.7039
 5HH  H17  H  HCR6  0   0.270   4.5440  -0.6581  -2.9419
 5HH  H18  H  HNC1  0   0.409   0.7740   2.1206  -1.0264
 5HH  H19  H  HCH2  0   0.254   0.4843   1.0585   1.7196
 5HH  H20  H  HCH2  0   0.246   0.6992   0.0036   0.3207
 5HH  H21  H  H     0   0.234  -3.8453   3.0880   1.2282
 5HH  H22  H  H     0   0.219  -3.6214   2.2902  -0.3139
 5HH  H24  H  HCH2  0   0.217  -3.6013   0.2007  -1.2438
 5HH  H25  H  HCH2  0   0.252  -3.0803  -1.4253  -0.8601
 5HH  H26  H  HCR6  0   0.242  -4.9835  -2.3218   1.1854
 5HH  H27  H  HCR6  0   0.253  -8.8148  -2.3746  -0.7299
 5HH  H3   H  HCR6  0   0.251  -7.3041  -3.1492   1.0734

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
 5HH  C2   C6   aromatic  1.369  0.020  1.369
 5HH  C2   C3   aromatic  1.411  0.020  1.411
 5HH  C6   C13  aromatic  1.413  0.020  1.413
 5HH  C3   C7   aromatic  1.368  0.020  1.368
 5HH  C13  C8   aromatic  1.416  0.020  1.416
 5HH  C13  C14  aromatic  1.419  0.020  1.419
 5HH  C8   C11  aromatic  1.364  0.020  1.364
 5HH  C7   C14  aromatic  1.414  0.020  1.414
 5HH  C14  C12  aromatic  1.413  0.020  1.413
 5HH  C11  C16  aromatic  1.413  0.020  1.413
 5HH  C12  C16  aromatic  1.367  0.020  1.367
 5HH  C16  S1   single    1.772  0.020  1.772
 5HH  C17  C19  single    1.527  0.020  1.527
 5HH  C17  C18  single    1.526  0.020  1.526
 5HH  C5   C10  aromatic  1.390  0.020  1.390
 5HH  C5   C1   aromatic  1.387  0.020  1.387
 5HH  C19  N1   single    1.455  0.020  1.455
 5HH  C10  C15  aromatic  1.391  0.020  1.391
 5HH  C1   C4   aromatic  1.391  0.020  1.391
 5HH  C18  C21  single    1.527  0.020  1.527
 5HH  S1   O2   double    1.454  0.020  1.454
 5HH  S1   O1   double    1.453  0.020  1.453
 5HH  S1   N2   single    1.643  0.020  1.643
 5HH  C15  C22  single    1.508  0.020  1.508
 5HH  C15  C9   aromatic  1.394  0.020  1.394
 5HH  C4   C9   aromatic  1.387  0.020  1.387
 5HH  N1   C22  single    1.450  0.020  1.450
 5HH  N1   C20  single    1.450  0.020  1.450
 5HH  C21  C20  single    1.533  0.020  1.533
 5HH  C21  C23  single    1.522  0.020  1.522
 5HH  N2   C23  single    1.461  0.020  1.461
 5HH  C2   H1   single    0.930  0.020  1.080
 5HH  C3   H2   single    0.930  0.020  1.080
 5HH  C4   H3   single    0.930  0.020  1.080
 5HH  C5   H4   single    0.930  0.020  1.080
 5HH  C6   H5   single    0.930  0.020  1.080
 5HH  C7   H6   single    0.930  0.020  1.080
 5HH  C10  H7   single    0.930  0.020  1.080
 5HH  C11  H8   single    0.930  0.020  1.080
 5HH  C12  H9   single    0.930  0.020  1.080
 5HH  C18  H10  single    0.970  0.020  1.090
 5HH  C18  H11  single    0.970  0.020  1.090
