# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:40:31 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: (2R)-2-[(1-benzylpiperidin-4-yl)methyl]-5,6-dimethoxy-2,3-dihydro-1H-inden-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2C[C@@H](CC3CCN(CC3)Cc4ccccc4)C(=O)c2cc1OC
#
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
 E20  E20  (2R)-2-[(1-benzylpiperidin-4-yl)methyl]-5,6-dimethoxy-2,3-dihydro-1H-inden-1-one  ligand  57  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 PERFECT
;

data_comp_E20
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
 E20  C1    C  CR6   0   0.312   0.4580  -0.2768   5.7979
 E20  C2    C  CR6   0   0.340  -0.9433  -0.2731   5.5353
 E20  C3    C  CR16  0  -0.456  -1.4214  -0.1395   4.2407
 E20  C4    C  CR56  0   0.095  -0.5111  -0.0057   3.1975
 E20  C5    C  CR56  0  -0.033   0.8442  -0.0071   3.4586
 E20  C6    C  CR16  0  -0.421   1.3487  -0.1385   4.7571
 E20  C7    C  CR5   0   0.378   1.5889   0.1501   2.2111
 E20  C8    C  CR15  0  -0.407   0.5861   0.1118   1.0649
 E20  C9    C  CH2   0  -0.491  -0.7958   0.1819   1.7367
 E20  C10   C  CH2   0  -0.420   0.8277   1.1839   0.0076
 E20  C11   C  CH1   0  -0.248  -0.0690   1.0371  -1.2209
 E20  C12   C  CH2   0  -0.420  -0.0106   2.2801  -2.1043
 E20  C13   C  CH2   0  -0.279  -0.8667   2.1147  -3.3490
 E20  N14   N  NT    0  -0.411  -0.4562   0.9517  -4.1126
 E20  C15   C  CH2   0  -0.270  -0.5599  -0.2619  -3.3238
 E20  C16   C  CH2   0  -0.427   0.2910  -0.1812  -2.0664
 E20  C17   C  CH2   0  -0.317  -1.1709   0.8412  -5.3644
 E20  C18   C  CR6   0   0.087  -0.5003  -0.0963  -6.3364
 E20  C19   C  CR16  0  -0.315  -1.2513  -0.9640  -7.1225
 E20  C20   C  CR16  0  -0.241  -0.6386  -1.7917  -8.0563
 E20  C21   C  CR16  0  -0.272   0.7403  -1.7649  -8.2099
 E20  C22   C  CR16  0  -0.242   1.5000  -0.9064  -7.4227
 E20  C23   C  CR16  0  -0.284   0.8845  -0.0798  -6.4944
 E20  O24   O  O     0  -0.416   2.7912   0.2721   2.0944
 E20  O25   O  O2    0  -0.463   0.7882  -0.4202   7.0928
 E20  C26   C  CH3   0  -0.439   2.1616  -0.4344   7.4247
 E20  O27   O  O2    0  -0.453  -1.7129  -0.4058   6.6188
 E20  C28   C  CH3   0  -0.442  -3.1198  -0.3704   6.4601
 E20  H3    H  HCR6  0   0.284  -2.4843  -0.1357   4.0376
 E20  H6    H  HCR6  0   0.283   2.4191  -0.1371   4.9182
 E20  H8    H  HCR5  0   0.292   0.7089  -0.8797   0.6117
 E20  H91   H  HCH2  0   0.263  -1.4913  -0.5655   1.3522
 E20  H92   H  HCH2  0   0.262  -1.2603   1.1573   1.5644
 E20  H101  H  HCH2  0   0.232   0.6573   2.1666   0.4604
 E20  H102  H  HCH2  0   0.230   1.8750   1.1640  -0.3092
 E20  H11   H  HCH1  0   0.224  -1.1083   0.9226  -0.8821
 E20  H121  H  HCH2  0   0.228  -0.3518   3.1575  -1.5488
 E20  H122  H  HCH2  0   0.213   1.0260   2.4714  -2.4023
 E20  H131  H  HCH2  0   0.182  -1.9295   2.0531  -3.0517
 E20  H132  H  HCH2  0   0.233  -0.7722   2.9989  -3.9849
 E20  H151  H  HCH2  0   0.185  -1.6100  -0.4637  -3.0437
 E20  H152  H  HCH2  0   0.237  -0.2306  -1.1079  -3.9309
 E20  H161  H  HCH2  0   0.213   1.3472  -0.1222  -2.3511
 E20  H162  H  HCH2  0   0.232   0.1672  -1.1070  -1.4990
 E20  H171  H  HCH2  0   0.208  -2.2205   0.5308  -5.2234
 E20  H172  H  HCH2  0   0.249  -1.2131   1.8370  -5.8181
 E20  H19   H  HCR6  0   0.246  -2.3282  -0.9965  -7.0012
 E20  H20   H  HCR6  0   0.252  -1.2406  -2.4613  -8.6572
 E20  H21   H  HCR6  0   0.252   1.2222  -2.4093  -8.9341
