# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 18:57:43 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (3R)-5-hydroxy-3-methyl-3-(phosphonooxy)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@](CCO)(CC(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
 3S4  3S4  '(3R)-5-hydroxy-3-methyl-3-(phosphonooxy)pentanoic acid'  ligand  27  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3S4
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
 3S4  C    C  CH3   0  -0.704   0.4624  -0.1270   1.9880
 3S4  O    O  OH1   0  -0.672  -0.7770   3.9097  -0.3939
 3S4  P    P  P     0   1.456  -1.4970  -1.2074  -0.1432
 3S4  C1   C  CT    0   0.205   0.4955   0.4982   0.5979
 3S4  O1   O  OH1   0  -0.598   3.8539  -0.5636  -0.6045
 3S4  C2   C  CH2   0  -0.474  -0.0918   1.9140   0.6728
 3S4  O2   O  O     0  -0.425   2.1266  -1.8573  -0.0533
 3S4  C3   C  CH2   0  -0.135  -0.3838   2.5816  -0.6621
 3S4  O3   O  O2    0  -0.606  -0.2501  -0.2554  -0.3857
 3S4  C4   C  CH2   0  -0.592   1.9225   0.5595   0.0565
 3S4  O4   O  O     0  -0.704  -1.3149  -2.4309   0.6579
 3S4  C5   C  C     0   0.558   2.6050  -0.7616  -0.1895
 3S4  O5   O  OH1   0  -0.746  -2.6559  -0.3150   0.5141
 3S4  O6   O  OH1   0  -0.731  -1.8647  -1.4064  -1.6849
 3S4  H    H  HCH3  0   0.252   1.0873   0.4688   2.6537
 3S4  HA   H  HCH3  0   0.243  -0.5448  -0.1192   2.4051
 3S4  HB   H  HCH3  0   0.265   0.8345  -1.1475   1.9946
 3S4  HO   H  HOH1  0   0.455  -1.0024   4.3275  -1.2298
 3S4  HO1  H  HOH1  0   0.480   4.2840  -1.4151  -0.7735
 3S4  H2   H  HCH2  0   0.248  -1.0097   1.8902   1.2671
 3S4  H2A  H  HCH2  0   0.249   0.6144   2.5335   1.2327
 3S4  H3   H  HCH2  0   0.193  -1.1734   2.0364  -1.1923
 3S4  H3A  H  HCH2  0   0.197   0.5010   2.5560  -1.3097
 3S4  H4   H  HCH2  0   0.299   1.9500   1.1141  -0.8858
 3S4  H4A  H  HCH2  0   0.295   2.5368   1.1405   0.7493
 3S4  HO5  H  HOH1  0   0.491  -2.9355   0.4611   0.0109
 3S4  HO6  H  HOH1  0   0.501  -2.4834  -2.1325  -1.8411

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
 3S4  C   C1   single  1.525  0.020  1.525
 3S4  C   H    single  0.970  0.020  1.090
 3S4  C   HA   single  0.970  0.020  1.090
 3S4  C   HB   single  0.970  0.020  1.090
 3S4  O   C3   single  1.411  0.020  1.411
 3S4  O   HO   single  0.850  0.020  0.980
 3S4  O4  P    double  1.474  0.020  1.474
 3S4  O5  P    single  1.604  0.020  1.604
 3S4  O6  P    single  1.597  0.020  1.597
 3S4  P   O3   single  1.587  0.020  1.587
 3S4  C2  C1   single  1.534  0.020  1.534
 3S4  O3  C1   single  1.446  0.020  1.446
 3S4  C1  C4   single  1.528  0.020  1.528
 3S4  C5  O1   single  1.331  0.020  1.331
 3S4  O1  HO1  single  0.850  0.020  0.980
 3S4  C3  C2   single  1.521  0.020  1.521
 3S4  C2  H2   single  0.970  0.020  1.090
 3S4  C2  H2A  single  0.970  0.020  1.090
 3S4  O2  C5   double  1.203  0.020  1.203
 3S4  C3  H3   single  0.970  0.020  1.090
 3S4  C3  H3A  single  0.970  0.020  1.090
 3S4  C4  C5   single  1.507  0.020  1.507
 3S4  C4  H4   single  0.970  0.020  1.090
 3S4  C4  H4A  single  0.970  0.020  1.090
 3S4  O5  HO5  single  0.850  0.020  0.980
 3S4  O6  HO6  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
 3S4  HB   C   HA  108.72  3.000
 3S4  HB   C   H   108.27  3.000
 3S4  HA   C   H   106.98  3.000
 3S4  HB   C   C1  112.54  3.000
 3S4  HA   C   C1  111.46  3.000
 3S4  H    C   C1  108.67  3.000
 3S4  HO   O   C3  108.01  3.000
 3S4  O6   P   O5  107.37  3.000
 3S4  O6   P   O4  116.72  3.000
 3S4  O5   P   O4  109.18  3.000
 3S4  O6   P   O3   96.20  3.000
 3S4  O5   P   O3  107.25  3.000
 3S4  O4   P   O3  118.94  3.000
 3S4  C4   C1  O3  105.16  3.000
 3S4  C4   C1  C2  109.74  3.000
 3S4  O3   C1  C2  108.46  3.000
 3S4  C4   C1  C   111.09  3.000
 3S4  O3   C1  C   113.28  3.000
 3S4  C2   C1  C   109.00  3.000
 3S4  HO1  O1  C5  109.89  3.000
 3S4  H2A  C2  H2  106.03  3.000
 3S4  H2A  C2  C3  108.95  3.000
 3S4  H2   C2  C3  108.98  3.000
 3S4  H2A  C2  C1  107.49  3.000
 3S4  H2   C2  C1  109.12  3.000
 3S4  C3   C2  C1  115.82  3.000
 3S4  H3A  C3  H3  106.49  3.000
 3S4  H3A  C3  C2  110.68  3.000
 3S4  H3   C3  C2  110.16  3.000
 3S4  H3A  C3  O   111.04  3.000
 3S4  H3   C3  O   111.06  3.000
 3S4  C2   C3  O   107.45  3.000
 3S4  C1   O3  P   127.85  3.000
 3S4  H4A  C4  H4  105.21  3.000
 3S4  H4A  C4  C5  108.34  3.000
 3S4  H4   C4  C5  107.00  3.000
 3S4  H4A  C4  C1  108.77  3.000
 3S4  H4   C4  C1  110.44  3.000
 3S4  C5   C4  C1  116.47  3.000
 3S4  C4   C5  O2  126.84  3.000
 3S4  C4   C5  O1  110.21  3.000
 3S4  O2   C5  O1  122.95  3.000
 3S4  HO5  O5  P   116.27  3.000
 3S4  HO6  O6  P   113.38  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
 3S4  CONST_01  HO1  O1  C5  O2     0.00   0.0  0
 3S4  Var_01    C1   C2  C3  O   -173.88  30.0  3
 3S4  Var_02    O4   P   O3  C1   -64.49  30.0  3
 3S4  Var_03    O1   C5  C4  C1  -177.42  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
 3S4  chir_01  C1  C2  O3  C4  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
 3S4  plan-1  O1   0.020
 3S4  plan-1  O2   0.020
 3S4  plan-1  C4   0.020
 3S4  plan-1  C5   0.020
 3S4  plan-1  HO1  0.020

