# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 21:05:23 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N-[(pyridin-2-ylcarbonyl)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)c2ccccn2)[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
 T68  T68  N-[(pyridin-2-ylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine  D-saccharide  40  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_T68
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
 T68  C1   C  CH1   0   0.208   1.6597   0.3062  -0.3610
 T68  N1   N  NH1   0  -0.734   0.2586   0.4232  -0.1323
 T68  C2   C  CH1   0  -0.028   2.3748   1.5859   0.0800
 T68  N2   N  NH1   0  -0.762  -1.9548  -0.0377  -0.4372
 T68  O2   O  OH1   0  -0.663   1.9955   2.6856  -0.7063
 T68  C3   C  CH1   0  -0.006   3.8766   1.3999  -0.0846
 T68  N3   N  N     0  -0.445  -4.1477   0.5081   0.9150
 T68  O3   O  OH1   0  -0.671   4.6028   2.4813   0.4477
 T68  C4   C  CH1   0   0.035   4.3464   0.1364   0.6269
 T68  O4   O  OH1   0  -0.672   5.6987  -0.1302   0.3512
 T68  C5   C  CH1   0  -0.015   3.5161  -1.0563   0.1502
 T68  O5   O  O2    0  -0.487   2.1452  -0.7951   0.3698
 T68  C6   C  CH2   0  -0.156   3.8701  -2.3266   0.8937
 T68  O6   O  OH1   0  -0.670   3.1447  -3.3959   0.3359
 T68  C7   C  C     0   0.766  -0.6635  -0.1814  -0.9304
 T68  O7   O  O     0  -0.473  -0.3971  -0.7590  -1.9604
 T68  C8   C  C     0   0.555  -3.1013  -0.5148  -1.0082
 T68  O8   O  O     0  -0.415  -3.1702  -1.1436  -2.0388
 T68  C9   C  CR6   0   0.120  -4.3278  -0.1766  -0.2090
 T68  C10  C  CR16  0  -0.293  -5.5752  -0.5803  -0.6606
 T68  C11  C  CR16  0  -0.143  -6.6834  -0.2506   0.1055
 T68  C12  C  CR16  0  -0.316  -6.4994   0.4602   1.2802
 T68  C13  C  CR16  0  -0.054  -5.2074   0.8192   1.6438
 T68  H1   H  HCH1  0   0.236   1.8251   0.1550  -1.4350
 T68  HN1  H  HNH1  0   0.409  -0.0311   0.7823   0.7662
 T68  H2   H  HCH1  0   0.227   2.1563   1.7566   1.1462
 T68  HN2  H  HNH1  0   0.426  -2.1053   0.4714   0.4275
 T68  HO2  H  HOH1  0   0.457   1.0836   2.9159  -0.5026
 T68  H3   H  HCH1  0   0.218   4.0888   1.2776  -1.1590
 T68  HO3  H  HOH1  0   0.458   4.4569   3.2523  -0.1093
 T68  H4   H  HCH1  0   0.213   4.1798   0.2628   1.7089
 T68  HO4  H  HOH1  0   0.455   6.2196   0.6220   0.6511
 T68  H5   H  HCH1  0   0.224   3.7042  -1.2050  -0.9261
 T68  H6   H  HCH2  0   0.213   4.9506  -2.4840   0.8144
 T68  H6A  H  HCH2  0   0.197   3.6411  -2.1886   1.9596
 T68  HO6  H  HOH1  0   0.457   3.4045  -4.2001   0.7936
 T68  H10  H  HCR6  0   0.282  -5.6782  -1.1355  -1.5819
 T68  H11  H  HCR6  0   0.286  -7.6746  -0.5442  -0.2120
 T68  H12  H  HCR6  0   0.284  -7.3358   0.7346   1.9076
 T68  H13  H  HCR6  0   0.278  -5.0254   1.3773   2.5542

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
 T68  C1   N1   single    1.424  0.020  1.424
 T68  C1   C2   single    1.531  0.020  1.531
 T68  C1   O5   single    1.408  0.020  1.408
 T68  N1   C7   single    1.361  0.020  1.361
 T68  C2   O2   single    1.404  0.020  1.404
