# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 21:28:43 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (2~{S})-2-(4-chlorophenyl)-3-methyl-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)c4ccc(Cl)cc4
#
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
 DOK  DOK  (2~{S})-2-(4-chlorophenyl)-3-methyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one  ligand  51  27  .  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_DOK
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
 DOK  C11  C   CR56  0   0.301  -4.9742   0.0177  -0.4821
 DOK  C15  C   CR16  0  -0.271  -7.1793  -0.8069  -0.2879
 DOK  C16  C   CR16  0  -0.270  -6.6949  -1.9643   0.3003
 DOK  C17  C   CR16  0  -0.356  -5.3228  -2.1536   0.5107
 DOK  C18  C   CH1   0  -0.458   2.0593   1.4283  -0.4991
 DOK  C19  C   CR16  0  -0.294   3.7823   0.3023   0.9802
 DOK  C20  C   CR16  0  -0.329   3.3576  -0.6228  -1.1834
 DOK  C21  C   CH1   0  -0.204   2.6903   2.8242  -0.6612
 DOK  C22  C   CR16  0  -0.194   4.7325  -0.6777   1.2202
 DOK  C23  C   CR16  0  -0.195   4.3065  -1.6109  -0.9618
 DOK  C24  C   CH3   0  -0.657   3.8171   2.7951  -1.6886
 DOK  C25  C   CH3   0  -0.665   1.6324   3.8412  -1.0825
 DOK  C26  C   CR6   0  -0.056   4.9856  -1.6295   0.2443
 DOK  C1   C   CH2   0  -0.342  -0.3522  -0.2925  -0.5866
 DOK  C2   C   CH2   0  -0.453  -1.6491   0.1873  -1.2337
 DOK  C3   C   CR5   0   0.445  -2.7659   0.2556  -0.2111
 DOK  C4   C   CH2   0  -0.451  -2.3535   1.0409   1.0252
 DOK  C5   C   CH2   0  -0.333  -1.0299   0.5255   1.5804
 DOK  N6   N   NT    0  -0.456  -0.0098   0.5490   0.5445
 DOK  C7   C   C     0   0.594   1.0309   1.4087   0.6320
 DOK  O8   O   O     0  -0.494   1.1931   2.1189   1.6158
 DOK  C9   C   CR6   0   0.169   3.0799   0.3448  -0.2232
 DOK  O10  O   O     0  -0.496  -3.9370   0.8318  -0.7942
 DOK  C12  C   CR56  0   0.312  -4.4892  -1.1399   0.1061
 DOK  O13  O   O     0  -0.492  -3.1384  -1.0766   0.1735
 DOK  C14  C   CR16  0  -0.355  -6.3159   0.2189  -0.6944
 DOK  CL   CL  CL    0  -0.132   6.1693  -2.8618   0.5389
 DOK  H1   H   HCR6  0   0.259  -8.2440  -0.6860  -0.4362
 DOK  H2   H   HCR6  0   0.259  -7.3849  -2.7390   0.6069
 DOK  H3   H   HCR6  0   0.271  -4.9404  -3.0564   0.9673
 DOK  H4   H   HCH1  0   0.264   1.5855   1.1996  -1.4567
 DOK  H5   H   HCR6  0   0.262   3.5936   1.0408   1.7487
 DOK  H6   H   HCR6  0   0.262   2.8314  -0.6071  -2.1303
 DOK  H7   H   HCH1  0   0.231   3.1088   3.1322   0.3002
 DOK  H8   H   HCR6  0   0.279   5.2684  -0.6973   2.1595
 DOK  H9   H   HCR6  0   0.279   4.5096  -2.3533  -1.7217
 DOK  H10  H   HCH3  0   0.216   3.4629   2.4337  -2.6572
 DOK  H11  H   HCH3  0   0.233   4.2146   3.8000  -1.8381
 DOK  H12  H   HCH3  0   0.234   4.6456   2.1587  -1.3776
 DOK  H13  H   HCH3  0   0.234   0.8220   3.9263  -0.3587
 DOK  H14  H   HCH3  0   0.234   2.0765   4.8316  -1.1932
 DOK  H15  H   HCH3  0   0.217   1.1952   3.5687  -2.0464
 DOK  H16  H   HCH2  0   0.266  -0.4597  -1.3214  -0.2333
 DOK  H17  H   HCH2  0   0.277   0.4370  -0.3110  -1.3295