 5HH  C19  H12  single    0.970  0.020  1.090
 5HH  C19  H13  single    0.970  0.020  1.090
 5HH  C20  H14  single    0.970  0.020  1.090
 5HH  C20  H15  single    0.970  0.020  1.090
 5HH  C21  H16  single    0.970  0.020  1.090
 5HH  C8   H17  single    0.930  0.020  1.080
 5HH  N2   H18  single    0.890  0.020  1.040
 5HH  C23  H19  single    0.970  0.020  1.090
 5HH  C23  H20  single    0.970  0.020  1.090
 5HH  C17  H21  single    0.970  0.020  1.090
 5HH  C17  H22  single    0.970  0.020  1.090
 5HH  C22  H24  single    0.970  0.020  1.090
 5HH  C22  H25  single    0.970  0.020  1.090
 5HH  C9   H26  single    0.930  0.020  1.080
 5HH  C1   H27  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
 5HH  H1   C2   C6   119.95  3.000
 5HH  H1   C2   C3   119.52  3.000
 5HH  C6   C2   C3   120.53  3.000
 5HH  H2   C3   C7   120.10  3.000
 5HH  H2   C3   C2   119.61  3.000
 5HH  C7   C3   C2   120.29  3.000
 5HH  H3   C4   C1   119.95  3.000
 5HH  H3   C4   C9   119.79  3.000
 5HH  C1   C4   C9   120.25  3.000
 5HH  H4   C5   C1   120.16  3.000
 5HH  H4   C5   C10  119.79  3.000
 5HH  C1   C5   C10  120.05  3.000
 5HH  H5   C6   C13  119.12  3.000
 5HH  H5   C6   C2   120.41  3.000
 5HH  C13  C6   C2   120.47  3.000
 5HH  H6   C7   C14  119.07  3.000
 5HH  H6   C7   C3   120.54  3.000
 5HH  C14  C7   C3   120.39  3.000
 5HH  H7   C10  C15  119.52  3.000
 5HH  H7   C10  C5   119.59  3.000
 5HH  C15  C10  C5   120.89  3.000
 5HH  H8   C11  C8   120.05  3.000
 5HH  H8   C11  C16  120.73  3.000
 5HH  C8   C11  C16  119.22  3.000
 5HH  H9   C12  C16  121.18  3.000
 5HH  H9   C12  C14  119.04  3.000
 5HH  C16  C12  C14  119.77  3.000
 5HH  C13  C14  C12  119.18  3.000
 5HH  C12  C14  C7   121.48  3.000
 5HH  C13  C14  C7   119.34  3.000
 5HH  S1   C16  C12  119.82  3.000
 5HH  S1   C16  C11  118.46  3.000
 5HH  C12  C16  C11  121.67  3.000
 5HH  H11  C18  H10  106.49  3.000
 5HH  H11  C18  C17  110.58  3.000
 5HH  H10  C18  C17  109.32  3.000
 5HH  H11  C18  C21  110.70  3.000
 5HH  H10  C18  C21  108.89  3.000
 5HH  C17  C18  C21  110.75  3.000
 5HH  H13  C19  H12  106.43  3.000
 5HH  H13  C19  N1   108.99  3.000
 5HH  H12  C19  N1   107.90  3.000
 5HH  H13  C19  C17  110.74  3.000
 5HH  H12  C19  C17  108.95  3.000
 5HH  N1   C19  C17  113.54  3.000
 5HH  H15  C20  H14  106.55  3.000
 5HH  H15  C20  N1   107.97  3.000
 5HH  H14  C20  N1   108.83  3.000
 5HH  H15  C20  C21  108.72  3.000
 5HH  H14  C20  C21  110.15  3.000
 5HH  N1   C20  C21  114.31  3.000
 5HH  H16  C21  C23  107.89  3.000
 5HH  H16  C21  C20  108.15  3.000
