# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:30:45 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 2-(4-chlorophenyl)-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(CC(=O)N2CCC3(CC2)Oc4ccccc4O3)cc1
#
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
 DLH  DLH  2-(4-chlorophenyl)-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethanone  ligand  42  24  .  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_DLH
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
 DLH  C10  C   CH2   0  -0.315  -0.8376  -0.4778  -1.2833
 DLH  C11  C   CH2   0  -0.309  -1.0071  -1.0004   1.0822
 DLH  C15  C   CR6   0  -0.052   6.1660   0.3385  -0.0321
 DLH  C17  C   CR16  0  -0.292   4.3692  -0.9554  -0.9336
 DLH  C18  C   CR16  0  -0.278   3.9560   1.2486  -0.1111
 DLH  C19  C   CR16  0  -0.179   5.7129  -0.8361  -0.6098
 DLH  C20  C   CR16  0  -0.183   5.2940   1.3873   0.2198
 DLH  C21  C   CR16  0  -0.332  -6.2073   1.4503   0.4727
 DLH  C22  C   CR16  0  -0.333  -6.0391  -1.3167  -0.1401
 DLH  C23  C   CR16  0  -0.250  -7.2700  -0.7044   0.1247
 DLH  C24  C   CR16  0  -0.251  -7.3520   0.6456   0.4241
 DLH  C1   C   CR5   0   0.447  -2.8470   0.3079  -0.0092
 DLH  C12  C   CH2   0  -0.701   2.0244  -0.0602  -1.0418
 DLH  C14  C   CR6   0   0.193   3.4752   0.0798  -0.6915
 DLH  C6   C   CR56  0   0.317  -4.9261  -0.5147  -0.0892
 DLH  C7   C   CR56  0   0.299  -5.0085   0.8355   0.2098
 DLH  C8   C   CH2   0  -0.441  -1.9108   0.6012  -1.1664
 DLH  C9   C   CH2   0  -0.443  -2.0788   0.0655   1.2767
 DLH  N2   N   NT    0  -0.461  -0.1347  -0.6424  -0.0238
 DLH  O13  O   O     0  -0.501   1.7113  -0.5810   1.2674
 DLH  O4   O   O     0  -0.491  -3.7662   1.3799   0.1775
 DLH  O5   O   O     0  -0.484  -3.6330  -0.8464  -0.3201
 DLH  H1   H   HCH2  0   0.265  -1.2916  -1.4321  -1.5637
 DLH  H2   H   HCH2  0   0.277  -0.1539  -0.2221  -2.0864
 DLH  H3   H   HCH2  0   0.276  -0.4231  -1.1130   1.9901
 DLH  H4   H   HCH2  0   0.254  -1.4683  -1.9696   0.8730
 DLH  H5   H   HCR6  0   0.233   4.0215  -1.8761  -1.3854
 DLH  H6   H   HCR6  0   0.232   3.2831   2.0743   0.0841
 DLH  H7   H   HCR6  0   0.259   6.3961  -1.6496  -0.8100
 DLH  H8   H   HCR6  0   0.258   5.6529   2.3033   0.6679
 DLH  H9   H   HCR6  0   0.251  -6.2683   2.5046   0.7036
 DLH  H10  H   HCR6  0   0.250  -5.9704  -2.3696  -0.3749
 DLH  H11  H   HCR6  0   0.240  -8.1701  -1.3024   0.0921
 DLH  H12  H   HCR6  0   0.241  -8.3156   1.0914   0.6276
 DLH  H13  H   HCH2  0   0.278   1.6516   0.8789  -1.4607
 DLH  H14  H   HCH2  0   0.283   1.9003  -0.8064  -1.8300
 DLH  H15  H   HCH2  0   0.238  -1.4396   1.5734  -1.0025
