# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 15:59:14 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: N-(phenylcarbonyl)-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)c2ccccc2)[C@H](O)[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
 OAK  OAK  N-(phenylcarbonyl)-beta-D-glucopyranosylamine  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 OK
;

data_comp_OAK
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
 OAK  C9   C  CR16  0  -0.265  -4.0735   0.9870   0.6415
 OAK  C10  C  CR16  0  -0.242  -5.3758   0.9108   0.1740
 OAK  C11  C  CR16  0  -0.249  -5.7335  -0.0765  -0.7357
 OAK  C12  C  CR16  0  -0.240  -4.7830  -0.9872  -1.1765
 OAK  C13  C  CR16  0  -0.288  -3.4757  -0.9040  -0.7198
 OAK  C8   C  CR6   0  -0.043  -3.1097   0.0882   0.1884
 OAK  C7   C  C     0   0.548  -1.7249   0.2058   0.7344
 OAK  O7   O  O     0  -0.468  -1.5139   0.7036   1.8265
 OAK  N1   N  NH1   0  -0.706  -0.7388  -0.2854  -0.0570
 OAK  C1   C  CH1   0   0.209   0.6419  -0.2617   0.3006
 OAK  O5   O  O2    0  -0.488   1.2336   0.8821  -0.2670
 OAK  C5   C  CH1   0  -0.014   2.5898   1.0504   0.0915
 OAK  C6   C  CH2   0  -0.157   3.0620   2.3666  -0.4885
 OAK  O6   O  OH1   0  -0.670   2.3384   3.4119   0.1153
 OAK  C4   C  CH1   0   0.035   3.4098  -0.1315  -0.4287
 OAK  O4   O  OH1   0  -0.672   4.7415   0.0412  -0.0132
 OAK  C3   C  CH1   0  -0.005   2.8271  -1.4340   0.1078
 OAK  O3   O  OH1   0  -0.672   3.5544  -2.4919  -0.4683
 OAK  C2   C  CH1   0  -0.030   1.3410  -1.5251  -0.2081
 OAK  O2   O  OH1   0  -0.662   0.8393  -2.6750   0.4234
 OAK  H9   H  HCR6  0   0.263  -3.8032   1.7545   1.3545
 OAK  H10  H  HCR6  0   0.264  -6.1139   1.6211   0.5224
 OAK  H11  H  HCR6  0   0.266  -6.7516  -0.1386  -1.0968
 OAK  H12  H  HCR6  0   0.266  -5.0588  -1.7693  -1.8714
 OAK  H13  H  HCR6  0   0.258  -2.7578  -1.6389  -1.0616
 OAK  HN1  H  HNH1  0   0.411  -0.9570  -0.5020  -1.0186
 OAK  H1   H  HCH1  0   0.234   0.7158  -0.2288   1.3945
 OAK  H5   H  HCH1  0   0.224   2.6883   1.0886   1.1890
 OAK  H6   H  HCH2  0   0.213   4.1373   2.4583  -0.3050
 OAK  H6A  H  HCH2  0   0.197   2.9208   2.3470  -1.5782
 OAK  HO6  H  HOH1  0   0.457   2.6767   4.2439  -0.2271
 OAK  H4   H  HCH1  0   0.213   3.3355  -0.1448  -1.5281
 OAK  HO4  H  HOH1  0   0.455   5.2566  -0.7040  -0.3393
 OAK  H3   H  HCH1  0   0.218   2.9438  -1.4310   1.2035
 OAK  HO3  H  HOH1  0   0.458   3.3298  -3.3064  -0.0079
 OAK  H2   H  HCH1  0   0.228   1.2166  -1.5787  -1.3008
 OAK  HO2  H  HOH1  0   0.455  -0.0364  -2.8676   0.0744

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
 OAK  C8   C9   aromatic  1.394  0.020  1.394
 OAK  C9   C10  aromatic  1.386  0.020  1.386
 OAK  C9   H9   single    0.930  0.020  1.080
 OAK  C10  C11  aromatic  1.389  0.020  1.389
