# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 23:50:05 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (2~{S},3~{S},4~{S},5~{S},6~{R})-2-(2-decoxyethoxy)-6-(hydroxymethyl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCOCCO[C@H]1O[C@H](CO)[C@@H](O)[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
 CQX  CQX  (2~{S},3~{S},4~{S},5~{S},6~{R})-2-(2-decoxyethoxy)-6-(hydroxymethyl)oxane-3,4,5-triol  ligand  61  25  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CQX
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
 CQX  C1   C  CH1   0  -0.030  -5.1027   0.0892  -1.3075
 CQX  C2   C  CH1   0   0.004  -4.0675   1.2075  -1.4090
 CQX  C3   C  CH1   0   0.032  -3.8550   1.8740  -0.0537
 CQX  C4   C  CH1   0  -0.013  -3.4995   0.8095   0.9863
 CQX  C6   C  CH1   0   0.248  -4.6919  -0.8773  -0.1928
 CQX  O49  O  OH1   0  -0.669  -6.3508   0.6665  -1.0183
 CQX  O55  O  OH1   0  -0.674  -4.4459   2.2099  -2.3230
 CQX  O7   O  OH1   0  -0.676  -2.7933   2.7976  -0.1022
 CQX  O5   O  O2    0  -0.499  -4.4973  -0.1977   1.0123
 CQX  C57  C  CH2   0  -0.159  -3.4168   1.3935   2.3802
 CQX  O61  O  OH1   0  -0.669  -2.9757   0.3945   3.2691
 CQX  O16  O  O2    0  -0.501  -3.5521  -1.5492  -0.6207
 CQX  C18  C  CH2   0  -0.185  -3.1261  -2.6009   0.2240
 CQX  C19  C  CH2   0  -0.173  -1.7611  -3.0584  -0.2181
 CQX  O22  O  O2    0  -0.478  -0.8291  -2.0392   0.0308
 CQX  C25  C  CH2   0  -0.119   0.4826  -2.3896  -0.3374
 CQX  C28  C  CH2   0  -0.458   1.4253  -1.2574   0.0159
 CQX  C31  C  CH2   0  -0.424   2.8682  -1.5778  -0.3539
 CQX  C34  C  CH2   0  -0.411   3.8365  -0.4648   0.0265
 CQX  C37  C  CH2   0  -0.412   5.2833  -0.7756  -0.3350
 CQX  C40  C  CH2   0  -0.411   6.2519   0.3275   0.0729
 CQX  C43  C  CH2   0  -0.411   7.7008   0.0255  -0.2886
 CQX  C46  C  CH2   0  -0.406   8.6674   1.1211   0.1432
 CQX  C49  C  CH2   0  -0.418  10.1173   0.8296  -0.2243
 CQX  C52  C  CH3   0  -0.662  11.0729   1.9272   0.2228
 CQX  H1   H  HCH1  0   0.230  -5.1311  -0.4650  -2.2563
 CQX  H2   H  HCH1  0   0.226  -3.1133   0.7525  -1.7055
 CQX  H3   H  HCH1  0   0.210  -4.7892   2.3669   0.2546
 CQX  H4   H  HCH1  0   0.230  -2.5228   0.3782   0.7232
 CQX  H5   H  HCH1  0   0.229  -5.5085  -1.5868   0.0102
 CQX  H6   H  HOH1  0   0.455  -7.0292  -0.0098  -1.1061
 CQX  H7   H  HOH1  0   0.456  -4.2701   1.8974  -3.2155
 CQX  H8   H  HOH1  0   0.452  -3.0039   3.4578  -0.7707
 CQX  H9   H  HCH2  0   0.209  -2.7293   2.2457   2.3584
 CQX  H10  H  HCH2  0   0.193  -4.4049   1.7835   2.6628
 CQX  H11  H  HOH1  0   0.455  -2.9018   0.7898   4.1422
 CQX  H12  H  HCH2  0   0.222  -3.0812  -2.2797   1.2696
 CQX  H13  H  HCH2  0   0.220  -3.8247  -3.4454   0.1674
 CQX  H14  H  HCH2  0   0.205  -1.5073  -3.9724   0.3379
 CQX  H15  H  HCH2  0   0.202  -1.7779  -3.3316  -1.2834
 CQX  H16  H  HCH2  0   0.189   0.7970  -3.3093   0.1796
 CQX  H17  H  HCH2  0   0.190   0.5389  -2.6031  -1.4156
