# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 11:52:15 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: [(2R,3R,4R,5R,6R)-2,4,5-trihydroxy-6-(sulfooxy)tetrahydro-2H-pyran-3-yl]sulfamic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1O[C@H](O[S](O)(=O)=O)[C@H](O)[C@H](O)[C@H]1N[S](O)(=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
 U9A  U9A  '[(2R,3R,4R,5R,6R)-2,4,5-trihydroxy-6-(sulfooxy)tetrahydro-2H-pyran-3-yl]sulfamic acid (non-preferred name)'  saccharide  28  19  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_U9A
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
 U9A  C4   C  CH1    0  -0.074  -0.2989  110.8278  291.0069
 U9A  C3   C  CH1    0   0.024   1.0804  110.1346  290.8930
 U9A  C2   C  CH1    0  -0.216   0.9115  108.6574  290.5350
 U9A  C5   C  CH1    0   0.270  -1.3465  110.1802  290.1127
 U9A  C1   C  CH1    0   0.342  -0.4330  108.1509  291.0719
 U9A  N2   N  NC1    0  -0.782   2.0023  107.8525  291.0739
 U9A  OAB  O  OS    -1  -0.732   3.6102  105.9626  290.9001
 U9A  OAF  O  OS     0  -0.759   1.5286  105.9427  289.5647
 U9A  OAH  O  OS     0  -0.733   3.3761  107.4203  288.9322
 U9A  O3   O  OH1    0  -0.663   1.9087  110.7432  289.9420
 U9A  O5   O  O2     0  -0.504  -1.5099  108.8371  290.4334
 U9A  O1   O  OH1    0  -0.687  -0.6454  106.8090  290.8826
 U9A  SAG  S  S      0   1.516   2.7046  106.7189  290.0340
 U9A  O5B  O  OC2    0  -0.627  -0.9440  110.3386  288.7702
 U9A  OBF  O  OS    -1  -0.734  -2.6135  112.0052  288.0073
 U9A  OBH  O  OS     0  -0.733  -3.1022  109.6166  287.7485
 U9A  OBI  O  OS     0  -0.724  -1.3028  110.6516  286.4188
 U9A  SBG  S  S      0   1.560  -2.1056  110.6829  287.6370
 U9A  O4   O  OH1    0  -0.660  -0.2031  112.1928  290.6863
 U9A  H6   H  HCH1   0   0.260  -0.6533  110.6968  292.0360
 U9A  H7   H  HCH1   0   0.216   1.5384  110.1937  291.8940
 U9A  H8   H  HCH1   0   0.265   0.8801  108.5930  289.4407
 U9A  H9   H  HCH1   0   0.240  -2.3118  110.6708  290.2807
 U9A  H10  H  HCH1   0   0.180  -0.4865  108.3555  292.1529
 U9A  HAM  H  HNC1   0   0.391   2.7203  108.4043  291.5311
 U9A  HAL  H  HOH1   0   0.444   1.6605  111.6762  289.9109
 U9A  HO1  H  HOH1   0   0.456   0.0527  106.4304  290.3069
 U9A  H2   H  HOH1   0   0.466  -0.0229  112.6888  291.4912

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
 U9A  OBI  SBG  deloc   1.459  0.020  1.459
 U9A  O5B  SBG  single  1.659  0.020  1.659
 U9A  O5B  C5   single  1.410  0.020  1.410
 U9A  SBG  OBH  deloc   1.464  0.020  1.464
 U9A  SBG  OBF  deloc   1.464  0.020  1.464
 U9A  O3   C3   single  1.400  0.020  1.400
 U9A  O5   C5   single  1.391  0.020  1.391
 U9A  O5   C1   single  1.428  0.020  1.428
 U9A  O1   C1   single  1.372  0.020  1.372
 U9A  C5   C4   single  1.522  0.020  1.522
 U9A  C3   C2   single  1.529  0.020  1.529
 U9A  C3   C4   single  1.548  0.020  1.548