 5HH  C23  C21  C20  109.34  3.000
 5HH  H16  C21  C18  108.80  3.000
 5HH  C23  C21  C18  112.87  3.000
 5HH  C20  C21  C18  109.66  3.000
 5HH  C8   C13  C14  119.11  3.000
 5HH  C14  C13  C6   118.98  3.000
 5HH  C8   C13  C6   121.91  3.000
 5HH  H17  C8   C13  119.09  3.000
 5HH  H17  C8   C11  119.87  3.000
 5HH  C13  C8   C11  121.04  3.000
 5HH  N2   S1   O2   106.20  3.000
 5HH  N2   S1   O1   107.31  3.000
 5HH  O2   S1   O1   120.05  3.000
 5HH  N2   S1   C16  106.45  3.000
 5HH  O1   S1   C16  108.02  3.000
 5HH  O2   S1   C16  108.06  3.000
 5HH  H18  N2   C23  113.61  3.000
 5HH  H18  N2   S1   111.63  3.000
 5HH  C23  N2   S1   119.12  3.000
 5HH  H20  C23  H19  107.55  3.000
 5HH  H20  C23  N2   111.25  3.000
 5HH  H19  C23  N2   108.47  3.000
 5HH  H20  C23  C21  109.66  3.000
 5HH  H19  C23  C21  109.66  3.000
 5HH  N2   C23  C21  110.19  3.000
 5HH  H22  C17  H21  106.32  3.000
 5HH  H22  C17  C19  110.26  3.000
 5HH  H21  C17  C19  109.49  3.000
 5HH  H22  C17  C18  109.69  3.000
 5HH  H21  C17  C18  110.39  3.000
 5HH  C19  C17  C18  110.61  3.000
 5HH  C22  N1   C20  113.88  3.000
 5HH  C20  N1   C19  111.04  3.000
 5HH  C22  N1   C19  113.69  3.000
 5HH  H25  C22  H24  105.68  3.000
 5HH  H25  C22  C15  108.58  3.000
 5HH  H24  C22  C15  108.63  3.000
 5HH  H25  C22  N1   107.49  3.000
 5HH  H24  C22  N1   113.99  3.000
 5HH  C15  C22  N1   112.15  3.000
 5HH  C9   C15  C22  120.69  3.000
 5HH  C9   C15  C10  118.63  3.000
 5HH  C22  C15  C10  120.67  3.000
 5HH  H26  C9   C15  119.33  3.000
 5HH  H26  C9   C4   119.98  3.000
 5HH  C15  C9   C4   120.69  3.000
 5HH  H27  C1   C5   120.25  3.000
 5HH  H27  C1   C4   120.26  3.000
 5HH  C5   C1   C4   119.49  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
 5HH  CONST_01  C8   C13  C6   C2   180.00   0.0  0
 5HH  CONST_02  C14  C13  C6   C2     0.00   0.0  0
 5HH  CONST_03  C14  C7   C3   C2     0.00   0.0  0
 5HH  CONST_04  C13  C6   C2   C3     0.00   0.0  0
 5HH  CONST_05  C13  C14  C7   C3     0.00   0.0  0
 5HH  CONST_06  C12  C14  C7   C3   180.00   0.0  0
 5HH  CONST_07  C10  C5   C1   C4     0.00   0.0  0
 5HH  CONST_08  C10  C15  C9   C4     0.00   0.0  0
 5HH  CONST_09  C9   C15  C10  C5     0.00   0.0  0
 5HH  CONST_10  C9   C4   C1   C5     0.00   0.0  0
 5HH  CONST_11  C7   C3   C2   C6     0.00   0.0  0
 5HH  CONST_12  C11  C8   C13  C6   180.00   0.0  0
 5HH  CONST_13  C7   C14  C13  C6     0.00   0.0  0
 5HH  CONST_14  C12  C14  C13  C6   180.00   0.0  0
 5HH  CONST_15  C8   C13  C14  C7   180.00   0.0  0
 5HH  CONST_16  C16  C12  C14  C7   180.00   0.0  0
