# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:41:40 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-(3-fluorobenzyl)-1-[(1R)-1-(naphthalen-1-yl)ethyl]piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N1CC[C@H](CC1)C(=O)NCc2cccc(F)c2)c3cccc4ccccc34
#
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
 S88  S88  N-(3-fluorobenzyl)-1-[(1R)-1-(naphthalen-1-yl)ethyl]piperidine-4-carboxamide  ligand  56  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S88
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
 S88  F29  F  F     0  -0.317  -5.8791  -1.3536   2.3124
 S88  C27  C  CR6   0   0.549  -6.2407  -0.7193   1.1841
 S88  C26  C  CR16  0  -0.424  -7.5425  -0.8474   0.7374
 S88  C25  C  CR16  0  -0.226  -7.8963  -0.1842  -0.4283
 S88  C24  C  CR16  0  -0.323  -6.9634   0.5781  -1.1195
 S88  C28  C  CR16  0  -0.458  -5.2955   0.0348   0.5192
 S88  C23  C  CR6   0   0.129  -5.6590   0.6958  -0.6510
 S88  C22  C  CH2   0  -0.361  -4.6622   1.5561  -1.3905
 S88  N21  N  NH1   0  -0.630  -3.3498   0.9683  -1.4860
 S88  C19  C  C     0   0.580  -2.3030   1.3233  -0.7172
 S88  O20  O  O     0  -0.498  -2.3619   2.2179   0.1155
 S88  C16  C  CH1   0  -0.401  -1.0498   0.4976  -0.9223
 S88  C15  C  CH2   0  -0.421  -0.9731  -0.5943   0.1486
 S88  C14  C  CH2   0  -0.284   0.3130  -1.3987   0.0266
 S88  N13  N  NT    0  -0.419   1.4745  -0.5317   0.1126
 S88  C18  C  CH2   0  -0.289   1.4456   0.4601  -0.9505
 S88  C17  C  CH2   0  -0.419   0.2146   1.3453  -0.8626
 S88  C11  C  CH1   0  -0.089   2.7580  -1.2244   0.1251
 S88  C12  C  CH3   0  -0.694   2.7728  -2.4580   1.0291
 S88  C10  C  CR6   0   0.056   3.8514  -0.2827   0.6038
 S88  C2   C  CR66  0   0.093   5.1828  -0.3647   0.0987
 S88  C1   C  CR16  0  -0.352   5.5756  -1.2762  -0.9152
 S88  C6   C  CR16  0  -0.248   6.8642  -1.3185  -1.3750
 S88  C5   C  CR16  0  -0.264   7.8428  -0.4522  -0.8488
 S88  C4   C  CR16  0  -0.310   7.5025   0.4376   0.1313
 S88  C3   C  CR66  0   0.108   6.1792   0.5035   0.6293
 S88  C7   C  CR16  0  -0.336   5.8379   1.4211   1.6485
 S88  C8   C  CR16  0  -0.241   4.5581   1.4752   2.1231
 S88  C9   C  CR16  0  -0.305   3.5701   0.6219   1.5969
 S88  H1   H  HCR6  0   0.280  -8.2561  -1.4521   1.2811
 S88  H2   H  HCR6  0   0.269  -8.9072  -0.2707  -0.8040
 S88  H3   H  HCR6  0   0.258  -7.2535   1.0788  -2.0349
 S88  H4   H  HCR6  0   0.270  -4.2912   0.1058   0.9168
 S88  H5   H  HCH2  0   0.271  -5.0329   1.7590  -2.3961
 S88  H6   H  HCH2  0   0.272  -4.5673   2.5209  -0.8910
 S88  H7   H  HNH1  0   0.403  -3.2335   0.2067  -2.1350
 S88  H8   H  HCH1  0   0.249  -1.0897   0.0056  -1.9014
 S88  H9   H  HCH2  0   0.231  -1.0130  -0.1369   1.1410
 S88  H10  H  HCH2  0   0.241  -1.8257  -1.2728   0.0666
 S88  H11  H  HCH2  0   0.252   0.3321  -2.1219   0.8406