 DLH  H16  H   HCH2  0   0.258  -2.4746   0.6622  -2.0992
 DLH  H17  H   HCH2  0   0.252  -2.7646  -0.2373   2.0718
 DLH  H18  H   HCH2  0   0.238  -1.6092   1.0020   1.5882
 DLH  C3   C   C     0   0.572   1.1867  -0.4488   0.1702
 DLH  CL   CL  CL    0  -0.115   7.8397   0.5028   0.3734

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
 DLH  O5   C6   single    1.355  0.020  1.355
 DLH  O5   C1   single    1.431  0.020  1.431
 DLH  C9   C1   single    1.517  0.020  1.517
 DLH  C9   C11  single    1.524  0.020  1.524
 DLH  C22  C6   aromatic  1.373  0.020  1.373
 DLH  C22  C23  aromatic  1.400  0.020  1.400
 DLH  C6   C7   aromatic  1.385  0.020  1.385
 DLH  O13  C3   double    1.223  0.020  1.223
 DLH  C1   C8   single    1.517  0.020  1.517
 DLH  C1   O4   single    1.424  0.020  1.424
 DLH  C8   C10  single    1.526  0.020  1.526
 DLH  C12  C3   single    1.524  0.020  1.524
 DLH  C12  C14  single    1.499  0.020  1.499
 DLH  C3   N2   single    1.350  0.020  1.350
 DLH  C11  N2   single    1.453  0.020  1.453
 DLH  C23  C24  aromatic  1.385  0.020  1.385
 DLH  N2   C10  single    1.452  0.020  1.452
 DLH  C17  C14  aromatic  1.389  0.020  1.389
 DLH  C17  C19  aromatic  1.387  0.020  1.387
 DLH  C14  C18  aromatic  1.391  0.020  1.391
 DLH  C7   O4   single    1.357  0.020  1.357
 DLH  C7   C21  aromatic  1.373  0.020  1.373
 DLH  C19  C15  aromatic  1.385  0.020  1.385
 DLH  C24  C21  aromatic  1.400  0.020  1.400
 DLH  C18  C20  aromatic  1.385  0.020  1.385
 DLH  C15  C20  aromatic  1.387  0.020  1.387
 DLH  C15  CL   single    1.730  0.020  1.730
 DLH  C10  H1   single    0.970  0.020  1.090
 DLH  C10  H2   single    0.970  0.020  1.090
 DLH  C11  H3   single    0.970  0.020  1.090
 DLH  C11  H4   single    0.970  0.020  1.090
 DLH  C17  H5   single    0.930  0.020  1.080
 DLH  C18  H6   single    0.930  0.020  1.080
 DLH  C19  H7   single    0.930  0.020  1.080
 DLH  C20  H8   single    0.930  0.020  1.080
 DLH  C21  H9   single    0.930  0.020  1.080
 DLH  C22  H10  single    0.930  0.020  1.080
 DLH  C23  H11  single    0.930  0.020  1.080
 DLH  C24  H12  single    0.930  0.020  1.080
 DLH  C12  H13  single    0.970  0.020  1.090
 DLH  C12  H14  single    0.970  0.020  1.090
 DLH  C8   H15  single    0.970  0.020  1.090
 DLH  C8   H16  single    0.970  0.020  1.090
 DLH  C9   H17  single    0.970  0.020  1.090
 DLH  C9   H18  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
 DLH  H2   C10  H1   106.11  3.000
 DLH  H2   C10  N2   111.33  3.000
 DLH  H1   C10  N2   108.94  3.000
 DLH  H2   C10  C8   109.46  3.000
 DLH  H1   C10  C8   110.17  3.000
 DLH  N2   C10  C8   110.74  3.000
 DLH  H4   C11  H3   107.16  3.000
 DLH  H4   C11  N2   109.02  3.000
