# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 20:41:27 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: S-nonyl-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCSC[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
 GT9  GT9  'S-nonyl-L-cysteine       '  L-peptide  40  16  .  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_GT9
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
 GT9  N    N  NH2    0  -0.800  10.7692   7.2596  27.8528
 GT9  CA   C  CH1    0  -0.220   9.4247   6.8201  27.5238
 GT9  CB   C  CH2    0  -0.522   9.4908   5.5534  26.6863
 GT9  SG   S  S2     0  -0.053  10.4433   4.2783  27.5689
 GT9  C    C  C      0   0.418   8.5608   6.6332  28.7996
 GT9  O    O  O      0  -0.598   8.9828   7.1584  29.8476
 GT9  OXT  O  OC    -1  -0.605   7.4868   6.0184  28.6495
 GT9  C1   C  CH2    0  -0.567   9.6991   2.7629  26.8937
 GT9  C2   C  CH2    0  -0.408   8.2912   2.4497  27.3819
 GT9  C3   C  CH2    0  -0.411   8.1788   2.2501  28.8863
 GT9  C4   C  CH2    0  -0.425   6.7781   1.8319  29.3183
 GT9  C5   C  CH2    0  -0.436   6.5684   1.8453  30.8304
 GT9  C6   C  CH2    0  -0.436   7.5228   0.9557  31.6266
 GT9  C7   C  CH2    0  -0.419   7.5082  -0.5206  31.2399
 GT9  C8   C  CH2    0  -0.421   6.1547  -1.1995  31.4152
 GT9  C9   C  CH3    0  -0.657   6.2125  -2.6976  31.1507
 GT9  H    H  HNH2   0   0.336  10.7142   7.9147  28.6207
 GT9  H2   H  HNH2   0   0.332  11.1818   7.7453  27.0672
 GT9  HA   H  HCH1   0   0.215   8.8816   7.5612  26.9102
 GT9  HB2  H  HCH2   0   0.257   8.4858   5.1833  26.4921
 GT9  HB3  H  HCH2   0   0.247   9.9668   5.7510  25.7227
 GT9  H11  H  HCH2   0   0.261   9.7238   2.8164  25.8031
 GT9  H12  H  HCH2   0   0.259  10.3799   1.9586  27.1827
 GT9  H21  H  HCH2   0   0.219   7.6001   3.2363  27.0650
 GT9  H22  H  HCH2   0   0.222   7.9615   1.5398  26.8682
 GT9  H31  H  HCH2   0   0.209   8.9097   1.4994  29.2041
 GT9  H32  H  HCH2   0   0.210   8.4541   3.1773  29.3964
 GT9  H41  H  HCH2   0   0.216   6.0490   2.5108  28.8639
 GT9  H42  H  HCH2   0   0.210   6.5524   0.8402  28.9122
 GT9  H51  H  HCH2   0   0.217   6.6749   2.8744  31.1883
 GT9  H52  H  HCH2   0   0.218   5.5348   1.5612  31.0482
 GT9  H61  H  HCH2   0   0.219   8.5438   1.3361  31.5298
 GT9  H62  H  HCH2   0   0.216   7.2743   1.0440  32.6892
 GT9  H71  H  HCH2   0   0.210   7.8415  -0.6420  30.2034
 GT9  H72  H  HCH2   0   0.214   8.2494  -1.0466  31.8504
 GT9  H81  H  HCH2   0   0.207   5.7894  -1.0197  32.4316
 GT9  H82  H  HCH2   0   0.215   5.4200  -0.7431  30.7460
 GT9  H91  H  HCH3   0   0.223   5.2348  -3.1651  31.2723
 GT9  H92  H  HCH3   0   0.214   6.5538  -2.9046  30.1346
 GT9  H93  H  HCH3   0   0.214   6.9036  -3.1926  31.8356

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
 GT9  N   CA   single  1.458  0.019  1.458
 GT9  N   H    single  0.860  0.020  0.860
 GT9  N   H2   single  0.890  0.020  1.040
 GT9  CA  CB   single  1.530  0.020  1.530
 GT9  CA  C    single  1.525  0.021  1.525
 GT9  CA  HA   single  0.970  0.020  0.970
 GT9  CB  SG   single  1.820  0.020  1.820
 GT9  CB  HB2  single  0.970  0.020  1.090
 GT9  CB  HB3  single  0.970  0.020  1.090
 GT9  SG  C1   single  1.818  0.020  1.818
 GT9  C   O    deloc   1.231  0.020  1.231
 GT9  C   OXT  deloc   1.247  0.020  1.247
 GT9  C1  C2   single  1.523  0.020  1.523
 GT9  C1  H11  single  0.970  0.020  1.090
 GT9  C1  H12  single  0.970  0.020  1.090
 GT9  C2  C3   single  1.522  0.020  1.522
 GT9  C2  H21  single  0.970  0.020  1.090
 GT9  C2  H22  single  0.970  0.020  1.090
 GT9  C3  C4   single  1.524  0.020  1.524
 GT9  C3  H31  single  0.970  0.020  1.090
 GT9  C3  H32  single  0.970  0.020  1.090
 GT9  C4  C5   single  1.527  0.020  1.527
 GT9  C4  H41  single  0.970  0.020  1.090
 GT9  C4  H42  single  0.970  0.020  1.090
 GT9  C5  C6   single  1.528  0.020  1.528
