# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 05:54:21 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: N~6~-propanoyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)NCCCC[C@H](N)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
 PRK  PRK  'N~6~-propanoyl-L-lysine  '  L-peptide  31  14  .  2012-08-28  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_PRK
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
 PRK  C     C  C      0   0.411  -4.3057  -10.1204  -6.2315
 PRK  N     N  NH2    0  -0.816  -2.3022  -10.0279  -4.7743
 PRK  O     O  O      0  -0.606  -5.5080   -9.8381  -6.4010
 PRK  CA    C  CH1    0  -0.219  -3.7581   -9.9749  -4.7868
 PRK  CB    C  CH2    0  -0.386  -4.2519   -8.6985  -4.1102
 PRK  CD    C  CH2    0  -0.421  -4.3591   -7.3393  -1.9660
 PRK  CE    C  CH2    0  -0.277  -3.9081   -7.2569  -0.5124
 PRK  CG    C  CH2    0  -0.425  -3.8128   -8.5817  -2.6564
 PRK  NZ    N  NH1    0  -0.638  -4.4138   -6.0978   0.1908
 PRK  CAA   C  CH3    0  -0.708  -5.7397   -4.0932   1.7183
 PRK  OAD   O  O      0  -0.513  -2.8046   -4.6828  -0.5020
 PRK  CAF   C  CH2    0  -0.538  -4.5046   -3.7628   0.8944
 PRK  CAL   C  C      0   0.530  -3.8341   -4.8892   0.1305
 PRK  OXT   O  OC    -1  -0.602  -3.5135  -10.5470  -7.0967
 PRK  H     H  HNH2   0   0.329  -1.9739  -10.4193  -3.9018
 PRK  H2    H  HNH2   0   0.332  -2.0097  -10.6588  -5.5091
 PRK  HA    H  HCH1   0   0.188  -4.1989  -10.8207  -4.2275
 PRK  HB2   H  HCH2   0   0.194  -3.8882   -7.8290  -4.6699
 PRK  HB3   H  HCH2   0   0.203  -5.3424   -8.6705  -4.1593
 PRK  HD2   H  HCH2   0   0.214  -5.4528   -7.3426  -2.0067
 PRK  HD3   H  HCH2   0   0.219  -4.0284   -6.4435  -2.4993
 PRK  HE2   H  HCH2   0   0.240  -4.2469   -8.1413   0.0297
 PRK  HE3   H  HCH2   0   0.233  -2.8180   -7.2552  -0.4607
 PRK  HG2   H  HCH2   0   0.203  -4.1405   -9.4741  -2.1091
 PRK  HG3   H  HCH2   0   0.210  -2.7198   -8.5709  -2.5975
 PRK  HZ    H  HNH1   0   0.407  -5.2816   -6.2027   0.6885
 PRK  HAA   H  HCH3   0   0.252  -6.1004   -3.1969   2.2213
 PRK  HAAA  H  HCH3   0   0.232  -6.5597   -4.4642   1.1011
 PRK  HAAB  H  HCH3   0   0.234  -5.5301   -4.8340   2.4911
 PRK  HAF   H  HCH2   0   0.260  -4.7443   -2.9909   0.1583
 PRK  HAFA  H  HCH2   0   0.259  -3.7355   -3.3244   1.5349

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
 PRK  C    O     deloc   1.231  0.020  1.231
 PRK  C    CA    single  1.525  0.021  1.525
 PRK  C    OXT   deloc   1.248  0.020  1.248
 PRK  N    CA    single  1.458  0.019  1.458
 PRK  CA   CB    single  1.530  0.020  1.530
 PRK  CB   CG    single  1.523  0.020  1.523
 PRK  CD   CE    single  1.524  0.020  1.524
 PRK  CD   CG    single  1.523  0.020  1.523
 PRK  CE   NZ    single  1.447  0.020  1.447
 PRK  NZ   CAL   single  1.342  0.020  1.342
 PRK  CAA  CAF   single  1.521  0.020  1.521
 PRK  OAD  CAL   double  1.226  0.020  1.226
 PRK  CAF  CAL   single  1.517  0.020  1.517
 PRK  N    H     single  0.860  0.020  0.860
 PRK  N    H2    single  0.890  0.020  1.040
 PRK  CA   HA    single  0.970  0.020  0.970
 PRK  CB   HB2   single  0.970  0.020  1.090
 PRK  CB   HB3   single  0.970  0.020  1.090
 PRK  CD   HD2   single  0.970  0.020  1.090
 PRK  CD   HD3   single  0.970  0.020  1.090
 PRK  CE   HE2   single  0.970  0.020  1.090
