# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 05:00:48 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (2~{R},3~{R})-2-(4-chlorophenyl)-3-oxidanyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[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
 DO5  DO5  (2~{R},3~{R})-2-(4-chlorophenyl)-3-oxidanyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one  ligand  49  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_DO5
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
 DO5  C10  C   CH2   0  -0.462   2.3230   1.5223  -1.1938
 DO5  C11  C   CH2   0  -0.331   0.9471   1.1384  -1.7315
 DO5  C13  C   C     0   0.585  -1.0596   1.7666  -0.4972
 DO5  C15  C   CR6   0   0.164  -2.8154   0.2889   0.4889
 DO5  C16  C   CR16  0  -0.313  -3.0543  -0.5834   1.5461
 DO5  C17  C   CR16  0  -0.200  -3.8543  -1.7063   1.3891
 DO5  C18  C   CR6   0  -0.056  -4.4200  -1.9580   0.1504
 DO5  C20  C   CR16  0  -0.198  -4.2008  -1.1059  -0.9207
 DO5  C21  C   CR16  0  -0.288  -3.4040   0.0146  -0.7427
 DO5  C22  C   CH1   0   0.087  -2.8412   2.7200   1.1010
 DO5  C23  C   CH3   0  -0.703  -2.0312   3.9661   1.4320
 DO5  C26  C   CH2   0  -0.337   0.4240  -0.1004   0.2783
 DO5  C27  C   CH2   0  -0.442   1.7759   0.2388   0.8970
 DO5  C1   C   CR16  0  -0.355   6.1247  -0.2431   0.9528
 DO5  C2   C   CR56  0   0.301   4.8882  -0.1161   0.3695
 DO5  C3   C   CR56  0   0.312   4.3305  -1.1265  -0.3984
 DO5  C4   C   CR16  0  -0.356   4.9839  -2.3137  -0.6220
 DO5  C5   C   CR16  0  -0.270   6.2478  -2.4583  -0.0351
 DO5  C6   C   CR16  0  -0.271   6.8042  -1.4484   0.7333
 DO5  O7   O   O     0  -0.492   3.1215  -0.7247  -0.8576
 DO5  C8   C   CR5   0   0.443   2.8126   0.5048  -0.1842
 DO5  O9   O   O     0  -0.496   4.0391   0.9396   0.4070
 DO5  N12  N   NT    0  -0.455   0.0109   0.9474  -0.6371
 DO5  C14  C   CH1   0  -0.513  -1.9655   1.5204   0.7068
 DO5  CL   CL  CL    0  -0.132  -5.4145  -3.3627  -0.0662
 DO5  O24  O   OH1   0  -0.659  -3.8095   2.9512   0.1068
 DO5  O25  O   O     0  -0.483  -1.3076   2.6425  -1.3122
 DO5  H1   H   HCH2  0   0.266   3.0376   1.6048  -2.0152
 DO5  H2   H   HCH2  0   0.260   2.2616   2.4981  -0.7063
 DO5  H3   H   HCH2  0   0.278   0.5794   1.9127  -2.3970
 DO5  H4   H   HCH2  0   0.256   1.0065   0.2133  -2.3127
 DO5  H5   H   HCR6  0   0.266  -2.6108  -0.3888   2.5155
 DO5  H6   H   HCR6  0   0.279  -4.0280  -2.3743   2.2218
 DO5  H7   H   HCR6  0   0.278  -4.6478  -1.3081  -1.8847
 DO5  H8   H   HCR6  0   0.259  -3.2453   0.6753  -1.5845
 DO5  H9   H   HCH1  0   0.217  -3.3327   2.3978   2.0307
 DO5  H10  H   HCH3  0   0.235  -2.6788   4.7312   1.8644
 DO5  H11  H   HCH3  0   0.224  -1.2621   3.7418   2.1732
 DO5  H12  H   HCH3  0   0.237  -1.5503   4.3880   0.5516
 DO5  H13  H   HCH2  0   0.264   0.4790  -1.0446  -0.2710
 DO5  H14  H   HCH2  0   0.284  -0.3061  -0.2522   1.0651
 DO5  H15  H   HCH2  0   0.259   1.6762   1.1322   1.5189
