# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 03:06:32 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (2~{S})-2-(3,4-dichlorophenyl)-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)c(Cl)c4
#
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
 DN5  DN5  (2~{S})-2-(3,4-dichlorophenyl)-3-methyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one  ligand  51  28  .  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_DN5
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
 DN5  C10  C   CR6   0   0.161  -2.3907   0.5410   0.6440
 DN5  C11  C   CR16  0  -0.324  -2.5109  -0.4147   1.6465
 DN5  C13  C   CR6   0  -0.021  -4.3357  -1.4597   0.4916
 DN5  C15  C   CR16  0  -0.249  -3.2619   0.4840  -0.4397
 DN5  C18  C   CH1   0  -0.205  -1.9729   3.0304   0.9805
 DN5  C19  C   CH3   0  -0.658  -2.9962   2.9965   2.1112
 DN5  C20  C   CH3   0  -0.665  -0.8777   4.0440   1.3037
 DN5  C22  C   CR56  0   0.312   4.8878  -1.2612  -0.3263
 DN5  C23  C   CR56  0   0.299   5.4869  -0.1375   0.2199
 DN5  C25  C   CR16  0  -0.355   6.7931  -0.1431   0.6439
 DN5  C26  C   CR16  0  -0.271   7.4982  -1.3449   0.4979
 DN5  C27  C   CR16  0  -0.270   6.8990  -2.4687  -0.0481
 DN5  C28  C   CR16  0  -0.355   5.5651  -2.4465  -0.4754
 DN5  C1   C   CH2   0  -0.338   1.4022   0.7151  -1.7468
 DN5  C2   C   CH2   0  -0.458   2.7976   1.1906  -1.3524
 DN5  C3   C   CR5   0   0.448   3.3419   0.3623  -0.2045
 DN5  C4   C   CH2   0  -0.442   2.3613   0.3011   0.9565
 DN5  C5   C   CH2   0  -0.343   0.9847  -0.1421   0.4710
 DN5  N6   N   NT    0  -0.454   0.5210   0.7339  -0.5897
 DN5  C7   C   C     0   0.595  -0.5032   1.6133  -0.5263
 DN5  O8   O   O     0  -0.492  -0.7888   2.3378  -1.4701
 DN5  C9   C   CH1   0  -0.464  -1.3560   1.6385   0.7445
 DN5  C12  C   CR16  0  -0.200  -3.4731  -1.4087   1.5743
 DN5  C14  C   CR6   0   0.023  -4.2275  -0.5062  -0.5155
 DN5  CL6  CL  CL    0  -0.097  -5.2929  -0.5423  -1.8696
 DN5  CL7  CL  CL    0  -0.098  -5.5283  -2.6994   0.4070
 DN5  O21  O   O     0  -0.493   3.6113  -0.9695  -0.6678
 DN5  O24  O   O     0  -0.497   4.5977   0.8846   0.2354
 DN5  H1   H   HCR6  0   0.270  -1.8518  -0.3886   2.5050
 DN5  H2   H   HCR6  0   0.282  -3.1983   1.2162  -1.2343
 DN5  H3   H   HCH1  0   0.233  -2.4811   3.3462   0.0664
 DN5  H4   H   HCH3  0   0.235  -3.3732   4.0018   2.3040
 DN5  H5   H   HCH3  0   0.234  -3.8529   2.3656   1.8754
 DN5  H6   H   HCH3  0   0.217  -2.5546   2.6281   3.0405
 DN5  H7   H   HCH3  0   0.218  -0.3711   3.7811   2.2356
 DN5  H8   H   HCH3  0   0.233  -0.1223   4.1132   0.5205
 DN5  H9   H   HCH3  0   0.236  -1.3041   5.0397   1.4336
 DN5  H11  H   HCR6  0   0.259   8.5293  -1.3921   0.8213
 DN5  H12  H   HCR6  0   0.259   7.4673  -3.3838  -0.1469
 DN5  H13  H   HCR6  0   0.271   5.0940  -3.3213  -0.9028
 DN5  H14  H   HCH2  0   0.281   0.9971   1.3493  -2.5290
 DN5  H15  H   HCH2  0   0.259   1.4432  -0.3035  -2.1423
 DN5  H16  H   HCH2  0   0.266   3.4721   1.1324  -2.2095
 DN5  H17  H   HCH2  0   0.259   2.7489   2.2359  -1.0388
 DN5  H18  H   HCH2  0   0.265   2.7268  -0.3820   1.7271
