# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 17:16:53 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N-[oxo(pyridin-2-ylamino)acetyl]-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)C(=O)Nc2ccccn2)[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
 475  475  N-[oxo(pyridin-2-ylamino)acetyl]-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_475
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
 475  C2   C  CH1   0  -0.033  -2.4989  -1.5701   0.0379
 475  N2   N  NH1   0  -0.720   3.1005   0.2007  -0.4356
 475  C3   C  CH1   0  -0.004  -3.9480  -1.3328  -0.3653
 475  C5   C  CH1   0  -0.017  -3.5539   1.1097  -0.0274
 475  C4   C  CH1   0   0.035  -4.4877  -0.0616   0.2812
 475  C10  C  CR16  0  -0.399   5.3478   0.7166  -1.0439
 475  C11  C  CR16  0  -0.141   6.6967   0.6645  -0.7573
 475  C12  C  CR16  0  -0.339   7.1171   0.0535   0.4185
 475  C13  C  CR16  0  -0.061   6.1487  -0.4771   1.2512
 475  N3   N  N     0  -0.424   4.8450  -0.4353   0.9913
 475  C9   C  CR6   0   0.530   4.4589   0.1459  -0.1288
 475  C8   C  C     0   0.441   2.0479  -0.2554   0.2688
 475  O8   O  O     0  -0.421   2.0538  -0.8072   1.3472
 475  O7   O  O     0  -0.453   0.7065   0.5767  -1.5536
 475  N1   N  NH1   0  -0.679  -0.3396  -0.4619   0.1828
 475  C1   C  CH1   0   0.214  -1.6874  -0.3082  -0.2643
 475  O5   O  O2    0  -0.486  -2.2427   0.7981   0.4005
 475  C6   C  CH2   0  -0.156  -3.9814   2.3778   0.6808
 475  O4   O  OH1   0  -0.671  -5.7650   0.2589  -0.2107
 475  O3   O  OH1   0  -0.671  -4.7816  -2.3955   0.0266
 475  O2   O  OH1   0  -0.662  -2.0225  -2.6709  -0.6927
 475  H2   H  HCH1  0   0.234  -2.4601  -1.7570   1.1217
 475  HN2  H  HNH1  0   0.429   2.8609   0.6411  -1.3145
 475  H3   H  HCH1  0   0.219  -3.9806  -1.1922  -1.4579
 475  H5   H  HCH1  0   0.227  -3.5605   1.2841  -1.1158
 475  HO6  H  HOH1  0   0.457  -3.4172   4.2265   0.7319
 475  H4   H  HCH1  0   0.215  -4.5087  -0.2084   1.3728
 475  H11  H  HCR6  0   0.280   7.4125   1.0957  -1.4445
 475  H12  H  HCR6  0   0.273   8.1631  -0.0097   0.6822
 475  H13  H  HCR6  0   0.267   6.4313  -0.9620   2.1785
 475  HN1  H  HNH1  0   0.417  -0.1730  -0.8634   1.0964
 475  H1   H  HCH1  0   0.238  -1.6745  -0.1404  -1.3491
 475  H6   H  HCH2  0   0.213  -5.0262   2.5799   0.4237
 475  H6A  H  HCH2  0   0.198  -3.9411   2.2108   1.7661
 475  HO4  H  HOH1  0   0.456  -6.3649  -0.4593   0.0158
 475  HO3  H  HOH1  0   0.457  -4.5671  -3.1663  -0.5083
 475  HO2  H  HOH1  0   0.459  -1.2425  -3.0260  -0.2559
 475  O6   O  OH1   0  -0.670  -3.1322   3.4266   0.2815
 475  C7   C  C     0   0.463   0.7232   0.0093  -0.4777
 475  H10  H  HCR6  0   0.286   4.9874   1.1825  -1.9519

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
 475  C2   C3   single    1.523  0.020  1.523
 475  C2   C1   single    1.530  0.020  1.530
 475  C2   O2   single    1.404  0.020  1.404
 475  N2   C9   single    1.394  0.020  1.394
 475  N2   C8   single    1.346  0.020  1.346
 475  C3   C4   single    1.525  0.020  1.525
