# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:14:11 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: N~6~-(sulfanylmethyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNCS)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
 9E7  9E7  N~6~-(sulfanylmethyl)-L-lysine  L-peptide  27  12  .  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_9E7
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
 9E7  C    C  C      0   0.398  19.4837  13.8680  -30.5509
 9E7  S    S  S2     0  -0.269  23.8271  10.7053  -34.5340
 9E7  N    N  NH2    0  -0.794  18.3900  16.1006  -30.1343
 9E7  CA   C  CH1    0  -0.197  18.9969  15.2171  -31.1291
 9E7  CB   C  CH2    0  -0.418  20.1490  15.9695  -31.8018
 9E7  CG   C  CH2    0  -0.441  20.8261  15.2195  -32.9562
 9E7  CD   C  CH2    0  -0.447  22.1133  14.4940  -32.5694
 9E7  CE   C  CH2    0  -0.271  22.7786  13.7639  -33.7262
 9E7  NZ   N  NH1    0  -0.588  22.0022  12.6216  -34.1743
 9E7  O    O  O      0  -0.614  19.2397  12.8372  -31.2111
 9E7  C1   C  CH2    0  -0.384  22.6055  11.8850  -35.2452
 9E7  OXT  O  OC    -1  -0.616  20.1022  13.9312  -29.4660
 9E7  H1   H  HSH1   0   0.212  24.7024  10.7064  -35.5457
 9E7  HA   H  HCH1   0   0.194  18.2411  15.0184  -31.8966
 9E7  HB2  H  HCH2   0   0.204  20.8946  16.2297  -31.0416
 9E7  HB3  H  HCH2   0   0.217  19.7462  16.9182  -32.1650
 9E7  HG2  H  HCH2   0   0.216  21.0687  15.9266  -33.7551
 9E7  HG3  H  HCH2   0   0.213  20.1076  14.5182  -33.3907
 9E7  HD2  H  HCH2   0   0.226  21.9334  13.7844  -31.7592
 9E7  HD3  H  HCH2   0   0.218  22.8226  15.2304  -32.1807
 9E7  HE2  H  HCH2   0   0.226  23.7561  13.3956  -33.4045
 9E7  HE3  H  HCH2   0   0.189  22.9727  14.4765  -34.5448
 9E7  HZ1  H  HNH1   0   0.363  21.0726  12.9051  -34.4529
 9E7  H17  H  HCH2   0   0.271  21.8364  11.3198  -35.7686
 9E7  H18  H  HCH2   0   0.240  23.1356  12.5009  -35.9816
 9E7  H2   H  HNH2   0   0.332  17.5523  15.6578  -29.7737
 9E7  H    H  HNH2   0   0.321  19.0205  16.1380  -29.3403

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
 9E7  C1  NZ   single  1.433  0.020  1.433
 9E7  C1  S    single  1.841  0.020  1.841
 9E7  CE  NZ   single  1.452  0.020  1.452
 9E7  CE  CD   single  1.521  0.020  1.521
 9E7  CD  CG   single  1.527  0.020  1.527
 9E7  CG  CB   single  1.534  0.020  1.534
 9E7  CB  CA   single  1.530  0.020  1.530
 9E7  O   C    deloc   1.231  0.020  1.231
 9E7  CA  C    single  1.525  0.021  1.525
 9E7  CA  N    single  1.458  0.019  1.458
 9E7  C   OXT  deloc   1.250  0.020  1.250
 9E7  S   H1   single  1.200  0.020  1.300
 9E7  N   H2   single  0.890  0.020  1.040
 9E7  N   H    single  0.860  0.020  0.860
 9E7  CA  HA   single  0.970  0.020  0.970
 9E7  CB  HB2  single  0.970  0.020  1.090
 9E7  CB  HB3  single  0.970  0.020  1.090
 9E7  CG  HG2  single  0.970  0.020  1.090
 9E7  CG  HG3  single  0.970  0.020  1.090
 9E7  CD  HD2  single  0.970  0.020  1.090
 9E7  CD  HD3  single  0.970  0.020  1.090
 9E7  CE  HE2  single  0.970  0.020  1.090
 9E7  CE  HE3  single  0.970  0.020  1.090
 9E7  NZ  HZ1  single  0.890  0.020  1.040
 9E7  C1  H17  single  0.970  0.020  1.090
 9E7  C1  H18  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
 9E7  OXT  C   O    126.68  3.000
 9E7  OXT  C   CA   115.85  3.000
 9E7  O    C   CA   120.80  1.700
 9E7  H1   S   C1    98.13  3.000
 9E7  H    N   H2   104.55  3.000
 9E7  H    N   CA   114.00  3.000
 9E7  H2   N   CA   108.73  3.000
 9E7  HA   CA  CB   109.00  3.000
 9E7  HA   CA  N    110.00  3.000
 9E7  CB   CA  N    110.50  1.700
 9E7  HA   CA  C    109.00  3.000
 9E7  N    CA  C    111.00  2.800
 9E7  CB   CA  C    110.10  1.900
 9E7  HB3  CB  HB2  105.97  3.000
 9E7  HB3  CB  CG   109.69  3.000
 9E7  HB2  CB  CG   109.74  3.000
 9E7  HB3  CB  CA   107.16  3.000
 9E7  HB2  CB  CA   108.89  3.000
 9E7  CG   CB  CA   114.98  3.000
 9E7  HG3  CG  HG2  105.66  3.000
 9E7  HG3  CG  CD   110.46  3.000
 9E7  HG2  CG  CD   107.76  3.000
 9E7  HG3  CG  CB   108.81  3.000
 9E7  HG2  CG  CB   109.36  3.000
 9E7  CD   CG  CB   114.43  3.000
 9E7  HD3  CD  HD2  106.30  3.000
 9E7  HD3  CD  CE   108.04  3.000
 9E7  HD2  CD  CE   108.93  3.000
 9E7  HD3  CD  CG   108.46  3.000
 9E7  HD2  CD  CG   110.96  3.000
 9E7  CE   CD  CG   113.83  3.000
 9E7  HE3  CE  HE2  106.19  3.000
 9E7  HE3  CE  NZ   111.93  3.000
 9E7  HE2  CE  NZ   107.69  3.000
 9E7  HE3  CE  CD   109.36  3.000
 9E7  HE2  CE  CD   109.21  3.000
 9E7  NZ   CE  CD   112.23  3.000
 9E7  HZ1  NZ  C1   108.99  3.000
 9E7  HZ1  NZ  CE   110.86  3.000
 9E7  C1   NZ  CE   114.20  3.000
 9E7  H18  C1  H17  108.08  3.000
 9E7  H18  C1  NZ   114.62  3.000
 9E7  H17  C1  NZ   109.20  3.000
 9E7  H18  C1  S    107.37  3.000
 9E7  H17  C1  S    108.77  3.000
 9E7  NZ   C1  S    108.66  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
 9E7  Var_01  CE  NZ  C1  S     83.28  30.0  3
 9E7  Var_02  CD  CG  CB  CA   -97.99  30.0  1
 9E7  Var_03  CE  CD  CG  CB  -179.56  30.0  1
 9E7  Var_04  NZ  CE  CD  CG   -68.67  30.0  1
 9E7  Var_05  C1  NZ  CE  CD  -178.71  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
 9E7  chir_01  CA  CB  C  N  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
 9E7  plan-1  C    0.020
 9E7  plan-1  CA   0.020
 9E7  plan-1  O    0.020
 9E7  plan-1  OXT  0.020

