# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 22:30:55 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (3~{R})-3-(4-aminophenyl)-3-ethyl-piperidine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@]1(CCC(=O)NC1=O)c2ccc(N)cc2
#
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
 9UQ  9UQ  (3~{R})-3-(4-aminophenyl)-3-ethyl-piperidine-2,6-dione  ligand  33  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9UQ
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
 9UQ  C12  C  CR16  0  -0.318   3.1138   0.4983  -0.8395
 9UQ  C2   C  CH2   0  -0.478  -1.2712  -0.9246   1.0048
 9UQ  C7   C  C     0   0.551  -3.4139   0.2354   0.3972
 9UQ  C6   C  C     0   0.610  -1.2192   1.0992  -0.4037
 9UQ  C5   C  CH2   0  -0.596  -2.7697  -1.0562   0.8041
 9UQ  C4   C  CR6   0   0.191   0.9208  -0.1118   0.0186
 9UQ  C3   C  CH2   0  -0.422  -0.8495  -1.0757  -1.4966
 9UQ  O2   O  O     0  -0.441  -4.5978   0.4648   0.5129
 9UQ  O1   O  O     0  -0.413  -0.6409   2.0733  -0.8245
 9UQ  N1   N  NH1   0  -0.681  -2.5725   1.1881  -0.1323
 9UQ  C1   C  CT    0  -0.341  -0.5772  -0.2694  -0.1964
 9UQ  C9   C  CR16  0  -0.317   1.5443  -0.4350   1.2207
 9UQ  C11  C  CR16  0  -0.310   2.9130  -0.2974   1.4034
 9UQ  C13  C  CR6   0   0.285   3.7299   0.1767   0.3758
 9UQ  N2   N  NH2   0  -0.860   5.0980   0.2715   0.5290
 9UQ  C10  C  CR16  0  -0.283   1.7487   0.3558  -1.0055
 9UQ  H1   H  HCR6  0   0.252   3.7127   0.8654  -1.6650
 9UQ  H2   H  HCH2  0   0.267  -1.0919  -0.3270   1.9019
 9UQ  H3   H  HCH2  0   0.274  -0.8419  -1.9072   1.2003
 9UQ  H4   H  HCH2  0   0.290  -3.0108  -1.8017   0.0407
 9UQ  H5   H  HCH2  0   0.300  -3.2540  -1.3968   1.7199
 9UQ  H6   H  HCH2  0   0.245  -1.9171  -1.0643  -1.7293
 9UQ  H7   H  HCH2  0   0.254  -0.3707  -0.5663  -2.3336
 9UQ  H8   H  HNH1  0   0.411  -3.0031   2.0759  -0.3664
 9UQ  H9   H  HCH3  0   0.241  -0.4889  -2.9881  -2.4115
 9UQ  H10  H  HCH3  0   0.232   0.6913  -2.5745  -1.1707
 9UQ  H11  H  HCH3  0   0.225  -0.9250  -3.1119  -0.7162
 9UQ  H12  H  HCR6  0   0.249   0.9728  -0.8085   2.0592
 9UQ  H13  H  HCR6  0   0.251   3.3496  -0.5664   2.3581
 9UQ  H14  H  HNH2  0   0.377   5.5559   0.9265  -0.0846
 9UQ  H15  H  HNH2  0   0.377   5.4200   0.3740   1.4784
 9UQ  H16  H  HCR6  0   0.242   1.3362   0.6207  -1.9694
 9UQ  C8   C  CH3   0  -0.665  -0.3643  -2.5157  -1.4372

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
 9UQ  O2   C7   double    1.211  0.020  1.211
 9UQ  C7   C5   single    1.500  0.020  1.500
 9UQ  C7   N1   single    1.377  0.020  1.377
 9UQ  C5   C2   single    1.518  0.020  1.518
 9UQ  N1   C6   single    1.383  0.020  1.383
 9UQ  C2   C1   single    1.534  0.020  1.534
