# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 21:36:51 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-deoxy-2-(ethanethioylamino)-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=S)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](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
 SN5  SN5  2-deoxy-2-(ethanethioylamino)-beta-D-glucopyranose  D-saccharide  30  15  .  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_SN5
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
 SN5  C1    C  CH1   0   0.312   0.0929  -1.0907  -0.6132
 SN5  S7    S  S1    0  -0.389  -3.2759  -0.0520   1.5608
 SN5  C2    C  CH1   0  -0.160  -0.5611   0.1562  -0.0120
 SN5  C3    C  CH1   0   0.042   0.3585   1.3574  -0.1990
 SN5  C4    C  CH1   0  -0.001   1.7517   1.0464   0.3421
 SN5  C5    C  CH1   0  -0.023   2.2702  -0.2571  -0.2738
 SN5  C6    C  CH2   0  -0.160   3.6079  -0.6673   0.3010
 SN5  C7    C  C     0   0.216  -3.0255   0.3249  -0.0435
 SN5  C8    C  CH3   0  -0.728  -4.1925   0.6313  -0.9356
 SN5  N2    N  NH1   0  -0.551  -1.8415   0.4009  -0.6266
 SN5  O3    O  OH1   0  -0.659  -0.2247   2.4571   0.4441
 SN5  O4    O  OH1   0  -0.672   2.5721   2.1455   0.0155
 SN5  O5    O  O2    0  -0.494   1.3456  -1.2925  -0.0106
 SN5  O6    O  OH1   0  -0.669   4.0709  -1.8042  -0.3863
 SN5  O1    O  OH1   0  -0.646  -0.7056  -2.1784  -0.3516
 SN5  H81C  H  HCH3  0   0.274  -4.6715   1.5502  -0.5989
 SN5  H82C  H  HCH3  0   0.249  -3.9115   0.7519  -1.9818
 SN5  H83C  H  HCH3  0   0.270  -4.9300  -0.1649  -0.8612
 SN5  H2    H  HNH1  0   0.411  -1.8267   0.6491  -1.6068
 SN5  HA    H  HCH1  0   0.279  -0.7336  -0.0148   1.0539
 SN5  H1    H  HCH1  0   0.190   0.2337  -0.9412  -1.6988
 SN5  H3    H  HCH1  0   0.212   0.4643   1.5480  -1.2810
 SN5  HB    H  HOH1  0   0.466  -0.4777  -2.8934  -0.9556
 SN5  HC    H  HOH1  0   0.452   0.3487   3.2185   0.3039
 SN5  H4    H  HCH1  0   0.230   1.6788   0.9151   1.4310
 SN5  HD    H  HOH1  0   0.464   3.2246   2.2724   0.7095
 SN5  H5    H  HCH1  0   0.224   2.3810  -0.1121  -1.3614
 SN5  H61C  H  HCH2  0   0.205   4.3009   0.1754   0.1971
 SN5  H62C  H  HCH2  0   0.200   3.4918  -0.8588   1.3768
 SN5  H6    H  HOH1  0   0.457   4.9444  -2.0210  -0.0484

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
 SN5  S7  C7    double  1.667  0.020  1.667
 SN5  C7  C8    single  1.501  0.020  1.501
 SN5  C7  N2    single  1.322  0.020  1.322
 SN5  N2  C2    single  1.441  0.020  1.441
 SN5  C2  C1    single  1.531  0.020  1.531
 SN5  C2  C3    single  1.524  0.020  1.524
 SN5  C1  O1    single  1.374  0.020  1.374
 SN5  C1  O5    single  1.405  0.020  1.405
 SN5  C3  O3    single  1.401  0.020  1.401
 SN5  C3  C4    single  1.527  0.020  1.527
 SN5  C4  O4    single  1.410  0.020  1.410
 SN5  C4  C5    single  1.532  0.020  1.532
 SN5  C5  O5    single  1.413  0.020  1.413
 SN5  C5  C6    single  1.513  0.020  1.513
 SN5  C6  O6    single  1.407  0.020  1.407
 SN5  C8  H81C  single  0.970  0.020  1.090
