# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:10:12 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: pentane-2,2,4,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(O)(O)CC(C)(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
 PBL  PBL  'pentane-2,2,4,4-tetrol   '  ligand  21  9  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PBL
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
 PBL  C1    C  CH3   0  -0.680   1.4094  -1.2442  -0.9205
 PBL  C2    C  CT    0   0.446   1.3304  -0.1075   0.0881
 PBL  O2    O  OH1   0  -0.664   1.6135   1.0690  -0.6244
 PBL  C3    C  CH2   0  -0.536   0.0019  -0.0098   0.8526
 PBL  C4    C  CT    0   0.456  -1.3271   0.0766   0.0912
 PBL  O4    O  OH1   0  -0.673  -2.3482   0.3893   1.0129
 PBL  C5    C  CH3   0  -0.699  -1.3917   1.1706  -0.9655
 PBL  O2'   O  OH1   0  -0.675   2.2848  -0.2970   1.1102
 PBL  O4'   O  OH1   0  -0.661  -1.5572  -1.1869  -0.4752
 PBL  H1    H  HCH3  0   0.229   2.4192  -1.3023  -1.3349
 PBL  H1A   H  HCH3  0   0.231   1.1851  -2.1968  -0.4435
 PBL  H1B   H  HCH3  0   0.236   0.7172  -1.1099  -1.7483
 PBL  H3    H  HCH2  0   0.247  -0.0654  -0.8745   1.5221
 PBL  H3A   H  HCH2  0   0.251   0.0622   0.8732   1.4984
 PBL  H5    H  HCH3  0   0.241  -0.7127   0.9662  -1.7890
 PBL  H5A   H  HCH3  0   0.233  -2.4050   1.2338  -1.3697
 PBL  H5B   H  HCH3  0   0.231  -1.1383   2.1458  -0.5506
 PBL  HO2   H  HOH1  0   0.447   1.4894   1.8262  -0.0401
 PBL  HO4   H  HOH1  0   0.445  -2.3013  -0.2309   1.7506
 PBL  HO2'  H  HOH1  0   0.446   3.1491  -0.4194   0.7000
 PBL  HO4'  H  HOH1  0   0.448  -2.3341  -1.1340  -1.0443

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
 PBL  C1   C2    single  1.522  0.020  1.522
 PBL  C2   O2    single  1.404  0.020  1.404
 PBL  C2   C3    single  1.536  0.020  1.536
 PBL  C2   O2'   single  1.411  0.020  1.411
 PBL  C3   C4    single  1.534  0.020  1.534
 PBL  C4   O4    single  1.411  0.020  1.411
 PBL  C4   C5    single  1.522  0.020  1.522
 PBL  C4   O4'   single  1.404  0.020  1.404
 PBL  C1   H1    single  0.970  0.020  1.090
 PBL  C1   H1A   single  0.970  0.020  1.090
 PBL  C1   H1B   single  0.970  0.020  1.090
 PBL  C3   H3    single  0.970  0.020  1.090
 PBL  C3   H3A   single  0.970  0.020  1.090
 PBL  C5   H5    single  0.970  0.020  1.090
 PBL  C5   H5A   single  0.970  0.020  1.090
 PBL  C5   H5B   single  0.970  0.020  1.090
 PBL  O2   HO2   single  0.850  0.020  0.980
 PBL  O4   HO4   single  0.850  0.020  0.980
 PBL  O2'  HO2'  single  0.850  0.020  0.980
 PBL  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
 PBL  H1B   C1   H1A  108.09  3.000
 PBL  H1B   C1   H1   107.82  3.000
 PBL  H1A   C1   H1   108.05  3.000
 PBL  H1B   C1   C2   112.29  3.000
 PBL  H1A   C1   C2   110.64  3.000
 PBL  H1    C1   C2   109.81  3.000
 PBL  O2'   C2   C3   103.47  3.000
 PBL  O2'   C2   O2   110.10  3.000
 PBL  C3    C2   O2   111.94  3.000
 PBL  O2'   C2   C1   110.16  3.000
 PBL  C3    C2   C1   114.98  3.000
 PBL  O2    C2   C1   106.21  3.000
 PBL  HO2   O2   C2   108.93  3.000
 PBL  H3A   C3   H3   106.22  3.000
 PBL  H3A   C3   C4   107.15  3.000
 PBL  H3    C3   C4   107.13  3.000
 PBL  H3A   C3   C2   107.29  3.000
 PBL  H3    C3   C2   107.89  3.000
 PBL  C4    C3   C2   120.39  3.000
 PBL  O4'   C4   C5   111.09  3.000
 PBL  O4'   C4   O4   110.15  3.000
 PBL  C5    C4   O4   105.27  3.000
 PBL  O4'   C4   C3   106.96  3.000
 PBL  C5    C4   C3   114.94  3.000
 PBL  O4    C4   C3   108.38  3.000
 PBL  HO4   O4   C4   108.78  3.000
 PBL  H5B   C5   H5A  107.75  3.000
 PBL  H5B   C5   H5   108.15  3.000
 PBL  H5A   C5   H5   108.06  3.000
 PBL  H5B   C5   C4   111.66  3.000
 PBL  H5A   C5   C4   109.73  3.000
 PBL  H5    C5   C4   111.36  3.000
 PBL  HO2'  O2'  C2   108.36  3.000
 PBL  HO4'  O4'  C4   108.71  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
 PBL  Var_01  C4  C3  C2  C1   -54.36  30.0  3
 PBL  Var_02  O4  C4  C3  C2  -169.91  30.0  3
 PBL  Var_03  H1  C1  C2  O2    61.68  30.0  3
 PBL  Var_04  H5  C5  C4  C3    67.04  30.0  3

