# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 12:04:40 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: [(1E,3R,4S)-4-fluoro-3,5-dihydroxy-4-methylpent-1-en-1-yl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](F)(CO)[C@H](O)/C=C/[P](O)(O)=O
#
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
 SG3  SG3  '[(1E,3R,4S)-4-fluoro-3,5-dihydroxy-4-methylpent-1-en-1-yl]phosphonic acid'  ligand  23  13  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SG3
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
 SG3  O3    O  OP    -1  -0.896   2.7009   1.5580  -0.5394
 SG3  P     P  P      0   1.144   2.9205   0.1249  -0.0447
 SG3  O4    O  OP    -1  -0.905   3.7742  -0.7384  -0.9812
 SG3  O2    O  O      0  -0.904   3.3443   0.0274   1.4254
 SG3  C5    C  C1     0  -0.572   1.2640  -0.6834  -0.0910
 SG3  C6    C  C1     0  -0.250   0.1436  -0.1070  -0.5219
 SG3  C7    C  CH1    0  -0.052  -1.2155  -0.7490  -0.5939
 SG3  O13   O  OH1    0  -0.663  -1.2578  -2.0450  -0.0506
 SG3  C8    C  CT     0   0.331  -2.3121   0.1382   0.0424
 SG3  C12   C  CH3    0  -0.719  -2.0879   0.3736   1.5219
 SG3  F11   F  F      0  -0.392  -2.2264   1.3847  -0.6062
 SG3  C9    C  CH2    0  -0.171  -3.6849  -0.4308  -0.2732
 SG3  O10   O  OH1    0  -0.672  -4.6820   0.3835   0.2926
 SG3  H5C2  H  H      0   0.195   1.2233  -1.7195   0.2485
 SG3  H6C2  H  H      0   0.228   0.1970   0.9165  -0.8797
 SG3  H7    H  HCH1   0   0.244  -1.4828  -0.8652  -1.6536
 SG3  H13   H  HOH1   0   0.449  -0.8139  -2.0324   0.8050
 SG3  H121  H  HCH3   0   0.247  -1.0756   0.7326   1.7100
 SG3  H122  H  HCH3   0   0.254  -2.7896   1.1075   1.9145
 SG3  H123  H  HCH3   0   0.231  -2.2292  -0.5454   2.0909
 SG3  H9C1  H  HCH2   0   0.207  -3.7902  -0.4971  -1.3658
 SG3  H9C2  H  HCH2   0   0.209  -3.7283  -1.4546   0.1126
 SG3  H10   H  HOH1   0   0.458  -5.5237  -0.0706   0.1986

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
 SG3  O3   P     deloc   1.532  0.020  1.532
 SG3  P    O4    deloc   1.533  0.020  1.533
 SG3  P    O2    deloc   1.533  0.020  1.533
 SG3  P    C5    single  1.844  0.020  1.844
 SG3  C5   C6    double  1.332  0.020  1.332
 SG3  C5   H5C2  single  0.930  0.020  1.080
 SG3  C6   C7    single  1.505  0.020  1.505
 SG3  C6   H6C2  single  0.930  0.020  1.080
 SG3  C7   O13   single  1.406  0.020  1.406
 SG3  C7   C8    single  1.547  0.020  1.547
 SG3  C7   H7    single  0.970  0.020  1.090
 SG3  O13  H13   single  0.850  0.020  0.980
 SG3  C8   C12   single  1.515  0.020  1.515
 SG3  C8   F11   single  1.408  0.020  1.408
 SG3  C8   C9    single  1.519  0.020  1.519
 SG3  C12  H121  single  0.970  0.020  1.090
 SG3  C12  H122  single  0.970  0.020  1.090
 SG3  C12  H123  single  0.970  0.020  1.090
 SG3  C9   O10   single  1.406  0.020  1.406
 SG3  C9   H9C1  single  0.970  0.020  1.090
 SG3  C9   H9C2  single  0.970  0.020  1.090
 SG3  O10  H10   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
 SG3  C5    P    O2    104.15  3.000
 SG3  C5    P    O4    103.77  3.000
 SG3  O2    P    O4    113.33  3.000
 SG3  C5    P    O3    105.86  3.000
 SG3  O2    P    O3    114.12  3.000
 SG3  O4    P    O3    114.16  3.000
 SG3  H5C2  C5   C6    118.71  3.000
 SG3  H5C2  C5   P     116.23  3.000
 SG3  C6    C5   P     125.05  3.000
 SG3  H6C2  C6   C7    115.52  3.000
 SG3  H6C2  C6   C5    118.26  3.000
 SG3  C7    C6   C5    126.21  3.000
 SG3  H7    C7   C8    106.54  3.000
 SG3  H7    C7   O13   105.53  3.000
 SG3  C8    C7   O13   110.38  3.000
 SG3  H7    C7   C6    108.12  3.000
 SG3  C8    C7   C6    112.08  3.000
 SG3  O13   C7   C6    113.70  3.000
 SG3  H13   O13  C7    108.49  3.000
 SG3  C9    C8   F11   106.92  3.000
 SG3  C9    C8   C12   113.26  3.000
 SG3  F11   C8   C12   107.66  3.000
 SG3  C9    C8   C7    109.89  3.000
 SG3  F11   C8   C7    105.97  3.000
 SG3  C12   C8   C7    112.69  3.000
 SG3  H123  C12  H122  107.25  3.000
 SG3  H123  C12  H121  107.93  3.000
 SG3  H122  C12  H121  108.32  3.000
 SG3  H123  C12  C8    111.08  3.000
 SG3  H122  C12  C8    111.19  3.000
 SG3  H121  C12  C8    110.92  3.000
 SG3  H9C2  C9   H9C1  106.86  3.000
 SG3  H9C2  C9   O10   111.81  3.000
 SG3  H9C1  C9   O10   111.52  3.000
 SG3  H9C2  C9   C8    108.23  3.000
 SG3  H9C1  C9   C8    108.39  3.000
 SG3  O10   C9   C8    109.89  3.000
 SG3  H10   O10  C9    107.94  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
 SG3  Var_01  C7  C6  C5  P   178.84   0.0  2
 SG3  Var_02  C6  C5  P   O3    2.14  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
 SG3  chir_01  C7  C6  O13  C8  negativ
 SG3  chir_02  C8  C9  C12  C7  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 SG3  plan-1  P     0.020
 SG3  plan-1  C5    0.020
 SG3  plan-1  C6    0.020
 SG3  plan-1  C7    0.020
 SG3  plan-1  H5C2  0.020
 SG3  plan-1  H6C2  0.020

