# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 15:24:51 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (1R,2R,3R,4S,5R)-4-(benzylamino)-5-(methylsulfanyl)cyclopentane-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@H]1[C@H](O)[C@H](O)[C@H](O)[C@@H]1NCc2ccccc2
#
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
 2SK  2SK  (1R,2R,3R,4S,5R)-4-(benzylamino)-5-(methylsulfanyl)cyclopentane-1,2,3-triol  ligand  37  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2SK
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
 2SK  C5   C  CH1   0  -0.053  -0.7728  -0.0181  -0.6596
 2SK  N5   N  NH1   0  -0.591   0.5623   0.2044  -0.1642
 2SK  C4   C  CH1   0  -0.007  -1.1799  -1.4861  -0.7737
 2SK  O4   O  OH1   0  -0.660  -0.8358  -2.1524   0.4118
 2SK  C3   C  CH1   0  -0.018  -2.6902  -1.3479  -0.9519
 2SK  O3   O  OH1   0  -0.670  -3.3440  -2.5719  -0.7292
 2SK  C2   C  CH1   0   0.076  -3.1205  -0.2413   0.0473
 2SK  O2   O  OH1   0  -0.677  -3.5997  -0.7783   1.2527
 2SK  C1   C  CH1   0  -0.421  -1.8297   0.5648   0.2889
 2SK  S6   S  S2    0  -0.024  -1.9623   2.3530   0.0373
 2SK  C7   C  CH3   0  -0.764  -2.8584   2.8229   1.5335
 2SK  C8   C  CH2   0  -0.332   1.6077  -0.1562  -1.1026
 2SK  C9   C  CR6   0   0.092   2.9643   0.0249  -0.4773
 2SK  C14  C  CR16  0  -0.285   3.2716  -0.6161   0.7224
 2SK  C13  C  CR16  0  -0.243   4.5203  -0.4630   1.3052
 2SK  C10  C  CR16  0  -0.320   3.9291   0.8299  -1.0721
 2SK  C11  C  CR16  0  -0.241   5.1824   0.9875  -0.4899
 2SK  C12  C  CR16  0  -0.270   5.4814   0.3404   0.6998
 2SK  H5   H  HCH1  0   0.224  -0.9246   0.4131  -1.6663
 2SK  HN5  H  HNH1  0   0.342   0.6595   1.1854   0.0729
 2SK  H4   H  HCH1  0   0.230  -0.7284  -1.9705  -1.6505
 2SK  HO4  H  HOH1  0   0.449  -1.2351  -3.0280   0.3883
 2SK  H3   H  HCH1  0   0.244  -2.8687  -0.9804  -1.9682
 2SK  HO3  H  HOH1  0   0.469  -4.1608  -2.5924  -1.2373
 2SK  H2   H  HCH1  0   0.212  -3.8876   0.3930  -0.4159
 2SK  HO2  H  HOH1  0   0.441  -3.8939  -1.6782   1.0609
 2SK  H1   H  HCH1  0   0.284  -1.5024   0.3932   1.3175
 2SK  H71  H  HCH3  0   0.274  -2.9726   3.9053   1.5225
 2SK  H72  H  HCH3  0   0.263  -3.8486   2.3712   1.5636
 2SK  H73  H  HCH3  0   0.263  -2.3025   2.5386   2.4260
 2SK  H81  H  HCH2  0   0.243   1.4804  -1.2084  -1.3729
 2SK  H82  H  HCH2  0   0.216   1.5585   0.4114  -2.0443
 2SK  H14  H  HCR6  0   0.247   2.5236  -1.2390   1.1979
 2SK  H13  H  HCR6  0   0.252   4.7471  -0.9690   2.2350
 2SK  H10  H  HCR6  0   0.248   3.6998   1.3399  -2.0006
 2SK  H11  H  HCR6  0   0.253   5.9208   1.6201  -0.9657
 2SK  H12  H  HCR6  0   0.253   6.4563   0.4599   1.1549

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
 2SK  C5   N5   single    1.441  0.020  1.441
 2SK  C5   C4   single    1.528  0.020  1.528
