# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 00:40:42 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-D-galacto-non-2-ulosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](NC(=O)CO)[C@@H](O)CC(=O)C(O)=O
#
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
 NGF  NGF  '3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-D-galacto-non-2-ulosonic acid'  D-saccharide  41  22  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NGF
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
 NGF  O10  O  O     0  -0.474  -0.4653   2.4147  -1.0824
 NGF  C10  C  C     0   0.511  -0.1571   2.2219   0.0779
 NGF  C11  C  CH2   0  -0.268  -0.0053   3.3507   1.0834
 NGF  N5   N  NH1   0  -0.658   0.0740   1.0005   0.6060
 NGF  C5   C  CH1   0  -0.161   0.0743  -0.2298  -0.1553
 NGF  C4   C  CH1   0   0.063  -1.1603  -1.0861   0.1668
 NGF  O4   O  OH1   0  -0.663  -1.1566  -1.5485   1.4976
 NGF  C3   C  CH2   0  -0.605  -2.4398  -0.3263  -0.1533
 NGF  C6   C  CH1   0   0.046   1.3874  -0.9926   0.0900
 NGF  O6   O  OH1   0  -0.664   1.3819  -2.2297  -0.5851
 NGF  C2   C  C     0   0.301  -3.6681  -1.1827  -0.1166
 NGF  O2   O  O     0  -0.341  -3.6781  -2.3805  -0.0314
 NGF  C1   C  C     0   0.485  -5.0005  -0.4215  -0.2361
 NGF  O1   O  O     0  -0.403  -5.0536   0.7744  -0.3435
 NGF  O3   O  OH1   0  -0.570  -6.0289  -1.2385  -0.2092
 NGF  C7   C  CH1   0  -0.025   2.6179  -0.1518  -0.2787
 NGF  O7   O  OH1   0  -0.662   2.5780   0.2665  -1.6268
 NGF  C8   C  CH1   0  -0.024   3.9352  -0.8806   0.0424
 NGF  O8   O  OH1   0  -0.659   3.9438  -1.3645   1.3655
 NGF  C9   C  CH2   0  -0.157   5.1309   0.0191  -0.2315
 NGF  O9   O  OH1   0  -0.671   6.3119  -0.7168  -0.0144
 NGF  O5   O  OH1   0  -0.657  -0.2382   4.5637   0.4328
 NGF  H1   H  HCH2  0   0.237  -0.7099   3.1704   1.9068
 NGF  H2   H  HCH2  0   0.235   1.0016   3.2924   1.5192
 NGF  H3   H  HNH1  0   0.399   0.3531   0.9526   1.5749
 NGF  H4   H  HCH1  0   0.267   0.0183   0.0425  -1.2120
 NGF  H5   H  HCH1  0   0.248  -1.1176  -1.9771  -0.4624
 NGF  H6   H  HOH1  0   0.443  -1.3337  -0.8089   2.0891
 NGF  H7   H  HCH2  0   0.285  -2.5734   0.5218   0.5253
 NGF  H8   H  HCH2  0   0.302  -2.3866   0.1204  -1.1526
 NGF  H9   H  HCH1  0   0.237   1.4527  -1.2322   1.1542
 NGF  H10  H  HOH1  0   0.444   1.1878  -2.0822  -1.5173
 NGF  H11  H  HOH1  0   0.494  -6.8586  -0.7412  -0.2810
 NGF  H12  H  HCH1  0   0.232   2.5924   0.7663   0.3191
 NGF  H13  H  HOH1  0   0.445   2.8336  -0.4678  -2.1961
 NGF  H14  H  HCH1  0   0.230   4.0078  -1.7675  -0.5978
 NGF  H15  H  HOH1  0   0.445   3.9526  -0.6126   1.9685
 NGF  H16  H  HCH2  0   0.204   5.0752   0.3967  -1.2581
