# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:40:58 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: N~6~-sulfo-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN[S](O)(=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
 4AK  4AK  'N~6~-sulfo-L-lysine      '  L-peptide  26  14  .  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_4AK
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
 4AK  N    N  NH2    0  -0.809  -1.0708  -7.5655  -2.7682
 4AK  CA   C  CH1    0  -0.155  -2.1123  -6.5481  -2.6341
 4AK  CB   C  CH2    0  -0.416  -1.5132  -5.3290  -1.9381
 4AK  C    C  C      0   0.385  -2.6699  -6.1529  -4.0239
 4AK  O    O  O      0  -0.607  -1.8403  -5.7749  -4.8748
 4AK  O2   O  OS    -1  -0.763  -4.1945  -0.0126   1.2772
 4AK  O3   O  OS     0  -0.757  -6.1303  -1.5402   1.0999
 4AK  CG   C  CH2    0  -0.438  -2.5048  -4.1987  -1.6989
 4AK  CD   C  CH2    0  -0.427  -1.8885  -3.0405  -0.9220
 4AK  CE   C  CH2    0  -0.284  -2.8115  -1.8411  -0.7695
 4AK  NZ   N  NC1    0  -0.756  -3.9775  -2.1730   0.0412
 4AK  S1   S  S      0   1.500  -5.0101  -0.8803   0.4142
 4AK  O4   O  OS     0  -0.761  -5.4029  -0.2241  -0.8471
 4AK  H    H  HNH2   0   0.330  -0.7726  -7.8489  -1.8419
 4AK  H2   H  HNH2   0   0.333  -1.4626  -8.4002  -3.1877
 4AK  HA   H  HCH1   0   0.164  -2.9571  -6.8996  -2.0220
 4AK  HB2  H  HCH2   0   0.205  -1.0933  -5.6412  -0.9740
 4AK  HB3  H  HCH2   0   0.204  -0.6727  -4.9631  -2.5354
 4AK  HG2  H  HCH2   0   0.216  -2.8789  -3.8202  -2.6557
 4AK  HG3  H  HCH2   0   0.208  -3.3747  -4.5922  -1.1625
 4AK  HD2  H  HCH2   0   0.215  -1.5678  -3.3817   0.0669
 4AK  HD3  H  HCH2   0   0.220  -0.9871  -2.7042  -1.4430
 4AK  HE2  H  HCH2   0   0.235  -2.2698  -1.0363  -0.2699
 4AK  HE3  H  HCH2   0   0.204  -3.0866  -1.4718  -1.7660
 4AK  HZ1  H  HNC1   0   0.371  -4.5284  -2.9026  -0.4005
 4AK  OXT  O  OC    -1  -0.613  -3.9080  -6.2234  -4.1690

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
 4AK  O   C    deloc   1.231  0.020  1.231
 4AK  C   CA   single  1.525  0.021  1.525
 4AK  N   CA   single  1.458  0.019  1.458
 4AK  CA  CB   single  1.530  0.020  1.530
 4AK  CB  CG   single  1.522  0.020  1.522
 4AK  CG  CD   single  1.525  0.020  1.525
 4AK  CD  CE   single  1.521  0.020  1.521
 4AK  CE  NZ   single  1.458  0.020  1.458
 4AK  O4  S1   deloc   1.475  0.020  1.475
 4AK  NZ  S1   single  1.696  0.020  1.696
 4AK  S1  O3   deloc   1.470  0.020  1.470
 4AK  S1  O2   deloc   1.471  0.020  1.471
 4AK  N   H    single  0.860  0.020  0.860
 4AK  N   H2   single  0.890  0.020  1.040
 4AK  CA  HA   single  0.970  0.020  0.970
 4AK  CB  HB2  single  0.970  0.020  1.090
 4AK  CB  HB3  single  0.970  0.020  1.090
 4AK  CG  HG2  single  0.970  0.020  1.090
 4AK  CG  HG3  single  0.970  0.020  1.090
 4AK  CD  HD2  single  0.970  0.020  1.090
 4AK  CD  HD3  single  0.970  0.020  1.090
 4AK  CE  HE2  single  0.970  0.020  1.090
 4AK  CE  HE3  single  0.970  0.020  1.090
 4AK  NZ  HZ1  single  0.890  0.020  1.040
 4AK  C   OXT  deloc   1.249  0.020  1.249

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
 4AK  H2   N   H    105.18  3.000
 4AK  H2   N   CA   109.62  3.000
 4AK  H    N   CA   114.00  3.000
 4AK  HA   CA  C    109.00  3.000
 4AK  HA   CA  CB   109.00  3.000
 4AK  C    CA  CB   110.10  1.900
 4AK  HA   CA  N    110.00  3.000
 4AK  CB   CA  N    110.50  1.700
 4AK  C    CA  N    111.00  2.800
 4AK  HB3  CB  HB2  106.32  3.000
 4AK  HB3  CB  CG   109.74  3.000
 4AK  HB2  CB  CG   108.82  3.000
 4AK  HB3  CB  CA   108.64  3.000
 4AK  HB2  CB  CA   108.89  3.000
 4AK  CG   CB  CA   114.14  3.000
 4AK  OXT  C   O    126.69  3.000
 4AK  OXT  C   CA   116.54  3.000
 4AK  O    C   CA   120.80  1.700
 4AK  HG3  CG  HG2  106.31  3.000
 4AK  HG3  CG  CD   110.15  3.000
 4AK  HG2  CG  CD   108.71  3.000
 4AK  HG3  CG  CB   109.12  3.000
 4AK  HG2  CG  CB   109.99  3.000
 4AK  CD   CG  CB   112.38  3.000
 4AK  HD3  CD  HD2  106.54  3.000
 4AK  HD3  CD  CE   107.77  3.000
 4AK  HD2  CD  CE   109.46  3.000
 4AK  HD3  CD  CG   108.89  3.000
 4AK  HD2  CD  CG   110.01  3.000
 4AK  CE   CD  CG   113.88  3.000
 4AK  HE3  CE  HE2  106.97  3.000
 4AK  HE3  CE  NZ   112.38  3.000
 4AK  HE2  CE  NZ   108.08  3.000
 4AK  HE3  CE  CD   109.05  3.000
 4AK  HE2  CE  CD   109.04  3.000
 4AK  NZ   CE  CD   111.18  3.000
 4AK  HZ1  NZ  S1   108.24  3.000
 4AK  HZ1  NZ  CE   110.82  3.000
 4AK  S1   NZ  CE   115.82  3.000
 4AK  O4   S1  NZ   108.25  3.000
 4AK  NZ   S1  O3   102.97  3.000
 4AK  O4   S1  O3   113.30  3.000
 4AK  O3   S1  O2   114.44  3.000
 4AK  NZ   S1  O2   103.96  3.000
 4AK  O4   S1  O2   112.77  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
 4AK  Var_01  CD  CG  CB  CA  176.26  30.0  3
 4AK  Var_02  CE  CD  CG  CB  174.91  30.0  3
 4AK  Var_03  CE  NZ  S1  O2  -65.92  30.0  2
 4AK  Var_04  NZ  CE  CD  CG   65.09  30.0  3
 4AK  Var_05  S1  NZ  CE  CD  174.24  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
 4AK  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
 4AK  plan-1  CA   0.020
 4AK  plan-1  C    0.020
 4AK  plan-1  O    0.020
 4AK  plan-1  OXT  0.020

