# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 21:30:42 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (3aS,5S,6S,7R,7aR)-5-fluoro-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]oxazole-6,7-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=N[C@@H]2[C@@H](O)[C@H](O)[C@@](F)(CO)O[C@@H]2O1
#
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
 5FN  5FN  (3aS,5S,6S,7R,7aR)-5-fluoro-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]oxazole-6,7-diol  ligand  27  15  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5FN
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
 5FN  F1    F  F     0  -0.374   0.4523   0.7564   1.4383
 5FN  C5    C  CT    0   0.579   1.1377   0.5819   0.2391
 5FN  C6    C  CH2   0  -0.235   2.4472   1.3372   0.3821
 5FN  O24   O  OH1   0  -0.668   3.2315   1.0705  -0.7508
 5FN  C4    C  CH1   0  -0.072   1.2929  -0.9159  -0.0267
 5FN  O22   O  OH1   0  -0.668   2.1512  -1.5322   0.8971
 5FN  C3    C  CH1   0   0.061  -0.0664  -1.5907   0.0812
 5FN  O21   O  OH1   0  -0.672  -0.0147  -2.9260  -0.3566
 5FN  O23   O  O2    0  -0.491   0.4083   1.1638  -0.7789
 5FN  C1    C  CR15  0   0.279  -0.8170   0.6147  -1.1380
 5FN  O1    O  O     0  -0.481  -1.8663   1.3297  -0.4960
 5FN  C7    C  CR5   0   0.488  -2.6905   0.4207   0.0639
 5FN  C9    C  CH3   0  -0.743  -3.8754   0.9708   0.7634
 5FN  N1    N  N     0  -0.423  -2.3844  -0.8007  -0.0522
 5FN  C2    C  CR15  0  -0.266  -1.1189  -0.8631  -0.7645
 5FN  H61C  H  HCH2  0   0.234   2.2230   2.4062   0.4933
 5FN  H62C  H  HCH2  0   0.229   2.9285   1.0092   1.3092
 5FN  H4    H  HCH1  0   0.253   1.6626  -1.0306  -1.0531
 5FN  H24   H  HOH1  0   0.469   4.1146   1.4153  -0.5924
 5FN  H22   H  HOH1  0   0.464   3.0539  -1.4742   0.5702
 5FN  H3    H  HCH1  0   0.231  -0.3848  -1.5463   1.1302
 5FN  H21   H  HOH1  0   0.453   0.5740  -3.4109   0.2315
 5FN  H2    H  HCR5  0   0.281  -1.2377  -1.4262  -1.6935
 5FN  H1    H  HCR5  0   0.268  -0.9094   0.7829  -2.2112
 5FN  H91C  H  HCH3  0   0.268  -3.5677   1.6417   1.5660
 5FN  H92C  H  HCH3  0   0.269  -4.4958   1.5460   0.0757
 5FN  H93C  H  HCH3  0   0.265  -4.4678   0.1647   1.1862

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
 5FN  F1   C5    single  1.392  0.020  1.392
 5FN  C5   C6    single  1.518  0.020  1.518
 5FN  C5   C4    single  1.529  0.020  1.529
 5FN  C5   O23   single  1.381  0.020  1.381
 5FN  C6   O24   single  1.404  0.020  1.404
 5FN  C4   O22   single  1.403  0.020  1.403
 5FN  C4   C3    single  1.521  0.020  1.521
 5FN  C3   O21   single  1.406  0.020  1.406
 5FN  C3   C2    single  1.534  0.020  1.534
 5FN  O23  C1    single  1.390  0.020  1.390
 5FN  C1   O1    single  1.423  0.020  1.423
 5FN  C1   C2    single  1.554  0.020  1.554
 5FN  O1   C7    single  1.349  0.020  1.349
 5FN  C7   C9    single  1.482  0.020  1.482
 5FN  C7   N1    double  1.265  0.020  1.265
