# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 08:23:20 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2~{S},3~{S},5~{S},6~{R})-2-heptoxy-6-(hydroxymethyl)oxane-3,5-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCO[C@H]1O[C@H](CO)[C@@H](O)C[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
 6KW  6KW  (2~{S},3~{S},5~{S},6~{R})-2-heptoxy-6-(hydroxymethyl)oxane-3,5-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 GRAND
;

data_comp_6KW
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
 6KW  C4   C  CH1   0   0.050  -3.5682   0.4285  -0.8747
 6KW  C5   C  CH1   0   0.002  -2.4544   1.0263  -0.0163
 6KW  C6   C  CH2   0  -0.160  -2.8415   2.3655   0.5736
 6KW  C3   C  CH2   0  -0.515  -3.1921  -0.9912  -1.2917
 6KW  CAR  C  CH3   0  -0.662   8.0220   0.5861  -0.1124
 6KW  CAQ  C  CH2   0  -0.418   6.7559   0.0199  -0.7400
 6KW  CAP  C  CH2   0  -0.406   5.5405   0.1252   0.1730
 6KW  CAO  C  CH2   0  -0.410   4.2725  -0.4471  -0.4473
 6KW  CAN  C  CH2   0  -0.423   3.0444  -0.2928   0.4407
 6KW  CAM  C  CH2   0  -0.463   1.7819  -0.8632  -0.1936
 6KW  CAL  C  CH2   0  -0.134   0.5573  -0.6232   0.6648
 6KW  O1   O  O2    0  -0.507  -0.5750  -1.1573   0.0026
 6KW  C1   C  CH1   0   0.252  -1.7557  -1.1307   0.7364
 6KW  O5   O  O2    0  -0.504  -2.1604   0.1645   1.0724
 6KW  O6   O  OH1   0  -0.670  -1.7236   2.9158   1.2307
 6KW  O4   O  OH1   0  -0.675  -3.7365   1.2682  -1.9966
 6KW  C2   C  CH1   0   0.004  -2.8211  -1.8498  -0.0940
 6KW  O2   O  OH1   0  -0.673  -3.9857  -2.0580   0.6730
 6KW  H1   H  HCH1  0   0.207  -4.4881   0.3974  -0.2736
 6KW  H2   H  HCH1  0   0.218  -1.5669   1.1655  -0.6513
 6KW  H3   H  HCH2  0   0.207  -3.1930   3.0133  -0.2368
 6KW  H4   H  HCH2  0   0.192  -3.6874   2.2201   1.2601
 6KW  H5   H  HCH2  0   0.251  -4.0154  -1.4592  -1.8393
 6KW  H6   H  HCH2  0   0.242  -2.3389  -0.9462  -1.9731
 6KW  H7   H  HCH3  0   0.215   7.8986   1.6387   0.1493
 6KW  H8   H  HCH3  0   0.216   8.2829   0.0493   0.8017
 6KW  H9   H  HCH3  0   0.225   8.8730   0.5132  -0.7910
 6KW  H10  H  HCH2  0   0.210   6.5447   0.5415  -1.6789
 6KW  H11  H  HCH2  0   0.210   6.9207  -1.0283  -1.0078
 6KW  H12  H  HCH2  0   0.206   5.7500  -0.3887   1.1180
 6KW  H13  H  HCH2  0   0.206   5.3752   1.1770   0.4313
 6KW  H14  H  HCH2  0   0.208   4.0839   0.0450  -1.4081
 6KW  H15  H  HCH2  0   0.209   4.4267  -1.5072  -0.6755
 6KW  H16  H  HCH2  0   0.214   3.2276  -0.7816   1.4037
 6KW  H17  H  HCH2  0   0.212   2.8930   0.7691   0.6626
 6KW  H18  H  HCH2  0   0.222   1.6269  -0.4047  -1.1754
 6KW  H19  H  HCH2  0   0.221   1.9078  -1.9370  -0.3621
 6KW  H20  H  HCH2  0   0.200   0.6817  -1.1001   1.6475
 6KW  H21  H  HCH2  0   0.208   0.4328   0.4513   0.8422
 6KW  H22  H  HCH1  0   0.226  -1.6162  -1.6374   1.7045
 6KW  H23  H  HOH1  0   0.454  -1.9768   3.7768   1.5750
