# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:26:34 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (2~{S})-3-methyl-2-phenyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](C(=O)N1CCC2(CC1)Oc3ccccc3O2)c4ccccc4
#
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
 DNK  DNK  (2~{S})-3-methyl-2-phenyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one  ligand  51  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DNK
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
 DNK  C10  C  CH2   0  -0.443   1.2639   0.2727   0.9759
 DNK  C11  C  CH2   0  -0.319  -0.0200  -0.2986   0.3832
 DNK  C13  C  C     0   0.600  -1.8400   1.1167  -0.5973
 DNK  C15  C  CH1   0  -0.204  -3.9135   1.7212   0.7436
 DNK  C16  C  CH3   0  -0.655  -4.9361   1.1984   1.7479
 DNK  C17  C  CH3   0  -0.663  -3.3420   3.0462   1.2422
 DNK  C18  C  CR6   0   0.158  -3.3221  -0.6869   0.1846
 DNK  C19  C  CR16  0  -0.291  -3.9599  -0.9239  -1.0323
 DNK  C20  C  CR16  0  -0.239  -4.4747  -2.1775  -1.3300
 DNK  C21  C  CR16  0  -0.270  -4.3573  -3.2180  -0.4169
 DNK  C22  C  CR16  0  -0.242  -3.7233  -2.9928   0.7968
 DNK  C23  C  CR16  0  -0.317  -3.2110  -1.7359   1.0924
 DNK  C25  C  CH2   0  -0.326   0.3304   0.9230  -1.6836
 DNK  C26  C  CH2   0  -0.460   1.6169   1.5460  -1.1517
 DNK  C1   C  CR16  0  -0.356   4.8341  -1.8071  -0.5601
 DNK  C2   C  CR56  0   0.313   4.0039  -0.7378  -0.3289
 DNK  C3   C  CR56  0   0.300   4.4133   0.3645   0.4049
 DNK  C4   C  CR16  0  -0.355   5.6723   0.4499   0.9467
 DNK  C5   C  CR16  0  -0.271   6.5316  -0.6334   0.7199
 DNK  C6   C  CR16  0  -0.270   6.1230  -1.7341  -0.0159
 DNK  O7   O  O     0  -0.496   3.4062   1.2696   0.4564
 DNK  C8   C  CR5   0   0.441   2.2540   0.6455  -0.1148
 DNK  O9   O  O     0  -0.491   2.7326  -0.5484  -0.7524
 DNK  N12  N  NT    0  -0.463  -0.5830   0.6147  -0.5951
 DNK  C14  C  CH1   0  -0.464  -2.7896   0.6902   0.5238
 DNK  O24  O  O     0  -0.497  -2.2348   1.8491  -1.4954
 DNK  H1   H  HCH2  0   0.258   1.0281   1.1681   1.5561
 DNK  H2   H  HCH2  0   0.263   1.7100  -0.4551   1.6583
 DNK  H3   H  HCH2  0   0.257   0.1757  -1.2627  -0.0958
 DNK  H4   H  HCH2  0   0.275  -0.7193  -0.4893   1.1886
 DNK  H5   H  HCH1  0   0.227  -4.4217   1.8917  -0.2094
 DNK  H6   H  HCH3  0   0.231  -5.7104   1.9467   1.9230
 DNK  H7   H  HCH3  0   0.234  -5.4293   0.2896   1.4038
 DNK  H8   H  HCH3  0   0.214  -4.4658   0.9774   2.7095
 DNK  H9   H  HCH3  0   0.215  -2.8627   2.9175   2.2161
 DNK  H10  H  HCH3  0   0.233  -2.6060   3.4710   0.5607
 DNK  H11  H  HCH3  0   0.231  -4.1357   3.7845   1.3657
 DNK  H12  H  HCR6  0   0.251  -4.0609  -0.1249  -1.7562
 DNK  H13  H  HCR6  0   0.255  -4.9693  -2.3425  -2.2788
 DNK  H14  H  HCR6  0   0.255  -4.7580  -4.1958  -0.6509
 DNK  H15  H  HCR6  0   0.255  -3.6267  -3.7949   1.5170
 DNK  H16  H  HCR6  0   0.250  -2.7267  -1.5694   2.0482
 DNK  H17  H  HCH2  0   0.279  -0.1514   1.6033  -2.3782
 DNK  H18  H  HCH2  0   0.253   0.5555   0.0027  -2.2318
 DNK  H19  H  HCH2  0   0.265   2.3119   1.7226  -1.9752
