# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 03:03:25 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: (1S,6S,7R,8R,8aR)-octahydroindolizine-1,6,7,8-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCN2C[C@H](O)[C@@H](O)[C@H](O)[C@@H]12
#
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
 CTS  CTS  (1S,6S,7R,8R,8aR)-octahydroindolizine-1,6,7,8-tetrol  ligand  28  13  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CTS
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
 CTS  C1   C  CH2   0  -0.316   1.7530   0.0872  -0.6491
 CTS  C2   C  CH1   0   0.028   0.8405  -0.3825  -1.7780
 CTS  C3   C  CH1   0   0.007  -0.5244   0.2842  -1.6575
 CTS  C4   C  CH1   0   0.053  -1.1296   0.0206  -0.2816
 CTS  C5   C  CH1   0  -0.094  -0.1510   0.4771   0.7847
 CTS  C6   C  CH1   0   0.055  -0.4978   0.1621   2.2343
 CTS  O2   O  OH1   0  -0.677   1.3598  -0.0483  -3.0470
 CTS  O3   O  OH1   0  -0.677  -1.4367  -0.1967  -2.6181
 CTS  O4   O  OH1   0  -0.678  -2.3325   0.7281  -0.0969
 CTS  O6   O  OH1   0  -0.675  -1.0162  -1.1468   2.3051
 CTS  N    N  NT    0  -0.448   1.1243  -0.1902   0.6161
 CTS  C7   C  CH2   0  -0.521   0.8744   0.2977   2.9177
 CTS  C8   C  CH2   0  -0.259   1.9114   0.1375   1.7914
 CTS  H11  H  HCH2  0   0.193   1.9716   1.1634  -0.7788
 CTS  H12  H  HCH2  0   0.241   2.7077  -0.4438  -0.7042
 CTS  H2   H  HCH1  0   0.208   0.7040  -1.4690  -1.6823
 CTS  H3   H  HCH1  0   0.199  -0.3815   1.3729  -1.7653
 CTS  H4   H  HCH1  0   0.205  -1.2861  -1.0621  -0.1793
 CTS  H5   H  HCH1  0   0.210  -0.0411   1.5772   0.7002
 CTS  H6   H  HCH1  0   0.216  -1.2139   0.8864   2.6370
 CTS  HO2  H  HOH1  0   0.456   2.0898  -0.6423  -3.2449
 CTS  HO3  H  HOH1  0   0.452  -1.0993   0.0212  -3.4927
 CTS  HO4  H  HOH1  0   0.450  -2.9605   0.4316  -0.7632
 CTS  HO6  H  HOH1  0   0.450  -1.1483  -1.3651   3.2322
 CTS  H71  H  HCH2  0   0.243   0.9664   1.2789   3.3836
 CTS  H72  H  HCH2  0   0.248   0.9935  -0.4422   3.7107
 CTS  H81  H  HCH2  0   0.200   2.4645   1.0795   1.6569
 CTS  H82  H  HCH2  0   0.231   2.6505  -0.6418   1.9894

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
 CTS  C1  C2   single  1.526  0.020  1.526
 CTS  C1  N    single  1.440  0.020  1.440
 CTS  C1  H11  single  0.970  0.020  1.090
 CTS  C1  H12  single  0.970  0.020  1.090
 CTS  C2  C3   single  1.524  0.020  1.524
 CTS  C2  O2   single  1.411  0.020  1.411
 CTS  C2  H2   single  0.970  0.020  1.090
 CTS  C3  C4   single  1.526  0.020  1.526
 CTS  C3  O3   single  1.409  0.020  1.409
 CTS  C3  H3   single  0.970  0.020  1.090
 CTS  C4  C5   single  1.518  0.020  1.518
 CTS  C4  O4   single  1.408  0.020  1.408
 CTS  C4  H4   single  0.970  0.020  1.090
 CTS  C5  C6   single  1.523  0.020  1.523
 CTS  C5  N    single  1.449  0.020  1.449
 CTS  C5  H5   single  0.970  0.020  1.090
 CTS  C6  O6   single  1.410  0.020  1.410