 DN5  H19  H   HCH2  0   0.256   2.2853   1.2957   1.4043
 DN5  H20  H   HCH2  0   0.268   1.0293  -1.1621   0.0804
 DN5  H21  H   HCH2  0   0.278   0.2902  -0.1728   1.3032
 DN5  H22  H   HCH1  0   0.269  -0.7330   1.4314   1.6185
 DN5  H23  H   HCR6  0   0.290  -3.5561  -2.1454   2.3614
 DN5  H10  H   HCR6  0   0.272   7.2571   0.7368   1.0685

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
 DN5  O21  C22  single    1.353  0.020  1.353
 DN5  O21  C3   single    1.436  0.020  1.436
 DN5  C28  C22  aromatic  1.373  0.020  1.373
 DN5  C28  C27  aromatic  1.401  0.020  1.401
 DN5  C2   C3   single    1.517  0.020  1.517
 DN5  C2   C1   single    1.526  0.020  1.526
 DN5  C20  C18  single    1.527  0.020  1.527
 DN5  C22  C23  aromatic  1.386  0.020  1.386
 DN5  C27  C26  aromatic  1.386  0.020  1.386
 DN5  C3   C4   single    1.521  0.020  1.521
 DN5  C3   O24  single    1.430  0.020  1.430
 DN5  C1   N6   single    1.455  0.020  1.455
 DN5  C19  C18  single    1.525  0.020  1.525
 DN5  C9   C18  single    1.541  0.020  1.541
 DN5  C9   C7   single    1.531  0.020  1.531
 DN5  C9   C10  single    1.512  0.020  1.512
 DN5  C4   C5   single    1.526  0.020  1.526
 DN5  N6   C7   single    1.351  0.020  1.351
 DN5  N6   C5   single    1.452  0.020  1.452
 DN5  C23  O24  single    1.355  0.020  1.355
 DN5  C23  C25  aromatic  1.373  0.020  1.373
 DN5  C7   O8   double    1.224  0.020  1.224
 DN5  C15  C10  aromatic  1.392  0.020  1.392
 DN5  C15  C14  aromatic  1.385  0.020  1.385
 DN5  C26  C25  aromatic  1.401  0.020  1.401
 DN5  CL6  C14  single    1.723  0.020  1.723
 DN5  C10  C11  aromatic  1.390  0.020  1.390
 DN5  C14  C13  aromatic  1.391  0.020  1.391
 DN5  C11  C12  aromatic  1.385  0.020  1.385
 DN5  C13  C12  aromatic  1.385  0.020  1.385
 DN5  C13  CL7  single    1.722  0.020  1.722
 DN5  C11  H1   single    0.930  0.020  1.080
 DN5  C15  H2   single    0.930  0.020  1.080
 DN5  C18  H3   single    0.970  0.020  1.090
 DN5  C19  H4   single    0.970  0.020  1.090
 DN5  C19  H5   single    0.970  0.020  1.090
 DN5  C19  H6   single    0.970  0.020  1.090
 DN5  C20  H7   single    0.970  0.020  1.090
 DN5  C20  H8   single    0.970  0.020  1.090
 DN5  C20  H9   single    0.970  0.020  1.090
 DN5  C25  H10  single    0.930  0.020  1.080
 DN5  C26  H11  single    0.930  0.020  1.080
 DN5  C27  H12  single    0.930  0.020  1.080
 DN5  C28  H13  single    0.930  0.020  1.080
 DN5  C1   H14  single    0.970  0.020  1.090
 DN5  C1   H15  single    0.970  0.020  1.090
 DN5  C2   H16  single    0.970  0.020  1.090
 DN5  C2   H17  single    0.970  0.020  1.090
 DN5  C4   H18  single    0.970  0.020  1.090
 DN5  C4   H19  single    0.970  0.020  1.090
 DN5  C5   H20  single    0.970  0.020  1.090
 DN5  C5   H21  single    0.970  0.020  1.090
 DN5  C9   H22  single    0.970  0.020  1.090
 DN5  C12  H23  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
 DN5  C9   C10  C15  120.66  3.000
 DN5  C15  C10  C11  118.64  3.000
 DN5  C9   C10  C11  120.68  3.000
 DN5  H1   C11  C12  118.78  3.000
 DN5  H1   C11  C10  120.17  3.000