 E20  H22   H  HCR6  0   0.251   2.5768  -0.8815  -7.5348
 E20  H23   H  HCR6  0   0.243   1.4793   0.5799  -5.8751
 E20  H261  H  HCH3  0   0.263   2.2182  -0.5421   8.5049
 E20  H262  H  HCH3  0   0.230   2.6848  -1.2740   6.9589
 E20  H263  H  HCH3  0   0.229   2.6593   0.4949   7.1349
 E20  H281  H  HCH3  0   0.266  -3.5426  -0.4565   7.4574
 E20  H282  H  HCH3  0   0.235  -3.4520   0.5693   6.0126
 E20  H283  H  HCH3  0   0.235  -3.4799  -1.2017   5.8493

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
 E20  C1   C2    aromatic  1.426  0.020  1.426
 E20  C1   C6    aromatic  1.377  0.020  1.377
 E20  C1   O25   single    1.344  0.020  1.344
 E20  C2   C3    aromatic  1.386  0.020  1.386
 E20  C2   O27   single    1.336  0.020  1.336
 E20  C3   C4    aromatic  1.391  0.020  1.391
 E20  C3   H3    single    0.930  0.020  1.080
 E20  C4   C5    aromatic  1.380  0.020  1.380
 E20  C4   C9    single    1.500  0.020  1.500
 E20  C5   C6    aromatic  1.399  0.020  1.399
 E20  C5   C7    single    1.461  0.020  1.461
 E20  C6   H6    single    0.930  0.020  1.080
 E20  C7   C8    single    1.523  0.020  1.523
 E20  C7   O24   double    1.214  0.020  1.214
 E20  C8   C9    single    1.538  0.020  1.538
 E20  C8   C10   single    1.525  0.020  1.525
 E20  C8   H8    single    0.970  0.020  1.090
 E20  C9   H91   single    0.970  0.020  1.090
 E20  C9   H92   single    0.970  0.020  1.090
 E20  C10  C11   single    1.528  0.020  1.528
 E20  C10  H101  single    0.970  0.020  1.090
 E20  C10  H102  single    0.970  0.020  1.090
 E20  C11  C12   single    1.526  0.020  1.526
 E20  C11  C16   single    1.526  0.020  1.526
 E20  C11  H11   single    0.970  0.020  1.090
 E20  C12  C13   single    1.520  0.020  1.520
 E20  C12  H121  single    0.970  0.020  1.090
 E20  C12  H122  single    0.970  0.020  1.090
 E20  C13  N14   single    1.451  0.020  1.451
 E20  C13  H131  single    0.970  0.020  1.090
 E20  C13  H132  single    0.970  0.020  1.090
 E20  N14  C15   single    1.451  0.020  1.451
 E20  N14  C17   single    1.446  0.020  1.446
 E20  C15  C16   single    1.520  0.020  1.520
 E20  C15  H151  single    0.970  0.020  1.090
 E20  C15  H152  single    0.970  0.020  1.090
 E20  C16  H161  single    0.970  0.020  1.090
 E20  C16  H162  single    0.970  0.020  1.090
 E20  C17  C18   single    1.508  0.020  1.508
 E20  C17  H171  single    0.970  0.020  1.090
 E20  C17  H172  single    0.970  0.020  1.090
 E20  C18  C19   aromatic  1.391  0.020  1.391
 E20  C18  C23   aromatic  1.394  0.020  1.394
 E20  C19  C20   aromatic  1.390  0.020  1.390
 E20  C19  H19   single    0.930  0.020  1.080
 E20  C20  C21   aromatic  1.388  0.020  1.388
 E20  C20  H20   single    0.930  0.020  1.080
 E20  C21  C22   aromatic  1.391  0.020  1.391
 E20  C21  H21   single    0.930  0.020  1.080
 E20  C22  C23   aromatic  1.387  0.020  1.387
 E20  C22  H22   single    0.930  0.020  1.080
 E20  C23  H23   single    0.930  0.020  1.080
 E20  O25  C26   single    1.413  0.020  1.413
 E20  C26  H261  single    0.970  0.020  1.090
 E20  C26  H262  single    0.970  0.020  1.090
 E20  C26  H263  single    0.970  0.020  1.090
 E20  O27  C28   single    1.416  0.020  1.416
 E20  C28  H281  single    0.970  0.020  1.090
 E20  C28  H282  single    0.970  0.020  1.090
 E20  C28  H283  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
 E20  O25   C1   C6    125.46  3.000
 E20  O25   C1   C2    114.78  3.000
