# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:14:26 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: N-{2-[(1S)-1-(3-ethoxy-4-methoxyphenyl)-2-(methylsulfonyl)ethyl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1cc(ccc1OC)[C@@H](C[S](C)(=O)=O)N2C(=O)c3cccc(NC(C)=O)c3C2=O
#
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
 A9L  A9L  N-{2-[(1S)-1-(3-ethoxy-4-methoxyphenyl)-2-(methylsulfonyl)ethyl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}acetamide  ligand  56  32  .  2022-03-11  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A9L
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
 A9L  C4   C  CR6   0   0.378  86.2175  156.4519  29.8299
 A9L  C14  C  CH3   0  -0.786  80.8707  161.3361  29.3440
 A9L  C5   C  CR56  0  -0.129  85.0912  156.8315  29.1052
 A9L  C6   C  CR56  0  -0.037  83.8889  156.1508  29.2036
 A9L  C11  C  CH1   0  -0.210  83.0005  158.8244  26.7915
 A9L  C7   C  CR5   0   0.619  84.9122  157.9346  28.1465
 A9L  C8   C  CR5   0   0.610  82.9169  156.8097  28.3000
 A9L  C9   C  C     0   0.513  88.6076  156.9839  30.2583
 A9L  C10  C  CH3   0  -0.797  89.6313  158.0018  29.8302
 A9L  C12  C  CH2   0  -0.649  81.8070  159.5398  27.4141
 A9L  C13  C  CR6   0   0.182  82.6944  158.1833  25.4562
 A9L  N1   N  NR5   0  -0.612  83.5954  157.8702  27.7158
 A9L  N2   N  NH1   0  -0.747  87.3849  157.1762  29.6726
 A9L  C3   C  CR16  0  -0.310  86.0602  155.3374  30.6734
 A9L  C1   C  CR16  0  -0.326  83.7269  155.0579  30.0196
 A9L  C15  C  CR16  0  -0.434  83.7770  157.9377  24.6039
 A9L  C16  C  CR6   0   0.342  83.5966  157.3363  23.3720
 A9L  C17  C  CR6   0   0.297  82.2928  156.9843  22.9569
 A9L  C18  C  CR16  0  -0.374  81.2256  157.2419  23.7976
 A9L  C19  C  CR16  0  -0.317  81.4255  157.8350  25.0445
 A9L  C2   C  CR16  0  -0.237  84.8468  154.6705  30.7561
 A9L  C20  C  CH2   0  -0.191  85.9236  157.3076  22.8743
 A9L  C21  C  CH3   0  -0.680  86.8182  156.8571  21.7452
 A9L  C22  C  CH3   0  -0.437  80.9215  156.0569  21.2670
 A9L  O1   O  O     0  -0.449  88.8442  156.0882  31.0427
 A9L  O2   O  O     0  -0.393  81.7723  156.5086  28.0841
 A9L  O3   O  O     0  -0.417  85.7301  158.7436  27.7738
 A9L  O4   O  OS    0  -0.676  83.4494  161.0850  28.7995
 A9L  O5   O  OS    0  -0.673  82.2946  159.2282  30.0237
 A9L  O6   O  O2    0  -0.465  84.5767  157.0527  22.4976
 A9L  O7   O  O2    0  -0.461  82.2045  156.4071  21.7465
 A9L  S1   S  S     0   1.204  82.2502  160.2711  28.9976
 A9L  H1   H  HCH3  0   0.315  81.0556  161.7927  30.3156
 A9L  H2   H  HCH3  0   0.297  80.7980  162.1040  28.5776
 A9L  H3   H  HCH3  0   0.298  79.9592  160.7434  29.3817
 A9L  H4   H  HCH1  0   0.315  83.7709  159.5794  26.6271