 9UQ  C6   C1   single    1.526  0.020  1.526
 9UQ  C6   O1   double    1.208  0.020  1.208
 9UQ  C1   C3   single    1.554  0.020  1.554
 9UQ  C1   C4   single    1.521  0.020  1.521
 9UQ  C3   C8   single    1.521  0.020  1.521
 9UQ  C4   C10  aromatic  1.397  0.020  1.397
 9UQ  C4   C9   aromatic  1.392  0.020  1.392
 9UQ  C10  C12  aromatic  1.383  0.020  1.383
 9UQ  C9   C11  aromatic  1.388  0.020  1.388
 9UQ  C12  C13  aromatic  1.400  0.020  1.400
 9UQ  C11  C13  aromatic  1.396  0.020  1.396
 9UQ  C13  N2   single    1.380  0.020  1.380
 9UQ  C12  H1   single    0.930  0.020  1.080
 9UQ  C2   H2   single    0.970  0.020  1.090
 9UQ  C2   H3   single    0.970  0.020  1.090
 9UQ  C5   H4   single    0.970  0.020  1.090
 9UQ  C5   H5   single    0.970  0.020  1.090
 9UQ  C3   H6   single    0.970  0.020  1.090
 9UQ  C3   H7   single    0.970  0.020  1.090
 9UQ  N1   H8   single    0.860  0.020  1.020
 9UQ  C8   H9   single    0.970  0.020  1.090
 9UQ  C8   H10  single    0.970  0.020  1.090
 9UQ  C8   H11  single    0.970  0.020  1.090
 9UQ  C9   H12  single    0.930  0.020  1.080
 9UQ  C11  H13  single    0.930  0.020  1.080
 9UQ  N2   H14  single    0.890  0.020  1.040
 9UQ  N2   H15  single    0.890  0.020  1.040
 9UQ  C10  H16  single    0.930  0.020  1.080

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
 9UQ  H1   C12  C10  119.27  3.000
 9UQ  H1   C12  C13  119.73  3.000
 9UQ  C10  C12  C13  121.00  3.000
 9UQ  H3   C2   H2   106.33  3.000
 9UQ  H3   C2   C1   110.32  3.000
 9UQ  H2   C2   C1   109.57  3.000
 9UQ  H3   C2   C5   109.54  3.000
 9UQ  H2   C2   C5   108.54  3.000
 9UQ  C1   C2   C5   112.34  3.000
 9UQ  N1   C7   O2   120.19  3.000
 9UQ  N1   C7   C5   115.97  3.000
 9UQ  O2   C7   C5   123.84  3.000
 9UQ  C1   C6   N1   116.28  3.000
 9UQ  C1   C6   O1   124.67  3.000
 9UQ  N1   C6   O1   119.00  3.000
 9UQ  H5   C5   H4   105.98  3.000
 9UQ  H5   C5   C7   107.83  3.000
 9UQ  H4   C5   C7   107.63  3.000
 9UQ  H5   C5   C2   110.77  3.000
 9UQ  H4   C5   C2   111.66  3.000
 9UQ  C7   C5   C2   112.66  3.000
 9UQ  C10  C4   C9   116.43  3.000
 9UQ  C9   C4   C1   122.61  3.000
 9UQ  C10  C4   C1   120.96  3.000
 9UQ  H7   C3   H6   105.10  3.000
 9UQ  H7   C3   C8   109.41  3.000
 9UQ  H6   C3   C8   109.26  3.000
 9UQ  H7   C3   C1   108.84  3.000
 9UQ  H6   C3   C1   110.12  3.000
 9UQ  C8   C3   C1   113.75  3.000
 9UQ  H8   N1   C6   115.24  3.000
 9UQ  H8   N1   C7   115.79  3.000
 9UQ  C6   N1   C7   128.97  3.000
 9UQ  C3   C1   C4   110.15  3.000
 9UQ  C4   C1   C6   109.91  3.000
 9UQ  C3   C1   C6   106.14  3.000
 9UQ  C4   C1   C2   112.27  3.000
 9UQ  C3   C1   C2   110.75  3.000
