# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:54:30 2021
#   Inital geometry file: a 45 line input string
#   Ligand name: 2-deoxy-2-fluoro-alpha-D-arabinofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@@H](F)[C@@H]1O
#
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
 V3M  V3M  2-deoxy-2-fluoro-alpha-D-arabinofuranose  D-saccharide  19  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 PERFECT
;

data_comp_V3M
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
 V3M  O1   O  OH1   0  -0.664  -2.1570   -7.1771  -18.1746
 V3M  O5   O  OH1   0  -0.669  -1.1512  -10.4567  -21.7474
 V3M  C5   C  CH2   0  -0.162  -1.8243   -9.2590  -22.0467
 V3M  C4   C  CH1   0   0.007  -2.3579   -8.6631  -20.7637
 V3M  O4   O  O2    0  -0.500  -1.2709   -8.3640  -19.8890
 V3M  C1   C  CH1   0   0.207  -1.4063   -7.0915  -19.3499
 V3M  C2   C  CH1   0   0.129  -2.1519   -6.3051  -20.4202
 V3M  F2   F  F     0  -0.377  -1.2374   -5.9404  -21.4065
 V3M  C3   C  CH1   0  -0.082  -3.1091   -7.3432  -21.0037
 V3M  O3   O  OH1   0  -0.663  -4.3381   -7.3831  -20.3294
 V3M  HO5  H  HOH1  0   0.457  -0.8365  -10.8373  -22.5721
 V3M  H51  H  HCH2  0   0.199  -1.1672   -8.5297  -22.5397
 V3M  H52  H  HCH2  0   0.206  -2.6777   -9.4269  -22.7169
 V3M  H4   H  HCH1  0   0.247  -3.0315   -9.3815  -20.2820
 V3M  H1   H  HCH1  0   0.244  -0.4063   -6.6856  -19.1568
 V3M  H2   H  HCH1  0   0.248  -2.6392   -5.4006  -20.0523
 V3M  H3   H  HCH1  0   0.254  -3.2489   -7.1530  -22.0759
 V3M  HO3  H  HOH1  0   0.458  -4.8496   -6.6088  -20.5843
 V3M  HO1  H  HOH1  0   0.463  -1.9325   -6.4347  -17.6046

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
 V3M  O1  C1   single  1.397  0.020  1.397
 V3M  O5  C5   single  1.406  0.020  1.406
 V3M  C5  C4   single  1.512  0.020  1.512
 V3M  C4  C3   single  1.538  0.020  1.538
 V3M  C4  O4   single  1.427  0.020  1.427
 V3M  O4  C1   single  1.389  0.020  1.389
 V3M  C1  C2   single  1.523  0.020  1.523
 V3M  C2  C3   single  1.528  0.020  1.528
 V3M  C2  F2   single  1.394  0.020  1.394
 V3M  C3  O3   single  1.402  0.020  1.402
 V3M  O5  HO5  single  0.850  0.020  0.980
 V3M  C5  H51  single  0.970  0.020  1.090
 V3M  C5  H52  single  0.970  0.020  1.090
 V3M  C4  H4   single  0.970  0.020  1.090
 V3M  C1  H1   single  0.970  0.020  1.090
 V3M  C2  H2   single  0.970  0.020  1.090
 V3M  C3  H3   single  0.970  0.020  1.090
 V3M  O3  HO3  single  0.850  0.020  0.980
 V3M  O1  HO1  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
 V3M  HO1  O1  C1   109.00  3.000
 V3M  HO5  O5  C5   108.14  3.000
 V3M  H52  C5  H51  107.00  3.000
 V3M  H52  C5  C4   107.69  3.000
 V3M  H51  C5  C4   109.29  3.000
 V3M  H52  C5  O5   111.82  3.000
 V3M  H51  C5  O5   112.01  3.000
 V3M  C4   C5  O5   108.91  3.000
 V3M  H4   C4  C3   109.32  3.000
 V3M  H4   C4  O4   109.64  3.000
 V3M  C3   C4  O4   106.73  3.000
 V3M  H4   C4  C5   109.36  3.000
 V3M  O4   C4  C5   109.51  3.000
 V3M  C3   C4  C5   112.23  3.000
 V3M  C1   O4  C4   110.84  3.000
 V3M  H1   C1  C2   112.28  3.000
 V3M  H1   C1  O4   108.58  3.000
 V3M  C2   C1  O4   104.36  3.000
 V3M  H1   C1  O1   111.38  3.000
 V3M  C2   C1  O1   111.09  3.000
 V3M  O4   C1  O1   108.83  3.000
 V3M  H2   C2  C3   114.34  3.000
 V3M  H2   C2  F2   108.34  3.000
 V3M  C3   C2  F2   108.58  3.000
 V3M  H2   C2  C1   114.18  3.000
 V3M  F2   C2  C1   108.14  3.000
 V3M  C3   C2  C1   102.96  3.000
 V3M  H3   C3  O3   111.28  3.000
 V3M  H3   C3  C2   109.58  3.000
 V3M  O3   C3  C2   112.63  3.000
 V3M  H3   C3  C4   111.31  3.000
 V3M  O3   C3  C4   109.19  3.000
 V3M  C2   C3  C4   102.57  3.000
 V3M  HO3  O3  C3   108.39  3.000

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
 V3M  chir_01  C4  C5  C3  O4  positiv
 V3M  chir_02  C1  O1  O4  C2  negativ
 V3M  chir_03  C2  F2  C3  C1  negativ
 V3M  chir_04  C3  O3  C2  C4  negativ