 475  C3   O3   single    1.406  0.020  1.406
 475  C5   C4   single    1.529  0.020  1.529
 475  C5   O5   single    1.414  0.020  1.414
 475  C5   C6   single    1.514  0.020  1.514
 475  O6   C6   single    1.407  0.020  1.407
 475  C4   O4   single    1.406  0.020  1.406
 475  C10  C11  aromatic  1.380  0.020  1.380
 475  C10  C9   aromatic  1.398  0.020  1.398
 475  C11  C12  aromatic  1.390  0.020  1.390
 475  C12  C13  aromatic  1.383  0.020  1.383
 475  C13  N3   aromatic  1.330  0.020  1.330
 475  N3   C9   aromatic  1.320  0.020  1.320
 475  C8   O8   double    1.211  0.020  1.211
 475  C8   C7   single    1.543  0.020  1.543
 475  C7   O7   double    1.216  0.020  1.216
 475  C7   N1   single    1.337  0.020  1.337
 475  N1   C1   single    1.428  0.020  1.428
 475  C1   O5   single    1.405  0.020  1.405
 475  C2   H2   single    0.970  0.020  1.090
 475  N2   HN2  single    0.860  0.020  1.020
 475  C3   H3   single    0.970  0.020  1.090
 475  C5   H5   single    0.970  0.020  1.090
 475  O6   HO6  single    0.850  0.020  0.980
 475  C4   H4   single    0.970  0.020  1.090
 475  C10  H10  single    0.930  0.020  1.080
 475  C11  H11  single    0.930  0.020  1.080
 475  C12  H12  single    0.930  0.020  1.080
 475  C13  H13  single    0.930  0.020  1.080
 475  N1   HN1  single    0.860  0.020  1.020
 475  C1   H1   single    0.970  0.020  1.090
 475  C6   H6   single    0.970  0.020  1.090
 475  C6   H6A  single    0.970  0.020  1.090
 475  O4   HO4  single    0.850  0.020  0.980
 475  O3   HO3  single    0.850  0.020  0.980
 475  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
 475  H2   C2   O2   111.55  3.000
 475  H2   C2   C1   108.41  3.000
 475  O2   C2   C1   111.33  3.000
 475  H2   C2   C3   108.71  3.000
 475  O2   C2   C3   107.90  3.000
 475  C1   C2   C3   108.89  3.000
 475  HN2  N2   C8   114.63  3.000
 475  HN2  N2   C9   116.05  3.000
 475  C8   N2   C9   129.32  3.000
 475  H3   C3   O3   110.80  3.000
 475  H3   C3   C4   107.67  3.000
 475  O3   C3   C4   107.58  3.000
 475  H3   C3   C2   108.09  3.000
 475  O3   C3   C2   111.87  3.000
 475  C4   C3   C2   110.77  3.000
 475  H5   C5   C6   109.12  3.000
 475  H5   C5   O5   109.83  3.000
 475  C6   C5   O5   107.75  3.000
 475  H5   C5   C4   108.47  3.000
 475  C6   C5   C4   112.00  3.000
 475  O5   C5   C4   109.65  3.000
 475  H4   C4   O4   111.09  3.000
 475  H4   C4   C5   108.28  3.000
 475  O4   C4   C5   108.03  3.000
 475  H4   C4   C3   108.41  3.000
 475  O4   C4   C3   111.30  3.000
 475  C5   C4   C3   109.68  3.000
 475  H10  C10  C9   120.88  3.000
 475  H10  C10  C11  121.06  3.000
 475  C9   C10  C11  118.06  3.000
 475  H11  C11  C12  120.82  3.000
 475  H11  C11  C10  119.99  3.000
 475  C12  C11  C10  119.19  3.000
 475  H12  C12  C13  120.56  3.000
 475  H12  C12  C11  121.65  3.000
 475  C13  C12  C11  117.79  3.000
 475  H13  C13  N3   115.90  3.000
 475  H13  C13  C12  120.27  3.000
 475  N3   C13  C12  123.82  3.000
 475  C9   N3   C13  117.81  3.000
