# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:16:40 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 5-[3,5-dimethoxy-4-[(3-oxidanylazetidin-1-yl)methyl]phenyl]-1,3-dimethyl-pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1CN2CC(O)C2)C3=CN(C)C(=O)C(=C3)C
#
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
 5U2  5U2  5-[3,5-dimethoxy-4-[(3-oxidanylazetidin-1-yl)methyl]phenyl]-1,3-dimethyl-pyridin-2-one  ligand  49  25  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5U2
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
 5U2  C4   C  CR16  0  -0.005  -2.9936  -0.7814   0.8848
 5U2  C6   C  CR6   0   0.550  -5.1705   0.1962   0.5491
 5U2  C8   C  CH3   0  -0.519  -4.9030  -1.6157   2.1377
 5U2  C10  C  CR6   0   0.407   1.1403   1.0208  -0.8500
 5U2  N12  N  N     0  -0.409   4.0132  -0.5370   0.0936
 5U2  C13  C  C     0   0.006   5.5718   0.0794   1.3353
 5U2  C15  C  CR6   0   0.151  -0.9512  -0.0515  -0.3041
 5U2  C17  C  CR6   0   0.410   1.0524  -1.3591  -0.5834
 5U2  C20  C  CH3   0  -0.438   1.2893   3.3835  -1.1096
 5U2  C22  C  CH3   0  -0.438   1.0369  -3.7278  -0.3752
 5U2  C24  C  C     0  -0.294   5.4693  -0.6635   0.0019
 5U2  C1   C  CR6   0  -0.117  -4.5539   1.0946  -0.4011
 5U2  C2   C  CR16  0  -0.203  -3.2223   1.0033  -0.6563
 5U2  C3   C  CR6   0  -0.049  -2.3929   0.0437  -0.0161
 5U2  N5   N  NR6   0  -0.505  -4.3180  -0.7102   1.1587
 5U2  O7   O  O     0  -0.506  -6.3670   0.2021   0.8296
 5U2  C9   C  CH3   0  -0.711  -5.4445   2.0854  -1.0784
 5U2  C14  C  CR16  0  -0.500  -0.2231   1.1035  -0.5696
 5U2  C16  C  CR16  0  -0.504  -0.3129  -1.2888  -0.3182
 5U2  C18  C  CR6   0  -0.127   1.8027  -0.2112  -0.8664
 5U2  O19  O  O2    0  -0.471   1.8929   2.1065  -1.1104
 5U2  O21  O  O2    0  -0.465   1.7305  -2.5202  -0.6147
 5U2  C23  C  C     0  -0.301   4.1516   0.5859   1.0247
 5U2  O25  O  OH1   0  -0.662   6.6231   0.9924   1.4239
 5U2  H1   H  HCR6  0   0.300  -2.4399  -1.5232   1.4429
 5U2  H2   H  HCH3  0   0.261  -5.3889  -1.0554   2.9332
 5U2  H3   H  HCH3  0   0.261  -5.6389  -2.2649   1.6672
 5U2  H4   H  HCH3  0   0.257  -4.1174  -2.2284   2.5688
 5U2  H6   H  H     0   0.214   5.5636  -0.6191   2.1790
 5U2  H7   H  HCH3  0   0.261   2.0794   4.0948  -1.3374
 5U2  H8   H  HCH3  0   0.227   0.5097   3.4706  -1.8710
 5U2  H9   H  HCH3  0   0.228   0.8610   3.6347  -0.1361
 5U2  H10  H  HCH3  0   0.261   1.7745  -4.5238  -0.4404
 5U2  H11  H  HCH3  0   0.227   0.5841  -3.7489   0.6193
 5U2  H12  H  HCH3  0   0.228   0.2584  -3.9094  -1.1205
 5U2  H13  H  H     0   0.229   5.8533  -1.6844  -0.0655
 5U2  H14  H  H     0   0.202   5.9064  -0.0631  -0.8097
 5U2  H15  H  HCR6  0   0.261  -2.7815   1.6710  -1.3878
 5U2  H16  H  HCH3  0   0.245  -6.2019   1.5899  -1.6889
 5U2  H17  H  HCH3  0   0.244  -5.9779   2.7028  -0.3542