 DOK  H18  H   HCH2  0   0.258  -1.4957   1.1846  -1.6537
 DOK  H19  H   HCH2  0   0.269  -1.9303  -0.4788  -2.0520
 DOK  H20  H   HCH2  0   0.257  -2.2457   2.0933   0.7520
 DOK  H21  H   HCH2  0   0.262  -3.1314   0.9770   1.7903
 DOK  H22  H   HCH2  0   0.279  -0.7126   1.1348   2.4209
 DOK  H23  H   HCH2  0   0.258  -1.1372  -0.5001   1.9446
 DOK  H24  H   HCR6  0   0.272  -6.6904   1.1233  -1.1544

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
 DOK  C17  C16  aromatic  1.401  0.020  1.401
 DOK  C17  C12  aromatic  1.373  0.020  1.373
 DOK  C16  C15  aromatic  1.386  0.020  1.386
 DOK  C25  C21  single    1.527  0.020  1.527
 DOK  O13  C12  single    1.354  0.020  1.354
 DOK  O13  C3   single    1.436  0.020  1.436
 DOK  C12  C11  aromatic  1.386  0.020  1.386
 DOK  C5   N6   single    1.454  0.020  1.454
 DOK  C5   C4   single    1.525  0.020  1.525
 DOK  C15  C14  aromatic  1.401  0.020  1.401
 DOK  C18  C21  single    1.540  0.020  1.540
 DOK  C18  C7   single    1.529  0.020  1.529
 DOK  C18  C9   single    1.514  0.020  1.514
 DOK  N6   C7   single    1.353  0.020  1.353
 DOK  N6   C1   single    1.451  0.020  1.451
 DOK  C4   C3   single    1.522  0.020  1.522
 DOK  C24  C21  single    1.525  0.020  1.525
 DOK  C20  C9   aromatic  1.391  0.020  1.391
 DOK  C20  C23  aromatic  1.388  0.020  1.388
 DOK  C3   O10  single    1.429  0.020  1.429
 DOK  C3   C2   single    1.516  0.020  1.516
 DOK  C7   O8   double    1.224  0.020  1.224
 DOK  C1   C2   single    1.527  0.020  1.527
 DOK  C11  C14  aromatic  1.373  0.020  1.373
 DOK  C11  O10  single    1.355  0.020  1.355
 DOK  C9   C19  aromatic  1.394  0.020  1.394
 DOK  C23  C26  aromatic  1.384  0.020  1.384
 DOK  C19  C22  aromatic  1.386  0.020  1.386
 DOK  C26  C22  aromatic  1.387  0.020  1.387
 DOK  C26  CL   single    1.734  0.020  1.734
 DOK  C15  H1   single    0.930  0.020  1.080
 DOK  C16  H2   single    0.930  0.020  1.080
 DOK  C17  H3   single    0.930  0.020  1.080
 DOK  C18  H4   single    0.970  0.020  1.090
 DOK  C19  H5   single    0.930  0.020  1.080
 DOK  C20  H6   single    0.930  0.020  1.080
 DOK  C21  H7   single    0.970  0.020  1.090
 DOK  C22  H8   single    0.930  0.020  1.080
 DOK  C23  H9   single    0.930  0.020  1.080
 DOK  C24  H10  single    0.970  0.020  1.090
 DOK  C24  H11  single    0.970  0.020  1.090
 DOK  C24  H12  single    0.970  0.020  1.090
 DOK  C25  H13  single    0.970  0.020  1.090
 DOK  C25  H14  single    0.970  0.020  1.090
 DOK  C25  H15  single    0.970  0.020  1.090
 DOK  C1   H16  single    0.970  0.020  1.090
 DOK  C1   H17  single    0.970  0.020  1.090
 DOK  C2   H18  single    0.970  0.020  1.090
 DOK  C2   H19  single    0.970  0.020  1.090
 DOK  C4   H20  single    0.970  0.020  1.090
 DOK  C4   H21  single    0.970  0.020  1.090
 DOK  C5   H22  single    0.970  0.020  1.090
 DOK  C5   H23  single    0.970  0.020  1.090
 DOK  C14  H24  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
 DOK  C14  C11  C12  121.99  3.000
 DOK  C14  C11  O10  128.63  3.000
 DOK  C12  C11  O10  109.37  3.000
 DOK  H1   C15  C14  119.01  3.000