 475  N3   C9   C10  123.33  3.000
 475  N3   C9   N2   119.30  3.000
 475  C10  C9   N2   117.37  3.000
 475  C7   C8   O8   120.85  3.000
 475  C7   C8   N2   111.10  3.000
 475  O8   C8   N2   128.05  3.000
 475  HN1  N1   C1   118.73  3.000
 475  HN1  N1   C7   117.07  3.000
 475  C1   N1   C7   123.88  3.000
 475  H1   C1   O5   110.60  3.000
 475  H1   C1   N1   108.34  3.000
 475  O5   C1   N1   108.03  3.000
 475  H1   C1   C2   109.11  3.000
 475  O5   C1   C2   110.26  3.000
 475  N1   C1   C2   110.47  3.000
 475  C1   O5   C5   113.38  3.000
 475  H6A  C6   H6   107.16  3.000
 475  H6A  C6   O6   111.80  3.000
 475  H6   C6   O6   111.82  3.000
 475  H6A  C6   C5   108.92  3.000
 475  H6   C6   C5   108.31  3.000
 475  O6   C6   C5   108.73  3.000
 475  HO4  O4   C4   108.29  3.000
 475  HO3  O3   C3   108.56  3.000
 475  HO2  O2   C2   109.16  3.000
 475  HO6  O6   C6   107.96  3.000
 475  N1   C7   O7   126.18  3.000
 475  N1   C7   C8   112.51  3.000
 475  O7   C7   C8   121.30  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
 475  CONST_01  C13  C12  C11  C10    0.00  0.0  0
 475  CONST_02  C13  N3   C9   C10    0.00  0.0  0
 475  CONST_03  N3   C9   C10  C11    0.00  0.0  0
 475  CONST_04  N3   C13  C12  C11    0.00  0.0  0
 475  CONST_05  C9   C10  C11  C12    0.00  0.0  0
 475  CONST_06  C9   N3   C13  C12    0.00  0.0  0
 475  CONST_07  C11  C10  C9   N2   180.00  0.0  0
 475  CONST_08  C13  N3   C9   N2   180.00  0.0  0
 475  CONST_09  H12  C12  C11  C10  180.00  0.0  0
 475  CONST_10  H13  C13  C12  C11  180.00  0.0  0
 475  CONST_11  H10  C10  C11  C12  180.00  0.0  0
 475  CONST_12  H11  C11  C12  C13  180.00  0.0  0
 475  CONST_13  C8   N2   C9   C10  180.00  0.0  0
 475  CONST_14  C8   N2   C9   N3     0.00  0.0  0
 475  CONST_15  HN2  N2   C9   C10    0.00  0.0  0
 475  CONST_16  O8   C8   N2   C9     0.00  0.0  0
 475  CONST_17  C7   C8   N2   C9   180.00  0.0  0
 475  CONST_18  C1   N1   C7   C8   180.00  0.0  0
 475  CONST_19  C1   N1   C7   O7     0.00  0.0  0
 475  CONST_20  N1   C7   C8   N2   180.00  0.0  0
 475  CONST_21  N1   C7   C8   O8     0.00  0.0  0
 475  CONST_22  HN1  N1   C7   C8     0.00  0.0  0

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
 475  chir_01  C2  C3  C1  O2  positiv
 475  chir_02  C3  O3  C2  C4  positiv
 475  chir_03  C5  O5  C4  C6  negativ
 475  chir_04  C4  O4  C5  C3  positiv
 475  chir_05  C1  O5  N1  C2  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
 475  plan-1  N2   0.020
 475  plan-1  C10  0.020
 475  plan-1  C11  0.020
 475  plan-1  C12  0.020
 475  plan-1  C13  0.020
 475  plan-1  N3   0.020
 475  plan-1  C9   0.020
 475  plan-1  H11  0.020
 475  plan-1  H12  0.020
 475  plan-1  H13  0.020
 475  plan-1  H10  0.020
 475  plan-2  N2   0.020
 475  plan-2  C9   0.020
 475  plan-2  C8   0.020
 475  plan-2  O8   0.020
 475  plan-2  O7   0.020
 475  plan-2  N1   0.020
 475  plan-2  C1   0.020
 475  plan-2  HN2  0.020
 475  plan-2  HN1  0.020
 475  plan-2  C7   0.020