 5U2  H18  H  HCH3  0   0.243  -4.8700   2.7463  -1.7253
 5U2  H19  H  HCH2  0   0.215   3.6405   0.5640  -1.6690
 5U2  H20  H  HCH2  0   0.241   3.4713  -1.1756  -1.7903
 5U2  H21  H  HCR6  0   0.272  -0.7207   2.0623  -0.5251
 5U2  H22  H  HCR6  0   0.270  -0.8913  -2.1871  -0.1531
 5U2  H23  H  H     0   0.203   4.1930   1.5621   0.5224
 5U2  H24  H  H     0   0.223   3.4135   0.6289   1.8291
 5U2  H25  H  HOH1  0   0.454   6.6156   1.3814   2.3037
 5U2  C11  C  CH2   0  -0.328   3.2789  -0.3243  -1.1336

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
 5U2  O25  C13  single    1.395  0.020  1.395
 5U2  C20  O19  single    1.412  0.020  1.412
 5U2  C13  C24  single    1.530  0.020  1.530
 5U2  C13  C23  single    1.540  0.020  1.540
 5U2  C24  N12  single    1.464  0.020  1.464
 5U2  O19  C10  single    1.346  0.020  1.346
 5U2  C23  N12  single    1.465  0.020  1.465
 5U2  C14  C10  aromatic  1.394  0.020  1.394
 5U2  C14  C15  aromatic  1.391  0.020  1.391
 5U2  C10  C18  aromatic  1.399  0.020  1.399
 5U2  N12  C11  single    1.446  0.020  1.446
 5U2  C15  C3   single    1.473  0.020  1.473
 5U2  C15  C16  aromatic  1.392  0.020  1.392
 5U2  C3   C2   single    1.421  0.020  1.421
 5U2  C3   C4   double    1.361  0.020  1.361
 5U2  C2   C1   double    1.359  0.020  1.359
 5U2  C4   N5   single    1.354  0.020  1.354
 5U2  C18  C11  single    1.505  0.020  1.505
 5U2  C18  C17  aromatic  1.400  0.020  1.400
 5U2  C1   C9   single    1.495  0.020  1.495
 5U2  C1   C6   single    1.446  0.020  1.446
 5U2  N5   C6   single    1.386  0.020  1.386
 5U2  N5   C8   single    1.456  0.020  1.456
 5U2  C6   O7   double    1.229  0.020  1.229
 5U2  C16  C17  aromatic  1.393  0.020  1.393
 5U2  C17  O21  single    1.345  0.020  1.345
 5U2  O21  C22  single    1.413  0.020  1.413
 5U2  C4   H1   single    0.930  0.020  1.080
 5U2  C8   H2   single    0.970  0.020  1.090
 5U2  C8   H3   single    0.970  0.020  1.090
 5U2  C8   H4   single    0.970  0.020  1.090
 5U2  C13  H6   single    0.970  0.020  1.090
 5U2  C20  H7   single    0.970  0.020  1.090
 5U2  C20  H8   single    0.970  0.020  1.090
 5U2  C20  H9   single    0.970  0.020  1.090
 5U2  C22  H10  single    0.970  0.020  1.090
 5U2  C22  H11  single    0.970  0.020  1.090
 5U2  C22  H12  single    0.970  0.020  1.090
 5U2  C24  H13  single    0.970  0.020  1.090
 5U2  C24  H14  single    0.970  0.020  1.090
 5U2  C2   H15  single    0.930  0.020  1.080
 5U2  C9   H16  single    0.970  0.020  1.090
 5U2  C9   H17  single    0.970  0.020  1.090
 5U2  C9   H18  single    0.970  0.020  1.090
 5U2  C11  H19  single    0.970  0.020  1.090
 5U2  C11  H20  single    0.970  0.020  1.090
 5U2  C14  H21  single    0.930  0.020  1.080
 5U2  C16  H22  single    0.930  0.020  1.080
 5U2  C23  H23  single    0.970  0.020  1.090
