# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:43:57 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: N~6~-[(3S)-3-hydroxybutanoyl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)CC(=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
 KHB  KHB  N~6~-[(3S)-3-hydroxybutanoyl]-L-lysine  L-peptide  35  16  .  2019-03-22  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_KHB
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
 KHB  N    N  NH2    0  -0.794  -12.3439  11.3229  -6.7836
 KHB  CA   C  CH1    0  -0.188  -11.0607  11.2017  -6.0923
 KHB  C    C  C      0   0.384  -10.0414  12.3025  -6.4683
 KHB  O    O  O      0  -0.612   -9.9044  12.5236  -7.6912
 KHB  CB   C  CH2    0  -0.410  -10.4806   9.8190  -6.3929
 KHB  CG   C  CH2    0  -0.428   -9.1760   9.5033  -5.6721
 KHB  CD   C  CH2    0  -0.446   -8.7203   8.0689  -5.9070
 KHB  CE   C  CH2    0  -0.249   -7.4161   7.7542  -5.1890
 KHB  C1   C  C      0   0.550   -6.4033   5.5844  -4.5669
 KHB  C2   C  CH2    0  -0.597   -5.9922   4.2317  -5.1169
 KHB  C3   C  CH1    0   0.047   -5.7145   3.1973  -4.0301
 KHB  C4   C  CH3    0  -0.672   -5.3628   1.8568  -4.6469
 KHB  NZ   N  NH1    0  -0.638   -6.9807   6.4006  -5.4605
 KHB  O2   O  OH1    0  -0.674   -6.8378   3.0085  -3.1932
 KHB  O1   O  O      0  -0.505   -6.2080   5.8982  -3.3967
 KHB  OXT  O  OC    -1  -0.613   -9.4310  12.8635  -5.5354
 KHB  H    H  HNH2   0   0.332  -12.7875  12.1897  -6.5012
 KHB  HN2  H  HNH2   0   0.321  -12.1450  11.4456  -7.7710
 KHB  HA   H  HCH1   0   0.192  -11.2597  11.2592  -5.0167
 KHB  HB2  H  HCH2   0   0.209  -11.2309   9.0687  -6.1239
 KHB  HB3  H  HCH2   0   0.201  -10.3290   9.7254  -7.4744
 KHB  HG2  H  HCH2   0   0.218   -8.3881  10.1876  -5.9994
 KHB  HG3  H  HCH2   0   0.210   -9.3011   9.6742  -4.5975
 KHB  HD2  H  HCH2   0   0.223   -9.4931   7.3726  -5.5682
 KHB  HD3  H  HCH2   0   0.220   -8.5970   7.8984  -6.9820
 KHB  HE2  H  HCH2   0   0.229   -6.6433   8.4692  -5.4910
 KHB  HE3  H  HCH2   0   0.239   -7.5468   7.8648  -4.1130
 KHB  H22  H  HCH2   0   0.256   -6.7582   3.8590  -5.8040
 KHB  H23  H  HCH2   0   0.272   -5.0871   4.3731  -5.7170
 KHB  H32  H  HCH1   0   0.200   -4.8528   3.5402  -3.4428
 KHB  H41  H  HCH3   0   0.235   -5.1197   1.1235  -3.8775
 KHB  H42  H  HCH3   0   0.222   -6.1913   1.4673  -5.2418
 KHB  H43  H  HCH3   0   0.227   -4.4972   1.9534  -5.3023
 KHB  H19  H  HNH1   0   0.398   -7.0696   6.0731  -6.4102
 KHB  HO2  H  HOH1   0   0.443   -6.9517   3.8188  -2.6852

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
 KHB  O   C    deloc   1.231  0.020  1.231
 KHB  N   CA   single  1.458  0.019  1.458
 KHB  CB  CA   single  1.530  0.020  1.530
 KHB  CB  CG   single  1.524  0.020  1.524
 KHB  C   CA   single  1.525  0.021  1.525
 KHB  CD  CG   single  1.523  0.020  1.523
 KHB  CD  CE   single  1.522  0.020  1.522
 KHB  NZ  CE   single  1.448  0.020  1.448
 KHB  NZ  C1   single  1.341  0.020  1.341
 KHB  C2  C1   single  1.517  0.020  1.517
 KHB  C2  C3   single  1.526  0.020  1.526
 KHB  C1  O1   double  1.227  0.020  1.227
 KHB  C4  C3   single  1.517  0.020  1.517
 KHB  C3  O2   single  1.413  0.020  1.413
 KHB  C   OXT  deloc   1.248  0.020  1.248
 KHB  N   H    single  0.860  0.020  0.860
 KHB  N   HN2  single  0.890  0.020  1.040
 KHB  CA  HA   single  0.970  0.020  0.970
 KHB  CB  HB2  single  0.970  0.020  1.090
 KHB  CB  HB3  single  0.970  0.020  1.090
 KHB  CG  HG2  single  0.970  0.020  1.090
 KHB  CG  HG3  single  0.970  0.020  1.090
