# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 10:14:06 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-(benzoylamino)-2-deoxy-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)[C@H](NC(=O)c2ccccc2)[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
 BG8  BG8  2-(benzoylamino)-2-deoxy-beta-D-glucopyranose  D-saccharide  37  20  .  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_BG8
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
 BG8  C01  C  CH1   0   0.033  -1.3734  -1.2749   0.3745
 BG8  C02  C  CH1   0  -0.153  -0.6081   0.0428   0.3903
 BG8  C03  C  CH1   0   0.310  -1.2506   1.0258  -0.5932
 BG8  O04  O  O2    0  -0.493  -2.6111   1.1896  -0.2806
 BG8  C05  C  CH1   0  -0.022  -3.3660   0.0060  -0.4356
 BG8  C06  C  CH1   0  -0.002  -2.8678  -1.0367   0.5704
 BG8  N07  N  NH1   0  -0.656   0.7766  -0.1748   0.0587
 BG8  O08  O  OH1   0  -0.672  -3.5052  -2.2834   0.4011
 BG8  O09  O  OH1   0  -0.662  -0.8394  -2.1011   1.3736
 BG8  C10  C  CH2   0  -0.158  -4.8232   0.3512  -0.2230
 BG8  O11  O  OH1   0  -0.646  -0.6210   2.2424  -0.4695
 BG8  O12  O  OH1   0  -0.667  -5.2313   1.2476  -1.2272
 BG8  C13  C  C     0   0.546   1.8072   0.3731   0.7273
 BG8  O15  O  O     0  -0.485   1.6743   1.0270   1.7517
 BG8  C14  C  CR16  0  -0.270   4.2600   0.1295   1.0087
 BG8  C16  C  CR6   0  -0.042   3.1628   0.1145   0.1498
 BG8  C17  C  CR16  0  -0.293   3.3685  -0.0977  -1.2122
 BG8  C18  C  CR16  0  -0.241   4.6487  -0.3090  -1.7041
 BG8  C19  C  CR16  0  -0.251   5.7345  -0.3134  -0.8395
 BG8  C20  C  CR16  0  -0.242   5.5372  -0.0930   0.5180
 BG8  H1   H  HCH1  0   0.210  -1.2446  -1.7325  -0.6224
 BG8  H2   H  HCH1  0   0.274  -0.6581   0.4775   1.3919
 BG8  H3   H  HCH1  0   0.184  -1.1609   0.6231  -1.6182
 BG8  H4   H  HCH1  0   0.221  -3.2398  -0.3966  -1.4547
 BG8  H5   H  HCH1  0   0.227  -3.0289  -0.6471   1.5859
 BG8  H6   H  HNH1  0   0.404   0.9713  -0.7776  -0.7254
 BG8  H7   H  HOH1  0   0.464  -4.2905  -2.3155   0.9543
 BG8  H8   H  HOH1  0   0.452  -1.3209  -2.9353   1.3557
 BG8  H9   H  HCH2  0   0.203  -5.4065  -0.5764  -0.2522
 BG8  H10  H  HCH2  0   0.200  -4.9452   0.7776   0.7826
 BG8  H11  H  HOH1  0   0.465  -0.7894   2.7720  -1.2559
 BG8  H12  H  HOH1  0   0.456  -6.1573   1.4589  -1.0792
 BG8  H14  H  HCR6  0   0.257   2.5403  -0.0747  -1.9095
 BG8  H15  H  HCR6  0   0.265   4.7967  -0.4628  -2.7647
 BG8  H16  H  HCR6  0   0.264   6.7324  -0.4830  -1.2223
 BG8  H17  H  HCR6  0   0.263   6.3803  -0.0907   1.1960
 BG8  H13  H  HCR6  0   0.262   4.1134   0.3051   2.0661

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
 BG8  O12  C10  single    1.407  0.020  1.407
 BG8  C10  C05  single    1.513  0.020  1.513
 BG8  O04  C05  single    1.412  0.020  1.412
