# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 06:18:05 2021
#   Inital geometry file: a 67 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R},6~{R})-4-methoxy-6-(methoxymethyl)oxane-2,3,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC[C@H]1O[C@@H](O)[C@H](O)[C@@H](OC)[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
 K3Q  K3Q  (2~{R},3~{R},4~{S},5~{R},6~{R})-4-methoxy-6-(methoxymethyl)oxane-2,3,5-triol  ligand  30  14  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K3Q
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
 K3Q  C1   C  CH1   0   0.298  -47.6346  -11.9964  21.7215
 K3Q  O1   O  OH1   0  -0.660  -47.6273  -11.7816  20.3513
 K3Q  C2   C  CH1   0  -0.037  -48.1822  -13.3727  22.0975
 K3Q  O2   O  OH1   0  -0.674  -49.5292  -13.4151  21.6836
 K3Q  O5   O  O2    0  -0.491  -46.2962  -11.9004  22.1038
 K3Q  C5   C  CH1   0  -0.030  -46.0959  -11.9831  23.5003
 K3Q  C4   C  CH1   0   0.032  -46.5668  -13.3485  24.0060
 K3Q  O4   O  OH1   0  -0.670  -46.4150  -13.3785  25.4024
 K3Q  C3   C  CH1   0  -0.008  -48.0232  -13.5656  23.6010
 K3Q  O3   O  O2    0  -0.505  -48.4045  -14.8648  23.9961
 K3Q  C6   C  CH2   0  -0.134  -44.6227  -11.7616  23.7676
 K3Q  O6   O  O2    0  -0.486  -44.2799  -10.4534  23.3966
 K3Q  C7   C  CH3   0  -0.408  -49.6588  -14.9550  24.6351
 K3Q  C8   C  CH3   0  -0.397  -42.9271  -10.1643  23.6399
 K3Q  H1   H  HCH1  0   0.179  -48.2316  -11.2220  22.2422
 K3Q  H2   H  HOH1  0   0.457  -48.4911  -12.0307  20.0024
 K3Q  H3   H  HCH1  0   0.231  -47.5845  -14.1307  21.5720
 K3Q  H4   H  HOH1  0   0.464  -49.7722  -14.3274  21.5037
 K3Q  H5   H  HCH1  0   0.228  -46.6763  -11.1986  24.0129
 K3Q  H6   H  HCH1  0   0.215  -45.9506  -14.1250  23.5250
 K3Q  H7   H  HOH1  0   0.455  -46.6703  -14.2544  25.7105
 K3Q  H8   H  HCH1  0   0.222  -48.6350  -12.8113  24.1203
 K3Q  H9   H  HCH2  0   0.217  -44.4229  -11.9332  24.8326
 K3Q  H10  H  HCH2  0   0.203  -44.0342  -12.5022  23.2051
 K3Q  H11  H  HCH3  0   0.234  -49.7933  -15.9906  24.9453
 K3Q  H12  H  HCH3  0   0.213  -49.7098  -14.3199  25.5257
 K3Q  H13  H  HCH3  0   0.209  -50.4876  -14.6832  23.9756
 K3Q  H14  H  HCH3  0   0.235  -42.7476   -9.1283  23.3554
 K3Q  H15  H  HCH3  0   0.204  -42.6647  -10.2824  24.6983
 K3Q  H16  H  HCH3  0   0.205  -42.2562  -10.8042  23.0543

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
 K3Q  O1  C1   single  1.387  0.020  1.387
 K3Q  C1  O5   single  1.395  0.020  1.395
 K3Q  C1  C2   single  1.528  0.020  1.528
 K3Q  O5  C5   single  1.413  0.020  1.413
 K3Q  O2  C2   single  1.410  0.020  1.410
 K3Q  C2  C3   single  1.524  0.020  1.524
 K3Q  C5  C6   single  1.514  0.020  1.514
 K3Q  C5  C4   single  1.530  0.020  1.530
 K3Q  O6  C6   single  1.402  0.020  1.402
 K3Q  O6  C8   single  1.405  0.020  1.405
 K3Q  C3  C4   single  1.527  0.020  1.527
 K3Q  C3  O3   single  1.410  0.020  1.410
 K3Q  C4  O4   single  1.405  0.020  1.405
 K3Q  O3  C7   single  1.411  0.020  1.411