 DLH  H3   C11  N2   109.82  3.000
 DLH  H4   C11  C9   110.35  3.000
 DLH  H3   C11  C9   110.13  3.000
 DLH  N2   C11  C9   110.30  3.000
 DLH  CL   C15  C20  119.60  3.000
 DLH  CL   C15  C19  119.65  3.000
 DLH  C20  C15  C19  120.75  3.000
 DLH  H5   C17  C14  119.98  3.000
 DLH  H5   C17  C19  118.78  3.000
 DLH  C14  C17  C19  121.24  3.000
 DLH  H6   C18  C14  120.08  3.000
 DLH  H6   C18  C20  118.74  3.000
 DLH  C14  C18  C20  121.19  3.000
 DLH  H7   C19  C17  120.28  3.000
 DLH  H7   C19  C15  120.57  3.000
 DLH  C17  C19  C15  119.15  3.000
 DLH  H8   C20  C18  120.31  3.000
 DLH  H8   C20  C15  120.48  3.000
 DLH  C18  C20  C15  119.22  3.000
 DLH  H9   C21  C7   121.80  3.000
 DLH  H9   C21  C24  121.46  3.000
 DLH  C7   C21  C24  116.74  3.000
 DLH  H10  C22  C6   121.70  3.000
 DLH  H10  C22  C23  121.53  3.000
 DLH  C6   C22  C23  116.77  3.000
 DLH  H11  C23  C24  119.75  3.000
 DLH  H11  C23  C22  118.97  3.000
 DLH  C24  C23  C22  121.27  3.000
 DLH  H12  C24  C23  119.69  3.000
 DLH  H12  C24  C21  119.03  3.000
 DLH  C23  C24  C21  121.28  3.000
 DLH  O5   C1   O4   106.33  3.000
 DLH  O4   C1   C9   109.63  3.000
 DLH  O5   C1   C9   109.48  3.000
 DLH  O4   C1   C8   110.66  3.000
 DLH  C9   C1   C8   111.40  3.000
 DLH  O5   C1   C8   109.22  3.000
 DLH  H14  C12  H13  105.75  3.000
 DLH  H14  C12  C3   109.71  3.000
 DLH  H13  C12  C3   109.65  3.000
 DLH  H14  C12  C14  110.02  3.000
 DLH  H13  C12  C14  109.83  3.000
 DLH  C3   C12  C14  111.72  3.000
 DLH  C12  C14  C18  120.70  3.000
 DLH  C18  C14  C17  118.46  3.000
 DLH  C12  C14  C17  120.84  3.000
 DLH  O5   C6   C7   109.40  3.000
 DLH  C7   C6   C22  121.95  3.000
 DLH  O5   C6   C22  128.65  3.000
 DLH  O4   C7   C6   109.36  3.000
 DLH  O4   C7   C21  128.64  3.000
 DLH  C6   C7   C21  121.99  3.000
 DLH  H16  C8   H15  107.52  3.000
 DLH  H16  C8   C1   110.12  3.000
 DLH  H15  C8   C1   108.88  3.000
 DLH  H16  C8   C10  109.71  3.000
 DLH  H15  C8   C10  109.71  3.000
 DLH  C1   C8   C10  110.84  3.000
 DLH  H18  C9   H17  107.44  3.000
 DLH  H18  C9   C1   108.79  3.000
 DLH  H17  C9   C1   110.07  3.000
 DLH  H18  C9   C11  109.49  3.000
 DLH  H17  C9   C11  109.90  3.000
 DLH  C1   C9   C11  111.07  3.000
 DLH  C3   N2   C11  120.91  3.000
 DLH  C11  N2   C10  113.42  3.000
 DLH  C3   N2   C10  125.63  3.000
 DLH  C7   O4   C1   106.98  3.000
 DLH  C6   O5   C1   106.85  3.000
 DLH  O13  C3   N2   122.23  3.000
 DLH  N2   C3   C12  117.42  3.000
 DLH  O13  C3   C12  120.35  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
 DLH  CONST_01  C14  C17  C19  C15     0.00   0.0  0
 DLH  CONST_02  C14  C18  C20  C15     0.00   0.0  0
