# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 12:31:25 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: (2~{S})-2-azanyl-3-(2-hydroxyethylsulfanyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CSCCO)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
 SWW  SWW  "(2~{S})-2-azanyl-3-(2-hydroxyethylsulfanyl)propanoic acid"  L-peptide  20  10  .  2022-08-11  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_SWW
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
 SWW  N     N  NH2    0  -0.791  -16.9485  13.8627  -2.0725
 SWW  CA    C  CH1    0  -0.187  -16.9552  13.7633  -0.6283
 SWW  C     C  C      0   0.403  -16.0182  12.6343  -0.1240
 SWW  O     O  O      0  -0.612  -16.1988  12.2697   1.0554
 SWW  C05   C  CH2    0  -0.580  -16.5476  15.0537   0.0959
 SWW  C07   C  CH2    0  -0.577  -19.1226  16.1816   0.4758
 SWW  C08   C  CH2    0  -0.136  -20.2808  16.0325  -0.4876
 SWW  O09   O  OH1    0  -0.651  -20.0973  14.8906  -1.2852
 SWW  S06   S  S2     0  -0.049  -17.5274  16.5245  -0.3340
 SWW  O1    O  OC    -1  -0.596  -15.1513  12.2177  -0.9154
 SWW  H1    H  HNH2   0   0.326  -17.4113  14.7222  -2.3454
 SWW  H041  H  HNH2   0   0.320  -15.9898  13.9259  -2.3918
 SWW  H031  H  HCH1   0   0.214  -17.9725  13.5194  -0.3084
 SWW  H052  H  HCH2   0   0.259  -16.5823  14.9209   1.1777
 SWW  H051  H  HCH2   0   0.261  -15.5202  15.3231  -0.1667
 SWW  H072  H  HCH2   0   0.270  -19.3424  17.0099   1.1507
 SWW  H071  H  HCH2   0   0.272  -19.0134  15.2874   1.0929
 SWW  H081  H  HCH2   0   0.199  -20.3667  16.9442  -1.0921
 SWW  H082  H  HCH2   0   0.203  -21.2005  15.9634   0.1100
 SWW  H091  H  HOH1   0   0.453  -20.8049  14.8579  -1.9350

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
 SWW  N    CA    single  1.458  0.019  1.458
 SWW  O09  C08   single  1.405  0.020  1.405
 SWW  C08  C07   single  1.514  0.020  1.514
 SWW  CA   C     single  1.525  0.021  1.525
 SWW  CA   C05   single  1.535  0.020  1.535
 SWW  C    O     deloc   1.231  0.020  1.231
 SWW  S06  C05   single  1.819  0.020  1.819
 SWW  S06  C07   single  1.821  0.020  1.821
 SWW  C    O1    deloc   1.246  0.020  1.246
 SWW  N    H1    single  0.890  0.020  1.040
 SWW  N    H041  single  0.890  0.020  1.040
 SWW  CA   H031  single  0.970  0.020  1.090
 SWW  C05  H052  single  0.970  0.020  1.090
 SWW  C05  H051  single  0.970  0.020  1.090
 SWW  C07  H072  single  0.970  0.020  1.090
 SWW  C07  H071  single  0.970  0.020  1.090
 SWW  C08  H081  single  0.970  0.020  1.090
 SWW  C08  H082  single  0.970  0.020  1.090
 SWW  O09  H091  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
 SWW  H041  N    H1    107.13  3.000
 SWW  H041  N    CA    108.86  3.000
 SWW  H1    N    CA    108.95  3.000
 SWW  H031  CA   C05   107.25  3.000
 SWW  H031  CA   C     107.72  3.000
 SWW  C05   CA   C     107.34  3.000
 SWW  H031  CA   N     108.14  3.000
 SWW  C05   CA   N     114.31  3.000
 SWW  C     CA   N     111.00  2.800
 SWW  O1    C    O     127.14  3.000
 SWW  O1    C    CA    117.21  3.000
 SWW  O     C    CA    120.80  1.700
 SWW  H051  C05  H052  107.33  3.000
 SWW  H051  C05  S06   104.48  3.000
 SWW  H052  C05  S06   108.41  3.000
 SWW  H051  C05  CA    110.08  3.000
 SWW  H052  C05  CA    110.93  3.000
 SWW  S06   C05  CA    115.17  3.000
 SWW  H071  C07  H072  106.99  3.000
 SWW  H071  C07  S06   108.53  3.000
 SWW  H072  C07  S06   107.98  3.000
 SWW  H071  C07  C08   110.82  3.000
 SWW  H072  C07  C08   108.32  3.000
 SWW  S06   C07  C08   113.93  3.000
 SWW  H082  C08  H081  106.63  3.000
 SWW  H082  C08  O09   111.52  3.000
 SWW  H081  C08  O09   111.89  3.000
 SWW  H082  C08  C07   107.49  3.000
 SWW  H081  C08  C07   109.19  3.000
 SWW  O09   C08  C07   109.96  3.000
 SWW  H091  O09  C08   108.38  3.000
 SWW  C07   S06  C05   102.39  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
 SWW  Var_01  C07   S06  C05  CA     72.06  30.0  1
 SWW  Var_02  C08   C07  S06  C05  -116.33  30.0  3
 SWW  Var_03  S06   C07  C08  O09    65.79  30.0  3
 SWW  Var_04  H072  C07  S06  C05   123.31  30.0  3
 SWW  Var_05  H071  C07  S06  C05     7.66  30.0  3
 SWW  Var_06  H052  C05  S06  C07   -52.86  30.0  3
 SWW  Var_07  H051  C05  S06  C07  -167.08  30.0  3
 SWW  Var_08  H072  C07  C08  O09  -174.03  30.0  3
 SWW  Var_09  H071  C07  C08  O09   -56.95  30.0  3
 SWW  Var_10  H081  C08  C07  S06   -57.32  30.0  3
 SWW  Var_11  H082  C08  C07  S06  -172.63  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
 SWW  chir_01  CA  N  C  C05  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
 SWW  plan-1  CA  0.020
 SWW  plan-1  C   0.020
 SWW  plan-1  O   0.020
 SWW  plan-1  O1  0.020