 DN5  C12  C11  C10  121.04  3.000
 DN5  CL7  C13  C14  120.77  3.000
 DN5  CL7  C13  C12  119.74  3.000
 DN5  C14  C13  C12  119.49  3.000
 DN5  H2   C15  C14  118.97  3.000
 DN5  H2   C15  C10  120.48  3.000
 DN5  C14  C15  C10  120.55  3.000
 DN5  H3   C18  C9   108.62  3.000
 DN5  H3   C18  C20  108.59  3.000
 DN5  C9   C18  C20  110.18  3.000
 DN5  H3   C18  C19  108.34  3.000
 DN5  C9   C18  C19  111.23  3.000
 DN5  C20  C18  C19  109.82  3.000
 DN5  H6   C19  H5   107.85  3.000
 DN5  H6   C19  H4   107.46  3.000
 DN5  H5   C19  H4   107.46  3.000
 DN5  H6   C19  C18  111.52  3.000
 DN5  H5   C19  C18  112.32  3.000
 DN5  H4   C19  C18  110.02  3.000
 DN5  H9   C20  H8   107.35  3.000
 DN5  H9   C20  H7   107.41  3.000
 DN5  H8   C20  H7   107.86  3.000
 DN5  H9   C20  C18  110.53  3.000
 DN5  H8   C20  C18  112.78  3.000
 DN5  H7   C20  C18  110.69  3.000
 DN5  O21  C22  C28  128.60  3.000
 DN5  C28  C22  C23  121.97  3.000
 DN5  O21  C22  C23  109.42  3.000
 DN5  O24  C23  C25  128.59  3.000
 DN5  C25  C23  C22  121.98  3.000
 DN5  O24  C23  C22  109.42  3.000
 DN5  H10  C25  C26  121.53  3.000
 DN5  H10  C25  C23  121.73  3.000
 DN5  C26  C25  C23  116.75  3.000
 DN5  H11  C26  C27  119.65  3.000
 DN5  H11  C26  C25  119.08  3.000
 DN5  C27  C26  C25  121.28  3.000
 DN5  H12  C27  C28  119.06  3.000
 DN5  H12  C27  C26  119.67  3.000
 DN5  C28  C27  C26  121.27  3.000
 DN5  H13  C28  C27  121.50  3.000
 DN5  H13  C28  C22  121.74  3.000
 DN5  C27  C28  C22  116.76  3.000
 DN5  H15  C1   H14  107.32  3.000
 DN5  H15  C1   N6   108.81  3.000
 DN5  H14  C1   N6   109.85  3.000
 DN5  H15  C1   C2   110.45  3.000
 DN5  H14  C1   C2   110.21  3.000
 DN5  N6   C1   C2   110.14  3.000
 DN5  H17  C2   H16  107.69  3.000
 DN5  H17  C2   C3   108.74  3.000
 DN5  H16  C2   C3   110.07  3.000
 DN5  H17  C2   C1   109.36  3.000
 DN5  H16  C2   C1   110.20  3.000
 DN5  C3   C2   C1   110.70  3.000
 DN5  O24  C3   O21  105.87  3.000
 DN5  O24  C3   C4   110.25  3.000
 DN5  O21  C3   C4   109.27  3.000
 DN5  O24  C3   C2   110.40  3.000
 DN5  C4   C3   C2   111.62  3.000
 DN5  O21  C3   C2   109.26  3.000
 DN5  H19  C4   H18  107.64  3.000
 DN5  H19  C4   C5   109.38  3.000
 DN5  H18  C4   C5   110.16  3.000
 DN5  H19  C4   C3   108.71  3.000
 DN5  H18  C4   C3   110.36  3.000
 DN5  C5   C4   C3   110.52  3.000
 DN5  H21  C5   H20  105.90  3.000
 DN5  H21  C5   N6   111.92  3.000
 DN5  H20  C5   N6   108.36  3.000
 DN5  H21  C5   C4   110.00  3.000
 DN5  H20  C5   C4   110.36  3.000
 DN5  N6   C5   C4   110.21  3.000
 DN5  C7   N6   C5   126.90  3.000
 DN5  C5   N6   C1   112.33  3.000
 DN5  C7   N6   C1   120.32  3.000
 DN5  C9   C7   O8   120.04  3.000
 DN5  O8   C7   N6   121.73  3.000
 DN5  C9   C7   N6   118.16  3.000
 DN5  H22  C9   C7   110.07  3.000
 DN5  H22  C9   C18  106.07  3.000
 DN5  C7   C9   C18  111.41  3.000
 DN5  H22  C9   C10  107.80  3.000
 DN5  C7   C9   C10  108.31  3.000
 DN5  C18  C9   C10  113.08  3.000
 DN5  H23  C12  C13  119.74  3.000
 DN5  H23  C12  C11  120.28  3.000
 DN5  C13  C12  C11  119.98  3.000
