# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 03:45:40 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 3-(2-hydroxyethyl)-2,2-bis(hydroxymethyl)pentane-1,5-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCC(CCO)C(CO)(CO)CO
#
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
 YES  YES  3-(2-hydroxyethyl)-2,2-bis(hydroxymethyl)pentane-1,5-diol  ligand  34  14  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YES
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
 YES  O1   O  OH1   0  -0.671   1.4693  -1.9515   1.5013
 YES  C1   C  CH2   0  -0.144   1.7438  -1.6159   0.1613
 YES  C2   C  CT    0  -0.196   1.1884  -0.2198  -0.1655
 YES  C3   C  CH2   0  -0.123   1.9340   0.8190   0.6831
 YES  O3   O  OH1   0  -0.677   3.3247   0.7167   0.4670
 YES  C4   C  CH2   0  -0.127   1.4819  -0.0276  -1.6580
 YES  O4   O  OH1   0  -0.665   1.1902   1.2839  -2.0787
 YES  C5   C  CH1   0  -0.213  -0.3301  -0.1471   0.1870
 YES  C6   C  CH2   0  -0.480  -0.9814   1.2390  -0.0260
 YES  C7   C  CH2   0  -0.149  -1.8412   1.6423   1.1601
 YES  O7   O  OH1   0  -0.676  -2.4264   2.9004   0.8979
 YES  C8   C  CH2   0  -0.473  -1.1433  -1.2552  -0.4973
 YES  C9   C  CH2   0  -0.140  -2.6042  -1.3006  -0.0856
 YES  O9   O  OH1   0  -0.676  -3.1959  -2.4338  -0.6891
 YES  H1   H  HCH2  0   0.217   2.8224  -1.6220  -0.0329
 YES  H3   H  HCH2  0   0.211   1.5875   1.8259   0.4371
 YES  H4   H  HCH2  0   0.202   2.5374  -0.2686  -1.8373
 YES  H4A  H  HCH2  0   0.202   0.8989  -0.7614  -2.2293
 YES  HO4  H  HOH1  0   0.453   1.4047   1.3467  -3.0136
 YES  H5   H  HCH1  0   0.226  -0.3771  -0.3532   1.2639
 YES  H6   H  HCH2  0   0.244  -0.2365   2.0188  -0.1710
 YES  H6A  H  HCH2  0   0.225  -1.5873   1.2374  -0.9373
 YES  H7   H  HCH2  0   0.193  -2.6089   0.8832   1.3530
 YES  H7A  H  HCH2  0   0.188  -1.2072   1.6750   2.0575
 YES  HO7  H  HOH1  0   0.451  -2.9921   3.1272   1.6412
 YES  H8   H  HCH2  0   0.222  -1.0938  -1.1441  -1.5849
 YES  H8A  H  HCH2  0   0.237  -0.7171  -2.2313  -0.2566
 YES  H9   H  HCH2  0   0.186  -2.6763  -1.3526   1.0101
 YES  H15  H  HOH1  0   0.454   1.8441  -2.8198   1.6717
 YES  H16  H  HCH2  0   0.203   1.3065  -2.3498  -0.5272
 YES  H17  H  HCH2  0   0.197   1.6826   0.6508   1.7390
 YES  H18  H  HOH1  0   0.453   3.7457   1.4725   0.8850
 YES  H19  H  HCH2  0   0.195  -3.1188  -0.3836  -0.3977
 YES  H20  H  HOH1  0   0.451  -4.1304  -2.4363  -0.4650

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
 YES  C1  O1   single  1.408  0.020  1.408
 YES  C1  H1   single  0.970  0.020  1.090
 YES  C2  C1   single  1.538  0.020  1.538
 YES  C2  C4   single  1.533  0.020  1.533
 YES  C2  C5   single  1.561  0.020  1.561
 YES  C3  C2   single  1.535  0.020  1.535
 YES  C3  H3   single  0.970  0.020  1.090
 YES  O3  C3   single  1.411  0.020  1.411
 YES  C4  H4   single  0.970  0.020  1.090
 YES  C4  H4A  single  0.970  0.020  1.090
 YES  O4  C4   single  1.408  0.020  1.408
 YES  O4  HO4  single  0.850  0.020  0.980
 YES  C5  C6   single  1.546  0.020  1.546
 YES  C5  H5   single  0.970  0.020  1.090
 YES  C6  C7   single  1.519  0.020  1.519