 A9L  H5   H  HCH3  0   0.272  90.6027  157.7492  30.2433
 A9L  H6   H  HCH3  0   0.272  89.7100  158.0489  28.7435
 A9L  H7   H  HCH3  0   0.278  89.3471  158.9951  30.1812
 A9L  H8   H  HCH2  0   0.333  81.5001  160.3616  26.7652
 A9L  H9   H  HCH2  0   0.317  80.9460  158.8991  27.5933
 A9L  H10  H  HNH1  0   0.425  87.3217  157.9507  29.0252
 A9L  H11  H  HCR6  0   0.300  86.8852  154.9877  31.2708
 A9L  H12  H  HCR6  0   0.274  82.7891  154.5249  30.0920
 A9L  H13  H  HCR6  0   0.275  84.7701  158.2302  24.9217
 A9L  H14  H  HCR6  0   0.285  80.2166  156.9847  23.5055
 A9L  H15  H  HCR6  0   0.250  80.5569  158.0136  25.6629
 A9L  H16  H  HCR6  0   0.282  84.7785  153.8183  31.4187
 A9L  H17  H  HCH2  0   0.224  86.1689  156.7686  23.7960
 A9L  H18  H  HCH2  0   0.226  86.0621  158.3761  23.0711
 A9L  H19  H  HCH3  0   0.238  87.8561  157.0632  22.0048
 A9L  H20  H  HCH3  0   0.235  86.7231  155.7870  21.5619
 A9L  H21  H  HCH3  0   0.235  86.5914  157.3902  20.8216
 A9L  H22  H  HCH3  0   0.261  81.0683  155.6188  20.2831
 A9L  H23  H  HCH3  0   0.229  80.4319  155.3210  21.9104
 A9L  H24  H  HCH3  0   0.229  80.2711  156.9303  21.1718

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
 A9L  C22  O7   single    1.414  0.020  1.414
 A9L  O7   C17  single    1.344  0.020  1.344
 A9L  C17  C18  aromatic  1.383  0.020  1.383
 A9L  C17  C16  aromatic  1.413  0.020  1.413
 A9L  C21  C20  single    1.509  0.020  1.509
 A9L  O6   C16  single    1.344  0.020  1.344
 A9L  O6   C20  single    1.422  0.020  1.422
 A9L  C18  C19  aromatic  1.395  0.020  1.395
 A9L  C16  C15  aromatic  1.383  0.020  1.383
 A9L  C19  C13  aromatic  1.379  0.020  1.379
 A9L  C15  C13  aromatic  1.400  0.020  1.400
 A9L  C13  C11  single    1.513  0.020  1.513
 A9L  C11  C12  single    1.524  0.020  1.524
 A9L  C11  N1   single    1.456  0.020  1.456
 A9L  C12  S1   single    1.800  0.020  1.800
 A9L  N1   C7   single    1.387  0.020  1.387
 A9L  N1   C8   single    1.388  0.020  1.388
 A9L  O3   C7   double    1.209  0.020  1.209
 A9L  O2   C8   double    1.203  0.020  1.203
 A9L  C7   C5   single    1.472  0.020  1.472
 A9L  C8   C6   single    1.482  0.020  1.482
 A9L  C5   C6   aromatic  1.385  0.020  1.385
 A9L  C5   C4   aromatic  1.392  0.020  1.392
 A9L  O4   S1   double    1.463  0.020  1.463
 A9L  C6   C1   aromatic  1.374  0.020  1.374
 A9L  S1   C14  single    1.777  0.020  1.777
 A9L  S1   O5   double    1.464  0.020  1.464
 A9L  O1   C9   double    1.214  0.020  1.214
 A9L  C9   C10  single    1.506  0.020  1.506
 A9L  C9   N2   single    1.369  0.020  1.369
 A9L  N2   C4   single    1.383  0.020  1.383
 A9L  C4   C3   aromatic  1.407  0.020  1.407
