# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 17:39:49 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{R},3~{S},4~{R},6~{S})-2-(hydroxymethyl)-6-methoxy-3-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1C[C@@H](C[C@@H]2O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](CO)O1
#
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
 DTK  DTK  (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{R},3~{S},4~{R},6~{S})-2-(hydroxymethyl)-6-methoxy-3-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol  ligand  48  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DTK
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
 DTK  O11  O  OH1   0  -0.674  -2.1554  -2.2479  -1.0157
 DTK  C11  C  CH1   0   0.058  -2.2338  -1.3015   0.0310
 DTK  C12  C  CH1   0  -0.003  -3.4804  -0.4233  -0.1402
 DTK  C13  C  CH2   0  -0.164  -4.7604  -1.2168   0.0135
 DTK  O13  O  OH1   0  -0.669  -5.8576  -0.3792  -0.2647
 DTK  O12  O  O2    0  -0.505  -3.5115   0.6005   0.8391
 DTK  C10  C  CH1   0  -0.277  -0.9633  -0.4502   0.0140
 DTK  C9   C  CH2   0  -0.483  -1.1124   0.6981   1.0123
 DTK  C8   C  CH1   0   0.286  -2.4081   1.4630   0.8240
 DTK  O8   O  O2    0  -0.497  -2.3220   2.1900  -0.3639
 DTK  CM   C  CH3   0  -0.409  -3.4157   3.0497  -0.5989
 DTK  C7   C  CH2   0  -0.439   0.2611  -1.3195   0.3098
 DTK  C1   C  CH1   0   0.025   1.5800  -0.5650   0.3364
 DTK  C2   C  CH1   0   0.021   2.7658  -1.4551   0.6896
 DTK  O2   O  OH1   0  -0.673   2.8182  -2.5306  -0.2180
 DTK  C3   C  CH1   0  -0.036   4.0663  -0.6444   0.6377
 DTK  O3   O  OH1   0  -0.670   4.0801   0.2096   1.7571
 DTK  C4   C  CH1   0   0.024   4.1578   0.1060  -0.6876
 DTK  O4   O  OH1   0  -0.673   5.3102   0.9151  -0.6326
 DTK  C5   C  CH1   0  -0.020   2.8845   0.9059  -1.0152
 DTK  O5   O  O2    0  -0.502   1.7653   0.0409  -0.9281
 DTK  C6   C  CH3   0  -0.693   2.6905   2.1999  -0.2358
 DTK  H1   H  HOH1  0   0.455  -2.6199  -3.0469  -0.7541
 DTK  H2   H  HCH1  0   0.206  -2.2961  -1.8058   1.0081
 DTK  H3   H  HCH1  0   0.215  -3.4550   0.0082  -1.1518
 DTK  H4   H  HCH2  0   0.196  -4.7291  -2.0688  -0.6755
 DTK  H5   H  HCH2  0   0.194  -4.8077  -1.6281   1.0322
 DTK  H6   H  HOH1  0   0.455  -6.6580  -0.9065  -0.1922
 DTK  H7   H  HCH1  0   0.234  -0.8653  -0.0271  -0.9917
 DTK  H8   H  HCH2  0   0.234  -1.1009   0.3023   2.0329
 DTK  H9   H  HCH2  0   0.251  -0.2756   1.3948   0.9370
 DTK  H10  H  HCH1  0   0.223  -2.5764   2.1446   1.6701
 DTK  H11  H  HCH3  0   0.216  -4.3500   2.5069  -0.7656
 DTK  H12  H  HCH3  0   0.207  -3.5686   3.7467   0.2333
 DTK  H13  H  HCH3  0   0.233  -3.1891   3.6283  -1.4932
 DTK  H14  H  HCH2  0   0.219   0.1330  -1.7894   1.2919
 DTK  H15  H  HCH2  0   0.243   0.3137  -2.1292  -0.4187
 DTK  H16  H  HCH1  0   0.224   1.5251   0.1974   1.1247
 DTK  H17  H  HCH1  0   0.226   2.6256  -1.8115   1.7206
 DTK  H18  H  HOH1  0   0.454   3.4908  -3.1483   0.0851
 DTK  H19  H  HCH1  0   0.224   4.9151  -1.3464   0.6879
 DTK  H20  H  HOH1  0   0.453   4.8102   0.8291   1.6549
 DTK  H21  H  HCH1  0   0.223   4.2591  -0.6585  -1.4703
