# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 00:35:42 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: (3R)-3-(4-methoxyphenyl)piperidine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@H]2CCC(=O)NC2=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
 9FT  9FT  "(3R)-3-(4-methoxyphenyl)piperidine-2,6-dione"
  ligand  29  16  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9FT
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
 9FT  C2   C  C     0   0.547  22.7455  16.3399   -7.3818
 9FT  C3   C  C     0   0.591  25.0555  16.7647   -8.1960
 9FT  C5   C  CH2   0  -0.439  23.5923  18.6981   -7.5523
 9FT  C6   C  CR6   0   0.187  25.9819  19.0846   -8.2921
 9FT  C7   C  CR16  0  -0.317  27.0472  19.6451   -7.6058
 9FT  C9   C  CR6   0   0.369  27.7492  20.8707   -9.5523
 9FT  C10  C  CR16  0  -0.328  26.6781  20.3129  -10.2565
 9FT  C11  C  CR16  0  -0.278  25.8130  19.4363   -9.6326
 9FT  C1   C  CH2   0  -0.591  22.6877  17.7282   -6.8127
 9FT  C12  C  CH3   0  -0.434  29.6249  22.3212   -9.5700
 9FT  C4   C  CH1   0  -0.529  25.0203  18.1576   -7.6006
 9FT  C8   C  CR16  0  -0.366  27.9303  20.5313   -8.2156
 9FT  N1   N  NH1   0  -0.688  23.9196  16.0009   -8.0237
 9FT  O1   O  O     0  -0.428  21.8489  15.5327   -7.2910
 9FT  O2   O  O     0  -0.413  26.0132  16.3022   -8.7703
 9FT  O3   O  O2    0  -0.467  28.5405  21.7139  -10.2417
 9FT  H1   H  HCH2  0   0.272  23.5916  19.6631   -7.0470
 9FT  H2   H  HCH2  0   0.255  23.2159  18.8680   -8.5642
 9FT  H3   H  HCR6  0   0.254  27.2045  19.3921   -6.5638
 9FT  H4   H  HCR6  0   0.260  26.5329  20.5748  -11.2974
 9FT  H5   H  HCR6  0   0.253  24.9915  19.0222  -10.2062
 9FT  H6   H  HCH2  0   0.290  21.6490  18.0573   -6.8175
 9FT  H7   H  HCH2  0   0.287  22.9935  17.6603   -5.7627
 9FT  H8   H  HCH3  0   0.258  30.1108  22.9735  -10.2915
 9FT  H9   H  HCH3  0   0.227  29.2939  22.9226   -8.7192
 9FT  H10  H  HCH3  0   0.227  30.3519  21.5847   -9.2174
 9FT  H11  H  HCH1  0   0.318  25.3567  18.0293   -6.5623
 9FT  H12  H  HCR6  0   0.276  28.7453  20.9388   -7.6328
 9FT  H13  H  HNH1  0   0.410  23.9636  15.0593   -8.3987

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
 9FT  C10  C9   aromatic  1.398  0.020  1.398
 9FT  C10  C11  aromatic  1.381  0.020  1.381
 9FT  O3   C9   single    1.346  0.020  1.346
 9FT  O3   C12  single    1.413  0.020  1.413
 9FT  C9   C8   aromatic  1.391  0.020  1.391
 9FT  C11  C6   aromatic  1.396  0.020  1.396
 9FT  O2   C3   double    1.209  0.020  1.209
 9FT  C6   C7   aromatic  1.386  0.020  1.386
 9FT  C6   C4   single    1.504  0.020  1.504
 9FT  C3   N1   single    1.380  0.020  1.380
 9FT  C3   C4   single    1.515  0.020  1.515
 9FT  N1   C2   single    1.380  0.020  1.380
 9FT  C8   C7   aromatic  1.392  0.020  1.392
 9FT  C4   C5   single    1.528  0.020  1.528
