# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 09:44:48 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (3S)-3-amino-1-hydroxy-5-methylhexan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C(=O)CO
#
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
 LEX  LEX  (3S)-3-amino-1-hydroxy-5-methylhexan-2-one  peptide  25  10  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LEX
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
 LEX  C     C  C     0   0.359  -1.4598   0.2472   0.1582
 LEX  N     N  NH2   0  -0.775   0.2278   1.9879  -0.4277
 LEX  O     O  O     0  -0.394  -2.0185   0.9326   0.9813
 LEX  CA    C  CH1   0  -0.224  -0.0658   0.5726  -0.3617
 LEX  CB    C  CH2   0  -0.410   0.9492  -0.1445   0.5403
 LEX  CG    C  CH1   0  -0.226   2.3945  -0.0928   0.0426
 LEX  CAC   C  CH2   0  -0.253  -2.0909  -0.9901  -0.4229
 LEX  CD1   C  CH3   0  -0.652   3.3239  -0.6663   1.1086
 LEX  CD2   C  CH3   0  -0.664   2.5703  -0.8457  -1.2723
 LEX  HN    H  HNH2  0   0.352  -0.3906   2.4400  -1.0897
 LEX  HA    H  HCH1  0   0.253   0.0148   0.1640  -1.3749
 LEX  HB    H  HCH2  0   0.233   0.8910   0.3020   1.5388
 LEX  HBA   H  HCH2  0   0.226   0.6597  -1.1944   0.6614
 LEX  HG    H  HCH1  0   0.222   2.6593   0.9558  -0.1208
 LEX  HAC   H  HCH2  0   0.230  -1.3493  -1.8023  -0.4013
 LEX  OXT   O  OH1   0  -0.659  -3.2661  -1.3039   0.2598
 LEX  HACA  H  HCH2  0   0.244  -2.2583  -0.7752  -1.4899
 LEX  HD1   H  HCH3  0   0.226   4.3659  -0.6291   0.7857
 LEX  HD1A  H  HCH3  0   0.224   3.2490  -0.1134   2.0469
 LEX  HD1B  H  HCH3  0   0.212   3.0800  -1.7111   1.3177
 LEX  HD2   H  HCH3  0   0.229   1.9872  -0.4109  -2.0849
 LEX  HD2A  H  HCH3  0   0.229   3.6146  -0.8374  -1.5893
 LEX  HD2B  H  HCH3  0   0.213   2.2659  -1.8901  -1.1650
 LEX  HXT   H  HOH1  0   0.462  -3.6779  -2.0492  -0.1867
 LEX  H2    H  HNH2  0   0.341   0.0420   2.4189   0.4703

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
 LEX  C    CAC   single  1.506  0.020  1.506
 LEX  C    CA    single  1.525  0.021  1.525
 LEX  N    HN    single  0.890  0.020  1.040
 LEX  O    C     double  1.231  0.020  1.231
 LEX  CA   N     single  1.458  0.019  1.458
 LEX  CA   HA    single  0.970  0.020  0.970
 LEX  CB   CA    single  1.530  0.020  1.530
 LEX  CB   HB    single  0.970  0.020  1.090
 LEX  CB   HBA   single  0.970  0.020  1.090
 LEX  CG   CB    single  1.529  0.020  1.529
 LEX  CG   CD2   single  1.525  0.020  1.525
 LEX  CG   CD1   single  1.526  0.020  1.526
 LEX  CG   HG    single  0.970  0.020  1.090
 LEX  CAC  HAC   single  0.970  0.020  1.090
 LEX  CAC  OXT   single  1.395  0.020  1.395
 LEX  CAC  HACA  single  0.970  0.020  1.090
 LEX  CD1  HD1   single  0.970  0.020  1.090
 LEX  CD1  HD1A  single  0.970  0.020  1.090
 LEX  CD1  HD1B  single  0.970  0.020  1.090
 LEX  CD2  HD2   single  0.970  0.020  1.090
 LEX  CD2  HD2A  single  0.970  0.020  1.090
 LEX  CD2  HD2B  single  0.970  0.020  1.090
 LEX  OXT  HXT   single  0.850  0.020  0.980
 LEX  N    H2    single  0.890  0.020  1.040

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
 LEX  CAC   C    CA    115.31  3.000
 LEX  CA    C    O     120.80  1.700
 LEX  CAC   C    O     122.37  3.000
 LEX  H2    N    HN    106.12  3.000
 LEX  H2    N    CA    109.78  3.000
 LEX  HN    N    CA    110.04  3.000
 LEX  HA    CA   CB    109.00  3.000
 LEX  CB    CA   N     110.50  1.700
 LEX  HA    CA   N     110.00  3.000
 LEX  CB    CA   C     110.10  1.900
 LEX  HA    CA   C     109.00  3.000
 LEX  N     CA   C     111.00  2.800
 LEX  HBA   CB   HB    106.01  3.000
 LEX  HBA   CB   CG    108.54  3.000
 LEX  HB    CB   CG    109.46  3.000
 LEX  CG    CB   CA    114.69  3.000
 LEX  HBA   CB   CA    109.74  3.000
 LEX  HB    CB   CA    108.05  3.000
 LEX  HG    CG   CD2   108.45  3.000
 LEX  HG    CG   CD1   108.49  3.000
 LEX  CD2   CG   CD1   110.28  3.000
 LEX  HG    CG   CB    108.04  3.000
 LEX  CD1   CG   CB    109.60  3.000
 LEX  CD2   CG   CB    111.88  3.000
 LEX  HACA  CAC  OXT   112.96  3.000
 LEX  HACA  CAC  HAC   105.40  3.000
 LEX  OXT   CAC  HAC   113.10  3.000
 LEX  HACA  CAC  C     106.10  3.000
 LEX  OXT   CAC  C     110.43  3.000
 LEX  HAC   CAC  C     108.46  3.000
 LEX  HD1B  CD1  HD1A  107.72  3.000
 LEX  HD1B  CD1  HD1   107.59  3.000
 LEX  HD1A  CD1  HD1   107.61  3.000
 LEX  HD1B  CD1  CG    110.91  3.000
 LEX  HD1A  CD1  CG    111.61  3.000
 LEX  HD1   CD1  CG    111.22  3.000
 LEX  HD2B  CD2  HD2A  107.59  3.000
 LEX  HD2B  CD2  HD2   107.77  3.000
 LEX  HD2A  CD2  HD2   106.99  3.000
 LEX  HD2B  CD2  CG    110.79  3.000
 LEX  HD2A  CD2  CG    110.91  3.000
 LEX  HD2   CD2  CG    112.58  3.000
 LEX  HXT   OXT  CAC   107.93  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
 LEX  Var_01  OXT  CAC  C   O     -8.69  30.0  3
 LEX  Var_02  CD2  CG   CB  CA   -65.07  30.0  2
 LEX  Var_03  HD2  CD2  CG  CB    62.74  30.0  3
 LEX  Var_04  HD1  CD1  CG  CB  -179.20  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
 LEX  chir_01  CA  C  N  CB  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
 LEX  plan-1  C    0.020
 LEX  plan-1  O    0.020
 LEX  plan-1  CA   0.020
 LEX  plan-1  CAC  0.020

