# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:46:53 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-5-thio-alpha-D-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@@H](O)S[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
 BBK  BBK  2-(acetylamino)-2-deoxy-5-thio-alpha-D-galactopyranose  D-saccharide  30  15  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BBK
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
 BBK  C1   C  CH1   0  -0.112  22.9790  -28.1695  -18.4074
 BBK  O1   O  OH1   0  -0.641  22.4614  -28.7567  -17.2457
 BBK  C2   C  CH1   0  -0.083  22.7897  -26.6430  -18.4246
 BBK  N2   N  NH1   0  -0.644  23.4195  -26.0693  -17.2520
 BBK  C3   C  CH1   0   0.038  21.3138  -26.2416  -18.4439
 BBK  O3   O  OH1   0  -0.664  21.2625  -24.8386  -18.3504
 BBK  C4   C  CH1   0   0.025  20.5795  -26.7437  -19.6884
 BBK  O4   O  OH1   0  -0.661  21.1845  -26.1847  -20.8234
 BBK  C5   C  CH1   0  -0.443  20.5461  -28.2728  -19.7206
 BBK  S5   S  S2    0   0.014  22.2292  -28.9553  -19.8447
 BBK  C6   C  CH2   0  -0.142  19.7545  -28.8461  -20.8890
 BBK  O6   O  OH1   0  -0.662  18.4363  -28.3613  -20.8044
 BBK  C7   C  C     0   0.508  24.7475  -25.8356  -17.1642
 BBK  O7   O  O     0  -0.484  25.5335  -26.1722  -18.0358
 BBK  C8   C  CH3   0  -0.780  25.1756  -25.1392  -15.8953
 BBK  H1   H  HCH1  0   0.272  24.0501  -28.3771  -18.5202
 BBK  HO1  H  HOH1  0   0.451  22.8802  -28.3284  -16.4881
 BBK  H2   H  HCH1  0   0.265  23.2858  -26.2580  -19.3190
 BBK  HN2  H  HNH1  0   0.406  22.8265  -25.6946  -16.5277
 BBK  H3   H  HCH1  0   0.225  20.8198  -26.7042  -17.5768
 BBK  HO3  H  HOH1  0   0.453  20.3541  -24.5806  -18.1633
 BBK  H4   H  HCH1  0   0.245  19.5379  -26.4033  -19.5928
 BBK  HO4  H  HOH1  0   0.457  20.5664  -26.2177  -21.5592
 BBK  H5   H  HCH1  0   0.281  20.0945  -28.6325  -18.7916
 BBK  H6   H  HCH2  0   0.206  20.2332  -28.5645  -21.8361
 BBK  H6A  H  HCH2  0   0.223  19.7869  -29.9416  -20.8327
 BBK  HO6  H  HOH1  0   0.458  17.9566  -28.6544  -21.5846
 BBK  H8   H  HCH3  0   0.260  26.2467  -24.9569  -15.9068
 BBK  H8A  H  HCH3  0   0.262  24.6565  -24.1872  -15.7777
 BBK  H8B  H  HCH3  0   0.265  24.9340  -25.7495  -15.0240

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
 BBK  S5  C1   single  1.802  0.020  1.802
 BBK  C2  C1   single  1.538  0.020  1.538
 BBK  C1  O1   single  1.401  0.020  1.401
 BBK  C1  H1   single  0.970  0.020  1.090
 BBK  O1  HO1  single  0.850  0.020  0.980
 BBK  C2  C3   single  1.530  0.020  1.530
 BBK  C2  N2   single  1.449  0.020  1.449
 BBK  C2  H2   single  0.970  0.020  1.090
 BBK  N2  C7   single  1.351  0.020  1.351
 BBK  N2  HN2  single  0.860  0.020  1.020
 BBK  C4  C3   single  1.530  0.020  1.530
 BBK  C3  O3   single  1.407  0.020  1.407
 BBK  C3  H3   single  0.970  0.020  1.090
 BBK  O3  HO3  single  0.850  0.020  0.980
 BBK  O4  C4   single  1.402  0.020  1.402
 BBK  C4  C5   single  1.530  0.020  1.530
 BBK  C4  H4   single  0.970  0.020  1.090
 BBK  O4  HO4  single  0.850  0.020  0.980