 GT9  C5  H51  single  0.970  0.020  1.090
 GT9  C5  H52  single  0.970  0.020  1.090
 GT9  C6  C7   single  1.526  0.020  1.526
 GT9  C6  H61  single  0.970  0.020  1.090
 GT9  C6  H62  single  0.970  0.020  1.090
 GT9  C7  C8   single  1.524  0.020  1.524
 GT9  C7  H71  single  0.970  0.020  1.090
 GT9  C7  H72  single  0.970  0.020  1.090
 GT9  C8  C9   single  1.522  0.020  1.522
 GT9  C8  H81  single  0.970  0.020  1.090
 GT9  C8  H82  single  0.970  0.020  1.090
 GT9  C9  H91  single  0.970  0.020  1.090
 GT9  C9  H92  single  0.970  0.020  1.090
 GT9  C9  H93  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
 GT9  H2   N   H    107.52  3.000
 GT9  H2   N   CA   110.30  3.000
 GT9  H    N   CA   114.00  3.000
 GT9  HA   CA  C    109.00  3.000
 GT9  HA   CA  CB   109.00  3.000
 GT9  C    CA  CB   110.10  1.900
 GT9  HA   CA  N    110.00  3.000
 GT9  C    CA  N    111.00  2.800
 GT9  CB   CA  N    110.50  1.700
 GT9  HB3  CB  HB2  107.84  3.000
 GT9  HB3  CB  SG   109.05  3.000
 GT9  HB2  CB  SG   109.36  3.000
 GT9  HB3  CB  CA   110.74  3.000
 GT9  HB2  CB  CA   109.97  3.000
 GT9  SG   CB  CA   109.84  3.000
 GT9  C1   SG  CB   100.93  3.000
 GT9  OXT  C   O    126.95  3.000
 GT9  OXT  C   CA   116.10  3.000
 GT9  O    C   CA   120.80  1.700
 GT9  H12  C1  H11  106.62  3.000
 GT9  H12  C1  C2   109.87  3.000
 GT9  H11  C1  C2   110.55  3.000
 GT9  H12  C1  SG   105.09  3.000
 GT9  H11  C1  SG   108.71  3.000
 GT9  C2   C1  SG   115.52  3.000
 GT9  H22  C2  H21  105.74  3.000
 GT9  H22  C2  C3   109.41  3.000
 GT9  H21  C2  C3   109.51  3.000
 GT9  H22  C2  C1   107.38  3.000
 GT9  H21  C2  C1   110.08  3.000
 GT9  C3   C2  C1   114.34  3.000
 GT9  H32  C3  H31  106.13  3.000
 GT9  H32  C3  C4   109.38  3.000
 GT9  H31  C3  C4   110.06  3.000
 GT9  H32  C3  C2   109.35  3.000
 GT9  H31  C3  C2   109.12  3.000
 GT9  C4   C3  C2   112.59  3.000
 GT9  H42  C4  H41  105.68  3.000
 GT9  H42  C4  C5   110.30  3.000
 GT9  H41  C4  C5   108.31  3.000
 GT9  H42  C4  C3   109.43  3.000
 GT9  H41  C4  C3   108.91  3.000
 GT9  C5   C4  C3   113.86  3.000
 GT9  H52  C5  H51  105.72  3.000
 GT9  H52  C5  C6   109.58  3.000
 GT9  H51  C5  C6   108.43  3.000
 GT9  H52  C5  C4   108.95  3.000
 GT9  H51  C5  C4   108.59  3.000
 GT9  C6   C5  C4   115.15  3.000
 GT9  H62  C6  H61  105.65  3.000
 GT9  H62  C6  C7   108.77  3.000
 GT9  H61  C6  C7   108.84  3.000
 GT9  H62  C6  C5   108.47  3.000
 GT9  H61  C6  C5   109.53  3.000
 GT9  C7   C6  C5   115.15  3.000
 GT9  H72  C7  H71  105.57  3.000
 GT9  H72  C7  C8   108.84  3.000
 GT9  H71  C7  C8   109.25  3.000
 GT9  H72  C7  C6   108.48  3.000
 GT9  H71  C7  C6   110.12  3.000
 GT9  C8   C7  C6   114.22  3.000
 GT9  H82  C8  H81  105.99  3.000
 GT9  H82  C8  C9   109.26  3.000
 GT9  H81  C8  C9   109.61  3.000
 GT9  H82  C8  C7   109.89  3.000
 GT9  H81  C8  C7   109.26  3.000
 GT9  C9   C8  C7   112.62  3.000
 GT9  H93  C9  H92  107.46  3.000
 GT9  H93  C9  H91  107.65  3.000
 GT9  H92  C9  H91  107.63  3.000
 GT9  H93  C9  C8   111.18  3.000
 GT9  H92  C9  C8   111.11  3.000
 GT9  H91  C9  C8   111.61  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
 GT9  Var_01  C2   C1  SG  CB   -72.53  30.0  3
 GT9  Var_02  C3   C2  C1  SG   -60.48  30.0  3
 GT9  Var_03  C4   C3  C2  C1  -175.50  30.0  3
 GT9  Var_04  C5   C4  C3  C2  -170.50  30.0  3
 GT9  Var_05  C6   C5  C4  C3   -58.02  30.0  3
 GT9  Var_06  C7   C6  C5  C4   -57.61  30.0  3
 GT9  Var_07  C8   C7  C6  C5   -60.25  30.0  3
 GT9  Var_08  C9   C8  C7  C6  -174.38  30.0  3
 GT9  Var_09  HB2  CB  SG  C1    31.43  30.0  1
 GT9  Var_10  H91  C9  C8  C7  -179.51  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
 GT9  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
 GT9  plan-1  CA   0.020
 GT9  plan-1  C    0.020
 GT9  plan-1  O    0.020
 GT9  plan-1  OXT  0.020

