# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:50:54 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 1-deoxy-1-fluoro-2-O-phosphono-alpha-D-gluco-hept-2-ulopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@](CF)(O[P](O)(O)=O)[C@H](O)[C@@H](O)[C@@H]1O
#
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
 JVS  JVS  1-deoxy-1-fluoro-2-O-phosphono-alpha-D-gluco-hept-2-ulopyranose  D-saccharide  30  18  .  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_JVS
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
 JVS  C02  C  CH1    0   0.008   2.1224  -0.9549   0.5694
 JVS  C03  C  CH1    0   0.033   2.4682   0.4747   0.1782
 JVS  C05  C  CH1    0   0.010   1.1954   1.2862  -0.1055
 JVS  C06  C  CH2    0  -0.161   1.5582   2.6268  -0.7099
 JVS  C09  C  CT     0   0.456  -0.0584  -0.6743  -0.6126
 JVS  C15  C  CH2    0  -0.027  -0.9003  -1.2118  -1.7723
 JVS  C17  C  CH1    0   0.017   1.1911  -1.5672  -0.4658
 JVS  F16  F  F      0  -0.308  -1.7968  -0.2665  -2.2412
 JVS  O07  O  OH1    0  -0.657   0.4089   3.4251  -0.8513
 JVS  O08  O  O2     0  -0.506   0.3906   0.5970  -1.0346
 JVS  O10  O  O2     0  -0.633  -0.6729  -0.6609   0.6060
 JVS  O1P  O  OP    -1  -0.908  -2.3592   1.3129   0.5600
 JVS  O2   O  OH1    0  -0.710   0.7830  -2.8664  -0.1150
 JVS  O2P  O  O      0  -0.904  -3.1916  -1.1038   0.2604
 JVS  O3   O  OH1    0  -0.682   3.2778  -1.7654   0.6367
 JVS  O3P  O  OP    -1  -0.958  -2.2218  -0.3523   2.5054
 JVS  O4   O  OH1    0  -0.695   3.2280   1.0303   1.2354
 JVS  P    P  P      0   1.202  -2.2728  -0.1369   0.9979
 JVS  H1   H  HCH1   0   0.202   1.6074  -0.9363   1.5398
 JVS  H2   H  HCH1   0   0.210   3.0656   0.4352  -0.7454
 JVS  H3   H  HCH1   0   0.210   0.6516   1.4523   0.8326
 JVS  H4   H  HCH2   0   0.191   2.2942   3.1085  -0.0531
 JVS  H5   H  HCH2   0   0.178   2.0560   2.4588  -1.6761
 JVS  H6   H  HCH2   0   0.168  -0.2504  -1.4807  -2.6096
 JVS  H7   H  HCH2   0   0.171  -1.4552  -2.0912  -1.4531
 JVS  H8   H  HCH1   0   0.288   1.7191  -1.5769  -1.4331
 JVS  H9   H  HOH1   0   0.448   0.6864   4.2646  -1.2285
 JVS  H11  H  HOH1   0   0.447   1.5706  -3.4155  -0.0510
 JVS  H12  H  HOH1   0   0.459   3.8412  -1.4170   1.3346
 JVS  H14  H  HOH1   0   0.452   3.8677   1.6457   0.8693

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
 JVS  O2P  P    deloc   1.524  0.020  1.524
 JVS  O3P  P    deloc   1.524  0.020  1.524
 JVS  P    O1P  deloc   1.517  0.020  1.517
 JVS  P    O10  single  1.729  0.020  1.729
 JVS  O10  C09  single  1.365  0.020  1.365
 JVS  C09  C15  single  1.531  0.020  1.531
 JVS  C09  O08  single  1.413  0.020  1.413
 JVS  C09  C17  single  1.543  0.020  1.543
 JVS  C05  O08  single  1.409  0.020  1.409
 JVS  C05  C06  single  1.515  0.020  1.515
 JVS  C05  C03  single  1.536  0.020  1.536
 JVS  C15  F16  single  1.385  0.020  1.385
 JVS  O2   C17  single  1.406  0.020  1.406
 JVS  C02  C17  single  1.521  0.020  1.521
 JVS  C02  C03  single  1.522  0.020  1.522
