# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 06:59:55 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-4-O-sulfo-alpha-D-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@H](O[S](O)(=O)=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
 NGK  NGK  2-(acetylamino)-2-deoxy-4-O-sulfo-alpha-D-galactopyranose  D-saccharide  33  19  .  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_NGK
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
 NGK  C1    C  CH1    0   0.270   1.6380   0.2339   1.5230
 NGK  C2    C  CH1    0  -0.167   0.1260   0.0183   1.6229
 NGK  C3    C  CH1    0   0.062  -0.3332  -1.0660   0.6404
 NGK  C4    C  CH1    0  -0.029   0.1298  -0.7008  -0.7663
 NGK  C5    C  CH1    0  -0.004   1.6437  -0.5071  -0.7415
 NGK  C6    C  CH2    0  -0.159   2.2195  -0.1089  -2.0832
 NGK  C7    C  C      0   0.519  -1.0417   0.4818   3.7466
 NGK  C8    C  CH3    0  -0.780  -1.2771  -0.0305   5.1450
 NGK  N     N  NH1    0  -0.643  -0.2643  -0.3042   2.9726
 NGK  O1    O  OH1    0  -0.670   2.2669  -0.8923   2.0504
 NGK  O3    O  OH1    0  -0.652  -1.7239  -1.2205   0.6518
 NGK  O4    O  OC2    0  -0.626  -0.5082   0.5039  -1.1706
 NGK  O5    O  O2     0  -0.498   2.0097   0.4898   0.1990
 NGK  O6    O  OH1    0  -0.673   3.6253  -0.1621  -1.9909
 NGK  O7    O  O      0  -0.498  -1.5297   1.5331   3.3582
 NGK  S     S  S      0   1.566  -1.4654   0.4990  -2.5096
 NGK  O1S   O  OS     0  -0.737  -1.9418   1.8802  -2.4900
 NGK  O2S   O  OS    -1  -0.730  -2.4968  -0.5115  -2.2784
 NGK  O3S   O  OS     0  -0.736  -0.5794   0.1751  -3.6316
 NGK  H1    H  HCH1   0   0.239   1.9165   1.1377   2.0763
 NGK  H2    H  HCH1   0   0.279  -0.3636   0.9562   1.3591
 NGK  H3    H  HCH1   0   0.218   0.1666  -2.0114   0.8996
 NGK  H4    H  HCH1   0   0.264  -0.1033  -1.5281  -1.4466
 NGK  H5    H  HCH1   0   0.228   2.0834  -1.4755  -0.4654
 NGK  H6C1  H  HCH2   0   0.203   1.8350  -0.8047  -2.8378
 NGK  H6C2  H  HCH2   0   0.202   1.8682   0.8912  -2.3582
 NGK  H8C1  H  HCH3   0   0.267  -2.3483  -0.1384   5.3140
 NGK  H8C2  H  HCH3   0   0.249  -0.7972  -0.9856   5.3502
 NGK  H8C3  H  HCH3   0   0.267  -0.9082   0.7029   5.8620
 NGK  H     H  HNH1   0   0.400   0.1454  -1.1255   3.3898
 NGK  HA    H  HOH1   0   0.466   3.1938  -0.6904   2.2169
 NGK  HB    H  HOH1   0   0.448  -1.9816  -1.4977   1.5373
 NGK  H6    H  HOH1   0   0.455   3.9880   0.1444  -2.8264

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
 NGK  C1  C2    single  1.530  0.020  1.530
 NGK  C1  O1    single  1.394  0.020  1.394
 NGK  C1  O5    single  1.399  0.020  1.399
 NGK  C1  H1    single  0.970  0.020  1.090
 NGK  C2  C3    single  1.534  0.020  1.534
 NGK  C2  N     single  1.442  0.020  1.442
 NGK  C2  H2    single  0.970  0.020  1.090
 NGK  C3  C4    single  1.525  0.020  1.525
 NGK  C3  O3    single  1.399  0.020  1.399
 NGK  C3  H3    single  0.970  0.020  1.090
 NGK  C4  C5    single  1.526  0.020  1.526
 NGK  C4  O4    single  1.422  0.020  1.422
 NGK  C4  H4    single  0.970  0.020  1.090
 NGK  C5  C6    single  1.513  0.020  1.513
 NGK  C5  O5    single  1.419  0.020  1.419
 NGK  C5  H5    single  0.970  0.020  1.090
 NGK  C6  O6    single  1.410  0.020  1.410
 NGK  C6  H6C1  single  0.970  0.020  1.090
 NGK  C6  H6C2  single  0.970  0.020  1.090
 NGK  C7  C8    single  1.508  0.020  1.508
 NGK  C7  N     single  1.350  0.020  1.350
