# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 00:32:08 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: methyl 2-(acetylamino)-2-deoxy-1-seleno-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Se][C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1NC(C)=O
#
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
 SNG  SNG  'methyl 2-(acetylamino)-2-deoxy-1-seleno-beta-D-glucopyranoside'  D-saccharide  33  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SNG
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
 SNG  C1    C   CH1   0  -0.115  37.4631  46.8521  13.8449
 SNG  C2    C   CH1   0  -0.140  36.1148  46.3327  14.3579
 SNG  C3    C   CH1   0   0.031  36.0908  44.8008  14.2882
 SNG  C4    C   CH1   0   0.021  36.4679  44.3340  12.8908
 SNG  C5    C   CH1   0   0.009  37.8275  44.9242  12.5248
 SNG  C6    C   CH2   0  -0.205  38.3130  44.5337  11.1383
 SNG  C7    C   C     0   0.501  34.8765  47.5441  16.1806
 SNG  C8    C   CH3   0  -0.812  33.8147  47.9762  15.2019
 SNG  N2    N   NH1   0  -0.614  35.8763  46.7638  15.7101
 SNG  O3    O   OH1   0  -0.664  34.8136  44.2975  14.5881
 SNG  O4    O   OH1   0  -0.672  36.5704  42.9354  12.8128
 SNG  O5    O   O2    0  -0.473  37.7552  46.3384  12.5800
 SNG  O6    O   OH1   0  -0.664  37.4139  44.8588  10.1070
 SNG  O7    O   O     0  -0.492  34.8407  47.8722  17.3574
 SNG  SE    SE  SE    0   0.071  37.5317  48.8037  13.7170
 SNG  H1    H   HCH1  0   0.262  38.2463  46.5867  14.5756
 SNG  H2    H   HCH1  0   0.279  35.3159  46.7055  13.7142
 SNG  H3    H   HCH1  0   0.220  36.8429  44.4088  14.9914
 SNG  H4    H   HCH1  0   0.216  35.7148  44.7198  12.1854
 SNG  H5    H   HCH1  0   0.224  38.5774  44.5583  13.2448
 SNG  H6C1  H   HCH2  0   0.238  39.2424  45.0727  10.9388
 SNG  H6C2  H   HCH2  0   0.222  38.5652  43.4688  11.1466
 SNG  H8C1  H   HCH3  0   0.263  33.3740  47.1279  14.6786
 SNG  H8C2  H   HCH3  0   0.274  33.0287  48.5044  15.7345
 SNG  H8C3  H   HCH3  0   0.266  34.2273  48.6503  14.4498
 SNG  HMC1  H   HCH3  0   0.274  36.7293  48.4996  11.3146
 SNG  HMC2  H   HCH3  0   0.258  35.3341  48.6207  12.4097
 SNG  HMC3  H   HCH3  0   0.277  36.2499  50.0699  11.9840
 SNG  HA    H   HNH1  0   0.392  36.5728  46.5011  16.3956
 SNG  HB    H   HOH1  0   0.459  34.6641  44.3777  15.5356
 SNG  HC    H   HOH1  0   0.455  35.7277  42.5554  13.0827
 SNG  H6    H   HOH1  0   0.454  36.7352  44.1795  10.0650
 SNG  CM    C   CH3   0  -0.813  36.3302  49.0035  12.1914

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
 SNG  C1  C2    single  1.533  0.020  1.533
 SNG  C1  O5    single  1.396  0.020  1.396
 SNG  C1  SE    single  1.957  0.020  1.957
 SNG  C1  H1    single  0.970  0.020  1.090
 SNG  C2  C3    single  1.534  0.020  1.534
 SNG  C2  N2    single  1.439  0.020  1.439
 SNG  C2  H2    single  0.970  0.020  1.090
 SNG  C3  C4    single  1.521  0.020  1.521
 SNG  C3  O3    single  1.405  0.020  1.405
 SNG  C3  H3    single  0.970  0.020  1.090
 SNG  C4  C5    single  1.527  0.020  1.527
 SNG  C4  O4    single  1.404  0.020  1.404
 SNG  C4  H4    single  0.970  0.020  1.090
 SNG  C5  C6    single  1.520  0.020  1.520
 SNG  C5  O5    single  1.417  0.020  1.417
 SNG  C5  H5    single  0.970  0.020  1.090
 SNG  C6  O6    single  1.406  0.020  1.406
 SNG  C6  H6C1  single  0.970  0.020  1.090
 SNG  C6  H6C2  single  0.970  0.020  1.090
 SNG  C7  C8    single  1.507  0.020  1.507