 BG8  O04  C03  single    1.406  0.020  1.406
 BG8  C05  C06  single    1.532  0.020  1.532
 BG8  C06  O08  single    1.410  0.020  1.410
 BG8  C06  C01  single    1.526  0.020  1.526
 BG8  O15  C13  double    1.223  0.020  1.223
 BG8  O11  C03  single    1.375  0.020  1.375
 BG8  C03  C02  single    1.532  0.020  1.532
 BG8  C02  C01  single    1.524  0.020  1.524
 BG8  C02  N07  single    1.440  0.020  1.440
 BG8  O09  C01  single    1.402  0.020  1.402
 BG8  C13  N07  single    1.345  0.020  1.345
 BG8  C13  C16  single    1.496  0.020  1.496
 BG8  C17  C16  aromatic  1.394  0.020  1.394
 BG8  C17  C18  aromatic  1.388  0.020  1.388
 BG8  C16  C14  aromatic  1.393  0.020  1.393
 BG8  C18  C19  aromatic  1.388  0.020  1.388
 BG8  C14  C20  aromatic  1.386  0.020  1.386
 BG8  C19  C20  aromatic  1.389  0.020  1.389
 BG8  C01  H1   single    0.970  0.020  1.090
 BG8  C02  H2   single    0.970  0.020  1.090
 BG8  C03  H3   single    0.970  0.020  1.090
 BG8  C05  H4   single    0.970  0.020  1.090
 BG8  C06  H5   single    0.970  0.020  1.090
 BG8  N07  H6   single    0.860  0.020  1.020
 BG8  O08  H7   single    0.850  0.020  0.980
 BG8  O09  H8   single    0.850  0.020  0.980
 BG8  C10  H9   single    0.970  0.020  1.090
 BG8  C10  H10  single    0.970  0.020  1.090
 BG8  O11  H11  single    0.850  0.020  0.980
 BG8  O12  H12  single    0.850  0.020  0.980
 BG8  C14  H13  single    0.930  0.020  1.080
 BG8  C17  H14  single    0.930  0.020  1.080
 BG8  C18  H15  single    0.930  0.020  1.080
 BG8  C19  H16  single    0.930  0.020  1.080
 BG8  C20  H17  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
 BG8  H1   C01  O09  110.78  3.000
 BG8  H1   C01  C06  107.14  3.000
 BG8  O09  C01  C06  111.93  3.000
 BG8  H1   C01  C02  108.00  3.000
 BG8  O09  C01  C02  108.11  3.000
 BG8  C06  C01  C02  110.83  3.000
 BG8  H2   C02  N07  108.36  3.000
 BG8  H2   C02  C03  108.30  3.000
 BG8  N07  C02  C03  110.63  3.000
 BG8  H2   C02  C01  109.29  3.000
 BG8  N07  C02  C01  110.47  3.000
 BG8  C03  C02  C01  109.73  3.000
 BG8  H3   C03  O11  111.63  3.000
 BG8  H3   C03  O04  109.11  3.000
 BG8  O11  C03  O04  108.66  3.000
 BG8  H3   C03  C02  109.13  3.000
 BG8  O11  C03  C02  108.53  3.000
 BG8  O04  C03  C02  109.75  3.000
 BG8  C05  O04  C03  113.28  3.000
 BG8  H4   C05  C10  108.87  3.000
 BG8  H4   C05  C06  108.73  3.000
 BG8  C10  C05  C06  112.10  3.000
 BG8  H4   C05  O04  110.25  3.000
 BG8  C06  C05  O04  108.94  3.000
 BG8  C10  C05  O04  107.95  3.000
 BG8  H5   C06  O08  110.98  3.000
 BG8  H5   C06  C05  108.52  3.000
 BG8  O08  C06  C05  112.07  3.000
 BG8  H5   C06  C01  108.50  3.000
 BG8  O08  C06  C01  106.81  3.000
 BG8  C05  C06  C01  109.90  3.000
 BG8  H6   N07  C13  118.83  3.000
 BG8  H6   N07  C02  117.07  3.000
 BG8  C13  N07  C02  124.10  3.000