 DN5  CL6  C14  C15  119.27  3.000
 DN5  CL6  C14  C13  120.43  3.000
 DN5  C15  C14  C13  120.30  3.000
 DN5  C3   O21  C22  107.19  3.000
 DN5  C3   O24  C23  107.30  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
 DN5  CONST_01  C13  C14  C15  C10    0.00   0.0  0
 DN5  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 DN5  CONST_03  C14  C15  C10  C11    0.00   0.0  0
 DN5  CONST_04  C14  C13  C12  C11    0.00   0.0  0
 DN5  CONST_05  C12  C11  C10  C15    0.00   0.0  0
 DN5  CONST_06  C12  C13  C14  C15    0.00   0.0  0
 DN5  CONST_07  C26  C27  C28  C22    0.00   0.0  0
 DN5  CONST_08  C26  C25  C23  C22    0.00   0.0  0
 DN5  CONST_09  C27  C28  C22  C23    0.00   0.0  0
 DN5  CONST_10  C27  C26  C25  C23    0.00   0.0  0
 DN5  CONST_11  C28  C22  C23  C25    0.00   0.0  0
 DN5  CONST_12  C28  C27  C26  C25    0.00   0.0  0
 DN5  CONST_13  CL6  C14  C15  C10  180.00   0.0  0
 DN5  CONST_14  CL7  C13  C12  C11  180.00   0.0  0
 DN5  CONST_15  CL7  C13  C14  C15  180.00   0.0  0
 DN5  CONST_16  C14  C15  C10  C9   180.00   0.0  0
 DN5  CONST_17  C12  C11  C10  C9   180.00   0.0  0
 DN5  CONST_18  CL6  C14  C13  C12  180.00   0.0  0
 DN5  CONST_19  H23  C12  C11  C10  180.00   0.0  0
 DN5  CONST_20  H2   C15  C10  C11  180.00   0.0  0
 DN5  CONST_21  H1   C11  C12  C13  180.00   0.0  0
 DN5  CONST_22  H12  C27  C28  C22  180.00   0.0  0
 DN5  CONST_23  H10  C25  C23  C22  180.00   0.0  0
 DN5  CONST_24  H13  C28  C22  C23  180.00   0.0  0
 DN5  CONST_25  H11  C26  C25  C23  180.00   0.0  0
 DN5  CONST_26  C9   C7   N6   C1   180.00   0.0  0
 DN5  CONST_27  O8   C7   N6   C1     0.00   0.0  0
 DN5  CONST_28  C9   C7   N6   C5     0.00   0.0  0
 DN5  CONST_29  O8   C7   N6   C5   180.00   0.0  0
 DN5  Var_01    C2   C3   O21  C22  127.56  30.0  1
 DN5  Var_02    O21  C3   O24  C23   -8.60  30.0  1
 DN5  Var_03    C4   C5   N6   C1    60.99  30.0  1
 DN5  Var_04    C5   C4   C3   C2    52.07  30.0  3
 DN5  Var_05    C5   N6   C1   C2   -60.80  30.0  1
 DN5  Var_06    N6   C1   C2   C3    55.34  30.0  1
 DN5  Var_07    N6   C5   C4   C3   -55.55  30.0  1
 DN5  Var_08    H7   C20  C18  C19   59.53  30.0  3
 DN5  Var_09    H4   C19  C18  C20   54.18  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
 DN5  chir_01  C9  C18  C7  C10  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
 DN5  plan-1  C10  0.020
 DN5  plan-1  C11  0.020
 DN5  plan-1  C13  0.020
 DN5  plan-1  C15  0.020
 DN5  plan-1  C9   0.020
 DN5  plan-1  C12  0.020
 DN5  plan-1  C14  0.020
 DN5  plan-1  CL6  0.020
 DN5  plan-1  CL7  0.020
 DN5  plan-1  H1   0.020
 DN5  plan-1  H2   0.020
 DN5  plan-1  H23  0.020
 DN5  plan-2  C22  0.020
 DN5  plan-2  C23  0.020
 DN5  plan-2  C25  0.020
 DN5  plan-2  C26  0.020
 DN5  plan-2  C27  0.020
 DN5  plan-2  C28  0.020
 DN5  plan-2  O21  0.020
 DN5  plan-2  O24  0.020
 DN5  plan-2  H11  0.020
 DN5  plan-2  H12  0.020
 DN5  plan-2  H13  0.020
 DN5  plan-2  H10  0.020
 DN5  plan-3  C1   0.020
 DN5  plan-3  C5   0.020
 DN5  plan-3  N6   0.020
 DN5  plan-3  C7   0.020
 DN5  plan-3  O8   0.020
 DN5  plan-3  C9   0.020