 6KW  H24  H  HOH1  0   0.454  -4.4827   0.9385  -2.5068
 6KW  H25  H  HCH1  0   0.227  -2.4033  -2.8041  -0.4403
 6KW  H26  H  HOH1  0   0.452  -3.7704  -2.6404   1.4084

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
 6KW  O6   C6   single  1.409  0.020  1.409
 6KW  O5   C1   single  1.398  0.020  1.398
 6KW  O5   C5   single  1.419  0.020  1.419
 6KW  CAP  CAQ  single  1.524  0.020  1.524
 6KW  CAP  CAO  single  1.523  0.020  1.523
 6KW  CAR  CAQ  single  1.522  0.020  1.522
 6KW  CAN  CAM  single  1.524  0.020  1.524
 6KW  CAN  CAO  single  1.523  0.020  1.523
 6KW  CAL  CAM  single  1.515  0.020  1.515
 6KW  CAL  O1   single  1.416  0.020  1.416
 6KW  C1   O1   single  1.390  0.020  1.390
 6KW  C1   C2   single  1.530  0.020  1.530
 6KW  C6   C5   single  1.514  0.020  1.514
 6KW  O2   C2   single  1.410  0.020  1.410
 6KW  C5   C4   single  1.528  0.020  1.528
 6KW  C2   C3   single  1.520  0.020  1.520
 6KW  C4   C3   single  1.527  0.020  1.527
 6KW  C4   O4   single  1.411  0.020  1.411
 6KW  C4   H1   single  0.970  0.020  1.090
 6KW  C5   H2   single  0.970  0.020  1.090
 6KW  C6   H3   single  0.970  0.020  1.090
 6KW  C6   H4   single  0.970  0.020  1.090
 6KW  C3   H5   single  0.970  0.020  1.090
 6KW  C3   H6   single  0.970  0.020  1.090
 6KW  CAR  H7   single  0.970  0.020  1.090
 6KW  CAR  H8   single  0.970  0.020  1.090
 6KW  CAR  H9   single  0.970  0.020  1.090
 6KW  CAQ  H10  single  0.970  0.020  1.090
 6KW  CAQ  H11  single  0.970  0.020  1.090
 6KW  CAP  H12  single  0.970  0.020  1.090
 6KW  CAP  H13  single  0.970  0.020  1.090
 6KW  CAO  H14  single  0.970  0.020  1.090
 6KW  CAO  H15  single  0.970  0.020  1.090
 6KW  CAN  H16  single  0.970  0.020  1.090
 6KW  CAN  H17  single  0.970  0.020  1.090
 6KW  CAM  H18  single  0.970  0.020  1.090
 6KW  CAM  H19  single  0.970  0.020  1.090
 6KW  CAL  H20  single  0.970  0.020  1.090
 6KW  CAL  H21  single  0.970  0.020  1.090
 6KW  C1   H22  single  0.970  0.020  1.090
 6KW  O6   H23  single  0.850  0.020  0.980
 6KW  O4   H24  single  0.850  0.020  0.980
 6KW  C2   H25  single  0.970  0.020  1.090
 6KW  O2   H26  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
 6KW  H1   C4   O4   110.59  3.000
 6KW  H1   C4   C3   109.22  3.000
 6KW  O4   C4   C3   111.44  3.000
 6KW  H1   C4   C5   108.29  3.000
 6KW  O4   C4   C5   107.50  3.000
 6KW  C3   C4   C5   109.73  3.000
 6KW  H2   C5   O5   110.64  3.000
 6KW  H2   C5   C6   108.62  3.000
 6KW  O5   C5   C6   106.93  3.000
 6KW  H2   C5   C4   108.26  3.000
 6KW  C6   C5   C4   112.25  3.000
 6KW  O5   C5   C4   110.14  3.000
 6KW  H4   C6   H3   107.06  3.000
 6KW  H4   C6   O6   111.78  3.000
 6KW  H3   C6   O6   111.63  3.000
 6KW  H4   C6   C5   108.86  3.000
 6KW  H3   C6   C5   108.48  3.000
 6KW  O6   C6   C5   108.93  3.000
 6KW  H6   C3   H5   107.04  3.000
