# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:31:37 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: [(2S)-3-methyl-5-oxo-2,5-dihydrofuran-2-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=O)O[C@H]1CC(O)=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
 3ML  3ML  '[(2S)-3-methyl-5-oxo-2,5-dihydrofuran-2-yl]acetic acid'  ligand  18  11  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3ML
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
 3ML  CAA   C  CH3    0  -0.739  -1.3492   2.6953   0.1894
 3ML  CAI   C  CR5    0   0.164  -1.3398   1.2146   0.1447
 3ML  CAE   C  CR15   0  -0.468  -2.3257   0.3771  -0.1820
 3ML  CAJ   C  CR5    0   0.545  -1.8275  -0.9916  -0.0630
 3ML  OAC   O  O      0  -0.458  -2.3912  -2.0396  -0.2599
 3ML  OAG   O  O      0  -0.460  -0.5468  -0.9451   0.3369
 3ML  CAK   C  CR15   0  -0.013  -0.1197   0.4128   0.4793
 3ML  CAF   C  CH2    0  -0.606   1.0624   0.6852  -0.4286
 3ML  CAH   C  C      0   0.428   2.3216  -0.1370  -0.0812
 3ML  OAD   O  O      0  -0.603   2.4594  -0.4808   1.1077
 3ML  OAB   O  OC    -1  -0.613   3.1091  -0.3500  -1.0218
 3ML  HAA   H  HCH3   0   0.264  -0.6389   3.1061  -0.5311
 3ML  HAAA  H  HCH3   0   0.263  -2.3349   3.0974  -0.0338
 3ML  HAAB  H  HCH3   0   0.262  -1.0396   3.0525   1.1733
 3ML  HAE   H  HCR5   0   0.275  -3.3333   0.6224  -0.4820
 3ML  HAK   H  HCR5   0   0.268   0.1703   0.5695   1.5229
 3ML  HAF   H  HCH2   0   0.237   0.7733   0.5327  -1.4722
 3ML  HAFA  H  HCH2   0   0.254   1.3242   1.7450  -0.3352

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
 3ML  CAA  CAI   single  1.481  0.020  1.481
 3ML  CAA  HAA   single  0.970  0.020  1.090
 3ML  CAA  HAAA  single  0.970  0.020  1.090
 3ML  CAA  HAAB  single  0.970  0.020  1.090
 3ML  CAI  CAK   single  1.498  0.020  1.498
 3ML  CAI  CAE   double  1.334  0.020  1.334
 3ML  CAE  CAJ   single  1.461  0.020  1.461
 3ML  CAE  HAE   single  0.930  0.020  1.080
 3ML  OAG  CAJ   single  1.343  0.020  1.343
 3ML  CAJ  OAC   double  1.206  0.020  1.206
 3ML  CAK  OAG   single  1.431  0.020  1.431
 3ML  CAF  CAK   single  1.515  0.020  1.515
 3ML  CAK  HAK   single  0.970  0.020  1.090
 3ML  CAF  CAH   single  1.543  0.020  1.543
 3ML  CAF  HAF   single  0.970  0.020  1.090
 3ML  CAF  HAFA  single  0.970  0.020  1.090
 3ML  OAD  CAH   deloc   1.245  0.020  1.245
 3ML  CAH  OAB   deloc   1.245  0.020  1.245

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
 3ML  HAAB  CAA  HAAA  108.72  3.000
 3ML  HAAB  CAA  HAA   106.69  3.000
 3ML  HAAA  CAA  HAA   108.36  3.000
 3ML  HAAB  CAA  CAI   110.64  3.000
 3ML  HAAA  CAA  CAI   111.65  3.000
 3ML  HAA   CAA  CAI   110.61  3.000
 3ML  CAK   CAI  CAE   108.70  3.000
 3ML  CAE   CAI  CAA   129.06  3.000
 3ML  CAK   CAI  CAA   122.24  3.000
 3ML  HAE   CAE  CAJ   123.62  3.000
 3ML  HAE   CAE  CAI   127.96  3.000
 3ML  CAJ   CAE  CAI   108.42  3.000
 3ML  OAG   CAJ  OAC   121.64  3.000
 3ML  OAC   CAJ  CAE   129.88  3.000
 3ML  OAG   CAJ  CAE   108.48  3.000
 3ML  CAK   OAG  CAJ   110.32  3.000
 3ML  HAK   CAK  CAF   109.81  3.000
 3ML  HAK   CAK  OAG   108.06  3.000
 3ML  CAF   CAK  OAG   110.11  3.000
 3ML  HAK   CAK  CAI   110.62  3.000
 3ML  CAF   CAK  CAI   113.91  3.000
 3ML  OAG   CAK  CAI   104.05  3.000
 3ML  HAFA  CAF  HAF   106.22  3.000
 3ML  HAFA  CAF  CAH   107.52  3.000
 3ML  HAF   CAF  CAH   110.87  3.000
 3ML  HAFA  CAF  CAK   108.01  3.000
 3ML  HAF   CAF  CAK   109.91  3.000
 3ML  CAH   CAF  CAK   113.94  3.000
 3ML  OAB   CAH  OAD   127.16  3.000
 3ML  OAB   CAH  CAF   115.92  3.000
 3ML  OAD   CAH  CAF   116.89  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
 3ML  Var_01  OAG  CAJ  CAE  CAI     0.10  30.0  1
 3ML  Var_02  CAK  CAI  CAE  CAJ     0.86  30.0  1
 3ML  Var_03  HAA  CAA  CAI  CAE  -117.31  30.0  3
 3ML  Var_04  OAD  CAH  CAF  CAK   -28.12  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
 3ML  chir_01  CAK  CAI  OAG  CAF  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
 3ML  plan-1  CAF  0.020
 3ML  plan-1  CAH  0.020
 3ML  plan-1  OAD  0.020
 3ML  plan-1  OAB  0.020
 3ML  plan-2  CAE  0.020
 3ML  plan-2  CAJ  0.020
 3ML  plan-2  OAC  0.020
 3ML  plan-2  OAG  0.020

