# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 14:14:43 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: (2~{S},3~{R})-2-azanyl-3-[oxidanyl(sulfanyl)phosphoryl]oxy-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O[P](O)(S)=O)[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
 T8L  T8L  '(2~{S},3~{R})-2-azanyl-3-[oxidanyl(sulfanyl)phosphoryl]oxy-butanoic acid'  L-peptide  20  12  .  2019-03-22  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T8L
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
 T8L  N    N  NH2    0  -0.790  -11.6364  83.6341   -5.2563
 T8L  CA   C  CH1    0  -0.201  -10.5250  82.8023   -5.7081
 T8L  C    C  C      0   0.379   -9.6860  82.2180   -4.5450
 T8L  O    O  O      0  -0.610   -9.2915  83.0466   -3.6958
 T8L  CB   C  CH1    0   0.067   -9.6203  83.6177   -6.6375
 T8L  OG1  O  O2     0  -0.604  -10.3850  84.0058   -7.7783
 T8L  CG2  C  CH3    0  -0.678   -8.4052  82.8373   -7.1129
 T8L  O1P  O  O      0  -0.758  -11.5900  85.5071   -9.3422
 T8L  O2P  O  OP    -1  -0.775  -10.5680  86.5254   -7.1477
 T8L  P    P  P      0   1.173  -10.5475  85.5449   -8.2751
 T8L  S1   S  S2     0  -0.525   -8.6289  85.9593   -9.1851
 T8L  H1   H  HNH2   0   0.336  -12.3024  83.0500   -4.7642
 T8L  H2   H  HNH2   0   0.323  -11.2745  84.2703   -4.5543
 T8L  H4   H  HCH1   0   0.197  -10.9394  81.9755   -6.2948
 T8L  H6   H  HCH1   0   0.195   -9.2820  84.5056   -6.0904
 T8L  H7   H  HCH3   0   0.226   -7.7376  82.5993   -6.2859
 T8L  H8   H  HCH3   0   0.216   -8.6965  81.9009   -7.5920
 T8L  H9   H  HCH3   0   0.229   -7.8373  83.4282   -7.8308
 T8L  H11  H  HSH1   0   0.208   -8.6759  85.0509  -10.1671
 T8L  O1   O  OC    -1  -0.607   -9.4692  80.9903   -4.5490

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
 T8L  O1P  P    deloc   1.492  0.020  1.492
 T8L  S1   P    single  2.163  0.020  2.163
 T8L  P    OG1  single  1.625  0.020  1.625
 T8L  P    O2P  deloc   1.494  0.020  1.494
 T8L  OG1  CB   single  1.427  0.020  1.427
 T8L  CG2  CB   single  1.520  0.020  1.520
 T8L  CB   CA   single  1.540  0.027  1.540
 T8L  CA   N    single  1.458  0.019  1.458
 T8L  CA   C    single  1.525  0.021  1.525
 T8L  C    O    deloc   1.231  0.020  1.231
 T8L  N    H1   single  0.890  0.020  1.040
 T8L  N    H2   single  0.890  0.020  1.040
 T8L  CA   H4   single  0.970  0.020  1.090
 T8L  CB   H6   single  0.970  0.020  1.090
 T8L  CG2  H7   single  0.970  0.020  1.090
 T8L  CG2  H8   single  0.970  0.020  1.090
 T8L  CG2  H9   single  0.970  0.020  1.090
 T8L  S1   H11  single  1.200  0.020  1.300
 T8L  C    O1   deloc   1.247  0.020  1.247

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
 T8L  H2   N    H1   105.06  3.000
 T8L  H2   N    CA   107.46  3.000
 T8L  H1   N    CA   108.80  3.000
 T8L  H4   CA   CB   107.47  3.000
 T8L  H4   CA   C    108.82  3.000
 T8L  CB   CA   C    109.10  2.200
 T8L  H4   CA   N    107.93  3.000
 T8L  C    CA   N    111.00  2.800
 T8L  CB   CA   N    111.50  1.700
 T8L  O1   C    O    126.86  3.000
 T8L  O1   C    CA   117.60  3.000
 T8L  O    C    CA   120.80  1.700
 T8L  H6   CB   CG2  108.97  3.000
 T8L  H6   CB   OG1  110.12  3.000
 T8L  CG2  CB   OG1  108.53  3.000
 T8L  H6   CB   CA   108.09  3.000
 T8L  CG2  CB   CA   112.86  3.000
 T8L  OG1  CB   CA   108.26  3.000
 T8L  P    OG1  CB   123.74  3.000
 T8L  H9   CG2  H8   108.37  3.000
 T8L  H9   CG2  H7   107.42  3.000
 T8L  H8   CG2  H7   108.03  3.000
 T8L  H9   CG2  CB   110.14  3.000
 T8L  H8   CG2  CB   111.36  3.000
 T8L  H7   CG2  CB   111.38  3.000
 T8L  S1   P    O2P  101.76  3.000
 T8L  O2P  P    O1P  123.13  3.000
 T8L  S1   P    O1P  108.88  3.000
 T8L  O2P  P    OG1  113.08  3.000
 T8L  S1   P    OG1  102.79  3.000
 T8L  O1P  P    OG1  105.33  3.000
 T8L  H11  S1   P     98.48  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
 T8L  Var_01  O1P  P  OG1  CB  -171.02  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
 T8L  chir_01  CA  CB   N   C    positiv
 T8L  chir_02  CB  OG1  CA  CG2  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
 T8L  plan-1  CA  0.020
 T8L  plan-1  C   0.020
 T8L  plan-1  O   0.020
 T8L  plan-1  O1  0.020

