# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 06:01:49 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (3S)-3-(2H-1,3-benzodioxol-5-yl)-1-[(3R,5S)-3,5-dimethylpiperidin-1-yl]-3-(2-hydroxy-4,6-dimethoxyphenyl)propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(O)c([C@@H](CC(=O)N2C[C@H](C)C[C@H](C)C2)c3ccc4OCOc4c3)c(OC)c1
#
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
 6Q6  6Q6  (3S)-3-(2H-1,3-benzodioxol-5-yl)-1-[(3R,5S)-3,5-dimethylpiperidin-1-yl]-3-(2-hydroxy-4,6-dimethoxyphenyl)propan-1-one  ligand  63  32  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6Q6
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
 6Q6  N1   N  NT    0  -0.465  -3.3921  -0.1288   0.2570
 6Q6  C2   C  CH1   0  -0.244  -5.4784  -0.5189  -0.9827
 6Q6  C4   C  CH2   0  -0.292  -4.6454   0.4695  -0.1698
 6Q6  C5   C  CH2   0  -0.295  -3.5856  -1.3033   1.0890
 6Q6  C6   C  CH3   0  -0.658  -6.8048   0.1036  -1.3933
 6Q6  C7   C  CH3   0  -0.658  -4.5977  -3.5929   1.2348
 6Q6  C13  C  CR16  0  -0.388   1.6252   2.1625  -0.6142
 6Q6  C14  C  CR6   0   0.395   2.0082  -1.2679   0.8545
 6Q6  C15  C  CR6   0   0.357   2.1017  -1.4031  -1.5230
 6Q6  C16  C  CR16  0  -0.327   0.0252   1.9662   1.1780
 6Q6  C17  C  CR56  0   0.309   1.9452   3.4021  -0.1247
 6Q6  C18  C  CR16  0  -0.334   0.3567   3.2365   1.6693
 6Q6  C19  C  CR56  0   0.274   1.3257   3.9328   0.9946
 6Q6  C20  C  CR16  0  -0.514   3.1011  -2.1168   0.9597
 6Q6  C24  C  CH3   0  -0.436   1.8683  -1.0474   3.2196
 6Q6  C8   C  C     0   0.580  -2.2352   0.1922  -0.3683
 6Q6  C3   C  CH2   0  -0.403  -5.6808  -1.8027  -0.1793
 6Q6  C1   C  CH1   0  -0.243  -4.3677  -2.3828   0.3412
 6Q6  C9   C  CH2   0  -0.635  -0.9864  -0.5674   0.0470
 6Q6  C10  C  CH1   0  -0.353   0.2947   0.0551  -0.5062
 6Q6  C11  C  CR6   0   0.180   0.6355   1.4238   0.0576
 6Q6  O5   O  O     0  -0.490   1.8521   5.1574   1.2631
 6Q6  C23  C  CH2   0   0.068   2.6540   5.4869   0.1384
 6Q6  O3   O  O     0  -0.490   2.8716   4.2832  -0.5844
 6Q6  C12  C  CR6   0  -0.073   1.4763  -0.8891  -0.3909
 6Q6  C21  C  CR16  0  -0.554   3.2030  -2.2616  -1.4468
 6Q6  C22  C  CR6   0   0.410   3.6952  -2.6144  -0.2007
 6Q6  O6   O  O2    0  -0.473   4.7455  -3.4337  -0.0117
 6Q6  C25  C  CH3   0  -0.437   5.3747  -4.0023  -1.1425
 6Q6  O2   O  O2    0  -0.459   1.3875  -0.7506   1.9263
 6Q6  H1   H  HCH1  0   0.224  -4.9116  -0.7649  -1.8889
 6Q6  H2   H  HCH2  0   0.231  -5.2028   0.7669   0.7260
 6Q6  H3   H  HCH2  0   0.258  -4.4423   1.3727  -0.7399
 6Q6  H4   H  HCH2  0   0.266  -2.6336  -1.6977   1.4351
 6Q6  H5   H  HCH2  0   0.238  -4.1431  -1.0031   1.9835
 6Q6  H6   H  HCH3  0   0.217  -7.3837   0.4095  -0.5184
 6Q6  H7   H  HCH3  0   0.229  -6.6561   0.9865  -2.0173
 6Q6  H8   H  HCH3  0   0.230  -7.4113  -0.6047  -1.9596
 6Q6  H9   H  HCH3  0   0.218  -5.1770  -3.3208   2.1201
 6Q6  H10  H  HCH3  0   0.233  -5.1492  -4.3711   0.7058
