# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 22:43:05 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 5-(2-hydroxyethyl)nonane-1,9-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCCCC(CCO)CCCCO
#
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
 5HD  5HD  5-(2-hydroxyethyl)nonane-1,9-diol  ligand  38  14  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5HD
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
 5HD  C1    C  CH2   0  -0.434  -2.1000  -0.6720   0.1747
 5HD  C2    C  CH2   0  -0.450  -3.5819  -0.6984  -0.1825
 5HD  C3    C  CH2   0  -0.139  -4.2435  -2.0021   0.2167
 5HD  O14   O  OH1   0  -0.676   5.2379  -2.6501   0.0443
 5HD  C13   C  CH2   0  -0.138   4.5848  -1.4248   0.3041
 5HD  C12   C  CH2   0  -0.452   3.1307  -1.5337  -0.1089
 5HD  C11   C  CH2   0  -0.435   2.3636  -0.2462   0.1677
 5HD  C10   C  CH2   0  -0.405   0.9043  -0.3341  -0.2680
 5HD  C6    C  CH1   0  -0.238   0.0152   0.8195   0.2055
 5HD  C7    C  CH2   0  -0.452   0.5659   2.1730  -0.2516
 5HD  C8    C  CH2   0  -0.141  -0.2025   3.3668   0.2871
 5HD  O9    O  OH1   0  -0.678   0.5281   4.5419  -0.0044
 5HD  C5    C  CH2   0  -0.407  -1.4361   0.6331  -0.2514
 5HD  O4    O  OH1   0  -0.676  -5.6040  -1.9680  -0.1623
 5HD  H1    H  HCH2  0   0.212  -1.9807  -0.8074   1.2554
 5HD  H1A   H  HCH2  0   0.219  -1.6054  -1.5256  -0.2969
 5HD  H2    H  HCH2  0   0.218  -4.0928   0.1353   0.3098
 5HD  H2A   H  HCH2  0   0.217  -3.6990  -0.5477  -1.2608
 5HD  H3    H  HCH2  0   0.185  -3.7163  -2.8368  -0.2654
 5HD  H3A   H  HCH2  0   0.188  -4.1340  -2.1463   1.3001
 5HD  HO14  H  HOH1  0   0.451   6.1587  -2.5595   0.3047
 5HD  H13   H  HCH2  0   0.186   4.6385  -1.1622   1.3697
 5HD  H13A  H  HCH2  0   0.187   5.0540  -0.5976  -0.2458
 5HD  H12   H  HCH2  0   0.218   3.0716  -1.7750  -1.1752
 5HD  H12A  H  HCH2  0   0.218   2.6599  -2.3633   0.4282
 5HD  H11   H  HCH2  0   0.212   2.4103  -0.0203   1.2395
 5HD  H11A  H  HCH2  0   0.219   2.8647   0.5827  -0.3397
 5HD  H10   H  HCH2  0   0.207   0.8511  -0.4079  -1.3608
 5HD  H10A  H  HCH2  0   0.225   0.4963  -1.2731   0.1163
 5HD  H6    H  HCH1  0   0.204   0.0264   0.8109   1.3046
 5HD  H7    H  HCH2  0   0.233   1.6026   2.2717   0.0812
 5HD  H7A   H  HCH2  0   0.213   0.5842   2.2089  -1.3472
 5HD  H8    H  HCH2  0   0.194  -1.2041   3.4134  -0.1560
 5HD  H8A   H  HCH2  0   0.184  -0.3425   3.2438   1.3711
 5HD  HO9   H  HOH1  0   0.451  -0.0041   5.2970   0.2608
 5HD  H5    H  HCH2  0   0.207  -1.4797   0.7180  -1.3443
 5HD  H5A   H  HCH2  0   0.222  -2.0415   1.4566   0.1382
 5HD  HO4   H  HOH1  0   0.451  -6.0198  -2.7790   0.1429

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
 5HD  C5   C1    single  1.525  0.020  1.525
 5HD  C1   C2    single  1.525  0.020  1.525
 5HD  C1   H1    single  0.970  0.020  1.090
 5HD  C1   H1A   single  0.970  0.020  1.090
 5HD  C2   C3    single  1.515  0.020  1.515
 5HD  C2   H2    single  0.970  0.020  1.090
 5HD  C2   H2A   single  0.970  0.020  1.090
 5HD  C3   O4    single  1.413  0.020  1.413
 5HD  C3   H3    single  0.970  0.020  1.090
 5HD  C3   H3A   single  0.970  0.020  1.090
 5HD  C13  O14   single  1.413  0.020  1.413
 5HD  O14  HO14  single  0.850  0.020  0.980
 5HD  C13  C12   single  1.516  0.020  1.516
 5HD  C13  H13   single  0.970  0.020  1.090
 5HD  C13  H13A  single  0.970  0.020  1.090
 5HD  C12  C11   single  1.524  0.020  1.524
 5HD  C12  H12   single  0.970  0.020  1.090
 5HD  C12  H12A  single  0.970  0.020  1.090
 5HD  C11  C10   single  1.525  0.020  1.525
 5HD  C11  H11   single  0.970  0.020  1.090
 5HD  C11  H11A  single  0.970  0.020  1.090
 5HD  C6   C10   single  1.531  0.020  1.531
 5HD  C10  H10   single  0.970  0.020  1.090