 5U2  C23  H24  single    0.970  0.020  1.090
 5U2  O25  H25  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
 5U2  H1   C4   N5   115.63  3.000
 5U2  H1   C4   C3   122.12  3.000
 5U2  N5   C4   C3   122.24  3.000
 5U2  O7   C6   N5   120.11  3.000
 5U2  O7   C6   C1   124.22  3.000
 5U2  N5   C6   C1   115.67  3.000
 5U2  H4   C8   H3   108.93  3.000
 5U2  H4   C8   H2   108.88  3.000
 5U2  H3   C8   H2   108.75  3.000
 5U2  H4   C8   N5   109.11  3.000
 5U2  H3   C8   N5   110.60  3.000
 5U2  H2   C8   N5   110.53  3.000
 5U2  O19  C10  C18  116.31  3.000
 5U2  C18  C10  C14  121.17  3.000
 5U2  O19  C10  C14  122.52  3.000
 5U2  C23  N12  C11  118.33  3.000
 5U2  C11  N12  C24  117.68  3.000
 5U2  C23  N12  C24   90.69  3.000
 5U2  H6   C13  O25  111.97  3.000
 5U2  H6   C13  C23  111.00  3.000
 5U2  O25  C13  C23  119.52  3.000
 5U2  H6   C13  C24  111.17  3.000
 5U2  C23  C13  C24   85.53  3.000
 5U2  O25  C13  C24  115.06  3.000
 5U2  C16  C15  C14  119.74  3.000
 5U2  C16  C15  C3   120.53  3.000
 5U2  C14  C15  C3   119.73  3.000
 5U2  O21  C17  C18  115.65  3.000
 5U2  O21  C17  C16  122.84  3.000
 5U2  C18  C17  C16  121.50  3.000
 5U2  H9   C20  H8   108.82  3.000
 5U2  H9   C20  H7   108.73  3.000
 5U2  H8   C20  H7   108.68  3.000
 5U2  H9   C20  O19  112.07  3.000
 5U2  H8   C20  O19  112.11  3.000
 5U2  H7   C20  O19  106.31  3.000
 5U2  H12  C22  H11  108.80  3.000
 5U2  H12  C22  H10  108.71  3.000
 5U2  H11  C22  H10  108.76  3.000
 5U2  H12  C22  O21  112.09  3.000
 5U2  H11  C22  O21  111.97  3.000
 5U2  H10  C22  O21  106.41  3.000
 5U2  H14  C24  H13  108.95  3.000
 5U2  H14  C24  C13  110.57  3.000
 5U2  H13  C24  C13  118.94  3.000
 5U2  H14  C24  N12  113.21  3.000
 5U2  H13  C24  N12  115.71  3.000
 5U2  C13  C24  N12   88.29  3.000
 5U2  C9   C1   C2   122.92  3.000
 5U2  C9   C1   C6   117.10  3.000
 5U2  C2   C1   C6   119.98  3.000
 5U2  H15  C2   C3   118.86  3.000
 5U2  H15  C2   C1   118.93  3.000
 5U2  C3   C2   C1   122.19  3.000
 5U2  C2   C3   C15  121.79  3.000
 5U2  C2   C3   C4   116.74  3.000
 5U2  C15  C3   C4   121.47  3.000
 5U2  C8   N5   C6   117.10  3.000
 5U2  C8   N5   C4   119.74  3.000
 5U2  C6   N5   C4   123.16  3.000
 5U2  H18  C9   H17  107.99  3.000
 5U2  H18  C9   H16  108.02  3.000
 5U2  H17  C9   H16  106.79  3.000
 5U2  H18  C9   C1   110.93  3.000
 5U2  H17  C9   C1   111.45  3.000
 5U2  H16  C9   C1   111.47  3.000
 5U2  H21  C14  C15  119.19  3.000
 5U2  H21  C14  C10  120.73  3.000
 5U2  C15  C14  C10  120.06  3.000
 5U2  H22  C16  C17  120.77  3.000
 5U2  H22  C16  C15  119.45  3.000
 5U2  C17  C16  C15  119.75  3.000
 5U2  C11  C18  C17  120.00  3.000
 5U2  C17  C18  C10  117.77  3.000
 5U2  C11  C18  C10  122.20  3.000
 5U2  C20  O19  C10  119.34  3.000
 5U2  C22  O21  C17  119.10  3.000