 NGF  H17  H  HCH2  0   0.191   5.0733   0.8963   0.4321
 NGF  H18  H  HOH1  0   0.455   7.0574  -0.1373  -0.1941
 NGF  H19  H  HOH1  0   0.462  -0.1395   5.2669   1.0809

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
 NGF  C9   O9   single  1.408  0.020  1.408
 NGF  C9   C8   single  1.521  0.020  1.521
 NGF  O7   C7   single  1.412  0.020  1.412
 NGF  C8   C7   single  1.539  0.020  1.539
 NGF  C8   O8   single  1.409  0.020  1.409
 NGF  C7   C6   single  1.535  0.020  1.535
 NGF  O5   C11  single  1.396  0.020  1.396
 NGF  C11  C10  single  1.519  0.020  1.519
 NGF  O6   C6   single  1.409  0.020  1.409
 NGF  C6   C5   single  1.538  0.020  1.538
 NGF  C10  O10  double  1.216  0.020  1.216
 NGF  C10  N5   single  1.351  0.020  1.351
 NGF  C5   N5   single  1.447  0.020  1.447
 NGF  C5   C4   single  1.537  0.020  1.537
 NGF  O1   C1   double  1.202  0.020  1.202
 NGF  C3   C4   single  1.522  0.020  1.522
 NGF  C3   C2   single  1.498  0.020  1.498
 NGF  C4   O4   single  1.409  0.020  1.409
 NGF  C1   C2   single  1.539  0.020  1.539
 NGF  C1   O3   single  1.314  0.020  1.314
 NGF  C2   O2   double  1.201  0.020  1.201
 NGF  C11  H1   single  0.970  0.020  1.090
 NGF  C11  H2   single  0.970  0.020  1.090
 NGF  N5   H3   single  0.860  0.020  1.020
 NGF  C5   H4   single  0.970  0.020  1.090
 NGF  C4   H5   single  0.970  0.020  1.090
 NGF  O4   H6   single  0.850  0.020  0.980
 NGF  C3   H7   single  0.970  0.020  1.090
 NGF  C3   H8   single  0.970  0.020  1.090
 NGF  C6   H9   single  0.970  0.020  1.090
 NGF  O6   H10  single  0.850  0.020  0.980
 NGF  O3   H11  single  0.850  0.020  0.980
 NGF  C7   H12  single  0.970  0.020  1.090
 NGF  O7   H13  single  0.850  0.020  0.980
 NGF  C8   H14  single  0.970  0.020  1.090
 NGF  O8   H15  single  0.850  0.020  0.980
 NGF  C9   H16  single  0.970  0.020  1.090
 NGF  C9   H17  single  0.970  0.020  1.090
 NGF  O9   H18  single  0.850  0.020  0.980
 NGF  O5   H19  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
 NGF  N5   C10  C11  113.33  3.000
 NGF  N5   C10  O10  124.05  3.000
 NGF  C11  C10  O10  122.62  3.000
 NGF  H2   C11  H1   106.36  3.000
 NGF  H2   C11  O5   112.58  3.000
 NGF  H1   C11  O5   112.64  3.000
 NGF  H2   C11  C10  108.34  3.000
 NGF  H1   C11  C10  108.06  3.000
 NGF  O5   C11  C10  108.69  3.000
 NGF  H3   N5   C5   117.69  3.000
 NGF  H3   N5   C10  117.74  3.000
 NGF  C5   N5   C10  124.28  3.000
 NGF  H4   C5   C6   108.75  3.000
 NGF  H4   C5   C4   107.48  3.000
 NGF  C6   C5   C4   112.09  3.000
 NGF  H4   C5   N5   107.27  3.000
 NGF  C4   C5   N5   111.31  3.000
 NGF  C6   C5   N5   109.75  3.000
 NGF  H5   C4   C3   108.61  3.000
 NGF  H5   C4   O4   106.05  3.000