 T68  C2   C3   single    1.522  0.020  1.522
 T68  N2   C7   single    1.390  0.020  1.390
 T68  N2   C8   single    1.367  0.020  1.367
 T68  C3   O3   single    1.407  0.020  1.407
 T68  C3   C4   single    1.524  0.020  1.524
 T68  N3   C9   aromatic  1.328  0.020  1.328
 T68  N3   C13  aromatic  1.323  0.020  1.323
 T68  C4   O4   single    1.406  0.020  1.406
 T68  C4   C5   single    1.529  0.020  1.529
 T68  C5   O5   single    1.413  0.020  1.413
 T68  C5   C6   single    1.514  0.020  1.514
 T68  C6   O6   single    1.407  0.020  1.407
 T68  C7   O7   double    1.211  0.020  1.211
 T68  C8   O8   double    1.209  0.020  1.209
 T68  C8   C9   single    1.502  0.020  1.502
 T68  C9   C10  aromatic  1.387  0.020  1.387
 T68  C10  C11  aromatic  1.387  0.020  1.387
 T68  C11  C12  aromatic  1.385  0.020  1.385
 T68  C12  C13  aromatic  1.389  0.020  1.389
 T68  C1   H1   single    0.970  0.020  1.090
 T68  N1   HN1  single    0.860  0.020  1.020
 T68  C2   H2   single    0.970  0.020  1.090
 T68  N2   HN2  single    0.860  0.020  1.020
 T68  O2   HO2  single    0.850  0.020  0.980
 T68  C3   H3   single    0.970  0.020  1.090
 T68  O3   HO3  single    0.850  0.020  0.980
 T68  C4   H4   single    0.970  0.020  1.090
 T68  O4   HO4  single    0.850  0.020  0.980
 T68  C5   H5   single    0.970  0.020  1.090
 T68  C6   H6   single    0.970  0.020  1.090
 T68  C6   H6A  single    0.970  0.020  1.090
 T68  O6   HO6  single    0.850  0.020  0.980
 T68  C10  H10  single    0.930  0.020  1.080
 T68  C11  H11  single    0.930  0.020  1.080
 T68  C12  H12  single    0.930  0.020  1.080
 T68  C13  H13  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
 T68  H1   C1   O5   110.39  3.000
 T68  H1   C1   C2   109.07  3.000
 T68  O5   C1   C2   110.07  3.000
 T68  H1   C1   N1   108.47  3.000
 T68  O5   C1   N1   108.67  3.000
 T68  C2   C1   N1   110.15  3.000
 T68  HN1  N1   C7   119.02  3.000
 T68  HN1  N1   C1   117.01  3.000
 T68  C7   N1   C1   122.39  3.000
 T68  H2   C2   C3   108.62  3.000
 T68  H2   C2   O2   111.54  3.000
 T68  C3   C2   O2   107.56  3.000
 T68  H2   C2   C1   108.40  3.000
 T68  C3   C2   C1   109.12  3.000
 T68  O2   C2   C1   111.54  3.000
 T68  HN2  N2   C8   114.00  3.000
 T68  HN2  N2   C7   119.48  3.000
 T68  C8   N2   C7   126.52  3.000
 T68  HO2  O2   C2   108.95  3.000
 T68  H3   C3   C4   107.68  3.000
 T68  H3   C3   O3   110.78  3.000
 T68  C4   C3   O3   107.54  3.000
 T68  H3   C3   C2   108.00  3.000
 T68  C4   C3   C2   110.79  3.000
 T68  O3   C3   C2   111.98  3.000
 T68  C13  N3   C9   118.59  3.000
 T68  HO3  O3   C3   108.58  3.000
 T68  H4   C4   C5   108.26  3.000
 T68  H4   C4   O4   111.09  3.000
 T68  C5   C4   O4   108.26  3.000
 T68  H4   C4   C3   108.46  3.000
 T68  C5   C4   C3   109.49  3.000
 T68  O4   C4   C3   111.23  3.000
 T68  HO4  O4   C4   108.13  3.000
 T68  H5   C5   C6   109.05  3.000
 T68  H5   C5   O5   110.02  3.000
 T68  C6   C5   O5   107.80  3.000
 T68  H5   C5   C4   108.47  3.000