 K3Q  C1  H1   single  0.970  0.020  1.090
 K3Q  O1  H2   single  0.850  0.020  0.980
 K3Q  C2  H3   single  0.970  0.020  1.090
 K3Q  O2  H4   single  0.850  0.020  0.980
 K3Q  C5  H5   single  0.970  0.020  1.090
 K3Q  C4  H6   single  0.970  0.020  1.090
 K3Q  O4  H7   single  0.850  0.020  0.980
 K3Q  C3  H8   single  0.970  0.020  1.090
 K3Q  C6  H9   single  0.970  0.020  1.090
 K3Q  C6  H10  single  0.970  0.020  1.090
 K3Q  C7  H11  single  0.970  0.020  1.090
 K3Q  C7  H12  single  0.970  0.020  1.090
 K3Q  C7  H13  single  0.970  0.020  1.090
 K3Q  C8  H14  single  0.970  0.020  1.090
 K3Q  C8  H15  single  0.970  0.020  1.090
 K3Q  C8  H16  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
 K3Q  H1   C1  O5   109.88  3.000
 K3Q  H1   C1  C2   108.71  3.000
 K3Q  O5   C1  C2   109.78  3.000
 K3Q  H1   C1  O1   111.03  3.000
 K3Q  C2   C1  O1   112.61  3.000
 K3Q  O5   C1  O1   104.77  3.000
 K3Q  H2   O1  C1   108.22  3.000
 K3Q  H3   C2  C3   109.12  3.000
 K3Q  H3   C2  O2   111.01  3.000
 K3Q  C3   C2  O2   112.67  3.000
 K3Q  H3   C2  C1   107.98  3.000
 K3Q  C3   C2  C1   108.62  3.000
 K3Q  O2   C2  C1   107.30  3.000
 K3Q  H4   O2  C2   108.97  3.000
 K3Q  C5   O5  C1   113.74  3.000
 K3Q  H5   C5  C6   109.04  3.000
 K3Q  H5   C5  C4   108.62  3.000
 K3Q  C6   C5  C4   111.82  3.000
 K3Q  H5   C5  O5   110.08  3.000
 K3Q  C4   C5  O5   109.58  3.000
 K3Q  C6   C5  O5   107.69  3.000
 K3Q  H6   C4  C3   108.50  3.000
 K3Q  H6   C4  O4   111.00  3.000
 K3Q  C3   C4  O4   111.32  3.000
 K3Q  H6   C4  C5   108.21  3.000
 K3Q  O4   C4  C5   108.31  3.000
 K3Q  C3   C4  C5   109.43  3.000
 K3Q  H7   O4  C4   107.98  3.000
 K3Q  H8   C3  O3   110.40  3.000
 K3Q  H8   C3  C4   107.89  3.000
 K3Q  O3   C3  C4   108.33  3.000
 K3Q  H8   C3  C2   108.69  3.000
 K3Q  O3   C3  C2   111.40  3.000
 K3Q  C4   C3  C2   110.07  3.000
 K3Q  C7   O3  C3   115.22  3.000
 K3Q  H10  C6  H9   107.07  3.000
 K3Q  H10  C6  O6   111.22  3.000
 K3Q  H9   C6  O6   110.99  3.000
 K3Q  H10  C6  C5   109.37  3.000
 K3Q  H9   C6  C5   109.01  3.000
 K3Q  O6   C6  C5   109.13  3.000
 K3Q  C8   O6  C6   112.43  3.000
 K3Q  H13  C7  H12  108.13  3.000
 K3Q  H13  C7  H11  108.32  3.000
 K3Q  H12  C7  H11  108.31  3.000
 K3Q  H13  C7  O3   112.63  3.000
 K3Q  H12  C7  O3   111.88  3.000
 K3Q  H11  C7  O3   107.43  3.000
 K3Q  H16  C8  H15  107.83  3.000
 K3Q  H16  C8  H14  108.35  3.000
 K3Q  H15  C8  H14  108.37  3.000
 K3Q  H16  C8  O6   112.12  3.000
 K3Q  H15  C8  O6   112.05  3.000
 K3Q  H14  C8  O6   108.01  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
 K3Q  Var_01  H11  C7  O3  C3  -176.11  30.0  3
 K3Q  Var_02  H14  C8  O6  C6  -178.34  30.0  3
 K3Q  Var_03  H9   C6  O6  C8    58.72  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
 K3Q  chir_01  C1  O1  O5  C2  positiv
 K3Q  chir_02  C2  O2  C1  C3  negativ
 K3Q  chir_03  C5  O5  C4  C6  negativ
 K3Q  chir_04  C4  O4  C3  C5  negativ
 K3Q  chir_05  C3  O3  C2  C4  positiv

