# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:57:15 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (2~{S})-2-(methylamino)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](NC)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
 9KK  9KK  '(2~{S})-2-(methylamino)hexanoic acid'  L-peptide  24  10  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9KK
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
 9KK  N    N  NH1    0  -0.584  22.7943  5.5678  -18.1647
 9KK  CE   C  CH3    0  -0.658  19.8961  1.0320  -18.9281
 9KK  CD   C  CH2    0  -0.412  20.0588  2.3467  -19.6774
 9KK  CG   C  CH2    0  -0.415  21.2600  3.1573  -19.2044
 9KK  CB   C  CH2    0  -0.412  21.4454  4.4547  -19.9812
 9KK  CA   C  CH1    0  -0.236  22.6993  5.2403  -19.5821
 9KK  CM   C  CH3    0  -0.525  21.7274  6.4009  -17.6533
 9KK  C    C  C      0   0.409  22.9339  6.5114  -20.4536
 9KK  O    O  O      0  -0.600  22.2109  6.6578  -21.4599
 9KK  OXT  O  OC    -1  -0.609  23.8554  7.2667  -20.0909
 9KK  H    H  HNH1   0   0.336  22.8328  4.7131  -17.6248
 9KK  HE3  H  HCH3   0   0.223  19.0258  0.4749  -19.2773
 9KK  HE2  H  HCH3   0   0.214  20.7714  0.3929  -19.0588
 9KK  HE1  H  HCH3   0   0.213  19.7708  1.2007  -17.8568
 9KK  HD2  H  HCH2   0   0.207  19.1520  2.9491  -19.5628
 9KK  HD3  H  HCH2   0   0.206  20.1544  2.1483  -20.7494
 9KK  HG2  H  HCH2   0   0.201  21.1410  3.3639  -18.1349
 9KK  HG3  H  HCH2   0   0.201  22.1659  2.5454  -19.2934
 9KK  HB2  H  HCH2   0   0.198  20.5499  5.0754  -19.8708
 9KK  HB3  H  HCH2   0   0.205  21.5092  4.2193  -21.0462
 9KK  HA   H  HCH1   0   0.211  23.5601  4.5846  -19.7805
 9KK  HM1  H  HCH3   0   0.222  21.8782  6.5638  -16.5850
 9KK  HM3  H  HCH3   0   0.217  21.7543  7.3808  -18.1332
 9KK  HM2  H  HCH3   0   0.188  20.7122  6.0004  -17.7801

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
 9KK  O   C    deloc   1.231  0.020  1.231
 9KK  C   CA   single  1.525  0.021  1.525
 9KK  CD  CG   single  1.524  0.020  1.524
 9KK  CD  CE   single  1.522  0.020  1.522
 9KK  CB  CA   single  1.521  0.033  1.521
 9KK  CB  CG   single  1.523  0.020  1.523
 9KK  CA  N    single  1.458  0.019  1.458
 9KK  N   CM   single  1.447  0.020  1.447
 9KK  C   OXT  deloc   1.245  0.020  1.245
 9KK  N   H    single  0.860  0.020  0.860
 9KK  CE  HE3  single  0.970  0.020  1.090
 9KK  CE  HE2  single  0.970  0.020  1.090
 9KK  CE  HE1  single  0.970  0.020  1.090
 9KK  CD  HD2  single  0.970  0.020  1.090
 9KK  CD  HD3  single  0.970  0.020  1.090
 9KK  CG  HG2  single  0.970  0.020  1.090
 9KK  CG  HG3  single  0.970  0.020  1.090
 9KK  CB  HB2  single  0.970  0.020  1.090
 9KK  CB  HB3  single  0.970  0.020  1.090
 9KK  CA  HA   single  0.970  0.020  0.970
 9KK  CM  HM1  single  0.970  0.020  1.090
 9KK  CM  HM3  single  0.970  0.020  1.090
 9KK  CM  HM2  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
 9KK  H    N   CM   109.02  3.000
 9KK  H    N   CA   114.00  3.000
 9KK  CM   N   CA   115.14  3.000
 9KK  HE1  CE  HE2  107.46  3.000
 9KK  HE1  CE  HE3  107.55  3.000
 9KK  HE2  CE  HE3  107.60  3.000
 9KK  HE1  CE  CD   111.22  3.000
 9KK  HE2  CE  CD   111.16  3.000
 9KK  HE3  CE  CD   111.65  3.000
 9KK  HD3  CD  HD2  105.94  3.000
 9KK  HD3  CD  CG   109.36  3.000
 9KK  HD2  CD  CG   109.13  3.000
 9KK  HD3  CD  CE   109.57  3.000
 9KK  HD2  CD  CE   109.59  3.000
 9KK  CG   CD  CE   113.01  3.000
 9KK  HG3  CG  HG2  105.90  3.000
 9KK  HG3  CG  CB   109.47  3.000
 9KK  HG2  CG  CB   110.51  3.000
 9KK  HG3  CG  CD   109.20  3.000
 9KK  HG2  CG  CD   108.51  3.000
 9KK  CB   CG  CD   112.99  3.000
 9KK  HB3  CB  HB2  105.55  3.000
 9KK  HB3  CB  CA   108.45  3.000
 9KK  HB2  CB  CA   110.62  3.000
 9KK  HB3  CB  CG   108.70  3.000
 9KK  HB2  CB  CG   109.38  3.000
 9KK  CA   CB  CG   113.78  3.000
 9KK  HA   CA  C    110.00  3.000
 9KK  HA   CA  CB   109.00  3.000
 9KK  C    CA  CB   110.50  1.500
 9KK  HA   CA  N    110.00  3.000
 9KK  CB   CA  N    110.40  1.500
 9KK  C    CA  N    111.00  2.800
 9KK  HM2  CM  HM3  107.42  3.000
 9KK  HM2  CM  HM1  107.16  3.000
 9KK  HM3  CM  HM1  107.04  3.000
 9KK  HM2  CM  N    115.51  3.000
 9KK  HM3  CM  N    110.09  3.000
 9KK  HM1  CM  N    109.28  3.000
 9KK  OXT  C   O    126.33  3.000
 9KK  OXT  C   CA   120.80  1.700
 9KK  O    C   CA   120.80  1.700

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
 9KK  Var_01  CB   CG  CD  CE   178.38  30.0  3
 9KK  Var_02  CA   CB  CG  CD  -176.27  30.0  1
 9KK  Var_03  HE3  CE  CD  CG   179.47  30.0  3
 9KK  Var_04  HM1  CM  N   CA   178.52  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
 9KK  chir_01  CA  C  CB  N  positiv

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
 9KK  plan-1  CA   0.020
 9KK  plan-1  C    0.020
 9KK  plan-1  O    0.020
 9KK  plan-1  OXT  0.020

