# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:23:25 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  32  18  .  2023-02-15  2023-02-16
;
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   0.001   2.1749  -1.0160   0.5560
 JVS  C03  C  CH1   0   0.023   2.5263   0.3959   0.0922
 JVS  C05  C  CH1   0  -0.086   1.2092   1.1514  -0.0340
 JVS  C06  C  CH2   0  -0.149   1.2865   2.6022  -0.4383
 JVS  C09  C  CT    0   0.428  -0.0226  -0.7669  -0.7031
 JVS  C15  C  CH2   0  -0.013  -0.7684  -1.3285  -1.9044
 JVS  C17  C  CH1   0   0.011   1.1757  -1.6785  -0.3910
 JVS  F16  F  F     0  -0.359  -1.9143  -0.5937  -2.1476
 JVS  O07  O  OH1   0  -0.679  -0.0186   3.1415  -0.2673
 JVS  O08  O  O2    0  -0.500   0.4142   0.5046  -1.0241
 JVS  O10  O  O2    0  -0.624  -0.8553  -0.7366   0.4422
 JVS  O1P  O  OH1   0  -0.777  -2.1405   1.4867  -0.1204
 JVS  O2   O  OH1   0  -0.661   0.6895  -2.8886   0.1183
 JVS  O2P  O  O     0  -0.703  -3.4482  -0.5584   0.5734
 JVS  O3   O  OH1   0  -0.670   3.2992  -1.8575   0.5994
 JVS  O3P  O  OH1   0  -0.738  -1.7744   0.5358   2.2372
 JVS  O4   O  OH1   0  -0.669   3.3703   0.9609   1.0651
 JVS  P    P  P     0   1.434  -2.1670   0.1557   0.7292
 JVS  H1   H  HCH1  0   0.223   1.7108  -0.9330   1.5516
 JVS  H2   H  HCH1  0   0.236   3.0187   0.3491  -0.8890
 JVS  H3   H  HCH1  0   0.240   0.7193   1.1223   0.9503
 JVS  H4   H  HCH2  0   0.227   2.0011   3.1263   0.2019
 JVS  H5   H  HCH2  0   0.235   1.6247   2.6959  -1.4743
 JVS  H6   H  HCH2  0   0.236  -0.1306  -1.2826  -2.7884
 JVS  H7   H  HCH2  0   0.233  -1.0520  -2.3636  -1.7183
 JVS  H8   H  HCH1  0   0.242   1.6917  -1.8320  -1.3519
 JVS  H9   H  HOH1  0   0.482  -0.1376   3.8993  -0.8484
 JVS  H10  H  HOH1  0   0.495  -1.3330   2.0610  -0.1573
 JVS  H11  H  HOH1  0   0.462   1.4052  -3.5317   0.1042
 JVS  H12  H  HOH1  0   0.457   3.9091  -1.5114   1.2590
 JVS  H13  H  HOH1  0   0.496  -2.5158   0.8890   2.7467
 JVS  H14  H  HOH1  0   0.465   3.9424   1.6109   0.6475

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    double  1.475  0.020  1.475
 JVS  O3P  P    single  1.604  0.020  1.604
 JVS  P    O1P  single  1.579  0.020  1.579
 JVS  P    O10  single  1.612  0.020  1.612
 JVS  O10  C09  single  1.416  0.020  1.416
 JVS  C09  C15  single  1.521  0.020  1.521
 JVS  C09  O08  single  1.382  0.020  1.382
 JVS  C09  C17  single  1.538  0.020  1.538
 JVS  C05  O08  single  1.425  0.020  1.425
 JVS  C05  C06  single  1.508  0.020  1.508
 JVS  C05  C03  single  1.524  0.020  1.524
 JVS  C15  F16  single  1.383  0.020  1.383
 JVS  O2   C17  single  1.400  0.020  1.400
 JVS  C02  C17  single  1.528  0.020  1.528
 JVS  C02  C03  single  1.527  0.020  1.527
 JVS  C02  O3   single  1.405  0.020  1.405
 JVS  C06  O07  single  1.422  0.020  1.422
 JVS  O4   C03  single  1.406  0.020  1.406
 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  O1P  H10  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  O3P  H13  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   110.75  3.000
 JVS  H1   C02  C17  108.51  3.000
 JVS  O3   C02  C17  106.42  3.000
 JVS  H1   C02  C03  107.57  3.000
 JVS  O3   C02  C03  112.27  3.000
 JVS  C17  C02  C03  111.29  3.000
 JVS  H2   C03  O4   111.46  3.000
 JVS  H2   C03  C05  109.55  3.000
 JVS  O4   C03  C05  112.14  3.000
 JVS  H2   C03  C02  109.57  3.000
 JVS  O4   C03  C02  107.42  3.000
 JVS  C05  C03  C02  106.54  3.000
 JVS  H3   C05  O08  111.18  3.000
 JVS  H3   C05  C06  106.75  3.000
 JVS  O08  C05  C06  106.20  3.000
 JVS  H3   C05  C03  107.33  3.000
 JVS  C06  C05  C03  117.06  3.000
 JVS  O08  C05  C03  108.35  3.000
 JVS  H5   C06  H4   108.15  3.000
 JVS  H5   C06  O07  111.41  3.000
 JVS  H4   C06  O07  110.34  3.000
 JVS  H5   C06  C05  110.62  3.000
 JVS  H4   C06  C05  109.74  3.000
 JVS  O07  C06  C05  106.58  3.000
 JVS  O10  C09  O08  110.73  3.000
 JVS  O08  C09  C17  110.26  3.000
 JVS  O10  C09  C17  107.87  3.000
 JVS  C17  C09  C15  108.87  3.000
 JVS  O08  C09  C15  108.13  3.000
 JVS  O10  C09  C15  110.99  3.000
 JVS  H7   C15  H6   109.30  3.000
 JVS  H7   C15  F16  108.62  3.000
 JVS  H6   C15  F16  108.63  3.000
 JVS  H7   C15  C09  110.09  3.000
 JVS  H6   C15  C09  109.73  3.000
 JVS  F16  C15  C09  110.42  3.000
 JVS  H8   C17  O2   111.08  3.000
 JVS  H8   C17  C09  105.70  3.000
 JVS  O2   C17  C09  108.39  3.000
 JVS  H8   C17  C02  107.15  3.000
 JVS  O2   C17  C02  112.11  3.000
 JVS  C09  C17  C02  112.23  3.000
 JVS  H9   O07  C06  109.84  3.000
 JVS  C09  O08  C05  115.62  3.000
 JVS  P    O10  C09  129.36  3.000
 JVS  H10  O1P  P    121.46  3.000
 JVS  H11  O2   C17  108.30  3.000
 JVS  H12  O3   C02  108.23  3.000
 JVS  H13  O3P  P    113.23  3.000
 JVS  H14  O4   C03  109.16  3.000
 JVS  O3P  P    O2P  115.25  3.000
 JVS  O3P  P    O1P  107.58  3.000
 JVS  O2P  P    O1P  111.46  3.000
 JVS  O1P  P    O10  110.92  3.000
 JVS  O3P  P    O10   95.71  3.000
 JVS  O2P  P    O10  114.83  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  102.23  30.0  2

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

