# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 22:53:22 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: D-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 DLY  DLY  'D-lysine                 '  D-peptide  23  10  .  2016-04-22  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_DLY
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
 DLY  N    N  NH2    0  -0.776  1.7090  -0.9385  -0.0470
 DLY  CA   C  CH1    0  -0.203  2.4568   0.1300   0.6016
 DLY  C    C  C      0   0.377  2.2535   1.5430  -0.0089
 DLY  O    O  O      0  -0.604  1.2265   1.7283  -0.6926
 DLY  CB   C  CH2    0  -0.426  2.1366   0.2004   2.0984
 DLY  CG   C  CH2    0  -0.416  2.3983  -1.0759   2.9046
 DLY  CD   C  CH2    0  -0.434  1.2204  -2.0416   2.9756
 DLY  CE   C  CH2    0  -0.302  1.4963  -3.2876   3.8154
 DLY  NZ   N  NH2    0  -0.791  1.7705  -3.0726   5.2300
 DLY  OXT  O  OC    -1  -0.619  3.1266   2.3917   0.2715
 DLY  H    H  HNH2   0   0.320  0.7336  -0.6632  -0.0732
 DLY  H2   H  HNH2   0   0.330  1.9848  -0.9789  -1.0214
 DLY  HA   H  HCH1   0   0.198  3.5207  -0.1207   0.5119
 DLY  HB2  H  HCH2   0   0.202  1.0897   0.5038   2.2283
 DLY  HB3  H  HCH2   0   0.221  2.7331   1.0143   2.5151
 DLY  HG2  H  HCH2   0   0.204  2.6734  -0.7851   3.9229
 DLY  HG3  H  HCH2   0   0.203  3.2720  -1.5964   2.4963
 DLY  HD2  H  HCH2   0   0.218  0.9436  -2.3465   1.9649
 DLY  HD3  H  HCH2   0   0.199  0.3501  -1.5178   3.3890
 DLY  HE2  H  HCH2   0   0.208  2.3453  -3.8295   3.3872
 DLY  HE3  H  HCH2   0   0.217  0.6400  -3.9632   3.7383
 DLY  HZ1  H  HNH2   0   0.334  1.0127  -2.5404   5.6411
 DLY  HZ2  H  HNH2   0   0.340  2.5959  -2.4961   5.3364

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
 DLY  N   CA   single  1.458  0.019  1.458
 DLY  N   H    single  0.860  0.020  0.860
 DLY  N   H2   single  0.890  0.020  1.040
 DLY  CA  C    single  1.525  0.021  1.525
 DLY  CA  CB   single  1.521  0.033  1.521
 DLY  CA  HA   single  0.970  0.020  0.970
 DLY  C   O    deloc   1.231  0.020  1.231
 DLY  C   OXT  deloc   1.249  0.020  1.249
 DLY  CB  CG   single  1.532  0.020  1.532
 DLY  CB  HB2  single  0.970  0.020  1.090
 DLY  CB  HB3  single  0.970  0.020  1.090
 DLY  CG  CD   single  1.525  0.020  1.525
 DLY  CG  HG2  single  0.970  0.020  1.090
 DLY  CG  HG3  single  0.970  0.020  1.090
 DLY  CD  CE   single  1.528  0.020  1.528
 DLY  CD  HD2  single  0.970  0.020  1.090
 DLY  CD  HD3  single  0.970  0.020  1.090
 DLY  CE  NZ   single  1.457  0.020  1.457
 DLY  CE  HE2  single  0.970  0.020  1.090
 DLY  CE  HE3  single  0.970  0.020  1.090
 DLY  NZ  HZ1  single  0.890  0.020  1.040
 DLY  NZ  HZ2  single  0.890  0.020  1.040

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
 DLY  H2   N   H    104.35  3.000
 DLY  H2   N   CA   108.52  3.000
 DLY  H    N   CA   114.00  3.000
 DLY  HA   CA  CB   109.00  3.000
 DLY  HA   CA  C    110.00  3.000
 DLY  CB   CA  C    110.50  1.500
 DLY  HA   CA  N    110.00  3.000
 DLY  CB   CA  N    110.40  1.500
 DLY  C    CA  N    111.00  2.800
 DLY  OXT  C   O    126.68  3.000
 DLY  OXT  C   CA   120.80  1.700
 DLY  O    C   CA   120.80  1.700
 DLY  HB3  CB  HB2  105.66  3.000
 DLY  HB3  CB  CG   109.08  3.000
 DLY  HB2  CB  CG   109.32  3.000
 DLY  HB3  CB  CA   107.04  3.000
 DLY  HB2  CB  CA   109.12  3.000
 DLY  CG   CB  CA   116.10  3.000
 DLY  HG3  CG  HG2  105.81  3.000
 DLY  HG3  CG  CD   109.42  3.000
 DLY  HG2  CG  CD   108.62  3.000
 DLY  HG3  CG  CB   109.62  3.000
 DLY  HG2  CG  CB   108.13  3.000
 DLY  CD   CG  CB   114.85  3.000
 DLY  HD3  CD  HD2  106.33  3.000
 DLY  HD3  CD  CE   109.01  3.000
 DLY  HD2  CD  CE   109.09  3.000
 DLY  HD3  CD  CG   109.16  3.000
 DLY  HD2  CD  CG   109.25  3.000
 DLY  CE   CD  CG   113.75  3.000
 DLY  HE3  CE  HE2  105.91  3.000
 DLY  HE3  CE  NZ   107.88  3.000
 DLY  HE2  CE  NZ   107.87  3.000
 DLY  HE3  CE  CD   108.89  3.000
 DLY  HE2  CE  CD   109.20  3.000
 DLY  NZ   CE  CD   116.58  3.000
 DLY  HZ2  NZ  HZ1  105.54  3.000
 DLY  HZ2  NZ  CE   109.85  3.000
 DLY  HZ1  NZ  CE   109.31  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
 DLY  Var_01  CD   CG  CB  CA   -89.50  30.0  3
 DLY  Var_02  CE   CD  CG  CB  -178.48  30.0  3
 DLY  Var_03  NZ   CE  CD  CG    62.83  30.0  3
 DLY  Var_04  HZ1  NZ  CE  CD    54.64  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
 DLY  chir_01  CA  N  C  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
 DLY  plan-1  CA   0.020
 DLY  plan-1  C    0.020
 DLY  plan-1  O    0.020
 DLY  plan-1  OXT  0.020

