# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 08:49:38 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-{[(3R)-1-benzylpiperidin-3-yl]methyl}-N-methylnaphthalene-2-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C[C@@H]1CCCN(C1)Cc2ccccc2)[S](=O)(=O)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
 5HB  5HB  N-{[(3R)-1-benzylpiperidin-3-yl]methyl}-N-methylnaphthalene-2-sulfonamide  ligand  57  29  .  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_5HB
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
 5HB  C10  C  CH2   0  -0.273   4.0439  -1.3994   0.6683
 5HB  C13  C  CR6   0   0.085   4.7651   1.3459  -0.3662
 5HB  C15  C  CR16  0  -0.242   4.3014   3.1888   1.1264
 5HB  C17  C  CR16  0  -0.242   6.5081   2.9159   0.2242
 5HB  C24  C  CR16  0  -0.248  -2.5392   0.0789  -1.5200
 5HB  C26  C  CR66  0   0.125  -4.1162   1.7350  -0.7259
 5HB  C28  C  CR16  0  -0.248  -5.6987   3.3798   0.0625
 5HB  N05  N  N     0  -0.553  -0.6366  -1.8989   0.6730
 5HB  C06  C  CH2   0  -0.302   0.4812  -1.2874  -0.0562
 5HB  C07  C  CH1   0  -0.246   1.5391  -2.3038  -0.4788
 5HB  C08  C  CH2   0  -0.443   2.1542  -3.0520   0.7021
 5HB  C09  C  CH2   0  -0.452   3.0411  -2.1384   1.5414
 5HB  N11  N  NT    0  -0.412   3.3786  -0.6844  -0.4065
 5HB  C12  C  CH2   0  -0.314   4.2943   0.1486  -1.1533
 5HB  C14  C  CR16  0  -0.288   3.8791   2.0604   0.4384
 5HB  C16  C  CR16  0  -0.272   5.6179   3.6233   1.0198
 5HB  C18  C  CR16  0  -0.315   6.0823   1.7833  -0.4599
 5HB  C19  C  CH2   0  -0.286   2.6399  -1.5957  -1.2609
 5HB  S20  S  S     0   1.370  -1.9953  -2.2637  -0.1778
 5HB  O21  O  OS    0  -0.650  -1.5704  -2.7359  -1.4863
 5HB  O22  O  OS    0  -0.652  -2.8204  -3.1194   0.6597
 5HB  C23  C  CR6   0  -0.195  -2.8613  -0.7343  -0.4106
 5HB  C25  C  CR16  0  -0.301  -3.1558   1.2889  -1.6639
 5HB  C27  C  CR16  0  -0.306  -4.7671   2.9829  -0.8577
 5HB  C29  C  CR16  0  -0.254  -6.0255   2.5495   1.1558
 5HB  C30  C  CR16  0  -0.303  -5.4119   1.3368   1.3093
 5HB  C31  C  CR66  0   0.128  -4.4416   0.9028   0.3759
 5HB  C32  C  CR16  0  -0.298  -3.7921  -0.3437   0.5141
 5HB  H1   H  HCH2  0   0.239   4.6059  -0.6871   1.2756
 5HB  H2   H  HCH2  0   0.186   4.7792  -2.1185   0.2624
 5HB  H3   H  HCR6  0   0.251   3.6020   3.7308   1.7504
 5HB  H4   H  HCR6  0   0.252   7.5377   3.2399   0.1398
 5HB  H6   H  HCR6  0   0.267  -6.1906   4.3375  -0.0447
 5HB  H7   H  HCH3  0   0.267  -1.5560  -2.0890   2.5575
 5HB  H8   H  HCH3  0   0.269   0.1201  -1.5800   2.5804
 5HB  H9   H  HCH3  0   0.241  -1.1329  -0.4182   2.1251
 5HB  H10  H  HCH2  0   0.256   0.1345  -0.7431  -0.9392
 5HB  H11  H  HCH2  0   0.271   0.9180  -0.5303   0.5944
 5HB  H12  H  HCH1  0   0.246   1.0626  -3.0237  -1.1489
 5HB  H13  H  HCH2  0   0.236   1.3751  -3.5139   1.3138