 DTK  H22  H  HOH1  0   0.457   5.4206   1.3602  -1.4789
 DTK  H23  H  HCH1  0   0.235   2.9407   1.1755  -2.0759
 DTK  H24  H  HCH3  0   0.232   3.5468   2.8593  -0.3729
 DTK  H25  H  HCH3  0   0.231   1.8112   2.7247  -0.6119
 DTK  H26  H  HCH3  0   0.234   2.5640   2.0470   0.8337

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
 DTK  C6   C5   single  1.523  0.020  1.523
 DTK  C5   C4   single  1.539  0.020  1.539
 DTK  C5   O5   single  1.417  0.020  1.417
 DTK  C4   O4   single  1.409  0.020  1.409
 DTK  C4   C3   single  1.526  0.020  1.526
 DTK  O5   C1   single  1.414  0.020  1.414
 DTK  C7   C1   single  1.520  0.020  1.520
 DTK  C7   C10  single  1.530  0.020  1.530
 DTK  C9   C10  single  1.529  0.020  1.529
 DTK  C9   C8   single  1.516  0.020  1.516
 DTK  C3   O3   single  1.408  0.020  1.408
 DTK  C3   C2   single  1.533  0.020  1.533
 DTK  C1   C2   single  1.524  0.020  1.524
 DTK  C10  C11  single  1.529  0.020  1.529
 DTK  C11  O11  single  1.413  0.020  1.413
 DTK  C11  C12  single  1.534  0.020  1.534
 DTK  O12  C8   single  1.401  0.020  1.401
 DTK  O12  C12  single  1.417  0.020  1.417
 DTK  C8   O8   single  1.395  0.020  1.395
 DTK  C2   O2   single  1.408  0.020  1.408
 DTK  C13  C12  single  1.514  0.020  1.514
 DTK  C13  O13  single  1.408  0.020  1.408
 DTK  O8   CM   single  1.411  0.020  1.411
 DTK  O11  H1   single  0.850  0.020  0.980
 DTK  C11  H2   single  0.970  0.020  1.090
 DTK  C12  H3   single  0.970  0.020  1.090
 DTK  C13  H4   single  0.970  0.020  1.090
 DTK  C13  H5   single  0.970  0.020  1.090
 DTK  O13  H6   single  0.850  0.020  0.980
 DTK  C10  H7   single  0.970  0.020  1.090
 DTK  C9   H8   single  0.970  0.020  1.090
 DTK  C9   H9   single  0.970  0.020  1.090
 DTK  C8   H10  single  0.970  0.020  1.090
 DTK  CM   H11  single  0.970  0.020  1.090
 DTK  CM   H12  single  0.970  0.020  1.090
 DTK  CM   H13  single  0.970  0.020  1.090
 DTK  C7   H14  single  0.970  0.020  1.090
 DTK  C7   H15  single  0.970  0.020  1.090
 DTK  C1   H16  single  0.970  0.020  1.090
 DTK  C2   H17  single  0.970  0.020  1.090
 DTK  O2   H18  single  0.850  0.020  0.980
 DTK  C3   H19  single  0.970  0.020  1.090
 DTK  O3   H20  single  0.850  0.020  0.980
 DTK  C4   H21  single  0.970  0.020  1.090
 DTK  O4   H22  single  0.850  0.020  0.980
 DTK  C5   H23  single  0.970  0.020  1.090
 DTK  C6   H24  single  0.970  0.020  1.090
 DTK  C6   H25  single  0.970  0.020  1.090
 DTK  C6   H26  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
 DTK  H1   O11  C11  109.18  3.000
 DTK  H2   C11  C10  108.16  3.000
 DTK  H2   C11  C12  108.37  3.000
 DTK  C10  C11  C12  110.79  3.000
 DTK  H2   C11  O11  110.71  3.000
 DTK  C12  C11  O11  110.23  3.000
 DTK  C10  C11  O11  108.57  3.000
 DTK  H3   C12  O12  110.65  3.000
 DTK  H3   C12  C13  108.57  3.000
 DTK  O12  C12  C13  106.86  3.000
 DTK  H3   C12  C11  107.96  3.000
 DTK  C13  C12  C11  112.06  3.000
 DTK  O12  C12  C11  110.75  3.000
 DTK  H5   C13  H4   107.03  3.000
 DTK  H5   C13  O13  111.84  3.000
 DTK  H4   C13  O13  111.13  3.000
 DTK  H5   C13  C12  109.05  3.000
 DTK  H4   C13  C12  108.63  3.000