 CQX  H18  H  HCH2  0   0.220   1.1063  -0.3450  -0.4976
 CQX  H19  H  HCH2  0   0.219   1.3586  -1.0542   1.0892
 CQX  H20  H  HCH2  0   0.212   3.1761  -2.5062   0.1395
 CQX  H21  H  HCH2  0   0.213   2.9382  -1.7686  -1.4302
 CQX  H22  H  HCH2  0   0.209   3.5297   0.4655  -0.4640
 CQX  H23  H  HCH2  0   0.208   3.7642  -0.2767   1.1034
 CQX  H24  H  HCH2  0   0.207   5.5842  -1.7147   0.1426
 CQX  H25  H  HCH2  0   0.207   5.3604  -0.9471  -1.4145
 CQX  H26  H  HCH2  0   0.206   5.9481   1.2687  -0.3989
 CQX  H27  H  HCH2  0   0.206   6.1751   0.4938   1.1533
 CQX  H28  H  HCH2  0   0.206   8.0009  -0.9226   0.1717
 CQX  H29  H  HCH2  0   0.206   7.7816  -0.1255  -1.3709
 CQX  H30  H  HCH2  0   0.205   8.3634   2.0719  -0.3090
 CQX  H31  H  HCH2  0   0.205   8.5908   1.2650   1.2269
 CQX  H32  H  HCH2  0   0.210  10.4195  -0.1227   0.2226
 CQX  H33  H  HCH2  0   0.209  10.1960   0.6934  -1.3076
 CQX  H34  H  HCH3  0   0.215  10.8032   2.8882  -0.2196
 CQX  H35  H  HCH3  0   0.215  11.0527   2.0490   1.3074
 CQX  H36  H  HCH3  0   0.226  12.1016   1.7076  -0.0659

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
 CQX  C52  C49  single  1.522  0.020  1.522
 CQX  C49  C46  single  1.524  0.020  1.524
 CQX  C46  C43  single  1.524  0.020  1.524
 CQX  C43  C40  single  1.524  0.020  1.524
 CQX  C40  C37  single  1.524  0.020  1.524
 CQX  C37  C34  single  1.523  0.020  1.523
 CQX  C34  C31  single  1.523  0.020  1.523
 CQX  C31  C28  single  1.524  0.020  1.524
 CQX  C28  C25  single  1.515  0.020  1.515
 CQX  C25  O22  single  1.407  0.020  1.407
 CQX  O22  C19  single  1.403  0.020  1.403
 CQX  O55  C2   single  1.408  0.020  1.408
 CQX  C1   O49  single  1.405  0.020  1.405
 CQX  C1   C2   single  1.527  0.020  1.527
 CQX  C1   C6   single  1.532  0.020  1.532
 CQX  O16  C18  single  1.415  0.020  1.415
 CQX  O16  C6   single  1.391  0.020  1.391
 CQX  C19  C18  single  1.506  0.020  1.506
 CQX  C2   C3   single  1.525  0.020  1.525
 CQX  C6   O5   single  1.397  0.020  1.397
 CQX  C3   O7   single  1.408  0.020  1.408
 CQX  C3   C4   single  1.530  0.020  1.530
 CQX  O5   C4   single  1.418  0.020  1.418
 CQX  C4   C57  single  1.514  0.020  1.514
 CQX  C57  O61  single  1.408  0.020  1.408
 CQX  C1   H1   single  0.970  0.020  1.090
 CQX  C2   H2   single  0.970  0.020  1.090
 CQX  C3   H3   single  0.970  0.020  1.090
 CQX  C4   H4   single  0.970  0.020  1.090
 CQX  C6   H5   single  0.970  0.020  1.090
 CQX  O49  H6   single  0.850  0.020  0.980
 CQX  O55  H7   single  0.850  0.020  0.980
 CQX  O7   H8   single  0.850  0.020  0.980
 CQX  C57  H9   single  0.970  0.020  1.090
 CQX  C57  H10  single  0.970  0.020  1.090
 CQX  O61  H11  single  0.850  0.020  0.980
 CQX  C18  H12  single  0.970  0.020  1.090
 CQX  C18  H13  single  0.970  0.020  1.090
 CQX  C19  H14  single  0.970  0.020  1.090
 CQX  C19  H15  single  0.970  0.020  1.090
 CQX  C25  H16  single  0.970  0.020  1.090