 DO5  H16  H   HCH2  0   0.262   2.1038  -0.5778   1.5448
 DO5  H17  H   HCR6  0   0.272   6.5562   0.5475   1.5517
 DO5  H18  H   HCR6  0   0.271   4.5462  -3.0996  -1.2227
 DO5  H19  H   HCR6  0   0.259   6.7938  -3.3800  -0.1851
 DO5  H20  H   HCR6  0   0.259   7.7805  -1.5898   1.1769
 DO5  H21  H   HCH1  0   0.286  -1.3373   1.3449   1.5851
 DO5  H22  H   HOH1  0   0.451  -4.4867   3.5203   0.4840

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
 DO5  C4   C5   aromatic  1.401  0.020  1.401
 DO5  C4   C3   aromatic  1.373  0.020  1.373
 DO5  C5   C6   aromatic  1.386  0.020  1.386
 DO5  O24  C22  single    1.407  0.020  1.407
 DO5  O7   C3   single    1.354  0.020  1.354
 DO5  O7   C8   single    1.435  0.020  1.435
 DO5  C11  N12  single    1.453  0.020  1.453
 DO5  C11  C10  single    1.526  0.020  1.526
 DO5  C3   C2   aromatic  1.386  0.020  1.386
 DO5  C23  C22  single    1.523  0.020  1.523
 DO5  C14  C22  single    1.537  0.020  1.537
 DO5  C14  C13  single    1.527  0.020  1.527
 DO5  C14  C15  single    1.512  0.020  1.512
 DO5  N12  C26  single    1.451  0.020  1.451
 DO5  N12  C13  single    1.355  0.020  1.355
 DO5  C6   C1   aromatic  1.401  0.020  1.401
 DO5  C10  C8   single    1.515  0.020  1.515
 DO5  C26  C27  single    1.525  0.020  1.525
 DO5  C13  O25  double    1.222  0.020  1.222
 DO5  C8   C27  single    1.521  0.020  1.521
 DO5  C8   O9   single    1.429  0.020  1.429
 DO5  C21  C15  aromatic  1.392  0.020  1.392
 DO5  C21  C20  aromatic  1.386  0.020  1.386
 DO5  C2   C1   aromatic  1.373  0.020  1.373
 DO5  C2   O9   single    1.355  0.020  1.355
 DO5  C15  C16  aromatic  1.391  0.020  1.391
 DO5  C20  C18  aromatic  1.386  0.020  1.386
 DO5  C16  C17  aromatic  1.388  0.020  1.388
 DO5  C18  C17  aromatic  1.385  0.020  1.385
 DO5  C18  CL   single    1.735  0.020  1.735
 DO5  C10  H1   single    0.970  0.020  1.090
 DO5  C10  H2   single    0.970  0.020  1.090
 DO5  C11  H3   single    0.970  0.020  1.090
 DO5  C11  H4   single    0.970  0.020  1.090
 DO5  C16  H5   single    0.930  0.020  1.080
 DO5  C17  H6   single    0.930  0.020  1.080
 DO5  C20  H7   single    0.930  0.020  1.080
 DO5  C21  H8   single    0.930  0.020  1.080
 DO5  C22  H9   single    0.970  0.020  1.090
 DO5  C23  H10  single    0.970  0.020  1.090
 DO5  C23  H11  single    0.970  0.020  1.090
 DO5  C23  H12  single    0.970  0.020  1.090
 DO5  C26  H13  single    0.970  0.020  1.090
 DO5  C26  H14  single    0.970  0.020  1.090
 DO5  C27  H15  single    0.970  0.020  1.090
 DO5  C27  H16  single    0.970  0.020  1.090
 DO5  C1   H17  single    0.930  0.020  1.080
 DO5  C4   H18  single    0.930  0.020  1.080
 DO5  C5   H19  single    0.930  0.020  1.080
 DO5  C6   H20  single    0.930  0.020  1.080
 DO5  C14  H21  single    0.970  0.020  1.090
 DO5  O24  H22  single    0.850  0.020  0.980

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
 DO5  H2   C10  H1   107.76  3.000
 DO5  H2   C10  C8   108.71  3.000
