# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:33:05 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 4-amino-2,4,5-trideoxy-5,5,5-trifluoro-L-threo-pentonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]([C@@H](O)CC(O)=O)C(F)(F)F
#
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
 F3T  F3T  '4-amino-2,4,5-trideoxy-5,5,5-trifluoro-L-threo-pentonic acid'  L-peptide  19  12  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F3T
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
 F3T  N    N  NH2    0  -0.801  -0.9619   1.8679  -0.5444
 F3T  C1   C  C      0   0.411   2.9820  -0.0744   0.2633
 F3T  F1   F  F      0  -0.311  -2.3540  -0.6506  -0.9956
 F3T  O1   O  OC    -1  -0.618   3.9692   0.5563  -0.1638
 F3T  C2   C  CH2    0  -0.604   1.6670   0.7137   0.4181
 F3T  F2   F  F      0  -0.318  -3.1882   0.4746   0.6321
 F3T  O2   O  O      0  -0.613   2.9615  -1.2717   0.6127
 F3T  C3   C  CH1    0   0.021   0.4429  -0.0778  -0.0098
 F3T  F3   F  F      0  -0.316  -1.9856  -1.2641   1.0357
 F3T  O3   O  OH1    0  -0.670   0.5127  -0.4419  -1.3733
 F3T  C4   C  CH1    0  -0.312  -0.8511   0.6986   0.2960
 F3T  C5   C  CT     0   1.001  -2.0883  -0.1907   0.2352
 F3T  HN   H  HNH2   0   0.351  -1.1950   1.6280  -1.4988
 F3T  HNA  H  HNH2   0   0.366  -1.6731   2.5027  -0.2100
 F3T  H2   H  HCH2   0   0.235   1.5613   0.9812   1.4758
 F3T  H2A  H  HCH2   0   0.218   1.7130   1.6577  -0.1311
 F3T  H3   H  HCH1   0   0.237   0.4393  -1.0127   0.5546
 F3T  HO3  H  HOH1   0   0.443   0.8006   0.3274  -1.8761
 F3T  H4   H  HCH1   0   0.279  -0.7872   1.0342   1.3358

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
 F3T  N   C4   single  1.444  0.020  1.444
 F3T  C1  O1   deloc   1.247  0.020  1.247
 F3T  C1  C2   single  1.541  0.020  1.541
 F3T  C1  O2   deloc   1.248  0.020  1.248
 F3T  F1  C5   single  1.341  0.020  1.341
 F3T  C2  C3   single  1.519  0.020  1.519
 F3T  F2  C5   single  1.345  0.020  1.345
 F3T  C3  O3   single  1.413  0.020  1.413
 F3T  C3  C4   single  1.540  0.020  1.540
 F3T  F3  C5   single  1.343  0.020  1.343
 F3T  C4  C5   single  1.525  0.020  1.525
 F3T  N   HN   single  0.890  0.020  1.040
 F3T  N   HNA  single  0.890  0.020  1.040
 F3T  C2  H2   single  0.970  0.020  1.090
 F3T  C2  H2A  single  0.970  0.020  1.090
 F3T  C3  H3   single  0.970  0.020  1.090
 F3T  O3  HO3  single  0.850  0.020  0.980
 F3T  C4  H4   single  0.970  0.020  1.090

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
 F3T  HNA  N   HN  107.41  3.000
 F3T  HNA  N   C4  111.72  3.000
 F3T  HN   N   C4  112.01  3.000
 F3T  O2   C1  C2  116.67  3.000
 F3T  O2   C1  O1  126.47  3.000
 F3T  C2   C1  O1  116.84  3.000
 F3T  H2A  C2  H2  106.15  3.000
 F3T  H2A  C2  C3  110.01  3.000
 F3T  H2   C2  C3  108.74  3.000
 F3T  H2A  C2  C1  110.81  3.000
 F3T  H2   C2  C1  107.71  3.000
 F3T  C3   C2  C1  113.13  3.000
 F3T  H3   C3  C4  109.04  3.000
 F3T  H3   C3  O3  106.16  3.000
 F3T  C4   C3  O3  111.29  3.000
 F3T  H3   C3  C2  107.65  3.000
 F3T  C4   C3  C2  111.01  3.000
 F3T  O3   C3  C2  111.49  3.000
 F3T  HO3  O3  C3  108.23  3.000
 F3T  H4   C4  C5  105.32  3.000
 F3T  H4   C4  C3  107.11  3.000
 F3T  C5   C4  C3  112.33  3.000
 F3T  H4   C4  N   108.00  3.000
 F3T  C5   C4  N   112.75  3.000
 F3T  C3   C4  N   110.92  3.000
 F3T  C4   C5  F3  112.35  3.000
 F3T  C4   C5  F2  111.29  3.000
 F3T  F3   C5  F2  106.38  3.000
 F3T  C4   C5  F1  113.42  3.000
 F3T  F3   C5  F1  106.75  3.000
 F3T  F2   C5  F1  106.17  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
 F3T  Var_01  C3  C2  C1  O1  139.89  30.0  3

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
 F3T  chir_01  C3  C2  O3  C4  positiv
 F3T  chir_02  C4  N   C3  C5  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 F3T  plan-1  C1  0.020
 F3T  plan-1  O1  0.020
 F3T  plan-1  C2  0.020
 F3T  plan-1  O2  0.020

