# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:29:07 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (1S,2R,8R,8aR)-octahydroindolizine-1,2,8-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCCN2C[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
 SWA  SWA  (1S,2R,8R,8aR)-octahydroindolizine-1,2,8-triol  ligand  27  12  .  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_SWA
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
 SWA  C1    C  CH1   0   0.081   0.9236   0.1477   1.4597
 SWA  O1    O  OH1   0  -0.680   2.1695  -0.4941   1.6277
 SWA  C3    C  CH1   0  -0.084   0.2555  -0.4545   0.2363
 SWA  N4    N  NT    0  -0.442  -1.0388   0.1651   0.0192
 SWA  C5    C  CH2   0  -0.278  -1.9658  -0.0306   1.1064
 SWA  C6    C  CH2   0  -0.444  -1.3800   0.5455   2.3872
 SWA  C2    C  CH2   0  -0.482   0.0035  -0.0370   2.6643
 SWA  C9    C  CH2   0  -0.279  -1.4965  -0.2586  -1.2902
 SWA  C8    C  CH1   0  -0.009  -0.2116  -0.6084  -2.0712
 SWA  O13   O  OH1   0  -0.681  -0.0295   0.0933  -3.2756
 SWA  C7    C  CH1   0   0.025   0.9402  -0.2649  -1.1081
 SWA  O11   O  OH1   0  -0.677   1.3679   1.0648  -1.2452
 SWA  HC1   H  HCH1  0   0.195   1.0552   1.2241   1.2863
 SWA  HO1   H  HOH1  0   0.449   2.6168  -0.0884   2.3763
 SWA  HC3   H  HCH1  0   0.202   0.1601  -1.5464   0.4081
 SWA  HC51  H  HCH2  0   0.184  -2.1974  -1.1016   1.2522
 SWA  HC52  H  HCH2  0   0.235  -2.9092   0.4661   0.8661
 SWA  HC61  H  HCH2  0   0.235  -2.0506   0.3437   3.2247
 SWA  HC62  H  HCH2  0   0.220  -1.3114   1.6325   2.2892
 SWA  HC21  H  HCH2  0   0.215  -0.0846  -1.1072   2.8821
 SWA  HC22  H  HCH2  0   0.237   0.4428   0.4343   3.5482
 SWA  HC91  H  HCH2  0   0.202  -2.1476  -1.1435  -1.2314
 SWA  HC92  H  HCH2  0   0.227  -2.0686   0.5324  -1.7844
 SWA  HC8   H  HCH1  0   0.224  -0.1891  -1.6891  -2.2499
 SWA  H13O  H  HOH1  0   0.462  -0.6904  -0.1962  -3.9112
 SWA  HC7   H  HCH1  0   0.215   1.7745  -0.9653  -1.2353
 SWA  H11O  H  HOH1  0   0.448   1.3826   1.2770  -2.1848

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
 SWA  C1   O1    single  1.411  0.020  1.411
 SWA  C1   C3    single  1.518  0.020  1.518
 SWA  C1   C2    single  1.527  0.020  1.527
 SWA  C1   HC1   single  0.970  0.020  1.090
 SWA  O1   HO1   single  0.850  0.020  0.980
 SWA  C3   N4    single  1.451  0.020  1.451
 SWA  C3   C7    single  1.521  0.020  1.521
 SWA  C3   HC3   single  0.970  0.020  1.090
 SWA  N4   C5    single  1.442  0.020  1.442
 SWA  N4   C9    single  1.450  0.020  1.450
 SWA  C5   C6    single  1.522  0.020  1.522
 SWA  C5   HC51  single  0.970  0.020  1.090
 SWA  C5   HC52  single  0.970  0.020  1.090
 SWA  C6   C2    single  1.526  0.020  1.526
 SWA  C6   HC61  single  0.970  0.020  1.090
 SWA  C6   HC62  single  0.970  0.020  1.090
 SWA  C2   HC21  single  0.970  0.020  1.090
 SWA  C2   HC22  single  0.970  0.020  1.090
