# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 21:55:00 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 5-hydroxy-3-oxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCC(=O)CC(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
 98J  98J  '5-hydroxy-3-oxopentanoic acid'  ligand  16  9  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_98J
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
 98J  C12   C  C      0   0.436  -1.7769  -0.2350   0.6313
 98J  O1    O  O      0  -0.426   0.3808   0.8300  -1.5496
 98J  O14   O  O      0  -0.595  -1.1763   0.6482   1.2716
 98J  O13   O  OC    -1  -0.603  -2.9076  -0.6972   0.8506
 98J  C3    C  CH2    0  -0.713  -1.0176  -0.8339  -0.5857
 98J  C2    C  C      0   0.417   0.2793  -0.1093  -0.7874
 98J  C9    C  CH2    0  -0.588   1.4527  -0.6229   0.0030
 98J  C10   C  CH2    0  -0.138   2.6340   0.3231   0.0461
 98J  O11   O  OH1    0  -0.675   3.6580  -0.2910   0.8007
 98J  H31C  H  HCH2   0   0.255  -0.8436  -1.8977  -0.3982
 98J  H32C  H  HCH2   0   0.259  -1.6412  -0.7549  -1.4790
 98J  H91C  H  HCH2   0   0.261   1.1138  -0.8687   1.0123
 98J  H92C  H  HCH2   0   0.264   1.7471  -1.5766  -0.4530
 98J  H101  H  HCH2   0   0.197   2.9691   0.5463  -0.9730
 98J  H102  H  HCH2   0   0.196   2.3218   1.2744   0.4947
 98J  H11   H  HOH1   0   0.453   4.4140   0.3023   0.8136

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
 98J  O1   C2    double  1.214  0.020  1.214
 98J  C2   C3    single  1.499  0.020  1.499
 98J  C2   C9    single  1.505  0.020  1.505
 98J  C3   C12   single  1.554  0.020  1.554
 98J  C12  O13   deloc   1.241  0.020  1.241
 98J  C12  O14   deloc   1.245  0.020  1.245
 98J  C9   C10   single  1.514  0.020  1.514
 98J  C10  O11   single  1.413  0.020  1.413
 98J  C3   H31C  single  0.970  0.020  1.090
 98J  C3   H32C  single  0.970  0.020  1.090
 98J  C9   H91C  single  0.970  0.020  1.090
 98J  C9   H92C  single  0.970  0.020  1.090
 98J  C10  H101  single  0.970  0.020  1.090
 98J  C10  H102  single  0.970  0.020  1.090
 98J  O11  H11   single  0.850  0.020  0.980

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
 98J  C3    C12  O13   116.10  3.000
 98J  O13   C12  O14   127.79  3.000
 98J  C3    C12  O14   116.11  3.000
 98J  H32C  C3   H31C  107.53  3.000
 98J  H32C  C3   C2    110.42  3.000
 98J  H31C  C3   C2    110.82  3.000
 98J  H32C  C3   C12   109.49  3.000
 98J  H31C  C3   C12   108.55  3.000
 98J  C2    C3   C12   109.98  3.000
 98J  C9    C2   C3    116.03  3.000
 98J  C9    C2   O1    121.91  3.000
 98J  C3    C2   O1    122.06  3.000
 98J  H92C  C9   H91C  105.76  3.000
 98J  H92C  C9   C10   110.21  3.000
 98J  H91C  C9   C10   110.87  3.000
 98J  H92C  C9   C2    106.71  3.000
 98J  H91C  C9   C2    108.67  3.000
 98J  C10   C9   C2    114.20  3.000
 98J  H102  C10  H101  106.90  3.000
 98J  H102  C10  O11   111.40  3.000
 98J  H101  C10  O11   111.33  3.000
 98J  H102  C10  C9    109.35  3.000
 98J  H101  C10  C9    109.84  3.000
 98J  O11   C10  C9    108.01  3.000
 98J  H11   O11  C10   108.00  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
 98J  Var_01  O1   C2   C3   C12   -93.81  30.0  1
 98J  Var_02  C10  C9   C2   O1     15.07  30.0  3
 98J  Var_03  C2   C3   C12  O14    -4.52  30.0  2
 98J  Var_04  O11  C10  C9   C2   -179.28  30.0  3

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
 98J  plan-1  O1   0.020
 98J  plan-1  C3   0.020
 98J  plan-1  C2   0.020
 98J  plan-1  C9   0.020
 98J  plan-2  C12  0.020
 98J  plan-2  O14  0.020
 98J  plan-2  O13  0.020
 98J  plan-2  C3   0.020