 E20  C6    C1   C2    119.76  3.000
 E20  O27   C2   C3    124.64  3.000
 E20  O27   C2   C1    114.62  3.000
 E20  C3    C2   C1    120.74  3.000
 E20  H3    C3   C4    120.12  3.000
 E20  H3    C3   C2    120.95  3.000
 E20  C4    C3   C2    118.94  3.000
 E20  C9    C4   C5    111.75  3.000
 E20  C9    C4   C3    128.18  3.000
 E20  C5    C4   C3    120.05  3.000
 E20  C7    C5   C6    128.21  3.000
 E20  C7    C5   C4    109.81  3.000
 E20  C6    C5   C4    121.98  3.000
 E20  H6    C6   C5    119.64  3.000
 E20  H6    C6   C1    121.83  3.000
 E20  C5    C6   C1    118.54  3.000
 E20  O24   C7   C8    125.60  3.000
 E20  O24   C7   C5    126.69  3.000
 E20  C8    C7   C5    107.71  3.000
 E20  H8    C8   C10   109.35  3.000
 E20  H8    C8   C9    108.80  3.000
 E20  C10   C8   C9    114.40  3.000
 E20  H8    C8   C7    105.06  3.000
 E20  C10   C8   C7    113.56  3.000
 E20  C9    C8   C7    105.17  3.000
 E20  H92   C9   H91   106.53  3.000
 E20  H92   C9   C8    110.69  3.000
 E20  H91   C9   C8    112.80  3.000
 E20  H92   C9   C4    110.21  3.000
 E20  H91   C9   C4    112.24  3.000
 E20  C8    C9   C4    104.43  3.000
 E20  H102  C10  H101  106.55  3.000
 E20  H102  C10  C11   109.10  3.000
 E20  H101  C10  C11   109.10  3.000
 E20  H102  C10  C8    109.85  3.000
 E20  H101  C10  C8    108.63  3.000
 E20  C11   C10  C8    113.38  3.000
 E20  H11   C11  C16   108.10  3.000
 E20  H11   C11  C12   107.42  3.000
 E20  C16   C11  C12   108.69  3.000
 E20  H11   C11  C10   108.49  3.000
 E20  C16   C11  C10   112.56  3.000
 E20  C12   C11  C10   111.39  3.000
 E20  H122  C12  H121  107.07  3.000
 E20  H122  C12  C13   109.23  3.000
 E20  H121  C12  C13   109.13  3.000
 E20  H122  C12  C11   109.63  3.000
 E20  H121  C12  C11   110.34  3.000
 E20  C13   C12  C11   111.34  3.000
 E20  H132  C13  H131  106.54  3.000
 E20  H132  C13  N14   108.53  3.000
 E20  H131  C13  N14   111.65  3.000
 E20  H132  C13  C12   109.86  3.000
 E20  H131  C13  C12   109.12  3.000
 E20  N14   C13  C12   111.04  3.000
 E20  C17   N14  C15   111.81  3.000
 E20  C17   N14  C13   112.16  3.000
 E20  C15   N14  C13   111.36  3.000
 E20  H152  C15  H151  106.61  3.000
 E20  H152  C15  C16   109.40  3.000
 E20  H151  C15  C16   109.38  3.000
 E20  H152  C15  N14   108.91  3.000
 E20  H151  C15  N14   110.99  3.000
 E20  C16   C15  N14   111.42  3.000
 E20  H162  C16  H161  106.84  3.000
 E20  H162  C16  C15   108.72  3.000
 E20  H161  C16  C15   109.12  3.000
 E20  H162  C16  C11   111.22  3.000
 E20  H161  C16  C11   109.17  3.000
 E20  C15   C16  C11   111.63  3.000
 E20  H172  C17  H171  105.78  3.000
 E20  H172  C17  C18   108.39  3.000
 E20  H171  C17  C18   109.30  3.000
 E20  H172  C17  N14   107.96  3.000
 E20  H171  C17  N14   112.39  3.000
 E20  C18   C17  N14   112.70  3.000
 E20  C23   C18  C19   118.67  3.000
 E20  C23   C18  C17   120.50  3.000
 E20  C19   C18  C17   120.80  3.000
 E20  H19   C19  C20   119.67  3.000
 E20  H19   C19  C18   119.46  3.000
 E20  C20   C19  C18   120.87  3.000
 E20  H20   C20  C21   120.20  3.000
 E20  H20   C20  C19   119.74  3.000
 E20  C21   C20  C19   120.05  3.000
 E20  H21   C21  C22   120.19  3.000
 E20  H21   C21  C20   120.32  3.000
 E20  C22   C21  C20   119.48  3.000
 E20  H22   C22  C23   119.79  3.000
 E20  H22   C22  C21   119.92  3.000
 E20  C23   C22  C21   120.28  3.000
 E20  H23   C23  C22   120.13  3.000
