# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 12:31:17 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (3~{S},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-5-sulfanyl-piperidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1NC[C@H](O)[C@@H](O)[C@@H]1S
#
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
 SGJ  SGJ  (3~{S},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-5-sulfanyl-piperidine-3,4-diol  ligand  24  11  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SGJ
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
 SGJ  O1   O  OH1   0  -0.665  -3.2639  -1.3674   0.1129
 SGJ  C1   C  CH2   0  -0.137  -2.4657  -0.3318  -0.4050
 SGJ  C2   C  CH1   0  -0.115  -1.0612  -0.4499   0.1679
 SGJ  N1   N  NH1   0  -0.569  -0.5109  -1.7497  -0.1671
 SGJ  C3   C  CH2   0  -0.353   0.8426  -1.9375   0.3098
 SGJ  C4   C  CH1   0   0.019   1.7979  -0.8620  -0.1992
 SGJ  O2   O  OH1   0  -0.676   3.0887  -0.9799   0.3610
 SGJ  C5   C  CH1   0   0.089   1.2687   0.5123   0.1909
 SGJ  O3   O  OH1   0  -0.670   2.0655   1.5416  -0.3414
 SGJ  C6   C  CH1   0  -0.417  -0.1569   0.7012  -0.3154
 SGJ  S1   S  S2    0  -0.246  -0.8442   2.2943   0.2779
 SGJ  H1   H  HOH1  0   0.455  -4.1661  -1.2177  -0.1828
 SGJ  H2   H  HCH2  0   0.192  -2.4002  -0.3759  -1.5028
 SGJ  H3   H  HCH2  0   0.212  -2.8810   0.6512  -0.1566
 SGJ  H4   H  HCH1  0   0.238  -1.1231  -0.3890   1.2628
 SGJ  H5   H  HNH1  0   0.344  -0.5479  -1.8896  -1.1715
 SGJ  H7   H  HCH2  0   0.227   0.8373  -1.9270   1.4050
 SGJ  H8   H  HCH2  0   0.247   1.1917  -2.9270   0.0051
 SGJ  H9   H  HCH1  0   0.208   1.8404  -0.9201  -1.2977
 SGJ  H10  H  HOH1  0   0.458   3.5449  -1.7099  -0.0680
 SGJ  H11  H  HCH1  0   0.205   1.2437   0.5634   1.2923
 SGJ  H12  H  HOH1  0   0.452   2.9664   1.4135  -0.0264
 SGJ  H13  H  HCH1  0   0.271  -0.1545   0.7144  -1.4105
 SGJ  H14  H  HSH1  0   0.232   0.1428   3.0810  -0.1605

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
 SGJ  C3  N1   single  1.447  0.020  1.447
 SGJ  C3  C4   single  1.526  0.020  1.526
 SGJ  O2  C4   single  1.412  0.020  1.412
 SGJ  C2  N1   single  1.451  0.020  1.451
 SGJ  C2  C6   single  1.542  0.020  1.542
 SGJ  C2  C1   single  1.522  0.020  1.522
 SGJ  S1  C6   single  1.834  0.020  1.834
 SGJ  C5  C4   single  1.523  0.020  1.523
 SGJ  C5  C6   single  1.525  0.020  1.525
 SGJ  C5  O3   single  1.406  0.020  1.406
 SGJ  C1  O1   single  1.406  0.020  1.406
 SGJ  O1  H1   single  0.850  0.020  0.980
 SGJ  C1  H2   single  0.970  0.020  1.090
 SGJ  C1  H3   single  0.970  0.020  1.090
 SGJ  C2  H4   single  0.970  0.020  1.090
 SGJ  N1  H5   single  0.890  0.020  1.040
 SGJ  C3  H7   single  0.970  0.020  1.090
 SGJ  C3  H8   single  0.970  0.020  1.090
 SGJ  C4  H9   single  0.970  0.020  1.090
 SGJ  O2  H10  single  0.850  0.020  0.980
 SGJ  C5  H11  single  0.970  0.020  1.090
 SGJ  O3  H12  single  0.850  0.020  0.980
 SGJ  C6  H13  single  0.970  0.020  1.090
 SGJ  S1  H14  single  1.200  0.020  1.300

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
 SGJ  H1   O1  C1  107.74  3.000
 SGJ  H3   C1  H2  106.54  3.000
 SGJ  H3   C1  C2  109.52  3.000
 SGJ  H2   C1  C2  108.51  3.000
 SGJ  H3   C1  O1  111.23  3.000
 SGJ  H2   C1  O1  111.81  3.000
 SGJ  C2   C1  O1  109.15  3.000
 SGJ  H4   C2  C6  107.71  3.000
 SGJ  H4   C2  N1  107.53  3.000
 SGJ  C6   C2  N1  111.97  3.000
 SGJ  H4   C2  C1  108.60  3.000
 SGJ  C6   C2  C1  111.44  3.000
 SGJ  N1   C2  C1  109.44  3.000
 SGJ  H5   N1  C3  110.02  3.000
 SGJ  H5   N1  C2  109.77  3.000
 SGJ  C3   N1  C2  113.26  3.000
 SGJ  H8   C3  H7  106.80  3.000
 SGJ  H8   C3  C4  110.20  3.000
 SGJ  H7   C3  C4  109.26  3.000
 SGJ  H8   C3  N1  108.93  3.000
 SGJ  H7   C3  N1  108.89  3.000
 SGJ  C4   C3  N1  112.59  3.000
 SGJ  H9   C4  C5  108.45  3.000
 SGJ  H9   C4  O2  110.87  3.000
 SGJ  C5   C4  O2  106.93  3.000
 SGJ  H9   C4  C3  108.65  3.000
 SGJ  C5   C4  C3  109.44  3.000
 SGJ  O2   C4  C3  112.40  3.000
 SGJ  H10  O2  C4  108.66  3.000
 SGJ  H11  C5  C6  107.74  3.000
 SGJ  H11  C5  O3  110.91  3.000
 SGJ  C6   C5  O3  108.26  3.000
 SGJ  H11  C5  C4  107.79  3.000
 SGJ  O3   C5  C4  111.50  3.000
 SGJ  C6   C5  C4  110.59  3.000
 SGJ  H12  O3  C5  107.99  3.000
 SGJ  H13  C6  S1  108.29  3.000
 SGJ  H13  C6  C5  109.36  3.000
 SGJ  S1   C6  C5  110.53  3.000
 SGJ  H13  C6  C2  108.89  3.000
 SGJ  C5   C6  C2  110.60  3.000
 SGJ  S1   C6  C2  109.11  3.000
 SGJ  H14  S1  C6   97.38  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
 SGJ  Var_01  C4  C3  N1  C2  -56.46  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
 SGJ  chir_01  C2  N1  C6  C1  negativ
 SGJ  chir_02  C4  O2  C3  C5  negativ
 SGJ  chir_03  C5  O3  C4  C6  positiv
 SGJ  chir_04  C6  S1  C5  C2  negativ

