# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 05:33:42 2021
#   Inital geometry file: a 69 line input string
#   Ligand name: (2R,3R,4S,5S,6S)-6-(dihydroxymethyl)-3,4-dimethoxytetrahydro-2H-pyran-2,5-diol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@H](O)O[C@H](C(O)O)[C@@H](O)[C@@H]1OC
#
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
 U9M  U9M  '(2R,3R,4S,5S,6S)-6-(dihydroxymethyl)-3,4-dimethoxytetrahydro-2H-pyran-2,5-diol (non-preferred name)'  D-saccharide  31  15  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U9M
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
 U9M  O4    O  OH1   0  -0.673  30.6287   1.6092  50.7326
 U9M  C4    C  CH1   0   0.020  29.9005   1.2463  51.8797
 U9M  C5    C  CH1   0  -0.018  28.6895   2.1691  51.9866
 U9M  O5    O  O2    0  -0.501  27.9689   1.8528  53.1526
 U9M  C6    C  CH1   0   0.252  27.7485   2.0584  50.7943
 U9M  O6    O  OH1   0  -0.671  27.2710   0.7477  50.7245
 U9M  O6B   O  OH1   0  -0.670  26.7239   2.9872  50.9910
 U9M  C3    C  CH1   0  -0.029  30.7509   1.4007  53.1431
 U9M  O3    O  O2    0  -0.488  31.9205   0.6175  53.0798
 U9M  C3M   C  CH3   0  -0.426  31.7706  -0.7749  53.2547
 U9M  C2    C  CH1   0  -0.018  29.9099   1.1745  54.3998
 U9M  O2    O  O2    0  -0.493  30.7145   1.4552  55.5135
 U9M  C2M   C  CH3   0  -0.405  30.4860   0.6555  56.6520
 U9M  C1    C  CH1   0   0.280  28.6921   2.1022  54.3359
 U9M  O1    O  OH1   0  -0.651  27.8658   1.8452  55.4060
 U9M  H4    H  HCH1  0   0.219  29.5356   0.2116  51.8058
 U9M  H5    H  HCH1  0   0.230  29.0520   3.2098  52.0274
 U9M  H61   H  HCH1  0   0.211  28.3154   2.3051  49.8880
 U9M  HO6   H  HOH1  0   0.462  27.0412   0.5427  49.8132
 U9M  H45   H  HOH1  0   0.457  26.2521   3.1088  50.1605
 U9M  H3    H  HCH1  0   0.244  31.1183   2.4354  53.1680
 U9M  H481  H  HCH3  0   0.245  32.7237  -1.2319  52.9923
 U9M  H482  H  HCH3  0   0.217  31.5400  -1.0460  54.2892
 U9M  H483  H  HCH3  0   0.216  31.0008  -1.2098  52.6106
 U9M  H2    H  HCH1  0   0.230  29.5347   0.1391  54.4278
 U9M  H4B1  H  HCH3  0   0.231  31.2760   0.8783  57.3685
 U9M  H4B2  H  HCH3  0   0.216  29.5224   0.8552  57.1248
 U9M  H4B3  H  HCH3  0   0.206  30.5358  -0.4132  56.4132
 U9M  H1    H  HCH1  0   0.190  29.0408   3.1500  54.3329
 U9M  HO4   H  HOH1  0   0.452  31.4415   1.0929  50.7168
 U9M  HO1   H  HOH1  0   0.466  27.2879   2.6016  55.5543

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
 U9M  O4   C4    single  1.406  0.020  1.406
 U9M  C4   C5    single  1.526  0.020  1.526
 U9M  C4   C3    single  1.531  0.020  1.531
 U9M  C4   H4    single  0.970  0.020  1.090
 U9M  C5   O5    single  1.407  0.020  1.407
 U9M  C5   C6    single  1.523  0.020  1.523
 U9M  C5   H5    single  0.970  0.020  1.090
 U9M  O5   C1    single  1.409  0.020  1.409
 U9M  C6   O6    single  1.397  0.020  1.397
 U9M  C6   O6B   single  1.397  0.020  1.397
 U9M  C6   H61   single  0.970  0.020  1.090
 U9M  O6   HO6   single  0.850  0.020  0.980
 U9M  O6B  H45   single  0.850  0.020  0.980
 U9M  C3   O3    single  1.409  0.020  1.409
 U9M  C3   C2    single  1.529  0.020  1.529