 S88  H12  H  HCH2  0   0.187   0.2979  -1.9774  -0.9149
 S88  H14  H  HCH2  0   0.247   2.3367   1.0851  -0.8804
 S88  H15  H  HCH2  0   0.192   1.4778  -0.0262  -1.9422
 S88  H16  H  HCH2  0   0.240   0.2331   2.0664  -1.6831
 S88  H17  H  HCH2  0   0.227   0.2418   1.9127   0.0702
 S88  H18  H  HCH1  0   0.211   2.9944  -1.5661  -0.8952
 S88  H19  H  HCH3  0   0.233   2.4164  -2.2110   2.0304
 S88  H20  H  HCH3  0   0.241   2.1669  -3.2726   0.6334
 S88  H21  H  HCH3  0   0.250   3.7922  -2.8327   1.1220
 S88  H22  H  HCR6  0   0.250   4.8541  -1.9567  -1.3454
 S88  H23  H  HCR6  0   0.257   7.1330  -2.0229  -2.1517
 S88  H24  H  HCR6  0   0.257   8.8577  -0.4941  -1.2218
 S88  H25  H  HCR6  0   0.254   8.2455   1.1099   0.5439
 S88  H26  H  HCR6  0   0.252   6.6037   2.0768   2.0450
 S88  H27  H  HCR6  0   0.253   4.2956   2.1756   2.9057
 S88  H28  H  HCR6  0   0.248   2.5557   0.6863   1.9691

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
 S88  C5   C6   aromatic  1.409  0.020  1.409
 S88  C5   C4   aromatic  1.367  0.020  1.367
 S88  C6   C1   aromatic  1.369  0.020  1.369
 S88  C4   C3   aromatic  1.415  0.020  1.415
 S88  C1   C2   aromatic  1.419  0.020  1.419
 S88  C3   C2   aromatic  1.424  0.020  1.424
 S88  C3   C7   aromatic  1.413  0.020  1.413
 S88  C2   C10  aromatic  1.426  0.020  1.426
 S88  C7   C8   aromatic  1.366  0.020  1.366
 S88  C10  C11  single    1.520  0.020  1.520
 S88  C10  C9   aromatic  1.372  0.020  1.372
 S88  C11  C12  single    1.529  0.020  1.529
 S88  C11  N13  single    1.459  0.020  1.459
 S88  C8   C9   aromatic  1.407  0.020  1.407
 S88  N13  C14  single    1.452  0.020  1.452
 S88  N13  C18  single    1.454  0.020  1.454
 S88  C14  C15  single    1.522  0.020  1.522
 S88  C18  C17  single    1.519  0.020  1.519
 S88  C16  C17  single    1.523  0.020  1.523
 S88  C16  C15  single    1.531  0.020  1.531
 S88  C16  C19  single    1.515  0.020  1.515
 S88  N21  C19  single    1.346  0.020  1.346
 S88  N21  C22  single    1.441  0.020  1.441
 S88  C19  O20  double    1.224  0.020  1.224
 S88  F29  C27  single    1.344  0.020  1.344
 S88  C27  C28  aromatic  1.380  0.020  1.380
 S88  C27  C26  aromatic  1.382  0.020  1.382
 S88  C28  C23  aromatic  1.392  0.020  1.392
 S88  C26  C25  aromatic  1.387  0.020  1.387
 S88  C23  C22  single    1.510  0.020  1.510
 S88  C23  C24  aromatic  1.391  0.020  1.391
 S88  C25  C24  aromatic  1.389  0.020  1.389
 S88  C26  H1   single    0.930  0.020  1.080
 S88  C25  H2   single    0.930  0.020  1.080
 S88  C24  H3   single    0.930  0.020  1.080
 S88  C28  H4   single    0.930  0.020  1.080
 S88  C22  H5   single    0.970  0.020  1.090
 S88  C22  H6   single    0.970  0.020  1.090
 S88  N21  H7   single    0.860  0.020  1.020
 S88  C16  H8   single    0.970  0.020  1.090
