# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 06:05:39 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 5-(acetylamino)-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@@H](F)[C@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
#
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
 FSI  FSI  '5-(acetylamino)-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid'  D-saccharide  39  22  .  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_FSI
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
 FSI  O2    O  OH1    0  -0.679   0.3577  -2.0759  -1.8104
 FSI  C1    C  C      0   0.379   0.0353  -3.3822   0.2269
 FSI  F1    F  F      0  -0.381   1.9460  -1.6541   1.3202
 FSI  C2    C  CT     0   0.300   0.3973  -2.0051  -0.4131
 FSI  C3    C  CH1    0   0.153   1.8289  -1.6083  -0.0675
 FSI  C4    C  CH1    0   0.021   2.1508  -0.1996  -0.5395
 FSI  O4    O  OH1    0  -0.663   3.4201   0.2222  -0.1124
 FSI  C5    C  CH1    0  -0.129   1.1109   0.7883  -0.0143
 FSI  N5    N  NH1    0  -0.633   1.3176   2.0915  -0.5932
 FSI  C6    C  CH1    0   0.038  -0.3005   0.2864  -0.3544
 FSI  O6    O  O2     0  -0.509  -0.4887  -1.0442   0.0809
 FSI  C7    C  CH1    0  -0.030  -1.3885   1.0999   0.3437
 FSI  O7    O  OH1    0  -0.664  -1.2766   0.9948   1.7436
 FSI  C8    C  CH1    0  -0.015  -2.7985   0.7042  -0.1355
 FSI  O8    O  OH1    0  -0.661  -2.9008   0.7804  -1.5396
 FSI  C9    C  CH2    0  -0.162  -3.8593   1.5500   0.5514
 FSI  O9    O  OH1    0  -0.671  -5.1317   1.1128   0.1318
 FSI  C10   C  C      0   0.525   1.7336   3.1780   0.0848
 FSI  O10   O  O      0  -0.501   1.9242   3.1894   1.2921
 FSI  C11   C  CH3    0  -0.783   1.9504   4.4078  -0.7625
 FSI  O1A   O  O      0  -0.575  -1.0022  -3.4550   0.8978
 FSI  O1B   O  OC    -1  -0.603   0.8428  -4.2892  -0.0439
 FSI  HO2   H  HOH1   0   0.456  -0.4851  -2.4500  -2.0912
 FSI  H3    H  HCH1   0   0.232   2.5340  -2.3306  -0.4845
 FSI  H4    H  HCH1   0   0.227   2.0901  -0.2068  -1.6366
 FSI  HO4   H  HOH1   0   0.455   4.0820  -0.1635  -0.6941
 FSI  H5    H  HCH1   0   0.267   1.2162   0.8856   1.0668
 FSI  HN5   H  HNH1   0   0.396   1.2296   2.1684  -1.5949
 FSI  H6    H  HCH1   0   0.225  -0.4405   0.3674  -1.4398
 FSI  H7    H  HCH1   0   0.240  -1.2315   2.1570   0.1003
 FSI  HO7   H  HOH1   0   0.445  -1.2793   0.0562   1.9673
 FSI  H8    H  HCH1   0   0.233  -2.9718  -0.3470   0.1179
 FSI  HO8   H  HOH1   0   0.443  -2.8155   1.7027  -1.8062
 FSI  H9    H  HCH2   0   0.208  -3.7415   1.4619   1.6358
 FSI  H9A   H  HCH2   0   0.186  -3.6932   2.6097   0.2995
 FSI  HO9   H  HOH1   0   0.454  -5.7902   1.5924   0.6417
 FSI  H11   H  HCH3   0   0.247   1.6377   4.2851  -1.7977
 FSI  H11A  H  HCH3   0   0.264   1.4064   5.2479  -0.3327
 FSI  H11B  H  HCH3   0   0.267   3.0095   4.6674  -0.7540

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
 FSI  C2   O2    single  1.400  0.020  1.400
 FSI  O2   HO2   single  0.850  0.020  0.980
 FSI  O1A  C1    deloc   1.238  0.020  1.238
 FSI  O1B  C1    deloc   1.244  0.020  1.244
 FSI  C1   C2    single  1.561  0.020  1.561
 FSI  F1   C3    single  1.393  0.020  1.393
 FSI  C2   O6    single  1.397  0.020  1.397
 FSI  C2   C3    single  1.525  0.020  1.525
 FSI  C3   C4    single  1.520  0.020  1.520
 FSI  C3   H3    single  0.970  0.020  1.090
 FSI  C5   C4    single  1.527  0.020  1.527
 FSI  C4   O4    single  1.404  0.020  1.404
 FSI  C4   H4    single  0.970  0.020  1.090
 FSI  O4   HO4   single  0.850  0.020  0.980
 FSI  C6   C5    single  1.536  0.020  1.536
 FSI  C5   N5    single  1.441  0.020  1.441
 FSI  C5   H5    single  0.970  0.020  1.090
 FSI  N5   C10   single  1.347  0.020  1.347
 FSI  N5   HN5   single  0.860  0.020  1.020
 FSI  O6   C6    single  1.413  0.020  1.413
 FSI  C7   C6    single  1.527  0.020  1.527
 FSI  C6   H6    single  0.970  0.020  1.090
 FSI  O7   C7    single  1.408  0.020  1.408
 FSI  C8   C7    single  1.541  0.020  1.541
 FSI  C7   H7    single  0.970  0.020  1.090
 FSI  O7   HO7   single  0.850  0.020  0.980