 DOK  H1   C15  C16  119.71  3.000
 DOK  C14  C15  C16  121.28  3.000
 DOK  H2   C16  C17  119.04  3.000
 DOK  H2   C16  C15  119.70  3.000
 DOK  C17  C16  C15  121.26  3.000
 DOK  H3   C17  C12  121.73  3.000
 DOK  H3   C17  C16  121.49  3.000
 DOK  C12  C17  C16  116.77  3.000
 DOK  H4   C18  C9   107.60  3.000
 DOK  H4   C18  C7   110.73  3.000
 DOK  C9   C18  C7   108.02  3.000
 DOK  H4   C18  C21  105.97  3.000
 DOK  C9   C18  C21  113.05  3.000
 DOK  C7   C18  C21  111.41  3.000
 DOK  H5   C19  C9   120.29  3.000
 DOK  H5   C19  C22  118.62  3.000
 DOK  C9   C19  C22  121.10  3.000
 DOK  H6   C20  C9   119.75  3.000
 DOK  H6   C20  C23  118.81  3.000
 DOK  C9   C20  C23  121.43  3.000
 DOK  H7   C21  C25  108.68  3.000
 DOK  H7   C21  C24  108.36  3.000
 DOK  C25  C21  C24  109.80  3.000
 DOK  H7   C21  C18  108.65  3.000
 DOK  C24  C21  C18  110.87  3.000
 DOK  C25  C21  C18  110.42  3.000
 DOK  H8   C22  C26  120.55  3.000
 DOK  H8   C22  C19  120.20  3.000
 DOK  C26  C22  C19  119.25  3.000
 DOK  H9   C23  C26  120.72  3.000
 DOK  H9   C23  C20  120.33  3.000
 DOK  C26  C23  C20  118.95  3.000
 DOK  H12  C24  H11  107.46  3.000
 DOK  H12  C24  H10  107.82  3.000
 DOK  H11  C24  H10  107.53  3.000
 DOK  H12  C24  C21  112.37  3.000
 DOK  H11  C24  C21  110.12  3.000
 DOK  H10  C24  C21  111.34  3.000
 DOK  H15  C25  H14  107.44  3.000
 DOK  H15  C25  H13  107.91  3.000
 DOK  H14  C25  H13  107.41  3.000
 DOK  H15  C25  C21  110.76  3.000
 DOK  H14  C25  C21  110.53  3.000
 DOK  H13  C25  C21  112.58  3.000
 DOK  CL   C26  C23  119.51  3.000
 DOK  CL   C26  C22  119.53  3.000
 DOK  C23  C26  C22  120.96  3.000
 DOK  H17  C1   H16  106.08  3.000
 DOK  H17  C1   N6   111.86  3.000
 DOK  H16  C1   N6   108.49  3.000
 DOK  H17  C1   C2   109.47  3.000
 DOK  H16  C1   C2   110.44  3.000
 DOK  N6   C1   C2   110.41  3.000
 DOK  H19  C2   H18  107.75  3.000
 DOK  H19  C2   C3   110.08  3.000
 DOK  H18  C2   C3   108.75  3.000
 DOK  H19  C2   C1   110.16  3.000
 DOK  H18  C2   C1   109.29  3.000
 DOK  C3   C2   C1   110.74  3.000
 DOK  O13  C3   O10  105.71  3.000
 DOK  O10  C3   C4   110.21  3.000
 DOK  O13  C3   C4   109.36  3.000
 DOK  O10  C3   C2   110.27  3.000
 DOK  C4   C3   C2   111.82  3.000
 DOK  O13  C3   C2   109.27  3.000
 DOK  H21  C4   H20  107.55  3.000
 DOK  H21  C4   C5   110.06  3.000
 DOK  H20  C4   C5   109.32  3.000
 DOK  H21  C4   C3   110.22  3.000
 DOK  H20  C4   C3   108.70  3.000
 DOK  C5   C4   C3   110.89  3.000
 DOK  H23  C5   H22  107.30  3.000
 DOK  H23  C5   N6   108.74  3.000
 DOK  H22  C5   N6   109.73  3.000
 DOK  H23  C5   C4   110.67  3.000
 DOK  H22  C5   C4   110.23  3.000
 DOK  N6   C5   C4   110.12  3.000
 DOK  C7   N6   C5   120.26  3.000
 DOK  C7   N6   C1   126.92  3.000
 DOK  C5   N6   C1   112.36  3.000
 DOK  O8   C7   N6   121.51  3.000
 DOK  O8   C7   C18  119.87  3.000
 DOK  N6   C7   C18  118.54  3.000
 DOK  C20  C9   C19  118.30  3.000
 DOK  C19  C9   C18  121.26  3.000
 DOK  C20  C9   C18  120.43  3.000
 DOK  C3   O10  C11  106.92  3.000
 DOK  O13  C12  C17  128.71  3.000
