# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 22:32:06 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (2S,3S)-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
 L3O  L3O  '(2S,3S)-3-amino-2-hydroxy-5-methylhexanoic acid'  L-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 PERFECT
;

data_comp_L3O
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
 L3O  CZ    C  CH1    0  -0.064  -1.1152  -0.4315   0.6371
 L3O  OZ    O  OH1    0  -0.692  -1.0460  -1.8343   0.5013
 L3O  CA    C  CH1    0  -0.120   0.0761   0.2298  -0.0787
 L3O  CB    C  CH2    0  -0.395   1.3938  -0.2555   0.5382
 L3O  CG    C  CH1    0  -0.244   2.6725   0.2943  -0.0987
 L3O  CD1   C  CH3    0  -0.648   3.8929  -0.1878   0.6797
 L3O  CD2   C  CH3    0  -0.655   2.7925  -0.0885  -1.5708
 L3O  N     N  NH2    0  -0.791  -0.0878   1.6773  -0.0814
 L3O  C     C  C      0   0.397  -2.4614   0.0609   0.0664
 L3O  O     O  O      0  -0.623  -2.8920  -0.6277  -0.8898
 L3O  OXT   O  OC    -1  -0.594  -3.0040   1.0503   0.5799
 L3O  HZ    H  HCH1   0   0.192  -1.0566  -0.1860   1.7059
 L3O  HA    H  HOH1   0   0.423  -1.6319  -2.0060  -0.2536
 L3O  HB    H  HCH1   0   0.209   0.0297  -0.0982  -1.1251
 L3O  HB1C  H  HCH2   0   0.205   1.3916   0.0089   1.6037
 L3O  HB2C  H  HCH2   0   0.208   1.4324  -1.3486   0.4955
 L3O  HN1   H  HNH2   0   0.330  -0.1394   2.0165   0.8725
 L3O  HN2   H  HNH2   0   0.343   0.7348   2.1120  -0.4810
 L3O  HG    H  HCH1   0   0.202   2.6579   1.3886  -0.0279
 L3O  HD11  H  HCH3   0   0.223   4.8139   0.2414   0.2810
 L3O  HD12  H  HCH3   0   0.222   3.8268   0.0885   1.7337
 L3O  HD13  H  HCH3   0   0.211   3.9853  -1.2756   0.6281
 L3O  HD21  H  HCH3   0   0.226   1.9827   0.3235  -2.1751
 L3O  HD22  H  HCH3   0   0.224   3.7308   0.2721  -1.9968
 L3O  HD23  H  HCH3   0   0.212   2.7722  -1.1748  -1.6903

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
 L3O  CZ   OZ    single  1.411  0.020  1.411
 L3O  CZ   CA    single  1.539  0.020  1.539
 L3O  CZ   C     single  1.543  0.020  1.543
 L3O  CA   CB    single  1.530  0.020  1.530
 L3O  CA   N     single  1.458  0.019  1.458
 L3O  CB   CG    single  1.531  0.020  1.531
 L3O  CG   CD1   single  1.526  0.020  1.526
 L3O  CG   CD2   single  1.526  0.020  1.526
 L3O  C    O     deloc   1.231  0.020  1.231
 L3O  C    OXT   deloc   1.240  0.020  1.240
 L3O  CZ   HZ    single  0.970  0.020  1.090
 L3O  OZ   HA    single  0.850  0.020  0.980
 L3O  CA   HB    single  0.970  0.020  1.090
 L3O  CB   HB1C  single  0.970  0.020  1.090
 L3O  CB   HB2C  single  0.970  0.020  1.090
 L3O  N    HN1   single  0.890  0.020  1.040
 L3O  N    HN2   single  0.890  0.020  1.040
 L3O  CG   HG    single  0.970  0.020  1.090
 L3O  CD1  HD11  single  0.970  0.020  1.090
 L3O  CD1  HD12  single  0.970  0.020  1.090
 L3O  CD1  HD13  single  0.970  0.020  1.090
 L3O  CD2  HD21  single  0.970  0.020  1.090
 L3O  CD2  HD22  single  0.970  0.020  1.090
 L3O  CD2  HD23  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
 L3O  HZ    CZ   C     109.59  3.000
 L3O  HZ    CZ   CA    108.38  3.000
 L3O  C     CZ   CA    111.49  3.000
 L3O  HZ    CZ   OZ    108.25  3.000
 L3O  C     CZ   OZ    108.93  3.000
 L3O  CA    CZ   OZ    110.15  3.000
 L3O  HA    OZ   CZ    102.77  3.000
 L3O  HB    CA   N     106.88  3.000
 L3O  HB    CA   CB    108.98  3.000
 L3O  N     CA   CB    110.50  1.700
 L3O  HB    CA   CZ    106.40  3.000
 L3O  N     CA   CZ    109.91  3.000
 L3O  CB    CA   CZ    110.00  3.000
 L3O  HB2C  CB   HB1C  106.17  3.000
 L3O  HB2C  CB   CG    108.24  3.000
 L3O  HB1C  CB   CG    108.60  3.000
 L3O  HB2C  CB   CA    109.30  3.000
 L3O  HB1C  CB   CA    108.21  3.000
 L3O  CG    CB   CA    115.89  3.000
 L3O  HG    CG   CD2   108.28  3.000
 L3O  HG    CG   CD1   107.04  3.000
 L3O  CD2   CG   CD1   110.49  3.000
 L3O  HG    CG   CB    108.69  3.000
 L3O  CD2   CG   CB    112.15  3.000
 L3O  CD1   CG   CB    110.02  3.000
 L3O  HD13  CD1  HD12  107.61  3.000
 L3O  HD13  CD1  HD11  107.62  3.000
 L3O  HD12  CD1  HD11  107.71  3.000
 L3O  HD13  CD1  CG    110.98  3.000
 L3O  HD12  CD1  CG    111.36  3.000
 L3O  HD11  CD1  CG    111.37  3.000
 L3O  HD23  CD2  HD22  107.55  3.000
 L3O  HD23  CD2  HD21  107.51  3.000
 L3O  HD22  CD2  HD21  107.28  3.000
 L3O  HD23  CD2  CG    110.70  3.000
 L3O  HD22  CD2  CG    111.17  3.000
 L3O  HD21  CD2  CG    112.41  3.000
 L3O  HN2   N    HN1   105.60  3.000
 L3O  HN2   N    CA    109.62  3.000
 L3O  HN1   N    CA    109.67  3.000
 L3O  OXT   C    O     127.12  3.000
 L3O  OXT   C    CZ    118.90  3.000
 L3O  O     C    CZ    113.97  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
 L3O  Var_01  CD1   CG   CB  CA   175.73  30.0  3
 L3O  Var_02  HD11  CD1  CG  CB  -176.50  30.0  3
 L3O  Var_03  HD21  CD2  CG  CB    62.33  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
 L3O  chir_01  CZ  OZ  CA  C   negativ
 L3O  chir_02  CA  N   CB  CZ  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
 L3O  plan-1  CZ   0.020
 L3O  plan-1  C    0.020
 L3O  plan-1  O    0.020
 L3O  plan-1  OXT  0.020

