# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 18:19:08 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 2,6-anhydro-5,7-dideoxy-5-fluoro-7-phosphono-D-glycero-D-manno-heptitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](C[P](O)(O)=O)[C@@H](F)[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
 JVA  JVA  2,6-anhydro-5,7-dideoxy-5-fluoro-7-phosphono-D-glycero-D-manno-heptitol  D-saccharide  30  16  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JVA
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
 JVA  C1   C  CH1   0  -0.059  -0.0759   0.9619   0.5416
 JVA  C2   C  CH1   0   0.176   1.2419   1.6731   0.2716
 JVA  C3   C  CH1   0  -0.037   2.1008   0.8853  -0.7034
 JVA  C4   C  CH1   0   0.028   2.2522  -0.5609  -0.2452
 JVA  C5   C  CH1   0  -0.004   0.8762  -1.1762   0.0350
 JVA  C6   C  CH2   0  -0.157   1.0275  -2.5424   0.6735
 JVA  C7   C  CH2   0  -0.831  -1.0266   1.1121  -0.6489
 JVA  O3   O  OH1   0  -0.671   3.3896   1.4316  -0.8377
 JVA  F2   F  F     0  -0.376   1.9268   1.7894   1.4795
 JVA  O1P  O  OH1   0  -0.750  -3.0947   0.4074   1.0281
 JVA  O2P  O  OH1   0  -0.747  -3.5301   1.0673  -1.4262
 JVA  O3P  O  O     0  -0.697  -2.5294  -1.2589  -0.7875
 JVA  O4   O  OH1   0  -0.672   2.8744  -1.3390  -1.2383
 JVA  O5   O  O2    0  -0.485   0.1438  -0.3685   0.9356
 JVA  O6   O  OH1   0  -0.659  -0.2351  -3.1424   0.8185
 JVA  P    P  P     0   1.388  -2.5705   0.1874  -0.4777
 JVA  H1   H  HCH1  0   0.277  -0.5420   1.4449   1.4045
 JVA  H2   H  HCH1  0   0.239   1.0589   2.6861  -0.0997
 JVA  H3   H  HCH1  0   0.234   1.5799   0.8760  -1.6707
 JVA  H4   H  HCH1  0   0.216   2.8369  -0.5746   0.6871
 JVA  H5   H  HCH1  0   0.225   0.3352  -1.2813  -0.9168
 JVA  H6   H  HCH2  0   0.208   1.6901  -3.1436   0.0416
 JVA  H7   H  HCH2  0   0.193   1.5340  -2.4189   1.6419
 JVA  H8   H  HCH2  0   0.313  -1.2662   2.1719  -0.7635
 JVA  H9   H  HCH2  0   0.300  -0.5807   0.7955  -1.5947
 JVA  H10  H  HOH1  0   0.461   3.3496   2.1863  -1.4330
 JVA  H11  H  HOH1  0   0.489  -3.2603   1.3233   1.2864
 JVA  H12  H  HOH1  0   0.492  -4.3627   0.6284  -1.6490
 JVA  H13  H  HOH1  0   0.454   3.7451  -0.9651  -1.4092
 JVA  H14  H  HOH1  0   0.452  -0.0997  -4.0083   1.2133

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
 JVA  O3P  P    double  1.480  0.020  1.480
 JVA  O2P  P    single  1.611  0.020  1.611
 JVA  P    O1P  single  1.610  0.020  1.610
 JVA  P    C7   single  1.808  0.020  1.808
 JVA  C7   C1   single  1.531  0.020  1.531
 JVA  C1   O5   single  1.405  0.020  1.405
 JVA  C1   C2   single  1.522  0.020  1.522
 JVA  O5   C5   single  1.414  0.020  1.414
 JVA  C5   C6   single  1.516  0.020  1.516
 JVA  C5   C4   single  1.533  0.020  1.533
 JVA  C6   O6   single  1.405  0.020  1.405
 JVA  C3   C2   single  1.519  0.020  1.519
 JVA  C3   C4   single  1.525  0.020  1.525
 JVA  C3   O3   single  1.406  0.020  1.406
