# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 00:53:24 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 4-(acetylamino)-4,6-dideoxy-beta-D-mannopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@@H]1NC(C)=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
 9WJ  9WJ  4-(acetylamino)-4,6-dideoxy-beta-D-mannopyranose  D-saccharide  29  14  .  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_9WJ
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
 9WJ  O3   O  OH1   0  -0.661  -0.0339  -2.3810   0.1242
 9WJ  C3   C  CH1   0   0.051   0.4749  -1.1972  -0.4274
 9WJ  C4   C  CH1   0  -0.119  -0.4319  -0.0436  -0.0006
 9WJ  O7   O  O     0  -0.503  -2.8543  -0.2961   1.4740
 9WJ  C8   C  CH3   0  -0.780  -4.1516  -0.5805  -0.5105
 9WJ  C5   C  CH1   0   0.048   0.1352   1.2936  -0.5067
 9WJ  O5   O  O2    0  -0.496   1.4810   1.4398  -0.1029
 9WJ  C1   C  CH1   0   0.266   2.3304   0.4294  -0.5861
 9WJ  C2   C  CH1   0  -0.044   1.9196  -0.9264  -0.0181
 9WJ  O2   O  OH1   0  -0.670   2.0028  -0.9555   1.3819
 9WJ  N4   N  NH1   0  -0.629  -1.7659  -0.2422  -0.5094
 9WJ  O1   O  OH1   0  -0.664   3.6164   0.7070  -0.1673
 9WJ  H1   H  HOH1  0   0.453   0.4592  -3.1241  -0.2377
 9WJ  H2   H  HCH1  0   0.213   0.4646  -1.2417  -1.5287
 9WJ  H3   H  HCH1  0   0.263  -0.4940  -0.0110   1.0886
 9WJ  H4   H  HCH3  0   0.247  -4.0190  -0.6368  -1.5891
 9WJ  H5   H  HCH3  0   0.265  -4.6245  -1.5019  -0.1713
 9WJ  H6   H  HCH3  0   0.266  -4.8405   0.2360  -0.2928
 9WJ  H10  H  HCH1  0   0.209   0.0788   1.2928  -1.6086
 9WJ  H11  H  HCH1  0   0.188   2.2611   0.3888  -1.6873
 9WJ  H12  H  HCH1  0   0.231   2.5630  -1.6952  -0.4755
 9WJ  H13  H  HOH1  0   0.451   2.9043  -0.7368   1.6390
 9WJ  H14  H  HNH1  0   0.397  -1.8691  -0.3345  -1.5080
 9WJ  H15  H  HOH1  0   0.467   3.9595   1.4635  -0.6553
 9WJ  C6   C  CH3   0  -0.681  -0.6346   2.4846   0.0237
 9WJ  H7   H  HCH3  0   0.230  -0.5935   2.5233   1.1135
 9WJ  C7   C  C     0   0.524  -2.8680  -0.3645   0.2528
 9WJ  H8   H  HCH3  0   0.244  -0.2272   3.4151  -0.3712
 9WJ  H9   H  HCH3  0   0.236  -1.6802   2.4286  -0.2736

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
 9WJ  C8  C7   single  1.509  0.020  1.509
 9WJ  C6  C5   single  1.514  0.020  1.514
 9WJ  C7  N4   single  1.346  0.020  1.346
 9WJ  C7  O7   double  1.223  0.020  1.223
 9WJ  N4  C4   single  1.441  0.020  1.441
 9WJ  C5  C4   single  1.538  0.020  1.538
 9WJ  C5  O5   single  1.413  0.020  1.413
 9WJ  C4  C3   single  1.528  0.020  1.528
 9WJ  O5  C1   single  1.406  0.020  1.406
 9WJ  C1  C2   single  1.526  0.020  1.526
 9WJ  C3  C2   single  1.526  0.020  1.526
 9WJ  C3  O3   single  1.402  0.020  1.402
 9WJ  C2  O2   single  1.403  0.020  1.403
 9WJ  C1  O1   single  1.381  0.020  1.381
 9WJ  O3  H1   single  0.850  0.020  0.980
 9WJ  C3  H2   single  0.970  0.020  1.090
 9WJ  C4  H3   single  0.970  0.020  1.090