 6Q6  H11  H  HCH3  0   0.230  -3.6546  -4.0248   1.5744
 6Q6  H12  H  HCR6  0   0.260   2.1188   1.7628  -1.4918
 6Q6  H13  H  HCR6  0   0.239  -0.7338   1.4073   1.7077
 6Q6  H14  H  HCR6  0   0.266  -0.1312   3.6405   2.5463
 6Q6  H15  H  HCR6  0   0.278   3.5092  -2.4077   1.9178
 6Q6  H16  H  HCH3  0   0.228   2.8975  -0.7078   3.3614
 6Q6  H17  H  HCH3  0   0.259   1.2250  -0.5140   3.9149
 6Q6  H18  H  HCH3  0   0.227   1.8164  -2.1166   3.4409
 6Q6  H19  H  HCH2  0   0.206  -6.3432  -1.5912   0.6709
 6Q6  H20  H  HCH2  0   0.234  -6.1989  -2.5466  -0.7921
 6Q6  H21  H  HCH1  0   0.224  -3.7605  -2.6905  -0.5200
 6Q6  H22  H  HCH2  0   0.280  -0.9352  -0.6741   1.1300
 6Q6  H23  H  HCH2  0   0.292  -1.0698  -1.5869  -0.3446
 6Q6  H24  H  HCH1  0   0.269   0.1192   0.2111  -1.5706
 6Q6  H25  H  HCH2  0   0.228   2.1280   6.2104  -0.4954
 6Q6  H26  H  HCH2  0   0.243   3.6078   5.8955   0.4713
 6Q6  H27  H  HOH1  0   0.477   2.1501  -1.4308  -3.4328
 6Q6  H28  H  HCR6  0   0.284   3.6491  -2.6316  -2.3614
 6Q6  H29  H  HCH3  0   0.229   4.6832  -4.6093  -1.7320
 6Q6  H30  H  HCH3  0   0.228   5.8164  -3.2413  -1.7909
 6Q6  H31  H  HCH3  0   0.261   6.1683  -4.6426  -0.7652
 6Q6  O4   O  OH1   0  -0.636   1.6167  -1.0437  -2.7302
 6Q6  O1   O  O     0  -0.498  -2.1863   1.0581  -1.2331

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
 6Q6  C25  O6   single    1.413  0.020  1.413
 6Q6  O6   C22  single    1.345  0.020  1.345
 6Q6  C22  C20  aromatic  1.395  0.020  1.395
 6Q6  C22  C21  aromatic  1.385  0.020  1.385
 6Q6  C20  C14  aromatic  1.388  0.020  1.388
 6Q6  C21  C15  aromatic  1.398  0.020  1.398
 6Q6  C14  O2   single    1.342  0.020  1.342
 6Q6  C14  C12  aromatic  1.406  0.020  1.406
 6Q6  C24  O2   single    1.411  0.020  1.411
 6Q6  C15  C12  aromatic  1.392  0.020  1.392
 6Q6  C15  O4   single    1.350  0.020  1.350
 6Q6  C12  C10  single    1.517  0.020  1.517
 6Q6  C5   C1   single    1.528  0.020  1.528
 6Q6  C5   N1   single    1.452  0.020  1.452
 6Q6  C1   C3   single    1.527  0.020  1.527
 6Q6  C1   C7   single    1.522  0.020  1.522
 6Q6  C2   C3   single    1.528  0.020  1.528
 6Q6  C2   C6   single    1.522  0.020  1.522
 6Q6  C2   C4   single    1.527  0.020  1.527
 6Q6  C13  C17  aromatic  1.371  0.020  1.371
 6Q6  C13  C11  aromatic  1.406  0.020  1.406
 6Q6  N1   C4   single    1.453  0.020  1.453
 6Q6  N1   C8   single    1.354  0.020  1.354
 6Q6  O3   C17  single    1.359  0.020  1.359
 6Q6  O3   C23  single    1.421  0.020  1.421
 6Q6  C10  C11  single    1.519  0.020  1.519
 6Q6  C10  C9   single    1.528  0.020  1.528
 6Q6  C17  C19  aromatic  1.385  0.020  1.385
 6Q6  C11  C16  aromatic  1.386  0.020  1.386
 6Q6  C23  O5   single    1.420  0.020  1.420
 6Q6  C19  O5   single    1.360  0.020  1.360
 6Q6  C19  C18  aromatic  1.371  0.020  1.371
 6Q6  C9   C8   single    1.520  0.020  1.520
 6Q6  C16  C18  aromatic  1.402  0.020  1.402