 9FT  C2   O1   double    1.210  0.020  1.210
 9FT  C2   C1   single    1.502  0.020  1.502
 9FT  C5   C1   single    1.519  0.020  1.519
 9FT  C5   H1   single    0.970  0.020  1.090
 9FT  C5   H2   single    0.970  0.020  1.090
 9FT  C7   H3   single    0.930  0.020  1.080
 9FT  C10  H4   single    0.930  0.020  1.080
 9FT  C11  H5   single    0.930  0.020  1.080
 9FT  C1   H6   single    0.970  0.020  1.090
 9FT  C1   H7   single    0.970  0.020  1.090
 9FT  C12  H8   single    0.970  0.020  1.090
 9FT  C12  H9   single    0.970  0.020  1.090
 9FT  C12  H10  single    0.970  0.020  1.090
 9FT  C4   H11  single    0.970  0.020  1.090
 9FT  C8   H12  single    0.930  0.020  1.080
 9FT  N1   H13  single    0.860  0.020  1.020

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
 9FT  O1   C2   N1   120.09  3.000
 9FT  O1   C2   C1   124.05  3.000
 9FT  N1   C2   C1   115.85  3.000
 9FT  O2   C3   N1   119.99  3.000
 9FT  N1   C3   C4   116.15  3.000
 9FT  O2   C3   C4   123.84  3.000
 9FT  H2   C5   H1   106.95  3.000
 9FT  H2   C5   C4   110.35  3.000
 9FT  H1   C5   C4   109.19  3.000
 9FT  H2   C5   C1   110.18  3.000
 9FT  H1   C5   C1   109.85  3.000
 9FT  C4   C5   C1   110.26  3.000
 9FT  C4   C6   C11  121.29  3.000
 9FT  C4   C6   C7   120.87  3.000
 9FT  C11  C6   C7   117.82  3.000
 9FT  H3   C7   C8   118.54  3.000
 9FT  H3   C7   C6   119.56  3.000
 9FT  C8   C7   C6   121.90  3.000
 9FT  O3   C9   C8   124.64  3.000
 9FT  C8   C9   C10  119.11  3.000
 9FT  O3   C9   C10  116.25  3.000
 9FT  H4   C10  C11  120.25  3.000
 9FT  H4   C10  C9   119.37  3.000
 9FT  C11  C10  C9   120.38  3.000
 9FT  H5   C11  C10  118.57  3.000
 9FT  H5   C11  C6   120.23  3.000
 9FT  C10  C11  C6   121.20  3.000
 9FT  H7   C1   H6   106.80  3.000
 9FT  H7   C1   C5   109.88  3.000
 9FT  H6   C1   C5   111.89  3.000
 9FT  H7   C1   C2   107.17  3.000
 9FT  H6   C1   C2   108.31  3.000
 9FT  C5   C1   C2   112.52  3.000
 9FT  H10  C12  H9   108.72  3.000
 9FT  H10  C12  H8   108.73  3.000
 9FT  H9   C12  H8   108.77  3.000
 9FT  H10  C12  O3   111.97  3.000
 9FT  H9   C12  O3   111.97  3.000
 9FT  H8   C12  O3   106.59  3.000
 9FT  H11  C4   C6   108.10  3.000
 9FT  H11  C4   C5   107.31  3.000
 9FT  C6   C4   C5   113.21  3.000
 9FT  H11  C4   C3   104.88  3.000
 9FT  C5   C4   C3   111.06  3.000
 9FT  C6   C4   C3   111.78  3.000
 9FT  H12  C8   C9   121.60  3.000
 9FT  H12  C8   C7   118.81  3.000
 9FT  C9   C8   C7   119.59  3.000
 9FT  H13  N1   C3   115.59  3.000
 9FT  H13  N1   C2   115.89  3.000
 9FT  C3   N1   C2   128.49  3.000
 9FT  C12  O3   C9   118.49  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
 9FT  CONST_01  C9   C10  C11  C6      0.00   0.0  0
 9FT  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 9FT  CONST_03  C10  C11  C6   C7      0.00   0.0  0