 DNK  H20  H  HCH2  0   0.259   1.3930   2.5103  -0.6898
 DNK  H21  H  HCR6  0   0.271   4.5117  -2.6638  -1.1366
 DNK  H22  H  HCR6  0   0.271   5.9889   1.3117   1.5185
 DNK  H23  H  HCR6  0   0.259   7.5314  -0.6060   1.1320
 DNK  H24  H  HCR6  0   0.259   6.8084  -2.5556  -0.1755
 DNK  H25  H  HCH1  0   0.264  -2.2505   0.6237   1.4732

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
 DNK  O9   C2   single    1.353  0.020  1.353
 DNK  O9   C8   single    1.436  0.020  1.436
 DNK  C26  C8   single    1.514  0.020  1.514
 DNK  C26  C25  single    1.525  0.020  1.525
 DNK  C1   C2   aromatic  1.373  0.020  1.373
 DNK  C1   C6   aromatic  1.401  0.020  1.401
 DNK  C2   C3   aromatic  1.386  0.020  1.386
 DNK  C17  C15  single    1.527  0.020  1.527
 DNK  C8   C10  single    1.520  0.020  1.520
 DNK  C8   O7   single    1.429  0.020  1.429
 DNK  C10  C11  single    1.525  0.020  1.525
 DNK  C6   C5   aromatic  1.386  0.020  1.386
 DNK  C25  N12  single    1.454  0.020  1.454
 DNK  C14  C15  single    1.541  0.020  1.541
 DNK  C14  C13  single    1.530  0.020  1.530
 DNK  C14  C18  single    1.515  0.020  1.515
 DNK  N12  C13  single    1.354  0.020  1.354
 DNK  N12  C11  single    1.452  0.020  1.452
 DNK  C15  C16  single    1.526  0.020  1.526
 DNK  C13  O24  double    1.224  0.020  1.224
 DNK  C19  C18  aromatic  1.394  0.020  1.394
 DNK  C19  C20  aromatic  1.387  0.020  1.387
 DNK  C3   O7   single    1.355  0.020  1.355
 DNK  C3   C4   aromatic  1.373  0.020  1.373
 DNK  C18  C23  aromatic  1.392  0.020  1.392
 DNK  C5   C4   aromatic  1.401  0.020  1.401
 DNK  C20  C21  aromatic  1.389  0.020  1.389
 DNK  C23  C22  aromatic  1.389  0.020  1.389
 DNK  C21  C22  aromatic  1.388  0.020  1.388
 DNK  C10  H1   single    0.970  0.020  1.090
 DNK  C10  H2   single    0.970  0.020  1.090
 DNK  C11  H3   single    0.970  0.020  1.090
 DNK  C11  H4   single    0.970  0.020  1.090
 DNK  C15  H5   single    0.970  0.020  1.090
 DNK  C16  H6   single    0.970  0.020  1.090
 DNK  C16  H7   single    0.970  0.020  1.090
 DNK  C16  H8   single    0.970  0.020  1.090
 DNK  C17  H9   single    0.970  0.020  1.090
 DNK  C17  H10  single    0.970  0.020  1.090
 DNK  C17  H11  single    0.970  0.020  1.090
 DNK  C19  H12  single    0.930  0.020  1.080
 DNK  C20  H13  single    0.930  0.020  1.080
 DNK  C21  H14  single    0.930  0.020  1.080
 DNK  C22  H15  single    0.930  0.020  1.080
 DNK  C23  H16  single    0.930  0.020  1.080
 DNK  C25  H17  single    0.970  0.020  1.090
 DNK  C25  H18  single    0.970  0.020  1.090
 DNK  C26  H19  single    0.970  0.020  1.090
 DNK  C26  H20  single    0.970  0.020  1.090
 DNK  C1   H21  single    0.930  0.020  1.080
 DNK  C4   H22  single    0.930  0.020  1.080
 DNK  C5   H23  single    0.930  0.020  1.080
 DNK  C6   H24  single    0.930  0.020  1.080
 DNK  C14  H25  single    0.970  0.020  1.090

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
 DNK  H2   C10  H1   107.59  3.000
 DNK  H2   C10  C8   110.22  3.000
 DNK  H1   C10  C8   108.70  3.000