 9UQ  C6   C1   C2   107.40  3.000
 9UQ  H12  C9   C11  116.97  3.000
 9UQ  H12  C9   C4   120.87  3.000
 9UQ  C11  C9   C4   122.16  3.000
 9UQ  H13  C11  C13  119.81  3.000
 9UQ  H13  C11  C9   119.26  3.000
 9UQ  C13  C11  C9   120.93  3.000
 9UQ  N2   C13  C11  121.46  3.000
 9UQ  N2   C13  C12  121.12  3.000
 9UQ  C11  C13  C12  117.36  3.000
 9UQ  H15  N2   H14  111.25  3.000
 9UQ  H15  N2   C13  115.36  3.000
 9UQ  H14  N2   C13  115.32  3.000
 9UQ  H16  C10  C4   120.61  3.000
 9UQ  H16  C10  C12  117.28  3.000
 9UQ  C4   C10  C12  122.11  3.000
 9UQ  H11  C8   H10  107.86  3.000
 9UQ  H11  C8   H9   107.18  3.000
 9UQ  H10  C8   H9   107.80  3.000
 9UQ  H11  C8   C3   112.30  3.000
 9UQ  H10  C8   C3   111.68  3.000
 9UQ  H9   C8   C3   109.82  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
 9UQ  CONST_01  C9   C4   C10  C12     0.00   0.0  0
 9UQ  CONST_02  C9   C11  C13  C12     0.00   0.0  0
 9UQ  CONST_03  C13  C12  C10  C4      0.00   0.0  0
 9UQ  CONST_04  C13  C11  C9   C4      0.00   0.0  0
 9UQ  CONST_05  C10  C4   C9   C11     0.00   0.0  0
 9UQ  CONST_06  C10  C12  C13  C11     0.00   0.0  0
 9UQ  CONST_07  C1   C4   C10  C12   180.00   0.0  0
 9UQ  CONST_08  C11  C9   C4   C1    180.00   0.0  0
 9UQ  CONST_09  C5   C7   N1   C6      0.00   0.0  0
 9UQ  CONST_10  N2   C13  C11  C9    180.00   0.0  0
 9UQ  CONST_11  C10  C12  C13  N2    180.00   0.0  0
 9UQ  CONST_12  O2   C7   N1   C6    180.00   0.0  0
 9UQ  CONST_13  H13  C11  C13  C12   180.00   0.0  0
 9UQ  CONST_14  H1   C12  C10  C4    180.00   0.0  0
 9UQ  CONST_15  H16  C10  C4   C1      0.00   0.0  0
 9UQ  CONST_16  H12  C9   C4   C1      0.00   0.0  0
 9UQ  CONST_17  H8   N1   C7   C5    180.00   0.0  0
 9UQ  Var_01    N1   C7   C5   C2     19.67  30.0  1
 9UQ  Var_02    C1   C2   C5   C7    -51.40  30.0  1
 9UQ  Var_03    C1   C6   N1   C7      5.36  30.0  1
 9UQ  Var_04    H9   C8   C3   C1   -173.95  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
 9UQ  chir_01  C1  C6  C2  C4  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
 9UQ  plan-1  C12  0.020
 9UQ  plan-1  C4   0.020
 9UQ  plan-1  C1   0.020
 9UQ  plan-1  C9   0.020
 9UQ  plan-1  C11  0.020
 9UQ  plan-1  C13  0.020
 9UQ  plan-1  N2   0.020
 9UQ  plan-1  C10  0.020
 9UQ  plan-1  H1   0.020
 9UQ  plan-1  H12  0.020
 9UQ  plan-1  H13  0.020
 9UQ  plan-1  H16  0.020
 9UQ  plan-2  C13  0.020
 9UQ  plan-2  N2   0.020
 9UQ  plan-2  H14  0.020
 9UQ  plan-2  H15  0.020
 9UQ  plan-3  C6   0.020
 9UQ  plan-3  O1   0.020
 9UQ  plan-3  N1   0.020
 9UQ  plan-3  C1   0.020
 9UQ  plan-4  C7   0.020
 9UQ  plan-4  C6   0.020
 9UQ  plan-4  C5   0.020
 9UQ  plan-4  O2   0.020
 9UQ  plan-4  N1   0.020
 9UQ  plan-4  H8   0.020