 CTS  C6  C7   single  1.539  0.020  1.539
 CTS  C6  H6   single  0.970  0.020  1.090
 CTS  O2  HO2  single  0.850  0.020  0.980
 CTS  O3  HO3  single  0.850  0.020  0.980
 CTS  O4  HO4  single  0.850  0.020  0.980
 CTS  O6  HO6  single  0.850  0.020  0.980
 CTS  N   C8   single  1.452  0.020  1.452
 CTS  C7  C8   single  1.539  0.020  1.539
 CTS  C7  H71  single  0.970  0.020  1.090
 CTS  C7  H72  single  0.970  0.020  1.090
 CTS  C8  H81  single  0.970  0.020  1.090
 CTS  C8  H82  single  0.970  0.020  1.090

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
 CTS  H12  C1  H11  107.10  3.000
 CTS  H12  C1  N    109.38  3.000
 CTS  H11  C1  N    112.14  3.000
 CTS  H12  C1  C2   109.59  3.000
 CTS  H11  C1  C2   109.34  3.000
 CTS  N    C1  C2   109.25  3.000
 CTS  H2   C2  O2   110.98  3.000
 CTS  H2   C2  C3   108.32  3.000
 CTS  O2   C2  C3   107.28  3.000
 CTS  H2   C2  C1   108.31  3.000
 CTS  O2   C2  C1   111.86  3.000
 CTS  C3   C2  C1   110.03  3.000
 CTS  H3   C3  O3   110.73  3.000
 CTS  H3   C3  C4   108.05  3.000
 CTS  O3   C3  C4   107.39  3.000
 CTS  H3   C3  C2   107.94  3.000
 CTS  O3   C3  C2   112.13  3.000
 CTS  C4   C3  C2   110.54  3.000
 CTS  H4   C4  O4   111.18  3.000
 CTS  H4   C4  C5   108.83  3.000
 CTS  O4   C4  C5   107.92  3.000
 CTS  H4   C4  C3   108.10  3.000
 CTS  O4   C4  C3   111.74  3.000
 CTS  C5   C4  C3   109.02  3.000
 CTS  H5   C5  N    111.15  3.000
 CTS  H5   C5  C6   107.47  3.000
 CTS  N    C5  C6   102.46  3.000
 CTS  H5   C5  C4   107.98  3.000
 CTS  N    C5  C4   110.32  3.000
 CTS  C6   C5  C4   117.36  3.000
 CTS  H6   C6  C7   111.18  3.000
 CTS  H6   C6  O6   110.80  3.000
 CTS  C7   C6  O6   112.80  3.000
 CTS  H6   C6  C5   111.22  3.000
 CTS  C7   C6  C5   101.62  3.000
 CTS  O6   C6  C5   108.88  3.000
 CTS  HO2  O2  C2   108.55  3.000
 CTS  HO3  O3  C3   108.38  3.000
 CTS  HO4  O4  C4   108.18  3.000
 CTS  HO6  O6  C6   108.05  3.000
 CTS  C8   N   C5   106.20  3.000
 CTS  C8   N   C1   115.53  3.000
 CTS  C5   N   C1   113.44  3.000
 CTS  H72  C7  H71  106.90  3.000
 CTS  H72  C7  C8   112.80  3.000
 CTS  H71  C7  C8   110.46  3.000
 CTS  H72  C7  C6   111.12  3.000
 CTS  H71  C7  C6   110.15  3.000
 CTS  C8   C7  C6   105.46  3.000
 CTS  H82  C8  H81  107.03  3.000
 CTS  H82  C8  C7   113.42  3.000
 CTS  H81  C8  C7   109.80  3.000
 CTS  H82  C8  N    110.65  3.000
 CTS  H81  C8  N    111.51  3.000
 CTS  C7   C8  N    104.51  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
 CTS  Var_01  C7  C8  N   C1  157.85  30.0  1
 CTS  Var_02  C5  N   C1  C2  -60.26  30.0  1
 CTS  Var_03  N   C8  C7  C6   -5.02  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
 CTS  chir_01  C2  C1  C3  O2  negativ
 CTS  chir_02  C3  O3  C2  C4  positiv
 CTS  chir_03  C4  O4  C3  C5  negativ
 CTS  chir_04  C5  N   C4  C6  negativ
 CTS  chir_05  C6  O6  C5  C7  positiv

