# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:25:45 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: (2S)-2-amino-4-(S-methylsulfonimidoyl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=N)(=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
 MSL  MSL  '(2S)-2-amino-4-(S-methylsulfonimidoyl)butanoic acid'  L-peptide  22  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_MSL
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
 MSL  OXT  O  OC    -1  -0.595  36.8369  16.7886  61.6980
 MSL  C    C  C      0   0.416  36.5118  17.9841  61.8432
 MSL  O    O  O      0  -0.601  36.7079  18.6947  62.8468
 MSL  CA   C  CH1    0  -0.218  35.8235  18.6753  60.6321
 MSL  N    N  NH2    0  -0.822  35.3839  17.6990  59.6469
 MSL  CB   C  CH2    0  -0.399  34.6484  19.5395  61.0948
 MSL  CG   C  CH2    0  -0.597  33.9935  20.2468  59.9209
 MSL  SD   S  S      0   1.065  32.5442  21.1670  60.4614
 MSL  OE   O  OS     0  -0.702  32.9745  22.1830  61.4309
 MSL  NE   N  N      0  -0.879  31.4349  20.2614  61.0178
 MSL  CE   C  CH3    0  -0.775  32.0493  21.9967  58.9529
 MSL  HA   H  HCH1   0   0.207  36.5810  19.3580  60.2124
 MSL  H    H  HNH2   0   0.338  35.9468  16.8676  59.7770
 MSL  H2   H  HNH2   0   0.334  35.5604  18.0326  58.7093
 MSL  HB2  H  HCH2   0   0.233  34.9990  20.2736  61.8186
 MSL  HB3  H  HCH2   0   0.221  33.9093  18.9061  61.5928
 MSL  HG2  H  HCH2   0   0.282  33.6441  19.5380  59.1671
 MSL  HG3  H  HCH2   0   0.279  34.6703  20.9593  59.4421
 MSL  HE   H  H      0   0.350  31.1589  19.5471  60.3508
 MSL  HE1  H  HCH3   0   0.283  31.7761  21.2508  58.2087
 MSL  HE2  H  HCH3   0   0.283  32.8618  22.6185  58.5826
 MSL  HE3  H  HCH3   0   0.298  31.1826  22.6095  59.1960

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
 MSL  OXT  C    deloc   1.247  0.020  1.247
 MSL  C    O    deloc   1.231  0.020  1.231
 MSL  C    CA   single  1.525  0.021  1.525
 MSL  CA   N    single  1.458  0.019  1.458
 MSL  CA   CB   single  1.530  0.020  1.530
 MSL  CA   HA   single  0.970  0.020  0.970
 MSL  N    H    single  0.860  0.020  0.860
 MSL  N    H2   single  0.890  0.020  1.040
 MSL  CB   CG   single  1.519  0.020  1.519
 MSL  CB   HB2  single  0.970  0.020  1.090
 MSL  CB   HB3  single  0.970  0.020  1.090
 MSL  CG   SD   single  1.800  0.020  1.800
 MSL  CG   HG2  single  0.970  0.020  1.090
 MSL  CG   HG3  single  0.970  0.020  1.090
 MSL  SD   OE   double  1.469  0.020  1.469
 MSL  SD   NE   double  1.536  0.020  1.536
 MSL  SD   CE   single  1.791  0.020  1.791
 MSL  NE   HE   single  0.890  0.020  1.040
 MSL  CE   HE1  single  0.970  0.020  1.090
 MSL  CE   HE2  single  0.970  0.020  1.090
 MSL  CE   HE3  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
 MSL  CA   C   O    120.80  1.700
 MSL  CA   C   OXT  116.79  3.000
 MSL  O    C   OXT  126.84  3.000
 MSL  HA   CA  CB   109.00  3.000
 MSL  HA   CA  N    110.00  3.000
 MSL  CB   CA  N    110.50  1.700
 MSL  HA   CA  C    110.00  3.000
 MSL  CB   CA  C    110.10  1.900
 MSL  N    CA  C    111.00  2.800
 MSL  H2   N   H    107.05  3.000
 MSL  H2   N   CA   110.72  3.000
 MSL  H    N   CA   114.00  3.000
 MSL  HB3  CB  HB2  107.79  3.000
 MSL  HB3  CB  CG   109.29  3.000
 MSL  HB2  CB  CG   109.79  3.000
 MSL  HB3  CB  CA   109.24  3.000
 MSL  HB2  CB  CA   109.54  3.000
 MSL  CG   CB  CA   111.12  3.000
 MSL  HG3  CG  HG2  108.59  3.000
 MSL  HG3  CG  SD   107.28  3.000
 MSL  HG2  CG  SD   106.35  3.000
 MSL  HG3  CG  CB   112.02  3.000
 MSL  HG2  CG  CB   111.66  3.000
 MSL  SD   CG  CB   110.68  3.000
 MSL  CE   SD  NE   112.24  3.000
 MSL  CE   SD  OE   108.44  3.000
 MSL  NE   SD  OE   112.35  3.000
 MSL  CE   SD  CG   101.91  3.000
 MSL  NE   SD  CG   112.88  3.000
 MSL  OE   SD  CG   108.42  3.000
 MSL  HE   NE  SD   111.90  3.000
 MSL  HE3  CE  HE2  110.41  3.000
 MSL  HE3  CE  HE1  109.78  3.000
 MSL  HE2  CE  HE1  110.26  3.000
 MSL  HE3  CE  SD   107.01  3.000
 MSL  HE2  CE  SD   110.18  3.000
 MSL  HE1  CE  SD   109.13  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
 MSL  Var_01  SD   CG  CB  CA  176.02  30.0  3
 MSL  Var_02  OE   SD  CG  CB   61.33  30.0  3
 MSL  Var_03  HE1  CE  SD  CG   62.90  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
 MSL  chir_01  CA  C   N   CB  negativ
 MSL  chir_02  SD  OE  NE  CE  both

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
 MSL  plan-1  OXT  0.020
 MSL  plan-1  C    0.020
 MSL  plan-1  O    0.020
 MSL  plan-1  CA   0.020