 6KW  H6   C3   C2   108.91  3.000
 6KW  H5   C3   C2   109.67  3.000
 6KW  H6   C3   C4   108.93  3.000
 6KW  H5   C3   C4   110.43  3.000
 6KW  C2   C3   C4   111.73  3.000
 6KW  H9   CAR  H8   107.56  3.000
 6KW  H9   CAR  H7   107.56  3.000
 6KW  H8   CAR  H7   107.48  3.000
 6KW  H9   CAR  CAQ  111.56  3.000
 6KW  H8   CAR  CAQ  111.17  3.000
 6KW  H7   CAR  CAQ  111.31  3.000
 6KW  H11  CAQ  H10  106.00  3.000
 6KW  H11  CAQ  CAP  109.44  3.000
 6KW  H10  CAQ  CAP  109.09  3.000
 6KW  H11  CAQ  CAR  109.39  3.000
 6KW  H10  CAQ  CAR  109.68  3.000
 6KW  CAP  CAQ  CAR  113.00  3.000
 6KW  H13  CAP  H12  106.01  3.000
 6KW  H13  CAP  CAO  109.34  3.000
 6KW  H12  CAP  CAO  109.52  3.000
 6KW  H13  CAP  CAQ  109.14  3.000
 6KW  H12  CAP  CAQ  109.38  3.000
 6KW  CAO  CAP  CAQ  113.21  3.000
 6KW  H15  CAO  H14  106.03  3.000
 6KW  H15  CAO  CAN  109.45  3.000
 6KW  H14  CAO  CAN  109.08  3.000
 6KW  H15  CAO  CAP  109.35  3.000
 6KW  H14  CAO  CAP  109.37  3.000
 6KW  CAN  CAO  CAP  113.31  3.000
 6KW  H17  CAN  H16  106.12  3.000
 6KW  H17  CAN  CAM  109.43  3.000
 6KW  H16  CAN  CAM  109.73  3.000
 6KW  H17  CAN  CAO  109.13  3.000
 6KW  H16  CAN  CAO  109.42  3.000
 6KW  CAM  CAN  CAO  112.80  3.000
 6KW  H19  CAM  H18  106.81  3.000
 6KW  H19  CAM  CAL  109.62  3.000
 6KW  H18  CAM  CAL  109.12  3.000
 6KW  H19  CAM  CAN  109.64  3.000
 6KW  H18  CAM  CAN  109.50  3.000
 6KW  CAL  CAM  CAN  112.01  3.000
 6KW  H21  CAL  H20  107.06  3.000
 6KW  H21  CAL  O1   110.77  3.000
 6KW  H20  CAL  O1   110.18  3.000
 6KW  H21  CAL  CAM  109.81  3.000
 6KW  H20  CAL  CAM  110.26  3.000
 6KW  O1   CAL  CAM  108.76  3.000
 6KW  C1   O1   CAL  115.14  3.000
 6KW  H22  C1   C2   110.42  3.000
 6KW  H22  C1   O5   104.57  3.000
 6KW  C2   C1   O5   111.36  3.000
 6KW  H22  C1   O1   110.33  3.000
 6KW  C2   C1   O1   107.20  3.000
 6KW  O5   C1   O1   112.98  3.000
 6KW  C1   O5   C5   115.98  3.000
 6KW  H23  O6   C6   107.94  3.000
 6KW  H24  O4   C4   108.07  3.000
 6KW  H25  C2   O2   110.95  3.000
 6KW  H25  C2   C1   108.34  3.000
 6KW  O2   C2   C1   110.44  3.000
 6KW  H25  C2   C3   109.60  3.000
 6KW  O2   C2   C3   108.09  3.000
 6KW  C1   C2   C3   109.40  3.000
 6KW  H26  O2   C2   108.68  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
 6KW  Var_01  H20  CAL  O1   C1     52.79  30.0  1
 6KW  Var_02  CAO  CAP  CAQ  CAR  -179.68  30.0  1
 6KW  Var_03  CAN  CAO  CAP  CAQ  -177.69  30.0  3
 6KW  Var_04  CAM  CAN  CAO  CAP   179.74  30.0  1
 6KW  Var_05  CAL  CAM  CAN  CAO  -176.41  30.0  3
 6KW  Var_06  O1   CAL  CAM  CAN   178.97  30.0  1
 6KW  Var_07  H7   CAR  CAQ  CAP   -58.95  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
 6KW  chir_01  C4  C5  C3  O4  positiv
 6KW  chir_02  C5  O5  C4  C6  negativ
 6KW  chir_03  C1  O1  O5  C2  negativ
 6KW  chir_04  C2  O2  C1  C3  positiv

