# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 23:43:06 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: 5-hydroxypentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCCCC(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
 SHO  SHO  '5-hydroxypentanoic acid  '  ligand  18  8  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SHO
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
 SHO  CA    C  CH2   0  -0.576  -0.6260  -0.0026  -0.9283
 SHO  CB    C  CH2   0  -0.430   0.2976  -0.0069   0.2785
 SHO  CG    C  CH2   0  -0.456  -0.4885   0.0003   1.5838
 SHO  CD    C  CH2   0  -0.137   0.4294  -0.0019   2.7903
 SHO  C     C  C     0   0.550   0.0969  -0.0246  -2.2463
 SHO  OXT   O  OH1   0  -0.598  -0.7489  -0.0163  -3.2732
 SHO  OE1   O  OH1   0  -0.675  -0.3532  -0.0021   3.9652
 SHO  O     O  O     0  -0.446   1.2947  -0.0470  -2.3849
 SHO  HAC1  H  HCH2  0   0.277  -1.3021  -0.8631  -0.8970
 SHO  HAC2  H  HCH2  0   0.277  -1.2754   0.8785  -0.9115
 SHO  HBC1  H  HCH2  0   0.230   0.9563   0.8650   0.2427
 SHO  HBC2  H  HCH2  0   0.230   0.9456  -0.8867   0.2458
 SHO  HGC1  H  HCH2  0   0.223  -1.1447  -0.8752   1.6244
 SHO  HGC2  H  HCH2  0   0.223  -1.1355   0.8827   1.6204
 SHO  HDC1  H  HCH2  0   0.189   1.0849   0.8784   2.7455
 SHO  HDC2  H  HCH2  0   0.188   1.0829  -0.8834   2.7439
 SHO  H     H  HOH1  0   0.478  -0.2558  -0.0303  -4.1069
 SHO  HE1   H  HOH1  0   0.452   0.2396   0.0034   4.7216

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
 SHO  CA   CB    single  1.520  0.020  1.520
 SHO  CA   C     single  1.503  0.020  1.503
 SHO  CA   HAC1  single  0.970  0.020  1.090
 SHO  CA   HAC2  single  0.970  0.020  1.090
 SHO  CB   CG    single  1.524  0.020  1.524
 SHO  CB   HBC1  single  0.970  0.020  1.090
 SHO  CB   HBC2  single  0.970  0.020  1.090
 SHO  CG   CD    single  1.516  0.020  1.516
 SHO  CG   HGC1  single  0.970  0.020  1.090
 SHO  CG   HGC2  single  0.970  0.020  1.090
 SHO  CD   OE1   single  1.412  0.020  1.412
 SHO  CD   HDC1  single  0.970  0.020  1.090
 SHO  CD   HDC2  single  0.970  0.020  1.090
 SHO  C    OXT   single  1.330  0.020  1.330
 SHO  C    O     double  1.206  0.020  1.206
 SHO  OXT  H     single  0.850  0.020  0.980
 SHO  OE1  HE1   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
 SHO  HAC2  CA   HAC1  105.41  3.000
 SHO  HAC2  CA   C     108.09  3.000
 SHO  HAC1  CA   C     108.09  3.000
 SHO  HAC2  CA   CB    110.52  3.000
 SHO  HAC1  CA   CB    110.51  3.000
 SHO  C     CA   CB    113.83  3.000
 SHO  HBC2  CB   HBC1  106.48  3.000
 SHO  HBC2  CB   CG    109.59  3.000
 SHO  HBC1  CB   CG    109.58  3.000
 SHO  HBC2  CB   CA    109.80  3.000
 SHO  HBC1  CB   CA    109.75  3.000
 SHO  CG    CB   CA    111.52  3.000
 SHO  HGC2  CG   HGC1  106.80  3.000
 SHO  HGC2  CG   CD    109.41  3.000
 SHO  HGC1  CG   CD    109.40  3.000
 SHO  HGC2  CG   CB    109.71  3.000
 SHO  HGC1  CG   CB    109.71  3.000
 SHO  CD    CG   CB    111.68  3.000
 SHO  HDC2  CD   HDC1  106.65  3.000
 SHO  HDC2  CD   OE1   111.40  3.000
 SHO  HDC1  CD   OE1   111.40  3.000
 SHO  HDC2  CD   CG    109.13  3.000
 SHO  HDC1  CD   CG    109.13  3.000
 SHO  OE1   CD   CG    109.07  3.000
 SHO  O     C    OXT   122.88  3.000
 SHO  O     C    CA    125.35  3.000
 SHO  OXT   C    CA    111.77  3.000
 SHO  H     OXT  C     109.92  3.000
 SHO  HE1   OE1  CD    108.24  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
 SHO  CONST_01  H    OXT  C   CA   180.00   0.0  0
 SHO  Var_01    CD   CG   CB  CA  -179.92  30.0  3
 SHO  Var_02    OXT  C    CA  CB  -179.82  30.0  3
 SHO  Var_03    OE1  CD   CG  CB  -179.70  30.0  3
 SHO  Var_04    C    CA   CB  CG  -179.37  30.0  1

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
 SHO  plan-1  CA   0.020
 SHO  plan-1  C    0.020
 SHO  plan-1  OXT  0.020
 SHO  plan-1  O    0.020
 SHO  plan-1  H    0.020