 NGF  C3   C4   O4   111.39  3.000
 NGF  H5   C4   C5   107.62  3.000
 NGF  O4   C4   C5   112.26  3.000
 NGF  C3   C4   C5   110.68  3.000
 NGF  H6   O4   C4   109.11  3.000
 NGF  H8   C3   H7   104.80  3.000
 NGF  H8   C3   C2   107.17  3.000
 NGF  H7   C3   C2   109.13  3.000
 NGF  H8   C3   C4   110.76  3.000
 NGF  H7   C3   C4   111.05  3.000
 NGF  C2   C3   C4   113.50  3.000
 NGF  H9   C6   C7   107.82  3.000
 NGF  H9   C6   O6   105.92  3.000
 NGF  C7   C6   O6   111.65  3.000
 NGF  H9   C6   C5   108.36  3.000
 NGF  O6   C6   C5   110.83  3.000
 NGF  C7   C6   C5   111.98  3.000
 NGF  H10  O6   C6   109.26  3.000
 NGF  C1   C2   O2   119.45  3.000
 NGF  O2   C2   C3   125.37  3.000
 NGF  C1   C2   C3   115.17  3.000
 NGF  O3   C1   O1   125.88  3.000
 NGF  O3   C1   C2   111.63  3.000
 NGF  O1   C1   C2   122.50  3.000
 NGF  H11  O3   C1   110.44  3.000
 NGF  H12  C7   C8   107.62  3.000
 NGF  H12  C7   O7   105.79  3.000
 NGF  C8   C7   O7   111.32  3.000
 NGF  H12  C7   C6   108.01  3.000
 NGF  C8   C7   C6   112.11  3.000
 NGF  O7   C7   C6   111.65  3.000
 NGF  H13  O7   C7   109.32  3.000
 NGF  H14  C8   C9   108.74  3.000
 NGF  H14  C8   O8   105.67  3.000
 NGF  C9   C8   O8   111.56  3.000
 NGF  H14  C8   C7   108.53  3.000
 NGF  O8   C8   C7   111.33  3.000
 NGF  C9   C8   C7   110.80  3.000
 NGF  H15  O8   C8   108.64  3.000
 NGF  H17  C9   H16  106.71  3.000
 NGF  H17  C9   O9   111.54  3.000
 NGF  H16  C9   O9   111.55  3.000
 NGF  H17  C9   C8   108.75  3.000
 NGF  H16  C9   C8   109.43  3.000
 NGF  O9   C9   C8   108.80  3.000
 NGF  H18  O9   C9   107.85  3.000
 NGF  H19  O5   C11  107.71  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
 NGF  CONST_01  C5   N5   C10  O10    0.00   0.0  0
 NGF  CONST_02  C5   N5   C10  C11  180.00   0.0  0
 NGF  CONST_03  H3   N5   C10  O10  180.00   0.0  0
 NGF  CONST_04  H11  O3   C1   C2   180.00   0.0  0
 NGF  Var_01    O5   C11  C10  O10   -1.60  30.0  1
 NGF  Var_02    C1   C2   C3   C4   171.70  30.0  3
 NGF  Var_03    O1   C1   C2   C3    -0.41  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
 NGF  chir_01  C5  C6  N5  C4  positiv
 NGF  chir_02  C4  O4  C5  C3  positiv
 NGF  chir_03  C6  O6  C5  C7  positiv
 NGF  chir_04  C7  O7  C6  C8  negativ
 NGF  chir_05  C8  O8  C7  C9  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
 NGF  plan-1  O10  0.020
 NGF  plan-1  C10  0.020
 NGF  plan-1  C11  0.020
 NGF  plan-1  N5   0.020
 NGF  plan-1  C5   0.020
 NGF  plan-1  H3   0.020
 NGF  plan-2  C3   0.020
 NGF  plan-2  C2   0.020
 NGF  plan-2  O2   0.020
 NGF  plan-2  C1   0.020
 NGF  plan-3  C2   0.020
 NGF  plan-3  C1   0.020
 NGF  plan-3  O1   0.020
 NGF  plan-3  O3   0.020
 NGF  plan-3  H11  0.020