 JVA  C2   F2   single  1.393  0.020  1.393
 JVA  C4   O4   single  1.407  0.020  1.407
 JVA  C1   H1   single  0.970  0.020  1.090
 JVA  C2   H2   single  0.970  0.020  1.090
 JVA  C3   H3   single  0.970  0.020  1.090
 JVA  C4   H4   single  0.970  0.020  1.090
 JVA  C5   H5   single  0.970  0.020  1.090
 JVA  C6   H6   single  0.970  0.020  1.090
 JVA  C6   H7   single  0.970  0.020  1.090
 JVA  C7   H8   single  0.970  0.020  1.090
 JVA  C7   H9   single  0.970  0.020  1.090
 JVA  O3   H10  single  0.850  0.020  0.980
 JVA  O1P  H11  single  0.850  0.020  0.980
 JVA  O2P  H12  single  0.850  0.020  0.980
 JVA  O4   H13  single  0.850  0.020  0.980
 JVA  O6   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
 JVA  H1   C1   O5   105.29  3.000
 JVA  H1   C1   C7   107.80  3.000
 JVA  O5   C1   C7   114.09  3.000
 JVA  H1   C1   C2   107.63  3.000
 JVA  O5   C1   C2   110.91  3.000
 JVA  C7   C1   C2   110.73  3.000
 JVA  H2   C2   F2   107.40  3.000
 JVA  H2   C2   C3   110.90  3.000
 JVA  F2   C2   C3   108.76  3.000
 JVA  H2   C2   C1   110.36  3.000
 JVA  F2   C2   C1   108.11  3.000
 JVA  C3   C2   C1   111.17  3.000
 JVA  H3   C3   O3   110.72  3.000
 JVA  H3   C3   C4   107.67  3.000
 JVA  O3   C3   C4   107.83  3.000
 JVA  H3   C3   C2   107.53  3.000
 JVA  O3   C3   C2   112.21  3.000
 JVA  C4   C3   C2   110.80  3.000
 JVA  H4   C4   O4   110.86  3.000
 JVA  H4   C4   C5   108.48  3.000
 JVA  O4   C4   C5   107.70  3.000
 JVA  H4   C4   C3   108.61  3.000
 JVA  O4   C4   C3   110.88  3.000
 JVA  C5   C4   C3   110.28  3.000
 JVA  H5   C5   O5   110.54  3.000
 JVA  H5   C5   C6   109.12  3.000
 JVA  O5   C5   C6   107.35  3.000
 JVA  H5   C5   C4   108.76  3.000
 JVA  C6   C5   C4   110.44  3.000
 JVA  O5   C5   C4   110.61  3.000
 JVA  H7   C6   H6   106.91  3.000
 JVA  H7   C6   O6   111.77  3.000
 JVA  H6   C6   O6   111.64  3.000
 JVA  H7   C6   C5   108.40  3.000
 JVA  H6   C6   C5   108.19  3.000
 JVA  O6   C6   C5   109.80  3.000
 JVA  H9   C7   H8   106.25  3.000
 JVA  H9   C7   P    106.40  3.000
 JVA  H8   C7   P    108.59  3.000
 JVA  H9   C7   C1   113.04  3.000
 JVA  H8   C7   C1   108.24  3.000
 JVA  P    C7   C1   113.99  3.000
 JVA  H10  O3   C3   109.01  3.000
 JVA  H11  O1P  P    115.82  3.000
 JVA  H12  O2P  P    113.61  3.000
 JVA  H13  O4   C4   108.09  3.000
 JVA  C5   O5   C1   116.31  3.000
 JVA  H14  O6   C6   107.48  3.000
 JVA  O3P  P    O2P  115.29  3.000
 JVA  O2P  P    O1P  106.39  3.000
 JVA  O3P  P    O1P  109.79  3.000
 JVA  O1P  P    C7   107.27  3.000
 JVA  O2P  P    C7    99.99  3.000
 JVA  O3P  P    C7   117.16  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
 JVA  Var_01  O3P  P  C7  C1  -80.38  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
 JVA  chir_01  C1  C7  O5  C2  negativ
 JVA  chir_02  C2  F2  C3  C1  negativ
 JVA  chir_03  C3  O3  C2  C4  positiv
 JVA  chir_04  C4  O4  C5  C3  positiv
 JVA  chir_05  C5  O5  C4  C6  negativ