 CQX  C25  H17  single  0.970  0.020  1.090
 CQX  C28  H18  single  0.970  0.020  1.090
 CQX  C28  H19  single  0.970  0.020  1.090
 CQX  C31  H20  single  0.970  0.020  1.090
 CQX  C31  H21  single  0.970  0.020  1.090
 CQX  C34  H22  single  0.970  0.020  1.090
 CQX  C34  H23  single  0.970  0.020  1.090
 CQX  C37  H24  single  0.970  0.020  1.090
 CQX  C37  H25  single  0.970  0.020  1.090
 CQX  C40  H26  single  0.970  0.020  1.090
 CQX  C40  H27  single  0.970  0.020  1.090
 CQX  C43  H28  single  0.970  0.020  1.090
 CQX  C43  H29  single  0.970  0.020  1.090
 CQX  C46  H30  single  0.970  0.020  1.090
 CQX  C46  H31  single  0.970  0.020  1.090
 CQX  C49  H32  single  0.970  0.020  1.090
 CQX  C49  H33  single  0.970  0.020  1.090
 CQX  C52  H34  single  0.970  0.020  1.090
 CQX  C52  H35  single  0.970  0.020  1.090
 CQX  C52  H36  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
 CQX  H1   C1   O49  111.21  3.000
 CQX  H1   C1   C6   108.48  3.000
 CQX  O49  C1   C6   110.35  3.000
 CQX  H1   C1   C2   109.23  3.000
 CQX  C6   C1   C2   109.19  3.000
 CQX  O49  C1   C2   108.35  3.000
 CQX  H2   C2   O55  110.68  3.000
 CQX  H2   C2   C3   107.46  3.000
 CQX  O55  C2   C3   107.65  3.000
 CQX  H2   C2   C1   107.67  3.000
 CQX  C3   C2   C1   110.82  3.000
 CQX  O55  C2   C1   112.47  3.000
 CQX  H3   C3   O7   110.85  3.000
 CQX  H3   C3   C4   108.57  3.000
 CQX  O7   C3   C4   107.73  3.000
 CQX  H3   C3   C2   109.05  3.000
 CQX  C4   C3   C2   109.41  3.000
 CQX  O7   C3   C2   111.17  3.000
 CQX  H4   C4   C57  108.86  3.000
 CQX  H4   C4   O5   110.54  3.000
 CQX  C57  C4   O5   107.20  3.000
 CQX  H4   C4   C3   108.46  3.000
 CQX  C57  C4   C3   111.73  3.000
 CQX  O5   C4   C3   110.06  3.000
 CQX  H5   C6   O16  110.70  3.000
 CQX  H5   C6   O5   104.94  3.000
 CQX  O16  C6   O5   112.72  3.000
 CQX  H5   C6   C1   110.00  3.000
 CQX  O5   C6   C1   110.99  3.000
 CQX  O16  C6   C1   107.51  3.000
 CQX  H6   O49  C1   108.58  3.000
 CQX  H7   O55  C2   108.78  3.000
 CQX  H8   O7   C3   107.98  3.000
 CQX  C6   O5   C4   115.32  3.000
 CQX  H10  C57  H9   107.06  3.000
 CQX  H10  C57  O61  111.77  3.000
 CQX  H9   C57  O61  111.59  3.000
 CQX  H10  C57  C4   108.94  3.000
 CQX  H9   C57  C4   108.43  3.000
 CQX  O61  C57  C4   108.95  3.000
 CQX  H11  O61  C57  107.80  3.000
 CQX  C18  O16  C6   114.98  3.000
 CQX  H13  C18  H12  107.52  3.000
 CQX  H13  C18  C19  109.15  3.000
 CQX  H12  C18  C19  109.41  3.000
 CQX  H13  C18  O16  110.46  3.000
 CQX  H12  C18  O16  111.38  3.000
 CQX  C19  C18  O16  108.88  3.000
 CQX  H15  C19  H14  106.66  3.000
 CQX  H15  C19  O22  111.24  3.000
 CQX  H14  C19  O22  111.15  3.000
 CQX  H15  C19  C18  110.24  3.000
 CQX  H14  C19  C18  108.26  3.000
 CQX  O22  C19  C18  109.22  3.000
 CQX  C25  O22  C19  113.07  3.000
 CQX  H17  C25  H16  106.46  3.000
 CQX  H17  C25  C28  109.97  3.000