 DNK  H2   C10  C11  109.69  3.000
 DNK  H1   C10  C11  109.37  3.000
 DNK  C8   C10  C11  111.19  3.000
 DNK  H4   C11  H3   106.60  3.000
 DNK  H4   C11  N12  111.18  3.000
 DNK  H3   C11  N12  109.19  3.000
 DNK  H4   C11  C10  108.68  3.000
 DNK  H3   C11  C10  110.46  3.000
 DNK  N12  C11  C10  110.65  3.000
 DNK  O24  C13  C14  120.27  3.000
 DNK  O24  C13  N12  121.50  3.000
 DNK  C14  C13  N12  118.16  3.000
 DNK  H5   C15  C14  108.60  3.000
 DNK  H5   C15  C17  108.87  3.000
 DNK  C14  C15  C17  110.75  3.000
 DNK  H5   C15  C16  108.40  3.000
 DNK  C14  C15  C16  110.70  3.000
 DNK  C17  C15  C16  109.47  3.000
 DNK  H8   C16  H7   107.69  3.000
 DNK  H8   C16  H6   107.63  3.000
 DNK  H7   C16  H6   107.55  3.000
 DNK  H8   C16  C15  111.10  3.000
 DNK  H7   C16  C15  112.41  3.000
 DNK  H6   C16  C15  110.26  3.000
 DNK  H11  C17  H10  107.36  3.000
 DNK  H11  C17  H9   107.33  3.000
 DNK  H10  C17  H9   107.89  3.000
 DNK  H11  C17  C15  110.61  3.000
 DNK  H10  C17  C15  112.77  3.000
 DNK  H9   C17  C15  110.67  3.000
 DNK  C14  C18  C23  120.73  3.000
 DNK  C23  C18  C19  118.54  3.000
 DNK  C14  C18  C19  120.71  3.000
 DNK  H12  C19  C20  119.25  3.000
 DNK  H12  C19  C18  120.04  3.000
 DNK  C20  C19  C18  120.70  3.000
 DNK  H13  C20  C21  120.03  3.000
 DNK  H13  C20  C19  119.68  3.000
 DNK  C21  C20  C19  120.29  3.000
 DNK  H14  C21  C22  120.32  3.000
 DNK  H14  C21  C20  120.22  3.000
 DNK  C22  C21  C20  119.46  3.000
 DNK  H15  C22  C23  119.74  3.000
 DNK  H15  C22  C21  120.16  3.000
 DNK  C23  C22  C21  120.10  3.000
 DNK  H16  C23  C22  119.42  3.000
 DNK  H16  C23  C18  119.66  3.000
 DNK  C22  C23  C18  120.91  3.000
 DNK  H18  C25  H17  107.33  3.000
 DNK  H18  C25  N12  109.02  3.000
 DNK  H17  C25  N12  109.46  3.000
 DNK  H18  C25  C26  110.16  3.000
 DNK  H17  C25  C26  109.98  3.000
 DNK  N12  C25  C26  110.82  3.000
 DNK  H20  C26  H19  107.85  3.000
 DNK  H20  C26  C8   108.77  3.000
 DNK  H19  C26  C8   110.18  3.000
 DNK  H20  C26  C25  109.58  3.000
 DNK  H19  C26  C25  109.87  3.000
 DNK  C8   C26  C25  110.54  3.000
 DNK  H21  C1   C6   121.50  3.000
 DNK  H21  C1   C2   121.74  3.000
 DNK  C6   C1   C2   116.76  3.000
 DNK  O9   C2   C3   109.38  3.000
 DNK  C3   C2   C1   121.99  3.000
 DNK  O9   C2   C1   128.62  3.000
 DNK  O7   C3   C4   128.67  3.000
 DNK  C4   C3   C2   121.95  3.000
 DNK  O7   C3   C2   109.38  3.000
 DNK  H22  C4   C5   121.47  3.000
 DNK  H22  C4   C3   121.77  3.000
 DNK  C5   C4   C3   116.77  3.000
 DNK  H23  C5   C6   119.67  3.000
 DNK  H23  C5   C4   119.05  3.000
 DNK  C6   C5   C4   121.28  3.000
 DNK  H24  C6   C5   119.66  3.000
 DNK  H24  C6   C1   119.08  3.000
 DNK  C5   C6   C1   121.26  3.000
 DNK  C8   O7   C3   106.99  3.000
 DNK  O9   C8   O7   105.78  3.000
 DNK  O7   C8   C26  110.68  3.000
 DNK  O9   C8   C26  109.32  3.000
 DNK  O7   C8   C10  110.21  3.000
 DNK  C26  C8   C10  111.30  3.000
 DNK  O9   C8   C10  109.39  3.000
 DNK  C8   O9   C2   106.90  3.000
 DNK  C25  N12  C13  120.23  3.000
