# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 21:48:50 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: N-[(phenylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)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
 BZD  BZD  N-[(phenylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine  D-saccharide  41  23  .  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_BZD
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
 BZD  O5    O  O2    0  -0.488   0.8477   0.3647  -2.1813
 BZD  C1    C  CH1   0   0.207  -0.2755  -0.2979  -1.6507
 BZD  C2    C  CH1   0  -0.028  -1.5473   0.1741  -2.3602
 BZD  O2    O  OH1   0  -0.663  -2.6744  -0.5410  -1.9243
 BZD  C3    C  CH1   0  -0.005  -1.3987  -0.0646  -3.8559
 BZD  O3    O  OH1   0  -0.671  -2.4706   0.4817  -4.5856
 BZD  C4    C  CH1   0   0.034  -0.1162   0.5732  -4.3774
 BZD  O4    O  OH1   0  -0.671   0.1157   0.2276  -5.7200
 BZD  C5    C  CH1   0  -0.014   1.0739   0.0873  -3.5479
 BZD  C6    C  CH2   0  -0.157   2.3614   0.7742  -3.9514
 BZD  O6    O  OH1   0  -0.670   3.4258   0.2034  -3.2291
 BZD  N1    N  NH1   0  -0.737  -0.3573  -0.0147  -0.2570
 BZD  C7    C  C     0   0.767   0.1842  -0.8300   0.6889
 BZD  O7    O  O     0  -0.470   0.7108  -1.8927   0.4492
 BZD  N2    N  NH1   0  -0.763   0.0262  -0.3144   1.9733
 BZD  C8    C  C     0   0.550   0.5456  -0.8461   3.1313
 BZD  O8    O  O     0  -0.420   1.3250  -1.7712   3.1546
 BZD  C9    C  CR6   0  -0.052   0.0939  -0.1735   4.3857
 BZD  C10   C  CR16  0  -0.260   0.9129  -0.2836   5.5089
 BZD  C11   C  CR16  0  -0.241   0.5411   0.3053   6.7062
 BZD  C12   C  CR16  0  -0.246  -0.6607   0.9962   6.7994
 BZD  C13   C  CR16  0  -0.239  -1.4898   1.0941   5.6906
 BZD  C14   C  CR16  0  -0.290  -1.1144   0.5145   4.4875
 BZD  H1    H  HCH1  0   0.237  -0.1761  -1.3829  -1.7787
 BZD  H2    H  HCH1  0   0.227  -1.6632   1.2555  -2.1856
 BZD  HO2   H  HOH1  0   0.457  -2.8834  -0.2747  -1.0234
 BZD  H3    H  HCH1  0   0.218  -1.3258  -1.1515  -4.0220
 BZD  HO3   H  HOH1  0   0.458  -3.2605  -0.0376  -4.4058
 BZD  H4    H  HCH1  0   0.213  -0.1979   1.6656  -4.2577
 BZD  HO4   H  HOH1  0   0.455  -0.6312   0.5376  -6.2428
 BZD  H5    H  HCH1  0   0.224   1.1837  -0.9993  -3.6991
 BZD  H61   H  HCH2  0   0.197   2.2642   1.8511  -3.7554
 BZD  H62   H  HCH2  0   0.213   2.4931   0.6546  -5.0317
 BZD  HO6   H  HOH1  0   0.457   4.2395   0.6277  -3.5151
 BZD  HN1   H  HNH1  0   0.410  -0.6547   0.9147   0.0038
 BZD  HN2   H  HNH1  0   0.428  -0.4973   0.5436   2.0596
 BZD  H101  H  HCR6  0   0.265   1.8478  -0.8243   5.4445
 BZD  H111  H  HCR6  0   0.267   1.1888   0.2229   7.5688
 BZD  H121  H  HCR6  0   0.268  -0.9522   1.4539   7.7357
 BZD  H131  H  HCR6  0   0.269  -2.4334   1.6186   5.7606
 BZD  H141  H  HCR6  0   0.265  -1.7927   0.5866   3.6466

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
 BZD  O5   C1    single    1.408  0.020  1.408
 BZD  O5   C5    single    1.413  0.020  1.413
 BZD  C1   C2    single    1.531  0.020  1.531
 BZD  C1   N1    single    1.425  0.020  1.425
 BZD  C1   H1    single    0.970  0.020  1.090
 BZD  C2   O2    single    1.404  0.020  1.404
