# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 23:16:13 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: (4S)-4-hydroxy-4-methoxybutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H](O)CCC(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
 HMB  HMB  '(4S)-4-hydroxy-4-methoxybutanoic acid'  ligand  18  9  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HMB
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
 HMB  CA   C  CH2    0  -0.584   1.0737  -0.4697  -0.2477
 HMB  CB   C  CH2    0  -0.497  -0.1086   0.4304   0.0706
 HMB  CG   C  CH1    0   0.310  -1.4486  -0.2212  -0.2260
 HMB  C    C  C      0   0.415   2.4604   0.1579  -0.0124
 HMB  OD1  O  OH1    0  -0.664  -1.6423  -1.4186   0.4709
 HMB  OD2  O  O2     0  -0.499  -2.4441   0.7211   0.0646
 HMB  O    O  O      0  -0.608   2.5079   1.3133   0.4532
 HMB  HA1  H  HCH2   0   0.225   1.0200  -1.3900   0.3425
 HMB  HA2  H  HCH2   0   0.221   1.0214  -0.7981  -1.2921
 HMB  HB1  H  HCH2   0   0.220  -0.0850   0.7299   1.1239
 HMB  HB2  H  HCH2   0   0.225  -0.0395   1.3503  -0.5140
 HMB  HG   H  HCH1   0   0.186  -1.5075  -0.5035  -1.2880
 HMB  HE1  H  HCH3   0   0.202  -3.7629   0.1245  -1.4321
 HMB  HE2  H  HCH3   0   0.209  -4.1333  -0.5049   0.1830
 HMB  HE3  H  HCH3   0   0.231  -4.3948   1.2063  -0.1802
 HMB  O4   O  OC    -1  -0.632   3.4384  -0.5607  -0.3078
 HMB  HD1  H  HOH1   0   0.446  -1.4029  -1.2822   1.3955
 HMB  CE   C  CH3    0  -0.407  -3.7371   0.3568  -0.3608

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
 HMB  CA   CB   single  1.520  0.020  1.520
 HMB  CA   C    single  1.540  0.020  1.540
 HMB  CA   HA1  single  0.970  0.020  1.090
 HMB  CA   HA2  single  0.970  0.020  1.090
 HMB  CB   CG   single  1.519  0.020  1.519
 HMB  CB   HB1  single  0.970  0.020  1.090
 HMB  CB   HB2  single  0.970  0.020  1.090
 HMB  CG   OD1  single  1.399  0.020  1.399
 HMB  CG   OD2  single  1.401  0.020  1.401
 HMB  CG   HG   single  0.970  0.020  1.090
 HMB  CE   OD2  single  1.409  0.020  1.409
 HMB  CE   HE1  single  0.970  0.020  1.090
 HMB  CE   HE2  single  0.970  0.020  1.090
 HMB  CE   HE3  single  0.970  0.020  1.090
 HMB  C    O    deloc   1.247  0.020  1.247
 HMB  C    O4   deloc   1.249  0.020  1.249
 HMB  OD1  HD1  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
 HMB  HA2  CA   HA1  105.04  3.000
 HMB  HA2  CA   C    108.09  3.000
 HMB  HA1  CA   C    107.72  3.000
 HMB  HA2  CA   CB   109.87  3.000
 HMB  HA1  CA   CB   110.30  3.000
 HMB  C    CA   CB   115.29  3.000
 HMB  HB2  CB   HB1  106.44  3.000
 HMB  HB2  CB   CG   108.22  3.000
 HMB  HB1  CB   CG   108.91  3.000
 HMB  HB2  CB   CA   109.73  3.000
 HMB  HB1  CB   CA   110.28  3.000
 HMB  CG   CB   CA   113.03  3.000
 HMB  HG   CG   OD2  109.55  3.000
 HMB  HG   CG   OD1  104.70  3.000
 HMB  OD2  CG   OD1  111.96  3.000
 HMB  HG   CG   CB   110.22  3.000
 HMB  OD2  CG   CB   107.32  3.000
 HMB  OD1  CG   CB   113.08  3.000
 HMB  O4   C    O    126.28  3.000
 HMB  O4   C    CA   115.75  3.000
 HMB  O    C    CA   117.97  3.000
 HMB  HD1  OD1  CG   108.79  3.000
 HMB  CE   OD2  CG   114.55  3.000
 HMB  HE3  CE   HE2  108.26  3.000
 HMB  HE3  CE   HE1  108.24  3.000
 HMB  HE2  CE   HE1  108.09  3.000
 HMB  HE3  CE   OD2  107.60  3.000
 HMB  HE2  CE   OD2  112.72  3.000
 HMB  HE1  CE   OD2  111.80  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
 HMB  Var_01  O    C   CA   CB    2.33  30.0  3
 HMB  Var_02  C    CA  CB   CG  177.96  30.0  1
 HMB  Var_03  HE1  CE  OD2  CG  -55.15  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
 HMB  chir_01  CG  CB  OD1  OD2  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
 HMB  plan-1  CA  0.020
 HMB  plan-1  C   0.020
 HMB  plan-1  O   0.020
 HMB  plan-1  O4  0.020

