# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:35:44 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 5-chloranyl-2-(2-oxidanylidene-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethyl)-3~{H}-pyridin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ClC1=CCC(=NC1=O)CC(=O)N2CCC3(CC2)Oc4ccccc4O3
#
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
 DL2  DL2  5-chloranyl-2-(2-oxidanylidene-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethyl)-3~{H}-pyridin-6-one  ligand  42  25  .  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_DL2
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
 DL2  C10  C   CH2   0  -0.453   2.2258   1.1733  -0.1148
 DL2  C11  C   CH2   0  -0.325   1.1396   0.9249   0.9263
 DL2  C13  C   C     0   0.589  -0.9877  -0.1033   0.3397
 DL2  C15  C   CR6   0   0.300  -3.2099  -1.0260  -0.1953
 DL2  C17  C   CR6   0   0.495  -5.0269  -0.4845  -1.5377
 DL2  C19  C   C     0  -0.569  -4.0015  -1.0064   1.0627
 DL2  C21  C   CH2   0  -0.332   1.1004  -1.4520   0.4027
 DL2  C22  C   CH2   0  -0.458   2.1909  -1.2772  -0.6507
 DL2  C23  C   CR6   0  -0.161  -5.8924  -0.4029  -0.3448
 DL2  C25  C   CR16  0  -0.124  -5.4219  -0.6443   0.8752
 DL2  C1   C   CR16  0  -0.355   6.2060   0.0122   1.3871
 DL2  C2   C   CR56  0   0.312   5.1184  -0.0250   0.5496
 DL2  C3   C   CR56  0   0.300   5.2227   0.2667  -0.8012
 DL2  C4   C   CR16  0  -0.355   6.4191   0.6095  -1.3814
 DL2  C5   C   CR16  0  -0.271   7.5388   0.6500  -0.5404
 DL2  C6   C   CR16  0  -0.270   7.4348   0.3586   0.8103
 DL2  O7   O   O     0  -0.496   4.0067   0.1368  -1.3847
 DL2  C8   C   CR5   0   0.445   3.0604  -0.0775  -0.3353
 DL2  O9   O   O     0  -0.493   3.8359  -0.3470   0.8417
 DL2  N12  N   NT    0  -0.464   0.3343  -0.2282   0.5568
 DL2  C14  C   CH2   0  -0.698  -1.7529  -1.3550  -0.0705
 DL2  N16  N   N     0  -0.428  -3.6796  -0.8093  -1.3623
 DL2  O18  O   O     0  -0.393  -5.4521  -0.2776  -2.6496
 DL2  O20  O   O     0  -0.490  -1.5858   0.9577   0.4584
 DL2  CL   CL  CL    0  -0.097  -7.5393   0.0144  -0.6292
 DL2  H1   H   HCH2  0   0.261   1.7650   1.4602  -1.0630
 DL2  H2   H   HCH2  0   0.263   2.8601   2.0025   0.2083
 DL2  H3   H   HCH2  0   0.259   1.5858   0.7454   1.9087
 DL2  H4   H   HCH2  0   0.280   0.5028   1.7997   1.0164
 DL2  H5   H   H     0   0.320  -3.9306  -1.9941   1.5347
 DL2  H6   H   H     0   0.320  -3.5272  -0.3295   1.7812
 DL2  H7   H   HCH2  0   0.291   0.4601  -2.2809   0.1186
 DL2  H8   H   HCH2  0   0.265   1.5418  -1.7174   1.3675
 DL2  H9   H   HCH2  0   0.270   2.8004  -2.1815  -0.7037
 DL2  H10  H   HCH2  0   0.262   1.7303  -1.1292  -1.6302
 DL2  H11  H   HCR6  0   0.308  -6.0570  -0.5906   1.7498
 DL2  H12  H   HCR6  0   0.271   6.1212  -0.2164   2.4409
 DL2  H13  H   HCR6  0   0.272   6.4967   0.8339  -2.4366
 DL2  H14  H   HCR6  0   0.259   8.4998   0.9174  -0.9585
 DL2  H15  H   HCR6  0   0.259   8.3154   0.3985   1.4373
 DL2  H16  H   HCH2  0   0.317  -1.3881  -1.7236  -1.0312
 DL2  H17  H   HCH2  0   0.310  -1.6123  -2.1508   0.6654

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
 DL2  C1   C2   aromatic  1.373  0.020  1.373
 DL2  C1   C6   aromatic  1.401  0.020  1.401
 DL2  O9   C2   single    1.354  0.020  1.354
 DL2  O9   C8   single    1.435  0.020  1.435
 DL2  C2   C3   aromatic  1.386  0.020  1.386
 DL2  C6   C5   aromatic  1.386  0.020  1.386
