# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 22:33:43 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: 3-O-acetyl-6-deoxy-alpha-L-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](O)[C@@H](O)[C@H](OC(C)=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
 98U  98U  "3-O-acetyl-6-deoxy-alpha-L-galactopyranose"  L-saccharide  28  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_98U
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
 98U  O4   O  OH1   0  -0.664  96.0386  39.4346  73.5548
 98U  C4   C  CH1   0  -0.001  95.5924  38.2185  74.0997
 98U  C3   C  CH1   0  -0.028  94.0831  38.2186  74.3409
 98U  C2   C  CH1   0  -0.018  93.3320  38.3484  73.0240
 98U  O2   O  OH1   0  -0.669  91.9424  38.2015  73.1775
 98U  O3   O  O2    0  -0.478  93.6965  39.3361  75.1477
 98U  C7   C  C     0   0.564  93.7060  39.2217  76.4797
 98U  C8   C  CH3   0  -0.771  93.2644  40.4988  77.1285
 98U  O7   O  O     0  -0.436  94.0295  38.2184  77.0595
 98U  C5   C  CH1   0   0.017  95.9153  37.0878  73.1282
 98U  C6   C  CH3   0  -0.680  97.3787  37.0339  72.7419
 98U  O5   O  O2    0  -0.492  95.1646  37.2247  71.9257
 98U  C1   C  CH1   0   0.256  93.7858  37.2398  72.0654
 98U  HO4  H  HOH1  0   0.453  95.9161  40.1318  74.2065
 98U  H4   H  HCH1  0   0.239  96.1030  37.9928  75.0463
 98U  H3   H  HCH1  0   0.255  93.7995  37.2851  74.8345
 98U  H2   H  HCH1  0   0.234  93.5824  39.3100  72.5589
 98U  HO2  H  HOH1  0   0.460  91.5984  38.9325  73.7003
 98U  H6   H  HCH3  0   0.262  93.2773  40.4000  78.2100
 98U  H7   H  HCH3  0   0.273  93.9213  41.3191  76.8374
 98U  H8   H  HCH3  0   0.273  92.2569  40.7620  76.8052
 98U  H5   H  HCH1  0   0.233  95.6527  36.1500  73.6326
 98U  H61  H  HCH3  0   0.232  97.9958  36.9471  73.6360
 98U  H62  H  HCH3  0   0.240  97.5773  36.1649  72.1151
 98U  H63  H  HCH3  0   0.234  97.6887  37.9266  72.2004
 98U  H1   H  HCH1  0   0.228  93.3916  37.4580  71.0635
 98U  O1   O  OH1   0  -0.666  93.3628  35.9787  72.5003
 98U  HO1  H  HOH1  0   0.453  92.4498  36.0448  72.8038

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
 98U  O5  C1   single  1.386  0.020  1.386
 98U  O5  C5   single  1.424  0.020  1.424
 98U  C1  C2   single  1.534  0.020  1.534
 98U  C6  C5   single  1.515  0.020  1.515
 98U  C2  O2   single  1.406  0.020  1.406
 98U  C2  C3   single  1.522  0.020  1.522
 98U  C5  C4   single  1.525  0.020  1.525
 98U  O4  C4   single  1.405  0.020  1.405
 98U  C4  C3   single  1.528  0.020  1.528
 98U  C3  O3   single  1.431  0.020  1.431
 98U  O3  C7   single  1.337  0.020  1.337
 98U  C7  O7   double  1.203  0.020  1.203
 98U  C7  C8   single  1.499  0.020  1.499
 98U  O4  HO4  single  0.850  0.020  0.980
 98U  C4  H4   single  0.970  0.020  1.090
 98U  C3  H3   single  0.970  0.020  1.090
 98U  C2  H2   single  0.970  0.020  1.090
 98U  O2  HO2  single  0.850  0.020  0.980
 98U  C8  H6   single  0.970  0.020  1.090
