# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 10:18:45 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2~{S},3~{S},4~{S},6~{S})-2-heptoxy-6-(hydroxymethyl)oxane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCO[C@H]1O[C@H](CO)C[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
 6KU  6KU  (2~{S},3~{S},4~{S},6~{S})-2-heptoxy-6-(hydroxymethyl)oxane-3,4-diol  D-saccharide  44  18  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6KU
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
 6KU  C4   C  CH2   0  -0.504  -3.6573  -0.5156   0.9480
 6KU  C5   C  CH1   0   0.005  -2.5380  -1.3526   0.3400
 6KU  C6   C  CH2   0  -0.154  -2.9959  -2.7709   0.0861
 6KU  C3   C  CH1   0   0.049  -3.2220   0.9416   1.0614
 6KU  CAR  C  CH3   0  -0.662   8.2060   0.0304   0.0783
 6KU  CAQ  C  CH2   0  -0.420   6.8887   0.6090   0.5755
 6KU  CAP  C  CH2   0  -0.407   5.6728   0.0001  -0.1120
 6KU  CAO  C  CH2   0  -0.411   4.3549   0.5897   0.3728
 6KU  CAN  C  CH2   0  -0.425   3.1346   0.0005  -0.3232
 6KU  CAM  C  CH2   0  -0.463   1.8300   0.6265   0.1542
 6KU  CAL  C  CH2   0  -0.133   0.6253   0.0555  -0.5653
 6KU  O1   O  O2    0  -0.507  -0.5412   0.6940  -0.0775
 6KU  C1   C  CH1   0   0.241  -1.6821   0.5193  -0.8539
 6KU  O5   O  O2    0  -0.499  -2.1116  -0.8079  -0.9005
 6KU  O6   O  OH1   0  -0.670  -1.9058  -3.5505  -0.3439
 6KU  O3   O  OH1   0  -0.672  -4.2482   1.7848   1.5290
 6KU  C2   C  CH1   0  -0.013  -2.7643   1.4535  -0.2959
 6KU  O2   O  OH1   0  -0.672  -3.8748   1.4798  -1.1585
 6KU  H41  H  HCH2  0   0.234  -4.5606  -0.5892   0.3355
 6KU  H42  H  HCH2  0   0.246  -3.8988  -0.9095   1.9393
 6KU  H5   H  HCH1  0   0.218  -1.6957  -1.3841   1.0456
 6KU  H62  H  HCH2  0   0.201  -3.4236  -3.1530   1.0218
 6KU  H61  H  HCH2  0   0.195  -3.8077  -2.7585  -0.6541
 6KU  H31  H  HCH1  0   0.215  -2.3529   0.9870   1.7313
 6KU  HAR  H  HCH3  0   0.216   8.3268   0.1919  -0.9946
 6KU  HAS  H  HCH3  0   0.226   9.0597   0.4877   0.5797
 6KU  HAT  H  HCH3  0   0.216   8.2570  -1.0457   0.2547
 6KU  HAQ  H  HCH2  0   0.211   6.8062   0.4581   1.6564
 6KU  HAU  H  HCH2  0   0.210   6.8836   1.6926   0.4215
 6KU  HAV  H  HCH2  0   0.207   5.7585   0.1451  -1.1948
 6KU  HAP  H  HCH2  0   0.207   5.6696  -1.0839   0.0476
 6KU  HAO  H  HCH2  0   0.209   4.2648   0.4388   1.4541
 6KU  HAW  H  HCH2  0   0.209   4.3672   1.6747   0.2201
 6KU  HAX  H  HCH2  0   0.213   3.2323   0.1405  -1.4053
 6KU  HAN  H  HCH2  0   0.214   3.1070  -1.0818  -0.1583
 6KU  HAM  H  HCH2  0   0.223   1.7219   0.4689   1.2319
 6KU  HAY  H  HCH2  0   0.220   1.8662   1.7087  -0.0049
 6KU  HAZ  H  HCH2  0   0.200   0.7215   0.2207  -1.6473
 6KU  HAL  H  HCH2  0   0.207   0.5704  -1.0283  -0.4097
 6KU  H1   H  HCH1  0   0.228  -1.4719   0.7827  -1.9022
 6KU  H63  H  HOH1  0   0.455  -2.2143  -4.4541  -0.4559
