# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:50:40 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: (4~{R},5~{R})-4,5,6-tris(oxidanyl)-2-oxidanylidene-hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H](O)CC(=O)C(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
 JBU  JBU  "(4R,5R)-4,5,6-tris(oxidanyl)-2-oxidanylidene-hexanoic acid"  ligand  21  12  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JBU
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
 JBU  C1   C  C      0   0.382  -19.0958  -36.3894  7.2530
 JBU  C2   C  C      0   0.244  -17.6213  -36.7240  7.5607
 JBU  C3   C  CH2    0  -0.601  -16.9987  -37.9211  6.8811
 JBU  C4   C  CH1    0   0.051  -15.9444  -37.5257  5.8309
 JBU  C5   C  CH1    0  -0.015  -16.5207  -36.6254  4.7325
 JBU  C6   C  CH2    0  -0.149  -15.4838  -36.3544  3.6568
 JBU  O8   O  OC    -1  -0.550  -19.7823  -35.9902  8.1941
 JBU  O9   O  O      0  -0.586  -19.4382  -36.5465  6.0560
 JBU  O10  O  O      0  -0.393  -16.9738  -36.0219  8.3054
 JBU  O11  O  OH1    0  -0.668  -15.3987  -38.6758  5.2282
 JBU  O12  O  OH1    0  -0.708  -17.6749  -37.1578  4.1445
 JBU  O7   O  OH1    0  -0.670  -15.9469  -35.3063  2.8340
 JBU  H1   H  HCH2   0   0.251  -17.7558  -38.5568  6.4220
 JBU  H2   H  HCH2   0   0.271  -16.4983  -38.5133  7.6536
 JBU  H3   H  HCH1   0   0.203  -15.1621  -36.9478  6.3436
 JBU  H4   H  HCH1   0   0.199  -16.7361  -35.6582  5.2174
 JBU  H5   H  HCH2   0   0.196  -15.3059  -37.2689  3.0790
 JBU  H6   H  HCH2   0   0.188  -14.5345  -36.0920  4.1436
 JBU  H8   H  HOH1   0   0.450  -14.9415  -39.1876  5.9027
 JBU  H9   H  HOH1   0   0.455  -18.4018  -36.9977  4.7881
 JBU  H10  H  HOH1   0   0.449  -15.3151  -35.1887  2.1196

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
 JBU  O7   C6   single  1.411  0.020  1.411
 JBU  C6   C5   single  1.518  0.020  1.518
 JBU  O12  C5   single  1.400  0.020  1.400
 JBU  C5   C4   single  1.533  0.020  1.533
 JBU  O11  C4   single  1.408  0.020  1.408
 JBU  C4   C3   single  1.540  0.020  1.540
 JBU  C3   C2   single  1.511  0.020  1.511
 JBU  O9   C1   deloc   1.255  0.020  1.255
 JBU  O8   C1   deloc   1.231  0.020  1.231
 JBU  C1   C2   single  1.543  0.020  1.543
 JBU  C2   O10  double  1.211  0.020  1.211
 JBU  C3   H1   single  0.970  0.020  1.090
 JBU  C3   H2   single  0.970  0.020  1.090
 JBU  C4   H3   single  0.970  0.020  1.090
 JBU  C5   H4   single  0.970  0.020  1.090
 JBU  C6   H5   single  0.970  0.020  1.090
 JBU  C6   H6   single  0.970  0.020  1.090
 JBU  O11  H8   single  0.850  0.020  0.980
 JBU  O12  H9   single  0.850  0.020  0.980
 JBU  O7   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
 JBU  O9   C1   O8   128.13  3.000
 JBU  O8   C1   C2   116.79  3.000
 JBU  O9   C1   C2   115.08  3.000
 JBU  O10  C2   C3   121.04  3.000
 JBU  O10  C2   C1   120.52  3.000
 JBU  C3   C2   C1   118.42  3.000
 JBU  H2   C3   H1   107.42  3.000
 JBU  H2   C3   C4   107.90  3.000
 JBU  H1   C3   C4   109.76  3.000
 JBU  H2   C3   C2   107.44  3.000
 JBU  H1   C3   C2   111.42  3.000
 JBU  C4   C3   C2   112.68  3.000
 JBU  H3   C4   O11  110.68  3.000
 JBU  H3   C4   C5   107.03  3.000
 JBU  O11  C4   C5   108.59  3.000
 JBU  H3   C4   C3   107.70  3.000
 JBU  O11  C4   C3   110.33  3.000
 JBU  C5   C4   C3   112.47  3.000
 JBU  H4   C5   O12  110.91  3.000
 JBU  H4   C5   C6   106.76  3.000
 JBU  O12  C5   C6   109.46  3.000
 JBU  H4   C5   C4   105.87  3.000
 JBU  O12  C5   C4   112.80  3.000
 JBU  C6   C5   C4   110.84  3.000
 JBU  H6   C6   H5   107.01  3.000
 JBU  H6   C6   O7   111.38  3.000
 JBU  H5   C6   O7   111.45  3.000
 JBU  H6   C6   C5   108.59  3.000
 JBU  H5   C6   C5   109.60  3.000
 JBU  O7   C6   C5   108.76  3.000
 JBU  H8   O11  C4   108.56  3.000
 JBU  H9   O12  C5   105.80  3.000
 JBU  H10  O7   C6   107.98  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
 JBU  Var_01  C4   C3  C2  C1    110.12  30.0  1
 JBU  Var_02  O9   C1  C2  C3    -39.17  30.0  2
 JBU  Var_03  O8   C1  C2  C3    141.67  30.0  2
 JBU  Var_04  O10  C2  C3  C4    -68.15  30.0  3
 JBU  Var_05  O10  C2  C1  O8    -40.05  30.0  2
 JBU  Var_06  O10  C2  C1  O9    139.11  30.0  2
 JBU  Var_07  H1   C3  C2  C1    -13.77  30.0  1
 JBU  Var_08  H2   C3  C2  C1   -131.17  30.0  1
 JBU  Var_09  H1   C3  C2  O10   167.97  30.0  1
 JBU  Var_10  H2   C3  C2  O10    50.56  30.0  1

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
 JBU  chir_01  C4  C5   O11  C3  positiv
 JBU  chir_02  C5  O12  C4   C6  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
 JBU  plan-1  C1   0.020
 JBU  plan-1  C2   0.020
 JBU  plan-1  C3   0.020
 JBU  plan-1  O10  0.020
 JBU  plan-2  C1   0.020
 JBU  plan-2  C2   0.020
 JBU  plan-2  O8   0.020
 JBU  plan-2  O9   0.020