 T68  C6   C5   C4   111.98  3.000
 T68  O5   C5   C4   109.52  3.000
 T68  C5   O5   C1   113.48  3.000
 T68  H6A  C6   H6   107.09  3.000
 T68  H6A  C6   O6   111.87  3.000
 T68  H6   C6   O6   111.76  3.000
 T68  H6A  C6   C5   108.80  3.000
 T68  H6   C6   C5   108.41  3.000
 T68  O6   C6   C5   108.81  3.000
 T68  HO6  O6   C6   107.92  3.000
 T68  O7   C7   N2   123.76  3.000
 T68  O7   C7   N1   124.17  3.000
 T68  N2   C7   N1   112.05  3.000
 T68  C9   C8   O8   121.59  3.000
 T68  C9   C8   N2   112.58  3.000
 T68  O8   C8   N2   125.83  3.000
 T68  C10  C9   C8   119.71  3.000
 T68  C10  C9   N3   123.21  3.000
 T68  C8   C9   N3   117.09  3.000
 T68  H10  C10  C11  121.13  3.000
 T68  H10  C10  C9   120.86  3.000
 T68  C11  C10  C9   118.01  3.000
 T68  H11  C11  C12  120.67  3.000
 T68  H11  C11  C10  120.37  3.000
 T68  C12  C11  C10  118.96  3.000
 T68  H12  C12  C13  120.14  3.000
 T68  H12  C12  C11  121.31  3.000
 T68  C13  C12  C11  118.56  3.000
 T68  H13  C13  C12  120.62  3.000
 T68  H13  C13  N3   116.71  3.000
 T68  C12  C13  N3   122.67  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
 T68  CONST_01  C11  C10  C9   N3     0.00   0.0  0
 T68  CONST_02  C11  C12  C13  N3     0.00   0.0  0
 T68  CONST_03  C12  C13  N3   C9     0.00   0.0  0
 T68  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 T68  CONST_05  C13  N3   C9   C10    0.00   0.0  0
 T68  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 T68  CONST_07  C13  N3   C9   C8   180.00   0.0  0
 T68  CONST_08  C11  C10  C9   C8   180.00   0.0  0
 T68  CONST_09  H10  C10  C9   N3   180.00   0.0  0
 T68  CONST_10  H12  C12  C13  N3   180.00   0.0  0
 T68  CONST_11  H13  C13  N3   C9   180.00   0.0  0
 T68  CONST_12  H11  C11  C10  C9   180.00   0.0  0
 T68  CONST_13  O7   C7   N1   C1     0.00   0.0  0
 T68  CONST_14  C9   C8   N2   C7   180.00   0.0  0
 T68  CONST_15  N2   C7   N1   C1   180.00   0.0  0
 T68  CONST_16  HN2  N2   C8   C9     0.00   0.0  0
 T68  CONST_17  O8   C8   N2   C7     0.00   0.0  0
 T68  CONST_18  C8   N2   C7   O7     0.00   0.0  0
 T68  CONST_19  C8   N2   C7   N1   180.00   0.0  0
 T68  CONST_20  HN1  N1   C7   O7   180.00   0.0  0
 T68  Var_01    N3   C9   C8   N2    -0.53  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
 T68  chir_01  C1  N1  C2  O5  negativ
 T68  chir_02  C2  O2  C1  C3  negativ
 T68  chir_03  C3  O3  C2  C4  positiv
 T68  chir_04  C4  O4  C5  C3  positiv
 T68  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
 T68  plan-1  N3   0.020
 T68  plan-1  C8   0.020
 T68  plan-1  C9   0.020
 T68  plan-1  C10  0.020
 T68  plan-1  C11  0.020
 T68  plan-1  C12  0.020
 T68  plan-1  C13  0.020
 T68  plan-1  H10  0.020
 T68  plan-1  H11  0.020
 T68  plan-1  H12  0.020
 T68  plan-1  H13  0.020
 T68  plan-2  C1   0.020
 T68  plan-2  N1   0.020
 T68  plan-2  N2   0.020
 T68  plan-2  C7   0.020
 T68  plan-2  O7   0.020
 T68  plan-2  C8   0.020
 T68  plan-2  O8   0.020
 T68  plan-2  C9   0.020
 T68  plan-2  HN1  0.020
 T68  plan-2  HN2  0.020

