# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:03:09 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: (2R,4S)-2-methyldihydrofuran-2,3,3,4(2H)-tetrol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(O)OC[C@H](O)C1(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
 PAV  PAV  '(2R,4S)-2-methyldihydrofuran-2,3,3,4(2H)-tetrol (non-preferred name)'  L-saccharide  20  10  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_PAV
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
 PAV  O3    O  OH1   0  -0.643   0.1959  -1.3701   1.7717
 PAV  C4    C  CT    0   0.486  -0.1035  -0.2023   1.0913
 PAV  C11   C  CH3   0  -0.671   0.1439   1.0219   1.9593
 PAV  O5    O  O2    0  -0.522  -1.4733  -0.2062   0.7025
 PAV  C6    C  CH2   0  -0.253  -1.6329   0.0401  -0.6846
 PAV  C7    C  CH1   0   0.013  -0.2929   0.5979  -1.1493
 PAV  O12   O  OH1   0  -0.637   0.0222   0.3678  -2.4933
 PAV  C8    C  CT    0   0.374   0.6709  -0.1820  -0.2499
 PAV  O1    O  OH1   0  -0.726   1.9109   0.4168  -0.0723
 PAV  O13   O  OH1   0  -0.630   0.7836  -1.4945  -0.6998
 PAV  HO3   H  HOH1  0   0.462  -0.0158  -1.2535   2.7045
 PAV  H111  H  HCH3  0   0.233  -0.5567   1.0192   2.7979
 PAV  H112  H  HCH3  0   0.244   1.1550   1.0299   2.3637
 PAV  H113  H  HCH3  0   0.196  -0.0079   1.9506   1.4107
 PAV  H61   H  HCH2  0   0.202  -1.8726  -0.8815  -1.2274
 PAV  H62   H  HCH2  0   0.250  -2.4553   0.7431  -0.8332
 PAV  H7    H  HCH1  0   0.249  -0.2306   1.6658  -0.9021
 PAV  H12   H  HOH1  0   0.468  -0.5300   0.9245  -3.0508
 PAV  HO1   H  HOH1  0   0.440   2.3050   0.6010  -0.9334
 PAV  H13   H  HOH1  0   0.465   0.8362  -1.4917  -1.6641

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
 PAV  O3   C4    single  1.384  0.020  1.384
 PAV  O3   HO3   single  0.850  0.020  0.980
 PAV  C4   C11   single  1.521  0.020  1.521
 PAV  C4   O5    single  1.424  0.020  1.424
 PAV  C4   C8    single  1.549  0.020  1.549
 PAV  C11  H111  single  0.970  0.020  1.090
 PAV  C11  H112  single  0.970  0.020  1.090
 PAV  C11  H113  single  0.970  0.020  1.090
 PAV  O5   C6    single  1.418  0.020  1.418
 PAV  C6   C7    single  1.524  0.020  1.524
 PAV  C6   H61   single  0.970  0.020  1.090
 PAV  C6   H62   single  0.970  0.020  1.090
 PAV  C7   O12   single  1.400  0.020  1.400
 PAV  C7   C8    single  1.532  0.020  1.532
 PAV  C7   H7    single  0.970  0.020  1.090
 PAV  O12  H12   single  0.850  0.020  0.980
 PAV  C8   O1    single  1.388  0.020  1.388
 PAV  C8   O13   single  1.392  0.020  1.392
 PAV  O1   HO1   single  0.850  0.020  0.980
 PAV  O13  H13   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
 PAV  HO3   O3   C4    109.04  3.000
 PAV  C8    C4   O5    104.16  3.000
 PAV  C8    C4   C11   113.72  3.000
 PAV  O5    C4   C11   108.33  3.000
 PAV  C8    C4   O3    109.18  3.000
 PAV  O5    C4   O3    109.87  3.000
 PAV  C11   C4   O3    111.30  3.000
 PAV  H113  C11  H112  108.07  3.000
 PAV  H113  C11  H111  107.42  3.000
 PAV  H112  C11  H111  108.08  3.000
 PAV  H113  C11  C4    112.10  3.000
 PAV  H112  C11  C4    111.64  3.000
 PAV  H111  C11  C4    109.38  3.000
 PAV  C6    O5   C4    112.02  3.000
 PAV  H62   C6   H61   108.01  3.000
 PAV  H62   C6   C7    112.64  3.000
 PAV  H61   C6   C7    110.44  3.000
 PAV  H62   C6   O5    109.25  3.000
 PAV  H61   C6   O5    111.29  3.000
 PAV  C7    C6   O5    105.24  3.000
 PAV  H7    C7   C8    109.11  3.000
 PAV  H7    C7   O12   111.31  3.000
 PAV  C8    C7   O12   109.78  3.000
 PAV  H7    C7   C6    109.71  3.000
 PAV  C8    C7   C6    100.83  3.000
 PAV  O12   C7   C6    115.50  3.000
 PAV  H12   O12  C7    109.40  3.000
 PAV  O13   C8   O1    112.07  3.000
 PAV  O13   C8   C7    109.95  3.000
 PAV  O1    C8   C7    114.68  3.000
 PAV  O13   C8   C4    107.94  3.000
 PAV  O1    C8   C4    109.96  3.000
 PAV  C7    C8   C4    101.57  3.000
 PAV  HO1   O1   C8    109.45  3.000
 PAV  H13   O13  C8    108.93  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
 PAV  Var_01  C7  C6  O5  C4  -15.45  30.0  1

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
 PAV  chir_01  C4  C11  O5  C8  negativ
 PAV  chir_02  C7  O12  C6  C8  negativ