 98U  C8  H7   single  0.970  0.020  1.090
 98U  C8  H8   single  0.970  0.020  1.090
 98U  C5  H5   single  0.970  0.020  1.090
 98U  C6  H61  single  0.970  0.020  1.090
 98U  C6  H62  single  0.970  0.020  1.090
 98U  C6  H63  single  0.970  0.020  1.090
 98U  C1  H1   single  0.970  0.020  1.090
 98U  C1  O1   single  1.399  0.020  1.399
 98U  O1  HO1  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
 98U  HO4  O4  C4   108.91  3.000
 98U  H4   C4  C5   107.34  3.000
 98U  H4   C4  C3   108.83  3.000
 98U  C5   C4  C3   108.03  3.000
 98U  H4   C4  O4   111.36  3.000
 98U  C3   C4  O4   112.00  3.000
 98U  C5   C4  O4   109.11  3.000
 98U  H3   C3  O3   110.00  3.000
 98U  H3   C3  C2   109.60  3.000
 98U  O3   C3  C2   106.73  3.000
 98U  H3   C3  C4   109.11  3.000
 98U  O3   C3  C4   110.84  3.000
 98U  C2   C3  C4   110.54  3.000
 98U  H2   C2  C1   107.52  3.000
 98U  H2   C2  O2   111.32  3.000
 98U  C1   C2  O2   106.56  3.000
 98U  H2   C2  C3   109.21  3.000
 98U  O2   C2  C3   112.61  3.000
 98U  C1   C2  C3   109.46  3.000
 98U  HO2  O2  C2   109.47  3.000
 98U  C7   O3  C3   119.53  3.000
 98U  O7   C7  C8   125.53  3.000
 98U  C8   C7  O3   110.87  3.000
 98U  O7   C7  O3   123.60  3.000
 98U  H8   C8  H7   107.21  3.000
 98U  H8   C8  H6   109.17  3.000
 98U  H7   C8  H6   109.09  3.000
 98U  H8   C8  C7   110.46  3.000
 98U  H7   C8  C7   110.35  3.000
 98U  H6   C8  C7   110.49  3.000
 98U  H5   C5  O5   110.14  3.000
 98U  H5   C5  C6   108.55  3.000
 98U  O5   C5  C6   107.30  3.000
 98U  H5   C5  C4   106.88  3.000
 98U  C6   C5  C4   113.16  3.000
 98U  O5   C5  C4   110.79  3.000
 98U  H63  C6  H62  108.41  3.000
 98U  H63  C6  H61  108.19  3.000
 98U  H62  C6  H61  107.77  3.000
 98U  H63  C6  C5   111.88  3.000
 98U  H62  C6  C5   110.56  3.000
 98U  H61  C6  C5   109.92  3.000
 98U  C1   O5  C5   116.12  3.000
 98U  O1   C1  H1   110.73  3.000
 98U  O1   C1  O5   108.79  3.000
 98U  H1   C1  O5   105.50  3.000
 98U  O1   C1  C2   111.57  3.000
 98U  H1   C1  C2   108.67  3.000
 98U  O5   C1  C2   111.41  3.000
 98U  HO1  O1  C1   108.79  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
 98U  Var_01  O7  C7  O3  C3     0.22  30.0  3
 98U  Var_02  C8  C7  O3  C3  -179.78  30.0  3
 98U  Var_03  H6  C8  C7  O3  -179.82  30.0  3
 98U  Var_04  H7  C8  C7  O3   -59.09  30.0  3
 98U  Var_05  H8  C8  C7  O3    59.28  30.0  3
 98U  Var_06  H6  C8  C7  O7     0.17  30.0  3
 98U  Var_07  H7  C8  C7  O7   120.90  30.0  3
 98U  Var_08  H8  C8  C7  O7  -120.73  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
 98U  chir_01  C4  C5  O4  C3  negativ
 98U  chir_02  C3  O3  C2  C4  negativ
 98U  chir_03  C2  O2  C3  C1  negativ
 98U  chir_04  C5  O5  C4  C6  positiv
 98U  chir_05  C1  O1  O5  C2  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
 98U  plan-1  O3  0.020
 98U  plan-1  C7  0.020
 98U  plan-1  C8  0.020
 98U  plan-1  O7  0.020