 DL2  C14  C13  single    1.523  0.020  1.523
 DL2  C14  C15  single    1.499  0.020  1.499
 DL2  C22  C8   single    1.515  0.020  1.515
 DL2  C22  C21  single    1.526  0.020  1.526
 DL2  C11  C10  single    1.525  0.020  1.525
 DL2  C11  N12  single    1.454  0.020  1.454
 DL2  C8   C10  single    1.520  0.020  1.520
 DL2  C8   O7   single    1.429  0.020  1.429
 DL2  C13  O20  double    1.224  0.020  1.224
 DL2  C13  N12  single    1.346  0.020  1.346
 DL2  N12  C21  single    1.452  0.020  1.452
 DL2  N16  C15  double    1.276  0.020  1.276
 DL2  N16  C17  single    1.397  0.020  1.397
 DL2  C3   O7   single    1.355  0.020  1.355
 DL2  C3   C4   aromatic  1.373  0.020  1.373
 DL2  C5   C4   aromatic  1.401  0.020  1.401
 DL2  C15  C19  single    1.486  0.020  1.486
 DL2  O18  C17  double    1.208  0.020  1.208
 DL2  C17  C23  single    1.476  0.020  1.476
 DL2  C19  C25  single    1.478  0.020  1.478
 DL2  C23  C25  double    1.330  0.020  1.330
 DL2  C23  CL   single    1.723  0.020  1.723
 DL2  C10  H1   single    0.970  0.020  1.090
 DL2  C10  H2   single    0.970  0.020  1.090
 DL2  C11  H3   single    0.970  0.020  1.090
 DL2  C11  H4   single    0.970  0.020  1.090
 DL2  C19  H5   single    0.970  0.020  1.090
 DL2  C19  H6   single    0.970  0.020  1.090
 DL2  C21  H7   single    0.970  0.020  1.090
 DL2  C21  H8   single    0.970  0.020  1.090
 DL2  C22  H9   single    0.970  0.020  1.090
 DL2  C22  H10  single    0.970  0.020  1.090
 DL2  C25  H11  single    0.930  0.020  1.080
 DL2  C1   H12  single    0.930  0.020  1.080
 DL2  C4   H13  single    0.930  0.020  1.080
 DL2  C5   H14  single    0.930  0.020  1.080
 DL2  C6   H15  single    0.930  0.020  1.080
 DL2  C14  H16  single    0.970  0.020  1.090
 DL2  C14  H17  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
 DL2  H2   C10  H1   107.59  3.000
 DL2  H2   C10  C8   110.40  3.000
 DL2  H1   C10  C8   108.77  3.000
 DL2  H2   C10  C11  109.59  3.000
 DL2  H1   C10  C11  109.57  3.000
 DL2  C8   C10  C11  110.86  3.000
 DL2  H4   C11  H3   107.27  3.000
 DL2  H4   C11  N12  109.59  3.000
 DL2  H3   C11  N12  108.91  3.000
 DL2  H4   C11  C10  110.07  3.000
 DL2  H3   C11  C10  110.45  3.000
 DL2  N12  C11  C10  110.50  3.000
 DL2  O20  C13  C14  119.53  3.000
 DL2  O20  C13  N12  123.03  3.000
 DL2  C14  C13  N12  117.44  3.000
 DL2  N16  C15  C14  118.11  3.000
 DL2  N16  C15  C19  125.13  3.000
 DL2  C14  C15  C19  116.75  3.000
 DL2  O18  C17  N16  119.66  3.000
 DL2  O18  C17  C23  121.86  3.000
 DL2  N16  C17  C23  118.48  3.000
 DL2  H6   C19  H5   104.26  3.000
 DL2  H6   C19  C25  110.37  3.000
 DL2  H5   C19  C25  109.71  3.000
 DL2  H6   C19  C15  109.44  3.000
 DL2  H5   C19  C15  108.53  3.000
 DL2  C25  C19  C15  114.06  3.000
 DL2  H8   C21  H7   106.48  3.000
 DL2  H8   C21  N12  108.90  3.000
 DL2  H7   C21  N12  111.11  3.000
 DL2  H8   C21  C22  110.38  3.000
 DL2  H7   C21  C22  109.17  3.000
 DL2  N12  C21  C22  110.71  3.000
 DL2  H10  C22  H9   107.70  3.000
 DL2  H10  C22  C8   108.74  3.000
 DL2  H9   C22  C8   110.22  3.000
 DL2  H10  C22  C21  109.46  3.000
 DL2  H9   C22  C21  109.72  3.000
 DL2  C8   C22  C21  110.92  3.000
 DL2  CL   C23  C25  122.26  3.000
 DL2  CL   C23  C17  116.14  3.000
 DL2  C25  C23  C17  121.60  3.000
 DL2  H11  C25  C23  121.66  3.000
 DL2  H11  C25  C19  118.28  3.000