 DNK  C13  N12  C11  126.47  3.000
 DNK  C25  N12  C11  113.22  3.000
 DNK  H25  C14  C18  108.20  3.000
 DNK  H25  C14  C15  106.05  3.000
 DNK  C18  C14  C15  112.57  3.000
 DNK  H25  C14  C13  110.30  3.000
 DNK  C18  C14  C13  107.91  3.000
 DNK  C15  C14  C13  111.76  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
 DNK  CONST_01  C21  C20  C19  C18    0.00   0.0  0
 DNK  CONST_02  C21  C22  C23  C18    0.00   0.0  0
 DNK  CONST_03  C22  C23  C18  C19    0.00   0.0  0
 DNK  CONST_04  C22  C21  C20  C19    0.00   0.0  0
 DNK  CONST_05  C23  C18  C19  C20    0.00   0.0  0
 DNK  CONST_06  C23  C22  C21  C20    0.00   0.0  0
 DNK  CONST_07  C4   C3   C2   C1     0.00   0.0  0
 DNK  CONST_08  C4   C5   C6   C1     0.00   0.0  0
 DNK  CONST_09  C5   C6   C1   C2     0.00   0.0  0
 DNK  CONST_10  C5   C4   C3   C2     0.00   0.0  0
 DNK  CONST_11  C6   C1   C2   C3     0.00   0.0  0
 DNK  CONST_12  C6   C5   C4   C3     0.00   0.0  0
 DNK  CONST_13  C14  C18  C19  C20  180.00   0.0  0
 DNK  CONST_14  C14  C18  C23  C22  180.00   0.0  0
 DNK  CONST_15  H13  C20  C19  C18  180.00   0.0  0
 DNK  CONST_16  H15  C22  C23  C18  180.00   0.0  0
 DNK  CONST_17  H16  C23  C18  C19  180.00   0.0  0
 DNK  CONST_18  H14  C21  C20  C19  180.00   0.0  0
 DNK  CONST_19  H12  C19  C20  C21  180.00   0.0  0
 DNK  CONST_20  H23  C5   C6   C1   180.00   0.0  0
 DNK  CONST_21  H24  C6   C1   C2   180.00   0.0  0
 DNK  CONST_22  H22  C4   C3   C2   180.00   0.0  0
 DNK  CONST_23  H21  C1   C2   C3   180.00   0.0  0
 DNK  CONST_24  C14  C13  N12  C11    0.00   0.0  0
 DNK  CONST_25  O24  C13  N12  C11  180.00   0.0  0
 DNK  CONST_26  C14  C13  N12  C25  180.00   0.0  0
 DNK  CONST_27  O24  C13  N12  C25    0.00   0.0  0
 DNK  Var_01    C25  C26  C8   C10  -52.84  30.0  3
 DNK  Var_02    C25  N12  C11  C10   57.95  30.0  1
 DNK  Var_03    O9   C8   C10  C11  -68.42  30.0  3
 DNK  Var_04    C26  C25  N12  C11  -58.78  30.0  1
 DNK  Var_05    N12  C25  C26  C8    55.23  30.0  1
 DNK  Var_06    N12  C11  C10  C8   -54.00  30.0  1
 DNK  Var_07    H9   C17  C15  C16   59.28  30.0  3
 DNK  Var_08    H6   C16  C15  C17   55.78  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
 DNK  chir_01  C14  C15  C13  C18  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
 DNK  plan-1  C18  0.020
 DNK  plan-1  C19  0.020
 DNK  plan-1  C20  0.020
 DNK  plan-1  C21  0.020
 DNK  plan-1  C22  0.020
 DNK  plan-1  C23  0.020
 DNK  plan-1  C14  0.020
 DNK  plan-1  H12  0.020
 DNK  plan-1  H13  0.020
 DNK  plan-1  H14  0.020
 DNK  plan-1  H15  0.020
 DNK  plan-1  H16  0.020
 DNK  plan-2  C1   0.020
 DNK  plan-2  C2   0.020
 DNK  plan-2  C3   0.020
 DNK  plan-2  C4   0.020
 DNK  plan-2  C5   0.020
 DNK  plan-2  C6   0.020
 DNK  plan-2  O7   0.020
 DNK  plan-2  O9   0.020
 DNK  plan-2  H21  0.020
 DNK  plan-2  H22  0.020
 DNK  plan-2  H23  0.020
 DNK  plan-2  H24  0.020
 DNK  plan-3  C11  0.020
 DNK  plan-3  C13  0.020
 DNK  plan-3  C25  0.020
 DNK  plan-3  N12  0.020
 DNK  plan-3  C14  0.020
 DNK  plan-3  O24  0.020

