# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 21:22:35 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  26  11  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.791   0.0349  -0.1178   1.6036
 L2O  C1   C  CH1   0  -0.135   0.1043  -0.1527   0.1563
 L2O  C2   C  CH2   0  -0.406   1.4024   0.4906  -0.3271
 L2O  C3   C  CH1   0  -0.220   2.6825  -0.1068   0.2576
 L2O  C4   C  CH3   0  -0.664   2.8213  -1.5915  -0.0612
 L2O  C5   C  CH3   0  -0.654   3.8935   0.6659  -0.2562
 L2O  C6   C  CH1   0  -0.066  -1.0994   0.5199  -0.5571
 L2O  O1   O  OH1   0  -0.652  -1.2560   1.8649  -0.2097
 L2O  C    C  C     0   0.497  -2.3736  -0.2537  -0.2759
 L2O  O    O  O     0  -0.438  -3.2447   0.1300   0.4644
 L2O  OXT  O  OH1   0  -0.587  -2.3997  -1.4173  -0.9086
 L2O  H    H  HNH2  0   0.340   0.0542   0.8319   1.9537
 L2O  H2   H  HNH2  0   0.352  -0.8000  -0.5601   1.9653
 L2O  H3   H  HCH1  0   0.245   0.1081  -1.2034  -0.1484
 L2O  H4   H  HCH2  0   0.218   1.4394   0.4112  -1.4198
 L2O  H5   H  HCH2  0   0.225   1.3746   1.5622  -0.1032
 L2O  H6   H  HCH1  0   0.216   2.6420   0.0058   1.3451
 L2O  H7   H  HCH3  0   0.228   2.0162  -2.1831   0.3764
 L2O  H8   H  HCH3  0   0.210   2.8112  -1.7606  -1.1414
 L2O  H9   H  HCH3  0   0.225   3.7621  -1.9882   0.3251
 L2O  H10  H  HCH3  0   0.222   3.8180   1.7292  -0.0207
 L2O  H11  H  HCH3  0   0.224   4.8191   0.2923   0.1854
 L2O  H12  H  HCH3  0   0.211   3.9855   0.5747  -1.3417
 L2O  HXT  H  HOH1  0   0.486  -3.2023  -1.9083  -0.6758
 L2O  H14  H  HOH1  0   0.441  -1.5700   1.9170   0.6999
 L2O  H15  H  HCH1  0   0.272  -0.9155   0.4884  -1.6357

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  1.449  0.020  1.449
 L2O  N    H    single  0.860  0.020  0.860
 L2O  N    H2   single  0.890  0.020  1.040
 L2O  C1   C2   single  1.527  0.020  1.527
 L2O  C1   C6   single  1.552  0.020  1.552
 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  1.517  0.020  1.517
 L2O  C6   O1   single  1.398  0.020  1.398
 L2O  C6   H15  single  0.970  0.020  1.090
 L2O  O1   H14  single  0.850  0.020  0.980
 L2O  C    O    double  1.231  0.020  1.231
 L2O  C    OXT  single  1.325  0.020  1.325
 L2O  OXT  HXT  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
 L2O  H2   N    H    107.60  3.000
 L2O  H2   N    C1   112.71  3.000
 L2O  H    N    C1   111.53  3.000
 L2O  H3   C1   C6   106.90  3.000
 L2O  H3   C1   C2   108.27  3.000
 L2O  C6   C1   C2   109.34  3.000
 L2O  H3   C1   N    107.54  3.000
 L2O  C6   C1   N    114.29  3.000
 L2O  C2   C1   N    110.28  3.000
 L2O  H5   C2   H4   105.99  3.000
 L2O  H5   C2   C3   108.99  3.000
 L2O  H4   C2   C3   108.94  3.000
 L2O  H5   C2   C1   109.02  3.000
 L2O  H4   C2   C1   108.28  3.000
 L2O  C3   C2   C1   115.22  3.000
 L2O  H6   C3   C5   108.18  3.000
 L2O  H6   C3   C4   108.14  3.000
 L2O  C5   C3   C4   110.52  3.000
 L2O  H6   C3   C2   108.00  3.000
 L2O  C5   C3   C2   109.75  3.000
 L2O  C4   C3   C2   112.13  3.000
 L2O  H9   C4   H8   107.54  3.000
 L2O  H9   C4   H7   107.28  3.000
 L2O  H8   C4   H7   107.80  3.000
 L2O  H9   C4   C3   111.00  3.000
 L2O  H8   C4   C3   110.87  3.000
 L2O  H7   C4   C3   112.15  3.000
 L2O  H12  C5   H11  107.57  3.000
 L2O  H12  C5   H10  107.54  3.000
 L2O  H11  C5   H10  107.74  3.000
 L2O  H12  C5   C3   111.03  3.000
 L2O  H11  C5   C3   111.32  3.000
 L2O  H10  C5   C3   111.45  3.000
 L2O  H15  C6   C    108.01  3.000
 L2O  H15  C6   O1   106.94  3.000
 L2O  C    C6   O1   110.51  3.000
 L2O  H15  C6   C1   108.06  3.000
 L2O  O1   C6   C1   112.92  3.000
 L2O  C    C6   C1   110.19  3.000
 L2O  H14  O1   C6   108.85  3.000
 L2O  OXT  C    O    123.95  3.000
 L2O  OXT  C    C6   112.08  3.000
 L2O  O    C    C6   123.95  3.000
 L2O  HXT  OXT  C    110.27  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  CONST_01  HXT  OXT  C   C6  180.00   0.0  0
 L2O  Var_01    C4   C3   C2  C1   59.36  30.0  3
 L2O  Var_02    H7   C4   C3  C2  -62.61  30.0  3
 L2O  Var_03    H10  C5   C3  C2   56.80  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
 L2O  plan-1  HXT  0.020