 S88  C15  H9   single    0.970  0.020  1.090
 S88  C15  H10  single    0.970  0.020  1.090
 S88  C14  H11  single    0.970  0.020  1.090
 S88  C14  H12  single    0.970  0.020  1.090
 S88  C18  H14  single    0.970  0.020  1.090
 S88  C18  H15  single    0.970  0.020  1.090
 S88  C17  H16  single    0.970  0.020  1.090
 S88  C17  H17  single    0.970  0.020  1.090
 S88  C11  H18  single    0.970  0.020  1.090
 S88  C12  H19  single    0.970  0.020  1.090
 S88  C12  H20  single    0.970  0.020  1.090
 S88  C12  H21  single    0.970  0.020  1.090
 S88  C1   H22  single    0.930  0.020  1.080
 S88  C6   H23  single    0.930  0.020  1.080
 S88  C5   H24  single    0.930  0.020  1.080
 S88  C4   H25  single    0.930  0.020  1.080
 S88  C7   H26  single    0.930  0.020  1.080
 S88  C8   H27  single    0.930  0.020  1.080
 S88  C9   H28  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
 S88  C28  C27  C26  122.69  3.000
 S88  C26  C27  F29  118.75  3.000
 S88  C28  C27  F29  118.57  3.000
 S88  H1   C26  C25  121.42  3.000
 S88  H1   C26  C27  120.70  3.000
 S88  C25  C26  C27  117.88  3.000
 S88  H2   C25  C24  119.91  3.000
 S88  H2   C25  C26  119.47  3.000
 S88  C24  C25  C26  120.62  3.000
 S88  H3   C24  C23  119.78  3.000
 S88  H3   C24  C25  119.64  3.000
 S88  C23  C24  C25  120.58  3.000
 S88  H4   C28  C23  121.32  3.000
 S88  H4   C28  C27  119.63  3.000
 S88  C23  C28  C27  119.05  3.000
 S88  C22  C23  C28  120.64  3.000
 S88  C22  C23  C24  120.15  3.000
 S88  C28  C23  C24  119.19  3.000
 S88  H6   C22  H5   106.68  3.000
 S88  H6   C22  N21  108.18  3.000
 S88  H5   C22  N21  108.92  3.000
 S88  H6   C22  C23  109.70  3.000
 S88  H5   C22  C23  109.46  3.000
 S88  N21  C22  C23  113.66  3.000
 S88  H7   N21  C19  118.52  3.000
 S88  H7   N21  C22  117.14  3.000
 S88  C19  N21  C22  124.24  3.000
 S88  C16  C19  O20  122.04  3.000
 S88  O20  C19  N21  122.95  3.000
 S88  C16  C19  N21  114.97  3.000
 S88  H8   C16  C17  108.35  3.000
 S88  H8   C16  C15  107.84  3.000
 S88  C17  C16  C15  109.13  3.000
 S88  H8   C16  C19  109.60  3.000
 S88  C15  C16  C19  109.60  3.000
 S88  C17  C16  C19  112.21  3.000
 S88  H10  C15  H9   107.42  3.000
 S88  H10  C15  C14  108.98  3.000
 S88  H9   C15  C14  108.95  3.000
 S88  H10  C15  C16  110.56  3.000
 S88  H9   C15  C16  109.55  3.000
 S88  C14  C15  C16  111.29  3.000
 S88  H12  C14  H11  106.81  3.000
 S88  H12  C14  N13  111.97  3.000
 S88  H11  C14  N13  109.77  3.000
 S88  H12  C14  C15  109.49  3.000
 S88  H11  C14  C15  107.81  3.000
 S88  N13  C14  C15  110.83  3.000
 S88  C11  N13  C18  110.35  3.000
 S88  C18  N13  C14  110.37  3.000
 S88  C11  N13  C14  114.89  3.000
 S88  H15  C18  H14  106.62  3.000
 S88  H15  C18  C17  109.39  3.000
 S88  H14  C18  C17  108.94  3.000
