# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 18:04:09 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (5S)-5-amino-3-oxo-hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)CC(=O)CC(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
 KMH  KMH  '(5S)-5-amino-3-oxo-hexanoic acid'  ligand  20  10  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KMH
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
 KMH  N     N  NH2    0  -0.792  -2.9395   0.8472  -1.0045
 KMH  CB    C  CH1    0  -0.101  -2.4243   0.1711   0.1800
 KMH  CG    C  CH3    0  -0.653  -3.4818  -0.7928   0.7022
 KMH  CE    C  C      0   0.436   2.1418  -0.8415   0.5702
 KMH  OF1   O  O      0  -0.594   1.6651  -0.4487   1.6507
 KMH  OF2   O  OC    -1  -0.606   3.1852  -1.4908   0.3917
 KMH  CA    C  CH2    0  -0.557  -1.1087  -0.5767  -0.0380
 KMH  C     C  C      0   0.418   0.0876   0.2714  -0.3856
 KMH  C2    C  CH2    0  -0.713   1.3499  -0.4715  -0.7154
 KMH  O     O  O      0  -0.428   0.0442   1.4854  -0.3816
 KMH  HN1   H  HNH2   0   0.343  -2.2573   1.5155  -1.3385
 KMH  HN2   H  HNH2   0   0.331  -3.0576   0.1719  -1.7521
 KMH  HB    H  HCH1   0   0.221  -2.2622   0.9393   0.9421
 KMH  HG1C  H  HCH3   0   0.214  -3.6674  -1.5952  -0.0164
 KMH  HG2C  H  HCH3   0   0.224  -3.1673  -1.2559   1.6382
 KMH  HG3C  H  HCH3   0   0.230  -4.4252  -0.2758   0.8793
 KMH  HA1C  H  HCH2   0   0.265  -0.8324  -1.1398   0.8605
 KMH  HA2C  H  HCH2   0   0.249  -1.2337  -1.3337  -0.8214
 KMH  H21C  H  HCH2   0   0.261   1.9883   0.1485  -1.3505
 KMH  H22C  H  HCH2   0   0.251   1.1273  -1.3864  -1.2712

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
 KMH  N   CB    single  1.458  0.020  1.458
 KMH  CB  CG    single  1.523  0.020  1.523
 KMH  CB  CA    single  1.529  0.020  1.529
 KMH  CE  OF2   deloc   1.242  0.020  1.242
 KMH  CE  OF1   deloc   1.245  0.020  1.245
 KMH  CE  C2    single  1.555  0.020  1.555
 KMH  CA  C     single  1.507  0.020  1.507
 KMH  C   O     double  1.215  0.020  1.215
 KMH  C   C2    single  1.501  0.020  1.501
 KMH  N   HN1   single  0.890  0.020  1.040
 KMH  N   HN2   single  0.890  0.020  1.040
 KMH  CB  HB    single  0.970  0.020  1.090
 KMH  CG  HG1C  single  0.970  0.020  1.090
 KMH  CG  HG2C  single  0.970  0.020  1.090
 KMH  CG  HG3C  single  0.970  0.020  1.090
 KMH  CA  HA1C  single  0.970  0.020  1.090
 KMH  CA  HA2C  single  0.970  0.020  1.090
 KMH  C2  H21C  single  0.970  0.020  1.090
 KMH  C2  H22C  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
 KMH  HN2   N   HN1   105.96  3.000
 KMH  HN2   N   CB    109.34  3.000
 KMH  HN1   N   CB    109.65  3.000
 KMH  HB    CB  CA    108.37  3.000
 KMH  HB    CB  CG    107.96  3.000
 KMH  CA    CB  CG    109.68  3.000
 KMH  HB    CB  N     107.01  3.000
 KMH  CA    CB  N     114.53  3.000
 KMH  CG    CB  N     109.07  3.000
 KMH  HG3C  CG  HG2C  108.15  3.000
 KMH  HG3C  CG  HG1C  107.94  3.000
 KMH  HG2C  CG  HG1C  107.54  3.000
 KMH  HG3C  CG  CB    110.88  3.000
 KMH  HG2C  CG  CB    111.27  3.000
 KMH  HG1C  CG  CB    110.91  3.000
 KMH  C2    CE  OF2   115.70  3.000
 KMH  C2    CE  OF1   116.60  3.000
 KMH  OF2   CE  OF1   127.70  3.000
 KMH  HA2C  CA  HA1C  105.06  3.000
 KMH  HA2C  CA  C     108.31  3.000
 KMH  HA1C  CA  C     106.15  3.000
 KMH  HA2C  CA  CB    109.96  3.000
 KMH  HA1C  CA  CB    110.58  3.000
 KMH  C     CA  CB    116.14  3.000
 KMH  O     C   C2    121.69  3.000
 KMH  C2    C   CA    116.08  3.000
 KMH  O     C   CA    122.23  3.000
 KMH  H22C  C2  H21C  107.34  3.000
 KMH  H22C  C2  C     110.77  3.000
 KMH  H21C  C2  C     109.75  3.000
 KMH  H22C  C2  CE    108.96  3.000
 KMH  H21C  C2  CE    108.53  3.000
 KMH  C     C2  CE    111.38  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
 KMH  Var_01  O   C  CA  CB    6.15  30.0  3
 KMH  Var_02  CA  C  C2  CE  -84.47  30.0  1

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
 KMH  chir_01  CB  N  CG  CA  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
 KMH  plan-1  CA   0.020
 KMH  plan-1  C    0.020
 KMH  plan-1  C2   0.020
 KMH  plan-1  O    0.020
 KMH  plan-2  CE   0.020
 KMH  plan-2  OF1  0.020
 KMH  plan-2  OF2  0.020
 KMH  plan-2  C2   0.020

