# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 20:08:27 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  21  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 GRAND
;

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  -0.789  -2.6693   1.1286  -0.7645
 KMH  CB    C  CH1   0  -0.101  -2.4436   0.1306   0.2720
 KMH  CG    C  CH3   0  -0.652  -3.6858  -0.7381   0.4179
 KMH  CE    C  C     0   0.535   2.5760  -0.2205  -0.3120
 KMH  OF1   O  O     0  -0.435   3.2291   0.4328  -1.0842
 KMH  OF2   O  OH1   0  -0.586   2.9487  -0.4787   0.9340
 KMH  CA    C  CH2   0  -0.561  -1.2219  -0.7609   0.0358
 KMH  C     C  C     0   0.409   0.1032  -0.0532   0.0085
 KMH  C2    C  CH2   0  -0.670   1.2392  -0.8338  -0.6236
 KMH  O     O  O     0  -0.394   0.2775   1.0576   0.4518
 KMH  HN1   H  HNH2  0   0.346  -1.8860   1.7670  -0.8120
 KMH  HN2   H  HNH2  0   0.335  -2.7186   0.6747  -1.6698
 KMH  HB    H  HCH1  0   0.231  -2.2970   0.6707   1.2116
 KMH  HG1C  H  HCH3  0   0.217  -3.8769  -1.3058  -0.4963
 KMH  HG2C  H  HCH3  0   0.226  -3.5730  -1.4528   1.2334
 KMH  HG3C  H  HCH3  0   0.234  -4.5634  -0.1246   0.6210
 KMH  HA1C  H  HCH2  0   0.282  -1.1386  -1.5149   0.8299
 KMH  HA2C  H  HCH2  0   0.264  -1.3372  -1.3383  -0.8885
 KMH  H21C  H  HCH2  0   0.317   1.0764  -0.8332  -1.7042
 KMH  H22C  H  HCH2  0   0.308   1.1953  -1.8764  -0.2995
 KMH  HF2   H  HOH1  0   0.484   3.7987  -0.0533   1.1240

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  1.456  0.020  1.456
 KMH  CB   CG    single  1.523  0.020  1.523
 KMH  CB   CA    single  1.531  0.020  1.531
 KMH  CE   OF2   single  1.326  0.020  1.326
 KMH  CE   OF1   double  1.204  0.020  1.204
 KMH  CE   C2    single  1.503  0.020  1.503
 KMH  CA   C     single  1.502  0.020  1.502
 KMH  C    O     double  1.209  0.020  1.209
 KMH  C    C2    single  1.516  0.020  1.516
 KMH  OF2  HF2   single  0.850  0.020  0.980
 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   106.16  3.000
 KMH  HN2   N    CB    109.65  3.000
 KMH  HN1   N    CB    110.23  3.000
 KMH  HB    CB   CA    108.25  3.000
 KMH  HB    CB   CG    107.99  3.000
 KMH  CA    CB   CG    109.49  3.000
 KMH  HB    CB   N     107.08  3.000
 KMH  CA    CB   N     114.39  3.000
 KMH  CG    CB   N     109.43  3.000
 KMH  HG3C  CG   HG2C  108.23  3.000
 KMH  HG3C  CG   HG1C  107.91  3.000
 KMH  HG2C  CG   HG1C  107.65  3.000
 KMH  HG3C  CG   CB    110.71  3.000
 KMH  HG2C  CG   CB    111.18  3.000
 KMH  HG1C  CG   CB    111.02  3.000
 KMH  C2    CE   OF2   111.43  3.000
 KMH  C2    CE   OF1   124.80  3.000
 KMH  OF2   CE   OF1   123.77  3.000
 KMH  HF2   OF2  CE    110.20  3.000
 KMH  HA2C  CA   HA1C  104.84  3.000
 KMH  HA2C  CA   C     109.00  3.000
 KMH  HA1C  CA   C     105.64  3.000
 KMH  HA2C  CA   CB    110.67  3.000
 KMH  HA1C  CA   CB    110.42  3.000
 KMH  C     CA   CB    115.62  3.000
 KMH  O     C    C2    121.19  3.000
 KMH  C2    C    CA    115.20  3.000
 KMH  O     C    CA    123.60  3.000
 KMH  H22C  C2   H21C  106.73  3.000
 KMH  H22C  C2   C     109.72  3.000
 KMH  H21C  C2   C     107.48  3.000
 KMH  H22C  C2   CE    111.31  3.000
 KMH  H21C  C2   CE    109.70  3.000
 KMH  C     C2   CE    111.70  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  CONST_01  HF2  OF2  CE  OF1     0.00   0.0  0
 KMH  Var_01    O    C    CA  CB     17.56  30.0  3
 KMH  Var_02    CA   C    C2  CE   -165.83  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
 KMH  plan-2  HF2  0.020