 5HB  H14  H  HCH2  0   0.227   2.7611  -3.8748   0.3103
 5HB  H15  H  HCH2  0   0.236   3.5782  -2.7207   2.2931
 5HB  H16  H  HCH2  0   0.219   2.4365  -1.4096   2.0892
 5HB  H18  H  HCH2  0   0.249   3.7725   0.5040  -2.0477
 5HB  H19  H  HCH2  0   0.209   5.1703  -0.4139  -1.5189
 5HB  H20  H  HCR6  0   0.248   2.8558   1.7189   0.5317
 5HB  H21  H  HCR6  0   0.252   5.9466   4.5042   1.5561
 5HB  H22  H  HCR6  0   0.247   6.7851   1.2320  -1.0743
 5HB  H23  H  HCH2  0   0.204   3.3006  -2.3527  -1.7195
 5HB  H24  H  HCH2  0   0.235   2.2008  -1.0257  -2.0849
 5HB  H25  H  HCR6  0   0.269  -2.9156   1.9181  -2.5119
 5HB  H26  H  HCR6  0   0.263  -4.5172   3.6216  -1.6959
 5HB  H27  H  HCR6  0   0.266  -6.7652   2.8783   1.8737
 5HB  H28  H  HCR6  0   0.264  -5.6617   0.6951   2.1454
 5HB  H29  H  HCR6  0   0.283  -4.0522  -0.9769   1.3532
 5HB  H5   H  HCR6  0   0.281  -1.8255  -0.2540  -2.2608
 5HB  C04  C  CH3   0  -0.547  -0.8242  -1.4653   2.0519

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
 5HB  C28  C27  aromatic  1.368  0.020  1.368
 5HB  C28  C29  aromatic  1.411  0.020  1.411
 5HB  C27  C26  aromatic  1.414  0.020  1.414
 5HB  C29  C30  aromatic  1.368  0.020  1.368
 5HB  C26  C25  aromatic  1.415  0.020  1.415
 5HB  C26  C31  aromatic  1.419  0.020  1.419
 5HB  C25  C24  aromatic  1.366  0.020  1.366
 5HB  C30  C31  aromatic  1.415  0.020  1.415
 5HB  C31  C32  aromatic  1.412  0.020  1.412
 5HB  C24  C23  aromatic  1.413  0.020  1.413
 5HB  C32  C23  aromatic  1.369  0.020  1.369
 5HB  C09  C10  single    1.521  0.020  1.521
 5HB  C09  C08  single    1.525  0.020  1.525
 5HB  C23  S20  single    1.773  0.020  1.773
 5HB  C10  N11  single    1.452  0.020  1.452
 5HB  C15  C16  aromatic  1.390  0.020  1.390
 5HB  C15  C14  aromatic  1.387  0.020  1.387
 5HB  C08  C07  single    1.527  0.020  1.527
 5HB  C16  C17  aromatic  1.388  0.020  1.388
 5HB  C14  C13  aromatic  1.394  0.020  1.394
 5HB  C17  C18  aromatic  1.390  0.020  1.390
 5HB  N05  S20  single    1.644  0.020  1.644
 5HB  N05  C04  single    1.458  0.020  1.458
 5HB  N05  C06  single    1.468  0.020  1.468
 5HB  C07  C06  single    1.527  0.020  1.527
 5HB  C07  C19  single    1.525  0.020  1.525
 5HB  S20  O22  double    1.454  0.020  1.454
 5HB  S20  O21  double    1.455  0.020  1.455
 5HB  C13  C18  aromatic  1.391  0.020  1.391
 5HB  C13  C12  single    1.508  0.020  1.508
 5HB  N11  C12  single    1.446  0.020  1.446
 5HB  N11  C19  single    1.451  0.020  1.451
 5HB  C10  H1   single    0.970  0.020  1.090
 5HB  C10  H2   single    0.970  0.020  1.090
 5HB  C15  H3   single    0.930  0.020  1.080
 5HB  C17  H4   single    0.930  0.020  1.080
 5HB  C24  H5   single    0.930  0.020  1.080
 5HB  C28  H6   single    0.930  0.020  1.080