 A9L  C1   C2   aromatic  1.395  0.020  1.395
 A9L  C3   C2   aromatic  1.387  0.020  1.387
 A9L  C14  H1   single    0.970  0.020  1.090
 A9L  C14  H2   single    0.970  0.020  1.090
 A9L  C14  H3   single    0.970  0.020  1.090
 A9L  C11  H4   single    0.970  0.020  1.090
 A9L  C10  H5   single    0.970  0.020  1.090
 A9L  C10  H6   single    0.970  0.020  1.090
 A9L  C10  H7   single    0.970  0.020  1.090
 A9L  C12  H8   single    0.970  0.020  1.090
 A9L  C12  H9   single    0.970  0.020  1.090
 A9L  N2   H10  single    0.860  0.020  1.020
 A9L  C3   H11  single    0.930  0.020  1.080
 A9L  C1   H12  single    0.930  0.020  1.080
 A9L  C15  H13  single    0.930  0.020  1.080
 A9L  C18  H14  single    0.930  0.020  1.080
 A9L  C19  H15  single    0.930  0.020  1.080
 A9L  C2   H16  single    0.930  0.020  1.080
 A9L  C20  H17  single    0.970  0.020  1.090
 A9L  C20  H18  single    0.970  0.020  1.090
 A9L  C21  H19  single    0.970  0.020  1.090
 A9L  C21  H20  single    0.970  0.020  1.090
 A9L  C21  H21  single    0.970  0.020  1.090
 A9L  C22  H22  single    0.970  0.020  1.090
 A9L  C22  H23  single    0.970  0.020  1.090
 A9L  C22  H24  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
 A9L  C3   C4   N2   125.28  3.000
 A9L  C3   C4   C5   115.96  3.000
 A9L  N2   C4   C5   118.75  3.000
 A9L  H3   C14  H2   110.68  3.000
 A9L  H3   C14  H1   109.85  3.000
 A9L  H2   C14  H1   110.12  3.000
 A9L  H3   C14  S1   109.31  3.000
 A9L  H2   C14  S1   109.74  3.000
 A9L  H1   C14  S1   107.06  3.000
 A9L  C7   C5   C6   107.99  3.000
 A9L  C6   C5   C4   122.10  3.000
 A9L  C7   C5   C4   129.91  3.000
 A9L  C1   C6   C8   129.70  3.000
 A9L  C1   C6   C5   122.38  3.000
 A9L  C8   C6   C5   107.91  3.000
 A9L  H4   C11  N1   105.11  3.000
 A9L  H4   C11  C13  107.65  3.000
 A9L  N1   C11  C13  111.44  3.000
 A9L  H4   C11  C12  106.83  3.000
 A9L  N1   C11  C12  111.61  3.000
 A9L  C13  C11  C12  113.65  3.000
 A9L  O3   C7   N1   125.28  3.000
 A9L  O3   C7   C5   128.29  3.000
 A9L  N1   C7   C5   106.43  3.000
 A9L  O2   C8   N1   125.51  3.000
 A9L  O2   C8   C6   128.48  3.000
 A9L  N1   C8   C6   106.01  3.000
 A9L  O1   C9   N2   123.64  3.000
 A9L  N2   C9   C10  112.99  3.000
 A9L  O1   C9   C10  123.37  3.000
 A9L  H7   C10  H6   107.46  3.000
 A9L  H7   C10  H5   108.82  3.000
 A9L  H6   C10  H5   108.95  3.000
 A9L  H7   C10  C9   110.29  3.000
 A9L  H6   C10  C9   111.19  3.000
 A9L  H5   C10  C9   110.05  3.000
 A9L  H9   C12  H8   108.59  3.000
 A9L  H9   C12  S1   106.81  3.000
 A9L  H8   C12  S1   106.65  3.000
 A9L  H9   C12  C11  114.23  3.000
 A9L  H8   C12  C11  109.31  3.000
 A9L  S1   C12  C11  110.93  3.000
