# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:39:01 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (3S)-3-hydroxyheptanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CCCC(O)=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
 HHD  HHD  '(3S)-3-hydroxyheptanedioic acid'  ligand  24  12  .  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_HHD
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
 HHD  O5    O  OH1   0  -0.598   4.9795  -0.6994   0.0995
 HHD  CZ    C  C     0   0.550   3.9062   0.0802  -0.0044
 HHD  O4    O  O     0  -0.446   3.9770   1.2764  -0.1401
 HHD  CE    C  CH2   0  -0.581   2.6309  -0.7124   0.0677
 HHD  CD    C  CH2   0  -0.417   1.3748   0.1380  -0.0270
 HHD  CG    C  CH2   0  -0.451   0.1199  -0.7222   0.0475
 HHD  CB    C  CH1   0   0.037  -1.1702   0.0798  -0.0801
 HHD  O3    O  OH1   0  -0.664  -1.2881   1.0753   0.9147
 HHD  CA    C  CH2   0  -0.598  -2.3820  -0.8472  -0.0673
 HHD  C     C  C     0   0.551  -3.6731  -0.1053  -0.2822
 HHD  O2    O  O     0  -0.448  -3.8045   0.8421  -1.0171
 HHD  O1    O  OH1   0  -0.592  -4.6807  -0.6314   0.4053
 HHD  H5    H  HOH1  0   0.478   5.7838  -0.1620   0.0453
 HHD  HE1C  H  HCH2  0   0.277   2.6528  -1.4608  -0.7314
 HHD  HE2C  H  HCH2  0   0.276   2.6385  -1.2849   1.0012
 HHD  HD1C  H  HCH2  0   0.232   1.3671   0.8762   0.7766
 HHD  HD2C  H  HCH2  0   0.229   1.3755   0.6970  -0.9668
 HHD  HG1C  H  HCH2  0   0.231   0.1429  -1.4705  -0.7509
 HHD  HG2C  H  HCH2  0   0.225   0.1082  -1.2852   0.9894
 HHD  HB    H  HCH1  0   0.233  -1.1522   0.6190  -1.0316
 HHD  H3    H  HOH1  0   0.443  -1.2334   0.6495   1.7777
 HHD  HA1C  H  HCH2  0   0.289  -2.2915  -1.5799  -0.8759
 HHD  HA2C  H  HCH2  0   0.266  -2.4187  -1.4190   0.8635
 HHD  H1    H  HOH1  0   0.478  -5.4995  -0.1518   0.2075

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
 HHD  O5  CZ    single  1.331  0.020  1.331
 HHD  CZ  O4    double  1.206  0.020  1.206
 HHD  CZ  CE    single  1.503  0.020  1.503
 HHD  CE  CD    single  1.520  0.020  1.520
 HHD  CD  CG    single  1.523  0.020  1.523
 HHD  CG  CB    single  1.524  0.020  1.524
 HHD  CB  O3    single  1.412  0.020  1.412
 HHD  CB  CA    single  1.526  0.020  1.526
 HHD  CA  C     single  1.504  0.020  1.504
 HHD  C   O2    double  1.206  0.020  1.206
 HHD  C   O1    single  1.328  0.020  1.328
 HHD  O5  H5    single  0.850  0.020  0.980
 HHD  CE  HE1C  single  0.970  0.020  1.090
 HHD  CE  HE2C  single  0.970  0.020  1.090
 HHD  CD  HD1C  single  0.970  0.020  1.090
 HHD  CD  HD2C  single  0.970  0.020  1.090
 HHD  CG  HG1C  single  0.970  0.020  1.090
 HHD  CG  HG2C  single  0.970  0.020  1.090
 HHD  CB  HB    single  0.970  0.020  1.090
 HHD  O3  H3    single  0.850  0.020  0.980
 HHD  CA  HA1C  single  0.970  0.020  1.090
 HHD  CA  HA2C  single  0.970  0.020  1.090
 HHD  O1  H1    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
 HHD  H5    O5  CZ    109.89  3.000
 HHD  CE    CZ  O4    125.32  3.000
 HHD  CE    CZ  O5    111.82  3.000
 HHD  O4    CZ  O5    122.86  3.000
 HHD  HE2C  CE  HE1C  105.35  3.000
 HHD  HE2C  CE  CD    110.58  3.000
 HHD  HE1C  CE  CD    110.70  3.000
 HHD  HE2C  CE  CZ    108.09  3.000
 HHD  HE1C  CE  CZ    107.96  3.000
 HHD  CD    CE  CZ    113.77  3.000
 HHD  HD2C  CD  HD1C  106.68  3.000
 HHD  HD2C  CD  CG    109.34  3.000
 HHD  HD1C  CD  CG    109.89  3.000
 HHD  HD2C  CD  CE    109.82  3.000
 HHD  HD1C  CD  CE    109.78  3.000
 HHD  CG    CD  CE    111.21  3.000
 HHD  HG2C  CG  HG1C  105.99  3.000
 HHD  HG2C  CG  CB    109.43  3.000
 HHD  HG1C  CG  CB    108.45  3.000
 HHD  HG2C  CG  CD    109.91  3.000
 HHD  HG1C  CG  CD    109.46  3.000
 HHD  CB    CG  CD    113.33  3.000
 HHD  HB    CB  CA    108.65  3.000
 HHD  HB    CB  O3    105.47  3.000
 HHD  CA    CB  O3    110.86  3.000
 HHD  HB    CB  CG    108.55  3.000
 HHD  CA    CB  CG    110.60  3.000
 HHD  O3    CB  CG    112.49  3.000
 HHD  H3    O3  CB    108.33  3.000
 HHD  HA2C  CA  HA1C  106.35  3.000
 HHD  HA2C  CA  C     110.54  3.000
 HHD  HA1C  CA  C     107.18  3.000
 HHD  HA2C  CA  CB    110.59  3.000
 HHD  HA1C  CA  CB    109.56  3.000
 HHD  C     CA  CB    112.38  3.000
 HHD  O1    C   O2    122.94  3.000
 HHD  O1    C   CA    112.44  3.000
 HHD  O2    C   CA    124.60  3.000
 HHD  H1    O1  C     109.83  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
 HHD  CONST_01  H5  O5  CZ  O4     0.00   0.0  0
 HHD  CONST_02  H1  O1  C   CA   180.00   0.0  0
 HHD  Var_01    CD  CE  CZ  O5   179.19  30.0  3
 HHD  Var_02    CG  CD  CE  CZ   179.82  30.0  3
 HHD  Var_03    CB  CG  CD  CE  -178.48  30.0  3
 HHD  Var_04    O2  C   CA  CB    36.48  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
 HHD  chir_01  CB  CG  O3  CA  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
 HHD  plan-1  O5  0.020
 HHD  plan-1  CZ  0.020
 HHD  plan-1  O4  0.020
 HHD  plan-1  CE  0.020
 HHD  plan-1  H5  0.020
 HHD  plan-2  CA  0.020
 HHD  plan-2  C   0.020
 HHD  plan-2  O2  0.020
 HHD  plan-2  O1  0.020
 HHD  plan-2  H1  0.020