 5HB  C04  H7   single    0.970  0.020  1.090
 5HB  C04  H8   single    0.970  0.020  1.090
 5HB  C04  H9   single    0.970  0.020  1.090
 5HB  C06  H10  single    0.970  0.020  1.090
 5HB  C06  H11  single    0.970  0.020  1.090
 5HB  C07  H12  single    0.970  0.020  1.090
 5HB  C08  H13  single    0.970  0.020  1.090
 5HB  C08  H14  single    0.970  0.020  1.090
 5HB  C09  H15  single    0.970  0.020  1.090
 5HB  C09  H16  single    0.970  0.020  1.090
 5HB  C12  H18  single    0.970  0.020  1.090
 5HB  C12  H19  single    0.970  0.020  1.090
 5HB  C14  H20  single    0.930  0.020  1.080
 5HB  C16  H21  single    0.930  0.020  1.080
 5HB  C18  H22  single    0.930  0.020  1.080
 5HB  C19  H23  single    0.970  0.020  1.090
 5HB  C19  H24  single    0.970  0.020  1.090
 5HB  C25  H25  single    0.930  0.020  1.080
 5HB  C27  H26  single    0.930  0.020  1.080
 5HB  C29  H27  single    0.930  0.020  1.080
 5HB  C30  H28  single    0.930  0.020  1.080
 5HB  C32  H29  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
 5HB  H2   C10  H1   106.63  3.000
 5HB  H2   C10  N11  110.68  3.000
 5HB  H1   C10  N11  109.05  3.000
 5HB  H2   C10  C09  109.46  3.000
 5HB  H1   C10  C09  109.70  3.000
 5HB  N11  C10  C09  111.22  3.000
 5HB  C18  C13  C14  118.66  3.000
 5HB  C18  C13  C12  120.66  3.000
 5HB  C14  C13  C12  120.65  3.000
 5HB  H3   C15  C16  119.96  3.000
 5HB  H3   C15  C14  119.76  3.000
 5HB  C16  C15  C14  120.29  3.000
 5HB  H4   C17  C18  119.79  3.000
 5HB  H4   C17  C16  120.14  3.000
 5HB  C18  C17  C16  120.06  3.000
 5HB  H5   C24  C25  119.91  3.000
 5HB  H5   C24  C23  120.75  3.000
 5HB  C25  C24  C23  119.32  3.000
 5HB  C31  C26  C27  118.99  3.000
 5HB  C31  C26  C25  119.06  3.000
 5HB  C27  C26  C25  121.95  3.000
 5HB  H6   C28  C29  119.49  3.000
 5HB  H6   C28  C27  119.98  3.000
 5HB  C29  C28  C27  120.53  3.000
 5HB  S20  N05  C06  117.69  3.000
 5HB  C06  N05  C04  116.36  3.000
 5HB  S20  N05  C04  116.69  3.000
 5HB  H11  C06  H10  105.27  3.000
 5HB  H11  C06  C07  110.49  3.000
 5HB  H10  C06  C07  109.12  3.000
 5HB  H11  C06  N05  107.34  3.000
 5HB  H10  C06  N05  111.53  3.000
 5HB  C07  C06  N05  112.82  3.000
 5HB  H12  C07  C19  107.83  3.000
 5HB  H12  C07  C08  109.09  3.000
 5HB  C19  C07  C08  109.47  3.000
 5HB  H12  C07  C06  107.83  3.000
 5HB  C19  C07  C06  109.45  3.000
 5HB  C08  C07  C06  113.03  3.000
 5HB  H14  C08  H13  106.13  3.000
 5HB  H14  C08  C09  108.95  3.000
 5HB  H13  C08  C09  111.08  3.000
 5HB  H14  C08  C07  108.34  3.000
 5HB  H13  C08  C07  110.65  3.000
 5HB  C09  C08  C07  111.48  3.000
 5HB  H16  C09  H15  106.40  3.000
 5HB  H16  C09  C08  110.69  3.000
 5HB  H15  C09  C08  110.21  3.000
 5HB  H16  C09  C10  109.15  3.000
 5HB  H15  C09  C10  109.26  3.000
 5HB  C08  C09  C10  111.01  3.000
