# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 22:11:37 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (3~{S})-3-ethyl-3-methyl-pyrrolidine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@]1(C)CC(=O)NC1=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
 9V2  9V2  (3~{S})-3-ethyl-3-methyl-pyrrolidine-2,5-dione  ligand  21  10  .  2022-07-24  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_9V2
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
 9V2  O1   O  O     0  -0.423   0.7240  -1.8817   0.7209
 9V2  C4   C  C     0   0.600   0.0716  -0.9365   0.3507
 9V2  N    N  NH1   0  -0.671  -1.1972  -1.0238  -0.1714
 9V2  C1   C  CT    0  -0.237   0.4838   0.5283   0.3406
 9V2  C3   C  CH2   0  -0.409   1.4046   0.7812  -0.8746
 9V2  C7   C  CH3   0  -0.668   2.7529   0.0765  -0.8730
 9V2  C5   C  CH3   0  -0.658   1.1511   0.9209   1.6513
 9V2  C2   C  CH2   0  -0.579  -0.8518   1.2497   0.1081
 9V2  C6   C  C     0   0.543  -1.8000   0.1908  -0.3907
 9V2  O2   O  O     0  -0.429  -2.8986   0.3393  -0.8677
 9V2  H1   H  HNH1  0   0.420  -1.6577  -1.9073  -0.3510
 9V2  H2   H  HCH2  0   0.239   0.8635   0.5189  -1.7893
 9V2  H3   H  HCH2  0   0.246   1.5646   1.8620  -0.9203
 9V2  H4   H  HCH3  0   0.226   3.3531   0.3377  -0.0014
 9V2  H5   H  HCH3  0   0.229   2.6559  -1.0077  -0.9017
 9V2  H6   H  HCH3  0   0.236   3.3191   0.3760  -1.7554
 9V2  H7   H  HCH3  0   0.245   2.0361   0.3205   1.8552
 9V2  H8   H  HCH3  0   0.244   1.4578   1.9669   1.6146
 9V2  H9   H  HCH3  0   0.245   0.4672   0.8027   2.4927
 9V2  H10  H  HCH2  0   0.306  -1.2628   1.6496   1.0396
 9V2  H11  H  HCH2  0   0.294  -0.7902   2.0786  -0.5975

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
 9V2  C7  C3   single  1.521  0.020  1.521
 9V2  C3  C1   single  1.545  0.020  1.545
 9V2  O1  C4   double  1.207  0.020  1.207
 9V2  N   C4   single  1.375  0.020  1.375
 9V2  N   C6   single  1.374  0.020  1.374
 9V2  C4  C1   single  1.522  0.020  1.522
 9V2  C1  C2   single  1.536  0.020  1.536
 9V2  C1  C5   single  1.522  0.020  1.522
 9V2  C6  O2   double  1.207  0.020  1.207
 9V2  C6  C2   single  1.506  0.020  1.506
 9V2  N   H1   single  0.860  0.020  1.020
 9V2  C3  H2   single  0.970  0.020  1.090
 9V2  C3  H3   single  0.970  0.020  1.090
 9V2  C7  H4   single  0.970  0.020  1.090
 9V2  C7  H5   single  0.970  0.020  1.090
 9V2  C7  H6   single  0.970  0.020  1.090
 9V2  C5  H7   single  0.970  0.020  1.090
 9V2  C5  H8   single  0.970  0.020  1.090
 9V2  C5  H9   single  0.970  0.020  1.090
 9V2  C2  H10  single  0.970  0.020  1.090
 9V2  C2  H11  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
 9V2  C1   C4  N    107.97  3.000
 9V2  C1   C4  O1   127.56  3.000
 9V2  N    C4  O1   124.46  3.000
 9V2  H1   N   C6   122.95  3.000
 9V2  H1   N   C4   122.85  3.000
 9V2  C6   N   C4   114.17  3.000
 9V2  C2   C1  C5   112.99  3.000
 9V2  C5   C1  C3   111.94  3.000
 9V2  C2   C1  C3   108.80  3.000
 9V2  C5   C1  C4   111.18  3.000
 9V2  C2   C1  C4   102.57  3.000
 9V2  C3   C1  C4   108.91  3.000
 9V2  H3   C3  H2   105.92  3.000
 9V2  H3   C3  C7   109.16  3.000
 9V2  H2   C3  C7   109.14  3.000
 9V2  H3   C3  C1   106.37  3.000
 9V2  H2   C3  C1   108.86  3.000
 9V2  C7   C3  C1   116.83  3.000
 9V2  H6   C7  H5   107.36  3.000
 9V2  H6   C7  H4   107.18  3.000
 9V2  H5   C7  H4   107.99  3.000
 9V2  H6   C7  C3   109.40  3.000
 9V2  H5   C7  C3   112.47  3.000
 9V2  H4   C7  C3   112.20  3.000
 9V2  H9   C5  H8   107.83  3.000
 9V2  H9   C5  H7   107.78  3.000
 9V2  H8   C5  H7   107.86  3.000
 9V2  H9   C5  C1   111.18  3.000
 9V2  H8   C5  C1   109.98  3.000
 9V2  H7   C5  C1   112.05  3.000
 9V2  H11  C2  H10  107.12  3.000
 9V2  H11  C2  C6   110.84  3.000
 9V2  H10  C2  C6   107.60  3.000
 9V2  H11  C2  C1   113.95  3.000
 9V2  H10  C2  C1   111.69  3.000
 9V2  C6   C2  C1   105.51  3.000
 9V2  O2   C6  C2   128.13  3.000
 9V2  C2   C6  N    107.01  3.000
 9V2  O2   C6  N    124.84  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
 9V2  CONST_01  C6  N   C4  C1    0.00   0.0  0
 9V2  CONST_02  C6  N   C4  O1  180.00   0.0  0
 9V2  CONST_03  H1  N   C4  C1  180.00   0.0  0
 9V2  Var_01    C2  C6  N   C4   -3.16  30.0  1
 9V2  Var_02    C1  C2  C6  N    12.55  30.0  1
 9V2  Var_03    H4  C7  C3  C1  -58.48  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
 9V2  chir_01  C1  C4  C2  C5  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
 9V2  plan-1  N   0.020
 9V2  plan-1  C2  0.020
 9V2  plan-1  C6  0.020
 9V2  plan-1  O2  0.020
 9V2  plan-2  O1  0.020
 9V2  plan-2  C4  0.020
 9V2  plan-2  N   0.020
 9V2  plan-2  C1  0.020
 9V2  plan-2  C6  0.020
 9V2  plan-2  H1  0.020

