# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 09:43:59 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  34  19  .  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_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   0.266   1.6668   0.2341   1.4455
 NGK  C2    C  CH1   0  -0.154   0.1539  -0.0124   1.4608
 NGK  C3    C  CH1   0   0.048  -0.2035  -1.1119   0.4586
 NGK  C4    C  CH1   0  -0.067   0.3329  -0.7548  -0.9189
 NGK  C5    C  CH1   0  -0.016   1.8300  -0.4950  -0.8172
 NGK  C6    C  CH2   0  -0.158   2.4350  -0.0676  -2.1401
 NGK  C7    C  C     0   0.520  -1.2535   0.3615   3.4463
 NGK  C8    C  CH3   0  -0.780  -1.5636  -0.1391   4.8331
 NGK  N     N  NH1   0  -0.645  -0.3110  -0.3443   2.7809
 NGK  O1    O  OH1   0  -0.665   2.2838  -0.8840   1.9935
 NGK  O3    O  OH1   0  -0.694  -1.6019  -1.3225   0.3762
 NGK  O4    O  OC2   0  -0.595  -0.2648   0.4706  -1.4028
 NGK  O5    O  O2    0  -0.492   2.1018   0.5079   0.1409
 NGK  O6    O  OH1   0  -0.668   3.8342  -0.1089  -2.0104
 NGK  O7    O  O     0  -0.489  -1.8228   1.3291   2.9662
 NGK  S     S  S     0   1.646  -1.6648   0.4920  -2.1704
 NGK  O1S   O  OS    0  -0.626  -1.7161   1.7658  -2.8307
 NGK  O2S   O  OS    0  -0.729  -2.7009   0.5535  -0.9931
 NGK  O3S   O  OS    0  -0.636  -1.8185  -0.7291  -2.9226
 NGK  H1    H  HCH1  0   0.254   1.8941   1.1401   2.0162
 NGK  H2    H  HCH1  0   0.289  -0.3394   0.9154   1.1679
 NGK  H3    H  HCH1  0   0.279   0.2805  -2.0514   0.7481
 NGK  H4    H  HCH1  0   0.314   0.1514  -1.5675  -1.6276
 NGK  H5    H  HCH1  0   0.257   2.2889  -1.4510  -0.5308
 NGK  H6C1  H  HCH2  0   0.209   2.0768  -0.7586  -2.9150
 NGK  H6C2  H  HCH2  0   0.214   2.0807   0.9340  -2.4075
 NGK  H8C1  H  HCH3  0   0.270  -2.6140  -0.4252   4.8855
 NGK  H8C2  H  HCH3  0   0.251  -0.9590  -0.9914   5.1371
 NGK  H8C3  H  HCH3  0   0.269  -1.4112   0.6677   5.5495
 NGK  H     H  HNH1  0   0.405   0.1419  -1.1095   3.2568
 NGK  HA    H  HOH1  0   0.471   3.1902  -0.6655   2.2363
 NGK  HB    H  HOH1  0   0.488  -1.9299  -1.6734   1.2135
 NGK  H6    H  HOH1  0   0.460   4.2200   0.2359  -2.8205
 NGK  H2S   H  H     0   0.503  -2.4943  -0.1733  -0.3290

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  1.533  0.020  1.533
 NGK  C1   O1    single  1.390  0.020  1.390
 NGK  C1   O5    single  1.402  0.020  1.402
 NGK  C1   H1    single  0.970  0.020  1.090
 NGK  C2   C3    single  1.530  0.020  1.530
 NGK  C2   N     single  1.438  0.020  1.438
 NGK  C2   H2    single  0.970  0.020  1.090
 NGK  C3   C4    single  1.521  0.020  1.521
 NGK  C3   O3    single  1.417  0.020  1.417
 NGK  C3   H3    single  0.970  0.020  1.090
 NGK  C4   C5    single  1.523  0.020  1.523
 NGK  C4   O4    single  1.447  0.020  1.447
 NGK  C4   H4    single  0.970  0.020  1.090
 NGK  C5   C6    single  1.516  0.020  1.516
 NGK  C5   O5    single  1.413  0.020  1.413
 NGK  C5   H5    single  0.970  0.020  1.090