 DLH  CONST_03  C20  C18  C14  C17     0.00   0.0  0
 DLH  CONST_04  C20  C15  C19  C17     0.00   0.0  0
 DLH  CONST_05  C19  C17  C14  C18     0.00   0.0  0
 DLH  CONST_06  C19  C15  C20  C18     0.00   0.0  0
 DLH  CONST_07  C22  C6   C7   C21     0.00   0.0  0
 DLH  CONST_08  C22  C23  C24  C21     0.00   0.0  0
 DLH  CONST_09  C7   C6   C22  C23     0.00   0.0  0
 DLH  CONST_10  C7   C21  C24  C23     0.00   0.0  0
 DLH  CONST_11  C6   C22  C23  C24     0.00   0.0  0
 DLH  CONST_12  C6   C7   C21  C24     0.00   0.0  0
 DLH  CONST_13  CL   C15  C19  C17   180.00   0.0  0
 DLH  CONST_14  CL   C15  C20  C18   180.00   0.0  0
 DLH  CONST_15  C12  C14  C17  C19   180.00   0.0  0
 DLH  CONST_16  C12  C14  C18  C20   180.00   0.0  0
 DLH  CONST_17  H5   C17  C19  C15   180.00   0.0  0
 DLH  CONST_18  H6   C18  C20  C15   180.00   0.0  0
 DLH  CONST_19  H8   C20  C15  C19   180.00   0.0  0
 DLH  CONST_20  H7   C19  C15  C20   180.00   0.0  0
 DLH  CONST_21  H11  C23  C24  C21   180.00   0.0  0
 DLH  CONST_22  H12  C24  C23  C22   180.00   0.0  0
 DLH  CONST_23  H9   C21  C24  C23   180.00   0.0  0
 DLH  CONST_24  H10  C22  C23  C24   180.00   0.0  0
 DLH  CONST_25  O13  C3   N2   C10   180.00   0.0  0
 DLH  CONST_26  C12  C3   N2   C10     0.00   0.0  0
 DLH  CONST_27  O13  C3   N2   C11     0.00   0.0  0
 DLH  CONST_28  C12  C3   N2   C11   180.00   0.0  0
 DLH  Var_01    O5   C1   C8   C10   -68.89  30.0  3
 DLH  Var_02    C9   C11  N2   C10   -58.71  30.0  1
 DLH  Var_03    C8   C10  N2   C11    58.61  30.0  1
 DLH  Var_04    C7   C6   O5   C1      6.56  30.0  1
 DLH  Var_05    N2   C11  C9   C1     54.75  30.0  1
 DLH  Var_06    N2   C10  C8   C1    -54.23  30.0  1
 DLH  Var_07    C6   C7   O4   C1     -6.27  30.0  1
 DLH  Var_08    C3   C12  C14  C17    98.12  30.0  3
 DLH  Var_09    N2   C3   C12  C14  -178.20  30.0  3

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
 DLH  plan-1  C15  0.020
 DLH  plan-1  C17  0.020
 DLH  plan-1  C18  0.020
 DLH  plan-1  C19  0.020
 DLH  plan-1  C20  0.020
 DLH  plan-1  C12  0.020
 DLH  plan-1  C14  0.020
 DLH  plan-1  H5   0.020
 DLH  plan-1  H6   0.020
 DLH  plan-1  H7   0.020
 DLH  plan-1  H8   0.020
 DLH  plan-1  CL   0.020
 DLH  plan-2  C21  0.020
 DLH  plan-2  C22  0.020
 DLH  plan-2  C23  0.020
 DLH  plan-2  C24  0.020
 DLH  plan-2  C6   0.020
 DLH  plan-2  C7   0.020
 DLH  plan-2  O4   0.020
 DLH  plan-2  O5   0.020
 DLH  plan-2  H9   0.020
 DLH  plan-2  H10  0.020
 DLH  plan-2  H11  0.020
 DLH  plan-2  H12  0.020
 DLH  plan-3  C10  0.020
 DLH  plan-3  C11  0.020
 DLH  plan-3  C12  0.020
 DLH  plan-3  N2   0.020
 DLH  plan-3  O13  0.020
 DLH  plan-3  C3   0.020