 CQX  H16  C25  C28  109.70  3.000
 CQX  H17  C25  O22  110.64  3.000
 CQX  H16  C25  O22  110.58  3.000
 CQX  C28  C25  O22  109.45  3.000
 CQX  H19  C28  H18  106.72  3.000
 CQX  H19  C28  C31  109.55  3.000
 CQX  H18  C28  C31  109.72  3.000
 CQX  H19  C28  C25  109.24  3.000
 CQX  H18  C28  C25  109.41  3.000
 CQX  C31  C28  C25  112.06  3.000
 CQX  H21  C31  H20  106.08  3.000
 CQX  H21  C31  C34  109.39  3.000
 CQX  H20  C31  C34  109.15  3.000
 CQX  H21  C31  C28  109.61  3.000
 CQX  H20  C31  C28  109.58  3.000
 CQX  C34  C31  C28  112.81  3.000
 CQX  H23  C34  H22  106.01  3.000
 CQX  H23  C34  C37  109.33  3.000
 CQX  H22  C34  C37  109.45  3.000
 CQX  H23  C34  C31  109.20  3.000
 CQX  H22  C34  C31  109.31  3.000
 CQX  C37  C34  C31  113.29  3.000
 CQX  H25  C37  H24  106.02  3.000
 CQX  H25  C37  C40  109.42  3.000
 CQX  H24  C37  C40  109.23  3.000
 CQX  H25  C37  C34  109.42  3.000
 CQX  H24  C37  C34  109.40  3.000
 CQX  C40  C37  C34  113.11  3.000
 CQX  H27  C40  H26  105.95  3.000
 CQX  H27  C40  C43  109.31  3.000
 CQX  H26  C40  C43  109.37  3.000
 CQX  H27  C40  C37  109.23  3.000
 CQX  H26  C40  C37  109.29  3.000
 CQX  C43  C40  C37  113.42  3.000
 CQX  H29  C43  H28  105.99  3.000
 CQX  H29  C43  C46  109.40  3.000
 CQX  H28  C43  C46  109.24  3.000
 CQX  H29  C43  C40  109.37  3.000
 CQX  H28  C43  C40  109.41  3.000
 CQX  C46  C43  C40  113.18  3.000
 CQX  H31  C46  H30  105.95  3.000
 CQX  H31  C46  C49  109.28  3.000
 CQX  H30  C46  C49  109.29  3.000
 CQX  H31  C46  C43  109.28  3.000
 CQX  H30  C46  C43  109.33  3.000
 CQX  C49  C46  C43  113.44  3.000
 CQX  H33  C49  H32  106.02  3.000
 CQX  H33  C49  C52  109.59  3.000
 CQX  H32  C49  C52  109.52  3.000
 CQX  H33  C49  C46  109.32  3.000
 CQX  H32  C49  C46  109.31  3.000
 CQX  C52  C49  C46  112.86  3.000
 CQX  H36  C52  H35  107.63  3.000
 CQX  H36  C52  H34  107.64  3.000
 CQX  H35  C52  H34  107.45  3.000
 CQX  H36  C52  C49  111.66  3.000
 CQX  H35  C52  C49  111.14  3.000
 CQX  H34  C52  C49  111.13  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
 CQX  Var_01  C19  C18  O16  C6   -169.53  30.0  3
 CQX  Var_02  O22  C19  C18  O16    67.59  30.0  1
 CQX  Var_03  C28  C25  O22  C19  -177.77  30.0  1
 CQX  Var_04  C31  C28  C25  O22   179.77  30.0  1
 CQX  Var_05  C34  C31  C28  C25  -178.53  30.0  2
 CQX  Var_06  C37  C34  C31  C28   179.85  30.0  1
 CQX  Var_07  C40  C37  C34  C31  -178.82  30.0  1
 CQX  Var_08  C43  C40  C37  C34  -179.86  30.0  1
 CQX  Var_09  C46  C43  C40  C37  -179.01  30.0  1
 CQX  Var_10  C49  C46  C43  C40  -179.59  30.0  1
 CQX  Var_11  C52  C49  C46  C43  -179.54  30.0  1
 CQX  Var_12  H34  C52  C49  C46   -58.76  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
 CQX  chir_01  C1  O49  C2  C6   negativ
 CQX  chir_02  C2  O55  C1  C3   positiv
 CQX  chir_03  C3  O7   C2  C4   negativ
 CQX  chir_04  C4  O5   C3  C57  negativ
 CQX  chir_05  C6  O16  O5  C1   negativ

