# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:58:41 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: ethyl (2~{R})-2-oxidanylpropanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)[C@@H](C)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
 9YL  9YL  'ethyl (2~{R})-2-oxidanylpropanoate'  ligand  18  8  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9YL
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
 9YL  C1   C  C     0   0.555  -0.2016   0.4468   0.0309
 9YL  O2   O  OH1   0  -0.651  -2.5564   0.4762  -0.4545
 9YL  C3   C  CH3   0  -0.693  -1.6223  -1.5401   0.5529
 9YL  C7   C  CH2   0  -0.181   2.1617   0.3741   0.1901
 9YL  C8   C  CH3   0  -0.688   3.2669  -0.5804  -0.1892
 9YL  C2   C  CH1   0  -0.075  -1.4300  -0.3505  -0.3858
 9YL  O1   O  O     0  -0.451  -0.2473   1.5407   0.5352
 9YL  OXT  O  O2    0  -0.453   0.9131  -0.2229  -0.2010
 9YL  H1   H  HOH1  0   0.447  -2.7302   0.8395   0.4208
 9YL  H2   H  HCH3  0   0.236  -1.7557  -1.2094   1.5848
 9YL  H3   H  HCH3  0   0.253  -2.5090  -2.1000   0.2576
 9YL  H4   H  HCH3  0   0.243  -0.7705  -2.2172   0.5202
 9YL  H5   H  HCH2  0   0.237   2.1560   0.5589   1.2660
 9YL  H6   H  HCH2  0   0.237   2.2839   1.3335  -0.3164
 9YL  H7   H  HCH3  0   0.236   3.1609  -1.5402   0.3166
 9YL  H8   H  HCH3  0   0.237   3.2969  -0.7530  -1.2650
 9YL  H9   H  HCH3  0   0.240   4.2242  -0.1514   0.1059
 9YL  H10  H  HCH1  0   0.269  -1.2612  -0.7261  -1.3987

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
 9YL  C8   C7   single  1.509  0.020  1.509
 9YL  C7   OXT  single  1.438  0.020  1.438
 9YL  O1   C1   double  1.205  0.020  1.205
 9YL  OXT  C1   single  1.321  0.020  1.321
 9YL  C1   C2   single  1.523  0.020  1.523
 9YL  C2   O2   single  1.399  0.020  1.399
 9YL  C2   C3   single  1.527  0.020  1.527
 9YL  O2   H1   single  0.850  0.020  0.980
 9YL  C3   H2   single  0.970  0.020  1.090
 9YL  C3   H3   single  0.970  0.020  1.090
 9YL  C3   H4   single  0.970  0.020  1.090
 9YL  C7   H5   single  0.970  0.020  1.090
 9YL  C7   H6   single  0.970  0.020  1.090
 9YL  C8   H7   single  0.970  0.020  1.090
 9YL  C8   H8   single  0.970  0.020  1.090
 9YL  C8   H9   single  0.970  0.020  1.090
 9YL  C2   H10  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
 9YL  OXT  C1   O1   124.44  3.000
 9YL  OXT  C1   C2   111.54  3.000
 9YL  O1   C1   C2   123.99  3.000
 9YL  H1   O2   C2   108.88  3.000
 9YL  H4   C3   H3   108.00  3.000
 9YL  H4   C3   H2   108.20  3.000
 9YL  H3   C3   H2   108.21  3.000
 9YL  H4   C3   C2   111.56  3.000
 9YL  H3   C3   C2   109.64  3.000
 9YL  H2   C3   C2   111.12  3.000
 9YL  H6   C7   H5   108.01  3.000
 9YL  H6   C7   OXT  109.63  3.000
 9YL  H5   C7   OXT  109.50  3.000
 9YL  H6   C7   C8   110.94  3.000
 9YL  H5   C7   C8   111.01  3.000
 9YL  OXT  C7   C8   107.75  3.000
 9YL  H9   C8   H8   107.79  3.000
 9YL  H9   C8   H7   107.84  3.000
 9YL  H8   C8   H7   108.74  3.000
 9YL  H9   C8   C7   109.05  3.000
 9YL  H8   C8   C7   111.62  3.000
 9YL  H7   C8   C7   111.66  3.000
 9YL  H10  C2   C3   108.74  3.000
 9YL  H10  C2   O2   106.37  3.000
 9YL  C3   C2   O2   112.89  3.000
 9YL  H10  C2   C1   107.99  3.000
 9YL  C3   C2   C1   109.95  3.000
 9YL  O2   C2   C1   110.71  3.000
 9YL  C7   OXT  C1   118.32  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
 9YL  Var_01  C8  C7  OXT  C1   -179.68  30.0  1
 9YL  Var_02  O1  C1  OXT  C7      1.05  30.0  3
 9YL  Var_03  H7  C8  C7   OXT   -60.47  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
 9YL  chir_01  C2  C1  O2  C3  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
 9YL  plan-1  C1   0.020
 9YL  plan-1  C2   0.020
 9YL  plan-1  O1   0.020
 9YL  plan-1  OXT  0.020

