# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:32:41 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: [(2~{R},3~{R},4~{R},5~{R},6~{R})-5-acetamido-4,6-bis(oxidanyl)-2-(sulfooxymethyl)oxan-3-yl] hydrogen sulfate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@H](O)O[C@H](CO[S](O)(=O)=O)[C@H](O[S](O)(=O)=O)[C@@H]1O
#
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
 8EX  8EX  '[(2~{R},3~{R},4~{R},5~{R},6~{R})-5-acetamido-4,6-bis(oxidanyl)-2-(sulfooxymethyl)oxan-3-yl] hydrogen sulfate'  D-saccharide  36  23  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8EX
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
 8EX  C1   C  CH1    0   0.319  -2.7911   0.5467  -0.1993
 8EX  C2   C  CH1    0  -0.171  -3.6786   0.7717   1.0342
 8EX  C3   C  CH1    0   0.070  -3.5831  -0.4373   1.9736
 8EX  C4   C  CH1    0  -0.081  -3.9018  -1.7036   1.1805
 8EX  C5   C  CH1    0  -0.008  -2.9681  -1.7811  -0.0212
 8EX  C6   C  CH2    0  -0.201  -3.2194  -3.0120  -0.8694
 8EX  C8   C  CH3    0  -0.779  -3.4844   4.1488   2.7464
 8EX  N2   N  NH1    0  -0.644  -3.2781   1.9831   1.7034
 8EX  O1   O  OH1    0  -0.650  -2.9672   1.5276  -1.1645
 8EX  O3   O  OH1    0  -0.687  -4.3418  -0.2639   3.1341
 8EX  O4   O  OC2    0  -0.624  -5.2411  -1.6574   0.6858
 8EX  O5   O  O2     0  -0.482  -3.1314  -0.6423  -0.8401
 8EX  O6   O  OC2    0  -0.608  -2.2733  -3.1135  -1.9227
 8EX  O7   O  O      0  -0.491  -5.2723   3.0506   1.6078
 8EX  O1S  O  OS     0  -0.728  -0.1659  -3.7617  -2.8603
 8EX  O2S  O  OS    -1  -0.735  -0.3731  -3.6359  -0.4041
 8EX  O3S  O  OS     0  -0.738  -1.4852  -5.4406  -1.6329
 8EX  S1   S  S      0   1.564  -0.9584  -4.0751  -1.6751
 8EX  S2   S  S      0   1.585  -6.3928  -2.5597   1.4322
 8EX  O5S  O  OS     0  -0.708  -7.5619  -2.2682   0.6156
 8EX  O6S  O  OS     0  -0.719  -5.9138  -3.9390   1.3821
 8EX  O4S  O  OS    -1  -0.742  -6.4588  -2.0148   2.8023
 8EX  H1   H  HCH1   0   0.175  -1.7360   0.5009   0.1369
 8EX  H2   H  HCH1   0   0.266  -4.7103   0.9004   0.7028
 8EX  H3   H  HCH1   0   0.221  -2.5329  -0.5336   2.2862
 8EX  H4   H  HCH1   0   0.275  -3.7387  -2.5849   1.8126
 8EX  H5   H  HCH1   0   0.244  -1.9415  -1.8257   0.3681
 8EX  H61  H  HCH2   0   0.247  -4.2029  -2.9580  -1.3385
 8EX  H62  H  HCH2   0   0.231  -3.2177  -3.8996  -0.2291
 8EX  H81  H  HCH3   0   0.264  -4.0360   4.2928   3.6756
 8EX  H82  H  HCH3   0   0.247  -2.4354   3.9920   2.9901
 8EX  H83  H  HCH3   0   0.264  -3.5724   5.0710   2.1725
 8EX  HN2  H  HNH1   0   0.400  -2.3481   2.0109   2.0938
 8EX  HO1  H  HOH1   0   0.458  -2.6581   2.3677  -0.8086
 8EX  HO3  H  HOH1   0   0.449  -5.1868  -0.7418   3.0559
 8EX  C7   C  C      0   0.516  -4.1059   3.0149   1.9692

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
 8EX  O1S  S1   deloc   1.460  0.020  1.460
 8EX  S1   O6   single  1.648  0.020  1.648
 8EX  S1   O3S  deloc   1.464  0.020  1.464
 8EX  S1   O2S  deloc   1.467  0.020  1.467
 8EX  O6   C6   single  1.419  0.020  1.419
 8EX  O5   C1   single  1.393  0.020  1.393
 8EX  O5   C5   single  1.412  0.020  1.412
 8EX  O1   C1   single  1.387  0.020  1.387
 8EX  C6   C5   single  1.516  0.020  1.516
 8EX  O5S  S2   deloc   1.456  0.020  1.456
 8EX  C1   C2   single  1.536  0.020  1.536
 8EX  C5   C4   single  1.524  0.020  1.524
 8EX  S2   O4   single  1.643  0.020  1.643
 8EX  S2   O6S  deloc   1.461  0.020  1.461
 8EX  S2   O4S  deloc   1.476  0.020  1.476
 8EX  O4   C4   single  1.429  0.020  1.429
 8EX  C2   N2   single  1.441  0.020  1.441
 8EX  C2   C3   single  1.534  0.020  1.534
 8EX  C4   C3   single  1.528  0.020  1.528
 8EX  O7   C7   double  1.222  0.020  1.222
 8EX  N2   C7   single  1.349  0.020  1.349