 NGK  C6   O6    single  1.406  0.020  1.406
 NGK  C6   H6C1  single  0.970  0.020  1.090
 NGK  C6   H6C2  single  0.970  0.020  1.090
 NGK  C7   C8    single  1.507  0.020  1.507
 NGK  C7   N     single  1.352  0.020  1.352
 NGK  C7   O7    double  1.221  0.020  1.221
 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  1.597  0.020  1.597
 NGK  O6   H6    single  0.850  0.020  0.980
 NGK  S    O1S   double  1.436  0.020  1.436
 NGK  S    O2S   single  1.570  0.020  1.570
 NGK  S    O3S   double  1.442  0.020  1.442
 NGK  O2S  H2S   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
 NGK  H1    C1   O5    105.02  3.000
 NGK  H1    C1   O1    111.60  3.000
 NGK  O5    C1   O1    112.72  3.000
 NGK  H1    C1   C2    109.44  3.000
 NGK  O5    C1   C2    110.30  3.000
 NGK  O1    C1   C2    107.75  3.000
 NGK  H2    C2   N     107.25  3.000
 NGK  H2    C2   C3    109.25  3.000
 NGK  N     C2   C3    111.09  3.000
 NGK  H2    C2   C1    107.87  3.000
 NGK  N     C2   C1    111.42  3.000
 NGK  C3    C2   C1    109.85  3.000
 NGK  H3    C3   O3    108.90  3.000
 NGK  H3    C3   C4    106.55  3.000
 NGK  O3    C3   C4    109.29  3.000
 NGK  H3    C3   C2    109.87  3.000
 NGK  O3    C3   C2    112.06  3.000
 NGK  C4    C3   C2    110.01  3.000
 NGK  H4    C4   O4    110.13  3.000
 NGK  H4    C4   C5    109.46  3.000
 NGK  O4    C4   C5    106.50  3.000
 NGK  H4    C4   C3    110.73  3.000
 NGK  O4    C4   C3    110.86  3.000
 NGK  C5    C4   C3    109.05  3.000
 NGK  H5    C5   O5    111.13  3.000
 NGK  H5    C5   C6    107.83  3.000
 NGK  O5    C5   C6    108.35  3.000
 NGK  H5    C5   C4    106.24  3.000
 NGK  O5    C5   C4    110.81  3.000
 NGK  C6    C5   C4    112.46  3.000
 NGK  H6C2  C6   H6C1  107.31  3.000
 NGK  H6C2  C6   O6    111.79  3.000
 NGK  H6C1  C6   O6    111.78  3.000
 NGK  H6C2  C6   C5    109.98  3.000
 NGK  H6C1  C6   C5    107.95  3.000
 NGK  O6    C6   C5    107.96  3.000
 NGK  O7    C7   N     123.02  3.000
 NGK  O7    C7   C8    121.96  3.000
 NGK  N     C7   C8    115.02  3.000
 NGK  H8C3  C8   H8C2  108.57  3.000
 NGK  H8C3  C8   H8C1  107.31  3.000
 NGK  H8C2  C8   H8C1  108.45  3.000
 NGK  H8C3  C8   C7    109.29  3.000
 NGK  H8C2  C8   C7    113.76  3.000
 NGK  H8C1  C8   C7    109.26  3.000
 NGK  H     N    C7    118.47  3.000
 NGK  H     N    C2    117.58  3.000
 NGK  C7    N    C2    123.80  3.000
 NGK  HA    O1   C1    109.55  3.000
 NGK  HB    O3   C3    109.82  3.000
 NGK  S     O4   C4    122.30  3.000
 NGK  C5    O5   C1    115.63  3.000
 NGK  H6    O6   C6    108.13  3.000
 NGK  O3S   S    O2S   110.73  3.000
 NGK  O3S   S    O1S   120.50  3.000
 NGK  O2S   S    O1S   106.66  3.000
 NGK  O3S   S    O4    109.43  3.000
 NGK  O2S   S    O4    102.63  3.000
 NGK  O1S   S    O4    105.33  3.000
 NGK  H2S   O2S  S     109.35  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  -162.83  30.0  3
 NGK  Var_02    H8C1  C8  C7  N   -119.31  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