 DOK  O13  C12  C11  109.34  3.000
 DOK  C17  C12  C11  121.95  3.000
 DOK  C12  O13  C3   106.79  3.000
 DOK  H24  C14  C15  121.48  3.000
 DOK  H24  C14  C11  121.77  3.000
 DOK  C15  C14  C11  116.75  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
 DOK  CONST_01  C16  C17  C12  C11    0.00   0.0  0
 DOK  CONST_02  C16  C15  C14  C11    0.00   0.0  0
 DOK  CONST_03  C12  C17  C16  C15    0.00   0.0  0
 DOK  CONST_04  C12  C11  C14  C15    0.00   0.0  0
 DOK  CONST_05  C14  C15  C16  C17    0.00   0.0  0
 DOK  CONST_06  C14  C11  C12  C17    0.00   0.0  0
 DOK  CONST_07  C23  C20  C9   C19    0.00   0.0  0
 DOK  CONST_08  C23  C26  C22  C19    0.00   0.0  0
 DOK  CONST_09  C22  C19  C9   C20    0.00   0.0  0
 DOK  CONST_10  C22  C26  C23  C20    0.00   0.0  0
 DOK  CONST_11  C9   C20  C23  C26    0.00   0.0  0
 DOK  CONST_12  C9   C19  C22  C26    0.00   0.0  0
 DOK  CONST_13  C23  C20  C9   C18  180.00   0.0  0
 DOK  CONST_14  C22  C19  C9   C18  180.00   0.0  0
 DOK  CONST_15  CL   C26  C22  C19  180.00   0.0  0
 DOK  CONST_16  CL   C26  C23  C20  180.00   0.0  0
 DOK  CONST_17  H3   C17  C12  C11  180.00   0.0  0
 DOK  CONST_18  H1   C15  C14  C11  180.00   0.0  0
 DOK  CONST_19  H24  C14  C15  C16  180.00   0.0  0
 DOK  CONST_20  H6   C20  C9   C19  180.00   0.0  0
 DOK  CONST_21  H5   C19  C9   C20  180.00   0.0  0
 DOK  CONST_22  H9   C23  C26  C22  180.00   0.0  0
 DOK  CONST_23  H8   C22  C26  C23  180.00   0.0  0
 DOK  CONST_24  H2   C16  C17  C12  180.00   0.0  0
 DOK  CONST_25  C5   N6   C7   C18  180.00   0.0  0
 DOK  CONST_26  C1   N6   C7   C18    0.00   0.0  0
 DOK  CONST_27  O8   C7   N6   C1   180.00   0.0  0
 DOK  CONST_28  O8   C7   N6   C5     0.00   0.0  0
 DOK  Var_01    O13  C3   O10  C11   13.23  30.0  1
 DOK  Var_02    C4   C5   N6   C1   -60.80  30.0  1
 DOK  Var_03    C5   C4   C3   C2   -51.36  30.0  3
 DOK  Var_04    C5   N6   C1   C2    60.90  30.0  1
 DOK  Var_05    N6   C5   C4   C3    55.01  30.0  1
 DOK  Var_06    C12  C11  O10  C3    -8.40  30.0  1
 DOK  Var_07    N6   C1   C2   C3   -55.09  30.0  1
 DOK  Var_08    H13  C25  C21  C18   59.62  30.0  3
 DOK  Var_09    H10  C24  C21  C18   57.41  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
 DOK  chir_01  C18  C21  C7  C9  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
 DOK  plan-1  C18  0.020
 DOK  plan-1  C19  0.020
 DOK  plan-1  C20  0.020
 DOK  plan-1  C22  0.020
 DOK  plan-1  C23  0.020
 DOK  plan-1  C26  0.020
 DOK  plan-1  C9   0.020
 DOK  plan-1  CL   0.020
 DOK  plan-1  H5   0.020
 DOK  plan-1  H6   0.020
 DOK  plan-1  H8   0.020
 DOK  plan-1  H9   0.020
 DOK  plan-2  C11  0.020
 DOK  plan-2  C15  0.020
 DOK  plan-2  C16  0.020
 DOK  plan-2  C17  0.020
 DOK  plan-2  O10  0.020
 DOK  plan-2  C12  0.020
 DOK  plan-2  O13  0.020
 DOK  plan-2  C14  0.020
 DOK  plan-2  H1   0.020
 DOK  plan-2  H2   0.020
 DOK  plan-2  H3   0.020
 DOK  plan-2  H24  0.020
 DOK  plan-3  C18  0.020
 DOK  plan-3  C1   0.020
 DOK  plan-3  C5   0.020
 DOK  plan-3  N6   0.020
 DOK  plan-3  C7   0.020
 DOK  plan-3  O8   0.020