 5HB  C19  N11  C12  112.34  3.000
 5HB  C19  N11  C10  111.09  3.000
 5HB  C12  N11  C10  112.07  3.000
 5HB  H19  C12  H18  105.85  3.000
 5HB  H19  C12  N11  112.35  3.000
 5HB  H18  C12  N11  107.89  3.000
 5HB  H19  C12  C13  109.26  3.000
 5HB  H18  C12  C13  108.50  3.000
 5HB  N11  C12  C13  112.68  3.000
 5HB  H20  C14  C15  120.09  3.000
 5HB  H20  C14  C13  119.26  3.000
 5HB  C15  C14  C13  120.64  3.000
 5HB  H21  C16  C17  120.27  3.000
 5HB  H21  C16  C15  120.26  3.000
 5HB  C17  C16  C15  119.47  3.000
 5HB  H22  C18  C17  119.65  3.000
 5HB  H22  C18  C13  119.48  3.000
 5HB  C17  C18  C13  120.87  3.000
 5HB  H24  C19  H23  106.52  3.000
 5HB  H24  C19  N11  108.70  3.000
 5HB  H23  C19  N11  111.74  3.000
 5HB  H24  C19  C07  109.79  3.000
 5HB  H23  C19  C07  109.06  3.000
 5HB  N11  C19  C07  110.92  3.000
 5HB  C23  S20  O22  107.82  3.000
 5HB  O22  S20  O21  119.53  3.000
 5HB  C23  S20  O21  107.74  3.000
 5HB  O21  S20  N05  107.23  3.000
 5HB  O22  S20  N05  107.54  3.000
 5HB  C23  S20  N05  106.27  3.000
 5HB  C32  C23  S20  119.31  3.000
 5HB  S20  C23  C24  119.23  3.000
 5HB  C32  C23  C24  121.42  3.000
 5HB  H25  C25  C26  119.12  3.000
 5HB  H25  C25  C24  119.81  3.000
 5HB  C26  C25  C24  121.07  3.000
 5HB  H26  C27  C28  120.43  3.000
 5HB  H26  C27  C26  119.12  3.000
 5HB  C28  C27  C26  120.46  3.000
 5HB  H27  C29  C30  120.12  3.000
 5HB  H27  C29  C28  119.57  3.000
 5HB  C30  C29  C28  120.31  3.000
 5HB  H28  C30  C31  119.06  3.000
 5HB  H28  C30  C29  120.56  3.000
 5HB  C31  C30  C29  120.38  3.000
 5HB  C32  C31  C30  121.45  3.000
 5HB  C32  C31  C26  119.22  3.000
 5HB  C30  C31  C26  119.33  3.000
 5HB  H29  C32  C31  118.78  3.000
 5HB  H29  C32  C23  121.32  3.000
 5HB  C31  C32  C23  119.90  3.000
 5HB  H9   C04  H8   108.25  3.000
 5HB  H9   C04  H7   109.17  3.000
 5HB  H8   C04  H7   107.33  3.000
 5HB  H9   C04  N05  112.60  3.000
 5HB  H8   C04  N05  108.45  3.000
 5HB  H7   C04  N05  110.87  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
 5HB  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 5HB  CONST_02  C16  C17  C18  C13     0.00   0.0  0
 5HB  CONST_03  C18  C17  C16  C15     0.00   0.0  0
 5HB  CONST_04  C18  C13  C14  C15     0.00   0.0  0
 5HB  CONST_05  C14  C15  C16  C17     0.00   0.0  0
 5HB  CONST_06  C14  C13  C18  C17     0.00   0.0  0
 5HB  CONST_07  C27  C26  C25  C24   180.00   0.0  0
 5HB  CONST_08  C31  C26  C25  C24     0.00   0.0  0
 5HB  CONST_09  C31  C32  C23  C24     0.00   0.0  0
 5HB  CONST_10  C29  C28  C27  C26     0.00   0.0  0
 5HB  CONST_11  C23  C24  C25  C26     0.00   0.0  0
 5HB  CONST_12  C29  C30  C31  C26     0.00   0.0  0
 5HB  CONST_13  C23  C32  C31  C26     0.00   0.0  0
 5HB  CONST_14  C25  C26  C27  C28   180.00   0.0  0