 A9L  C19  C13  C15  119.06  3.000
 A9L  C15  C13  C11  117.09  3.000
 A9L  C19  C13  C11  123.84  3.000
 A9L  C8   N1   C7   111.65  3.000
 A9L  C8   N1   C11  124.64  3.000
 A9L  C7   N1   C11  123.70  3.000
 A9L  H10  N2   C9   115.92  3.000
 A9L  H10  N2   C4   114.91  3.000
 A9L  C9   N2   C4   129.17  3.000
 A9L  H11  C3   C2   118.75  3.000
 A9L  H11  C3   C4   120.28  3.000
 A9L  C2   C3   C4   120.96  3.000
 A9L  H12  C1   C2   121.61  3.000
 A9L  H12  C1   C6   122.30  3.000
 A9L  C2   C1   C6   116.09  3.000
 A9L  H13  C15  C16  119.91  3.000
 A9L  H13  C15  C13  118.90  3.000
 A9L  C16  C15  C13  121.19  3.000
 A9L  O6   C16  C17  115.43  3.000
 A9L  O6   C16  C15  125.20  3.000
 A9L  C17  C16  C15  119.37  3.000
 A9L  O7   C17  C18  125.23  3.000
 A9L  C18  C17  C16  119.16  3.000
 A9L  O7   C17  C16  115.61  3.000
 A9L  H14  C18  C19  118.44  3.000
 A9L  H14  C18  C17  120.77  3.000
 A9L  C19  C18  C17  120.79  3.000
 A9L  H15  C19  C18  117.80  3.000
 A9L  H15  C19  C13  121.80  3.000
 A9L  C18  C19  C13  120.41  3.000
 A9L  H16  C2   C1   119.43  3.000
 A9L  H16  C2   C3   118.07  3.000
 A9L  C1   C2   C3   122.50  3.000
 A9L  H18  C20  H17  107.48  3.000
 A9L  H18  C20  O6   110.02  3.000
 A9L  H17  C20  O6   110.30  3.000
 A9L  H18  C20  C21  110.52  3.000
 A9L  H17  C20  C21  110.48  3.000
 A9L  O6   C20  C21  108.05  3.000
 A9L  H21  C21  H20  108.63  3.000
 A9L  H21  C21  H19  107.91  3.000
 A9L  H20  C21  H19  107.99  3.000
 A9L  H21  C21  C20  111.38  3.000
 A9L  H20  C21  C20  111.54  3.000
 A9L  H19  C21  C20  109.27  3.000
 A9L  H24  C22  H23  108.82  3.000
 A9L  H24  C22  H22  108.88  3.000
 A9L  H23  C22  H22  108.78  3.000
 A9L  H24  C22  O7   111.81  3.000
 A9L  H23  C22  O7   111.94  3.000
 A9L  H22  C22  O7   106.51  3.000
 A9L  C20  O6   C16  118.74  3.000
 A9L  C22  O7   C17  118.13  3.000
 A9L  O5   S1   O4   117.81  3.000
 A9L  O5   S1   C12  109.56  3.000
 A9L  O4   S1   C12  107.99  3.000
 A9L  O5   S1   C14  108.30  3.000
 A9L  O4   S1   C14  109.23  3.000
 A9L  C12  S1   C14  102.94  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
 A9L  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 A9L  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 A9L  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 A9L  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 A9L  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 A9L  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 A9L  CONST_07  C17  C18  C19  C13     0.00   0.0  0
 A9L  CONST_08  C17  C16  C15  C13     0.00   0.0  0
 A9L  CONST_09  C18  C17  C16  C15     0.00   0.0  0
 A9L  CONST_10  C18  C19  C13  C15     0.00   0.0  0
