# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 04:18:20 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 6-deoxy-alpha-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]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
 XXR  XXR  6-deoxy-alpha-D-mannopyranose  D-saccharide  23  11  .  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_XXR
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
 XXR  O4   O  OH1   0  -0.672  13.7757  40.1007  -1.2215
 XXR  C4   C  CH1   0   0.051  12.6696  39.2373  -1.1143
 XXR  C5   C  CH1   0   0.022  12.7002  38.2952  -2.3176
 XXR  C6   C  CH3   0  -0.681  13.9146  37.3892  -2.3144
 XXR  C3   C  CH1   0  -0.030  11.3557  40.0059  -1.1007
 XXR  O3   O  OH1   0  -0.670  11.3337  40.8015   0.0687
 XXR  C2   C  CH1   0  -0.046  10.1733  39.0391  -1.1296
 XXR  O2   O  OH1   0  -0.666  10.1031  38.2647   0.0417
 XXR  C1   C  CH1   0   0.246  10.3186  38.0714  -2.3062
 XXR  O5   O  O2    0  -0.491  11.5573  37.4479  -2.3075
 XXR  O1   O  OH1   0  -0.664  10.1587  38.7354  -3.5300
 XXR  HO4  H  HOH1  0   0.449  13.7515  40.7062  -0.4735
 XXR  H4   H  HCH1  0   0.202  12.7333  38.6284  -0.1995
 XXR  H5   H  HCH1  0   0.218  12.7129  38.9051  -3.2308
 XXR  H61  H  HCH3  0   0.236  14.8301  37.9753  -2.3651
 XXR  H62  H  HCH3  0   0.225  13.9477  36.7825  -1.4078
 XXR  H63  H  HCH3  0   0.238  13.8992  36.7217  -3.1762
 XXR  H3   H  HCH1  0   0.224  11.3148  40.6320  -2.0014
 XXR  HO3  H  HOH1  0   0.458  10.6840  41.5029  -0.0470
 XXR  H2   H  HCH1  0   0.221   9.2448  39.6174  -1.2673
 XXR  HO2  H  HOH1  0   0.447  10.1917  38.8632   0.7919
 XXR  H1   H  HCH1  0   0.226   9.5834  37.2621  -2.1986
 XXR  HO1  H  HOH1  0   0.456   9.2856  39.1416  -3.5577

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
 XXR  O1  C1   single  1.401  0.020  1.401
 XXR  O5  C5   single  1.423  0.020  1.423
 XXR  O5  C1   single  1.387  0.020  1.387
 XXR  C5  C6   single  1.515  0.020  1.515
 XXR  C5  C4   single  1.529  0.020  1.529
 XXR  C1  C2   single  1.530  0.020  1.530
 XXR  O4  C4   single  1.407  0.020  1.407
 XXR  C4  C3   single  1.522  0.020  1.522
 XXR  C3  C2   single  1.528  0.020  1.528
 XXR  C3  O3   single  1.415  0.020  1.415
 XXR  C2  O2   single  1.406  0.020  1.406
 XXR  O4  HO4  single  0.850  0.020  0.980
 XXR  C4  H4   single  0.970  0.020  1.090
 XXR  C5  H5   single  0.970  0.020  1.090
 XXR  C6  H61  single  0.970  0.020  1.090
 XXR  C6  H62  single  0.970  0.020  1.090
 XXR  C6  H63  single  0.970  0.020  1.090
 XXR  C3  H3   single  0.970  0.020  1.090
 XXR  O3  HO3  single  0.850  0.020  0.980
 XXR  C2  H2   single  0.970  0.020  1.090
 XXR  O2  HO2  single  0.850  0.020  0.980
 XXR  C1  H1   single  0.970  0.020  1.090
 XXR  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
 XXR  HO4  O4  C4   107.88  3.000
 XXR  H4   C4  C3   108.77  3.000
 XXR  H4   C4  C5   108.19  3.000
 XXR  C3   C4  C5   109.60  3.000
 XXR  H4   C4  O4   110.93  3.000
 XXR  C3   C4  O4   111.67  3.000
 XXR  C5   C4  O4   107.61  3.000
 XXR  H5   C5  O5   110.24  3.000
 XXR  H5   C5  C6   108.94  3.000
 XXR  O5   C5  C6   106.72  3.000
 XXR  H5   C5  C4   108.21  3.000
 XXR  C6   C5  C4   112.51  3.000
 XXR  O5   C5  C4   110.21  3.000
 XXR  H63  C6  H62  108.47  3.000
 XXR  H63  C6  H61  107.74  3.000
 XXR  H62  C6  H61  108.22  3.000
 XXR  H63  C6  C5   110.68  3.000
 XXR  H62  C6  C5   111.01  3.000
 XXR  H61  C6  C5   110.62  3.000
 XXR  H3   C3  C2   108.46  3.000
 XXR  H3   C3  O3   110.91  3.000
 XXR  C2   C3  O3   111.07  3.000
 XXR  H3   C3  C4   108.23  3.000
 XXR  O3   C3  C4   107.75  3.000
 XXR  C2   C3  C4   110.39  3.000
 XXR  HO3  O3  C3   108.72  3.000
 XXR  H2   C2  C1   108.40  3.000
 XXR  H2   C2  O2   110.55  3.000
 XXR  C1   C2  O2   107.27  3.000
 XXR  H2   C2  C3   108.80  3.000
 XXR  O2   C2  C3   111.81  3.000
 XXR  C1   C2  C3   109.95  3.000
 XXR  HO2  O2  C2   107.57  3.000
 XXR  H1   C1  O1   110.99  3.000
 XXR  H1   C1  O5   105.46  3.000
 XXR  O1   C1  O5   108.31  3.000
 XXR  H1   C1  C2   109.08  3.000
 XXR  O5   C1  C2   111.71  3.000
 XXR  O1   C1  C2   111.16  3.000
 XXR  C1   O5  C5   116.73  3.000
 XXR  HO1  O1  C1   109.17  3.000

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
 XXR  chir_01  C4  C5  O4  C3  negativ
 XXR  chir_02  C5  O5  C4  C6  negativ
 XXR  chir_03  C3  O3  C4  C2  negativ
 XXR  chir_04  C2  O2  C3  C1  negativ
 XXR  chir_05  C1  O5  O1  C2  positiv