 DTK  O13  C13  C12  109.08  3.000
 DTK  H6   O13  C13  107.92  3.000
 DTK  C8   O12  C12  114.85  3.000
 DTK  H7   C10  C7   108.98  3.000
 DTK  H7   C10  C9   108.55  3.000
 DTK  C7   C10  C9   112.23  3.000
 DTK  H7   C10  C11  107.42  3.000
 DTK  C9   C10  C11  109.26  3.000
 DTK  C7   C10  C11  110.26  3.000
 DTK  H9   C9   H8   106.69  3.000
 DTK  H9   C9   C8   108.94  3.000
 DTK  H8   C9   C8   107.89  3.000
 DTK  H9   C9   C10  111.07  3.000
 DTK  H8   C9   C10  109.65  3.000
 DTK  C8   C9   C10  112.40  3.000
 DTK  H10  C8   O8   109.98  3.000
 DTK  H10  C8   C9   110.36  3.000
 DTK  O8   C8   C9   108.41  3.000
 DTK  H10  C8   O12  104.65  3.000
 DTK  O8   C8   O12  112.25  3.000
 DTK  C9   C8   O12  111.17  3.000
 DTK  CM   O8   C8   114.29  3.000
 DTK  H13  CM   H12  108.34  3.000
 DTK  H13  CM   H11  108.44  3.000
 DTK  H12  CM   H11  108.19  3.000
 DTK  H13  CM   O8   107.41  3.000
 DTK  H12  CM   O8   111.66  3.000
 DTK  H11  CM   O8   112.67  3.000
 DTK  H15  C7   H14  106.61  3.000
 DTK  H15  C7   C1   109.78  3.000
 DTK  H14  C7   C1   107.37  3.000
 DTK  H15  C7   C10  109.34  3.000
 DTK  H14  C7   C10  108.86  3.000
 DTK  C1   C7   C10  114.56  3.000
 DTK  H16  C1   O5   110.55  3.000
 DTK  H16  C1   C2   106.14  3.000
 DTK  O5   C1   C2   110.82  3.000
 DTK  H16  C1   C7   108.29  3.000
 DTK  C2   C1   C7   112.91  3.000
 DTK  O5   C1   C7   108.11  3.000
 DTK  H17  C2   C3   108.13  3.000
 DTK  H17  C2   O2   111.18  3.000
 DTK  C3   C2   O2   110.51  3.000
 DTK  H17  C2   C1   107.89  3.000
 DTK  O2   C2   C1   109.00  3.000
 DTK  C3   C2   C1   110.07  3.000
 DTK  H18  O2   C2   108.26  3.000
 DTK  H19  C3   C4   107.85  3.000
 DTK  H19  C3   O3   110.02  3.000
 DTK  C4   C3   O3   113.06  3.000
 DTK  H19  C3   C2   108.35  3.000
 DTK  O3   C3   C2   107.58  3.000
 DTK  C4   C3   C2   109.90  3.000
 DTK  H20  O3   C3   108.26  3.000
 DTK  H21  C4   C5   106.63  3.000
 DTK  H21  C4   O4   110.60  3.000
 DTK  C5   C4   O4   112.73  3.000
 DTK  H21  C4   C3   106.38  3.000
 DTK  O4   C4   C3   107.31  3.000
 DTK  C5   C4   C3   113.01  3.000
 DTK  H22  O4   C4   108.97  3.000
 DTK  H23  C5   C6   107.03  3.000
 DTK  H23  C5   O5   104.48  3.000
 DTK  C6   C5   O5   112.74  3.000
 DTK  H23  C5   C4   106.95  3.000
 DTK  O5   C5   C4   108.85  3.000
 DTK  C6   C5   C4   115.98  3.000
 DTK  C5   O5   C1   114.83  3.000
 DTK  H26  C6   H25  108.23  3.000
 DTK  H26  C6   H24  107.47  3.000
 DTK  H25  C6   H24  107.40  3.000
 DTK  H26  C6   C5   113.49  3.000
 DTK  H25  C6   C5   109.57  3.000
 DTK  H24  C6   C5   110.47  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
 DTK  Var_01  H11  CM  O8  C8  -66.15  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
 DTK  chir_01  C11  C10  O11  C12  positiv
 DTK  chir_02  C12  O12  C11  C13  negativ
 DTK  chir_03  C10  C7   C9   C11  positiv
 DTK  chir_04  C8   O8   O12  C9   negativ
 DTK  chir_05  C1   O5   C7   C2   negativ
 DTK  chir_06  C2   O2   C1   C3   positiv
 DTK  chir_07  C3   O3   C2   C4   negativ
 DTK  chir_08  C4   O4   C5   C3   positiv
 DTK  chir_09  C5   O5   C4   C6   positiv