 U9M  C3   H3    single  0.970  0.020  1.090
 U9M  O3   C3M   single  1.411  0.020  1.411
 U9M  C3M  H481  single  0.970  0.020  1.090
 U9M  C3M  H482  single  0.970  0.020  1.090
 U9M  C3M  H483  single  0.970  0.020  1.090
 U9M  C2   O2    single  1.402  0.020  1.402
 U9M  C2   C1    single  1.532  0.020  1.532
 U9M  C2   H2    single  0.970  0.020  1.090
 U9M  O2   C2M   single  1.410  0.020  1.410
 U9M  C2M  H4B1  single  0.970  0.020  1.090
 U9M  C2M  H4B2  single  0.970  0.020  1.090
 U9M  C2M  H4B3  single  0.970  0.020  1.090
 U9M  C1   O1    single  1.376  0.020  1.376
 U9M  C1   H1    single  0.970  0.020  1.090
 U9M  O4   HO4   single  0.850  0.020  0.980
 U9M  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
 U9M  HO4   O4   C4    108.18  3.000
 U9M  H4    C4   C3    109.56  3.000
 U9M  H4    C4   C5    108.08  3.000
 U9M  C3    C4   C5    108.78  3.000
 U9M  H4    C4   O4    111.09  3.000
 U9M  C3    C4   O4    111.07  3.000
 U9M  C5    C4   O4    108.18  3.000
 U9M  H5    C5   C6    107.50  3.000
 U9M  H5    C5   O5    110.48  3.000
 U9M  C6    C5   O5    108.43  3.000
 U9M  H5    C5   C4    108.20  3.000
 U9M  C6    C5   C4    113.04  3.000
 U9M  O5    C5   C4    109.18  3.000
 U9M  C1    O5   C5    113.17  3.000
 U9M  H61   C6   O6B   110.23  3.000
 U9M  H61   C6   O6    110.27  3.000
 U9M  O6B   C6   O6    112.35  3.000
 U9M  H61   C6   C5    108.13  3.000
 U9M  O6B   C6   C5    107.13  3.000
 U9M  O6    C6   C5    108.58  3.000
 U9M  HO6   O6   C6    109.21  3.000
 U9M  H45   O6B  C6    108.77  3.000
 U9M  H3    C3   C2    107.75  3.000
 U9M  H3    C3   O3    104.30  3.000
 U9M  C2    C3   O3    114.28  3.000
 U9M  H3    C3   C4    107.43  3.000
 U9M  C2    C3   C4    110.97  3.000
 U9M  O3    C3   C4    111.59  3.000
 U9M  C3M   O3   C3    117.05  3.000
 U9M  H483  C3M  H482  108.05  3.000
 U9M  H483  C3M  H481  107.89  3.000
 U9M  H482  C3M  H481  107.95  3.000
 U9M  H483  C3M  O3    113.20  3.000
 U9M  H482  C3M  O3    112.59  3.000
 U9M  H481  C3M  O3    106.93  3.000
 U9M  H2    C2   C1    107.42  3.000
 U9M  H2    C2   O2    111.31  3.000
 U9M  C1    C2   O2    111.59  3.000
 U9M  H2    C2   C3    110.32  3.000
 U9M  C1    C2   C3    108.26  3.000
 U9M  O2    C2   C3    107.91  3.000
 U9M  C2M   O2   C2    115.77  3.000
 U9M  H4B3  C2M  H4B2  108.23  3.000
 U9M  H4B3  C2M  H4B1  108.04  3.000
 U9M  H4B2  C2M  H4B1  108.53  3.000
 U9M  H4B3  C2M  O2    111.70  3.000
 U9M  H4B2  C2M  O2    112.89  3.000
 U9M  H4B1  C2M  O2    107.30  3.000
 U9M  H1    C1   O1    111.65  3.000
 U9M  H1    C1   C2    108.88  3.000
 U9M  O1    C1   C2    109.37  3.000
 U9M  H1    C1   O5    109.13  3.000
 U9M  O1    C1   O5    108.17  3.000
 U9M  C2    C1   O5    109.62  3.000
 U9M  HO1   O1   C1    109.46  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
 U9M  Var_01  H481  C3M  O3  C3  169.62  30.0  3
 U9M  Var_02  H4B1  C2M  O2  C2  171.30  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
 U9M  chir_01  C4  O4  C5  C3  positiv
 U9M  chir_02  C5  O5  C4  C6  negativ
 U9M  chir_03  C3  O3  C2  C4  positiv
 U9M  chir_04  C2  O2  C1  C3  negativ
 U9M  chir_05  C1  O1  O5  C2  positiv

