# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 10:33:43 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: (2S)-2-amino-4-(methylsulfonyl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)CC[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
 OMT  OMT  '(2S)-2-amino-4-(methylsulfonyl)butanoic acid'  L-peptide  21  11  .  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_OMT
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
 OMT  N    N  NH2    0  -0.811  56.5767  15.2541  10.5563
 OMT  CA   C  CH1    0  -0.212  56.3807  16.5551  11.1868
 OMT  CB   C  CH2    0  -0.454  56.4461  16.3536  12.7013
 OMT  CG   C  CH2    0  -0.610  56.0122  17.4940  13.6119
 OMT  SD   S  S      0   1.192  54.3014  18.0260  13.4995
 OMT  CE   C  CH3    0  -0.811  53.3410  16.5285  13.4084
 OMT  C    C  C      0   0.426  57.4302  17.5562  10.6383
 OMT  O    O  O      0  -0.604  57.7308  17.4242   9.4349
 OMT  OXT  O  OC    -1  -0.591  57.8617  18.4257  11.4205
 OMT  OD1  O  OS     0  -0.690  53.9673  18.7087  14.7522
 OMT  OD2  O  OS     0  -0.683  54.0893  18.7764  12.2588
 OMT  H    H  HNH2   0   0.334  56.7434  15.4103   9.5708
 OMT  H2   H  HNH2   0   0.331  55.7266  14.7084  10.6248
 OMT  HA   H  HCH1   0   0.204  55.3977  16.9820  10.9296
 OMT  HB2  H  HCH2   0   0.237  55.8689  15.4618  12.9628
 OMT  HB3  H  HCH2   0   0.252  57.4764  16.1203  12.9813
 OMT  HG2  H  HCH2   0   0.291  56.1454  17.2064  14.6559
 OMT  HG3  H  HCH2   0   0.309  56.5914  18.3971  13.4196
 OMT  HE1  H  HCH3   0   0.308  52.2936  16.8286  13.4030
 OMT  HE2  H  HCH3   0   0.291  53.5708  15.9895  12.4919
 OMT  HE3  H  HCH3   0   0.291  53.5439  15.9046  14.2763

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
 OMT  N   CA   single  1.458  0.019  1.458
 OMT  N   H    single  0.860  0.020  0.860
 OMT  N   H2   single  0.890  0.020  1.040
 OMT  CA  CB   single  1.530  0.020  1.530
 OMT  CA  C    single  1.525  0.021  1.525
 OMT  CA  HA   single  0.970  0.020  0.970
 OMT  CB  CG   single  1.522  0.020  1.522
 OMT  CB  HB2  single  0.970  0.020  1.090
 OMT  CB  HB3  single  0.970  0.020  1.090
 OMT  CG  SD   single  1.795  0.020  1.795
 OMT  CG  HG2  single  0.970  0.020  1.090
 OMT  CG  HG3  single  0.970  0.020  1.090
 OMT  SD  CE   single  1.781  0.020  1.781
 OMT  SD  OD1  double  1.465  0.020  1.465
 OMT  SD  OD2  double  1.465  0.020  1.465
 OMT  CE  HE1  single  0.970  0.020  1.090
 OMT  CE  HE2  single  0.970  0.020  1.090
 OMT  CE  HE3  single  0.970  0.020  1.090
 OMT  C   O    deloc   1.231  0.020  1.231
 OMT  C   OXT  deloc   1.247  0.020  1.247

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
 OMT  H2   N   H    106.71  3.000
 OMT  H2   N   CA   109.79  3.000
 OMT  H    N   CA   114.00  3.000
 OMT  HA   CA  C    110.00  3.000
 OMT  HA   CA  CB   109.00  3.000
 OMT  C    CA  CB   110.10  1.900
 OMT  HA   CA  N    110.00  3.000
 OMT  C    CA  N    111.00  2.800
 OMT  CB   CA  N    110.50  1.700
 OMT  HB3  CB  HB2  105.20  3.000
 OMT  HB3  CB  CG   105.98  3.000
 OMT  HB2  CB  CG   108.50  3.000
 OMT  HB3  CB  CA   108.80  3.000
 OMT  HB2  CB  CA   108.76  3.000
 OMT  CG   CB  CA   118.78  3.000
 OMT  HG3  CG  HG2  108.80  3.000
 OMT  HG3  CG  SD   104.46  3.000
 OMT  HG2  CG  SD   104.74  3.000
 OMT  HG3  CG  CB   111.33  3.000
 OMT  HG2  CG  CB   109.88  3.000
 OMT  SD   CG  CB   117.14  3.000
 OMT  OD2  SD  OD1  116.89  3.000
 OMT  OD2  SD  CE   108.01  3.000
 OMT  OD1  SD  CE   108.21  3.000
 OMT  OD2  SD  CG   110.04  3.000
 OMT  OD1  SD  CG   107.57  3.000
 OMT  CE   SD  CG   105.53  3.000
 OMT  HE3  CE  HE2  110.40  3.000
 OMT  HE3  CE  HE1  109.95  3.000
 OMT  HE2  CE  HE1  109.60  3.000
 OMT  HE3  CE  SD   109.92  3.000
 OMT  HE2  CE  SD   110.23  3.000
 OMT  HE1  CE  SD   106.67  3.000
 OMT  OXT  C   O    126.57  3.000
 OMT  OXT  C   CA   117.55  3.000
 OMT  O    C   CA   120.80  1.700

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
 OMT  Var_01  SD   CG  CB  CA   62.39  30.0  3
 OMT  Var_02  CE   SD  CG  CB   42.83  30.0  3
 OMT  Var_03  HE1  CE  SD  CG  176.51  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
 OMT  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
 OMT  plan-1  CA   0.020
 OMT  plan-1  C    0.020
 OMT  plan-1  O    0.020
 OMT  plan-1  OXT  0.020