 SN5  C8  H82C  single  0.970  0.020  1.090
 SN5  C8  H83C  single  0.970  0.020  1.090
 SN5  N2  H2    single  0.860  0.020  1.020
 SN5  C2  HA    single  0.970  0.020  1.090
 SN5  C1  H1    single  0.970  0.020  1.090
 SN5  C3  H3    single  0.970  0.020  1.090
 SN5  O1  HB    single  0.850  0.020  0.980
 SN5  O3  HC    single  0.850  0.020  0.980
 SN5  C4  H4    single  0.970  0.020  1.090
 SN5  O4  HD    single  0.850  0.020  0.980
 SN5  C5  H5    single  0.970  0.020  1.090
 SN5  C6  H61C  single  0.970  0.020  1.090
 SN5  C6  H62C  single  0.970  0.020  1.090
 SN5  O6  H6    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
 SN5  H1    C1  O1    111.60  3.000
 SN5  H1    C1  O5    109.11  3.000
 SN5  O1    C1  O5    108.83  3.000
 SN5  H1    C1  C2    109.27  3.000
 SN5  O5    C1  C2    109.24  3.000
 SN5  O1    C1  C2    108.76  3.000
 SN5  HA    C2  N2    107.59  3.000
 SN5  HA    C2  C3    109.76  3.000
 SN5  N2    C2  C3    110.48  3.000
 SN5  HA    C2  C1    108.84  3.000
 SN5  C3    C2  C1    109.63  3.000
 SN5  N2    C2  C1    110.51  3.000
 SN5  H3    C3  O3    110.74  3.000
 SN5  H3    C3  C4    107.16  3.000
 SN5  O3    C3  C4    112.15  3.000
 SN5  H3    C3  C2    108.31  3.000
 SN5  C4    C3  C2    110.28  3.000
 SN5  O3    C3  C2    108.13  3.000
 SN5  H4    C4  O4    111.17  3.000
 SN5  H4    C4  C5    108.60  3.000
 SN5  O4    C4  C5    111.92  3.000
 SN5  H4    C4  C3    108.36  3.000
 SN5  C5    C4  C3    109.86  3.000
 SN5  O4    C4  C3    106.87  3.000
 SN5  H5    C5  O5    110.23  3.000
 SN5  H5    C5  C6    108.75  3.000
 SN5  O5    C5  C6    108.01  3.000
 SN5  H5    C5  C4    108.58  3.000
 SN5  C6    C5  C4    112.17  3.000
 SN5  O5    C5  C4    109.10  3.000
 SN5  H62C  C6  H61C  107.08  3.000
 SN5  H62C  C6  O6    111.85  3.000
 SN5  H61C  C6  O6    111.53  3.000
 SN5  H62C  C6  C5    109.01  3.000
 SN5  H61C  C6  C5    108.34  3.000
 SN5  O6    C6  C5    108.94  3.000
 SN5  N2    C7  C8    115.00  3.000
 SN5  N2    C7  S7    124.90  3.000
 SN5  C8    C7  S7    120.10  3.000
 SN5  H83C  C8  H82C  108.75  3.000
 SN5  H83C  C8  H81C  107.34  3.000
 SN5  H82C  C8  H81C  108.46  3.000
 SN5  H83C  C8  C7    109.70  3.000
 SN5  H82C  C8  C7    113.13  3.000
 SN5  H81C  C8  C7    109.29  3.000
 SN5  H2    N2  C7    117.05  3.000
 SN5  H2    N2  C2    116.24  3.000
 SN5  C7    N2  C2    126.71  3.000
 SN5  HC    O3  C3    107.80  3.000
 SN5  HD    O4  C4    109.32  3.000
 SN5  C5    O5  C1    113.48  3.000
 SN5  H6    O6  C6    108.03  3.000
 SN5  HB    O1  C1    109.30  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
 SN5  Var_01  C2    N2  C7  S7   1.13  30.0  2
 SN5  Var_02  H81C  C8  C7  S7  65.51  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
 SN5  chir_01  C1  C2  O1  O5  positiv
 SN5  chir_02  C2  N2  C3  C1  positiv
 SN5  chir_03  C3  O3  C2  C4  positiv
 SN5  chir_04  C4  O4  C5  C3  positiv
 SN5  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
 SN5  plan-1  S7  0.020
 SN5  plan-1  C7  0.020
 SN5  plan-1  C8  0.020
 SN5  plan-1  N2  0.020