 8EX  C7   C8   single  1.509  0.020  1.509
 8EX  C3   O3   single  1.397  0.020  1.397
 8EX  C1   H1   single  0.970  0.020  1.090
 8EX  C2   H2   single  0.970  0.020  1.090
 8EX  C3   H3   single  0.970  0.020  1.090
 8EX  C4   H4   single  0.970  0.020  1.090
 8EX  C5   H5   single  0.970  0.020  1.090
 8EX  C6   H61  single  0.970  0.020  1.090
 8EX  C6   H62  single  0.970  0.020  1.090
 8EX  C8   H81  single  0.970  0.020  1.090
 8EX  C8   H82  single  0.970  0.020  1.090
 8EX  C8   H83  single  0.970  0.020  1.090
 8EX  N2   HN2  single  0.860  0.020  1.020
 8EX  O1   HO1  single  0.850  0.020  0.980
 8EX  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
 8EX  H1   C1  O5   109.68  3.000
 8EX  H1   C1  O1   111.17  3.000
 8EX  O5   C1  O1   104.62  3.000
 8EX  H1   C1  C2   108.21  3.000
 8EX  O1   C1  C2   112.45  3.000
 8EX  O5   C1  C2   110.68  3.000
 8EX  H2   C2  N2   107.74  3.000
 8EX  H2   C2  C3   109.74  3.000
 8EX  N2   C2  C3   111.16  3.000
 8EX  H2   C2  C1   108.64  3.000
 8EX  C3   C2  C1   109.90  3.000
 8EX  N2   C2  C1   109.60  3.000
 8EX  H3   C3  O3   107.05  3.000
 8EX  H3   C3  C4   105.91  3.000
 8EX  O3   C3  C4   114.88  3.000
 8EX  H3   C3  C2   107.61  3.000
 8EX  O3   C3  C2   112.15  3.000
 8EX  C4   C3  C2   108.81  3.000
 8EX  H4   C4  O4   111.41  3.000
 8EX  H4   C4  C5   108.82  3.000
 8EX  O4   C4  C5   107.64  3.000
 8EX  H4   C4  C3   109.63  3.000
 8EX  O4   C4  C3   110.39  3.000
 8EX  C5   C4  C3   108.89  3.000
 8EX  H5   C5  O5   110.26  3.000
 8EX  H5   C5  C6   108.67  3.000
 8EX  O5   C5  C6   108.13  3.000
 8EX  H5   C5  C4   107.16  3.000
 8EX  C6   C5  C4   112.39  3.000
 8EX  O5   C5  C4   110.22  3.000
 8EX  H62  C6  H61  107.05  3.000
 8EX  H62  C6  O6   112.03  3.000
 8EX  H61  C6  O6   106.58  3.000
 8EX  H62  C6  C5   109.33  3.000
 8EX  H61  C6  C5   110.48  3.000
 8EX  O6   C6  C5   111.27  3.000
 8EX  H83  C8  H82  108.52  3.000
 8EX  H83  C8  H81  107.23  3.000
 8EX  H82  C8  H81  108.41  3.000
 8EX  H83  C8  C7   109.36  3.000
 8EX  H82  C8  C7   113.84  3.000
 8EX  H81  C8  C7   109.27  3.000
 8EX  HN2  N2  C7   117.92  3.000
 8EX  HN2  N2  C2   117.32  3.000
 8EX  C7   N2  C2   124.33  3.000
 8EX  HO1  O1  C1   108.59  3.000
 8EX  HO3  O3  C3   110.09  3.000
 8EX  S2   O4  C4   118.83  3.000
 8EX  C5   O5  C1   113.17  3.000
 8EX  S1   O6  C6   117.53  3.000
 8EX  O3S  S1  O2S  113.44  3.000
 8EX  O2S  S1  O1S  115.00  3.000
 8EX  O3S  S1  O1S  114.76  3.000
 8EX  O2S  S1  O6   105.90  3.000
 8EX  O3S  S1  O6   105.16  3.000
 8EX  O1S  S1  O6   100.72  3.000
 8EX  O4S  S2  O6S  113.27  3.000
 8EX  O4S  S2  O5S  114.27  3.000
 8EX  O6S  S2  O5S  115.67  3.000
 8EX  O4S  S2  O4   104.50  3.000
 8EX  O6S  S2  O4   105.85  3.000
 8EX  O5S  S2  O4   101.44  3.000
 8EX  O7   C7  N2   123.36  3.000
 8EX  N2   C7  C8   115.06  3.000
 8EX  O7   C7  C8   121.59  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
 8EX  CONST_01  O7   C7  N2  C2     0.00   0.0  0
 8EX  CONST_02  C8   C7  N2  C2   180.00   0.0  0
 8EX  CONST_03  HN2  N2  C7  C8     0.00   0.0  0
 8EX  Var_01    O5S  S2  O4  C4  -178.21  30.0  3
 8EX  Var_02    O1S  S1  O6  C6  -172.08  30.0  3
 8EX  Var_03    H81  C8  C7  N2  -120.94  30.0  3
 8EX  Var_04    H61  C6  O6  S1  -143.25  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
 8EX  chir_01  C1  O5  O1  C2  negativ
 8EX  chir_02  C2  N2  C3  C1  positiv
 8EX  chir_03  C3  O3  C2  C4  positiv
 8EX  chir_04  C4  O4  C5  C3  negativ
 8EX  chir_05  C5  O5  C4  C6  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
 8EX  plan-1  C2   0.020
 8EX  plan-1  C8   0.020
 8EX  plan-1  N2   0.020
 8EX  plan-1  O7   0.020
 8EX  plan-1  HN2  0.020
 8EX  plan-1  C7   0.020