 BZD  C2   C3    single    1.522  0.020  1.522
 BZD  C2   H2    single    0.970  0.020  1.090
 BZD  O2   HO2   single    0.850  0.020  0.980
 BZD  C3   O3    single    1.407  0.020  1.407
 BZD  C3   C4    single    1.524  0.020  1.524
 BZD  C3   H3    single    0.970  0.020  1.090
 BZD  O3   HO3   single    0.850  0.020  0.980
 BZD  C4   O4    single    1.406  0.020  1.406
 BZD  C4   C5    single    1.530  0.020  1.530
 BZD  C4   H4    single    0.970  0.020  1.090
 BZD  O4   HO4   single    0.850  0.020  0.980
 BZD  C5   C6    single    1.514  0.020  1.514
 BZD  C5   H5    single    0.970  0.020  1.090
 BZD  C6   O6    single    1.407  0.020  1.407
 BZD  C6   H61   single    0.970  0.020  1.090
 BZD  C6   H62   single    0.970  0.020  1.090
 BZD  O6   HO6   single    0.850  0.020  0.980
 BZD  N1   C7    single    1.361  0.020  1.361
 BZD  N1   HN1   single    0.860  0.020  1.020
 BZD  C7   O7    double    1.210  0.020  1.210
 BZD  C7   N2    single    1.393  0.020  1.393
 BZD  N2   C8    single    1.376  0.020  1.376
 BZD  N2   HN2   single    0.860  0.020  1.020
 BZD  C8   O8    double    1.210  0.020  1.210
 BZD  C8   C9    single    1.493  0.020  1.493
 BZD  C9   C10   aromatic  1.394  0.020  1.394
 BZD  C9   C14   aromatic  1.394  0.020  1.394
 BZD  C10  C11   aromatic  1.385  0.020  1.385
 BZD  C10  H101  single    0.930  0.020  1.080
 BZD  C11  C12   aromatic  1.389  0.020  1.389
 BZD  C11  H111  single    0.930  0.020  1.080
 BZD  C12  C13   aromatic  1.388  0.020  1.388
 BZD  C12  H121  single    0.930  0.020  1.080
 BZD  C13  C14   aromatic  1.387  0.020  1.387
 BZD  C13  H131  single    0.930  0.020  1.080
 BZD  C14  H141  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
 BZD  C5    O5   C1   113.57  3.000
 BZD  H1    C1   N1   108.42  3.000
 BZD  H1    C1   C2   109.03  3.000
 BZD  N1    C1   C2   110.14  3.000
 BZD  H1    C1   O5   110.44  3.000
 BZD  N1    C1   O5   108.72  3.000
 BZD  C2    C1   O5   110.06  3.000
 BZD  H2    C2   C3   108.67  3.000
 BZD  H2    C2   O2   111.49  3.000
 BZD  C3    C2   O2   107.67  3.000
 BZD  H2    C2   C1   108.46  3.000
 BZD  C3    C2   C1   109.03  3.000
 BZD  O2    C2   C1   111.46  3.000
 BZD  HO2   O2   C2   108.90  3.000
 BZD  H3    C3   C4   107.79  3.000
 BZD  H3    C3   O3   110.81  3.000
 BZD  C4    C3   O3   107.52  3.000
 BZD  H3    C3   C2   108.01  3.000
 BZD  C4    C3   C2   110.65  3.000
 BZD  O3    C3   C2   111.99  3.000
 BZD  HO3   O3   C3   108.60  3.000
 BZD  H4    C4   C5   108.28  3.000
 BZD  H4    C4   O4   111.08  3.000
 BZD  C5    C4   O4   108.15  3.000
 BZD  H4    C4   C3   108.37  3.000
 BZD  C5    C4   C3   109.64  3.000
 BZD  O4    C4   C3   111.26  3.000
 BZD  HO4   O4   C4   108.15  3.000
 BZD  H5    C5   C6   109.02  3.000
 BZD  H5    C5   C4   108.43  3.000
 BZD  C6    C5   C4   111.89  3.000
 BZD  H5    C5   O5   110.01  3.000
 BZD  C6    C5   O5   107.75  3.000
 BZD  C4    C5   O5   109.73  3.000
 BZD  H62   C6   H61  107.08  3.000
 BZD  H62   C6   O6   111.79  3.000
 BZD  H61   C6   O6   111.89  3.000
 BZD  H62   C6   C5   108.40  3.000
 BZD  H61   C6   C5   108.78  3.000
 BZD  O6    C6   C5   108.80  3.000