 6Q6  C8   O1   double    1.225  0.020  1.225
 6Q6  C2   H1   single    0.970  0.020  1.090
 6Q6  C4   H2   single    0.970  0.020  1.090
 6Q6  C4   H3   single    0.970  0.020  1.090
 6Q6  C5   H4   single    0.970  0.020  1.090
 6Q6  C5   H5   single    0.970  0.020  1.090
 6Q6  C6   H6   single    0.970  0.020  1.090
 6Q6  C6   H7   single    0.970  0.020  1.090
 6Q6  C6   H8   single    0.970  0.020  1.090
 6Q6  C7   H9   single    0.970  0.020  1.090
 6Q6  C7   H10  single    0.970  0.020  1.090
 6Q6  C7   H11  single    0.970  0.020  1.090
 6Q6  C13  H12  single    0.930  0.020  1.080
 6Q6  C16  H13  single    0.930  0.020  1.080
 6Q6  C18  H14  single    0.930  0.020  1.080
 6Q6  C20  H15  single    0.930  0.020  1.080
 6Q6  C24  H16  single    0.970  0.020  1.090
 6Q6  C24  H17  single    0.970  0.020  1.090
 6Q6  C24  H18  single    0.970  0.020  1.090
 6Q6  C3   H19  single    0.970  0.020  1.090
 6Q6  C3   H20  single    0.970  0.020  1.090
 6Q6  C1   H21  single    0.970  0.020  1.090
 6Q6  C9   H22  single    0.970  0.020  1.090
 6Q6  C9   H23  single    0.970  0.020  1.090
 6Q6  C10  H24  single    0.970  0.020  1.090
 6Q6  C23  H25  single    0.970  0.020  1.090
 6Q6  C23  H26  single    0.970  0.020  1.090
 6Q6  O4   H27  single    0.850  0.020  0.980
 6Q6  C21  H28  single    0.930  0.020  1.080
 6Q6  C25  H29  single    0.970  0.020  1.090
 6Q6  C25  H30  single    0.970  0.020  1.090
 6Q6  C25  H31  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
 6Q6  C8   N1   C5   124.77  3.000
 6Q6  C8   N1   C4   120.26  3.000
 6Q6  C5   N1   C4   112.73  3.000
 6Q6  H1   C2   C3   108.33  3.000
 6Q6  H1   C2   C6   108.62  3.000
 6Q6  C3   C2   C6   111.72  3.000
 6Q6  H1   C2   C4   107.65  3.000
 6Q6  C6   C2   C4   110.75  3.000
 6Q6  C3   C2   C4   109.65  3.000
 6Q6  H3   C4   H2   107.34  3.000
 6Q6  H3   C4   C2   111.13  3.000
 6Q6  H2   C4   C2   109.47  3.000
 6Q6  H3   C4   N1   109.57  3.000
 6Q6  H2   C4   N1   108.07  3.000
 6Q6  C2   C4   N1   111.13  3.000
 6Q6  H5   C5   H4   106.57  3.000
 6Q6  H5   C5   C1   109.42  3.000
 6Q6  H4   C5   C1   110.34  3.000
 6Q6  H5   C5   N1   108.29  3.000
 6Q6  H4   C5   N1   111.04  3.000
 6Q6  C1   C5   N1   111.04  3.000
 6Q6  H8   C6   H7   107.71  3.000
 6Q6  H8   C6   H6   107.62  3.000
 6Q6  H7   C6   H6   107.67  3.000
 6Q6  H8   C6   C2   111.04  3.000
 6Q6  H7   C6   C2   111.50  3.000
 6Q6  H6   C6   C2   111.12  3.000
 6Q6  H11  C7   H10  107.78  3.000
 6Q6  H11  C7   H9   107.73  3.000
 6Q6  H10  C7   H9   107.62  3.000
 6Q6  H11  C7   C1   111.52  3.000
 6Q6  H10  C7   C1   111.05  3.000
 6Q6  H9   C7   C1   110.98  3.000
 6Q6  H12  C13  C11  120.93  3.000
 6Q6  H12  C13  C17  121.10  3.000
 6Q6  C11  C13  C17  117.96  3.000
 6Q6  O2   C14  C12  115.37  3.000
 6Q6  C12  C14  C20  121.99  3.000
 6Q6  O2   C14  C20  122.64  3.000
 6Q6  C21  C15  O4   119.68  3.000