 DO5  H1   C10  C8   109.91  3.000
 DO5  H2   C10  C11  109.34  3.000
 DO5  H1   C10  C11  110.12  3.000
 DO5  C8   C10  C11  110.93  3.000
 DO5  H4   C11  H3   107.21  3.000
 DO5  H4   C11  N12  108.91  3.000
 DO5  H3   C11  N12  109.72  3.000
 DO5  H4   C11  C10  110.54  3.000
 DO5  H3   C11  C10  110.00  3.000
 DO5  N12  C11  C10  110.40  3.000
 DO5  O25  C13  C14  121.41  3.000
 DO5  O25  C13  N12  121.66  3.000
 DO5  C14  C13  N12  116.91  3.000
 DO5  C14  C15  C21  121.70  3.000
 DO5  C21  C15  C16  118.43  3.000
 DO5  C14  C15  C16  119.85  3.000
 DO5  H5   C16  C17  118.84  3.000
 DO5  H5   C16  C15  119.79  3.000
 DO5  C17  C16  C15  121.36  3.000
 DO5  H6   C17  C18  120.71  3.000
 DO5  H6   C17  C16  120.35  3.000
 DO5  C18  C17  C16  118.93  3.000
 DO5  CL   C18  C20  119.47  3.000
 DO5  CL   C18  C17  119.54  3.000
 DO5  C20  C18  C17  120.99  3.000
 DO5  H7   C20  C21  120.20  3.000
 DO5  H7   C20  C18  120.55  3.000
 DO5  C21  C20  C18  119.24  3.000
 DO5  H8   C21  C20  118.56  3.000
 DO5  H8   C21  C15  120.40  3.000
 DO5  C20  C21  C15  121.05  3.000
 DO5  H9   C22  O24  109.75  3.000
 DO5  H9   C22  C14  104.06  3.000
 DO5  O24  C22  C14  109.83  3.000
 DO5  H9   C22  C23  107.08  3.000
 DO5  C14  C22  C23  113.05  3.000
 DO5  O24  C22  C23  112.66  3.000
 DO5  H12  C23  H11  108.52  3.000
 DO5  H12  C23  H10  108.11  3.000
 DO5  H11  C23  H10  107.04  3.000
 DO5  H12  C23  C22  112.12  3.000
 DO5  H11  C23  C22  110.75  3.000
 DO5  H10  C23  C22  110.12  3.000
 DO5  H14  C26  H13  106.11  3.000
 DO5  H14  C26  N12  111.54  3.000
 DO5  H13  C26  N12  108.71  3.000
 DO5  H14  C26  C27  109.50  3.000
 DO5  H13  C26  C27  110.56  3.000
 DO5  N12  C26  C27  110.34  3.000
 DO5  H16  C27  H15  107.51  3.000
 DO5  H16  C27  C8   110.34  3.000
 DO5  H15  C27  C8   108.88  3.000
 DO5  H16  C27  C26  109.90  3.000
 DO5  H15  C27  C26  109.37  3.000
 DO5  C8   C27  C26  110.78  3.000
 DO5  H17  C1   C6   121.48  3.000
 DO5  H17  C1   C2   121.79  3.000
 DO5  C6   C1   C2   116.73  3.000
 DO5  O9   C2   C3   109.33  3.000
 DO5  O9   C2   C1   128.64  3.000
 DO5  C3   C2   C1   122.02  3.000
 DO5  O7   C3   C4   128.75  3.000
 DO5  O7   C3   C2   109.31  3.000
 DO5  C4   C3   C2   121.93  3.000
 DO5  H18  C4   C5   121.51  3.000
 DO5  H18  C4   C3   121.73  3.000
 DO5  C5   C4   C3   116.76  3.000
 DO5  H19  C5   C6   119.68  3.000
 DO5  H19  C5   C4   119.03  3.000
 DO5  C6   C5   C4   121.29  3.000
 DO5  H20  C6   C5   119.64  3.000
 DO5  H20  C6   C1   119.08  3.000
 DO5  C5   C6   C1   121.28  3.000
 DO5  C8   O7   C3   106.69  3.000
 DO5  O9   C8   O7   105.66  3.000
 DO5  O9   C8   C27  110.12  3.000
 DO5  O7   C8   C27  109.28  3.000
 DO5  O9   C8   C10  110.41  3.000
 DO5  C27  C8   C10  111.77  3.000
 DO5  O7   C8   C10  109.41  3.000
 DO5  C8   O9   C2   106.81  3.000
 DO5  C26  N12  C13  126.59  3.000
 DO5  C13  N12  C11  120.49  3.000
 DO5  C26  N12  C11  112.74  3.000
 DO5  H21  C14  C22  104.27  3.000