 5HH  CONST_17  C14  C13  C8   C11    0.00   0.0  0
 5HH  CONST_18  C14  C12  C16  C11    0.00   0.0  0
 5HH  CONST_19  C8   C13  C14  C12    0.00   0.0  0
 5HH  CONST_20  C8   C11  C16  C12    0.00   0.0  0
 5HH  CONST_21  C13  C8   C11  C16    0.00   0.0  0
 5HH  CONST_22  C13  C14  C12  C16    0.00   0.0  0
 5HH  CONST_23  C1   C5   C10  C15    0.00   0.0  0
 5HH  CONST_24  C1   C4   C9   C15    0.00   0.0  0
 5HH  CONST_25  C22  C15  C9   C4   180.00   0.0  0
 5HH  CONST_26  C22  C15  C10  C5   180.00   0.0  0
 5HH  CONST_27  S1   C16  C12  C14  180.00   0.0  0
 5HH  CONST_28  S1   C16  C11  C8   180.00   0.0  0
 5HH  CONST_29  H6   C7   C3   C2   180.00   0.0  0
 5HH  CONST_30  H5   C6   C2   C3   180.00   0.0  0
 5HH  CONST_31  H4   C5   C1   C4   180.00   0.0  0
 5HH  CONST_32  H3   C4   C1   C5   180.00   0.0  0
 5HH  CONST_33  H2   C3   C2   C6   180.00   0.0  0
 5HH  CONST_34  H17  C8   C13  C6     0.00   0.0  0
 5HH  CONST_35  H1   C2   C3   C7   180.00   0.0  0
 5HH  CONST_36  H9   C12  C14  C7     0.00   0.0  0
 5HH  CONST_37  H27  C1   C5   C10  180.00   0.0  0
 5HH  CONST_38  H26  C9   C15  C10  180.00   0.0  0
 5HH  CONST_39  H8   C11  C16  C12  180.00   0.0  0
 5HH  CONST_40  H7   C10  C15  C9   180.00   0.0  0
 5HH  Var_01    N1   C19  C17  C18  -54.62  30.0  1
 5HH  Var_02    C21  C18  C17  C19   53.19  30.0  1
 5HH  Var_03    C21  C20  N1   C19  -55.32  30.0  1
 5HH  Var_04    C17  C19  N1   C20   54.87  30.0  1
 5HH  Var_05    N1   C22  C15  C10  136.92  30.0  2
 5HH  Var_06    C15  C22  N1   C19  -69.80  30.0  3
 5HH  Var_07    O2   S1   C16  C11  -36.02  30.0  2
 5HH  Var_08    C23  N2   S1   C16   60.21  30.0  3
 5HH  Var_09    S1   N2   C23  C21  170.51  30.0  1

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
 5HH  chir_01  C21  C18  C20  C23  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
 5HH  plan-1  C4   0.020
 5HH  plan-1  C5   0.020
 5HH  plan-1  C10  0.020
 5HH  plan-1  C22  0.020
 5HH  plan-1  C15  0.020
 5HH  plan-1  C9   0.020
 5HH  plan-1  C1   0.020
 5HH  plan-1  H4   0.020
 5HH  plan-1  H7   0.020
 5HH  plan-1  H26  0.020
 5HH  plan-1  H27  0.020
 5HH  plan-1  H3   0.020
 5HH  plan-2  C2   0.020
 5HH  plan-2  C3   0.020
 5HH  plan-2  C6   0.020
 5HH  plan-2  C7   0.020
 5HH  plan-2  C11  0.020
 5HH  plan-2  C12  0.020
 5HH  plan-2  C14  0.020
 5HH  plan-2  C16  0.020
 5HH  plan-2  C13  0.020
 5HH  plan-2  C8   0.020
 5HH  plan-2  S1   0.020
 5HH  plan-2  H1   0.020
 5HH  plan-2  H2   0.020
 5HH  plan-2  H5   0.020
 5HH  plan-2  H6   0.020
 5HH  plan-2  H8   0.020
 5HH  plan-2  H9   0.020
 5HH  plan-2  H17  0.020