 S88  H15  C18  N13  110.81  3.000
 S88  H14  C18  N13  109.13  3.000
 S88  C17  C18  N13  111.80  3.000
 S88  H17  C17  H16  107.35  3.000
 S88  H17  C17  C18  109.39  3.000
 S88  H16  C17  C18  109.12  3.000
 S88  H17  C17  C16  110.07  3.000
 S88  H16  C17  C16  110.61  3.000
 S88  C18  C17  C16  110.25  3.000
 S88  H18  C11  C10  109.23  3.000
 S88  H18  C11  C12  107.17  3.000
 S88  C10  C11  C12  107.85  3.000
 S88  H18  C11  N13  109.16  3.000
 S88  C12  C11  N13  113.37  3.000
 S88  C10  C11  N13  109.96  3.000
 S88  H21  C12  H20  107.10  3.000
 S88  H21  C12  H19  107.76  3.000
 S88  H20  C12  H19  108.71  3.000
 S88  H21  C12  C11  109.67  3.000
 S88  H20  C12  C11  112.52  3.000
 S88  H19  C12  C11  110.89  3.000
 S88  C9   C10  C2   119.04  3.000
 S88  C9   C10  C11  119.25  3.000
 S88  C2   C10  C11  121.61  3.000
 S88  C3   C2   C1   117.66  3.000
 S88  C3   C2   C10  119.08  3.000
 S88  C1   C2   C10  123.26  3.000
 S88  H22  C1   C6   118.37  3.000
 S88  H22  C1   C2   120.26  3.000
 S88  C6   C1   C2   121.37  3.000
 S88  H23  C6   C5   119.71  3.000
 S88  H23  C6   C1   119.67  3.000
 S88  C5   C6   C1   120.62  3.000
 S88  H24  C5   C4   120.39  3.000
 S88  H24  C5   C6   119.93  3.000
 S88  C4   C5   C6   119.68  3.000
 S88  H25  C4   C3   118.56  3.000
 S88  H25  C4   C5   120.41  3.000
 S88  C3   C4   C5   121.02  3.000
 S88  C7   C3   C4   120.65  3.000
 S88  C7   C3   C2   119.71  3.000
 S88  C4   C3   C2   119.64  3.000
 S88  H26  C7   C8   120.75  3.000
 S88  H26  C7   C3   119.09  3.000
 S88  C8   C7   C3   120.17  3.000
 S88  H27  C8   C9   119.49  3.000
 S88  H27  C8   C7   120.26  3.000
 S88  C9   C8   C7   120.25  3.000
 S88  H28  C9   C8   119.55  3.000
 S88  H28  C9   C10  118.69  3.000
 S88  C8   C9   C10  121.75  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
 S88  CONST_01  C24  C23  C28  C27     0.00   0.0  0
 S88  CONST_02  C24  C25  C26  C27     0.00   0.0  0
 S88  CONST_03  C23  C28  C27  C26     0.00   0.0  0
 S88  CONST_04  C23  C24  C25  C26     0.00   0.0  0
 S88  CONST_05  C28  C27  C26  C25     0.00   0.0  0
 S88  CONST_06  C28  C23  C24  C25     0.00   0.0  0
 S88  CONST_07  C6   C1   C2   C10   180.00   0.0  0
 S88  CONST_08  C4   C3   C2   C10   180.00   0.0  0
 S88  CONST_09  C7   C3   C2   C10     0.00   0.0  0
 S88  CONST_10  C7   C8   C9   C10     0.00   0.0  0
 S88  CONST_11  C5   C6   C1   C2      0.00   0.0  0
 S88  CONST_12  C5   C4   C3   C2      0.00   0.0  0
 S88  CONST_13  C8   C7   C3   C2      0.00   0.0  0
 S88  CONST_14  C8   C9   C10  C2      0.00   0.0  0
 S88  CONST_15  C4   C5   C6   C1      0.00   0.0  0
 S88  CONST_16  C4   C3   C2   C1      0.00   0.0  0
 S88  CONST_17  C7   C3   C2   C1    180.00   0.0  0
 S88  CONST_18  C9   C10  C2   C1    180.00   0.0  0
 S88  CONST_19  C3   C4   C5   C6      0.00   0.0  0