 DL2  C23  C25  C19  120.06  3.000
 DL2  H12  C1   C6   121.48  3.000
 DL2  H12  C1   C2   121.76  3.000
 DL2  C6   C1   C2   116.76  3.000
 DL2  O9   C2   C3   109.36  3.000
 DL2  C3   C2   C1   121.95  3.000
 DL2  O9   C2   C1   128.68  3.000
 DL2  O7   C3   C4   128.60  3.000
 DL2  C4   C3   C2   122.00  3.000
 DL2  O7   C3   C2   109.39  3.000
 DL2  H13  C4   C5   121.49  3.000
 DL2  H13  C4   C3   121.77  3.000
 DL2  C5   C4   C3   116.74  3.000
 DL2  H14  C5   C6   119.70  3.000
 DL2  H14  C5   C4   119.03  3.000
 DL2  C6   C5   C4   121.27  3.000
 DL2  H15  C6   C5   119.74  3.000
 DL2  H15  C6   C1   118.98  3.000
 DL2  C5   C6   C1   121.28  3.000
 DL2  C8   O7   C3   107.00  3.000
 DL2  O9   C8   O7   105.82  3.000
 DL2  O7   C8   C22  110.24  3.000
 DL2  O9   C8   C22  109.40  3.000
 DL2  O7   C8   C10  110.29  3.000
 DL2  C22  C8   C10  111.52  3.000
 DL2  O9   C8   C10  109.41  3.000
 DL2  C8   O9   C2   106.87  3.000
 DL2  C21  N12  C13  125.42  3.000
 DL2  C21  N12  C11  113.77  3.000
 DL2  C13  N12  C11  120.76  3.000
 DL2  H17  C14  H16  107.68  3.000
 DL2  H17  C14  C15  109.94  3.000
 DL2  H16  C14  C15  109.00  3.000
 DL2  H17  C14  C13  110.63  3.000
 DL2  H16  C14  C13  110.27  3.000
 DL2  C15  C14  C13  109.29  3.000
 DL2  C17  N16  C15  120.61  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
 DL2  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 DL2  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 DL2  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 DL2  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 DL2  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 DL2  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 DL2  CONST_07  H14  C5   C6   C1   180.00   0.0  0
 DL2  CONST_08  H15  C6   C1   C2   180.00   0.0  0
 DL2  CONST_09  H13  C4   C3   C2   180.00   0.0  0
 DL2  CONST_10  H12  C1   C2   C3   180.00   0.0  0
 DL2  CONST_11  C14  C13  N12  C11  180.00   0.0  0
 DL2  CONST_12  O20  C13  N12  C11    0.00   0.0  0
 DL2  CONST_13  C14  C13  N12  C21    0.00   0.0  0
 DL2  CONST_14  O20  C13  N12  C21  180.00   0.0  0
 DL2  Var_01    C21  N12  C11  C10   58.17  30.0  1
 DL2  Var_02    C21  C22  C8   C10  -52.48  30.0  3
 DL2  Var_03    O9   C8   C10  C11  -68.43  30.0  3
 DL2  Var_04    C22  C21  N12  C11  -58.00  30.0  1
 DL2  Var_05    C23  C17  N16  C15   -0.21  30.0  1
 DL2  Var_06    C23  C25  C19  C15    1.60  30.0  1
 DL2  Var_07    C19  C15  N16  C17    2.01  30.0  1
 DL2  Var_08    C19  C25  C23  C17   -0.08  30.0  1
 DL2  Var_09    N16  C15  C19  C25   -2.69  30.0  1
 DL2  Var_10    N16  C17  C23  C25   -0.75  30.0  1
 DL2  Var_11    N12  C21  C22  C8    54.04  30.0  1
 DL2  Var_12    N12  C11  C10  C8   -54.36  30.0  1
 DL2  Var_13    N12  C13  C14  C15  177.15  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
 DL2  plan-1  C11  0.020
 DL2  plan-1  C13  0.020
 DL2  plan-1  C21  0.020
 DL2  plan-1  N12  0.020
 DL2  plan-1  C14  0.020
 DL2  plan-1  O20  0.020
 DL2  plan-2  C1   0.020
 DL2  plan-2  C2   0.020
 DL2  plan-2  C3   0.020
 DL2  plan-2  C4   0.020
 DL2  plan-2  C5   0.020
 DL2  plan-2  C6   0.020
 DL2  plan-2  O7   0.020
 DL2  plan-2  O9   0.020
 DL2  plan-2  H12  0.020
 DL2  plan-2  H13  0.020
 DL2  plan-2  H14  0.020
 DL2  plan-2  H15  0.020
 DL2  plan-3  C17  0.020
 DL2  plan-3  C23  0.020
 DL2  plan-3  N16  0.020
 DL2  plan-3  O18  0.020

