# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 03:13:13 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  24  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  -0.699   0.4833  -0.2131   1.9457
 3S4  O    O  OH1    0  -0.680  -0.8087   3.8707  -0.3596
 3S4  P    P  P      0   1.214  -1.5818  -0.9772  -0.3481
 3S4  C1   C  CT     0   0.228   0.5715   0.4734   0.5817
 3S4  O1   O  OC    -1  -0.770   2.9860  -0.8655  -1.4368
 3S4  C2   C  CH2    0  -0.453  -0.0589   1.8780   0.7083
 3S4  O2   O  O      0  -0.431   3.0617  -1.4461   0.7056
 3S4  C3   C  CH2    0  -0.127  -0.4082   2.5325  -0.6134
 3S4  O3   O  O2     0  -0.580  -0.0443  -0.2736  -0.4416
 3S4  C4   C  CH2    0  -0.606   2.0461   0.6388   0.1559
 3S4  O4   O  O      0  -0.896  -1.4107  -2.2810   0.4239
 3S4  C5   C  C      0   0.381   2.7492  -0.6719  -0.2254
 3S4  O5   O  OP    -1  -0.964  -2.4969   0.0370   0.3414
 3S4  O6   O  OP    -1  -0.948  -1.8857  -1.1750  -1.8349
 3S4  H    H  HCH3   0   0.220   1.0337   0.3614   2.6943
 3S4  HA   H  HCH3   0   0.174  -0.5547  -0.2813   2.2667
 3S4  HB   H  HCH3   0   0.255   0.9053  -1.2124   1.9069
 3S4  HO   H  HOH1   0   0.451  -1.0864   4.2579  -1.1942
 3S4  H2   H  HCH2   0   0.227  -0.9717   1.8095   1.3033
 3S4  H2A  H  HCH2   0   0.188   0.6395   2.5197   1.2570
 3S4  H3   H  HCH2   0   0.204  -1.2138   1.9635  -1.0859
 3S4  H3A  H  HCH2   0   0.128   0.4494   2.5091  -1.2976
 3S4  H4   H  HCH2   0   0.214   2.0939   1.3271  -0.6926
 3S4  H4A  H  HCH2   0   0.270   2.5858   1.1167   0.9803

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  1.529  0.020  1.529
 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  1.420  0.020  1.420
 3S4  O   HO   single  0.850  0.020  0.980
 3S4  O4  P    deloc   1.525  0.020  1.525
 3S4  O5  P    deloc   1.530  0.020  1.530
 3S4  O6  P    deloc   1.530  0.020  1.530
 3S4  P   O3   single  1.693  0.020  1.693
 3S4  C2  C1   single  1.545  0.020  1.545
 3S4  O3  C1   single  1.409  0.020  1.409
 3S4  C1  C4   single  1.544  0.020  1.544
 3S4  C5  O1   deloc   1.249  0.020  1.249
 3S4  C3  C2   single  1.516  0.020  1.516
 3S4  C2  H2   single  0.970  0.020  1.090
 3S4  C2  H2A  single  0.970  0.020  1.090
 3S4  O2  C5   deloc   1.251  0.020  1.251
 3S4  C3  H3   single  0.970  0.020  1.090
 3S4  C3  H3A  single  0.970  0.020  1.090
 3S4  C4  C5   single  1.535  0.020  1.535
 3S4  C4  H4   single  0.970  0.020  1.090
 3S4  C4  H4A  single  0.970  0.020  1.090

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  108.88  3.000
 3S4  HB   C   H   108.23  3.000
 3S4  HA   C   H   108.13  3.000
 3S4  HB   C   C1  111.04  3.000
 3S4  HA   C   C1  110.25  3.000
 3S4  H    C   C1  110.24  3.000
 3S4  HO   O   C3  107.82  3.000
 3S4  O6   P   O5  113.87  3.000
 3S4  O6   P   O4  113.81  3.000
 3S4  O5   P   O4  113.93  3.000
 3S4  O6   P   O3  100.39  3.000
 3S4  O5   P   O3  107.00  3.000
 3S4  O4   P   O3  106.34  3.000
 3S4  C4   C1  O3  105.90  3.000
 3S4  C4   C1  C2  108.36  3.000
 3S4  O3   C1  C2  111.30  3.000
 3S4  C4   C1  C   110.44  3.000
 3S4  O3   C1  C   112.62  3.000
 3S4  C2   C1  C   108.15  3.000
 3S4  H2A  C2  H2  107.26  3.000
 3S4  H2A  C2  C3  109.31  3.000
 3S4  H2   C2  C3  108.04  3.000
 3S4  H2A  C2  C1  108.27  3.000
 3S4  H2   C2  C1  109.20  3.000
 3S4  C3   C2  C1  114.54  3.000
 3S4  H3A  C3  H3  107.17  3.000
 3S4  H3A  C3  C2  110.76  3.000
 3S4  H3   C3  C2  108.77  3.000
 3S4  H3A  C3  O   110.61  3.000
 3S4  H3   C3  O   111.09  3.000
 3S4  C2   C3  O   108.43  3.000
 3S4  C1   O3  P   125.25  3.000
 3S4  H4A  C4  H4  106.73  3.000
 3S4  H4A  C4  C5  109.50  3.000
 3S4  H4   C4  C5  108.95  3.000
 3S4  H4A  C4  C1  108.04  3.000
 3S4  H4   C4  C1  108.85  3.000
 3S4  C5   C4  C1  114.48  3.000
 3S4  C4   C5  O2  117.26  3.000
 3S4  C4   C5  O1  117.37  3.000
 3S4  O2   C5  O1  125.35  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  Var_01  C1  C2  C3  O   -172.44  30.0  3
 3S4  Var_02  O4  P   O3  C1   -80.76  30.0  3
 3S4  Var_03  O1  C5  C4  C1   107.38  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

