# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 03:30:09 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H]1O[C@@](O)(C[C@H](O)[C@H]1NC(=O)CO)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
 NGE  NGE  '3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid'  D-saccharide  40  22  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NGE
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
 NGE  O9    O  OH1    0  -0.676   8.1315   -5.5601  -17.2196
 NGE  C9    C  CH2    0  -0.180   7.2369   -6.4291  -16.5564
 NGE  C8    C  CH1    0  -0.018   8.0481   -7.4064  -15.7233
 NGE  O8    O  OH1    0  -0.665   8.8723   -8.2074  -16.5432
 NGE  C7    C  CH1    0  -0.010   8.8830   -6.7063  -14.6311
 NGE  O7    O  OH1    0  -0.666   8.0883   -5.8530  -13.8422
 NGE  C6    C  CH1    0   0.023   9.6217   -7.7204  -13.7552
 NGE  O6    O  O2     0  -0.528   8.6138   -8.3873  -13.0285
 NGE  C3    C  CH2    0  -0.514  10.0200   -8.7739  -11.1156
 NGE  C4    C  CH1    0   0.051  11.1794   -8.0926  -11.8214
 NGE  O4    O  OH1    0  -0.658  12.0001   -7.5028  -10.8435
 NGE  C5    C  CH1    0  -0.120  10.6336   -7.0600  -12.8089
 NGE  N5    N  NH1    0  -0.640  11.7135   -6.4676  -13.5617
 NGE  C2    C  CT     0   0.361   9.0130   -9.3755  -12.0960
 NGE  C10   C  C      0   0.472  11.9934   -5.1558  -13.6111
 NGE  O10   O  O      0  -0.489  11.3923   -4.2889  -12.9952
 NGE  C11   C  CH2    0  -0.278  13.1791   -4.7839  -14.4941
 NGE  O11   O  OH1    0  -0.652  13.6718   -5.8227  -15.2980
 NGE  HO9   H  HOH1   0   0.458   7.6564   -5.1062  -17.9205
 NGE  H91   H  HCH2   0   0.200   6.5361   -5.8861  -15.9129
 NGE  H92   H  HCH2   0   0.214   6.6356   -7.0050  -17.2708
 NGE  H8    H  HCH1   0   0.237   7.3372   -8.0858  -15.2424
 NGE  HO8   H  HOH1   0   0.439   9.3903   -7.6152  -17.1004
 NGE  H7    H  HCH1   0   0.241   9.6248   -6.0713  -15.1256
 NGE  HO7   H  HOH1   0   0.440   7.5447   -6.4081  -13.2699
 NGE  H6    H  HCH1   0   0.221  10.1668   -8.4149  -14.4110
 NGE  H5    H  HCH1   0   0.257  10.1418   -6.2688  -12.2386
 NGE  H31   H  HCH2   0   0.252  10.3911   -9.5538  -10.4457
 NGE  H32   H  HCH2   0   0.244   9.5043   -8.0338  -10.5005
 NGE  H4    H  HCH1   0   0.196  11.7611   -8.8339  -12.3962
 NGE  HO4   H  HOH1   0   0.448  12.7743   -7.1329  -11.2810
 NGE  HN5   H  HNH1   0   0.398  12.2872   -7.0796  -14.1255
 NGE  H111  H  HCH2   0   0.245  12.8895   -3.9026  -15.0752
 NGE  H112  H  HCH2   0   0.260  13.9865   -4.4676  -13.8286
 NGE  HO11  H  HOH1   0   0.461  13.1192   -5.8933  -16.0830
 NGE  C1    C  C      0   0.380   7.6848   -9.7652  -11.3642
 NGE  O2    O  OH1    0  -0.665   9.5182  -10.4965  -12.7510
 NGE  HO2   H  HOH1   0   0.444  10.4495  -10.3783  -12.9658
