# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 18:05:53 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  22  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  OC    -1  -0.636   5.0176  -0.6947   0.1136
 HHD  CZ    C  C      0   0.410   3.9878   0.0021  -0.0160
 HHD  O4    O  O      0  -0.610   3.9540   1.2345  -0.2026
 HHD  CE    C  CH2    0  -0.581   2.6499  -0.7545   0.0588
 HHD  CD    C  CH2    0  -0.399   1.3920   0.0968  -0.0077
 HHD  CG    C  CH2    0  -0.435   0.1224  -0.7425   0.0759
 HHD  CB    C  CH1    0   0.042  -1.1708   0.0597  -0.0353
 HHD  O3    O  OH1    0  -0.674  -1.2523   1.0654   0.9628
 HHD  CA    C  CH2    0  -0.582  -2.3981  -0.8406  -0.0033
 HHD  C     C  C      0   0.407  -3.7225  -0.0836  -0.1973
 HHD  O2    O  O      0  -0.620  -3.7560   0.7513  -1.1248
 HHD  O1    O  OC    -1  -0.622  -4.6674  -0.3792   0.5627
 HHD  HE1C  H  HCH2   0   0.216   2.6358  -1.4953  -0.7503
 HHD  HE2C  H  HCH2   0   0.213   2.6441  -1.3485   0.9806
 HHD  HD1C  H  HCH2   0   0.203   1.4012   0.8311   0.8007
 HHD  HD2C  H  HCH2   0   0.198   1.3828   0.6720  -0.9389
 HHD  HG1C  H  HCH2   0   0.209   0.1299  -1.4903  -0.7248
 HHD  HG2C  H  HCH2   0   0.202   0.1153  -1.3129   1.0147
 HHD  HB    H  HCH1   0   0.203  -1.1647   0.6015  -0.9860
 HHD  H3    H  HOH1   0   0.434  -1.2468   0.6275   1.8208
 HHD  HA1C  H  HCH2   0   0.223  -2.3052  -1.5802  -0.8072
 HHD  HA2C  H  HCH2   0   0.199  -2.4111  -1.4100   0.9331

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    deloc   1.250  0.020  1.250
 HHD  CZ  O4    deloc   1.247  0.020  1.247
 HHD  CZ  CE    single  1.539  0.020  1.539
 HHD  CE  CD    single  1.520  0.020  1.520
 HHD  CD  CG    single  1.524  0.020  1.524
 HHD  CG  CB    single  1.526  0.020  1.526
 HHD  CB  O3    single  1.419  0.020  1.419
 HHD  CB  CA    single  1.522  0.020  1.522
 HHD  CA  C     single  1.538  0.020  1.538
 HHD  C   O2    deloc   1.248  0.020  1.248
 HHD  C   O1    deloc   1.248  0.020  1.248
 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

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  CE    CZ  O4    118.01  3.000
 HHD  CE    CZ  O5    115.92  3.000
 HHD  O4    CZ  O5    126.07  3.000
 HHD  HE2C  CE  HE1C  104.72  3.000
 HHD  HE2C  CE  CD    109.61  3.000
 HHD  HE1C  CE  CD    109.59  3.000
 HHD  HE2C  CE  CZ    108.17  3.000
 HHD  HE1C  CE  CZ    107.90  3.000
 HHD  CD    CE  CZ    116.23  3.000
 HHD  HD2C  CD  HD1C  106.05  3.000
 HHD  HD2C  CD  CG    109.21  3.000
 HHD  HD1C  CD  CG    109.67  3.000
 HHD  HD2C  CD  CE    109.78  3.000
 HHD  HD1C  CD  CE    109.70  3.000
 HHD  CG    CD  CE    112.24  3.000
 HHD  HG2C  CG  HG1C  105.68  3.000
 HHD  HG2C  CG  CB    109.25  3.000
 HHD  HG1C  CG  CB    108.14  3.000
 HHD  HG2C  CG  CD    109.77  3.000
 HHD  HG1C  CG  CD    109.27  3.000
 HHD  CB    CG  CD    114.36  3.000
 HHD  HB    CB  CA    108.39  3.000
 HHD  HB    CB  O3    105.09  3.000
 HHD  CA    CB  O3    110.98  3.000
 HHD  HB    CB  CG    108.60  3.000
 HHD  CA    CB  CG    111.77  3.000
 HHD  O3    CB  CG    111.71  3.000
 HHD  H3    O3  CB    107.69  3.000
 HHD  HA2C  CA  HA1C  106.08  3.000
 HHD  HA2C  CA  C     110.69  3.000
 HHD  HA1C  CA  C     108.21  3.000
 HHD  HA2C  CA  CB    109.56  3.000
 HHD  HA1C  CA  CB    108.38  3.000
 HHD  C     CA  CB    113.61  3.000
 HHD  O1    C   O2    126.19  3.000
 HHD  O1    C   CA    117.30  3.000
 HHD  O2    C   CA    116.49  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  Var_01  CD  CE  CZ  O5   176.18  30.0  3
 HHD  Var_02  CG  CD  CE  CZ  -179.92  30.0  3
 HHD  Var_03  CB  CG  CD  CE  -177.97  30.0  3
 HHD  Var_04  O2  C   CA  CB    46.15  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
 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-2  CA  0.020
 HHD  plan-2  C   0.020
 HHD  plan-2  O2  0.020
 HHD  plan-2  O1  0.020

