# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 03:02:56 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: (2S)-2-amino-7-sulfanylheptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCCS)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
 U2M  U2M  '(2S)-2-amino-7-sulfanylheptanoic acid'  L-peptide  25  11  .  2022-03-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_U2M
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
 U2M  N    N  NH2    0  -0.805  74.1292  32.3636  -0.9143
 U2M  CA   C  CH1    0  -0.161  72.8308  32.5444  -1.5570
 U2M  C    C  C      0   0.385  72.4558  34.0403  -1.6864
 U2M  O    O  O      0  -0.615  71.7434  34.3367  -2.6690
 U2M  CB   C  CH2    0  -0.422  71.7853  31.7939  -0.7255
 U2M  CG   C  CH2    0  -0.416  70.3748  31.7801  -1.3015
 U2M  CD   C  CH2    0  -0.409  69.4493  30.8398  -0.5389
 U2M  CE   C  CH2    0  -0.413  68.0151  30.8755  -1.0545
 U2M  CZ   C  CH2    0  -0.548  67.1259  29.8871  -0.3165
 U2M  SH   S  S2     0  -0.262  65.4228  30.0008  -0.9651
 U2M  H1   H  HNH2   0   0.328  74.4073  31.3938  -1.0091
 U2M  H2   H  HNH2   0   0.331  74.8334  32.8973  -1.4084
 U2M  H4   H  HCH1   0   0.169  72.8057  32.1192  -2.5722
 U2M  H6   H  HCH2   0   0.206  72.1257  30.7570  -0.6124
 U2M  H7   H  HCH2   0   0.204  71.7687  32.2179   0.2840
 U2M  H8   H  HCH2   0   0.213  69.9558  32.7890  -1.2906
 U2M  H9   H  HCH2   0   0.203  70.4075  31.4761  -2.3529
 U2M  H10  H  HCH2   0   0.212  69.8333  29.8164  -0.6060
 U2M  H11  H  HCH2   0   0.212  69.4576  31.0993   0.5251
 U2M  H12  H  HCH2   0   0.226  68.0040  30.6491  -2.1249
 U2M  H13  H  HCH2   0   0.227  67.6146  31.8875  -0.9443
 U2M  H14  H  HCH2   0   0.260  67.1187  30.1048   0.7518
 U2M  H15  H  HCH2   0   0.260  67.4950  28.8703  -0.4537
 U2M  H16  H  HSH1   0   0.219  64.8656  29.0652  -0.1882
 U2M  OXT  O  OC    -1  -0.603  72.8650  34.8187  -0.8034

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
 U2M  O   C    deloc   1.231  0.020  1.231
 U2M  CA  C    single  1.525  0.021  1.525
 U2M  CA  N    single  1.458  0.019  1.458
 U2M  CA  CB   single  1.521  0.033  1.521
 U2M  CG  CB   single  1.524  0.020  1.524
 U2M  CG  CD   single  1.524  0.020  1.524
 U2M  SH  CZ   single  1.826  0.020  1.826
 U2M  CE  CZ   single  1.521  0.020  1.521
 U2M  CE  CD   single  1.524  0.020  1.524
 U2M  N   H1   single  0.890  0.020  1.040
 U2M  N   H2   single  0.890  0.020  1.040
 U2M  CA  H4   single  0.970  0.020  1.090
 U2M  CB  H6   single  0.970  0.020  1.090
 U2M  CB  H7   single  0.970  0.020  1.090
 U2M  CG  H8   single  0.970  0.020  1.090
 U2M  CG  H9   single  0.970  0.020  1.090
 U2M  CD  H10  single  0.970  0.020  1.090
 U2M  CD  H11  single  0.970  0.020  1.090
 U2M  CE  H12  single  0.970  0.020  1.090
 U2M  CE  H13  single  0.970  0.020  1.090
 U2M  CZ  H14  single  0.970  0.020  1.090
 U2M  CZ  H15  single  0.970  0.020  1.090
 U2M  SH  H16  single  1.200  0.020  1.300
 U2M  C   OXT  deloc   1.246  0.020  1.246

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
 U2M  H2   N   H1   105.54  3.000
 U2M  H2   N   CA   109.79  3.000
 U2M  H1   N   CA   108.75  3.000
 U2M  H4   CA  CB   107.19  3.000
 U2M  H4   CA  C    106.90  3.000
 U2M  CB   CA  C    110.50  1.500
 U2M  H4   CA  N    112.23  3.000
 U2M  CB   CA  N    110.40  1.500
 U2M  C    CA  N    111.00  2.800
 U2M  OXT  C   O    126.61  3.000
 U2M  OXT  C   CA   120.80  1.700
 U2M  O    C   CA   120.80  1.700
 U2M  H7   CB  H6   106.00  3.000
 U2M  H7   CB  CG   109.76  3.000
 U2M  H6   CB  CG   108.52  3.000
 U2M  H7   CB  CA   108.72  3.000
 U2M  H6   CB  CA   107.89  3.000
 U2M  CG   CB  CA   115.53  3.000
 U2M  H9   CG  H8   106.10  3.000
 U2M  H9   CG  CD   109.11  3.000
 U2M  H8   CG  CD   109.38  3.000
 U2M  H9   CG  CB   109.75  3.000
 U2M  H8   CG  CB   110.06  3.000
 U2M  CD   CG  CB   112.25  3.000
 U2M  H11  CD  H10  106.16  3.000
 U2M  H11  CD  CE   109.28  3.000
 U2M  H10  CD  CE   109.33  3.000
 U2M  H11  CD  CG   109.59  3.000
 U2M  H10  CD  CG   109.45  3.000
 U2M  CE   CD  CG   112.81  3.000
 U2M  H13  CE  H12  106.64  3.000
 U2M  H13  CE  CZ   109.77  3.000
 U2M  H12  CE  CZ   109.53  3.000
 U2M  H13  CE  CD   109.39  3.000
 U2M  H12  CE  CD   109.61  3.000
 U2M  CZ   CE  CD   111.76  3.000
 U2M  H15  CZ  H14  108.16  3.000
 U2M  H15  CZ  SH   109.22  3.000
 U2M  H14  CZ  SH   109.24  3.000
 U2M  H15  CZ  CE   110.31  3.000
 U2M  H14  CZ  CE   110.46  3.000
 U2M  SH   CZ  CE   109.43  3.000
 U2M  H16  SH  CZ    97.97  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
 U2M  Var_01  CD  CG  CB  CA  171.06  30.0  1
 U2M  Var_02  CE  CD  CG  CB  176.73  30.0  3
 U2M  Var_03  CZ  CE  CD  CG  177.61  30.0  1
 U2M  Var_04  SH  CZ  CE  CD  179.14  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
 U2M  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
 U2M  plan-1  CA   0.020
 U2M  plan-1  C    0.020
 U2M  plan-1  O    0.020
 U2M  plan-1  OXT  0.020