 6KU  H32  H  HOH1  0   0.450  -4.4579   1.5259   2.4317
 6KU  H21  H  HCH1  0   0.231  -2.3265   2.4549  -0.1820
 6KU  H22  H  HOH1  0   0.454  -3.6137   1.9091  -1.9790

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
 6KU  CAR  CAQ  single  1.522  0.020  1.522
 6KU  CAQ  CAP  single  1.524  0.020  1.524
 6KU  CAP  CAO  single  1.523  0.020  1.523
 6KU  CAO  CAN  single  1.523  0.020  1.523
 6KU  CAN  CAM  single  1.524  0.020  1.524
 6KU  CAM  CAL  single  1.515  0.020  1.515
 6KU  CAL  O1   single  1.416  0.020  1.416
 6KU  O1   C1   single  1.391  0.020  1.391
 6KU  C1   O5   single  1.396  0.020  1.396
 6KU  C1   C2   single  1.535  0.020  1.535
 6KU  O5   C5   single  1.420  0.020  1.420
 6KU  C5   C6   single  1.512  0.020  1.512
 6KU  C5   C4   single  1.524  0.020  1.524
 6KU  C2   C3   single  1.521  0.020  1.521
 6KU  C2   O2   single  1.406  0.020  1.406
 6KU  C3   C4   single  1.525  0.020  1.525
 6KU  C3   O3   single  1.408  0.020  1.408
 6KU  C6   O6   single  1.407  0.020  1.407
 6KU  C4   H41  single  0.970  0.020  1.090
 6KU  C4   H42  single  0.970  0.020  1.090
 6KU  C5   H5   single  0.970  0.020  1.090
 6KU  C6   H62  single  0.970  0.020  1.090
 6KU  C6   H61  single  0.970  0.020  1.090
 6KU  C3   H31  single  0.970  0.020  1.090
 6KU  CAR  HAR  single  0.970  0.020  1.090
 6KU  CAR  HAS  single  0.970  0.020  1.090
 6KU  CAR  HAT  single  0.970  0.020  1.090
 6KU  CAQ  HAQ  single  0.970  0.020  1.090
 6KU  CAQ  HAU  single  0.970  0.020  1.090
 6KU  CAP  HAV  single  0.970  0.020  1.090
 6KU  CAP  HAP  single  0.970  0.020  1.090
 6KU  CAO  HAO  single  0.970  0.020  1.090
 6KU  CAO  HAW  single  0.970  0.020  1.090
 6KU  CAN  HAX  single  0.970  0.020  1.090
 6KU  CAN  HAN  single  0.970  0.020  1.090
 6KU  CAM  HAM  single  0.970  0.020  1.090
 6KU  CAM  HAY  single  0.970  0.020  1.090
 6KU  CAL  HAZ  single  0.970  0.020  1.090
 6KU  CAL  HAL  single  0.970  0.020  1.090
 6KU  C1   H1   single  0.970  0.020  1.090
 6KU  O6   H63  single  0.850  0.020  0.980
 6KU  O3   H32  single  0.850  0.020  0.980
 6KU  C2   H21  single  0.970  0.020  1.090
 6KU  O2   H22  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
 6KU  H42  C4   H41  107.51  3.000
 6KU  H42  C4   C3   109.86  3.000
 6KU  H41  C4   C3   109.97  3.000
 6KU  H42  C4   C5   109.02  3.000
 6KU  H41  C4   C5   110.25  3.000
 6KU  C3   C4   C5   110.17  3.000
 6KU  H5   C5   O5   109.97  3.000
 6KU  H5   C5   C6   108.25  3.000
 6KU  O5   C5   C6   107.70  3.000
 6KU  H5   C5   C4   108.81  3.000
 6KU  C6   C5   C4   111.08  3.000
 6KU  O5   C5   C4   110.99  3.000
 6KU  H61  C6   H62  106.89  3.000
 6KU  H61  C6   O6   111.88  3.000
 6KU  H62  C6   O6   111.68  3.000
 6KU  H61  C6   C5   109.05  3.000
 6KU  H62  C6   C5   107.54  3.000
 6KU  O6   C6   C5   109.65  3.000
 6KU  H31  C3   C2   107.00  3.000
