# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:33:14 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: N~6~-carboxy-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(O)=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
 KCX  KCX  'N~6~-carboxy-L-lysine    '  L-peptide  25  13  .  2015-10-07  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_KCX
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
 KCX  N    N  NH2    0  -0.791  28.3696  43.4430  28.4276
 KCX  CA   C  CH1    0  -0.226  28.1749  43.3151  29.8666
 KCX  CB   C  CH2    0  -0.406  28.9722  42.1298  30.4128
 KCX  CG   C  CH2    0  -0.450  30.4864  42.2918  30.3063
 KCX  CD   C  CH2    0  -0.427  31.2781  41.2540  31.0987
 KCX  CE   C  CH2    0  -0.290  31.0196  41.2927  32.6097
 KCX  NZ   N  NH1    0  -0.661  31.1447  42.5930  33.2213
 KCX  C    C  C      0   0.389  28.4501  44.5996  30.6979
 KCX  O    O  O      0  -0.599  28.7332  45.6406  30.0753
 KCX  CX   C  C      0   0.493  32.4011  43.2173  33.3686
 KCX  OXT  O  OC    -1  -0.615  28.3393  44.4838  31.9400
 KCX  OQ1  O  O      0  -0.644  33.4084  42.4765  33.3654
 KCX  OQ2  O  OC    -1  -0.655  32.3771  44.4576  33.5312
 KCX  H    H  HNH2   0   0.329  27.7913  44.2053  28.0955
 KCX  HN2  H  HNH2   0   0.326  29.3148  43.7676  28.2579
 KCX  HA   H  HCH1   0   0.215  27.1144  43.0749  30.0198
 KCX  HB2  H  HCH2   0   0.214  28.6839  41.9913  31.4551
 KCX  HB3  H  HCH2   0   0.202  28.6703  41.2183  29.8865
 KCX  HG2  H  HCH2   0   0.214  30.7908  42.2378  29.2567
 KCX  HG3  H  HCH2   0   0.211  30.7791  43.2896  30.6480
 KCX  HD2  H  HCH2   0   0.201  31.0471  40.2486  30.7296
 KCX  HD3  H  HCH2   0   0.211  32.3450  41.4094  30.9193
 KCX  HE2  H  HCH2   0   0.207  30.0128  40.9201  32.8171
 KCX  HE3  H  HCH2   0   0.216  31.7000  40.5978  33.1035
 KCX  HZ   H  HNH1   0   0.336  30.3994  43.2312  32.9812

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
 KCX  N   CA   single  1.458  0.019  1.458
 KCX  N   H    single  0.860  0.020  0.860
 KCX  N   HN2  single  0.890  0.020  1.040
 KCX  CA  CB   single  1.530  0.020  1.530
 KCX  CA  C    single  1.525  0.021  1.525
 KCX  CA  HA   single  0.970  0.020  0.970
 KCX  CB  CG   single  1.527  0.020  1.527
 KCX  CB  HB2  single  0.970  0.020  1.090
 KCX  CB  HB3  single  0.970  0.020  1.090
 KCX  CG  CD   single  1.527  0.020  1.527
 KCX  CG  HG2  single  0.970  0.020  1.090
 KCX  CG  HG3  single  0.970  0.020  1.090
 KCX  CD  CE   single  1.533  0.020  1.533
 KCX  CD  HD2  single  0.970  0.020  1.090
 KCX  CD  HD3  single  0.970  0.020  1.090
 KCX  CE  NZ   single  1.442  0.020  1.442
 KCX  CE  HE2  single  0.970  0.020  1.090
 KCX  CE  HE3  single  0.970  0.020  1.090
 KCX  NZ  CX   single  1.411  0.020  1.411
 KCX  NZ  HZ   single  0.890  0.020  1.040
 KCX  C   O    deloc   1.231  0.020  1.231
 KCX  C   OXT  deloc   1.252  0.020  1.252
 KCX  CX  OQ1  deloc   1.250  0.020  1.250
 KCX  CX  OQ2  deloc   1.251  0.020  1.251

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
 KCX  HN2  N   H    103.68  3.000
 KCX  HN2  N   CA   108.53  3.000
 KCX  H    N   CA   114.00  3.000
 KCX  HA   CA  C    109.00  3.000
 KCX  HA   CA  CB   109.00  3.000
 KCX  C    CA  CB   110.10  1.900
 KCX  HA   CA  N    110.00  3.000
 KCX  C    CA  N    111.00  2.800
 KCX  CB   CA  N    110.50  1.700
 KCX  HB3  CB  HB2  106.31  3.000
 KCX  HB3  CB  CG   109.16  3.000
 KCX  HB2  CB  CG   110.03  3.000
 KCX  HB3  CB  CA   109.25  3.000
 KCX  HB2  CB  CA   107.58  3.000
 KCX  CG   CB  CA   114.20  3.000
 KCX  HG3  CG  HG2  105.67  3.000
 KCX  HG3  CG  CD   108.59  3.000
 KCX  HG2  CG  CD   108.67  3.000
 KCX  HG3  CG  CB   109.89  3.000
 KCX  HG2  CG  CB   109.73  3.000
 KCX  CD   CG  CB   113.95  3.000
 KCX  HD3  CD  HD2  106.32  3.000
 KCX  HD3  CD  CE   108.83  3.000
 KCX  HD2  CD  CE   108.64  3.000
 KCX  HD3  CD  CG   108.92  3.000
 KCX  HD2  CD  CG   109.85  3.000
 KCX  CE   CD  CG   114.00  3.000
 KCX  HE3  CE  HE2  105.75  3.000
 KCX  HE3  CE  NZ   109.17  3.000
 KCX  HE2  CE  NZ   107.85  3.000
 KCX  HE3  CE  CD   108.95  3.000
 KCX  HE2  CE  CD   109.48  3.000
 KCX  NZ   CE  CD   115.21  3.000
 KCX  HZ   NZ  CX   113.73  3.000
 KCX  HZ   NZ  CE   113.88  3.000
 KCX  CX   NZ  CE   121.36  3.000
 KCX  OXT  C   O    126.38  3.000
 KCX  OXT  C   CA   116.00  3.000
 KCX  O    C   CA   120.80  1.700
 KCX  OQ2  CX  OQ1  127.10  3.000
 KCX  OQ2  CX  NZ   115.79  3.000
 KCX  OQ1  CX  NZ   117.07  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
 KCX  Var_01  CD   CG  CB  CA  168.19  30.0  3
 KCX  Var_02  CE   CD  CG  CB  -61.49  30.0  3
 KCX  Var_03  NZ   CE  CD  CG  -50.93  30.0  3
 KCX  Var_04  CX   NZ  CE  CD  -70.51  30.0  3
 KCX  Var_05  OQ1  CX  NZ  CE  -22.56  30.0  2

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
 KCX  chir_01  CA  N  CB  C  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
 KCX  plan-1  CA   0.020
 KCX  plan-1  C    0.020
 KCX  plan-1  O    0.020
 KCX  plan-1  OXT  0.020
 KCX  plan-2  NZ   0.020
 KCX  plan-2  CX   0.020
 KCX  plan-2  OQ1  0.020
 KCX  plan-2  OQ2  0.020