 2SK  C5   C1   single    1.535  0.020  1.535
 2SK  C5   H5   single    0.970  0.020  1.090
 2SK  N5   C8   single    1.450  0.020  1.450
 2SK  N5   HN5  single    0.890  0.020  1.040
 2SK  C4   O4   single    1.403  0.020  1.403
 2SK  C4   C3   single    1.527  0.020  1.527
 2SK  C4   H4   single    0.970  0.020  1.090
 2SK  O4   HO4  single    0.850  0.020  0.980
 2SK  C3   O3   single    1.405  0.020  1.405
 2SK  C3   C2   single    1.552  0.020  1.552
 2SK  C3   H3   single    0.970  0.020  1.090
 2SK  O3   HO3  single    0.850  0.020  0.980
 2SK  C2   O2   single    1.404  0.020  1.404
 2SK  C2   C1   single    1.541  0.020  1.541
 2SK  C2   H2   single    0.970  0.020  1.090
 2SK  O2   HO2  single    0.850  0.020  0.980
 2SK  C1   S6   single    1.811  0.020  1.811
 2SK  C1   H1   single    0.970  0.020  1.090
 2SK  S6   C7   single    1.806  0.020  1.806
 2SK  C7   H71  single    0.970  0.020  1.090
 2SK  C7   H72  single    0.970  0.020  1.090
 2SK  C7   H73  single    0.970  0.020  1.090
 2SK  C8   C9   single    1.505  0.020  1.505
 2SK  C8   H81  single    0.970  0.020  1.090
 2SK  C8   H82  single    0.970  0.020  1.090
 2SK  C9   C14  aromatic  1.394  0.020  1.394
 2SK  C9   C10  aromatic  1.390  0.020  1.390
 2SK  C14  C13  aromatic  1.386  0.020  1.386
 2SK  C14  H14  single    0.930  0.020  1.080
 2SK  C13  C12  aromatic  1.391  0.020  1.391
 2SK  C13  H13  single    0.930  0.020  1.080
 2SK  C10  C11  aromatic  1.391  0.020  1.391
 2SK  C10  H10  single    0.930  0.020  1.080
 2SK  C11  C12  aromatic  1.387  0.020  1.387
 2SK  C11  H11  single    0.930  0.020  1.080
 2SK  C12  H12  single    0.930  0.020  1.080

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
 2SK  H5   C5   C1   108.66  3.000
 2SK  H5   C5   C4   105.67  3.000
 2SK  C1   C5   C4   103.16  3.000
 2SK  H5   C5   N5   112.32  3.000
 2SK  C1   C5   N5   111.52  3.000
 2SK  C4   C5   N5   114.89  3.000
 2SK  HN5  N5   C8   108.83  3.000
 2SK  HN5  N5   C5   108.57  3.000
 2SK  C8   N5   C5   114.02  3.000
 2SK  H4   C4   C3   110.68  3.000
 2SK  H4   C4   O4   111.35  3.000
 2SK  C3   C4   O4   112.60  3.000
 2SK  H4   C4   C5   111.95  3.000
 2SK  C3   C4   C5   100.68  3.000
 2SK  O4   C4   C5   109.14  3.000
 2SK  HO4  O4   C4   108.04  3.000
 2SK  H3   C3   C2   108.24  3.000
 2SK  H3   C3   O3   111.31  3.000
 2SK  C2   C3   O3   112.96  3.000
 2SK  H3   C3   C4   107.45  3.000
 2SK  C2   C3   C4   105.29  3.000
 2SK  O3   C3   C4   111.27  3.000
 2SK  HO3  O3   C3   109.25  3.000
 2SK  H2   C2   C1   110.44  3.000
 2SK  H2   C2   O2   110.17  3.000
 2SK  C1   C2   O2   110.57  3.000
 2SK  H2   C2   C3   109.52  3.000
 2SK  C1   C2   C3   103.99  3.000
 2SK  O2   C2   C3   112.01  3.000
 2SK  HO2  O2   C2   106.84  3.000