 6KU  H31  C3   O3   110.45  3.000
 6KU  C2   C3   O3   108.31  3.000
 6KU  H31  C3   C4   108.10  3.000
 6KU  O3   C3   C4   112.88  3.000
 6KU  C2   C3   C4   109.94  3.000
 6KU  HAT  CAR  HAS  107.61  3.000
 6KU  HAT  CAR  HAR  107.42  3.000
 6KU  HAS  CAR  HAR  107.64  3.000
 6KU  HAT  CAR  CAQ  111.25  3.000
 6KU  HAS  CAR  CAQ  111.59  3.000
 6KU  HAR  CAR  CAQ  111.14  3.000
 6KU  HAU  CAQ  HAQ  105.96  3.000
 6KU  HAU  CAQ  CAP  109.17  3.000
 6KU  HAQ  CAQ  CAP  109.29  3.000
 6KU  HAU  CAQ  CAR  109.54  3.000
 6KU  HAQ  CAQ  CAR  109.60  3.000
 6KU  CAP  CAQ  CAR  113.04  3.000
 6KU  HAP  CAP  HAV  105.96  3.000
 6KU  HAP  CAP  CAO  109.52  3.000
 6KU  HAV  CAP  CAO  109.33  3.000
 6KU  HAP  CAP  CAQ  109.38  3.000
 6KU  HAV  CAP  CAQ  109.30  3.000
 6KU  CAO  CAP  CAQ  113.09  3.000
 6KU  HAW  CAO  HAO  105.95  3.000
 6KU  HAW  CAO  CAN  109.17  3.000
 6KU  HAO  CAO  CAN  109.38  3.000
 6KU  HAW  CAO  CAP  109.23  3.000
 6KU  HAO  CAO  CAP  109.39  3.000
 6KU  CAN  CAO  CAP  113.45  3.000
 6KU  HAN  CAN  HAX  106.10  3.000
 6KU  HAN  CAN  CAM  109.71  3.000
 6KU  HAX  CAN  CAM  109.47  3.000
 6KU  HAN  CAN  CAO  109.49  3.000
 6KU  HAX  CAN  CAO  109.30  3.000
 6KU  CAM  CAN  CAO  112.57  3.000
 6KU  HAY  CAM  HAM  106.78  3.000
 6KU  HAY  CAM  CAL  109.27  3.000
 6KU  HAM  CAM  CAL  109.56  3.000
 6KU  HAY  CAM  CAN  109.41  3.000
 6KU  HAM  CAM  CAN  109.51  3.000
 6KU  CAL  CAM  CAN  112.16  3.000
 6KU  HAL  CAL  HAZ  107.03  3.000
 6KU  HAL  CAL  O1   110.83  3.000
 6KU  HAZ  CAL  O1   110.09  3.000
 6KU  HAL  CAL  CAM  110.18  3.000
 6KU  HAZ  CAL  CAM  109.96  3.000
 6KU  O1   CAL  CAM  108.75  3.000
 6KU  C1   O1   CAL  115.25  3.000
 6KU  H1   C1   C2   109.59  3.000
 6KU  H1   C1   O5   104.73  3.000
 6KU  C2   C1   O5   111.96  3.000
 6KU  H1   C1   O1   110.17  3.000
 6KU  C2   C1   O1   107.40  3.000
 6KU  O5   C1   O1   112.98  3.000
 6KU  C1   O5   C5   115.33  3.000
 6KU  H63  O6   C6   107.92  3.000
 6KU  H32  O3   C3   108.02  3.000
 6KU  H21  C2   O2   111.17  3.000
 6KU  H21  C2   C1   108.15  3.000
 6KU  O2   C2   C1   110.19  3.000
 6KU  H21  C2   C3   109.51  3.000
 6KU  O2   C2   C3   108.42  3.000
 6KU  C1   C2   C3   109.37  3.000
 6KU  H22  O2   C2   108.49  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
 6KU  Var_01  HAZ  CAL  O1   C1     44.53  30.0  1
 6KU  Var_02  CAO  CAP  CAQ  CAR  -179.32  30.0  3
 6KU  Var_03  CAN  CAO  CAP  CAQ   179.20  30.0  3
 6KU  Var_04  CAM  CAN  CAO  CAP  -178.71  30.0  3
 6KU  Var_05  CAL  CAM  CAN  CAO   178.75  30.0  3
 6KU  Var_06  O1   CAL  CAM  CAN  -179.44  30.0  3
 6KU  Var_07  HAR  CAR  CAQ  CAP    59.39  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
 6KU  chir_01  C5  O5  C6  C4  positiv
 6KU  chir_02  C3  O3  C2  C4  positiv
 6KU  chir_03  C1  O1  O5  C2  negativ
 6KU  chir_04  C2  O2  C1  C3  positiv