 NGK  C7  O7    double  1.222  0.020  1.222
 NGK  C8  H8C1  single  0.970  0.020  1.090
 NGK  C8  H8C2  single  0.970  0.020  1.090
 NGK  C8  H8C3  single  0.970  0.020  1.090
 NGK  N   H     single  0.860  0.020  1.020
 NGK  O1  HA    single  0.850  0.020  0.980
 NGK  O3  HB    single  0.850  0.020  0.980
 NGK  O4  S     single  1.646  0.020  1.646
 NGK  O6  H6    single  0.850  0.020  0.980
 NGK  S   O1S   deloc   1.461  0.020  1.461
 NGK  S   O2S   deloc   1.462  0.020  1.462
 NGK  S   O3S   deloc   1.466  0.020  1.466

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
 NGK  H1    C1  O5    105.04  3.000
 NGK  H1    C1  O1    111.15  3.000
 NGK  O5    C1  O1    112.71  3.000
 NGK  H1    C1  C2    109.54  3.000
 NGK  O5    C1  C2    110.49  3.000
 NGK  O1    C1  C2    107.90  3.000
 NGK  H2    C2  N     107.30  3.000
 NGK  H2    C2  C3    108.59  3.000
 NGK  N     C2  C3    111.13  3.000
 NGK  H2    C2  C1    107.86  3.000
 NGK  N     C2  C1    111.10  3.000
 NGK  C3    C2  C1    110.71  3.000
 NGK  H3    C3  O3    110.77  3.000
 NGK  H3    C3  C4    106.56  3.000
 NGK  O3    C3  C4    109.61  3.000
 NGK  H3    C3  C2    108.70  3.000
 NGK  O3    C3  C2    111.74  3.000
 NGK  C4    C3  C2    109.31  3.000
 NGK  H4    C4  O4    111.56  3.000
 NGK  H4    C4  C5    108.47  3.000
 NGK  O4    C4  C5    110.01  3.000
 NGK  H4    C4  C3    109.09  3.000
 NGK  O4    C4  C3    109.20  3.000
 NGK  C5    C4  C3    108.45  3.000
 NGK  H5    C5  O5    110.46  3.000
 NGK  H5    C5  C6    107.60  3.000
 NGK  O5    C5  C6    107.74  3.000
 NGK  H5    C5  C4    106.80  3.000
 NGK  O5    C5  C4    110.85  3.000
 NGK  C6    C5  C4    113.35  3.000
 NGK  H6C2  C6  H6C1  107.12  3.000
 NGK  H6C2  C6  O6    111.76  3.000
 NGK  H6C1  C6  O6    111.77  3.000
 NGK  H6C2  C6  C5    109.93  3.000
 NGK  H6C1  C6  C5    108.05  3.000
 NGK  O6    C6  C5    108.15  3.000
 NGK  O7    C7  N     123.27  3.000
 NGK  O7    C7  C8    121.64  3.000
 NGK  N     C7  C8    115.09  3.000
 NGK  H8C3  C8  H8C2  108.49  3.000
 NGK  H8C3  C8  H8C1  107.29  3.000
 NGK  H8C2  C8  H8C1  108.50  3.000
 NGK  H8C3  C8  C7    109.19  3.000
 NGK  H8C2  C8  C7    113.84  3.000
 NGK  H8C1  C8  C7    109.33  3.000
 NGK  H     N   C7    118.11  3.000
 NGK  H     N   C2    117.37  3.000
 NGK  C7    N   C2    124.24  3.000
 NGK  HA    O1  C1    109.29  3.000
 NGK  HB    O3  C3    107.77  3.000
 NGK  S     O4  C4    119.32  3.000
 NGK  C5    O5  C1    115.50  3.000
 NGK  H6    O6  C6    107.91  3.000
 NGK  O3S   S   O2S   113.25  3.000
 NGK  O3S   S   O1S   114.59  3.000
 NGK  O2S   S   O1S   114.91  3.000
 NGK  O3S   S   O4    105.77  3.000
 NGK  O2S   S   O4    106.48  3.000
 NGK  O1S   S   O4    100.13  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
 NGK  CONST_01  C8    C7  N   C2   180.00   0.0  0
 NGK  CONST_02  O7    C7  N   C2     0.00   0.0  0
 NGK  CONST_03  H     N   C7  C8     0.00   0.0  0
 NGK  Var_01    O1S   S   O4  C4   177.14  30.0  3
 NGK  Var_02    H8C1  C8  C7  N   -122.34  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
 NGK  chir_01  C1  C2  O1  O5  negativ
 NGK  chir_02  C2  N   C3  C1  positiv
 NGK  chir_03  C3  O3  C2  C4  positiv
 NGK  chir_04  C4  O4  C5  C3  negativ
 NGK  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
 NGK  plan-1  C2  0.020
 NGK  plan-1  C7  0.020
 NGK  plan-1  C8  0.020
 NGK  plan-1  N   0.020
 NGK  plan-1  O7  0.020
 NGK  plan-1  H   0.020