 5HD  C10  H10A  single  0.970  0.020  1.090
 5HD  C7   C6    single  1.531  0.020  1.531
 5HD  C6   C5    single  1.533  0.020  1.533
 5HD  C6   H6    single  0.970  0.020  1.090
 5HD  C8   C7    single  1.518  0.020  1.518
 5HD  C7   H7    single  0.970  0.020  1.090
 5HD  C7   H7A   single  0.970  0.020  1.090
 5HD  O9   C8    single  1.414  0.020  1.414
 5HD  C8   H8    single  0.970  0.020  1.090
 5HD  C8   H8A   single  0.970  0.020  1.090
 5HD  O9   HO9   single  0.850  0.020  0.980
 5HD  C5   H5    single  0.970  0.020  1.090
 5HD  C5   H5A   single  0.970  0.020  1.090
 5HD  O4   HO4   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
 5HD  H1A   C1   H1   106.24  3.000
 5HD  H1A   C1   C5   110.53  3.000
 5HD  H1    C1   C5   109.51  3.000
 5HD  H1A   C1   C2   108.97  3.000
 5HD  H1    C1   C2   109.56  3.000
 5HD  C5    C1   C2   111.87  3.000
 5HD  H2A   C2   H2   106.75  3.000
 5HD  H2A   C2   C3   109.34  3.000
 5HD  H2    C2   C3   109.45  3.000
 5HD  H2A   C2   C1   109.41  3.000
 5HD  H2    C2   C1   109.57  3.000
 5HD  C3    C2   C1   112.18  3.000
 5HD  H3A   C3   H3   106.57  3.000
 5HD  H3A   C3   O4   111.33  3.000
 5HD  H3    C3   O4   111.26  3.000
 5HD  H3A   C3   C2   109.23  3.000
 5HD  H3    C3   C2   109.18  3.000
 5HD  O4    C3   C2   109.20  3.000
 5HD  HO14  O14  C13  108.14  3.000
 5HD  H13A  C13  H13  106.54  3.000
 5HD  H13A  C13  C12  109.12  3.000
 5HD  H13   C13  C12  109.17  3.000
 5HD  H13A  C13  O14  111.33  3.000
 5HD  H13   C13  O14  111.28  3.000
 5HD  C12   C13  O14  109.34  3.000
 5HD  H12A  C12  H12  106.72  3.000
 5HD  H12A  C12  C11  109.55  3.000
 5HD  H12   C12  C11  109.62  3.000
 5HD  H12A  C12  C13  109.48  3.000
 5HD  H12   C12  C13  109.45  3.000
 5HD  C11   C12  C13  111.89  3.000
 5HD  H11A  C11  H11  106.14  3.000
 5HD  H11A  C11  C10  110.46  3.000
 5HD  H11   C11  C10  109.38  3.000
 5HD  H11A  C11  C12  108.99  3.000
 5HD  H11   C11  C12  109.27  3.000
 5HD  C10   C11  C12  112.40  3.000
 5HD  H10A  C10  H10  105.92  3.000
 5HD  H10A  C10  C6   108.76  3.000
 5HD  H10   C10  C6   109.31  3.000
 5HD  H10A  C10  C11  107.81  3.000
 5HD  H10   C10  C11  109.56  3.000
 5HD  C6    C10  C11  115.07  3.000
 5HD  H6    C6   C5   107.86  3.000
 5HD  H6    C6   C7   107.57  3.000
 5HD  C5    C6   C7   111.04  3.000
 5HD  H6    C6   C10  107.30  3.000
 5HD  C5    C6   C10  111.46  3.000
 5HD  C7    C6   C10  111.39  3.000
 5HD  H7A   C7   H7   106.58  3.000
 5HD  H7A   C7   C8   109.70  3.000
 5HD  H7    C7   C8   107.51  3.000
 5HD  H7A   C7   C6   109.47  3.000
 5HD  H7    C7   C6   109.27  3.000
 5HD  C8    C7   C6   114.02  3.000
 5HD  H8A   C8   H8   106.67  3.000
 5HD  H8A   C8   O9   111.22  3.000
 5HD  H8    C8   O9   110.70  3.000
 5HD  H8A   C8   C7   109.03  3.000
 5HD  H8    C8   C7   110.63  3.000
 5HD  O9    C8   C7   108.59  3.000
 5HD  HO9   O9   C8   108.05  3.000
 5HD  H5A   C5   H5   105.94  3.000
 5HD  H5A   C5   C6   109.04  3.000
 5HD  H5    C5   C6   108.97  3.000
 5HD  H5A   C5   C1   107.69  3.000
 5HD  H5    C5   C1   109.11  3.000
 5HD  C6    C5   C1   115.65  3.000
 5HD  HO4   O4   C3   108.12  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
 5HD  Var_01  C10  C6   C5   C1     56.43  30.0  2
 5HD  Var_02  O4   C3   C2   C1   -179.01  30.0  3
 5HD  Var_03  C6   C5   C1   C2    173.36  30.0  1
 5HD  Var_04  C5   C1   C2   C3    179.02  30.0  1
 5HD  Var_05  C11  C12  C13  O14   179.09  30.0  3
 5HD  Var_06  C10  C11  C12  C13   178.92  30.0  3
 5HD  Var_07  C6   C10  C11  C12   169.42  30.0  3
 5HD  Var_08  C7   C6   C10  C11    56.61  30.0  2
 5HD  Var_09  C8   C7   C6   C10  -174.95  30.0  2
 5HD  Var_10  O9   C8   C7   C6    169.86  30.0  1

