# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 06:29:45 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  20  12  .  2022-03-18  2022-11-17
;
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  -0.806  -0.9104   1.8030  -0.6397
 F3T  C1   C  C     0   0.552   2.9527  -0.1260   0.2839
 F3T  F1   F  F     0  -0.310  -2.3165  -0.7636  -0.8900
 F3T  O1   O  OH1   0  -0.591   3.9946   0.6648   0.0568
 F3T  C2   C  CH2   0  -0.609   1.6774   0.6527   0.4670
 F3T  F2   F  F     0  -0.313  -3.1573   0.5293   0.6062
 F3T  O2   O  O     0  -0.444   3.0419  -1.3254   0.3681
 F3T  C3   C  CH1   0   0.019   0.4585  -0.1252  -0.0133
 F3T  F3   F  F     0  -0.313  -1.9744  -1.1702   1.1971
 F3T  O3   O  OH1   0  -0.659   0.5704  -0.4544  -1.3746
 F3T  C4   C  CH1   0  -0.321  -0.8166   0.6905   0.2758
 F3T  C5   C  CT    0   1.005  -2.0644  -0.1835   0.2914
 F3T  HN   H  HNH2  0   0.360  -1.2949   1.5370  -1.5365
 F3T  HNA  H  HNH2  0   0.374  -1.4885   2.5436  -0.2699
 F3T  HO1  H  HOH1  0   0.480   4.8040   0.1351  -0.0062
 F3T  H2   H  HCH2  0   0.295   1.5858   0.8637   1.5377
 F3T  H2A  H  HCH2  0   0.278   1.7392   1.6213  -0.0328
 F3T  H3   H  HCH1  0   0.262   0.4214  -1.0720   0.5288
 F3T  HO3  H  HOH1  0   0.447   0.6912   0.3630  -1.8725
 F3T  H4   H  HCH1  0   0.293  -0.7304   1.0923   1.2897

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   single  1.328  0.020  1.328
 F3T  C1  C2   single  1.505  0.020  1.505
 F3T  C1  O2   double  1.206  0.020  1.206
 F3T  F1  C5   single  1.340  0.020  1.340
 F3T  C2  C3   single  1.524  0.020  1.524
 F3T  F2  C5   single  1.342  0.020  1.342
 F3T  C3  O3   single  1.405  0.020  1.405
 F3T  C3  C4   single  1.541  0.020  1.541
 F3T  F3  C5   single  1.342  0.020  1.342
 F3T  C4  C5   single  1.524  0.020  1.524
 F3T  N   HN   single  0.890  0.020  1.040
 F3T  N   HNA  single  0.890  0.020  1.040
 F3T  O1  HO1  single  0.850  0.020  0.980
 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  107.46  3.000
 F3T  HNA  N   C4  111.73  3.000
 F3T  HN   N   C4  112.60  3.000
 F3T  O2   C1  C2  124.66  3.000
 F3T  O2   C1  O1  123.12  3.000
 F3T  C2   C1  O1  112.18  3.000
 F3T  HO1  O1  C1  109.93  3.000
 F3T  H2A  C2  H2  106.34  3.000
 F3T  H2A  C2  C3  110.73  3.000
 F3T  H2   C2  C3  109.86  3.000
 F3T  H2A  C2  C1  110.81  3.000
 F3T  H2   C2  C1  106.83  3.000
 F3T  C3   C2  C1  112.04  3.000
 F3T  H3   C3  C4  109.75  3.000
 F3T  H3   C3  O3  106.30  3.000
 F3T  C4   C3  O3  111.82  3.000
 F3T  H3   C3  C2  108.26  3.000
 F3T  C4   C3  C2  109.43  3.000
 F3T  O3   C3  C2  111.18  3.000
 F3T  HO3  O3  C3  108.15  3.000
 F3T  H4   C4  C5  105.41  3.000
 F3T  H4   C4  C3  107.64  3.000
 F3T  C5   C4  C3  112.08  3.000
 F3T  H4   C4  N   108.05  3.000
 F3T  C5   C4  N   113.29  3.000
 F3T  C3   C4  N   110.04  3.000
 F3T  C4   C5  F3  111.94  3.000
 F3T  C4   C5  F2  111.38  3.000
 F3T  F3   C5  F2  106.66  3.000
 F3T  C4   C5  F1  113.16  3.000
 F3T  F3   C5  F1  106.81  3.000
 F3T  F2   C5  F1  106.47  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  CONST_01  HO1  O1  C1  C2  180.00   0.0  0
 F3T  Var_01    C3   C2  C1  O1  149.08  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
 F3T  plan-1  HO1  0.020