 SWA  C9   C8    single  1.544  0.020  1.544
 SWA  C9   HC91  single  0.970  0.020  1.090
 SWA  C9   HC92  single  0.970  0.020  1.090
 SWA  C8   O13   single  1.406  0.020  1.406
 SWA  C8   C7    single  1.540  0.020  1.540
 SWA  C8   HC8   single  0.970  0.020  1.090
 SWA  O13  H13O  single  0.850  0.020  0.980
 SWA  C7   O11   single  1.404  0.020  1.404
 SWA  C7   HC7   single  0.970  0.020  1.090
 SWA  O11  H11O  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
 SWA  HC1   C1   C2    108.38  3.000
 SWA  HC1   C1   C3    108.31  3.000
 SWA  C2    C1   C3    108.81  3.000
 SWA  HC1   C1   O1    111.02  3.000
 SWA  C2    C1   O1    112.52  3.000
 SWA  C3    C1   O1    107.70  3.000
 SWA  HO1   O1   C1    108.14  3.000
 SWA  HC3   C3   C7    107.36  3.000
 SWA  HC3   C3   N4    111.51  3.000
 SWA  C7    C3   N4    102.48  3.000
 SWA  HC3   C3   C1    107.66  3.000
 SWA  C7    C3   C1    117.69  3.000
 SWA  N4    C3   C1    110.10  3.000
 SWA  C9    N4   C5    115.98  3.000
 SWA  C9    N4   C3    106.97  3.000
 SWA  C5    N4   C3    113.74  3.000
 SWA  HC52  C5   HC51  106.77  3.000
 SWA  HC52  C5   C6    110.20  3.000
 SWA  HC51  C5   C6    109.66  3.000
 SWA  HC52  C5   N4    109.11  3.000
 SWA  HC51  C5   N4    111.44  3.000
 SWA  C6    C5   N4    109.62  3.000
 SWA  HC62  C6   HC61  106.92  3.000
 SWA  HC62  C6   C2    109.80  3.000
 SWA  HC61  C6   C2    110.30  3.000
 SWA  HC62  C6   C5    108.96  3.000
 SWA  HC61  C6   C5    109.84  3.000
 SWA  C2    C6   C5    110.93  3.000
 SWA  HC22  C2   HC21  107.01  3.000
 SWA  HC22  C2   C6    110.26  3.000
 SWA  HC21  C2   C6    109.63  3.000
 SWA  HC22  C2   C1    110.08  3.000
 SWA  HC21  C2   C1    108.87  3.000
 SWA  C6    C2   C1    110.90  3.000
 SWA  HC92  C9   HC91  107.23  3.000
 SWA  HC92  C9   C8    111.74  3.000
 SWA  HC91  C9   C8    109.72  3.000
 SWA  HC92  C9   N4    111.20  3.000
 SWA  HC91  C9   N4    111.93  3.000
 SWA  C8    C9   N4    105.08  3.000
 SWA  HC8   C8   C7    107.86  3.000
 SWA  HC8   C8   O13   110.48  3.000
 SWA  C7    C8   O13   109.12  3.000
 SWA  HC8   C8   C9    108.85  3.000
 SWA  C7    C8   C9    104.81  3.000
 SWA  O13   C8   C9    115.35  3.000
 SWA  H13O  O13  C8    109.09  3.000
 SWA  HC7   C7   O11   111.21  3.000
 SWA  HC7   C7   C8    110.73  3.000
 SWA  O11   C7   C8    112.21  3.000
 SWA  HC7   C7   C3    111.44  3.000
 SWA  O11   C7   C3    109.98  3.000
 SWA  C8    C7   C3    100.85  3.000
 SWA  H11O  O11  C7    107.98  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
 SWA  Var_01  C5  C6  C2  C1   53.93  30.0  1
 SWA  Var_02  C8  C9  N4  C3  -24.67  30.0  1
 SWA  Var_03  C2  C6  C5  N4  -54.26  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
 SWA  chir_01  C1  O1   C3  C2  negativ
 SWA  chir_02  C3  N4   C7  C1  negativ
 SWA  chir_03  C8  O13  C7  C9  negativ
 SWA  chir_04  C7  O11  C3  C8  negativ

