# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 15:16:45 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  28  16  .  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_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  -0.044  -0.0348   0.9269   0.6125
 JVA  C2   C  CH1    0   0.177   1.2897   1.6370   0.3838
 JVA  C3   C  CH1    0  -0.035   2.1143   0.9090  -0.6634
 JVA  C4   C  CH1    0   0.023   2.2542  -0.5689  -0.3187
 JVA  C5   C  CH1    0   0.019   0.8899  -1.1887   0.0185
 JVA  C6   C  CH2    0  -0.161   1.1012  -2.5743   0.5980
 JVA  C7   C  CH2    0  -0.779  -0.9814   1.1109  -0.5659
 JVA  O3   O  OH1    0  -0.677   3.4141   1.4390  -0.7999
 JVA  F2   F  F      0  -0.388   2.0135   1.6641   1.5825
 JVA  O1P  O  OP    -1  -0.913  -3.1120   0.6993   1.0475
 JVA  O2P  O  OP    -1  -0.919  -3.5037   1.0527  -1.4661
 JVA  O3P  O  O      0  -0.886  -2.5054  -1.1558  -0.6373
 JVA  O4   O  OH1    0  -0.676   2.8062  -1.2869  -1.3986
 JVA  O5   O  O2     0  -0.493   0.2255  -0.4131   0.9848
 JVA  O6   O  OH1    0  -0.661  -0.1329  -3.2156   0.8053
 JVA  P    P  P      0   1.177  -2.6748   0.3439  -0.3817
 JVA  H1   H  HCH1   0   0.230  -0.5221   1.3690   1.4864
 JVA  H2   H  HCH1   0   0.216   1.1204   2.6775   0.0888
 JVA  H3   H  HCH1   0   0.226   1.5680   0.9799  -1.6126
 JVA  H4   H  HCH1   0   0.202   2.8960  -0.6530   0.5721
 JVA  H5   H  HCH1   0   0.215   0.2844  -1.2622  -0.8945
 JVA  H6   H  HCH2   0   0.201   1.7352  -3.1417  -0.0928
 JVA  H7   H  HCH2   0   0.184   1.6666  -2.4732   1.5367
 JVA  H8   H  HCH2   0   0.207  -1.1141   2.1920  -0.6868
 JVA  H9   H  HCH2   0   0.204  -0.5392   0.7653  -1.5057
 JVA  H10  H  HOH1   0   0.456   3.3656   2.2483  -1.3179
 JVA  H13  H  HOH1   0   0.450   3.6601  -0.8953  -1.6095
 JVA  H14  H  HOH1   0   0.449   0.0557  -4.0915   1.1534

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    deloc   1.531  0.020  1.531
 JVA  O2P  P    deloc   1.538  0.020  1.538
 JVA  P    O1P  deloc   1.536  0.020  1.536
 JVA  P    C7   single  1.868  0.020  1.868
 JVA  C7   C1   single  1.523  0.020  1.523
 JVA  C1   O5   single  1.415  0.020  1.415
 JVA  C1   C2   single  1.520  0.020  1.520
 JVA  O5   C5   single  1.406  0.020  1.406
 JVA  C5   C6   single  1.517  0.020  1.517
 JVA  C5   C4   single  1.536  0.020  1.536
 JVA  C6   O6   single  1.406  0.020  1.406
 JVA  C3   C2   single  1.519  0.020  1.519
 JVA  C3   C4   single  1.524  0.020  1.524
 JVA  C3   O3   single  1.410  0.020  1.410
 JVA  C2   F2   single  1.401  0.020  1.401
 JVA  C4   O4   single  1.409  0.020  1.409
 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  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   104.74  3.000
 JVA  H1   C1  C7   107.01  3.000
 JVA  O5   C1  C7   115.63  3.000
 JVA  H1   C1  C2   108.63  3.000
 JVA  O5   C1  C2   108.76  3.000
 JVA  C7   C1  C2   111.64  3.000
 JVA  H2   C2  F2   106.99  3.000
 JVA  H2   C2  C3   110.72  3.000
 JVA  F2   C2  C3   108.59  3.000
 JVA  H2   C2  C1   110.48  3.000
 JVA  F2   C2  C1   109.31  3.000
 JVA  C3   C2  C1   110.66  3.000
 JVA  H3   C3  O3   110.54  3.000
 JVA  H3   C3  C4   107.69  3.000
 JVA  O3   C3  C4   107.56  3.000
 JVA  H3   C3  C2   107.17  3.000
 JVA  O3   C3  C2   112.77  3.000
 JVA  C4   C3  C2   111.02  3.000
 JVA  H4   C4  O4   110.65  3.000
 JVA  H4   C4  C5   108.01  3.000
 JVA  O4   C4  C5   108.09  3.000
 JVA  H4   C4  C3   108.09  3.000
 JVA  O4   C4  C3   110.90  3.000
 JVA  C5   C4  C3   111.07  3.000
 JVA  H5   C5  O5   110.35  3.000
 JVA  H5   C5  C6   109.48  3.000
 JVA  O5   C5  C6   107.89  3.000
 JVA  H5   C5  C4   109.53  3.000
 JVA  C6   C5  C4   109.19  3.000
 JVA  O5   C5  C4   110.36  3.000
 JVA  H7   C6  H6   106.74  3.000
 JVA  H7   C6  O6   111.53  3.000
 JVA  H6   C6  O6   111.37  3.000
 JVA  H7   C6  C5   108.28  3.000
 JVA  H6   C6  C5   108.23  3.000
 JVA  O6   C6  C5   110.53  3.000
 JVA  H9   C7  H8   105.40  3.000
 JVA  H9   C7  P    108.74  3.000
 JVA  H8   C7  P    107.83  3.000
 JVA  H9   C7  C1   112.03  3.000
 JVA  H8   C7  C1   106.25  3.000
 JVA  P    C7  C1   115.95  3.000
 JVA  H10  O3  C3   108.77  3.000
 JVA  H13  O4  C4   107.93  3.000
 JVA  C5   O5  C1   115.38  3.000
 JVA  H14  O6  C6   107.27  3.000
 JVA  O3P  P   O2P  113.17  3.000
 JVA  O2P  P   O1P  113.32  3.000
 JVA  O3P  P   O1P  114.43  3.000
 JVA  O1P  P   C7   104.76  3.000
 JVA  O2P  P   C7   103.29  3.000
 JVA  O3P  P   C7   106.59  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  -77.74  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
 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