 NGE  O1A   O  O      0  -0.582   7.3268  -10.9500  -11.4251
 NGE  O1B   O  OC    -1  -0.598   7.1194   -8.8202  -10.7857

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
 NGE  O9   C9    single  1.413  0.020  1.413
 NGE  C9   C8    single  1.519  0.020  1.519
 NGE  C8   O8    single  1.412  0.020  1.412
 NGE  C8   C7    single  1.543  0.020  1.543
 NGE  C7   O7    single  1.408  0.020  1.408
 NGE  C7   C6    single  1.530  0.020  1.530
 NGE  C6   O6    single  1.410  0.020  1.410
 NGE  C6   C5    single  1.535  0.020  1.535
 NGE  O6   C2    single  1.416  0.020  1.416
 NGE  C1   O1A   deloc   1.239  0.020  1.239
 NGE  C1   O1B   deloc   1.244  0.020  1.244
 NGE  C1   C2    single  1.566  0.020  1.566
 NGE  O2   C2    single  1.393  0.020  1.393
 NGE  C3   C4    single  1.519  0.020  1.519
 NGE  C3   C2    single  1.529  0.020  1.529
 NGE  C4   O4    single  1.406  0.020  1.406
 NGE  C4   C5    single  1.529  0.020  1.529
 NGE  C5   N5    single  1.444  0.020  1.444
 NGE  N5   C10   single  1.342  0.020  1.342
 NGE  C10  O10   double  1.222  0.020  1.222
 NGE  C10  C11   single  1.524  0.020  1.524
 NGE  C11  O11   single  1.403  0.020  1.403
 NGE  O9   HO9   single  0.850  0.020  0.980
 NGE  C9   H91   single  0.970  0.020  1.090
 NGE  C9   H92   single  0.970  0.020  1.090
 NGE  C8   H8    single  0.970  0.020  1.090
 NGE  O8   HO8   single  0.850  0.020  0.980
 NGE  C7   H7    single  0.970  0.020  1.090
 NGE  O7   HO7   single  0.850  0.020  0.980
 NGE  C6   H6    single  0.970  0.020  1.090
 NGE  C5   H5    single  0.970  0.020  1.090
 NGE  O2   HO2   single  0.850  0.020  0.980
 NGE  C3   H31   single  0.970  0.020  1.090
 NGE  C3   H32   single  0.970  0.020  1.090
 NGE  C4   H4    single  0.970  0.020  1.090
 NGE  O4   HO4   single  0.850  0.020  0.980
 NGE  N5   HN5   single  0.860  0.020  1.020
 NGE  C11  H111  single  0.970  0.020  1.090
 NGE  C11  H112  single  0.970  0.020  1.090
 NGE  O11  HO11  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
 NGE  HO9   O9   C9    108.65  3.000
 NGE  H92   C9   H91   106.99  3.000
 NGE  H92   C9   C8    108.18  3.000
 NGE  H91   C9   C8    109.78  3.000
 NGE  H92   C9   O9    111.37  3.000
 NGE  H91   C9   O9    112.09  3.000
 NGE  C8    C9   O9    108.36  3.000
 NGE  H8    C8   C7    108.79  3.000
 NGE  H8    C8   O8    106.39  3.000
 NGE  C7    C8   O8    110.65  3.000
 NGE  H8    C8   C9    107.06  3.000
 NGE  C7    C8   C9    112.66  3.000
 NGE  O8    C8   C9    111.00  3.000
 NGE  HO8   O8   C8    107.50  3.000
 NGE  H7    C7   C6    108.42  3.000
 NGE  H7    C7   O7    106.50  3.000
 NGE  C6    C7   O7    110.70  3.000
 NGE  H7    C7   C8    108.07  3.000
 NGE  C6    C7   C8    111.45  3.000
