# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:05:44 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: 3-(methylsulfonyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)C[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
 KNB  KNB  3-(methylsulfonyl)-L-alanine  L-peptide  18  10  .  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_KNB
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
 KNB  C     C  C      0   0.424  15.0510  -23.0211  -17.8435
 KNB  O     O  O      0  -0.594  14.0252  -22.9695  -18.5447
 KNB  CA    C  CH1    0  -0.217  16.3121  -23.6401  -18.5255
 KNB  CB    C  CH2    0  -0.613  15.8946  -24.9008  -19.2762
 KNB  S     S  S      0   1.201  17.2362  -25.7199  -20.1498
 KNB  O2    O  OS     0  -0.688  18.1854  -24.7154  -20.6398
 KNB  CS    C  CH3    0  -0.793  18.0546  -26.7243  -18.9277
 KNB  O1    O  OS     0  -0.693  16.6471  -26.6284  -21.1393
 KNB  N     N  NH2    0  -0.819  17.3674  -23.9068  -17.5656
 KNB  H21   H  HCH1   0   0.235  16.6291  -22.9074  -19.2791
 KNB  H111  H  HCH2   0   0.286  15.4628  -25.6524  -18.6102
 KNB  H112  H  HCH2   0   0.300  15.1626  -24.6717  -20.0513
 KNB  H281  H  HCH3   0   0.294  18.8713  -27.2395  -19.4322
 KNB  H282  H  HCH3   0   0.290  18.4258  -26.0885  -18.1292
 KNB  H283  H  HCH3   0   0.282  17.3466  -27.4488  -18.5306
 KNB  HN1   H  HNH2   0   0.342  18.2545  -23.5633  -17.9059
 KNB  OXT   O  OC    -1  -0.584  15.1950  -22.6144  -16.6762
 KNB  H2    H  HNH2   0   0.346  17.1437  -23.3849  -16.7263

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
 KNB  C   CA    single  1.525  0.021  1.525
 KNB  C   O     deloc   1.231  0.020  1.231
 KNB  CA  CB    single  1.521  0.033  1.521
 KNB  CA  N     single  1.458  0.019  1.458
 KNB  CA  H21   single  0.970  0.020  1.090
 KNB  CB  S     single  1.798  0.020  1.798
 KNB  CB  H111  single  0.970  0.020  1.090
 KNB  CB  H112  single  0.970  0.020  1.090
 KNB  S   O1    double  1.467  0.020  1.467
 KNB  S   O2    double  1.466  0.020  1.466
 KNB  S   CS    single  1.781  0.020  1.781
 KNB  CS  H281  single  0.970  0.020  1.090
 KNB  CS  H282  single  0.970  0.020  1.090
 KNB  CS  H283  single  0.970  0.020  1.090
 KNB  N   HN1   single  0.890  0.020  1.040
 KNB  C   OXT   deloc   1.244  0.020  1.244
 KNB  N   H2    single  0.890  0.020  1.040

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
 KNB  OXT   C   CA    116.47  3.000
 KNB  OXT   C   O     127.64  3.000
 KNB  CA    C   O     120.80  1.700
 KNB  H21   CA  N     111.51  3.000
 KNB  H21   CA  CB    107.02  3.000
 KNB  N     CA  CB    110.40  1.500
 KNB  H21   CA  C     105.57  3.000
 KNB  N     CA  C     111.00  2.800
 KNB  CB    CA  C     110.50  1.500
 KNB  H112  CB  H111  108.20  3.000
 KNB  H112  CB  S     104.54  3.000
 KNB  H111  CB  S     106.11  3.000
 KNB  H112  CB  CA    111.10  3.000
 KNB  H111  CB  CA    112.12  3.000
 KNB  S     CB  CA    114.29  3.000
 KNB  O1    S   CS    107.35  3.000
 KNB  CS    S   O2    108.55  3.000
 KNB  O1    S   O2    117.31  3.000
 KNB  CS    S   CB    105.45  3.000
 KNB  O2    S   CB    109.46  3.000
 KNB  O1    S   CB    108.07  3.000
 KNB  H283  CS  H282  110.11  3.000
 KNB  H283  CS  H281  110.00  3.000
 KNB  H282  CS  H281  111.16  3.000
 KNB  H283  CS  S     109.08  3.000
 KNB  H282  CS  S     109.35  3.000
 KNB  H281  CS  S     107.06  3.000
 KNB  H2    N   HN1   107.32  3.000
 KNB  H2    N   CA    107.02  3.000
 KNB  HN1   N   CA    110.68  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
 KNB  Var_01  O1    S   CB  CA  -162.43  30.0  3
 KNB  Var_02  H281  CS  S   CB   179.64  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
 KNB  chir_01  CA  C  CB  N  positiv

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

