# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 22:01:24 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (1R,2R,3S,4S,5r)-5-(benzylamino)cyclopentane-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O)[C@@H](NCc2ccccc2)[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
 SK3  SK3  (1R,2R,3S,4S,5r)-5-(benzylamino)cyclopentane-1,2,3,4-tetrol  ligand  34  17  .  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_SK3
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
 SK3  C5   C  CH1   0  -0.137   1.0471   0.5511   0.6629
 SK3  N5   N  NH1   0  -0.553  -0.2986   0.5583   0.1470
 SK3  C4   C  CH1   0   0.019   1.6012  -0.8487   0.9500
 SK3  O4   O  OH1   0  -0.674   1.3937  -1.7495  -0.1106
 SK3  C3   C  CH1   0  -0.041   3.0893  -0.5394   1.1671
 SK3  O3   O  OH1   0  -0.681   3.9370  -1.6425   1.0907
 SK3  C2   C  CH1   0   0.009   3.4284   0.6172   0.1796
 SK3  O2   O  OH1   0  -0.661   4.2003   0.1677  -0.9121
 SK3  C1   C  CH1   0  -0.043   2.0553   1.1358  -0.3305
 SK3  O1   O  OH1   0  -0.691   1.7920   0.6321  -1.6245
 SK3  C6   C  CH2   0  -0.360  -1.3035   0.1913   1.1200
 SK3  C7   C  CR6   0   0.111  -2.6675   0.0767   0.4932
 SK3  C12  C  CR16  0  -0.313  -2.8199  -0.3765  -0.8133
 SK3  C11  C  CR16  0  -0.171  -4.0852  -0.5246  -1.3672
 SK3  C8   C  CR16  0  -0.352  -3.8078   0.3956   1.2274
 SK3  C9   C  CR16  0  -0.165  -5.0745   0.2440   0.6785
 SK3  C10  C  CR16  0  -0.333  -5.2176  -0.2186  -0.6232
 SK3  H5   H  HCH1  0   0.284   1.1496   1.1333   1.5959
 SK3  HN5  H  HNH1  0   0.351  -0.5174   1.4753  -0.2237
 SK3  H4   H  HCH1  0   0.236   1.1730  -1.2952   1.8534
 SK3  HO4  H  HOH1  0   0.432   1.2561  -1.2266  -0.9122
 SK3  H3   H  HCH1  0   0.259   3.1945  -0.1465   2.1831
 SK3  HO3  H  HOH1  0   0.425   3.8349  -2.0405   0.2200
 SK3  H2   H  HCH1  0   0.268   3.9489   1.4141   0.7139
 SK3  HO2  H  HOH1  0   0.445   4.9894   0.7073  -0.9915
 SK3  H1   H  HCH1  0   0.246   2.0174   2.2328  -0.3380
 SK3  HO1  H  HOH1  0   0.439   2.6605   0.4554  -2.0165
 SK3  H61  H  HCH2  0   0.234  -1.0351  -0.7825   1.5405
 SK3  H62  H  HCH2  0   0.217  -1.3507   0.8830   1.9752
 SK3  H12  H  HCR6  0   0.230  -1.9414  -0.6018  -1.4043
 SK3  H11  H  HCR6  0   0.260  -4.1850  -0.8753  -2.3869
 SK3  H8   H  HCR6  0   0.220  -3.7040   0.7629   2.2422
 SK3  H9   H  HCR6  0   0.260  -5.9496   0.4921   1.2658
 SK3  H10  H  HCR6  0   0.229  -6.2032  -0.3318  -1.0557

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
 SK3  C5   N5   single    1.441  0.020  1.441
 SK3  C5   C4   single    1.533  0.020  1.533
 SK3  C5   C1   single    1.531  0.020  1.531
 SK3  C5   H5   single    0.970  0.020  1.090
 SK3  N5   C6   single    1.446  0.020  1.446
 SK3  N5   HN5  single    0.890  0.020  1.040
 SK3  C4   O4   single    1.407  0.020  1.407
 SK3  C4   C3   single    1.535  0.020  1.535
 SK3  C4   H4   single    0.970  0.020  1.090
 SK3  O4   HO4  single    0.850  0.020  0.980
 SK3  C3   O3   single    1.393  0.020  1.393
 SK3  C3   C2   single    1.558  0.020  1.558
 SK3  C3   H3   single    0.970  0.020  1.090
 SK3  O3   HO3  single    0.850  0.020  0.980
 SK3  C2   O2   single    1.411  0.020  1.411
 SK3  C2   C1   single    1.554  0.020  1.554
 SK3  C2   H2   single    0.970  0.020  1.090
 SK3  O2   HO2  single    0.850  0.020  0.980
 SK3  C1   O1   single    1.413  0.020  1.413
 SK3  C1   H1   single    0.970  0.020  1.090
 SK3  O1   HO1  single    0.850  0.020  0.980
 SK3  C6   C7   single    1.506  0.020  1.506
 SK3  C6   H61  single    0.970  0.020  1.090
 SK3  C6   H62  single    0.970  0.020  1.090
 SK3  C7   C12  aromatic  1.391  0.020  1.391
 SK3  C7   C8   aromatic  1.393  0.020  1.393
 SK3  C12  C11  aromatic  1.389  0.020  1.389
 SK3  C12  H12  single    0.930  0.020  1.080
 SK3  C11  C10  aromatic  1.389  0.020  1.389
 SK3  C11  H11  single    0.930  0.020  1.080
