# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 04:15:05 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (3S)-1,3-dihydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-2-methylbut-2-ylium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C+](CO)[C@H](O)CO[P](O)(=O)O[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
 43Q  43Q  (3S)-1,3-dihydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-2-methylbut-2-ylium  ligand  29  16  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_43Q
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
 43Q  O6   O  OH1   0  -0.712   4.2899   0.6422  -1.0534
 43Q  P1   P  P     0   1.474   3.2777  -0.3948  -0.4220
 43Q  O5   O  OH1   0  -0.721   2.8959  -1.4687  -1.5238
 43Q  O4   O  O     0  -0.681   3.7052  -0.8581   0.9038
 43Q  O3   O  O2    0  -0.675   1.8721   0.4351  -0.4091
 43Q  P    P  P     0   1.509   0.6748   0.2487   0.6403
 43Q  O8   O  O     0  -0.698   0.3390  -1.1442   1.0060
 43Q  O7   O  OH1   0  -0.707   1.0273   1.1034   1.9182
 43Q  O2   O  O2    0  -0.557  -0.4416   1.0164  -0.1999
 43Q  C4   C  CH2   0  -0.221  -1.8026   1.0597   0.2165
 43Q  C3   C  CH1   0  -0.063  -2.5512  -0.2361  -0.1982
 43Q  C1   C  C     1   0.254  -3.9891   0.0494  -0.3267
 43Q  C    C  CH2   0  -0.210  -4.9228  -0.7064   0.4793
 43Q  O    O  OH1   0  -0.630  -6.2338  -0.3312   0.2856
 43Q  C2   C  CH3   0  -0.751  -4.4629   1.0566  -1.2542
 43Q  O1   O  OH1   0  -0.664  -2.3394  -1.3086   0.6430
 43Q  H1   H  HOH1  0   0.509   4.1355   0.9059  -1.9715
 43Q  H2   H  HOH1  0   0.513   3.5656  -2.1513  -1.6751
 43Q  H3   H  HOH1  0   0.514   1.2868   2.0253   1.7717
 43Q  H4   H  HCH2  0   0.294  -1.8985   1.1892   1.2969
 43Q  H5   H  HCH2  0   0.302  -2.2222   1.9375  -0.2671
 43Q  H6   H  HCH1  0   0.331  -2.2515  -0.4414  -1.2469
 43Q  H8   H  HCH2  0   0.324  -4.7105  -1.7709   0.2603
 43Q  H9   H  HCH2  0   0.315  -4.5643  -0.6005   1.5237
 43Q  H10  H  HOH1  0   0.488  -6.8057  -0.9592   0.7384
 43Q  H11  H  HCH3  0   0.340  -5.2764   0.6375  -1.8545
 43Q  H12  H  HCH3  0   0.341  -4.9438   1.8518  -0.6677
 43Q  H13  H  HCH3  0   0.301  -3.6939   1.4794  -1.8916
 43Q  H14  H  HOH1  0   0.482  -1.3796  -1.4480   0.7730

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
 43Q  C   O    single  1.377  0.020  1.377
 43Q  C   C1   single  1.447  0.020  1.447
 43Q  O1  C3   single  1.379  0.020  1.379
 43Q  C1  C3   single  1.472  0.020  1.472
 43Q  C1  C2   single  1.449  0.020  1.449
 43Q  C3  C4   single  1.553  0.020  1.553
 43Q  O4  P1   double  1.468  0.020  1.468
 43Q  C4  O2   single  1.424  0.020  1.424
 43Q  O6  P1   single  1.581  0.020  1.581
 43Q  P1  O3   single  1.632  0.020  1.632
 43Q  P1  O5   single  1.585  0.020  1.585
 43Q  O2  P    single  1.594  0.020  1.594
 43Q  O3  P    single  1.603  0.020  1.603
 43Q  P   O8   double  1.479  0.020  1.479
 43Q  P   O7   single  1.577  0.020  1.577
 43Q  O6  H1   single  0.850  0.020  0.980
 43Q  O5  H2   single  0.850  0.020  0.980
 43Q  O7  H3   single  0.850  0.020  0.980
 43Q  C4  H4   single  0.970  0.020  1.090
 43Q  C4  H5   single  0.970  0.020  1.090
 43Q  C3  H6   single  0.970  0.020  1.090
 43Q  C   H8   single  0.970  0.020  1.090
 43Q  C   H9   single  0.970  0.020  1.090
 43Q  O   H10  single  0.850  0.020  0.980
 43Q  C2  H11  single  0.970  0.020  1.090
 43Q  C2  H12  single  0.970  0.020  1.090
 43Q  C2  H13  single  0.970  0.020  1.090
 43Q  O1  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
 43Q  H1   O6  P1   117.10  3.000
 43Q  O3   P1  O4   113.83  3.000
 43Q  O3   P1  O5    98.20  3.000
 43Q  O4   P1  O5   118.95  3.000
 43Q  O5   P1  O6   108.72  3.000
 43Q  O3   P1  O6   102.77  3.000
 43Q  O4   P1  O6   112.41  3.000
 43Q  H2   O5  P1   114.81  3.000
 43Q  P    O3  P1   126.10  3.000
 43Q  O2   P   O7   108.82  3.000
 43Q  O7   P   O8   111.15  3.000
 43Q  O2   P   O8   115.15  3.000
 43Q  O7   P   O3   107.48  3.000
 43Q  O8   P   O3   116.18  3.000
 43Q  O2   P   O3    97.01  3.000
 43Q  H3   O7  P    116.93  3.000
 43Q  C4   O2  P    121.99  3.000
 43Q  H5   C4  H4   108.09  3.000
 43Q  H5   C4  C3   111.67  3.000
 43Q  H4   C4  C3   108.71  3.000
 43Q  H5   C4  O2   105.28  3.000
 43Q  H4   C4  O2   112.13  3.000
 43Q  C3   C4  O2   110.93  3.000
 43Q  H6   C3  O1   113.01  3.000
 43Q  H6   C3  C1   102.54  3.000
 43Q  O1   C3  C1   110.74  3.000
 43Q  H6   C3  C4   106.05  3.000
 43Q  C1   C3  C4   109.42  3.000
 43Q  O1   C3  C4   114.33  3.000
 43Q  C2   C1  C    120.58  3.000
 43Q  C2   C1  C3   120.68  3.000
 43Q  C    C1  C3   118.73  3.000
 43Q  H9   C   H8   102.48  3.000
 43Q  H9   C   O    114.46  3.000
 43Q  H8   C   O    114.61  3.000
 43Q  H9   C   C1   105.43  3.000
 43Q  H8   C   C1   105.56  3.000
 43Q  O    C   C1   113.19  3.000
 43Q  H10  O   C    108.77  3.000
 43Q  H13  C2  H12  109.99  3.000
 43Q  H13  C2  H11  110.74  3.000
 43Q  H12  C2  H11  104.15  3.000
 43Q  H13  C2  C1   114.54  3.000
 43Q  H12  C2  C1   107.73  3.000
 43Q  H11  C2  C1   109.14  3.000
 43Q  H14  O1  C3   110.02  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
 43Q  Var_01  O2   P   O3  P1  -164.23  30.0  3
 43Q  Var_02  C3   C4  O2  P    -81.81  30.0  1
 43Q  Var_03  O    C   C1  C3   178.95  30.0  2
 43Q  Var_04  H11  C2  C1  C3   130.96  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
 43Q  chir_02  C3  O1  C1  C4  negativ
 43Q  chir_03  P   O3  O8  O7  both

