# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:32:20 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (2~{R})-2-oxidanylhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@@H](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
 7N6  7N6  '(2~{R})-2-oxidanylhexanoic acid'  ligand  21  9  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7N6
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
 7N6  C2   C  CH2   0  -0.422   2.8949  -0.5563  -0.4262
 7N6  C3   C  CH2   0  -0.406   1.7397   0.1638   0.2589
 7N6  C6   C  C     0   0.507  -2.1066  -0.2205  -0.0273
 7N6  O8   O  O     0  -0.438  -2.8833   0.3928  -0.7138
 7N6  O9   O  OH1   0  -0.652  -0.7807   1.7382   0.3762
 7N6  C5   C  CH1   0  -0.064  -0.7918   0.3449   0.4869
 7N6  O7   O  OH1   0  -0.591  -2.2858  -1.4792   0.3491
 7N6  C4   C  CH2   0  -0.473   0.3836  -0.3321  -0.2258
 7N6  C1   C  CH3   0  -0.662   4.2562  -0.0699   0.0506
 7N6  H1   H  HCH2  0   0.214   2.8069  -1.6327  -0.2501
 7N6  H2   H  HCH2  0   0.214   2.8149  -0.4192  -1.5090
 7N6  H3   H  HCH2  0   0.215   1.8136   0.0199   1.3425
 7N6  H4   H  HCH2  0   0.219   1.8300   1.2391   0.0845
 7N6  H5   H  HOH1  0   0.447  -0.8150   1.9782  -0.5565
 7N6  H6   H  HCH1  0   0.269  -0.7232   0.1210   1.5565
 7N6  H7   H  HOH1  0   0.484  -3.1089  -1.8288  -0.0249
 7N6  H8   H  HCH2  0   0.235   0.2959  -0.1726  -1.3068
 7N6  H9   H  HCH2  0   0.242   0.3186  -1.4117  -0.0697
 7N6  H10  H  HCH3  0   0.217   4.3841   0.9964  -0.1445
 7N6  H11  H  HCH3  0   0.217   4.3751  -0.2234   1.1248
 7N6  H12  H  HCH3  0   0.227   5.0682  -0.5976  -0.4506

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
 7N6  C5  C4   single  1.532  0.020  1.532
 7N6  C5  C6   single  1.521  0.020  1.521
 7N6  C5  O9   single  1.398  0.020  1.398
 7N6  C4  C3   single  1.523  0.020  1.523
 7N6  O8  C6   double  1.204  0.020  1.204
 7N6  C6  O7   single  1.326  0.020  1.326
 7N6  C3  C2   single  1.524  0.020  1.524
 7N6  C1  C2   single  1.522  0.020  1.522
 7N6  C2  H1   single  0.970  0.020  1.090
 7N6  C2  H2   single  0.970  0.020  1.090
 7N6  C3  H3   single  0.970  0.020  1.090
 7N6  C3  H4   single  0.970  0.020  1.090
 7N6  O9  H5   single  0.850  0.020  0.980
 7N6  C5  H6   single  0.970  0.020  1.090
 7N6  O7  H7   single  0.850  0.020  0.980
 7N6  C4  H8   single  0.970  0.020  1.090
 7N6  C4  H9   single  0.970  0.020  1.090
 7N6  C1  H10  single  0.970  0.020  1.090
 7N6  C1  H11  single  0.970  0.020  1.090
 7N6  C1  H12  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
 7N6  H2   C2  H1   106.05  3.000
 7N6  H2   C2  C1   109.60  3.000
 7N6  H1   C2  C1   109.62  3.000
 7N6  H2   C2  C3   109.28  3.000
 7N6  H1   C2  C3   109.36  3.000
 7N6  C1   C2  C3   112.71  3.000
 7N6  H4   C3  H3   106.34  3.000
 7N6  H4   C3  C4   110.06  3.000
 7N6  H3   C3  C4   109.39  3.000
 7N6  H4   C3  C2   109.30  3.000
 7N6  H3   C3  C2   109.36  3.000
 7N6  C4   C3  C2   112.21  3.000
 7N6  O7   C6  C5   111.95  3.000
 7N6  O7   C6  O8   123.92  3.000
 7N6  C5   C6  O8   124.12  3.000
 7N6  H5   O9  C5   108.94  3.000
 7N6  H6   C5  C4   108.41  3.000
 7N6  H6   C5  O9   106.30  3.000
 7N6  C4   C5  O9   113.42  3.000
 7N6  H6   C5  C6   107.97  3.000
 7N6  O9   C5  C6   110.53  3.000
 7N6  C4   C5  C6   109.98  3.000
 7N6  H7   O7  C6   110.34  3.000
 7N6  H9   C4  H8   106.25  3.000
 7N6  H9   C4  C5   108.93  3.000
 7N6  H8   C4  C5   109.45  3.000
 7N6  H9   C4  C3   109.22  3.000
 7N6  H8   C4  C3   109.74  3.000
 7N6  C5   C4  C3   113.03  3.000
 7N6  H12  C1  H11  107.64  3.000
 7N6  H12  C1  H10  107.65  3.000
 7N6  H11  C1  H10  107.49  3.000
 7N6  H12  C1  C2   111.55  3.000
 7N6  H11  C1  C2   111.15  3.000
 7N6  H10  C1  C2   111.16  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
 7N6  CONST_01  H7   O7  C6  O8     0.00   0.0  0
 7N6  Var_01    C5   C4  C3  C2   177.98  30.0  1
 7N6  Var_02    C1   C2  C3  C4  -179.96  30.0  3
 7N6  Var_03    H10  C1  C2  C3   -59.88  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
 7N6  chir_01  C5  C4  C6  O9  positiv

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
 7N6  plan-1  C6  0.020
 7N6  plan-1  O8  0.020
 7N6  plan-1  C5  0.020
 7N6  plan-1  O7  0.020
 7N6  plan-1  H7  0.020

