# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 01:41:06 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: (4S)-nonane-1,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](O)CCCO
#
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
 HND  HND  '(4S)-nonane-1,4-diol     '  ligand  31  11  .  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_HND
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
 HND  C1    C  CH2   0  -0.137  -4.2869  -0.7214   0.1256
 HND  C2    C  CH2   0  -0.451  -3.0990   0.1514  -0.2275
 HND  C3    C  CH2   0  -0.453  -1.7920  -0.4349   0.2903
 HND  C4    C  CH1   0   0.042  -0.5570   0.3630  -0.1177
 HND  C5    C  CH2   0  -0.439   0.7298  -0.3342   0.3140
 HND  C6    C  CH2   0  -0.411   1.9948   0.3147  -0.2320
 HND  C7    C  CH2   0  -0.407   3.2657  -0.4165   0.1814
 HND  C8    C  CH2   0  -0.418   4.5290   0.1915  -0.4153
 HND  C9    C  CH3   0  -0.662   5.7966  -0.5408   0.0018
 HND  O10   O  OH1   0  -0.670  -0.6131   1.6997   0.3469
 HND  O11   O  OH1   0  -0.676  -5.4634  -0.1304  -0.3863
 HND  H2    H  HCH2  0   0.217  -3.0428   0.2569  -1.3159
 HND  H3    H  HCH2  0   0.217  -1.8242  -0.5211   1.3834
 HND  H4    H  HCH1  0   0.210  -0.5506   0.4419  -1.2117
 HND  H5    H  HCH2  0   0.212   0.7713  -0.3737   1.4099
 HND  H5A   H  HCH2  0   0.216   0.6864  -1.3756  -0.0203
 HND  HO10  H  HOH1  0   0.438  -0.6242   1.6753   1.3101
 HND  H6    H  HCH2  0   0.206   1.9365   0.3432  -1.3260
 HND  H6A   H  HCH2  0   0.212   2.0530   1.3563   0.0963
 HND  H7    H  HCH2  0   0.206   3.3460  -0.4198   1.2741
 HND  H7A   H  HCH2  0   0.205   3.1942  -1.4684  -0.1177
 HND  H8    H  HCH2  0   0.210   4.4481   0.1889  -1.5069
 HND  H8A   H  HCH2  0   0.210   4.5997   1.2433  -0.1208
 HND  H9    H  HCH3  0   0.215   5.9271  -0.5183   1.0854
 HND  H9A   H  HCH3  0   0.215   5.7652  -1.5888  -0.3026
 HND  H9B   H  HCH3  0   0.226   6.6843  -0.0935  -0.4470
 HND  H1    H  HCH2  0   0.187  -4.1330  -1.7274  -0.2886
 HND  HO11  H  HOH1  0   0.451  -6.2022  -0.7103  -0.1823
 HND  H2A   H  HCH2  0   0.222  -3.2501   1.1536   0.1816
 HND  H1A   H  HCH2  0   0.186  -4.3411  -0.8370   1.2173
 HND  H3A   H  HCH2  0   0.221  -1.6762  -1.4556  -0.0879

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
 HND  H1    C1   single  0.970  0.020  1.090
 HND  C2    C1   single  1.516  0.020  1.516
 HND  C1    O11  single  1.413  0.020  1.413
 HND  C1    H1A  single  0.970  0.020  1.090
 HND  H2    C2   single  0.970  0.020  1.090
 HND  H2A   C2   single  0.970  0.020  1.090
 HND  C2    C3   single  1.523  0.020  1.523
 HND  C4    C3   single  1.526  0.020  1.526
 HND  C3    H3   single  0.970  0.020  1.090
 HND  C3    H3A  single  0.970  0.020  1.090
 HND  H4    C4   single  0.970  0.020  1.090
 HND  C5    C4   single  1.526  0.020  1.526
 HND  C4    O10  single  1.416  0.020  1.416
 HND  H5A   C5   single  0.970  0.020  1.090
 HND  C6    C5   single  1.523  0.020  1.523
 HND  C5    H5   single  0.970  0.020  1.090
 HND  C7    C6   single  1.523  0.020  1.523