 BG8  H7   O08  C06  109.24  3.000
 BG8  H8   O09  C01  107.86  3.000
 BG8  H10  C10  H9   107.08  3.000
 BG8  H10  C10  O12  111.95  3.000
 BG8  H9   C10  O12  111.46  3.000
 BG8  H10  C10  C05  108.91  3.000
 BG8  H9   C10  C05  108.41  3.000
 BG8  O12  C10  C05  108.94  3.000
 BG8  H11  O11  C03  109.45  3.000
 BG8  H12  O12  C10  108.04  3.000
 BG8  C16  C13  O15  120.96  3.000
 BG8  C16  C13  N07  115.60  3.000
 BG8  O15  C13  N07  123.44  3.000
 BG8  H13  C14  C20  119.80  3.000
 BG8  H13  C14  C16  119.83  3.000
 BG8  C20  C14  C16  120.37  3.000
 BG8  C17  C16  C14  119.19  3.000
 BG8  C14  C16  C13  118.28  3.000
 BG8  C17  C16  C13  122.50  3.000
 BG8  H14  C17  C18  118.73  3.000
 BG8  H14  C17  C16  120.87  3.000
 BG8  C18  C17  C16  120.38  3.000
 BG8  H15  C18  C19  120.21  3.000
 BG8  H15  C18  C17  119.69  3.000
 BG8  C19  C18  C17  120.09  3.000
 BG8  H16  C19  C20  120.10  3.000
 BG8  H16  C19  C18  120.10  3.000
 BG8  C20  C19  C18  119.80  3.000
 BG8  H17  C20  C19  120.13  3.000
 BG8  H17  C20  C14  119.73  3.000
 BG8  C19  C20  C14  120.14  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
 BG8  CONST_01  C18  C17  C16  C14    0.00   0.0  0
 BG8  CONST_02  C18  C19  C20  C14    0.00   0.0  0
 BG8  CONST_03  C19  C18  C17  C16    0.00   0.0  0
 BG8  CONST_04  C19  C20  C14  C16    0.00   0.0  0
 BG8  CONST_05  C20  C14  C16  C17    0.00   0.0  0
 BG8  CONST_06  C20  C19  C18  C17    0.00   0.0  0
 BG8  CONST_07  C18  C17  C16  C13  180.00   0.0  0
 BG8  CONST_08  C20  C14  C16  C13  180.00   0.0  0
 BG8  CONST_09  H14  C17  C16  C14  180.00   0.0  0
 BG8  CONST_10  H16  C19  C20  C14  180.00   0.0  0
 BG8  CONST_11  H15  C18  C17  C16  180.00   0.0  0
 BG8  CONST_12  H17  C20  C14  C16  180.00   0.0  0
 BG8  CONST_13  H13  C14  C16  C17  180.00   0.0  0
 BG8  CONST_14  C16  C13  N07  C02  180.00   0.0  0
 BG8  CONST_15  O15  C13  N07  C02    0.00   0.0  0
 BG8  CONST_16  H6   N07  C13  C16    0.00   0.0  0
 BG8  Var_01    C17  C16  C13  N07   28.76  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
 BG8  chir_01  C01  C06  C02  O09  negativ
 BG8  chir_02  C02  N07  C01  C03  positiv
 BG8  chir_03  C03  O04  O11  C02  negativ
 BG8  chir_04  C05  O04  C06  C10  negativ
 BG8  chir_05  C06  O08  C05  C01  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
 BG8  plan-1  C13  0.020
 BG8  plan-1  C14  0.020
 BG8  plan-1  C16  0.020
 BG8  plan-1  C17  0.020
 BG8  plan-1  C18  0.020
 BG8  plan-1  C19  0.020
 BG8  plan-1  C20  0.020
 BG8  plan-1  H14  0.020
 BG8  plan-1  H15  0.020
 BG8  plan-1  H16  0.020
 BG8  plan-1  H17  0.020
 BG8  plan-1  H13  0.020
 BG8  plan-2  C02  0.020
 BG8  plan-2  N07  0.020
 BG8  plan-2  C13  0.020
 BG8  plan-2  O15  0.020
 BG8  plan-2  C16  0.020
 BG8  plan-2  H6   0.020