 S88  CONST_20  C3   C2   C1   C6      0.00   0.0  0
 S88  CONST_21  C7   C3   C4   C5    180.00   0.0  0
 S88  CONST_22  C8   C7   C3   C4    180.00   0.0  0
 S88  CONST_23  C9   C10  C2   C3      0.00   0.0  0
 S88  CONST_24  C9   C8   C7   C3      0.00   0.0  0
 S88  CONST_25  C23  C28  C27  F29   180.00   0.0  0
 S88  CONST_26  C25  C26  C27  F29   180.00   0.0  0
 S88  CONST_27  C22  C23  C28  C27   180.00   0.0  0
 S88  CONST_28  C22  C23  C24  C25   180.00   0.0  0
 S88  CONST_29  C1   C2   C10  C11     0.00   0.0  0
 S88  CONST_30  C3   C2   C10  C11   180.00   0.0  0
 S88  CONST_31  C8   C9   C10  C11   180.00   0.0  0
 S88  CONST_32  H2   C25  C26  C27   180.00   0.0  0
 S88  CONST_33  H4   C28  C27  C26   180.00   0.0  0
 S88  CONST_34  H3   C24  C25  C26   180.00   0.0  0
 S88  CONST_35  H1   C26  C25  C24   180.00   0.0  0
 S88  CONST_36  H22  C1   C2   C10     0.00   0.0  0
 S88  CONST_37  H27  C8   C9   C10   180.00   0.0  0
 S88  CONST_38  H23  C6   C1   C2    180.00   0.0  0
 S88  CONST_39  H25  C4   C3   C2    180.00   0.0  0
 S88  CONST_40  H26  C7   C3   C2    180.00   0.0  0
 S88  CONST_41  H28  C9   C10  C2    180.00   0.0  0
 S88  CONST_42  H24  C5   C6   C1    180.00   0.0  0
 S88  CONST_43  C16  C19  N21  C22   180.00   0.0  0
 S88  CONST_44  H7   N21  C19  C16     0.00   0.0  0
 S88  CONST_45  O20  C19  N21  C22     0.00   0.0  0
 S88  Var_01    N13  C18  C17  C16   -57.90  30.0  1
 S88  Var_02    N13  C14  C15  C16    57.07  30.0  1
 S88  Var_03    C18  N13  C14  C15   -59.67  30.0  1
 S88  Var_04    C17  C18  N13  C14    60.69  30.0  1
 S88  Var_05    N21  C22  C23  C24  -138.76  30.0  2
 S88  Var_06    C19  N21  C22  C23  -102.05  30.0  2

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
 S88  chir_01  C16  C17  C15  C19  negativ
 S88  chir_02  C11  N13  C10  C12  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
 S88  plan-1  F29  0.020
 S88  plan-1  C27  0.020
 S88  plan-1  C26  0.020
 S88  plan-1  C25  0.020
 S88  plan-1  C24  0.020
 S88  plan-1  C28  0.020
 S88  plan-1  C23  0.020
 S88  plan-1  C22  0.020
 S88  plan-1  H1   0.020
 S88  plan-1  H2   0.020
 S88  plan-1  H3   0.020
 S88  plan-1  H4   0.020
 S88  plan-2  C11  0.020
 S88  plan-2  C10  0.020
 S88  plan-2  C2   0.020
 S88  plan-2  C1   0.020
 S88  plan-2  C6   0.020
 S88  plan-2  C5   0.020
 S88  plan-2  C4   0.020
 S88  plan-2  C3   0.020
 S88  plan-2  C7   0.020
 S88  plan-2  C8   0.020
 S88  plan-2  C9   0.020
 S88  plan-2  H22  0.020
 S88  plan-2  H23  0.020
 S88  plan-2  H24  0.020
 S88  plan-2  H25  0.020
 S88  plan-2  H26  0.020
 S88  plan-2  H27  0.020
 S88  plan-2  H28  0.020
 S88  plan-3  C22  0.020
 S88  plan-3  N21  0.020
 S88  plan-3  C19  0.020
 S88  plan-3  O20  0.020
 S88  plan-3  C16  0.020
 S88  plan-3  H7   0.020