 FSI  C9   C8    single  1.521  0.020  1.521
 FSI  C8   O8    single  1.410  0.020  1.410
 FSI  C8   H8    single  0.970  0.020  1.090
 FSI  O8   HO8   single  0.850  0.020  0.980
 FSI  C9   O9    single  1.409  0.020  1.409
 FSI  C9   H9    single  0.970  0.020  1.090
 FSI  C9   H9A   single  0.970  0.020  1.090
 FSI  O9   HO9   single  0.850  0.020  0.980
 FSI  O10  C10   double  1.222  0.020  1.222
 FSI  C10  C11   single  1.509  0.020  1.509
 FSI  C11  H11   single  0.970  0.020  1.090
 FSI  C11  H11A  single  0.970  0.020  1.090
 FSI  C11  H11B  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
 FSI  HO2   O2   C2    109.59  3.000
 FSI  O1B   C1   O1A   128.25  3.000
 FSI  O1B   C1   C2    113.79  3.000
 FSI  O1A   C1   C2    117.94  3.000
 FSI  O6    C2   C3    109.64  3.000
 FSI  C3    C2   C1    110.75  3.000
 FSI  O6    C2   C1    108.34  3.000
 FSI  C3    C2   O2    105.42  3.000
 FSI  O6    C2   O2    111.70  3.000
 FSI  C1    C2   O2    110.98  3.000
 FSI  H3    C3   C4    110.95  3.000
 FSI  H3    C3   C2    110.33  3.000
 FSI  C4    C3   C2    111.68  3.000
 FSI  H3    C3   F1    107.71  3.000
 FSI  C4    C3   F1    108.78  3.000
 FSI  C2    C3   F1    107.22  3.000
 FSI  H4    C4   C5    108.06  3.000
 FSI  H4    C4   O4    110.83  3.000
 FSI  C5    C4   O4    108.46  3.000
 FSI  H4    C4   C3    106.99  3.000
 FSI  O4    C4   C3    112.05  3.000
 FSI  C5    C4   C3    110.39  3.000
 FSI  HO4   O4   C4    108.52  3.000
 FSI  H5    C5   C6    109.71  3.000
 FSI  H5    C5   N5    107.68  3.000
 FSI  C6    C5   N5    109.78  3.000
 FSI  H5    C5   C4    109.44  3.000
 FSI  N5    C5   C4    110.44  3.000
 FSI  C6    C5   C4    109.76  3.000
 FSI  HN5   N5   C10   117.74  3.000
 FSI  HN5   N5   C5    117.10  3.000
 FSI  C10   N5   C5    124.88  3.000
 FSI  H6    C6   C7    108.78  3.000
 FSI  H6    C6   O6    110.93  3.000
 FSI  C7    C6   O6    105.43  3.000
 FSI  H6    C6   C5    108.18  3.000
 FSI  C7    C6   C5    112.29  3.000
 FSI  O6    C6   C5    111.22  3.000
 FSI  C6    O6   C2    117.02  3.000
 FSI  H7    C7   C8    108.04  3.000
 FSI  H7    C7   O7    106.34  3.000
 FSI  C8    C7   O7    111.26  3.000
 FSI  H7    C7   C6    108.07  3.000
 FSI  C8    C7   C6    111.90  3.000
 FSI  O7    C7   C6    110.98  3.000
 FSI  HO7   O7   C7    107.62  3.000
 FSI  H8    C8   C9    108.60  3.000
 FSI  H8    C8   O8    105.72  3.000
 FSI  C9    C8   O8    111.67  3.000
 FSI  H8    C8   C7    108.62  3.000
 FSI  O8    C8   C7    111.23  3.000
 FSI  C9    C8   C7    110.79  3.000
 FSI  HO8   O8   C8    108.71  3.000
 FSI  H9A   C9   H9    106.72  3.000
 FSI  H9A   C9   O9    111.50  3.000
 FSI  H9    C9   O9    111.54  3.000
 FSI  H9A   C9   C8    109.06  3.000
 FSI  H9    C9   C8    109.13  3.000
 FSI  O9    C9   C8    108.83  3.000
 FSI  HO9   O9   C9    107.81  3.000
 FSI  C11   C10  O10   121.64  3.000
 FSI  C11   C10  N5    114.79  3.000
 FSI  O10   C10  N5    123.57  3.000
 FSI  H11B  C11  H11A  107.37  3.000
 FSI  H11B  C11  H11   108.26  3.000
 FSI  H11A  C11  H11   108.59  3.000
 FSI  H11B  C11  C10   109.22  3.000
 FSI  H11A  C11  C10   109.59  3.000
 FSI  H11   C11  C10   113.63  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
 FSI  CONST_01  O10  C10  N5   C5     0.00   0.0  0
 FSI  CONST_02  C11  C10  N5   C5   180.00   0.0  0
 FSI  CONST_03  HN5  N5   C10  O10  180.00   0.0  0
 FSI  Var_01    H11  C11  C10  N5     6.29  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
 FSI  chir_01  C2  C1  O6  C3  negativ
 FSI  chir_02  C3  F1  C2  C4  negativ
 FSI  chir_03  C4  O4  C3  C5  negativ
 FSI  chir_04  C5  N5  C6  C4  negativ
 FSI  chir_05  C6  O6  C7  C5  negativ
 FSI  chir_06  C7  O7  C6  C8  negativ
 FSI  chir_07  C8  O8  C7  C9  negativ

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
 FSI  plan-1  C5   0.020
 FSI  plan-1  N5   0.020
 FSI  plan-1  C10  0.020
 FSI  plan-1  O10  0.020
 FSI  plan-1  C11  0.020
 FSI  plan-1  HN5  0.020
 FSI  plan-2  C1   0.020
 FSI  plan-2  C2   0.020
 FSI  plan-2  O1A  0.020
 FSI  plan-2  O1B  0.020