 BZD  HO6   O6   C6   107.97  3.000
 BZD  HN1   N1   C7   119.26  3.000
 BZD  HN1   N1   C1   116.91  3.000
 BZD  C7    N1   C1   122.54  3.000
 BZD  N2    C7   O7   123.86  3.000
 BZD  N2    C7   N1   111.96  3.000
 BZD  O7    C7   N1   124.16  3.000
 BZD  HN2   N2   C8   116.91  3.000
 BZD  HN2   N2   C7   116.91  3.000
 BZD  C8    N2   C7   126.16  3.000
 BZD  C9    C8   O8   121.53  3.000
 BZD  C9    C8   N2   114.76  3.000
 BZD  O8    C8   N2   123.70  3.000
 BZD  C14   C9   C10  119.29  3.000
 BZD  C14   C9   C8   123.07  3.000
 BZD  C10   C9   C8   117.61  3.000
 BZD  H101  C10  C11  119.73  3.000
 BZD  H101  C10  C9   119.93  3.000
 BZD  C11   C10  C9   120.34  3.000
 BZD  H111  C11  C12  120.15  3.000
 BZD  H111  C11  C10  119.75  3.000
 BZD  C12   C11  C10  120.10  3.000
 BZD  H121  C12  C13  120.03  3.000
 BZD  H121  C12  C11  120.09  3.000
 BZD  C13   C12  C11  119.89  3.000
 BZD  H131  C13  C14  119.65  3.000
 BZD  H131  C13  C12  120.24  3.000
 BZD  C14   C13  C12  120.11  3.000
 BZD  H141  C14  C13  118.44  3.000
 BZD  H141  C14  C9   121.27  3.000
 BZD  C13   C14  C9   120.26  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
 BZD  CONST_01  C12   C11  C10  C9      0.00   0.0  0
 BZD  CONST_02  C12   C13  C14  C9      0.00   0.0  0
 BZD  CONST_03  C13   C14  C9   C10     0.00   0.0  0
 BZD  CONST_04  C13   C12  C11  C10     0.00   0.0  0
 BZD  CONST_05  C14   C9   C10  C11     0.00   0.0  0
 BZD  CONST_06  C14   C13  C12  C11     0.00   0.0  0
 BZD  CONST_07  C11   C10  C9   C8    180.00   0.0  0
 BZD  CONST_08  C13   C14  C9   C8    180.00   0.0  0
 BZD  CONST_09  H111  C11  C10  C9    180.00   0.0  0
 BZD  CONST_10  H131  C13  C14  C9    180.00   0.0  0
 BZD  CONST_11  H141  C14  C9   C10   180.00   0.0  0
 BZD  CONST_12  H121  C12  C11  C10   180.00   0.0  0
 BZD  CONST_13  H101  C10  C11  C12   180.00   0.0  0
 BZD  CONST_14  O7    C7   N1   C1      0.00   0.0  0
 BZD  CONST_15  C9    C8   N2   C7    180.00   0.0  0
 BZD  CONST_16  N2    C7   N1   C1    180.00   0.0  0
 BZD  CONST_17  HN2   N2   C8   C9      0.00   0.0  0
 BZD  CONST_18  O8    C8   N2   C7      0.00   0.0  0
 BZD  CONST_19  C8    N2   C7   O7      0.00   0.0  0
 BZD  CONST_20  C8    N2   C7   N1    180.00   0.0  0
 BZD  CONST_21  HN1   N1   C7   O7    180.00   0.0  0
 BZD  Var_01    C10   C9   C8   N2   -156.15  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
 BZD  chir_01  C1  O5  C2  N1  positiv
 BZD  chir_02  C2  O2  C1  C3  negativ
 BZD  chir_03  C3  O3  C2  C4  positiv
 BZD  chir_04  C4  O4  C5  C3  positiv
 BZD  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
 BZD  plan-1  C8    0.020
 BZD  plan-1  C9    0.020
 BZD  plan-1  C10   0.020
 BZD  plan-1  C11   0.020
 BZD  plan-1  C12   0.020
 BZD  plan-1  C13   0.020
 BZD  plan-1  C14   0.020
 BZD  plan-1  H101  0.020
 BZD  plan-1  H111  0.020
 BZD  plan-1  H121  0.020
 BZD  plan-1  H131  0.020
 BZD  plan-1  H141  0.020
 BZD  plan-2  C1    0.020
 BZD  plan-2  N1    0.020
 BZD  plan-2  C7    0.020
 BZD  plan-2  O7    0.020
 BZD  plan-2  N2    0.020
 BZD  plan-2  C8    0.020
 BZD  plan-2  O8    0.020
 BZD  plan-2  C9    0.020
 BZD  plan-2  HN1   0.020
 BZD  plan-2  HN2   0.020