 9WJ  C8  H4   single  0.970  0.020  1.090
 9WJ  C8  H5   single  0.970  0.020  1.090
 9WJ  C8  H6   single  0.970  0.020  1.090
 9WJ  C6  H7   single  0.970  0.020  1.090
 9WJ  C6  H8   single  0.970  0.020  1.090
 9WJ  C6  H9   single  0.970  0.020  1.090
 9WJ  C5  H10  single  0.970  0.020  1.090
 9WJ  C1  H11  single  0.970  0.020  1.090
 9WJ  C2  H12  single  0.970  0.020  1.090
 9WJ  O2  H13  single  0.850  0.020  0.980
 9WJ  N4  H14  single  0.860  0.020  1.020
 9WJ  O1  H15  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
 9WJ  H1   O3  C3  108.55  3.000
 9WJ  H2   C3  C2  106.50  3.000
 9WJ  H2   C3  C4  107.69  3.000
 9WJ  C2   C3  C4  110.67  3.000
 9WJ  H2   C3  O3  110.84  3.000
 9WJ  C2   C3  O3  112.83  3.000
 9WJ  C4   C3  O3  108.20  3.000
 9WJ  H3   C4  N4  107.68  3.000
 9WJ  H3   C4  C5  108.87  3.000
 9WJ  N4   C4  C5  110.17  3.000
 9WJ  H3   C4  C3  109.57  3.000
 9WJ  C5   C4  C3  110.22  3.000
 9WJ  N4   C4  C3  110.28  3.000
 9WJ  H6   C8  H5  107.28  3.000
 9WJ  H6   C8  H4  108.28  3.000
 9WJ  H5   C8  H4  108.52  3.000
 9WJ  H6   C8  C7  109.23  3.000
 9WJ  H5   C8  C7  109.43  3.000
 9WJ  H4   C8  C7  113.90  3.000
 9WJ  H10  C5  O5  109.53  3.000
 9WJ  H10  C5  C6  108.93  3.000
 9WJ  O5   C5  C6  107.63  3.000
 9WJ  H10  C5  C4  108.00  3.000
 9WJ  O5   C5  C4  110.31  3.000
 9WJ  C6   C5  C4  112.40  3.000
 9WJ  C1   O5  C5  113.77  3.000
 9WJ  H11  C1  O1  111.61  3.000
 9WJ  H11  C1  C2  108.76  3.000
 9WJ  O1   C1  C2  108.44  3.000
 9WJ  H11  C1  O5  109.36  3.000
 9WJ  O1   C1  O5  108.30  3.000
 9WJ  C2   C1  O5  110.36  3.000
 9WJ  H12  C2  O2  111.42  3.000
 9WJ  H12  C2  C1  107.95  3.000
 9WJ  O2   C2  C1  111.95  3.000
 9WJ  H12  C2  C3  108.52  3.000
 9WJ  O2   C2  C3  108.67  3.000
 9WJ  C1   C2  C3  108.22  3.000
 9WJ  H13  O2  C2  108.50  3.000
 9WJ  H14  N4  C7  117.97  3.000
 9WJ  H14  N4  C4  117.19  3.000
 9WJ  C7   N4  C4  124.79  3.000
 9WJ  H15  O1  C1  109.63  3.000
 9WJ  H9   C6  H8  107.70  3.000
 9WJ  H9   C6  H7  108.10  3.000
 9WJ  H8   C6  H7  108.52  3.000
 9WJ  H9   C6  C5  110.63  3.000
 9WJ  H8   C6  C5  110.76  3.000
 9WJ  H7   C6  C5  111.01  3.000
 9WJ  N4   C7  C8  115.04  3.000
 9WJ  N4   C7  O7  123.45  3.000
 9WJ  C8   C7  O7  121.51  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
 9WJ  CONST_01  C8   C7  N4  C4   180.00   0.0  0
 9WJ  CONST_02  O7   C7  N4  C4     0.00   0.0  0
 9WJ  CONST_03  H14  N4  C7  O7   180.00   0.0  0
 9WJ  Var_01    H4   C8  C7  O7  -179.11  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
 9WJ  chir_01  C3  C4  C2  O3  negativ
 9WJ  chir_02  C4  N4  C5  C3  positiv
 9WJ  chir_03  C5  O5  C4  C6  negativ
 9WJ  chir_04  C1  O5  O1  C2  negativ
 9WJ  chir_05  C2  O2  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
 9WJ  plan-1  C4   0.020
 9WJ  plan-1  O7   0.020
 9WJ  plan-1  C8   0.020
 9WJ  plan-1  N4   0.020
 9WJ  plan-1  H14  0.020
 9WJ  plan-1  C7   0.020