 PRK  CE   HE3   single  0.970  0.020  1.090
 PRK  CG   HG2   single  0.970  0.020  1.090
 PRK  CG   HG3   single  0.970  0.020  1.090
 PRK  NZ   HZ    single  0.860  0.020  1.020
 PRK  CAA  HAA   single  0.970  0.020  1.090
 PRK  CAA  HAAA  single  0.970  0.020  1.090
 PRK  CAA  HAAB  single  0.970  0.020  1.090
 PRK  CAF  HAF   single  0.970  0.020  1.090
 PRK  CAF  HAFA  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
 PRK  OXT   C    CA    116.96  3.000
 PRK  OXT   C    O     126.53  3.000
 PRK  CA    C    O     120.80  1.700
 PRK  H2    N    H     106.95  3.000
 PRK  H2    N    CA    107.78  3.000
 PRK  H     N    CA    114.00  3.000
 PRK  HA    CA   CB    109.00  3.000
 PRK  HA    CA   N     110.00  3.000
 PRK  CB    CA   N     110.50  1.700
 PRK  HA    CA   C     109.00  3.000
 PRK  CB    CA   C     110.10  1.900
 PRK  N     CA   C     111.00  2.800
 PRK  HB3   CB   HB2   106.74  3.000
 PRK  HB3   CB   CG    109.20  3.000
 PRK  HB2   CB   CG    109.33  3.000
 PRK  HB3   CB   CA    108.94  3.000
 PRK  HB2   CB   CA    109.24  3.000
 PRK  CG    CB   CA    113.19  3.000
 PRK  HD3   CD   HD2   106.65  3.000
 PRK  HD3   CD   CG    109.80  3.000
 PRK  HD2   CD   CG    109.83  3.000
 PRK  HD3   CD   CE    109.34  3.000
 PRK  HD2   CD   CE    109.35  3.000
 PRK  CG    CD   CE    111.74  3.000
 PRK  HE3   CE   HE2   106.73  3.000
 PRK  HE3   CE   NZ    108.96  3.000
 PRK  HE2   CE   NZ    107.42  3.000
 PRK  HE3   CE   CD    109.92  3.000
 PRK  HE2   CE   CD    109.76  3.000
 PRK  NZ    CE   CD    113.79  3.000
 PRK  HG3   CG   HG2   106.23  3.000
 PRK  HG3   CG   CD    109.01  3.000
 PRK  HG2   CG   CD    109.29  3.000
 PRK  HG3   CG   CB    109.88  3.000
 PRK  HG2   CG   CB    109.13  3.000
 PRK  CD    CG   CB    113.07  3.000
 PRK  HZ    NZ   CAL   119.26  3.000
 PRK  HZ    NZ   CE    117.29  3.000
 PRK  CAL   NZ   CE    123.28  3.000
 PRK  HAAB  CAA  HAAA  108.31  3.000
 PRK  HAAB  CAA  HAA   107.17  3.000
 PRK  HAAA  CAA  HAA   106.99  3.000
 PRK  HAAB  CAA  CAF   112.04  3.000
 PRK  HAAA  CAA  CAF   112.19  3.000
 PRK  HAA   CAA  CAF   109.89  3.000
 PRK  HAFA  CAF  HAF   105.41  3.000
 PRK  HAFA  CAF  CAL   106.37  3.000
 PRK  HAF   CAF  CAL   106.38  3.000
 PRK  HAFA  CAF  CAA   109.95  3.000
 PRK  HAF   CAF  CAA   109.88  3.000
 PRK  CAL   CAF  CAA   118.06  3.000
 PRK  CAF   CAL  OAD   120.39  3.000
 PRK  CAF   CAL  NZ    117.08  3.000
 PRK  OAD   CAL  NZ    122.53  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
 PRK  CONST_01  OAD  CAL  NZ   CE      0.00   0.0  0
 PRK  CONST_02  CAF  CAL  NZ   CE    180.00   0.0  0
 PRK  CONST_03  HZ   NZ   CAL  OAD   180.00   0.0  0
 PRK  Var_01    CD   CG   CB   CA   -177.39  30.0  3
 PRK  Var_02    CE   CD   CG   CB    179.68  30.0  1
 PRK  Var_03    CAL  NZ   CE   CD    -83.42  30.0  3
 PRK  Var_04    NZ   CE   CD   CG   -179.42  30.0  3
 PRK  Var_05    CAA  CAF  CAL  NZ      2.70  30.0  1
 PRK  Var_06    HAA  CAA  CAF  CAL   179.04  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
 PRK  chir_01  CA  C  N  CB  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
 PRK  plan-1  CE   0.020
 PRK  plan-1  NZ   0.020
 PRK  plan-1  OAD  0.020
 PRK  plan-1  CAF  0.020
 PRK  plan-1  CAL  0.020
 PRK  plan-1  HZ   0.020
 PRK  plan-2  C    0.020
 PRK  plan-2  O    0.020
 PRK  plan-2  CA   0.020
 PRK  plan-2  OXT  0.020

