# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 14:46:10 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: (2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}ethyl)(trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCC[B-](O)(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
 S2C  S2C  (2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}ethyl)(trihydroxy)borate(1-)  L-peptide  25  13  .  2016-05-13  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_S2C
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
 S2C  OXT  O  OC    -1  -0.601  68.0545   9.4033  29.9413
 S2C  N    N  NH2    0  -0.805  64.5452  10.1401  30.0935
 S2C  CA   C  CH1    0  -0.227  65.8701  10.2678  29.5078
 S2C  C    C  C      0   0.422  66.8359   9.1977  30.0962
 S2C  O    O  O      0  -0.597  66.3065   8.2080  30.6375
 S2C  CB   C  CH2    0  -0.510  66.4184  11.6713  29.7291
 S2C  SG   S  S2     0  -0.090  65.3670  12.9306  28.9395
 S2C  CD   C  CH2    0  -0.537  66.1909  14.4509  29.5255
 S2C  CE   C  CH2    0  -0.657  65.4581  15.7082  29.0893
 S2C  B    B  B     -1   0.471  66.1557  17.1032  29.6631
 S2C  O1   O  OB     0  -0.739  67.5696  17.2399  29.2539
 S2C  O2   O  OB     0  -0.739  65.3998  18.2206  29.0722
 S2C  O3   O  OB     0  -0.747  66.1325  17.1245  31.1504
 S2C  HA   H  HCH1   0   0.201  65.8634  10.0862  28.4181
 S2C  HB1  H  HCH2   0   0.234  66.4639  11.8841  30.8010
 S2C  HB2  H  HCH2   0   0.243  67.4259  11.7479  29.3229
 S2C  HD1  H  HCH2   0   0.226  66.2481  14.3926  30.6154
 S2C  HD2  H  HCH2   0   0.225  67.2166  14.4458  29.1468
 S2C  HE1  H  HCH2   0   0.166  65.4132  15.7260  27.9926
 S2C  HE2  H  HCH2   0   0.164  64.4133  15.6345  29.4233
 S2C  HO1  H  H      0   0.411  68.0967  16.5899  29.7235
 S2C  HO2  H  H      0   0.417  65.7273  19.0413  29.4500
 S2C  HO3  H  H      0   0.407  65.2753  16.8081  31.4450
 S2C  H    H  HNH2   0   0.330  63.8447  10.5069  29.4634
 S2C  HN2  H  HNH2   0   0.334  64.3536   9.1540  30.2113

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
 S2C  OXT  C    deloc   1.245  0.020  1.245
 S2C  N    CA   single  1.458  0.019  1.458
 S2C  N    H    single  0.860  0.020  0.860
 S2C  N    HN2  single  0.890  0.020  1.040
 S2C  CA   C    single  1.525  0.021  1.525
 S2C  CA   CB   single  1.530  0.020  1.530
 S2C  CA   HA   single  0.970  0.020  0.970
 S2C  C    O    deloc   1.231  0.020  1.231
 S2C  CB   SG   single  1.821  0.020  1.821
 S2C  CB   HB1  single  0.970  0.020  1.090
 S2C  CB   HB2  single  0.970  0.020  1.090
 S2C  SG   CD   single  1.826  0.020  1.826
 S2C  CD   CE   single  1.519  0.020  1.519
 S2C  CD   HD1  single  0.970  0.020  1.090
 S2C  CD   HD2  single  0.970  0.020  1.090
 S2C  CE   B    single  1.662  0.020  1.662
 S2C  CE   HE1  single  0.970  0.020  1.090
 S2C  CE   HE2  single  0.970  0.020  1.090
 S2C  B    O1   single  1.478  0.020  1.478
 S2C  B    O2   single  1.473  0.020  1.473
 S2C  B    O3   single  1.488  0.020  1.488
 S2C  O1   HO1  single  0.850  0.020  0.980
 S2C  O2   HO2  single  0.850  0.020  0.980
 S2C  O3   HO3  single  0.850  0.020  0.980

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
 S2C  HN2  N   H    107.16  3.000
 S2C  HN2  N   CA   107.77  3.000
 S2C  H    N   CA   114.00  3.000
 S2C  HA   CA  CB   109.00  3.000
 S2C  HA   CA  C    109.00  3.000
 S2C  CB   CA  C    110.10  1.900
 S2C  HA   CA  N    110.00  3.000
 S2C  CB   CA  N    110.50  1.700
 S2C  C    CA  N    111.00  2.800
 S2C  O    C   CA   120.80  1.700
 S2C  O    C   OXT  126.93  3.000
 S2C  CA   C   OXT  116.52  3.000
 S2C  HB2  CB  HB1  108.26  3.000
 S2C  HB2  CB  SG   108.89  3.000
 S2C  HB1  CB  SG   108.33  3.000
 S2C  HB2  CB  CA   110.10  3.000
 S2C  HB1  CB  CA   109.68  3.000
 S2C  SG   CB  CA   111.50  3.000
 S2C  CD   SG  CB   100.15  3.000
 S2C  HD2  CD  HD1  107.22  3.000
 S2C  HD2  CD  CE   110.91  3.000
 S2C  HD1  CD  CE   110.84  3.000
 S2C  HD2  CD  SG   107.95  3.000
 S2C  HD1  CD  SG   107.41  3.000
 S2C  CE   CD  SG   112.29  3.000
 S2C  HE2  CE  HE1  105.41  3.000
 S2C  HE2  CE  B    110.51  3.000
 S2C  HE1  CE  B    110.40  3.000
 S2C  HE2  CE  CD   108.40  3.000
 S2C  HE1  CE  CD   108.66  3.000
 S2C  B    CE  CD   113.14  3.000
 S2C  O3   B   O2   112.47  3.000
 S2C  O3   B   O1   106.88  3.000
 S2C  O2   B   O1   108.04  3.000
 S2C  O3   B   CE   110.53  3.000
 S2C  O2   B   CE   106.43  3.000
 S2C  O1   B   CE   112.56  3.000
 S2C  HO1  O1  B    109.11  3.000
 S2C  HO2  O2  B    108.38  3.000
 S2C  HO3  O3  B    108.42  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
 S2C  Var_01  CE   CD  SG  CB  -176.09  30.0  3
 S2C  Var_02  B    CE  CD  SG   177.67  30.0  3
 S2C  Var_03  O1   B   CE  CD    57.51  30.0  3
 S2C  Var_04  HB1  CB  SG  CD    53.88  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
 S2C  chir_01  CA  N  C  CB  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
 S2C  plan-1  OXT  0.020
 S2C  plan-1  CA   0.020
 S2C  plan-1  C    0.020
 S2C  plan-1  O    0.020

