# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 21:17:02 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (2S,3R)-3-amino-2-hydroxy-5-methylhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@@H](N)[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
 L2O  L2O  '(2S,3R)-3-amino-2-hydroxy-5-methylhexanoic acid'  peptide  25  11  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_L2O
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
 L2O  N    N  NH2    0  -0.796   0.0464  -0.2936   1.5221
 L2O  C1   C  CH1    0  -0.109   0.1307  -0.1771   0.0733
 L2O  C2   C  CH2    0  -0.396   1.4362   0.5066  -0.3295
 L2O  C3   C  CH1    0  -0.214   2.7089  -0.1175   0.2425
 L2O  C4   C  CH3    0  -0.663   2.8522  -1.5863  -0.1406
 L2O  C5   C  CH3    0  -0.653   3.9307   0.6754  -0.2114
 L2O  C6   C  CH1    0  -0.084  -1.0715   0.5399  -0.5618
 L2O  O1   O  OH1    0  -0.700  -1.1908   1.8576  -0.0829
 L2O  C    C  C      0   0.388  -2.3872  -0.2194  -0.2869
 L2O  O    O  O      0  -0.609  -3.2722   0.4501   0.2955
 L2O  OXT  O  OC    -1  -0.596  -2.4598  -1.4023  -0.6557
 L2O  H    H  HNH2   0   0.327  -0.1405   0.6192   1.9214
 L2O  H2   H  HNH2   0   0.342  -0.7395  -0.8784   1.7788
 L2O  H3   H  HCH1   0   0.215   0.1345  -1.1918  -0.3336
 L2O  H4   H  HCH2   0   0.202   1.5011   0.5045  -1.4246
 L2O  H5   H  HCH2   0   0.213   1.3966   1.5610  -0.0342
 L2O  H6   H  HCH1   0   0.209   2.6477  -0.0572   1.3332
 L2O  H7   H  HCH3   0   0.227   2.0390  -2.1926   0.2595
 L2O  H8   H  HCH3   0   0.207   2.8559  -1.7082  -1.2272
 L2O  H9   H  HCH3   0   0.221   3.7874  -2.0029   0.2393
 L2O  H10  H  HCH3   0   0.219   3.8499   1.7278   0.0683
 L2O  H11  H  HCH3   0   0.221   4.8480   0.2833   0.2320
 L2O  H12  H  HCH3   0   0.208   4.0458   0.6319  -1.2978
 L2O  H14  H  HOH1   0   0.426  -2.0852   1.8502   0.3080
 L2O  H15  H  HCH1   0   0.193  -0.9180   0.5502  -1.6533

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
 L2O  N   C1   single  1.456  0.020  1.456
 L2O  N   H    single  0.860  0.020  0.860
 L2O  N   H2   single  0.890  0.020  1.040
 L2O  C1  C2   single  1.528  0.020  1.528
 L2O  C1  C6   single  1.537  0.020  1.537
 L2O  C1  H3   single  0.970  0.020  1.090
 L2O  C2  C3   single  1.529  0.020  1.529
 L2O  C2  H4   single  0.970  0.020  1.090
 L2O  C2  H5   single  0.970  0.020  1.090
 L2O  C3  C4   single  1.525  0.020  1.525
 L2O  C3  C5   single  1.526  0.020  1.526
 L2O  C3  H6   single  0.970  0.020  1.090
 L2O  C4  H7   single  0.970  0.020  1.090
 L2O  C4  H8   single  0.970  0.020  1.090
 L2O  C4  H9   single  0.970  0.020  1.090
 L2O  C5  H10  single  0.970  0.020  1.090
 L2O  C5  H11  single  0.970  0.020  1.090
 L2O  C5  H12  single  0.970  0.020  1.090
 L2O  C6  C    single  1.544  0.020  1.544
 L2O  C6  O1   single  1.407  0.020  1.407
 L2O  C6  H15  single  0.970  0.020  1.090
 L2O  O1  H14  single  0.850  0.020  0.980
 L2O  C   O    deloc   1.231  0.020  1.231
 L2O  C   OXT  deloc   1.241  0.020  1.241

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
 L2O  H2   N   H    106.08  3.000
 L2O  H2   N   C1   110.08  3.000
 L2O  H    N   C1   109.30  3.000
 L2O  H3   C1  C6   106.37  3.000
 L2O  H3   C1  C2   108.31  3.000
 L2O  C6   C1  C2   110.53  3.000
 L2O  H3   C1  N    107.23  3.000
 L2O  C6   C1  N    113.78  3.000
 L2O  C2   C1  N    110.34  3.000
 L2O  H5   C2  H4   105.84  3.000
 L2O  H5   C2  C3   108.79  3.000
 L2O  H4   C2  C3   108.87  3.000
 L2O  H5   C2  C1   109.19  3.000
 L2O  H4   C2  C1   108.23  3.000
 L2O  C3   C2  C1   115.48  3.000
 L2O  H6   C3  C5   108.23  3.000
 L2O  H6   C3  C4   107.99  3.000
 L2O  C5   C3  C4   110.53  3.000
 L2O  H6   C3  C2   107.69  3.000
 L2O  C5   C3  C2   110.07  3.000
 L2O  C4   C3  C2   112.18  3.000
 L2O  H9   C4  H8   107.48  3.000
 L2O  H9   C4  H7   107.39  3.000
 L2O  H8   C4  H7   107.77  3.000
 L2O  H9   C4  C3   111.14  3.000
 L2O  H8   C4  C3   110.95  3.000
 L2O  H7   C4  C3   111.92  3.000
 L2O  H12  C5  H11  107.51  3.000
 L2O  H12  C5  H10  107.50  3.000
 L2O  H11  C5  H10  107.72  3.000
 L2O  H12  C5  C3   111.06  3.000
 L2O  H11  C5  C3   111.43  3.000
 L2O  H10  C5  C3   111.43  3.000
 L2O  H15  C6  C    107.44  3.000
 L2O  H15  C6  O1   109.88  3.000
 L2O  C    C6  O1   109.13  3.000
 L2O  H15  C6  C1   107.74  3.000
 L2O  O1   C6  C1   111.25  3.000
 L2O  C    C6  C1   111.32  3.000
 L2O  H14  O1  C6   101.94  3.000
 L2O  OXT  C   O    127.30  3.000
 L2O  OXT  C   C6   117.75  3.000
 L2O  O    C   C6   114.95  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
 L2O  Var_01  C4   C3  C2  C1   57.68  30.0  3
 L2O  Var_02  H7   C4  C3  C2  -62.43  30.0  3
 L2O  Var_03  H10  C5  C3  C2   56.33  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
 L2O  chir_01  C1  N   C2  C6  positiv
 L2O  chir_02  C6  O1  C1  C   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
 L2O  plan-1  C6   0.020
 L2O  plan-1  C    0.020
 L2O  plan-1  O    0.020
 L2O  plan-1  OXT  0.020