 6Q6  O4   C15  C12  117.88  3.000
 6Q6  C21  C15  C12  122.43  3.000
 6Q6  H13  C16  C11  120.18  3.000
 6Q6  H13  C16  C18  117.56  3.000
 6Q6  C11  C16  C18  122.26  3.000
 6Q6  O3   C17  C19  109.26  3.000
 6Q6  C19  C17  C13  122.06  3.000
 6Q6  O3   C17  C13  128.67  3.000
 6Q6  H14  C18  C19  121.88  3.000
 6Q6  H14  C18  C16  121.06  3.000
 6Q6  C19  C18  C16  117.06  3.000
 6Q6  O5   C19  C18  129.34  3.000
 6Q6  C18  C19  C17  121.29  3.000
 6Q6  O5   C19  C17  109.36  3.000
 6Q6  H15  C20  C22  118.70  3.000
 6Q6  H15  C20  C14  121.93  3.000
 6Q6  C22  C20  C14  119.36  3.000
 6Q6  H18  C24  H17  108.80  3.000
 6Q6  H18  C24  H16  108.81  3.000
 6Q6  H17  C24  H16  108.77  3.000
 6Q6  H18  C24  O2   112.03  3.000
 6Q6  H17  C24  O2   106.34  3.000
 6Q6  H16  C24  O2   111.98  3.000
 6Q6  C9   C8   O1   120.90  3.000
 6Q6  O1   C8   N1   121.87  3.000
 6Q6  C9   C8   N1   117.23  3.000
 6Q6  H20  C3   H19  106.20  3.000
 6Q6  H20  C3   C1   109.86  3.000
 6Q6  H19  C3   C1   109.14  3.000
 6Q6  H20  C3   C2   109.85  3.000
 6Q6  H19  C3   C2   108.98  3.000
 6Q6  C1   C3   C2   112.61  3.000
 6Q6  H21  C1   C3   108.34  3.000
 6Q6  H21  C1   C7   108.74  3.000
 6Q6  C3   C1   C7   111.85  3.000
 6Q6  H21  C1   C5   107.39  3.000
 6Q6  C7   C1   C5   110.59  3.000
 6Q6  C3   C1   C5   109.79  3.000
 6Q6  H23  C9   H22  105.53  3.000
 6Q6  H23  C9   C10  108.28  3.000
 6Q6  H22  C9   C10  111.13  3.000
 6Q6  H23  C9   C8   107.76  3.000
 6Q6  H22  C9   C8   111.05  3.000
 6Q6  C10  C9   C8   112.73  3.000
 6Q6  H24  C10  C12  106.78  3.000
 6Q6  H24  C10  C11  105.64  3.000
 6Q6  C12  C10  C11  110.97  3.000
 6Q6  H24  C10  C9   106.08  3.000
 6Q6  C11  C10  C9   114.89  3.000
 6Q6  C12  C10  C9   111.84  3.000
 6Q6  C10  C11  C16  123.62  3.000
 6Q6  C16  C11  C13  119.37  3.000
 6Q6  C10  C11  C13  117.00  3.000
 6Q6  C23  O5   C19  105.74  3.000
 6Q6  H26  C23  H25  110.43  3.000
 6Q6  H26  C23  O3   109.82  3.000
 6Q6  H25  C23  O3   109.78  3.000
 6Q6  H26  C23  O5   109.83  3.000
 6Q6  H25  C23  O5   109.88  3.000
 6Q6  O3   C23  O5   107.02  3.000
 6Q6  C23  O3   C17  105.84  3.000
 6Q6  C10  C12  C15  121.21  3.000
 6Q6  C10  C12  C14  121.98  3.000
 6Q6  C15  C12  C14  116.80  3.000
 6Q6  H28  C21  C22  121.76  3.000
 6Q6  H28  C21  C15  119.22  3.000
 6Q6  C22  C21  C15  119.02  3.000
 6Q6  O6   C22  C21  123.97  3.000
 6Q6  C21  C22  C20  120.39  3.000
 6Q6  O6   C22  C20  115.64  3.000
 6Q6  C25  O6   C22  118.69  3.000
 6Q6  H31  C25  H30  108.72  3.000
 6Q6  H31  C25  H29  108.78  3.000
 6Q6  H30  C25  H29  108.81  3.000
 6Q6  H31  C25  O6   106.51  3.000
 6Q6  H30  C25  O6   111.99  3.000
 6Q6  H29  C25  O6   111.92  3.000
 6Q6  C24  O2   C14  119.55  3.000
 6Q6  H27  O4   C15  110.27  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
 6Q6  CONST_01  C18  C19  C17  C13     0.00   0.0  0
 6Q6  CONST_02  C18  C16  C11  C13     0.00   0.0  0
