# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 04:15:07 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (2S)-2-amino-4-[(R)-({[(2R)-2-amino-2-carboxyethyl]sulfanyl}amino)sulfinyl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC[S@@](=O)NSC[C@H](N)C(O)=O)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
 K1R  K1R  '(2S)-2-amino-4-[(R)-({[(2R)-2-amino-2-carboxyethyl]sulfanyl}amino)sulfinyl]butanoic acid'  L-peptide  30  17  .  2022-09-22  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_K1R
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
 K1R  N1    N  NH2    0  -0.787  -0.5039   0.6189   1.0567
 K1R  CA1   C  CH1    0  -0.210   0.2003   0.2292  -0.1535
 K1R  C1    C  C      0   0.388   1.6948   0.6393  -0.2231
 K1R  O11   O  OC    -1  -0.621   2.3552   0.1283  -1.1512
 K1R  O12   O  O      0  -0.604   2.1084   1.4517   0.6263
 K1R  CB1   C  CH2    0  -0.430  -0.5187   0.7893  -1.3854
 K1R  CG1   C  CH2    0  -0.625  -1.9633   0.3256  -1.4608
 K1R  OE1   O  O      0  -0.756  -2.0082   0.4899  -4.1168
 K1R  N2    N  NH2    0  -0.798  -6.9502   0.4262  -6.2979
 K1R  CA2   C  CH1    0  -0.238  -6.4913  -0.9037  -5.9332
 K1R  C2    C  C      0   0.422  -7.5609  -1.6562  -5.1019
 K1R  SAG   S  S3     0   0.907  -2.7572   1.0187  -2.9353
 K1R  NAF   N  NH1    0  -0.832  -4.1703   0.0525  -2.8215
 K1R  O2    O  O      0  -0.607  -8.7314  -1.2346  -5.1759
 K1R  O21   O  OC    -1  -0.607  -7.1664  -2.6554  -4.4725
 K1R  CB2   C  CH2    0  -0.515  -5.1760  -0.7678  -5.1892
 K1R  SG2   S  S2     0   0.152  -5.3990   0.5213  -3.9259
 K1R  H1N1  H  HNH2   0   0.325  -0.2904   1.5923   1.2440
 K1R  H1N2  H  HNH2   0   0.338  -0.1028   0.1179   1.8402
 K1R  HA1   H  HCH1   0   0.218   0.1558  -0.8640  -0.2219
 K1R  HB11  H  HCH2   0   0.242   0.0171   0.4704  -2.2795
 K1R  HB12  H  HCH2   0   0.230  -0.4779   1.8846  -1.3599
 K1R  HG11  H  HCH2   0   0.281  -2.0333  -0.7628  -1.5366
 K1R  HG12  H  HCH2   0   0.281  -2.5314   0.6600  -0.5916
 K1R  HA2   H  HCH1   0   0.229  -6.2977  -1.5420  -6.8129
 K1R  HA    H  HNH1   0   0.418  -4.5064  -0.0715  -1.8711
 K1R  HB21  H  HCH2   0   0.254  -4.3644  -0.4765  -5.8579
 K1R  HB22  H  HCH2   0   0.264  -4.9022  -1.6953  -4.6918
 K1R  H2N1  H  HNH2   0   0.342  -7.9304   0.3798  -6.5408
 K1R  H2N2  H  HNH2   0   0.339  -6.4492   0.7631  -7.1097

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
 K1R  N1   CA1   single  1.453  0.020  1.453
 K1R  N1   H1N1  single  0.890  0.020  1.040
 K1R  N1   H1N2  single  0.890  0.020  1.040
 K1R  CA1  C1    single  1.551  0.020  1.551
 K1R  CA1  CB1   single  1.532  0.020  1.532
 K1R  CA1  HA1   single  0.970  0.020  1.090
 K1R  C1   O11   deloc   1.248  0.020  1.248
 K1R  C1   O12   deloc   1.246  0.020  1.246
 K1R  CB1  CG1   single  1.519  0.020  1.519
 K1R  CB1  HB11  single  0.970  0.020  1.090
 K1R  CB1  HB12  single  0.970  0.020  1.090
 K1R  CG1  SAG   single  1.812  0.020  1.812
 K1R  CG1  HG11  single  0.970  0.020  1.090
 K1R  CG1  HG12  single  0.970  0.020  1.090
 K1R  OE1  SAG   double  1.495  0.020  1.495
 K1R  N2   CA2   single  1.453  0.020  1.453