 2SK  H1   C1   S6   107.92  3.000
 2SK  H1   C1   C2   108.43  3.000
 2SK  S6   C1   C2   115.69  3.000
 2SK  H1   C1   C5   108.40  3.000
 2SK  S6   C1   C5   109.85  3.000
 2SK  C2   C1   C5   106.33  3.000
 2SK  C7   S6   C1   100.26  3.000
 2SK  H73  C7   H72  109.47  3.000
 2SK  H73  C7   H71  108.75  3.000
 2SK  H72  C7   H71  108.51  3.000
 2SK  H73  C7   S6   110.96  3.000
 2SK  H72  C7   S6   111.48  3.000
 2SK  H71  C7   S6   107.60  3.000
 2SK  H82  C8   H81  106.23  3.000
 2SK  H82  C8   C9   109.50  3.000
 2SK  H81  C8   C9   108.87  3.000
 2SK  H82  C8   N5   113.15  3.000
 2SK  H81  C8   N5   108.36  3.000
 2SK  C9   C8   N5   110.55  3.000
 2SK  C10  C9   C14  118.77  3.000
 2SK  C10  C9   C8   121.17  3.000
 2SK  C14  C9   C8   120.06  3.000
 2SK  H14  C14  C13  120.05  3.000
 2SK  H14  C14  C9   119.33  3.000
 2SK  C13  C14  C9   120.62  3.000
 2SK  H13  C13  C12  119.93  3.000
 2SK  H13  C13  C14  119.88  3.000
 2SK  C12  C13  C14  120.20  3.000
 2SK  H10  C10  C11  119.73  3.000
 2SK  H10  C10  C9   119.49  3.000
 2SK  C11  C10  C9   120.79  3.000
 2SK  H11  C11  C12  120.17  3.000
 2SK  H11  C11  C10  119.79  3.000
 2SK  C12  C11  C10  120.03  3.000
 2SK  H12  C12  C11  120.22  3.000
 2SK  H12  C12  C13  120.19  3.000
 2SK  C11  C12  C13  119.59  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
 2SK  CONST_01  C12  C13  C14  C9      0.00   0.0  0
 2SK  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 2SK  CONST_03  C11  C10  C9   C14     0.00   0.0  0
 2SK  CONST_04  C11  C12  C13  C14     0.00   0.0  0
 2SK  CONST_05  C10  C9   C14  C13     0.00   0.0  0
 2SK  CONST_06  C10  C11  C12  C13     0.00   0.0  0
 2SK  CONST_07  C13  C14  C9   C8    180.00   0.0  0
 2SK  CONST_08  C11  C10  C9   C8    180.00   0.0  0
 2SK  CONST_09  H13  C13  C14  C9    180.00   0.0  0
 2SK  CONST_10  H11  C11  C10  C9    180.00   0.0  0
 2SK  CONST_11  H10  C10  C9   C14   180.00   0.0  0
 2SK  CONST_12  H12  C12  C13  C14   180.00   0.0  0
 2SK  CONST_13  H14  C14  C9   C10   180.00   0.0  0
 2SK  Var_01    C9   C8   N5   C5   -176.45  30.0  3
 2SK  Var_02    C14  C9   C8   N5     55.47  30.0  2
 2SK  Var_03    H71  C7   S6   C1    177.90  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
 2SK  chir_01  C5  N5  C4  C1  negativ
 2SK  chir_02  C4  O4  C3  C5  negativ
 2SK  chir_03  C3  O3  C2  C4  negativ
 2SK  chir_04  C2  O2  C3  C1  positiv
 2SK  chir_05  C1  S6  C5  C2  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
 2SK  plan-1  C8   0.020
 2SK  plan-1  C9   0.020
 2SK  plan-1  C14  0.020
 2SK  plan-1  C13  0.020
 2SK  plan-1  C10  0.020
 2SK  plan-1  C11  0.020
 2SK  plan-1  C12  0.020
 2SK  plan-1  H14  0.020
 2SK  plan-1  H13  0.020
 2SK  plan-1  H10  0.020
 2SK  plan-1  H11  0.020
 2SK  plan-1  H12  0.020