 SK3  C8   C9   aromatic  1.389  0.020  1.389
 SK3  C8   H8   single    0.930  0.020  1.080
 SK3  C9   C10  aromatic  1.389  0.020  1.389
 SK3  C9   H9   single    0.930  0.020  1.080
 SK3  C10  H10  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
 SK3  H5   C5   C1   106.60  3.000
 SK3  H5   C5   C4   106.84  3.000
 SK3  C1   C5   C4   103.43  3.000
 SK3  H5   C5   N5   112.73  3.000
 SK3  C1   C5   N5   112.37  3.000
 SK3  C4   C5   N5   114.15  3.000
 SK3  HN5  N5   C6   109.02  3.000
 SK3  HN5  N5   C5   109.70  3.000
 SK3  C6   N5   C5   114.00  3.000
 SK3  H4   C4   C3   110.15  3.000
 SK3  H4   C4   O4   107.65  3.000
 SK3  C3   C4   O4   112.24  3.000
 SK3  H4   C4   C5   112.69  3.000
 SK3  C3   C4   C5   101.12  3.000
 SK3  O4   C4   C5   112.97  3.000
 SK3  HO4  O4   C4   107.44  3.000
 SK3  H3   C3   C2   107.52  3.000
 SK3  H3   C3   O3   106.06  3.000
 SK3  C2   C3   O3   114.87  3.000
 SK3  H3   C3   C4   107.27  3.000
 SK3  C2   C3   C4   105.72  3.000
 SK3  O3   C3   C4   114.99  3.000
 SK3  HO3  O3   C3   108.20  3.000
 SK3  H2   C2   C1   109.78  3.000
 SK3  H2   C2   O2   110.53  3.000
 SK3  C1   C2   O2   109.63  3.000
 SK3  H2   C2   C3   109.60  3.000
 SK3  C1   C2   C3   105.27  3.000
 SK3  O2   C2   C3   111.90  3.000
 SK3  HO2  O2   C2   109.57  3.000
 SK3  H1   C1   O1   110.09  3.000
 SK3  H1   C1   C2   111.49  3.000
 SK3  O1   C1   C2   110.26  3.000
 SK3  H1   C1   C5   111.30  3.000
 SK3  O1   C1   C5   109.58  3.000
 SK3  C2   C1   C5   103.97  3.000
 SK3  HO1  O1   C1   105.57  3.000
 SK3  H62  C6   H61  105.73  3.000
 SK3  H62  C6   C7   109.42  3.000
 SK3  H61  C6   C7   108.33  3.000
 SK3  H62  C6   N5   113.14  3.000
 SK3  H61  C6   N5   108.30  3.000
 SK3  C7   C6   N5   111.64  3.000
 SK3  C8   C7   C12  118.68  3.000
 SK3  C8   C7   C6   120.31  3.000
 SK3  C12  C7   C6   121.00  3.000
 SK3  H12  C12  C11  119.96  3.000
 SK3  H12  C12  C7   119.45  3.000
 SK3  C11  C12  C7   120.59  3.000
 SK3  H11  C11  C10  120.04  3.000
 SK3  H11  C11  C12  119.60  3.000
 SK3  C10  C11  C12  120.36  3.000
 SK3  H8   C8   C9   119.62  3.000
 SK3  H8   C8   C7   119.50  3.000
 SK3  C9   C8   C7   120.88  3.000
 SK3  H9   C9   C10  120.10  3.000
 SK3  H9   C9   C8   119.85  3.000
 SK3  C10  C9   C8   120.05  3.000
 SK3  H10  C10  C9   120.21  3.000
 SK3  H10  C10  C11  120.35  3.000
 SK3  C9   C10  C11  119.43  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
 SK3  CONST_01  C10  C11  C12  C7      0.00   0.0  0
 SK3  CONST_02  C10  C9   C8   C7      0.00   0.0  0
 SK3  CONST_03  C9   C8   C7   C12     0.00   0.0  0
 SK3  CONST_04  C9   C10  C11  C12     0.00   0.0  0
 SK3  CONST_05  C8   C7   C12  C11     0.00   0.0  0
 SK3  CONST_06  C8   C9   C10  C11     0.00   0.0  0
 SK3  CONST_07  C11  C12  C7   C6    180.00   0.0  0
 SK3  CONST_08  C9   C8   C7   C6    180.00   0.0  0
 SK3  CONST_09  H11  C11  C12  C7    180.00   0.0  0
 SK3  CONST_10  H9   C9   C8   C7    180.00   0.0  0
 SK3  CONST_11  H8   C8   C7   C12   180.00   0.0  0
 SK3  CONST_12  H10  C10  C11  C12   180.00   0.0  0
 SK3  CONST_13  H12  C12  C7   C8    180.00   0.0  0
 SK3  Var_01    C7   C6   N5   C5   -174.08  30.0  3
 SK3  Var_02    C12  C7   C6   N5     33.69  30.0  2

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
 SK3  chir_01  C5  N5  C4  C1  negativ
 SK3  chir_02  C4  O4  C5  C3  positiv
 SK3  chir_03  C3  O3  C4  C2  positiv
 SK3  chir_04  C2  O2  C3  C1  positiv
 SK3  chir_05  C1  O1  C2  C5  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
 SK3  plan-1  C6   0.020
 SK3  plan-1  C7   0.020
 SK3  plan-1  C12  0.020
 SK3  plan-1  C11  0.020
 SK3  plan-1  C8   0.020
 SK3  plan-1  C9   0.020
 SK3  plan-1  C10  0.020
 SK3  plan-1  H12  0.020
 SK3  plan-1  H11  0.020
 SK3  plan-1  H8   0.020
 SK3  plan-1  H9   0.020
 SK3  plan-1  H10  0.020