 YES  C6  H6   single  0.970  0.020  1.090
 YES  C6  H6A  single  0.970  0.020  1.090
 YES  C7  H7   single  0.970  0.020  1.090
 YES  C7  H7A  single  0.970  0.020  1.090
 YES  O7  C7   single  1.412  0.020  1.412
 YES  O7  HO7  single  0.850  0.020  0.980
 YES  C8  C5   single  1.535  0.020  1.535
 YES  C8  H8   single  0.970  0.020  1.090
 YES  C8  H8A  single  0.970  0.020  1.090
 YES  C9  C8   single  1.518  0.020  1.518
 YES  C9  H9   single  0.970  0.020  1.090
 YES  O9  C9   single  1.414  0.020  1.414
 YES  O1  H15  single  0.850  0.020  0.980
 YES  C1  H16  single  0.970  0.020  1.090
 YES  C3  H17  single  0.970  0.020  1.090
 YES  O3  H18  single  0.850  0.020  0.980
 YES  C9  H19  single  0.970  0.020  1.090
 YES  O9  H20  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
 YES  H15  O1  C1  107.94  3.000
 YES  H16  C1  H1  106.10  3.000
 YES  H16  C1  C2  109.27  3.000
 YES  H1   C1  C2  108.84  3.000
 YES  H16  C1  O1  111.10  3.000
 YES  C2   C1  O1  110.37  3.000
 YES  H1   C1  O1  111.04  3.000
 YES  C5   C2  C4  113.59  3.000
 YES  C5   C2  C3  108.44  3.000
 YES  C4   C2  C3  111.13  3.000
 YES  C3   C2  C1  108.76  3.000
 YES  C5   C2  C1  110.23  3.000
 YES  C4   C2  C1  104.57  3.000
 YES  H17  C3  H3  106.55  3.000
 YES  H17  C3  O3  111.21  3.000
 YES  H3   C3  O3  110.17  3.000
 YES  H17  C3  C2  108.46  3.000
 YES  O3   C3  C2  110.19  3.000
 YES  H3   C3  C2  110.19  3.000
 YES  H18  O3  C3  107.95  3.000
 YES  H4A  C4  H4  106.20  3.000
 YES  H4A  C4  O4  110.93  3.000
 YES  H4   C4  O4  110.79  3.000
 YES  O4   C4  C2  111.60  3.000
 YES  H4A  C4  C2  108.74  3.000
 YES  H4   C4  C2  108.40  3.000
 YES  HO4  O4  C4  107.78  3.000
 YES  H5   C5  C8  106.21  3.000
 YES  C8   C5  C6  111.25  3.000
 YES  H5   C5  C6  106.59  3.000
 YES  C8   C5  C2  112.40  3.000
 YES  H5   C5  C2  104.74  3.000
 YES  C6   C5  C2  114.86  3.000
 YES  H6A  C6  H6  105.61  3.000
 YES  H6A  C6  C7  109.71  3.000
 YES  H6   C6  C7  107.53  3.000
 YES  H6A  C6  C5  110.28  3.000
 YES  H6   C6  C5  111.86  3.000
 YES  C7   C6  C5  111.64  3.000
 YES  H7A  C7  H7  106.31  3.000
 YES  H7A  C7  O7  111.35  3.000
 YES  H7   C7  O7  111.05  3.000
 YES  O7   C7  C6  109.03  3.000
 YES  H7A  C7  C6  108.59  3.000
 YES  H7   C7  C6  110.47  3.000
 YES  HO7  O7  C7  108.09  3.000
 YES  H8A  C8  H8  106.99  3.000
 YES  H8A  C8  C9  106.80  3.000
 YES  H8   C8  C9  108.42  3.000
 YES  C9   C8  C5  114.22  3.000
 YES  H8A  C8  C5  109.89  3.000
 YES  H8   C8  C5  110.22  3.000
 YES  H19  C9  H9  107.00  3.000
 YES  H19  C9  O9  110.63  3.000
 YES  H9   C9  O9  111.11  3.000
 YES  H19  C9  C8  110.44  3.000
 YES  O9   C9  C8  108.11  3.000
 YES  H9   C9  C8  109.56  3.000
 YES  H20  O9  C9  108.03  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
 YES  Var_01  C4  C2  C1  O1  -176.71  30.0  1
 YES  Var_02  O4  C4  C2  C1  -172.18  30.0  3
 YES  Var_03  C6  C5  C2  C1   176.73  30.0  3
 YES  Var_04  O3  C3  C2  C1    55.74  30.0  1
 YES  Var_05  C7  C6  C5  C2  -133.84  30.0  3
 YES  Var_06  C9  C8  C5  C2   174.77  30.0  1
 YES  Var_07  O7  C7  C6  C5  -178.94  30.0  3
 YES  Var_08  O9  C9  C8  C5  -174.59  30.0  1

