# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 05:00:03 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2S,4R)-2-amino-4H-1,3-benzoxathiin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1Oc2ccccc2[C@H](O)S1
#
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
 STH  STH  (2S,4R)-2-amino-4H-1,3-benzoxathiin-4-ol  ligand  21  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_STH
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
 STH  C8    C  CH1   0  -0.195   0.4091  -1.5040  -0.1546
 STH  O8    O  OH1   0  -0.627   0.5756  -2.1199   1.0851
 STH  C1    C  CR6   0   0.023  -0.7677  -0.5688  -0.0723
 STH  C2    C  CR6   0   0.371  -0.6633   0.8186   0.0493
 STH  C3    C  CR16  0  -0.348  -1.8132   1.6086   0.0848
 STH  C4    C  CR16  0  -0.248  -3.0635   1.0253   0.0170
 STH  C5    C  CR16  0  -0.267  -3.1868  -0.3570  -0.0857
 STH  C6    C  CR16  0  -0.274  -2.0438  -1.1326  -0.1286
 STH  C7    C  CH1   0   0.066   1.6638   0.7607   0.4528
 STH  O2    O  O2    0  -0.458   0.5113   1.4877   0.1051
 STH  N7    N  NH2   0  -0.814   2.7627   1.6613   0.3541
 STH  S7    S  S2    0  -0.020   1.9040  -0.6162  -0.7133
 STH  H8    H  HCH1  0   0.282   0.2212  -2.2353  -0.9482
 STH  HO8   H  HOH1  0   0.463   1.2164  -2.8339   0.9884
 STH  H3    H  HCR6  0   0.268  -1.7104   2.6833   0.1673
 STH  H4    H  HCR6  0   0.263  -3.9449   1.6525   0.0474
 STH  H5    H  HCR6  0   0.257  -4.1627  -0.8205  -0.1382
 STH  H6    H  HCR6  0   0.263  -2.1309  -2.2086  -0.2233
 STH  H7    H  HCH1  0   0.252   1.5071   0.3190   1.4468
 STH  HN71  H  HNH2  0   0.372   2.7409   2.3122   1.1307
 STH  HN72  H  HNH2  0   0.370   3.6371   1.1574   0.4276

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
 STH  C8  O8    single    1.394  0.020  1.394
 STH  C8  C1    single    1.505  0.020  1.505
 STH  C8  S7    single    1.826  0.020  1.826
 STH  C8  H8    single    0.970  0.020  1.090
 STH  O8  HO8   single    0.850  0.020  0.980
 STH  C1  C2    aromatic  1.397  0.020  1.397
 STH  C1  C6    aromatic  1.396  0.020  1.396
 STH  C2  C3    aromatic  1.396  0.020  1.396
 STH  C2  O2    single    1.353  0.020  1.353
 STH  C3  C4    aromatic  1.381  0.020  1.381
 STH  C3  H3    single    0.930  0.020  1.080
 STH  C4  C5    aromatic  1.392  0.020  1.392
 STH  C4  H4    single    0.930  0.020  1.080
 STH  C5  C6    aromatic  1.382  0.020  1.382
 STH  C5  H5    single    0.930  0.020  1.080
 STH  C6  H6    single    0.930  0.020  1.080
 STH  C7  O2    single    1.406  0.020  1.406
 STH  C7  N7    single    1.424  0.020  1.424
 STH  C7  S7    single    1.820  0.020  1.820
 STH  C7  H7    single    0.970  0.020  1.090
 STH  N7  HN71  single    0.890  0.020  1.040
 STH  N7  HN72  single    0.890  0.020  1.040

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
 STH  H8    C8  S7    104.08  3.000
 STH  H8    C8  C1    108.68  3.000
 STH  S7    C8  C1    110.77  3.000
 STH  H8    C8  O8    111.70  3.000
 STH  S7    C8  O8    112.89  3.000
 STH  C1    C8  O8    108.61  3.000
 STH  HO8   O8  C8    108.50  3.000
 STH  C6    C1  C2    118.23  3.000
 STH  C6    C1  C8    117.48  3.000
 STH  C2    C1  C8    124.29  3.000
 STH  O2    C2  C3    115.74  3.000
 STH  O2    C2  C1    124.04  3.000
 STH  C3    C2  C1    120.19  3.000
 STH  H3    C3  C4    120.58  3.000
 STH  H3    C3  C2    119.05  3.000
 STH  C4    C3  C2    120.37  3.000
 STH  H4    C4  C5    120.37  3.000
 STH  H4    C4  C3    119.41  3.000
 STH  C5    C4  C3    120.22  3.000
 STH  H5    C5  C6    120.28  3.000
 STH  H5    C5  C4    120.61  3.000
 STH  C6    C5  C4    119.11  3.000
 STH  H6    C6  C5    119.57  3.000
 STH  H6    C6  C1    118.55  3.000
 STH  C5    C6  C1    121.87  3.000
 STH  H7    C7  S7    107.11  3.000
 STH  H7    C7  N7    115.26  3.000
 STH  S7    C7  N7    109.40  3.000
 STH  H7    C7  O2    108.33  3.000
 STH  S7    C7  O2    109.93  3.000
 STH  N7    C7  O2    106.76  3.000
 STH  C7    O2  C2    117.78  3.000
 STH  HN72  N7  HN71  106.42  3.000
 STH  HN72  N7  C7    110.29  3.000
 STH  HN71  N7  C7    109.66  3.000
 STH  C7    S7  C8     93.65  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
 STH  CONST_01  C4  C3  C2  C1    0.00  0.0  0
 STH  CONST_02  C4  C5  C6  C1    0.00  0.0  0
 STH  CONST_03  C5  C6  C1  C2    0.00  0.0  0
 STH  CONST_04  C5  C4  C3  C2    0.00  0.0  0
 STH  CONST_05  C6  C1  C2  C3    0.00  0.0  0
 STH  CONST_06  C6  C5  C4  C3    0.00  0.0  0
 STH  CONST_07  H6  C6  C1  C8    0.00  0.0  0
 STH  CONST_08  H3  C3  C2  C1  180.00  0.0  0
 STH  CONST_09  H5  C5  C6  C1  180.00  0.0  0
 STH  CONST_10  H4  C4  C3  C2  180.00  0.0  0

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
 STH  chir_01  C8  O8  C1  S7  negativ
 STH  chir_02  C7  S7  O2  N7  positiv

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
 STH  plan-1  C8  0.020
 STH  plan-1  C1  0.020
 STH  plan-1  C2  0.020
 STH  plan-1  C3  0.020
 STH  plan-1  C4  0.020
 STH  plan-1  C5  0.020
 STH  plan-1  C6  0.020
 STH  plan-1  O2  0.020
 STH  plan-1  H3  0.020
 STH  plan-1  H4  0.020
 STH  plan-1  H5  0.020
 STH  plan-1  H6  0.020