 SNG  C7  N2    single  1.353  0.020  1.353
 SNG  C7  O7    double  1.222  0.020  1.222
 SNG  C8  H8C1  single  0.970  0.020  1.090
 SNG  C8  H8C2  single  0.970  0.020  1.090
 SNG  C8  H8C3  single  0.970  0.020  1.090
 SNG  CM  SE    single  1.952  0.020  1.952
 SNG  CM  HMC1  single  0.970  0.020  1.090
 SNG  CM  HMC2  single  0.970  0.020  1.090
 SNG  CM  HMC3  single  0.970  0.020  1.090
 SNG  N2  HA    single  0.860  0.020  1.020
 SNG  O3  HB    single  0.850  0.020  0.980
 SNG  O4  HC    single  0.850  0.020  0.980
 SNG  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
 SNG  H1    C1  SE    104.97  3.000
 SNG  H1    C1  O5    111.28  3.000
 SNG  SE    C1  O5    107.48  3.000
 SNG  H1    C1  C2    108.73  3.000
 SNG  SE    C1  C2    112.99  3.000
 SNG  O5    C1  C2    111.25  3.000
 SNG  H2    C2  N2    109.30  3.000
 SNG  H2    C2  C3    107.63  3.000
 SNG  N2    C2  C3    109.83  3.000
 SNG  H2    C2  C1    109.31  3.000
 SNG  N2    C2  C1    111.01  3.000
 SNG  C3    C2  C1    109.69  3.000
 SNG  H3    C3  O3    110.90  3.000
 SNG  H3    C3  C4    107.94  3.000
 SNG  O3    C3  C4    108.16  3.000
 SNG  H3    C3  C2    108.40  3.000
 SNG  O3    C3  C2    111.24  3.000
 SNG  C4    C3  C2    110.15  3.000
 SNG  H4    C4  O4    111.29  3.000
 SNG  H4    C4  C5    108.65  3.000
 SNG  O4    C4  C5    107.85  3.000
 SNG  H4    C4  C3    108.14  3.000
 SNG  O4    C4  C3    112.01  3.000
 SNG  C5    C4  C3    108.81  3.000
 SNG  H5    C5  O5    109.91  3.000
 SNG  H5    C5  C6    107.06  3.000
 SNG  O5    C5  C6    107.95  3.000
 SNG  H5    C5  C4    108.72  3.000
 SNG  O5    C5  C4    109.33  3.000
 SNG  C6    C5  C4    113.82  3.000
 SNG  H6C2  C6  H6C1  106.58  3.000
 SNG  H6C2  C6  O6    112.20  3.000
 SNG  H6C1  C6  O6    107.21  3.000
 SNG  H6C2  C6  C5    108.46  3.000
 SNG  H6C1  C6  C5    108.15  3.000
 SNG  O6    C6  C5    113.91  3.000
 SNG  O7    C7  N2    120.75  3.000
 SNG  O7    C7  C8    121.84  3.000
 SNG  N2    C7  C8    117.40  3.000
 SNG  H8C3  C8  H8C2  108.13  3.000
 SNG  H8C3  C8  H8C1  107.64  3.000
 SNG  H8C2  C8  H8C1  108.74  3.000
 SNG  H8C3  C8  C7    111.00  3.000
 SNG  H8C2  C8  C7    109.31  3.000
 SNG  H8C1  C8  C7    111.93  3.000
 SNG  HA    N2  C7    115.02  3.000
 SNG  HA    N2  C2    116.40  3.000
 SNG  C7    N2  C2    128.47  3.000
 SNG  HB    O3  C3    108.75  3.000
 SNG  HC    O4  C4    108.27  3.000
 SNG  C5    O5  C1    114.41  3.000
 SNG  H6    O6  C6    108.67  3.000
 SNG  CM    SE  C1     97.56  3.000
 SNG  HMC3  CM  HMC2  108.34  3.000
 SNG  HMC3  CM  HMC1  109.10  3.000
 SNG  HMC2  CM  HMC1  109.54  3.000
 SNG  HMC3  CM  SE    107.12  3.000
 SNG  HMC2  CM  SE    111.73  3.000
 SNG  HMC1  CM  SE    110.91  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
 SNG  CONST_01  C8    C7  N2  C2    0.00   0.0  0
 SNG  CONST_02  O7    C7  N2  C2  180.00   0.0  0
 SNG  CONST_03  HA    N2  C7  C8  180.00   0.0  0
 SNG  Var_01    HMC1  CM  SE  C1  -61.38  30.0  3
 SNG  Var_02    H8C1  C8  C7  N2   53.58  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
 SNG  chir_01  C1  C2  O5  SE  negativ
 SNG  chir_02  C2  N2  C3  C1  positiv
 SNG  chir_03  C3  O3  C2  C4  positiv
 SNG  chir_04  C4  O4  C5  C3  positiv
 SNG  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
 SNG  plan-1  C2  0.020
 SNG  plan-1  C7  0.020
 SNG  plan-1  C8  0.020
 SNG  plan-1  N2  0.020
 SNG  plan-1  O7  0.020
 SNG  plan-1  HA  0.020

