# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:40:57 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: N~6~-ethyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNCCCC[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
 LDH  LDH  'N~6~-ethyl-L-lysine      '  L-peptide  29  12  .  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_LDH
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
 LDH  N    N  NH2    0  -0.773  -22.6656   1.5041  -17.4608
 LDH  CA   C  CH1    0  -0.208  -22.5841   1.9434  -18.8480
 LDH  CB   C  CH2    0  -0.418  -21.9455   3.3351  -18.9337
 LDH  CG   C  CH2    0  -0.438  -22.8181   4.5351  -18.5609
 LDH  CD   C  CH2    0  -0.428  -23.3342   4.5911  -17.1203
 LDH  CE   C  CH2    0  -0.258  -24.7132   3.9676  -16.9512
 LDH  NZ   N  NH1    0  -0.593  -25.0368   3.7710  -15.5506
 LDH  CH   C  CH2    0  -0.261  -26.3481   3.1839  -15.3510
 LDH  C1   C  CH3    0  -0.674  -26.6086   2.9027  -13.8822
 LDH  C    C  C      0   0.381  -21.8473   0.9580  -19.8000
 LDH  O    O  O      0  -0.618  -21.9270   1.2173  -21.0200
 LDH  OXT  O  OC    -1  -0.602  -21.2409  -0.0003  -19.2813
 LDH  HN1  H  HNH2   0   0.327  -23.1538   0.6170  -17.4312
 LDH  HN2  H  HNH2   0   0.320  -21.7257   1.2813  -17.1525
 LDH  HA   H  HCH1   0   0.202  -23.6104   2.0301  -19.2264
 LDH  HB1  H  HCH2   0   0.201  -21.0409   3.3428  -18.3129
 LDH  HB2  H  HCH2   0   0.217  -21.6073   3.4924  -19.9596
 LDH  HG1  H  HCH2   0   0.218  -22.2273   5.4334  -18.7608
 LDH  HG2  H  HCH2   0   0.206  -23.6666   4.5861  -19.2532
 LDH  HD1  H  HCH2   0   0.208  -22.6216   4.0879  -16.4614
 LDH  HD2  H  HCH2   0   0.210  -23.3811   5.6298  -16.7815
 LDH  HE1  H  HCH2   0   0.202  -25.4626   4.6380  -17.3870
 LDH  HE2  H  HCH2   0   0.199  -24.7688   3.0325  -17.5247
 LDH  HNZ  H  HNH1   0   0.326  -24.3436   3.1405  -15.1610
 LDH  HH1  H  HCH2   0   0.210  -27.0988   3.8855  -15.7272
 LDH  HH2  H  HCH2   0   0.181  -26.4846   2.2556  -15.9294
 LDH  H11  H  HCH3   0   0.219  -25.8852   2.1885  -13.4835
 LDH  H12  H  HCH3   0   0.220  -26.5409   3.8149  -13.2883
 LDH  H13  H  HCH3   0   0.225  -27.6022   2.4782  -13.7382

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
 LDH  N   CA   single  1.458  0.019  1.458
 LDH  N   HN1  single  0.890  0.020  1.040
 LDH  N   HN2  single  0.890  0.020  1.040
 LDH  CA  CB   single  1.530  0.020  1.530
 LDH  CA  C    single  1.525  0.021  1.525
 LDH  CA  HA   single  0.970  0.020  0.970
 LDH  CB  CG   single  1.530  0.020  1.530
 LDH  CB  HB1  single  0.970  0.020  1.090
 LDH  CB  HB2  single  0.970  0.020  1.090
 LDH  CG  CD   single  1.531  0.020  1.531
 LDH  CG  HG1  single  0.970  0.020  1.090
 LDH  CG  HG2  single  0.970  0.020  1.090
 LDH  CD  CE   single  1.523  0.020  1.523
 LDH  CD  HD1  single  0.970  0.020  1.090
 LDH  CD  HD2  single  0.970  0.020  1.090