 K1R  N2   H2N1  single  0.890  0.020  1.040
 K1R  N2   H2N2  single  0.890  0.020  1.040
 K1R  CA2  C2    single  1.550  0.020  1.550
 K1R  CA2  CB2   single  1.517  0.020  1.517
 K1R  CA2  HA2   single  0.970  0.020  1.090
 K1R  C2   O2    deloc   1.246  0.020  1.246
 K1R  C2   O21   deloc   1.245  0.020  1.245
 K1R  SAG  NAF   single  1.716  0.020  1.716
 K1R  NAF  SG2   single  1.717  0.020  1.717
 K1R  NAF  HA    single  0.890  0.020  1.040
 K1R  CB2  SG2   single  1.819  0.020  1.819
 K1R  CB2  HB21  single  0.970  0.020  1.090
 K1R  CB2  HB22  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
 K1R  H1N2  N1   H1N1  104.39  3.000
 K1R  H1N2  N1   CA1   108.64  3.000
 K1R  H1N1  N1   CA1   108.01  3.000
 K1R  HA1   CA1  CB1   107.17  3.000
 K1R  HA1   CA1  C1    107.46  3.000
 K1R  CB1   CA1  C1    108.62  3.000
 K1R  HA1   CA1  N1    107.43  3.000
 K1R  CB1   CA1  N1    110.12  3.000
 K1R  C1    CA1  N1    115.68  3.000
 K1R  O12   C1   O11   126.73  3.000
 K1R  O12   C1   CA1   117.49  3.000
 K1R  O11   C1   CA1   115.77  3.000
 K1R  HB12  CB1  HB11  107.04  3.000
 K1R  HB12  CB1  CG1   109.97  3.000
 K1R  HB11  CB1  CG1   109.72  3.000
 K1R  HB12  CB1  CA1   109.21  3.000
 K1R  HB11  CB1  CA1   108.77  3.000
 K1R  CG1   CB1  CA1   111.99  3.000
 K1R  HG12  CG1  HG11  109.09  3.000
 K1R  HG12  CG1  SAG   107.63  3.000
 K1R  HG11  CG1  SAG   107.23  3.000
 K1R  HG12  CG1  CB1   111.23  3.000
 K1R  HG11  CG1  CB1   111.60  3.000
 K1R  SAG   CG1  CB1   109.89  3.000
 K1R  H2N2  N2   H2N1  107.62  3.000
 K1R  H2N2  N2   CA2   110.47  3.000
 K1R  H2N1  N2   CA2   108.93  3.000
 K1R  HA2   CA2  CB2   106.89  3.000
 K1R  HA2   CA2  C2    105.53  3.000
 K1R  CB2   CA2  C2    112.26  3.000
 K1R  HA2   CA2  N2    112.61  3.000
 K1R  CB2   CA2  N2    108.35  3.000
 K1R  C2    CA2  N2    111.16  3.000
 K1R  O21   C2   O2    126.80  3.000
 K1R  O21   C2   CA2   116.25  3.000
 K1R  O2    C2   CA2   116.88  3.000
 K1R  NAF   SAG  OE1   105.41  3.000
 K1R  NAF   SAG  CG1    95.25  3.000
 K1R  OE1   SAG  CG1   106.74  3.000
 K1R  HA    NAF  SG2   113.48  3.000
 K1R  HA    NAF  SAG   113.79  3.000
 K1R  SG2   NAF  SAG   113.13  3.000
 K1R  HB22  CB2  HB21  108.71  3.000
 K1R  HB22  CB2  SG2   108.53  3.000
 K1R  HB21  CB2  SG2   109.13  3.000
 K1R  HB22  CB2  CA2   111.48  3.000
 K1R  HB21  CB2  CA2   111.60  3.000
 K1R  SG2   CB2  CA2   107.33  3.000
 K1R  CB2   SG2  NAF    99.52  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
 K1R  Var_01  SAG   CG1  CB1  CA1  -179.97  30.0  3
 K1R  Var_02  OE1   SAG  CG1  CB1    61.68  30.0  3
 K1R  Var_03  SG2   NAF  SAG  CG1   171.25  30.0  2
 K1R  Var_04  HB21  CB2  SG2  NAF   -82.64  30.0  1

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
 K1R  chir_01  CA1  N1  C1  CB1  positiv
 K1R  chir_02  CA2  N2  C2  CB2  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
 K1R  plan-1  CA1  0.020
 K1R  plan-1  C1   0.020
 K1R  plan-1  O11  0.020
 K1R  plan-1  O12  0.020
 K1R  plan-2  CA2  0.020
 K1R  plan-2  C2   0.020
 K1R  plan-2  O2   0.020
 K1R  plan-2  O21  0.020
 K1R  plan-3  CG1  0.020
 K1R  plan-3  OE1  0.020
 K1R  plan-3  SAG  0.020
 K1R  plan-3  NAF  0.020

