# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 00:11:23 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: [(2S)-2-methyl-5-oxo-2,5-dihydrofuran-2-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(CC(O)=O)OC(=O)C=C1
#
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
 4ML  4ML  '[(2S)-2-methyl-5-oxo-2,5-dihydrofuran-2-yl]acetic acid'  ligand  18  11  .  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_4ML
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
 4ML  CAF   C  C1     0  -0.137   1.2723  -1.4236  -0.5279
 4ML  CAE   C  C1     0  -0.403   2.3356  -0.6429  -0.6775
 4ML  CAJ   C  C      0   0.526   2.0254   0.6516  -0.0574
 4ML  OAC   O  O      0  -0.452   2.7077   1.6411   0.0358
 4ML  OAH   O  O2     0  -0.454   0.7835   0.5991   0.4382
 4ML  CAK   C  CT     0   0.144   0.1852  -0.6872   0.1949
 4ML  CAA   C  CH3    0  -0.656  -0.1247  -1.3628   1.5243
 4ML  CAG   C  CH2    0  -0.585  -1.0296  -0.5272  -0.7157
 4ML  CAI   C  C      0   0.427  -2.2054   0.3405  -0.2145
 4ML  OAD   O  O      0  -0.589  -2.0952   0.9323   0.8734
 4ML  OAB   O  OC    -1  -0.620  -3.1823   0.3732  -0.9884
 4ML  HAF   H  H      0   0.293   1.1515  -2.4454  -0.8597
 4ML  HAE   H  H      0   0.282   3.2771  -0.8674  -1.1543
 4ML  HAA   H  HCH3   0   0.258  -0.8607  -0.7914   2.0832
 4ML  HAAA  H  HCH3   0   0.233  -0.5259  -2.3604   1.3433
 4ML  HAAB  H  HCH3   0   0.237   0.7790  -1.4706   2.1253
 4ML  HAG   H  HCH2   0   0.251  -0.6964  -0.1187  -1.6761
 4ML  HAGA  H  HCH2   0   0.245  -1.4079  -1.5280  -0.9454

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
 4ML  CAE  CAF   double  1.328  0.020  1.328
 4ML  CAK  CAF   single  1.499  0.020  1.499
 4ML  CAF  HAF   single  0.930  0.020  1.080
 4ML  CAJ  CAE   single  1.468  0.020  1.468
 4ML  CAE  HAE   single  0.930  0.020  1.080
 4ML  OAC  CAJ   double  1.206  0.020  1.206
 4ML  CAJ  OAH   single  1.338  0.020  1.338
 4ML  OAH  CAK   single  1.439  0.020  1.439
 4ML  CAK  CAG   single  1.527  0.020  1.527
 4ML  CAK  CAA   single  1.523  0.020  1.523
 4ML  CAA  HAA   single  0.970  0.020  1.090
 4ML  CAA  HAAA  single  0.970  0.020  1.090
 4ML  CAA  HAAB  single  0.970  0.020  1.090
 4ML  CAI  CAG   single  1.545  0.020  1.545
 4ML  CAG  HAG   single  0.970  0.020  1.090
 4ML  CAG  HAGA  single  0.970  0.020  1.090
 4ML  OAD  CAI   deloc   1.243  0.020  1.243
 4ML  CAI  OAB   deloc   1.247  0.020  1.247

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
 4ML  HAF   CAF  CAK   122.10  3.000
 4ML  HAF   CAF  CAE   127.64  3.000
 4ML  CAK   CAF  CAE   110.26  3.000
 4ML  HAE   CAE  CAJ   123.67  3.000
 4ML  HAE   CAE  CAF   128.78  3.000
 4ML  CAJ   CAE  CAF   107.56  3.000
 4ML  OAH   CAJ  OAC   121.92  3.000
 4ML  OAH   CAJ  CAE   108.53  3.000
 4ML  OAC   CAJ  CAE   129.54  3.000
 4ML  CAK   OAH  CAJ   110.99  3.000
 4ML  CAG   CAK  CAA   113.90  3.000
 4ML  CAA   CAK  OAH   109.48  3.000
 4ML  CAG   CAK  OAH   109.75  3.000
 4ML  CAA   CAK  CAF   110.52  3.000
 4ML  CAG   CAK  CAF   109.94  3.000
 4ML  OAH   CAK  CAF   102.66  3.000
 4ML  HAAB  CAA  HAAA  107.82  3.000
 4ML  HAAB  CAA  HAA   109.25  3.000
 4ML  HAAA  CAA  HAA   108.50  3.000
 4ML  HAAB  CAA  CAK   110.87  3.000
 4ML  HAAA  CAA  CAK   109.62  3.000
 4ML  HAA   CAA  CAK   110.70  3.000
 4ML  HAGA  CAG  HAG   105.20  3.000
 4ML  HAGA  CAG  CAI   108.58  3.000
 4ML  HAG   CAG  CAI   107.85  3.000
 4ML  HAGA  CAG  CAK   107.72  3.000
 4ML  HAG   CAG  CAK   108.66  3.000
 4ML  CAI   CAG  CAK   118.10  3.000
 4ML  OAB   CAI  OAD   126.87  3.000
 4ML  OAB   CAI  CAG   114.19  3.000
 4ML  OAD   CAI  CAG   118.93  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
 4ML  Var_01  OAH  CAJ  CAE  CAF  -0.19  30.0  1
 4ML  Var_02  CAK  CAF  CAE  CAJ   0.40  30.0  1
 4ML  Var_03  OAD  CAI  CAG  CAK   3.75  30.0  2

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
 4ML  chir_01  CAK  OAH  CAF  CAA  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
 4ML  plan-1  CAG  0.020
 4ML  plan-1  CAI  0.020
 4ML  plan-1  OAD  0.020
 4ML  plan-1  OAB  0.020
 4ML  plan-2  CAE  0.020
 4ML  plan-2  CAJ  0.020
 4ML  plan-2  OAC  0.020
 4ML  plan-2  OAH  0.020

