# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:45:49 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  17  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  -0.577  -0.6743  -0.0181  -0.9118
 SHO  CB    C  CH2    0  -0.414   0.2649  -0.0035   0.2834
 SHO  CG    C  CH2    0  -0.451  -0.4815   0.0168   1.6127
 SHO  CD    C  CH2    0  -0.136   0.4656   0.0253   2.7958
 SHO  C     C  C      0   0.410  -0.0034  -0.0256  -2.2968
 SHO  OXT   O  OC     0  -0.634  -0.7719  -0.1410  -3.2756
 SHO  OE1   O  OH1    0  -0.677  -0.2819   0.0524   3.9947
 SHO  O     O  O     -1  -0.610   1.2370   0.0917  -2.3452
 SHO  HAC1  H  HCH2   0   0.215  -1.3421  -0.8846  -0.8460
 SHO  HAC2  H  HCH2   0   0.219  -1.3391   0.8532  -0.8638
 SHO  HBC1  H  HCH2   0   0.205   0.9244   0.8669   0.2232
 SHO  HBC2  H  HCH2   0   0.204   0.9200  -0.8795   0.2482
 SHO  HGC1  H  HCH2   0   0.213  -1.1398  -0.8561   1.6808
 SHO  HGC2  H  HCH2   0   0.213  -1.1275   0.9003   1.6586
 SHO  HDC1  H  HCH2   0   0.184   1.1284   0.8980   2.7194
 SHO  HDC2  H  HCH2   0   0.185   1.1100  -0.8630   2.7474
 SHO  HE1   H  HOH1   0   0.450   0.3337   0.0523   4.7326

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  1.539  0.020  1.539
 SHO  CA   HAC1  single  0.970  0.020  1.090
 SHO  CA   HAC2  single  0.970  0.020  1.090
 SHO  CB   CG    single  1.525  0.020  1.525
 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  1.413  0.020  1.413
 SHO  CD   HDC1  single  0.970  0.020  1.090
 SHO  CD   HDC2  single  0.970  0.020  1.090
 SHO  C    OXT   deloc   1.250  0.020  1.250
 SHO  C    O     deloc   1.247  0.020  1.247
 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  104.84  3.000
 SHO  HAC2  CA   C     107.91  3.000
 SHO  HAC1  CA   C     108.41  3.000
 SHO  HAC2  CA   CB    109.41  3.000
 SHO  HAC1  CA   CB    109.69  3.000
 SHO  C     CA   CB    115.99  3.000
 SHO  HBC2  CB   HBC1  105.92  3.000
 SHO  HBC2  CB   CG    109.38  3.000
 SHO  HBC1  CB   CG    109.42  3.000
 SHO  HBC2  CB   CA    109.69  3.000
 SHO  HBC1  CB   CA    109.69  3.000
 SHO  CG    CB   CA    112.53  3.000
 SHO  HGC2  CG   HGC1  106.60  3.000
 SHO  HGC2  CG   CD    109.35  3.000
 SHO  HGC1  CG   CD    109.36  3.000
 SHO  HGC2  CG   CB    109.64  3.000
 SHO  HGC1  CG   CB    109.74  3.000
 SHO  CD    CG   CB    112.01  3.000
 SHO  HDC2  CD   HDC1  106.58  3.000
 SHO  HDC2  CD   OE1   111.30  3.000
 SHO  HDC1  CD   OE1   111.29  3.000
 SHO  HDC2  CD   CG    109.12  3.000
 SHO  HDC1  CD   CG    109.10  3.000
 SHO  OE1   CD   CG    109.38  3.000
 SHO  O     C    OXT   126.16  3.000
 SHO  O     C    CA    117.92  3.000
 SHO  OXT   C    CA    115.92  3.000
 SHO  HE1   OE1  CD    108.21  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  Var_01  CD   CG  CB  CA  179.76  30.0  3
 SHO  Var_02  OXT  C   CA  CB  174.72  30.0  3
 SHO  Var_03  OE1  CD  CG  CB  179.64  30.0  3
 SHO  Var_04  C    CA  CB  CG  179.44  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