 U9A  C1   C2   single  1.534  0.020  1.534
 U9A  OAF  SAG  deloc   1.485  0.020  1.485
 U9A  C2   N2   single  1.459  0.020  1.459
 U9A  O4   C4   single  1.405  0.020  1.405
 U9A  SAG  N2   single  1.691  0.020  1.691
 U9A  SAG  OAH  deloc   1.469  0.020  1.469
 U9A  SAG  OAB  deloc   1.464  0.020  1.464
 U9A  C4   H6   single  0.970  0.020  1.090
 U9A  C3   H7   single  0.970  0.020  1.090
 U9A  C2   H8   single  0.970  0.020  1.090
 U9A  C5   H9   single  0.970  0.020  1.090
 U9A  C1   H10  single  0.970  0.020  1.090
 U9A  N2   HAM  single  0.890  0.020  1.040
 U9A  O3   HAL  single  0.850  0.020  0.980
 U9A  O1   HO1  single  0.850  0.020  0.980
 U9A  O4   H2   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
 U9A  H6   C4   O4   110.62  3.000
 U9A  H6   C4   C5   106.15  3.000
 U9A  O4   C4   C5   109.04  3.000
 U9A  H6   C4   C3   107.68  3.000
 U9A  O4   C4   C3   110.94  3.000
 U9A  C5   C4   C3   112.31  3.000
 U9A  H7   C3   O3   110.34  3.000
 U9A  H7   C3   C2   108.07  3.000
 U9A  O3   C3   C2   109.03  3.000
 U9A  H7   C3   C4   106.22  3.000
 U9A  C2   C3   C4   110.57  3.000
 U9A  O3   C3   C4   112.49  3.000
 U9A  H8   C2   N2   110.96  3.000
 U9A  H8   C2   C1   107.74  3.000
 U9A  N2   C2   C1   110.12  3.000
 U9A  H8   C2   C3   107.06  3.000
 U9A  N2   C2   C3   111.34  3.000
 U9A  C1   C2   C3   109.50  3.000
 U9A  H9   C5   O5B  110.31  3.000
 U9A  H9   C5   O5   107.07  3.000
 U9A  O5B  C5   O5   111.19  3.000
 U9A  H9   C5   C4   109.01  3.000
 U9A  O5   C5   C4   110.87  3.000
 U9A  O5B  C5   C4   108.36  3.000
 U9A  H10  C1   O1   108.03  3.000
 U9A  H10  C1   O5   108.24  3.000
 U9A  O1   C1   O5   106.96  3.000
 U9A  H10  C1   C2   108.95  3.000
 U9A  O1   C1   C2   114.24  3.000
 U9A  O5   C1   C2   110.24  3.000
 U9A  HAM  N2   SAG  110.36  3.000
 U9A  HAM  N2   C2   113.30  3.000
 U9A  SAG  N2   C2   116.95  3.000
 U9A  HAL  O3   C3   106.84  3.000
 U9A  C1   O5   C5   118.61  3.000
 U9A  HO1  O1   C1   110.39  3.000
 U9A  OAH  SAG  OAF  112.00  3.000
 U9A  OAH  SAG  OAB  114.07  3.000
 U9A  OAF  SAG  OAB  114.00  3.000
 U9A  OAB  SAG  N2   103.86  3.000
 U9A  OAH  SAG  N2   109.34  3.000
 U9A  OAF  SAG  N2   102.47  3.000
 U9A  SBG  O5B  C5   118.27  3.000
 U9A  OBI  SBG  OBH  114.99  3.000
 U9A  OBH  SBG  OBF  113.73  3.000
 U9A  OBI  SBG  OBF  114.92  3.000
 U9A  OBF  SBG  O5B  104.93  3.000
 U9A  OBH  SBG  O5B  105.87  3.000
 U9A  OBI  SBG  O5B  100.41  3.000
 U9A  H2   O4   C4   108.81  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
 U9A  Var_01  OAF  SAG  N2   C2   -53.46  30.0  3
 U9A  Var_02  OBI  SBG  O5B  C5  -175.56  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
 U9A  chir_01  C4  C5  C3   O4  negativ
 U9A  chir_02  C3  O3  C4   C2  negativ
 U9A  chir_03  C2  N2  C3   C1  positiv
 U9A  chir_04  C5  O5  O5B  C4  positiv
 U9A  chir_05  C1  O1  O5   C2  positiv

