# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:05:22 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: methyl 4-amino-2,4,5-trideoxy-5,5,5-trifluoro-L-threo-pentonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)C[C@H](O)[C@@H](N)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
 F3M  F3M  'methyl 4-amino-2,4,5-trideoxy-5,5,5-trifluoro-L-threo-pentonate'  L-peptide  23  13  .  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_F3M
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
 F3M  N    N  NH2   0  -0.804  -1.3253   1.9020  -0.4067
 F3M  C1   C  C     0   0.609   2.5729  -0.1683   0.3235
 F3M  F1   F  F     0  -0.312  -2.7361  -0.3240  -1.2113
 F3M  O1   O  O2    0  -0.451   3.6192   0.5734  -0.0079
 F3M  C2   C  CH2   0  -0.624   1.3106   0.6529   0.3920
 F3M  F2   F  F     0  -0.311  -3.5362   0.4755   0.6132
 F3M  O2   O  O     0  -0.449   2.6418  -1.3458   0.5711
 F3M  C3   C  CH1   0   0.009   0.0745  -0.1681   0.0518
 F3M  F3   F  F     0  -0.314  -2.4164  -1.3594   0.6502
 F3M  O3   O  OH1   0  -0.658   0.1354  -0.6632  -1.2642
 F3M  C4   C  CH1   0  -0.338  -1.1964   0.6604   0.3235
 F3M  C5   C  CT    0   1.035  -2.4686  -0.1419   0.0887
 F3M  CA   C  CH3   0  -0.426   4.8968  -0.0648  -0.0449
 F3M  HN   H  HNH2  0   0.375  -0.7331   2.6173  -0.0100
 F3M  HNA  H  HNH2  0   0.351  -1.0756   1.8042  -1.3824
 F3M  H2   H  HCH2  0   0.301   1.2326   1.0415   1.4132
 F3M  H2A  H  HCH2  0   0.271   1.3960   1.5248  -0.2603
 F3M  H3   H  HCH1  0   0.259   0.0587  -1.0448   0.7026
 F3M  HO3  H  HOH1  0   0.447   0.3220   0.0598  -1.8729
 F3M  H4   H  HCH1  0   0.295  -1.1898   0.9005   1.3912
 F3M  HA   H  HCH3  0   0.240   5.1710  -0.4630   0.9317
 F3M  HAA  H  HCH3  0   0.240   4.9186  -0.8685  -0.7801
 F3M  HAB  H  HCH3  0   0.253   5.6062   0.7055  -0.3321

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
 F3M  N   C4   single  1.446  0.020  1.446
 F3M  C1  O1   single  1.325  0.020  1.325
 F3M  C1  C2   single  1.507  0.020  1.507
 F3M  C1  O2   double  1.205  0.020  1.205
 F3M  F1  C5   single  1.340  0.020  1.340
 F3M  O1  CA   single  1.429  0.020  1.429
 F3M  C2  C3   single  1.522  0.020  1.522
 F3M  F2  C5   single  1.340  0.020  1.340
 F3M  C3  O3   single  1.407  0.020  1.407
 F3M  C3  C4   single  1.541  0.020  1.541
 F3M  F3  C5   single  1.342  0.020  1.342
 F3M  C4  C5   single  1.522  0.020  1.522
 F3M  N   HN   single  0.890  0.020  1.040
 F3M  N   HNA  single  0.890  0.020  1.040
 F3M  C2  H2   single  0.970  0.020  1.090
 F3M  C2  H2A  single  0.970  0.020  1.090
 F3M  C3  H3   single  0.970  0.020  1.090
 F3M  O3  HO3  single  0.850  0.020  0.980
 F3M  C4  H4   single  0.970  0.020  1.090
 F3M  CA  HA   single  0.970  0.020  0.970
 F3M  CA  HAA  single  0.970  0.020  1.090
 F3M  CA  HAB  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
 F3M  HNA  N   HN   107.61  3.000
 F3M  HNA  N   C4   112.45  3.000
 F3M  HN   N   C4   110.95  3.000
 F3M  O2   C1  C2   124.80  3.000
 F3M  O2   C1  O1   123.59  3.000
 F3M  C2   C1  O1   111.58  3.000
 F3M  CA   O1  C1   117.56  3.000
 F3M  H2A  C2  H2   106.21  3.000
 F3M  H2A  C2  C3   111.13  3.000
 F3M  H2   C2  C3   109.99  3.000
 F3M  H2A  C2  C1   110.01  3.000
 F3M  H2   C2  C1   107.17  3.000
 F3M  C3   C2  C1   112.08  3.000
 F3M  H3   C3  C4   108.34  3.000
 F3M  H3   C3  O3   105.99  3.000
 F3M  C4   C3  O3   112.93  3.000
 F3M  H3   C3  C2   108.15  3.000
 F3M  C4   C3  C2   109.89  3.000
 F3M  O3   C3  C2   111.32  3.000
 F3M  HO3  O3  C3   109.59  3.000
 F3M  H4   C4  C5   105.73  3.000
 F3M  H4   C4  C3   106.56  3.000
 F3M  C5   C4  C3   112.25  3.000
 F3M  H4   C4  N    107.74  3.000
 F3M  C5   C4  N    107.46  3.000
 F3M  C3   C4  N    116.49  3.000
 F3M  C4   C5  F3   112.41  3.000
 F3M  C4   C5  F2   111.26  3.000
 F3M  F3   C5  F2   106.57  3.000
 F3M  C4   C5  F1   112.85  3.000
 F3M  F3   C5  F1   106.89  3.000
 F3M  F2   C5  F1   106.46  3.000
 F3M  HAB  CA  HAA  109.37  3.000
 F3M  HAB  CA  HA   109.38  3.000
 F3M  HAA  CA  HA   109.28  3.000
 F3M  HAB  CA  O1   105.91  3.000
 F3M  HAA  CA  O1   111.40  3.000
 F3M  HA   CA  O1   111.42  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
 F3M  Var_01  C3  C2  C1  O1  150.39  30.0  3
 F3M  Var_02  HA  CA  O1  C1  -61.09  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
 F3M  chir_01  C3  C2  O3  C4  positiv
 F3M  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
 F3M  plan-1  C1  0.020
 F3M  plan-1  O1  0.020
 F3M  plan-1  C2  0.020
 F3M  plan-1  O2  0.020