 LDH  CE  NZ   single  1.451  0.020  1.451
 LDH  CE  HE1  single  0.970  0.020  1.090
 LDH  CE  HE2  single  0.970  0.020  1.090
 LDH  NZ  CH   single  1.451  0.020  1.451
 LDH  NZ  HNZ  single  0.890  0.020  1.040
 LDH  CH  C1   single  1.518  0.020  1.518
 LDH  CH  HH1  single  0.970  0.020  1.090
 LDH  CH  HH2  single  0.970  0.020  1.090
 LDH  C1  H11  single  0.970  0.020  1.090
 LDH  C1  H12  single  0.970  0.020  1.090
 LDH  C1  H13  single  0.970  0.020  1.090
 LDH  C   O    deloc   1.231  0.020  1.231
 LDH  C   OXT  deloc   1.247  0.020  1.247

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
 LDH  HN2  N   HN1  104.20  3.000
 LDH  HN2  N   CA   107.69  3.000
 LDH  HN1  N   CA   108.58  3.000
 LDH  HA   CA  C    109.00  3.000
 LDH  HA   CA  CB   109.00  3.000
 LDH  C    CA  CB   110.10  1.900
 LDH  HA   CA  N    110.00  3.000
 LDH  C    CA  N    111.00  2.800
 LDH  CB   CA  N    110.50  1.700
 LDH  HB2  CB  HB1  105.98  3.000
 LDH  HB2  CB  CG   107.03  3.000
 LDH  HB1  CB  CG   109.08  3.000
 LDH  HB2  CB  CA   108.19  3.000
 LDH  HB1  CB  CA   108.54  3.000
 LDH  CG   CB  CA   117.44  3.000
 LDH  HG2  CG  HG1  105.34  3.000
 LDH  HG2  CG  CD   109.36  3.000
 LDH  HG1  CG  CD   108.91  3.000
 LDH  HG2  CG  CB   108.90  3.000
 LDH  HG1  CG  CB   106.95  3.000
 LDH  CD   CG  CB   116.76  3.000
 LDH  HD2  CD  HD1  106.17  3.000
 LDH  HD2  CD  CE   108.40  3.000
 LDH  HD1  CD  CE   109.56  3.000
 LDH  HD2  CD  CG   109.92  3.000
 LDH  HD1  CD  CG   109.30  3.000
 LDH  CE   CD  CG   113.25  3.000
 LDH  HE2  CE  HE1  106.18  3.000
 LDH  HE2  CE  NZ   112.17  3.000
 LDH  HE1  CE  NZ   108.32  3.000
 LDH  HE2  CE  CD   109.66  3.000
 LDH  HE1  CE  CD   108.95  3.000
 LDH  NZ   CE  CD   111.38  3.000
 LDH  HNZ  NZ  CH   108.25  3.000
 LDH  HNZ  NZ  CE   107.61  3.000
 LDH  CH   NZ  CE   112.91  3.000
 LDH  HH2  CH  HH1  105.94  3.000
 LDH  HH2  CH  C1   109.29  3.000
 LDH  HH1  CH  C1   109.49  3.000
 LDH  HH2  CH  NZ   112.37  3.000
 LDH  HH1  CH  NZ   108.27  3.000
 LDH  C1   CH  NZ   111.30  3.000
 LDH  H13  C1  H12  108.09  3.000
 LDH  H13  C1  H11  107.51  3.000
 LDH  H12  C1  H11  107.89  3.000
 LDH  H13  C1  CH   110.88  3.000
 LDH  H12  C1  CH   111.18  3.000
 LDH  H11  C1  CH   111.15  3.000
 LDH  OXT  C   O    126.62  3.000
 LDH  OXT  C   CA   117.55  3.000
 LDH  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
 LDH  Var_01  CD   CG  CB  CA   62.40  30.0  3
 LDH  Var_02  CE   CD  CG  CB  -93.12  30.0  3
 LDH  Var_03  NZ   CE  CD  CG  167.26  30.0  3
 LDH  Var_04  CH   NZ  CE  CD  179.72  30.0  3
 LDH  Var_05  C1   CH  NZ  CE  175.93  30.0  3
 LDH  Var_06  H11  C1  CH  NZ  -61.48  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
 LDH  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
 LDH  plan-1  CA   0.020
 LDH  plan-1  C    0.020
 LDH  plan-1  O    0.020
 LDH  plan-1  OXT  0.020

