# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 19:54:45 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: methyl 6-deoxy-alpha-L-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@@H](C)[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
 RAO  RAO  'methyl 6-deoxy-alpha-L-mannopyranoside'  L-saccharide  26  12  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RAO
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
 RAO  C1    C  CH1   0   0.261   -6.3348  13.6225  34.5288
 RAO  O1    O  O2    0  -0.495   -5.8502  12.5985  33.7210
 RAO  C7    C  CH3   0  -0.406   -4.9009  11.7587  34.3411
 RAO  O2    O  OH1   0  -0.668   -7.4500  15.6920  34.3803
 RAO  C2    C  CH1   0  -0.018   -7.1970  14.5204  33.6449
 RAO  C3    C  CH1   0   0.003   -8.4868  13.7950  33.2731
 RAO  O3    O  OH1   0  -0.672   -9.2837  14.6940  32.5382
 RAO  C4    C  CH1   0   0.014   -9.1865  13.2999  34.5310
 RAO  O4    O  OH1   0  -0.672  -10.3265  12.5751  34.1206
 RAO  C5    C  CH1   0   0.014   -8.2299  12.4262  35.3476
 RAO  O5    O  O2    0  -0.498   -7.0418  13.1544  35.6390
 RAO  C6    C  CH3   0  -0.695   -8.8248  11.9909  36.6701
 RAO  H1    H  HCH1  0   0.232   -5.5037  14.2068  34.9502
 RAO  HC71  H  HCH3  0   0.236   -4.5003  11.1000  33.5725
 RAO  HC72  H  HCH3  0   0.210   -4.0729  12.3329  34.7711
 RAO  HC73  H  HCH3  0   0.216   -5.3377  11.1413  35.1304
 RAO  HO2   H  HOH1  0   0.450   -8.0990  16.2111  33.8932
 RAO  H2    H  HCH1  0   0.231   -6.6341  14.7456  32.7278
 RAO  H3    H  HCH1  0   0.213   -8.2233  12.9196  32.6610
 RAO  HO3   H  HOH1  0   0.450  -10.1608  14.3068  32.4428
 RAO  H4    H  HCH1  0   0.216   -9.4744  14.1670  35.1416
 RAO  HO4   H  HOH1  0   0.458  -10.9891  12.6151  34.8158
 RAO  H5    H  HCH1  0   0.216   -7.9903  11.5312  34.7567
 RAO  H61   H  HCH3  0   0.244   -8.1102  11.3952  37.2384
 RAO  H62   H  HCH3  0   0.227   -9.1178  12.8502  37.2765
 RAO  H63   H  HCH3  0   0.233   -9.7059  11.3709  36.5080

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
 RAO  C1  O1    single  1.391  0.020  1.391
 RAO  C1  C2    single  1.527  0.020  1.527
 RAO  C1  O5    single  1.397  0.020  1.397
 RAO  C1  H1    single  0.970  0.020  1.090
 RAO  O1  C7    single  1.411  0.020  1.411
 RAO  C7  HC71  single  0.970  0.020  1.090
 RAO  C7  HC72  single  0.970  0.020  1.090
 RAO  C7  HC73  single  0.970  0.020  1.090
 RAO  O2  C2    single  1.406  0.020  1.406
 RAO  O2  HO2   single  0.850  0.020  0.980
 RAO  C2  C3    single  1.526  0.020  1.526
 RAO  C2  H2    single  0.970  0.020  1.090
 RAO  C3  O3    single  1.408  0.020  1.408
 RAO  C3  C4    single  1.522  0.020  1.522
 RAO  C3  H3    single  0.970  0.020  1.090
 RAO  O3  HO3   single  0.850  0.020  0.980
 RAO  C4  O4    single  1.412  0.020  1.412
 RAO  C4  C5    single  1.531  0.020  1.531
 RAO  C4  H4    single  0.970  0.020  1.090
 RAO  O4  HO4   single  0.850  0.020  0.980
 RAO  C5  O5    single  1.424  0.020  1.424
 RAO  C5  C6    single  1.514  0.020  1.514
 RAO  C5  H5    single  0.970  0.020  1.090
 RAO  C6  H61   single  0.970  0.020  1.090
 RAO  C6  H62   single  0.970  0.020  1.090
 RAO  C6  H63   single  0.970  0.020  1.090

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
 RAO  H1    C1  O5    104.83  3.000
 RAO  H1    C1  C2    109.65  3.000
 RAO  O5    C1  C2    111.80  3.000
 RAO  H1    C1  O1    110.50  3.000
 RAO  O5    C1  O1    113.02  3.000
 RAO  C2    C1  O1    107.06  3.000
 RAO  C7    O1  C1    114.66  3.000
 RAO  HC73  C7  HC72  108.34  3.000
 RAO  HC73  C7  HC71  108.37  3.000
 RAO  HC72  C7  HC71  108.43  3.000
 RAO  HC73  C7  O1    112.62  3.000
 RAO  HC72  C7  O1    111.66  3.000
 RAO  HC71  C7  O1    107.30  3.000
 RAO  HO2   O2  C2    107.80  3.000
 RAO  H2    C2  C3    109.09  3.000
 RAO  H2    C2  O2    110.96  3.000
 RAO  C3    C2  O2    111.80  3.000
 RAO  H2    C2  C1    108.32  3.000
 RAO  C3    C2  C1    109.81  3.000
 RAO  O2    C2  C1    106.78  3.000
 RAO  H3    C3  C4    108.12  3.000
 RAO  H3    C3  O3    110.68  3.000
 RAO  C4    C3  O3    112.26  3.000
 RAO  H3    C3  C2    108.14  3.000
 RAO  C4    C3  C2    109.99  3.000
 RAO  O3    C3  C2    107.58  3.000
 RAO  HO3   O3  C3    108.07  3.000
 RAO  H4    C4  C5    108.51  3.000
 RAO  H4    C4  O4    110.80  3.000
 RAO  C5    C4  O4    111.50  3.000
 RAO  H4    C4  C3    108.84  3.000
 RAO  C5    C4  C3    109.82  3.000
 RAO  O4    C4  C3    107.33  3.000
 RAO  HO4   O4  C4    108.96  3.000
 RAO  H5    C5  C6    108.74  3.000
 RAO  H5    C5  O5    110.16  3.000
 RAO  C6    C5  O5    107.23  3.000
 RAO  H5    C5  C4    108.31  3.000
 RAO  C6    C5  C4    112.60  3.000
 RAO  O5    C5  C4    109.79  3.000
 RAO  C5    O5  C1    115.54  3.000
 RAO  H63   C6  H62   108.28  3.000
 RAO  H63   C6  H61   107.26  3.000
 RAO  H62   C6  H61   108.45  3.000
 RAO  H63   C6  C5    110.57  3.000
 RAO  H62   C6  C5    111.37  3.000
 RAO  H61   C6  C5    110.78  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
 RAO  Var_01  HC71  C7  O1  C1  -172.02  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
 RAO  chir_01  C1  O1  C2  O5  negativ
 RAO  chir_02  C2  O2  C1  C3  negativ
 RAO  chir_03  C3  O3  C2  C4  negativ
 RAO  chir_04  C4  O4  C5  C3  negativ
 RAO  chir_05  C5  O5  C4  C6  positiv