 OAK  C10  H10  single    0.930  0.020  1.080
 OAK  C12  C11  aromatic  1.388  0.020  1.388
 OAK  C11  H11  single    0.930  0.020  1.080
 OAK  C13  C12  aromatic  1.387  0.020  1.387
 OAK  C12  H12  single    0.930  0.020  1.080
 OAK  C8   C13  aromatic  1.394  0.020  1.394
 OAK  C13  H13  single    0.930  0.020  1.080
 OAK  C7   C8   single    1.493  0.020  1.493
 OAK  N1   C7   single    1.356  0.020  1.356
 OAK  C7   O7   double    1.219  0.020  1.219
 OAK  C1   N1   single    1.426  0.020  1.426
 OAK  N1   HN1  single    0.860  0.020  1.020
 OAK  C2   C1   single    1.531  0.020  1.531
 OAK  C1   O5   single    1.407  0.020  1.407
 OAK  C1   H1   single    0.970  0.020  1.090
 OAK  C5   O5   single    1.413  0.020  1.413
 OAK  C4   C5   single    1.530  0.020  1.530
 OAK  C5   C6   single    1.514  0.020  1.514
 OAK  C5   H5   single    0.970  0.020  1.090
 OAK  O6   C6   single    1.407  0.020  1.407
 OAK  C6   H6   single    0.970  0.020  1.090
 OAK  C6   H6A  single    0.970  0.020  1.090
 OAK  O6   HO6  single    0.850  0.020  0.980
 OAK  O4   C4   single    1.406  0.020  1.406
 OAK  C3   C4   single    1.524  0.020  1.524
 OAK  C4   H4   single    0.970  0.020  1.090
 OAK  O4   HO4  single    0.850  0.020  0.980
 OAK  O3   C3   single    1.407  0.020  1.407
 OAK  C3   C2   single    1.522  0.020  1.522
 OAK  C3   H3   single    0.970  0.020  1.090
 OAK  O3   HO3  single    0.850  0.020  0.980
 OAK  O2   C2   single    1.405  0.020  1.405
 OAK  C2   H2   single    0.970  0.020  1.090
 OAK  O2   HO2  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
 OAK  H9   C9   C8   119.93  3.000
 OAK  H9   C9   C10  119.74  3.000
 OAK  C8   C9   C10  120.32  3.000
 OAK  H10  C10  C11  120.12  3.000
 OAK  H10  C10  C9   119.76  3.000
 OAK  C11  C10  C9   120.12  3.000
 OAK  H11  C11  C12  120.04  3.000
 OAK  H11  C11  C10  120.10  3.000
 OAK  C12  C11  C10  119.86  3.000
 OAK  H12  C12  C13  119.67  3.000
 OAK  H12  C12  C11  120.24  3.000
 OAK  C13  C12  C11  120.08  3.000
 OAK  H13  C13  C8   120.97  3.000
 OAK  H13  C13  C12  118.70  3.000
 OAK  C8   C13  C12  120.31  3.000
 OAK  C7   C8   C13  122.53  3.000
 OAK  C7   C8   C9   118.15  3.000
 OAK  C13  C8   C9   119.29  3.000
 OAK  N1   C7   O7   123.02  3.000
 OAK  O7   C7   C8   121.36  3.000
 OAK  N1   C7   C8   115.62  3.000
 OAK  HN1  N1   C1   116.84  3.000
 OAK  HN1  N1   C7   118.44  3.000
 OAK  C1   N1   C7   123.47  3.000
 OAK  H1   C1   C2   108.99  3.000
 OAK  H1   C1   O5   110.46  3.000
 OAK  C2   C1   O5   110.17  3.000
 OAK  H1   C1   N1   108.40  3.000
 OAK  O5   C1   N1   108.63  3.000
 OAK  C2   C1   N1   110.19  3.000
 OAK  C5   O5   C1   113.46  3.000
 OAK  H5   C5   C4   108.50  3.000
 OAK  H5   C5   C6   108.87  3.000
 OAK  C4   C5   C6   111.98  3.000