 BBK  C6  C5   single  1.523  0.020  1.523
 BBK  C5  S5   single  1.820  0.020  1.820
 BBK  C5  H5   single  0.970  0.020  1.090
 BBK  C6  O6   single  1.407  0.020  1.407
 BBK  C6  H6   single  0.970  0.020  1.090
 BBK  C6  H6A  single  0.970  0.020  1.090
 BBK  O6  HO6  single  0.850  0.020  0.980
 BBK  O7  C7   double  1.221  0.020  1.221
 BBK  C7  C8   single  1.509  0.020  1.509
 BBK  C8  H8   single  0.970  0.020  1.090
 BBK  C8  H8A  single  0.970  0.020  1.090
 BBK  C8  H8B  single  0.970  0.020  1.090

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
 BBK  H1   C1  S5   104.00  3.000
 BBK  H1   C1  C2   107.87  3.000
 BBK  S5   C1  C2   111.88  3.000
 BBK  H1   C1  O1   111.52  3.000
 BBK  C2   C1  O1   112.32  3.000
 BBK  S5   C1  O1   108.97  3.000
 BBK  HO1  O1  C1   107.72  3.000
 BBK  H2   C2  C3   109.59  3.000
 BBK  H2   C2  N2   108.99  3.000
 BBK  C3   C2  N2   109.00  3.000
 BBK  H2   C2  C1   107.63  3.000
 BBK  N2   C2  C1   109.29  3.000
 BBK  C3   C2  C1   112.29  3.000
 BBK  HN2  N2  C7   117.84  3.000
 BBK  HN2  N2  C2   118.21  3.000
 BBK  C7   N2  C2   123.24  3.000
 BBK  H3   C3  C4   106.72  3.000
 BBK  H3   C3  O3   110.52  3.000
 BBK  C4   C3  O3   111.34  3.000
 BBK  H3   C3  C2   108.24  3.000
 BBK  O3   C3  C2   107.21  3.000
 BBK  C4   C3  C2   112.79  3.000
 BBK  HO3  O3  C3   108.33  3.000
 BBK  H4   C4  C5   106.89  3.000
 BBK  H4   C4  O4   110.82  3.000
 BBK  C5   C4  O4   113.00  3.000
 BBK  H4   C4  C3   106.40  3.000
 BBK  C5   C4  C3   110.84  3.000
 BBK  O4   C4  C3   108.69  3.000
 BBK  HO4  O4  C4   109.17  3.000
 BBK  H5   C5  C6   108.25  3.000
 BBK  H5   C5  S5   108.44  3.000
 BBK  C6   C5  S5   106.68  3.000
 BBK  H5   C5  C4   108.66  3.000
 BBK  S5   C5  C4   110.85  3.000
 BBK  C6   C5  C4   113.81  3.000
 BBK  C5   S5  C1    99.61  3.000
 BBK  H6A  C6  H6   106.70  3.000
 BBK  H6A  C6  O6   111.63  3.000
 BBK  H6   C6  O6   111.84  3.000
 BBK  H6A  C6  C5   108.72  3.000
 BBK  H6   C6  C5   109.79  3.000
 BBK  O6   C6  C5   108.12  3.000
 BBK  HO6  O6  C6   108.27  3.000
 BBK  C8   C7  O7   123.01  3.000
 BBK  C8   C7  N2   114.40  3.000
 BBK  O7   C7  N2   122.59  3.000
 BBK  H8B  C8  H8A  107.26  3.000
 BBK  H8B  C8  H8   108.70  3.000
 BBK  H8A  C8  H8   108.89  3.000
 BBK  H8B  C8  C7   110.52  3.000
 BBK  H8A  C8  C7   111.00  3.000
 BBK  H8   C8  C7   110.37  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
 BBK  CONST_01  O7   C7  N2  C2     0.00   0.0  0
 BBK  CONST_02  C8   C7  N2  C2   180.00   0.0  0
 BBK  CONST_03  HN2  N2  C7  O7   180.00   0.0  0
 BBK  Var_01    H8   C8  C7  N2  -178.25  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
 BBK  chir_01  C1  S5  C2  O1  negativ
 BBK  chir_02  C2  N2  C3  C1  positiv
 BBK  chir_03  C3  O3  C2  C4  positiv
 BBK  chir_04  C4  O4  C5  C3  negativ
 BBK  chir_05  C5  S5  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
 BBK  plan-1  C2   0.020
 BBK  plan-1  N2   0.020
 BBK  plan-1  C7   0.020
 BBK  plan-1  O7   0.020
 BBK  plan-1  C8   0.020
 BBK  plan-1  HN2  0.020