 DO5  H21  C14  C15  107.92  3.000
 DO5  C22  C14  C15  110.64  3.000
 DO5  H21  C14  C13  108.56  3.000
 DO5  C15  C14  C13  110.56  3.000
 DO5  C22  C14  C13  114.49  3.000
 DO5  H22  O24  C22  107.74  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
 DO5  CONST_01  C18  C20  C21  C15    0.00   0.0  0
 DO5  CONST_02  C18  C17  C16  C15    0.00   0.0  0
 DO5  CONST_03  C20  C21  C15  C16    0.00   0.0  0
 DO5  CONST_04  C20  C18  C17  C16    0.00   0.0  0
 DO5  CONST_05  C21  C15  C16  C17    0.00   0.0  0
 DO5  CONST_06  C21  C20  C18  C17    0.00   0.0  0
 DO5  CONST_07  C4   C5   C6   C1     0.00   0.0  0
 DO5  CONST_08  C4   C3   C2   C1     0.00   0.0  0
 DO5  CONST_09  C5   C4   C3   C2     0.00   0.0  0
 DO5  CONST_10  C5   C6   C1   C2     0.00   0.0  0
 DO5  CONST_11  C6   C5   C4   C3     0.00   0.0  0
 DO5  CONST_12  C6   C1   C2   C3     0.00   0.0  0
 DO5  CONST_13  CL   C18  C17  C16  180.00   0.0  0
 DO5  CONST_14  C14  C15  C16  C17  180.00   0.0  0
 DO5  CONST_15  C14  C15  C21  C20  180.00   0.0  0
 DO5  CONST_16  CL   C18  C20  C21  180.00   0.0  0
 DO5  CONST_17  H7   C20  C21  C15  180.00   0.0  0
 DO5  CONST_18  H6   C17  C16  C15  180.00   0.0  0
 DO5  CONST_19  H8   C21  C15  C16  180.00   0.0  0
 DO5  CONST_20  H5   C16  C17  C18  180.00   0.0  0
 DO5  CONST_21  H19  C5   C6   C1   180.00   0.0  0
 DO5  CONST_22  H18  C4   C3   C2   180.00   0.0  0
 DO5  CONST_23  H20  C6   C1   C2   180.00   0.0  0
 DO5  CONST_24  H17  C1   C2   C3   180.00   0.0  0
 DO5  CONST_25  C14  C13  N12  C11  180.00   0.0  0
 DO5  CONST_26  O25  C13  N12  C11    0.00   0.0  0
 DO5  CONST_27  C14  C13  N12  C26    0.00   0.0  0
 DO5  CONST_28  O25  C13  N12  C26  180.00   0.0  0
 DO5  Var_01    C26  N12  C11  C10  -60.02  30.0  1
 DO5  Var_02    C26  C27  C8   C10   51.62  30.0  3
 DO5  Var_03    C27  C26  N12  C11   60.23  30.0  1
 DO5  Var_04    O7   C8   C10  C11   69.71  30.0  3
 DO5  Var_05    N12  C11  C10  C8    54.64  30.0  1
 DO5  Var_06    N12  C26  C27  C8   -54.92  30.0  1

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
 DO5  chir_01  C22  O24  C23  C14  positiv
 DO5  chir_02  C14  C22  C13  C15  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
 DO5  plan-1  C15  0.020
 DO5  plan-1  C16  0.020
 DO5  plan-1  C17  0.020
 DO5  plan-1  C18  0.020
 DO5  plan-1  C20  0.020
 DO5  plan-1  C21  0.020
 DO5  plan-1  C14  0.020
 DO5  plan-1  CL   0.020
 DO5  plan-1  H5   0.020
 DO5  plan-1  H6   0.020
 DO5  plan-1  H7   0.020
 DO5  plan-1  H8   0.020
 DO5  plan-2  C1   0.020
 DO5  plan-2  C2   0.020
 DO5  plan-2  C3   0.020
 DO5  plan-2  C4   0.020
 DO5  plan-2  C5   0.020
 DO5  plan-2  C6   0.020
 DO5  plan-2  O7   0.020
 DO5  plan-2  O9   0.020
 DO5  plan-2  H17  0.020
 DO5  plan-2  H18  0.020
 DO5  plan-2  H19  0.020
 DO5  plan-2  H20  0.020
 DO5  plan-3  C11  0.020
 DO5  plan-3  C13  0.020
 DO5  plan-3  C26  0.020
 DO5  plan-3  N12  0.020
 DO5  plan-3  C14  0.020
 DO5  plan-3  O25  0.020