 E20  H23   C23  C18   119.22  3.000
 E20  C22   C23  C18   120.64  3.000
 E20  C26   O25  C1    117.78  3.000
 E20  H263  C26  H262  108.78  3.000
 E20  H263  C26  H261  108.90  3.000
 E20  H262  C26  H261  108.80  3.000
 E20  H263  C26  O25   111.82  3.000
 E20  H262  C26  O25   111.88  3.000
 E20  H261  C26  O25   106.56  3.000
 E20  C28   O27  C2    118.62  3.000
 E20  H283  C28  H282  108.98  3.000
 E20  H283  C28  H281  108.93  3.000
 E20  H282  C28  H281  109.01  3.000
 E20  H283  C28  O27   111.78  3.000
 E20  H282  C28  O27   111.68  3.000
 E20  H281  C28  O27   106.36  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
 E20  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 E20  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 E20  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 E20  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 E20  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 E20  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 E20  CONST_07  C21   C20  C19  C18     0.00   0.0  0
 E20  CONST_08  C21   C22  C23  C18     0.00   0.0  0
 E20  CONST_09  C22   C23  C18  C19     0.00   0.0  0
 E20  CONST_10  C22   C21  C20  C19     0.00   0.0  0
 E20  CONST_11  C23   C18  C19  C20     0.00   0.0  0
 E20  CONST_12  C23   C22  C21  C20     0.00   0.0  0
 E20  CONST_13  O25   C1   C2   C3    180.00   0.0  0
 E20  CONST_14  O27   C2   C3   C4    180.00   0.0  0
 E20  CONST_15  O25   C1   C6   C5    180.00   0.0  0
 E20  CONST_16  O27   C2   C1   C6    180.00   0.0  0
 E20  CONST_17  C20   C19  C18  C17   180.00   0.0  0
 E20  CONST_18  C22   C23  C18  C17   180.00   0.0  0
 E20  CONST_19  H3    C3   C2   C1    180.00   0.0  0
 E20  CONST_20  H6    C6   C1   C2    180.00   0.0  0
 E20  CONST_21  H20   C20  C19  C18   180.00   0.0  0
 E20  CONST_22  H22   C22  C23  C18   180.00   0.0  0
 E20  CONST_23  H23   C23  C18  C19   180.00   0.0  0
 E20  CONST_24  H21   C21  C20  C19   180.00   0.0  0
 E20  CONST_25  H19   C19  C20  C21   180.00   0.0  0
 E20  Var_01    C8    C9   C4   C3   -174.04  30.0  1
 E20  Var_02    C8    C7   C5   C4     -5.80  30.0  1
 E20  Var_03    N14   C13  C12  C11   -57.42  30.0  1
 E20  Var_04    N14   C15  C16  C11    55.98  30.0  1
 E20  Var_05    C15   N14  C13  C12    59.23  30.0  1
 E20  Var_06    C16   C15  N14  C13   -58.54  30.0  1
 E20  Var_07    C18   C17  N14  C13   163.25  30.0  3
 E20  Var_08    C19   C18  C17  N14   139.92  30.0  2
 E20  Var_09    H261  C26  O25  C1    179.14  30.0  3
 E20  Var_10    H281  C28  O27  C2   -177.88  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
 E20  chir_01  C8   C7   C9   C10  negativ
 E20  chir_02  C11  C16  C12  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
 E20  plan-1  C17  0.020
 E20  plan-1  C18  0.020
 E20  plan-1  C19  0.020
 E20  plan-1  C20  0.020
 E20  plan-1  C21  0.020
 E20  plan-1  C22  0.020
 E20  plan-1  C23  0.020
 E20  plan-1  H19  0.020
 E20  plan-1  H20  0.020
 E20  plan-1  H21  0.020
 E20  plan-1  H22  0.020
 E20  plan-1  H23  0.020
 E20  plan-2  C1   0.020
 E20  plan-2  C2   0.020
 E20  plan-2  C3   0.020
 E20  plan-2  C4   0.020
 E20  plan-2  C5   0.020
 E20  plan-2  C6   0.020
 E20  plan-2  C7   0.020
 E20  plan-2  C9   0.020
 E20  plan-2  O25  0.020
 E20  plan-2  O27  0.020
 E20  plan-2  H3   0.020
 E20  plan-2  H6   0.020
 E20  plan-3  C5   0.020
 E20  plan-3  C7   0.020
 E20  plan-3  C8   0.020
 E20  plan-3  O24  0.020