 KHB  CD  HD2  single  0.970  0.020  1.090
 KHB  CD  HD3  single  0.970  0.020  1.090
 KHB  CE  HE2  single  0.970  0.020  1.090
 KHB  CE  HE3  single  0.970  0.020  1.090
 KHB  C2  H22  single  0.970  0.020  1.090
 KHB  C2  H23  single  0.970  0.020  1.090
 KHB  C3  H32  single  0.970  0.020  1.090
 KHB  C4  H41  single  0.970  0.020  1.090
 KHB  C4  H42  single  0.970  0.020  1.090
 KHB  C4  H43  single  0.970  0.020  1.090
 KHB  NZ  H19  single  0.860  0.020  1.020
 KHB  O2  HO2  single  0.850  0.020  0.980

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
 KHB  HN2  N   H    104.68  3.000
 KHB  HN2  N   CA   107.34  3.000
 KHB  H    N   CA   114.00  3.000
 KHB  HA   CA  CB   109.00  3.000
 KHB  HA   CA  C    109.00  3.000
 KHB  CB   CA  C    110.10  1.900
 KHB  HA   CA  N    110.00  3.000
 KHB  C    CA  N    111.00  2.800
 KHB  CB   CA  N    110.50  1.700
 KHB  OXT  C   O    126.73  3.000
 KHB  OXT  C   CA   117.42  3.000
 KHB  O    C   CA   120.80  1.700
 KHB  HB3  CB  HB2  106.19  3.000
 KHB  HB3  CB  CG   109.31  3.000
 KHB  HB2  CB  CG   109.18  3.000
 KHB  HB3  CB  CA   108.89  3.000
 KHB  HB2  CB  CA   108.14  3.000
 KHB  CG   CB  CA   114.78  3.000
 KHB  HG3  CG  HG2  106.16  3.000
 KHB  HG3  CG  CD   109.42  3.000
 KHB  HG2  CG  CD   109.12  3.000
 KHB  HG3  CG  CB   109.52  3.000
 KHB  HG2  CG  CB   110.22  3.000
 KHB  CD   CG  CB   112.23  3.000
 KHB  HD3  CD  HD2  106.52  3.000
 KHB  HD3  CD  CE   109.53  3.000
 KHB  HD2  CD  CE   109.13  3.000
 KHB  HD3  CD  CG   109.37  3.000
 KHB  HD2  CD  CG   109.90  3.000
 KHB  CE   CD  CG   112.23  3.000
 KHB  HE3  CE  HE2  106.90  3.000
 KHB  HE3  CE  NZ   108.43  3.000
 KHB  HE2  CE  NZ   110.27  3.000
 KHB  HE3  CE  CD   110.01  3.000
 KHB  HE2  CE  CD   109.86  3.000
 KHB  NZ   CE  CD   111.26  3.000
 KHB  O1   C1  NZ   123.26  3.000
 KHB  O1   C1  C2   122.05  3.000
 KHB  NZ   C1  C2   114.70  3.000
 KHB  H23  C2  H22  106.16  3.000
 KHB  H23  C2  C3   109.11  3.000
 KHB  H22  C2  C3   110.11  3.000
 KHB  H23  C2  C1   107.91  3.000
 KHB  H22  C2  C1   109.98  3.000
 KHB  C3   C2  C1   113.30  3.000
 KHB  H32  C3  O2   110.41  3.000
 KHB  H32  C3  C4   108.15  3.000
 KHB  O2   C3  C4   107.87  3.000
 KHB  H32  C3  C2   108.19  3.000
 KHB  O2   C3  C2   111.57  3.000
 KHB  C4   C3  C2   110.59  3.000
 KHB  H43  C4  H42  107.86  3.000
 KHB  H43  C4  H41  107.87  3.000
 KHB  H42  C4  H41  108.28  3.000
 KHB  H43  C4  C3   110.51  3.000
 KHB  H42  C4  C3   111.15  3.000
 KHB  H41  C4  C3   111.04  3.000
 KHB  H19  NZ  C1   117.90  3.000
 KHB  H19  NZ  CE   116.99  3.000
 KHB  C1   NZ  CE   125.00  3.000
 KHB  HO2  O2  C3   107.09  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
 KHB  CONST_01  C2   C1  NZ  CE   180.00   0.0  0
 KHB  CONST_02  O1   C1  NZ  CE     0.00   0.0  0
 KHB  CONST_03  H19  NZ  C1  C2     0.00   0.0  0
 KHB  Var_01    CD   CG  CB  CA   174.53  30.0  3
 KHB  Var_02    CE   CD  CG  CB   179.90  30.0  1
 KHB  Var_03    NZ   CE  CD  CG  -178.18  30.0  3
 KHB  Var_04    C1   NZ  CE  CD  -141.98  30.0  1
 KHB  Var_05    NZ   C1  C2  C3  -163.57  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
 KHB  chir_01  CA  N   CB  C   negativ
 KHB  chir_02  C3  C2  C4  O2  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
 KHB  plan-1  CE   0.020
 KHB  plan-1  C1   0.020
 KHB  plan-1  C2   0.020
 KHB  plan-1  NZ   0.020
 KHB  plan-1  O1   0.020
 KHB  plan-1  H19  0.020
 KHB  plan-2  CA   0.020
 KHB  plan-2  C    0.020
 KHB  plan-2  O    0.020
 KHB  plan-2  OXT  0.020