 5HB  CONST_15  C31  C26  C27  C28     0.00   0.0  0
 5HB  CONST_16  C31  C30  C29  C28     0.00   0.0  0
 5HB  CONST_17  C30  C31  C32  C23   180.00   0.0  0
 5HB  CONST_18  C30  C31  C26  C25   180.00   0.0  0
 5HB  CONST_19  C32  C31  C26  C25     0.00   0.0  0
 5HB  CONST_20  C32  C23  C24  C25     0.00   0.0  0
 5HB  CONST_21  C30  C29  C28  C27     0.00   0.0  0
 5HB  CONST_22  C30  C31  C26  C27     0.00   0.0  0
 5HB  CONST_23  C32  C31  C26  C27   180.00   0.0  0
 5HB  CONST_24  C32  C31  C30  C29   180.00   0.0  0
 5HB  CONST_25  C12  C13  C14  C15   180.00   0.0  0
 5HB  CONST_26  C12  C13  C18  C17   180.00   0.0  0
 5HB  CONST_27  C25  C24  C23  S20   180.00   0.0  0
 5HB  CONST_28  C31  C32  C23  S20   180.00   0.0  0
 5HB  CONST_29  H3   C15  C14  C13   180.00   0.0  0
 5HB  CONST_30  H4   C17  C18  C13   180.00   0.0  0
 5HB  CONST_31  H29  C32  C23  C24   180.00   0.0  0
 5HB  CONST_32  H6   C28  C27  C26   180.00   0.0  0
 5HB  CONST_33  H5   C24  C25  C26   180.00   0.0  0
 5HB  CONST_34  H28  C30  C31  C26   180.00   0.0  0
 5HB  CONST_35  H21  C16  C15  C14   180.00   0.0  0
 5HB  CONST_36  H22  C18  C13  C14   180.00   0.0  0
 5HB  CONST_37  H20  C14  C15  C16   180.00   0.0  0
 5HB  CONST_38  H25  C25  C24  C23   180.00   0.0  0
 5HB  CONST_39  H26  C27  C26  C25     0.00   0.0  0
 5HB  CONST_40  H27  C29  C28  C27   180.00   0.0  0
 5HB  Var_01    C07  C08  C09  C10   -50.92  30.0  1
 5HB  Var_02    C07  C19  N11  C10    62.23  30.0  1
 5HB  Var_03    N11  C10  C09  C08    54.24  30.0  1
 5HB  Var_04    C19  N11  C10  C09   -60.15  30.0  1
 5HB  Var_05    C13  C12  N11  C10   -70.65  30.0  3
 5HB  Var_06    C14  C13  C12  N11   -40.68  30.0  3
 5HB  Var_07    N05  S20  C23  C24    86.81  30.0  2
 5HB  Var_08    C23  S20  N05  C04    68.01  30.0  3
 5HB  Var_09    C07  C06  N05  C04   117.15  30.0  3
 5HB  Var_10    H7   C04  N05  C06  -170.21  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
 5HB  chir_01  C07  C08  C06  C19  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
 5HB  plan-1  C13  0.020
 5HB  plan-1  C15  0.020
 5HB  plan-1  C17  0.020
 5HB  plan-1  C12  0.020
 5HB  plan-1  C14  0.020
 5HB  plan-1  C16  0.020
 5HB  plan-1  C18  0.020
 5HB  plan-1  H3   0.020
 5HB  plan-1  H4   0.020
 5HB  plan-1  H20  0.020
 5HB  plan-1  H21  0.020
 5HB  plan-1  H22  0.020
 5HB  plan-2  C24  0.020
 5HB  plan-2  C26  0.020
 5HB  plan-2  C28  0.020
 5HB  plan-2  S20  0.020
 5HB  plan-2  C23  0.020
 5HB  plan-2  C25  0.020
 5HB  plan-2  C27  0.020
 5HB  plan-2  C29  0.020
 5HB  plan-2  C30  0.020
 5HB  plan-2  C31  0.020
 5HB  plan-2  C32  0.020
 5HB  plan-2  H6   0.020
 5HB  plan-2  H25  0.020
 5HB  plan-2  H26  0.020
 5HB  plan-2  H27  0.020
 5HB  plan-2  H28  0.020
 5HB  plan-2  H29  0.020
 5HB  plan-2  H5   0.020