 JVS  C02  O3   single  1.413  0.020  1.413
 JVS  C06  O07  single  1.406  0.020  1.406
 JVS  O4   C03  single  1.415  0.020  1.415
 JVS  C02  H1   single  0.970  0.020  1.090
 JVS  C03  H2   single  0.970  0.020  1.090
 JVS  C05  H3   single  0.970  0.020  1.090
 JVS  C06  H4   single  0.970  0.020  1.090
 JVS  C06  H5   single  0.970  0.020  1.090
 JVS  C15  H6   single  0.970  0.020  1.090
 JVS  C15  H7   single  0.970  0.020  1.090
 JVS  C17  H8   single  0.970  0.020  1.090
 JVS  O07  H9   single  0.850  0.020  0.980
 JVS  O2   H11  single  0.850  0.020  0.980
 JVS  O3   H12  single  0.850  0.020  0.980
 JVS  O4   H14  single  0.850  0.020  0.980

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
 JVS  H1   C02  O3   110.54  3.000
 JVS  H1   C02  C17  108.72  3.000
 JVS  O3   C02  C17  107.59  3.000
 JVS  H1   C02  C03  108.52  3.000
 JVS  O3   C02  C03  111.42  3.000
 JVS  C17  C02  C03  110.02  3.000
 JVS  H2   C03  O4   110.46  3.000
 JVS  H2   C03  C05  108.28  3.000
 JVS  O4   C03  C05  112.05  3.000
 JVS  H2   C03  C02  107.77  3.000
 JVS  O4   C03  C02  107.38  3.000
 JVS  C05  C03  C02  110.82  3.000
 JVS  H3   C05  O08  110.77  3.000
 JVS  H3   C05  C06  109.02  3.000
 JVS  O08  C05  C06  107.85  3.000
 JVS  H3   C05  C03  109.44  3.000
 JVS  C06  C05  C03  110.05  3.000
 JVS  O08  C05  C03  109.68  3.000
 JVS  H5   C06  H4   106.81  3.000
 JVS  H5   C06  O07  111.61  3.000
 JVS  H4   C06  O07  111.04  3.000
 JVS  H5   C06  C05  108.89  3.000
 JVS  H4   C06  C05  108.07  3.000
 JVS  O07  C06  C05  110.29  3.000
 JVS  O10  C09  O08  113.64  3.000
 JVS  O08  C09  C17  106.97  3.000
 JVS  O10  C09  C17  106.58  3.000
 JVS  C17  C09  C15  108.32  3.000
 JVS  O08  C09  C15  105.34  3.000
 JVS  O10  C09  C15  115.62  3.000
 JVS  H7   C15  H6   109.22  3.000
 JVS  H7   C15  F16  108.73  3.000
 JVS  H6   C15  F16  107.06  3.000
 JVS  H7   C15  C09  110.01  3.000
 JVS  H6   C15  C09  109.85  3.000
 JVS  F16  C15  C09  111.90  3.000
 JVS  H8   C17  O2   110.48  3.000
 JVS  H8   C17  C09  108.04  3.000
 JVS  O2   C17  C09  108.87  3.000
 JVS  H8   C17  C02  107.91  3.000
 JVS  O2   C17  C02  112.32  3.000
 JVS  C09  C17  C02  109.13  3.000
 JVS  H9   O07  C06  107.41  3.000
 JVS  C09  O08  C05  115.13  3.000
 JVS  P    O10  C09  128.47  3.000
 JVS  H11  O2   C17  107.84  3.000
 JVS  H12  O3   C02  107.80  3.000
 JVS  H14  O4   C03  108.93  3.000
 JVS  O3P  P    O2P  114.15  3.000
 JVS  O3P  P    O1P  115.00  3.000
 JVS  O2P  P    O1P  115.62  3.000
 JVS  O1P  P    O10  106.08  3.000
 JVS  O3P  P    O10   98.65  3.000
 JVS  O2P  P    O10  104.83  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
 JVS  Var_01  O2P  P  O10  C09  64.48  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
 JVS  chir_01  C02  C17  C03  O3   positiv
 JVS  chir_02  C03  O4   C05  C02  positiv
 JVS  chir_03  C05  O08  C03  C06  negativ
 JVS  chir_04  C09  O08  C17  C15  positiv
 JVS  chir_05  C17  O2   C09  C02  negativ