 A9L  CONST_11  C19  C18  C17  C16     0.00   0.0  0
 A9L  CONST_12  C19  C13  C15  C16     0.00   0.0  0
 A9L  CONST_13  C8   N1   C7   C5      0.00   0.0  0
 A9L  CONST_14  N2   C4   C5   C6    180.00   0.0  0
 A9L  CONST_15  C18  C19  C13  C11   180.00   0.0  0
 A9L  CONST_16  C16  C15  C13  C11   180.00   0.0  0
 A9L  CONST_17  N2   C4   C5   C7      0.00   0.0  0
 A9L  CONST_18  O6   C16  C15  C13   180.00   0.0  0
 A9L  CONST_19  C2   C3   C4   N2    180.00   0.0  0
 A9L  CONST_20  O7   C17  C16  C15   180.00   0.0  0
 A9L  CONST_21  O6   C16  C17  C18   180.00   0.0  0
 A9L  CONST_22  O7   C17  C18  C19   180.00   0.0  0
 A9L  CONST_23  C11  N1   C7   C5    180.00   0.0  0
 A9L  CONST_24  O3   C7   N1   C8    180.00   0.0  0
 A9L  CONST_25  H16  C2   C3   C4    180.00   0.0  0
 A9L  CONST_26  H12  C1   C6   C5    180.00   0.0  0
 A9L  CONST_27  H11  C3   C4   C5    180.00   0.0  0
 A9L  CONST_28  H14  C18  C19  C13   180.00   0.0  0
 A9L  CONST_29  H15  C19  C13  C15   180.00   0.0  0
 A9L  CONST_30  H13  C15  C16  C17   180.00   0.0  0
 A9L  CONST_31  C9   N2   C4   C5    180.00   0.0  0
 A9L  CONST_32  C3   C4   N2   C9      0.00   0.0  0
 A9L  CONST_33  O3   C7   N1   C11     0.00   0.0  0
 A9L  CONST_34  H10  N2   C4   C5      0.00   0.0  0
 A9L  CONST_35  O1   C9   N2   C4      0.00   0.0  0
 A9L  CONST_36  C10  C9   N2   C4    180.00   0.0  0
 A9L  Var_01    C21  C20  O6   C16   177.92  30.0  3
 A9L  Var_02    H22  C22  O7   C17   179.51  30.0  3
 A9L  Var_03    C11  C12  S1   C14   167.51  30.0  1
 A9L  Var_04    H1   C14  S1   C12   178.12  30.0  3
 A9L  Var_05    H5   C10  C9   N2   -174.44  30.0  3
 A9L  Var_06    H19  C21  C20  O6    178.81  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
 A9L  chir_01  C11  C13  C12  N1  negativ

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
 A9L  plan-1  C11  0.020
 A9L  plan-1  C13  0.020
 A9L  plan-1  C15  0.020
 A9L  plan-1  C16  0.020
 A9L  plan-1  C17  0.020
 A9L  plan-1  C18  0.020
 A9L  plan-1  C19  0.020
 A9L  plan-1  O6   0.020
 A9L  plan-1  O7   0.020
 A9L  plan-1  H13  0.020
 A9L  plan-1  H14  0.020
 A9L  plan-1  H15  0.020
 A9L  plan-2  C4   0.020
 A9L  plan-2  C5   0.020
 A9L  plan-2  C6   0.020
 A9L  plan-2  C11  0.020
 A9L  plan-2  C7   0.020
 A9L  plan-2  C8   0.020
 A9L  plan-2  N1   0.020
 A9L  plan-2  N2   0.020
 A9L  plan-2  C3   0.020
 A9L  plan-2  C1   0.020
 A9L  plan-2  C2   0.020
 A9L  plan-2  O2   0.020
 A9L  plan-2  O3   0.020
 A9L  plan-2  H11  0.020
 A9L  plan-2  H12  0.020
 A9L  plan-2  H16  0.020
 A9L  plan-3  C4   0.020
 A9L  plan-3  C9   0.020
 A9L  plan-3  C10  0.020
 A9L  plan-3  N2   0.020
 A9L  plan-3  O1   0.020
 A9L  plan-3  H10  0.020