 NGE  O7    C7   C8    111.48  3.000
 NGE  HO7   O7   C7    107.55  3.000
 NGE  H6    C6   C5    108.22  3.000
 NGE  H6    C6   O6    111.28  3.000
 NGE  C5    C6   O6    110.91  3.000
 NGE  H6    C6   C7    108.45  3.000
 NGE  C5    C6   C7    112.71  3.000
 NGE  O6    C6   C7    105.27  3.000
 NGE  C2    O6   C6    117.89  3.000
 NGE  H32   C3   H31   107.38  3.000
 NGE  H32   C3   C2    108.48  3.000
 NGE  H31   C3   C2    109.63  3.000
 NGE  H32   C3   C4    108.56  3.000
 NGE  H31   C3   C4    110.22  3.000
 NGE  C2    C3   C4    112.42  3.000
 NGE  H4    C4   C5    107.77  3.000
 NGE  H4    C4   O4    109.65  3.000
 NGE  C5    C4   O4    111.97  3.000
 NGE  H4    C4   C3    110.07  3.000
 NGE  C5    C4   C3    109.29  3.000
 NGE  O4    C4   C3    108.09  3.000
 NGE  HO4   O4   C4    108.32  3.000
 NGE  H5    C5   N5    108.16  3.000
 NGE  H5    C5   C4    108.22  3.000
 NGE  N5    C5   C4    110.29  3.000
 NGE  H5    C5   C6    109.68  3.000
 NGE  N5    C5   C6    110.38  3.000
 NGE  C4    C5   C6    110.05  3.000
 NGE  HN5   N5   C10   116.92  3.000
 NGE  HN5   N5   C5    117.84  3.000
 NGE  C10   N5   C5    125.20  3.000
 NGE  C3    C2   O2    112.29  3.000
 NGE  C3    C2   C1    110.92  3.000
 NGE  O2    C2   C1    109.09  3.000
 NGE  C3    C2   O6    109.47  3.000
 NGE  O2    C2   O6    110.74  3.000
 NGE  C1    C2   O6    104.02  3.000
 NGE  C11   C10  O10   120.11  3.000
 NGE  C11   C10  N5    114.96  3.000
 NGE  O10   C10  N5    124.91  3.000
 NGE  H112  C11  H111  106.60  3.000
 NGE  H112  C11  O11   107.68  3.000
 NGE  H111  C11  O11   112.64  3.000
 NGE  H112  C11  C10   107.01  3.000
 NGE  H111  C11  C10   107.34  3.000
 NGE  O11   C11  C10   115.12  3.000
 NGE  HO11  O11  C11   108.67  3.000
 NGE  C2    C1   O1B   114.44  3.000
 NGE  C2    C1   O1A   117.40  3.000
 NGE  O1B   C1   O1A   128.16  3.000
 NGE  HO2   O2   C2    110.90  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
 NGE  CONST_01  O10  C10  N5   C5     0.00   0.0  0
 NGE  CONST_02  C11  C10  N5   C5   180.00   0.0  0
 NGE  CONST_03  HN5  N5   C10  O10  180.00   0.0  0
 NGE  Var_01    O11  C11  C10  N5    10.00  30.0  3

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
 NGE  chir_01  C8  C9  O8  C7  negativ
 NGE  chir_02  C7  O7  C8  C6  positiv
 NGE  chir_03  C6  O6  C5  C7  positiv
 NGE  chir_04  C4  O4  C5  C3  positiv
 NGE  chir_05  C5  N5  C6  C4  negativ
 NGE  chir_06  C2  O6  C1  C3  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
 NGE  plan-1  C5   0.020
 NGE  plan-1  N5   0.020
 NGE  plan-1  C10  0.020
 NGE  plan-1  O10  0.020
 NGE  plan-1  C11  0.020
 NGE  plan-1  HN5  0.020
 NGE  plan-2  C2   0.020
 NGE  plan-2  C1   0.020
 NGE  plan-2  O1A  0.020
 NGE  plan-2  O1B  0.020