 OAK  H5   C5   O5   110.03  3.000
 OAK  C6   C5   O5   107.80  3.000
 OAK  C4   C5   O5   109.65  3.000
 OAK  H6A  C6   H6   107.09  3.000
 OAK  H6A  C6   O6   111.88  3.000
 OAK  H6   C6   O6   111.77  3.000
 OAK  H6A  C6   C5   108.93  3.000
 OAK  H6   C6   C5   108.36  3.000
 OAK  O6   C6   C5   108.72  3.000
 OAK  HO6  O6   C6   108.00  3.000
 OAK  H4   C4   C3   108.36  3.000
 OAK  H4   C4   O4   111.11  3.000
 OAK  C3   C4   O4   111.29  3.000
 OAK  H4   C4   C5   108.21  3.000
 OAK  C3   C4   C5   109.61  3.000
 OAK  O4   C4   C5   108.21  3.000
 OAK  HO4  O4   C4   108.16  3.000
 OAK  H3   C3   C2   108.05  3.000
 OAK  H3   C3   O3   110.76  3.000
 OAK  C2   C3   O3   112.00  3.000
 OAK  H3   C3   C4   107.89  3.000
 OAK  C2   C3   C4   110.57  3.000
 OAK  O3   C3   C4   107.50  3.000
 OAK  HO3  O3   C3   108.66  3.000
 OAK  H2   C2   O2   111.46  3.000
 OAK  H2   C2   C3   108.61  3.000
 OAK  O2   C2   C3   107.73  3.000
 OAK  H2   C2   C1   108.56  3.000
 OAK  O2   C2   C1   111.29  3.000
 OAK  C3   C2   C1   109.12  3.000
 OAK  HO2  O2   C2   109.02  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
 OAK  CONST_01  C12  C13  C8   C9      0.00   0.0  0
 OAK  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 OAK  CONST_03  C13  C8   C9   C10     0.00   0.0  0
 OAK  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 OAK  CONST_05  C8   C9   C10  C11     0.00   0.0  0
 OAK  CONST_06  C8   C13  C12  C11     0.00   0.0  0
 OAK  CONST_07  C7   C8   C9   C10   180.00   0.0  0
 OAK  CONST_08  C7   C8   C13  C12   180.00   0.0  0
 OAK  CONST_09  H13  C13  C8   C9    180.00   0.0  0
 OAK  CONST_10  H11  C11  C10  C9    180.00   0.0  0
 OAK  CONST_11  H12  C12  C11  C10   180.00   0.0  0
 OAK  CONST_12  H9   C9   C10  C11   180.00   0.0  0
 OAK  CONST_13  H10  C10  C11  C12   180.00   0.0  0
 OAK  CONST_14  C1   N1   C7   C8    180.00   0.0  0
 OAK  CONST_15  C1   N1   C7   O7      0.00   0.0  0
 OAK  CONST_16  HN1  N1   C7   C8      0.00   0.0  0
 OAK  Var_01    N1   C7   C8   C9   -155.26  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
 OAK  chir_01  C1  N1  C2  O5  negativ
 OAK  chir_02  C5  O5  C6  C4  positiv
 OAK  chir_03  C4  O4  C5  C3  positiv
 OAK  chir_04  C3  O3  C2  C4  positiv
 OAK  chir_05  C2  O2  C3  C1  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
 OAK  plan-1  C9   0.020
 OAK  plan-1  C10  0.020
 OAK  plan-1  C11  0.020
 OAK  plan-1  C12  0.020
 OAK  plan-1  C13  0.020
 OAK  plan-1  C8   0.020
 OAK  plan-1  C7   0.020
 OAK  plan-1  H9   0.020
 OAK  plan-1  H10  0.020
 OAK  plan-1  H11  0.020
 OAK  plan-1  H12  0.020
 OAK  plan-1  H13  0.020
 OAK  plan-2  C8   0.020
 OAK  plan-2  C7   0.020
 OAK  plan-2  O7   0.020
 OAK  plan-2  N1   0.020
 OAK  plan-2  C1   0.020
 OAK  plan-2  HN1  0.020

