# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 10:42:52 2019
#
#   Ligand name: 6-deoxy-6-fluoro-1-O-phosphono-alpha-D-glucopyranose
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](O)[C@@H](CF)O[C@H](O[P](O)(O)=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
JV4        JV4 '6-deoxy-6-fluoro-1-O-phosphono-alpha-D-glucopyranose' ligand 26 16 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_JV4
#
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
JV4         C02    C   CH1    0    .      -0.5130    0.5424   -1.5172
JV4         C03    C   CH1    0    .       0.9710    0.5485   -1.5176
JV4         C05    C   CH1    0    .       1.5666    0.5602   -0.0830
JV4         C06    C   CH2    0    .       1.2516    1.7736    0.5573
JV4         C09    C   CH1    0    .      -0.5363   -0.6107    0.6560
JV4         C15    C   CH1    0    .      -1.0715   -0.5696   -0.7273
JV4         F07    F   F      0    .       1.9738    1.8792    1.7134
JV4         O08    O   O2     0    .       0.9396   -0.6257    0.6914
JV4         O10    O   O2     0    .      -1.0109   -1.7568    1.2858
JV4         O1P    O   OP    -1    .      -1.8988   -0.7364    3.4788
JV4         O2     O   OH1    0    .      -0.7414   -1.8365   -1.3978
JV4         O2P    O   O      0    .      -1.4902   -3.1665    3.4001
JV4         O3     O   OH1    0    .      -0.9871    1.8058   -0.9486
JV4         O3P    O   OP    -1    .       0.4100   -1.5875    3.4345
JV4         O4     O   OH1    0    .       1.4339   -0.6146   -2.1952
JV4         P11    P   P      0    .      -0.9976   -1.8108    2.9349
JV4         H1     H   HCH1   0    .      -0.8616    0.4572   -2.5343
JV4         H2     H   HCH1   0    .       1.3177    1.4331   -2.0481
JV4         H3     H   HCH1   0    .       2.6479    0.4340   -0.1339
JV4         H4     H   HCH2   0    .       0.1948    1.7957    0.7894
JV4         H5     H   HCH2   0    .       1.4964    2.6075   -0.1022
JV4         H6     H   HCH1   0    .      -0.8895    0.2626    1.1924
JV4         H7     H   HCH1   0    .      -2.1529   -0.4599   -0.6824
JV4         H9     H   HOH1   0    .      -1.5293   -2.2098   -1.7762
JV4         H10    H   HOH1   0    .      -1.5442    2.2446   -1.5752
JV4         H12    H   HOH1   0    .       2.0211   -0.3596   -2.8950
#
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
JV4   O2P     P11   deloc         1.516 0.020     1.516
JV4   O3P     P11   deloc         1.510 0.020     1.510
JV4   P11     O1P   deloc         1.504 0.020     1.504
JV4   P11     O10   single        1.650 0.020     1.650
JV4   O10     C09   single        1.391 0.020     1.391
JV4   C09     O08   single        1.476 0.020     1.476
JV4   C09     C15   single        1.484 0.020     1.484
JV4   O08     C05   single        1.549 0.020     1.549
JV4   C05     C06   single        1.408 0.020     1.408
JV4   C05     C03   single        1.553 0.020     1.553
JV4   O2      C15   single        1.471 0.020     1.471
JV4   C06     F07   single        1.367 0.020     1.367
JV4   C02     C15   single        1.474 0.020     1.474
JV4   C02     C03   single        1.484 0.020     1.484
JV4   C02     O3    single        1.464 0.020     1.464
JV4   C03     O4    single        1.423 0.020     1.423
JV4   C02     H1    single        0.970 0.020     1.090
JV4   C03     H2    single        0.970 0.020     1.090
JV4   C05     H3    single        0.970 0.020     1.090
JV4   C06     H4    single        0.970 0.020     1.090
JV4   C06     H5    single        0.970 0.020     1.090
JV4   C09     H6    single        0.970 0.020     1.090
JV4   C15     H7    single        0.970 0.020     1.090
JV4   O2      H9    single        0.850 0.020     0.980
JV4   O3      H10   single        0.850 0.020     0.980
JV4   O4      H12   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
JV4   H1      C02     O3          109.26 3.000
JV4   H1      C02     C15         108.86 3.000
JV4   O3      C02     C15         108.67 3.000
JV4   H1      C02     C03         108.86 3.000
JV4   O3      C02     C03         108.68 3.000
JV4   C15     C02     C03         112.47 3.000
JV4   H2      C03     O4          109.18 3.000
JV4   H2      C03     C05         108.78 3.000
JV4   O4      C03     C05         108.73 3.000
JV4   H2      C03     C02         108.79 3.000
JV4   O4      C03     C02         108.78 3.000
JV4   C05     C03     C02         112.53 3.000
JV4   H3      C05     O08         109.65 3.000
JV4   H3      C05     C06         110.06 3.000
JV4   O08     C05     C06         110.00 3.000
JV4   H3      C05     C03         109.66 3.000
JV4   C06     C05     C03         109.92 3.000
JV4   O08     C05     C03         107.51 3.000
JV4   H5      C06     H4          109.46 3.000
JV4   H5      C06     F07         109.49 3.000
JV4   H4      C06     F07         109.45 3.000
JV4   H5      C06     C05         109.49 3.000
JV4   H4      C06     C05         109.49 3.000
JV4   F07     C06     C05         109.45 3.000
JV4   H6      C09     O10         109.18 3.000
JV4   H6      C09     O08         108.78 3.000
JV4   O10     C09     O08         108.77 3.000
JV4   H6      C09     C15         108.75 3.000
JV4   O08     C09     C15         112.53 3.000
JV4   O10     C09     C15         108.78 3.000
JV4   H7      C15     O2          109.19 3.000
JV4   H7      C15     C09         108.84 3.000
JV4   O2      C15     C09         108.67 3.000
JV4   H7      C15     C02         108.83 3.000
JV4   O2      C15     C02         108.69 3.000
JV4   C09     C15     C02         112.58 3.000
JV4   C09     O08     C05         112.64 3.000
JV4   P11     O10     C09         118.47 3.000
JV4   H9      O2      C15         109.49 3.000
JV4   H10     O3      C02         109.48 3.000
JV4   H12     O4      C03         109.44 3.000
JV4   O3P     P11     O2P         109.49 3.000
JV4   O3P     P11     O1P         109.47 3.000
JV4   O2P     P11     O1P         109.46 3.000
JV4   O1P     P11     O10         109.46 3.000
JV4   O3P     P11     O10         109.47 3.000
JV4   O2P     P11     O10         109.48 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
JV4 Var_01         O2P     P11     O10     C09        -177.24  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
JV4 chir_01   C02     C15     C03     O3    positiv
JV4 chir_02   C03     O4      C02     C05   negativ
JV4 chir_03   C05     O08     C03     C06   negativ
JV4 chir_04   C09     O08     O10     C15   positiv
JV4 chir_05   C15     O2      C09     C02   negativ