 5U2  H24  C23  H23  109.10  3.000
 5U2  H24  C23  C13  119.18  3.000
 5U2  H23  C23  C13  110.48  3.000
 5U2  H24  C23  N12  115.74  3.000
 5U2  H23  C23  N12  113.20  3.000
 5U2  C13  C23  N12   87.89  3.000
 5U2  H25  O25  C13  108.46  3.000
 5U2  H20  C11  H19  106.22  3.000
 5U2  H20  C11  C18  109.77  3.000
 5U2  H19  C11  C18  110.41  3.000
 5U2  H20  C11  N12  107.83  3.000
 5U2  H19  C11  N12  111.44  3.000
 5U2  C18  C11  N12  111.02  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
 5U2  CONST_01  C16  C15  C14  C10     0.00   0.0  0
 5U2  CONST_02  C16  C17  C18  C10     0.00   0.0  0
 5U2  CONST_03  C18  C10  C14  C15     0.00   0.0  0
 5U2  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 5U2  CONST_05  C14  C10  C18  C17     0.00   0.0  0
 5U2  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 5U2  CONST_07  C3   C15  C14  C10   180.00   0.0  0
 5U2  CONST_08  C3   C15  C16  C17   180.00   0.0  0
 5U2  CONST_09  C1   C6   N5   C4      0.00   0.0  0
 5U2  CONST_10  O21  C17  C18  C10   180.00   0.0  0
 5U2  CONST_11  O19  C10  C14  C15   180.00   0.0  0
 5U2  CONST_12  O21  C17  C16  C15   180.00   0.0  0
 5U2  CONST_13  O19  C10  C18  C17   180.00   0.0  0
 5U2  CONST_14  C14  C10  C18  C11   180.00   0.0  0
 5U2  CONST_15  C16  C17  C18  C11   180.00   0.0  0
 5U2  CONST_16  O7   C6   N5   C4    180.00   0.0  0
 5U2  CONST_17  C1   C6   N5   C8    180.00   0.0  0
 5U2  CONST_18  H21  C14  C15  C3      0.00   0.0  0
 5U2  CONST_19  H22  C16  C15  C3      0.00   0.0  0
 5U2  CONST_20  O7   C6   N5   C8      0.00   0.0  0
 5U2  Var_01    C14  C15  C3   C4   -144.34  30.0  2
 5U2  Var_02    C23  N12  C24  C13    21.18  30.0  1
 5U2  Var_03    N12  C11  C18  C10   102.35  30.0  2
 5U2  Var_04    C18  C11  N12  C24  -179.79  30.0  3
 5U2  Var_05    C14  C10  O19  C20    -0.33  30.0  2
 5U2  Var_06    C18  C17  O21  C22  -178.33  30.0  2
 5U2  Var_07    H2   C8   N5   C4    122.59  30.0  3
 5U2  Var_08    H16  C9   C1   C6    -62.92  30.0  3
 5U2  Var_09    H7   C20  O19  C10   179.77  30.0  3
 5U2  Var_10    H10  C22  O21  C17  -179.50  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
 5U2  chir_01  C13  O25  C24  C23  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
 5U2  plan-1  C4   0.020
 5U2  plan-1  C6   0.020
 5U2  plan-1  C8   0.020
 5U2  plan-1  C15  0.020
 5U2  plan-1  C1   0.020
 5U2  plan-1  C2   0.020
 5U2  plan-1  C3   0.020
 5U2  plan-1  N5   0.020
 5U2  plan-1  O7   0.020
 5U2  plan-1  C9   0.020
 5U2  plan-1  H1   0.020
 5U2  plan-1  H15  0.020
 5U2  plan-2  C10  0.020
 5U2  plan-2  C15  0.020
 5U2  plan-2  C17  0.020
 5U2  plan-2  C3   0.020
 5U2  plan-2  C14  0.020
 5U2  plan-2  C16  0.020
 5U2  plan-2  C18  0.020
 5U2  plan-2  O19  0.020
 5U2  plan-2  O21  0.020
 5U2  plan-2  H21  0.020
 5U2  plan-2  H22  0.020
 5U2  plan-2  C11  0.020