 6Q6  CONST_03  C21  C22  C20  C14     0.00   0.0  0
 6Q6  CONST_04  C21  C15  C12  C14     0.00   0.0  0
 6Q6  CONST_05  C20  C22  C21  C15     0.00   0.0  0
 6Q6  CONST_06  C20  C14  C12  C15     0.00   0.0  0
 6Q6  CONST_07  C17  C13  C11  C16     0.00   0.0  0
 6Q6  CONST_08  C17  C19  C18  C16     0.00   0.0  0
 6Q6  CONST_09  C11  C13  C17  C19     0.00   0.0  0
 6Q6  CONST_10  C11  C16  C18  C19     0.00   0.0  0
 6Q6  CONST_11  C22  C20  C14  C12     0.00   0.0  0
 6Q6  CONST_12  C22  C21  C15  C12     0.00   0.0  0
 6Q6  CONST_13  O6   C22  C20  C14   180.00   0.0  0
 6Q6  CONST_14  O4   C15  C12  C14   180.00   0.0  0
 6Q6  CONST_15  O6   C22  C21  C15   180.00   0.0  0
 6Q6  CONST_16  O2   C14  C12  C15   180.00   0.0  0
 6Q6  CONST_17  C10  C11  C13  C17   180.00   0.0  0
 6Q6  CONST_18  C10  C11  C16  C18   180.00   0.0  0
 6Q6  CONST_19  C10  C12  C14  C20   180.00   0.0  0
 6Q6  CONST_20  C21  C15  C12  C10   180.00   0.0  0
 6Q6  CONST_21  C22  C21  C15  O4    180.00   0.0  0
 6Q6  CONST_22  O2   C14  C20  C22   180.00   0.0  0
 6Q6  CONST_23  H13  C16  C11  C13   180.00   0.0  0
 6Q6  CONST_24  H12  C13  C11  C16   180.00   0.0  0
 6Q6  CONST_25  H14  C18  C19  C17   180.00   0.0  0
 6Q6  CONST_26  H28  C21  C22  C20   180.00   0.0  0
 6Q6  CONST_27  H15  C20  C14  C12   180.00   0.0  0
 6Q6  CONST_28  C9   C8   N1   C4    180.00   0.0  0
 6Q6  CONST_29  O1   C8   N1   C4      0.00   0.0  0
 6Q6  CONST_30  C9   C8   N1   C5      0.00   0.0  0
 6Q6  CONST_31  O1   C8   N1   C5    180.00   0.0  0
 6Q6  Var_01    C5   N1   C4   C2    -59.98  30.0  1
 6Q6  Var_02    C1   C5   N1   C4     59.80  30.0  1
 6Q6  Var_03    O5   C23  O3   C17    16.19  30.0  1
 6Q6  Var_04    O3   C23  O5   C19   -16.24  30.0  1
 6Q6  Var_05    C12  C14  O2   C24  -178.51  30.0  2
 6Q6  Var_06    C10  C9   C8   N1   -168.47  30.0  2
 6Q6  Var_07    H16  C24  O2   C14    60.54  30.0  3
 6Q6  Var_08    H29  C25  O6   C22   -59.68  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
 6Q6  chir_01  C2   C3   C6   C4  negativ
 6Q6  chir_02  C1   C7   C3   C5  negativ
 6Q6  chir_03  C10  C12  C11  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
 6Q6  plan-1  C14  0.020
 6Q6  plan-1  C15  0.020
 6Q6  plan-1  C20  0.020
 6Q6  plan-1  C10  0.020
 6Q6  plan-1  C12  0.020
 6Q6  plan-1  C21  0.020
 6Q6  plan-1  C22  0.020
 6Q6  plan-1  O6   0.020
 6Q6  plan-1  O2   0.020
 6Q6  plan-1  H15  0.020
 6Q6  plan-1  H28  0.020
 6Q6  plan-1  O4   0.020
 6Q6  plan-2  C13  0.020
 6Q6  plan-2  C16  0.020
 6Q6  plan-2  C17  0.020
 6Q6  plan-2  C18  0.020
 6Q6  plan-2  C19  0.020
 6Q6  plan-2  C10  0.020
 6Q6  plan-2  C11  0.020
 6Q6  plan-2  O5   0.020
 6Q6  plan-2  O3   0.020
 6Q6  plan-2  H12  0.020
 6Q6  plan-2  H13  0.020
 6Q6  plan-2  H14  0.020
 6Q6  plan-3  N1   0.020
 6Q6  plan-3  C4   0.020
 6Q6  plan-3  C5   0.020
 6Q6  plan-3  C8   0.020
 6Q6  plan-3  C9   0.020
 6Q6  plan-3  O1   0.020