 9FT  CONST_04  C10  C9   C8   C7      0.00   0.0  0
 9FT  CONST_05  C8   C9   C10  C11     0.00   0.0  0
 9FT  CONST_06  C8   C7   C6   C11     0.00   0.0  0
 9FT  CONST_07  C4   C6   C11  C10   180.00   0.0  0
 9FT  CONST_08  C8   C7   C6   C4    180.00   0.0  0
 9FT  CONST_09  C1   C2   N1   C3      0.00   0.0  0
 9FT  CONST_10  O3   C9   C8   C7    180.00   0.0  0
 9FT  CONST_11  O3   C9   C10  C11   180.00   0.0  0
 9FT  CONST_12  O1   C2   N1   C3    180.00   0.0  0
 9FT  CONST_13  H4   C10  C11  C6    180.00   0.0  0
 9FT  CONST_14  H12  C8   C7   C6    180.00   0.0  0
 9FT  CONST_15  H5   C11  C6   C7    180.00   0.0  0
 9FT  CONST_16  H5   C11  C10  C9    180.00   0.0  0
 9FT  CONST_17  H3   C7   C8   C9    180.00   0.0  0
 9FT  CONST_18  H12  C8   C9   C10   180.00   0.0  0
 9FT  CONST_19  H3   C7   C6   C11   180.00   0.0  0
 9FT  CONST_20  H5   C11  C6   C4      0.00   0.0  0
 9FT  CONST_21  H3   C7   C6   C4      0.00   0.0  0
 9FT  CONST_22  H4   C10  C9   C8    180.00   0.0  0
 9FT  CONST_23  H13  N1   C2   C1    180.00   0.0  0
 9FT  CONST_24  H13  N1   C2   O1      0.00   0.0  0
 9FT  Var_01    C4   C3   N1   C2      0.29  30.0  1
 9FT  Var_02    C4   C5   C1   C2    -54.14  30.0  1
 9FT  Var_03    N1   C2   C1   C5     26.60  30.0  1
 9FT  Var_04    O2   C3   N1   C2    178.79  30.0  1
 9FT  Var_05    O1   C2   C1   C5   -154.31  30.0  1
 9FT  Var_06    H1   C5   C1   C2   -174.51  30.0  1
 9FT  Var_07    H2   C5   C1   C2     67.91  30.0  1
 9FT  Var_08    H13  N1   C3   C4   -178.05  30.0  1
 9FT  Var_09    H6   C1   C5   C4   -176.36  30.0  1
 9FT  Var_10    H7   C1   C5   C4     65.19  30.0  1
 9FT  Var_11    H6   C1   C2   N1    150.82  30.0  1
 9FT  Var_12    H7   C1   C2   N1    -94.29  30.0  1
 9FT  Var_13    C12  O3   C9   C10   179.01  30.0  2
 9FT  Var_14    C8   C9   O3   C12    -0.98  30.0  2
 9FT  Var_15    H6   C1   C2   O1    -30.09  30.0  1
 9FT  Var_16    H7   C1   C2   O1     84.80  30.0  1
 9FT  Var_17    H13  N1   C3   O2      0.45  30.0  1
 9FT  Var_18    H8   C12  O3   C9   -178.59  30.0  3
 9FT  Var_19    H9   C12  O3   C9    -59.77  30.0  3
 9FT  Var_20    H10  C12  O3   C9     62.63  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
 9FT  chir_01  C4  C6  C3  C5  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
 9FT  plan-1  C6   0.020
 9FT  plan-1  C7   0.020
 9FT  plan-1  C9   0.020
 9FT  plan-1  C10  0.020
 9FT  plan-1  C11  0.020
 9FT  plan-1  C4   0.020
 9FT  plan-1  C8   0.020
 9FT  plan-1  O3   0.020
 9FT  plan-1  H3   0.020
 9FT  plan-1  H4   0.020
 9FT  plan-1  H5   0.020
 9FT  plan-1  H12  0.020
 9FT  plan-2  C2   0.020
 9FT  plan-2  C3   0.020
 9FT  plan-2  C1   0.020
 9FT  plan-2  N1   0.020
 9FT  plan-2  O1   0.020
 9FT  plan-2  H13  0.020
 9FT  plan-3  C3   0.020
 9FT  plan-3  C4   0.020
 9FT  plan-3  N1   0.020
 9FT  plan-3  O2   0.020