 5FN  N1   C2    single  1.454  0.020  1.454
 5FN  C6   H61C  single  0.970  0.020  1.090
 5FN  C6   H62C  single  0.970  0.020  1.090
 5FN  C4   H4    single  0.970  0.020  1.090
 5FN  O24  H24   single  0.850  0.020  0.980
 5FN  O22  H22   single  0.850  0.020  0.980
 5FN  C3   H3    single  0.970  0.020  1.090
 5FN  O21  H21   single  0.850  0.020  0.980
 5FN  C2   H2    single  0.970  0.020  1.090
 5FN  C1   H1    single  0.970  0.020  1.090
 5FN  C9   H91C  single  0.970  0.020  1.090
 5FN  C9   H92C  single  0.970  0.020  1.090
 5FN  C9   H93C  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
 5FN  O23   C5   C4    109.77  3.000
 5FN  O23   C5   C6    108.38  3.000
 5FN  C4    C5   C6    114.58  3.000
 5FN  O23   C5   F1    108.79  3.000
 5FN  C4    C5   F1    108.81  3.000
 5FN  C6    C5   F1    106.32  3.000
 5FN  H62C  C6   H61C  107.20  3.000
 5FN  H62C  C6   O24   112.39  3.000
 5FN  H61C  C6   O24   112.38  3.000
 5FN  H62C  C6   C5    108.05  3.000
 5FN  H61C  C6   C5    108.53  3.000
 5FN  O24   C6   C5    108.14  3.000
 5FN  H24   O24  C6    108.19  3.000
 5FN  H4    C4   C3    108.73  3.000
 5FN  H4    C4   O22   111.34  3.000
 5FN  C3    C4   O22   107.76  3.000
 5FN  H4    C4   C5    107.41  3.000
 5FN  C3    C4   C5    109.35  3.000
 5FN  O22   C4   C5    112.20  3.000
 5FN  H22   O22  C4    108.89  3.000
 5FN  H3    C3   C2    108.00  3.000
 5FN  H3    C3   O21   110.29  3.000
 5FN  C2    C3   O21   107.70  3.000
 5FN  H3    C3   C4    108.01  3.000
 5FN  C2    C3   C4    111.32  3.000
 5FN  O21   C3   C4    111.48  3.000
 5FN  H21   O21  C3    108.09  3.000
 5FN  C1    O23  C5    119.32  3.000
 5FN  H1    C1   C2    111.52  3.000
 5FN  H1    C1   O1    107.70  3.000
 5FN  C2    C1   O1    103.07  3.000
 5FN  H1    C1   O23   105.55  3.000
 5FN  C2    C1   O23   119.01  3.000
 5FN  O1    C1   O23   109.58  3.000
 5FN  C7    O1   C1    107.42  3.000
 5FN  N1    C7   C9    126.55  3.000
 5FN  N1    C7   O1    117.71  3.000
 5FN  C9    C7   O1    115.74  3.000
 5FN  H93C  C9   H92C  109.07  3.000
 5FN  H93C  C9   H91C  108.91  3.000
 5FN  H92C  C9   H91C  107.47  3.000
 5FN  H93C  C9   C7    110.14  3.000
 5FN  H92C  C9   C7    110.68  3.000
 5FN  H91C  C9   C7    110.50  3.000
 5FN  C2    N1   C7    107.29  3.000
 5FN  H2    C2   N1    110.13  3.000
 5FN  H2    C2   C1    107.87  3.000
 5FN  N1    C2   C1    104.25  3.000
 5FN  H2    C2   C3    107.39  3.000
 5FN  N1    C2   C3    110.34  3.000
 5FN  C1    C2   C3    116.77  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
 5FN  Var_01  N1    C7  O1  C1    1.41  30.0  1
 5FN  Var_02  H91C  C9  C7  O1  -59.07  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
 5FN  chir_01  C5  C6   C4   O23  positiv
 5FN  chir_02  C4  O22  C5   C3   positiv
 5FN  chir_03  C3  O21  C2   C4   positiv
 5FN  chir_04  C1  O1   O23  C2   negativ
 5FN  chir_05  C2  N1   C3   C1   positiv