 HND  H6    C6   single  0.970  0.020  1.090
 HND  C6    H6A  single  0.970  0.020  1.090
 HND  H7    C7   single  0.970  0.020  1.090
 HND  H7A   C7   single  0.970  0.020  1.090
 HND  C7    C8   single  1.524  0.020  1.524
 HND  C9    C8   single  1.522  0.020  1.522
 HND  C8    H8   single  0.970  0.020  1.090
 HND  C8    H8A  single  0.970  0.020  1.090
 HND  H9    C9   single  0.970  0.020  1.090
 HND  H9A   C9   single  0.970  0.020  1.090
 HND  C9    H9B  single  0.970  0.020  1.090
 HND  HO10  O10  single  0.850  0.020  0.980
 HND  HO11  O11  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
 HND  H1A   C1   H1   106.57  3.000
 HND  H1A   C1   O11  111.27  3.000
 HND  H1    C1   O11  111.29  3.000
 HND  H1A   C1   C2   109.31  3.000
 HND  O11   C1   C2   109.11  3.000
 HND  H1    C1   C2   109.25  3.000
 HND  H2A   C2   H2   106.91  3.000
 HND  H2A   C2   C3   110.14  3.000
 HND  H2    C2   C3   109.33  3.000
 HND  C3    C2   C1   111.81  3.000
 HND  H2A   C2   C1   109.42  3.000
 HND  H2    C2   C1   109.10  3.000
 HND  H3A   C3   H3   105.91  3.000
 HND  H3A   C3   C4   108.03  3.000
 HND  H3    C3   C4   109.35  3.000
 HND  H3A   C3   C2   109.41  3.000
 HND  H3    C3   C2   110.11  3.000
 HND  C4    C3   C2   113.72  3.000
 HND  H4    C4   O10  105.04  3.000
 HND  O10   C4   C5   111.83  3.000
 HND  H4    C4   C5   108.07  3.000
 HND  O10   C4   C3   111.94  3.000
 HND  C5    C4   C3   111.59  3.000
 HND  H4    C4   C3   108.00  3.000
 HND  H5A   C5   H5   105.80  3.000
 HND  H5    C5   C6   110.00  3.000
 HND  H5A   C5   C6   109.20  3.000
 HND  H5    C5   C4   109.32  3.000
 HND  C6    C5   C4   113.85  3.000
 HND  H5A   C5   C4   108.35  3.000
 HND  H6A   C6   H6   106.13  3.000
 HND  H6A   C6   C7   109.34  3.000
 HND  H6    C6   C7   109.13  3.000
 HND  H6A   C6   C5   110.02  3.000
 HND  H6    C6   C5   108.95  3.000
 HND  C7    C6   C5   113.02  3.000
 HND  H7A   C7   H7   105.91  3.000
 HND  H7A   C7   C8   109.28  3.000
 HND  H7    C7   C8   109.33  3.000
 HND  C8    C7   C6   113.19  3.000
 HND  H7A   C7   C6   109.40  3.000
 HND  H7    C7   C6   109.47  3.000
 HND  H8A   C8   H8   105.99  3.000
 HND  H8A   C8   C9   109.56  3.000
 HND  H8    C8   C9   109.49  3.000
 HND  H8A   C8   C7   109.37  3.000
 HND  H8    C8   C7   109.17  3.000
 HND  C9    C8   C7   113.03  3.000
 HND  H9B   C9   H9A  107.60  3.000
 HND  H9B   C9   H9   107.62  3.000
 HND  H9A   C9   H9   107.45  3.000
 HND  H9B   C9   C8   111.58  3.000
 HND  H9A   C9   C8   111.19  3.000
 HND  H9    C9   C8   111.20  3.000
 HND  HO10  O10  C4   107.73  3.000
 HND  HO11  O11  C1   108.11  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
 HND  Var_01  C4   C3  C2  C1   176.30  30.0  3
 HND  Var_02  O11  C1  C2  C3  -179.68  30.0  3
 HND  Var_03  C7   C6  C5  C4  -178.55  30.0  1
 HND  Var_04  C8   C7  C6  C5   177.34  30.0  1
 HND  Var_05  C9   C8  C7  C6   179.92  30.0  3
 HND  Var_06  H9   C9  C8  C7   -60.47  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
 HND  chir_01  C4  C3  C5  O10  positiv

