# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 01:44:23 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{R})-6-(cyclohexylmethoxy)-2-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@H](OCC3CCCCC3)O[C@@H]2CO)[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
 GKC  GKC  (2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{R})-6-(cyclohexylmethoxy)-2-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol  ligand  64  30  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GKC
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
 GKC  O1   O  O     0  -0.503  -24.4411   -7.7717  -58.0520
 GKC  C1   C  CR16  0   0.279  -25.6574   -8.2875  -58.5410
 GKC  C10  C  CH2   0  -0.174  -22.4424   -9.6705  -59.9836
 GKC  C11  C  CH1   0   0.002  -25.4366  -12.7463  -59.7194
 GKC  C12  C  CH1   0   0.312  -24.1323  -12.8707  -60.4970
 GKC  C14  C  CH1   0  -0.273  -22.6340  -16.0137  -61.3914
 GKC  C15  C  CH2   0  -0.414  -23.9640  -16.4520  -62.0031
 GKC  C16  C  CH2   0  -0.423  -21.4664  -16.4516  -62.2765
 GKC  C17  C  CH2   0  -0.431  -23.9923  -17.9518  -62.2795
 GKC  C18  C  CH2   0  -0.427  -22.8256  -18.3782  -63.1635
 GKC  C19  C  CH2   0  -0.428  -21.4942  -17.9503  -62.5564
 GKC  C2   C  CR16  0  -0.004  -26.6512   -7.1600  -58.8436
 GKC  C3   C  CR16  0  -0.011  -24.5248   -7.1881  -56.7602
 GKC  C4   C  CR16  0   0.034  -26.4749   -6.0583  -57.7912
 GKC  C5   C  CR16  0  -0.059  -25.9347   -6.6355  -56.4853
 GKC  C6   C  CH2   0  -0.173  -24.0041   -8.1305  -55.6933
 GKC  C7   C  CH1   0   0.015  -24.8901  -10.3140  -59.4718
 GKC  C8   C  CH1   0  -0.021  -25.9619  -11.3242  -59.8776
 GKC  C9   C  CH1   0   0.006  -23.6312  -10.5658  -60.3074
 GKC  O11  O  O2    0  -0.495  -23.5874  -14.1087  -60.2737
 GKC  O2   O  OH1   0  -0.662  -26.4612   -6.6818  -60.1500
 GKC  O3   O  OH1   0  -0.669  -27.7092   -5.4095  -57.6199
 GKC  O4   O  OH1   0  -0.670  -25.8772   -5.5976  -55.5338
 GKC  O5   O  O2    0  -0.500  -25.3916   -9.0080  -59.6838
 GKC  O6   O  OH1   0  -0.663  -24.8387   -9.2606  -55.6028
 GKC  O7   O  O2    0  -0.507  -23.2177  -11.8958  -60.0569
 GKC  O8   O  OH1   0  -0.667  -27.1268  -11.2138  -59.0936
 GKC  O9   O  OH1   0  -0.665  -26.3396  -13.6951  -60.2213
 GKC  H1   H  HCR6  0   0.211  -26.1173   -8.9340  -57.7810
 GKC  H2   H  HCH2  0   0.201  -22.3850   -9.5043  -58.9012
 GKC  H3   H  HCH2  0   0.205  -21.5337  -10.2137  -60.2751
 GKC  H4   H  HCH1  0   0.215  -25.2171  -12.9208  -58.6533
 GKC  H5   H  HCH1  0   0.186  -24.3354  -12.7162  -61.5748
 GKC  H6   H  HCH2  0   0.219  -21.5863  -14.2302  -60.7852
 GKC  H7   H  HCH2  0   0.200  -22.6934  -14.0025  -62.1425
 GKC  H8   H  HCH1  0   0.218  -22.5190  -16.5080  -60.4173
 GKC  H9   H  HCH2  0   0.227  -24.7932  -16.1751  -61.3493
 GKC  H10  H  HCH2  0   0.202  -24.1154  -15.9118  -62.9462
 GKC  H11  H  HCH2  0   0.227  -20.5186  -16.1755  -61.8051
 GKC  H12  H  HCH2  0   0.208  -21.5121  -15.9030  -63.2253
 GKC  H13  H  HCH2  0   0.224  -24.9413  -18.2257  -62.7473
 GKC  H14  H  HCH2  0   0.207  -23.9475  -18.5000  -61.3317
 GKC  H15  H  HCH2  0   0.206  -22.9363  -17.9205  -64.1527
 GKC  H16  H  HCH2  0   0.224  -22.8414  -19.4598  -63.3189
 GKC  H17  H  HCH2  0   0.225  -20.6688  -18.2219  -63.2187
 GKC  H18  H  HCH2  0   0.208  -21.3329  -18.4938  -61.6190
 GKC  H19  H  HCR6  0   0.216  -27.6597   -7.5834  -58.7219
 GKC  H20  H  HCR6  0   0.242  -23.8512   -6.3235  -56.7734
 GKC  H21  H  HCR6  0   0.209  -25.7186   -5.3549  -58.1768
 GKC  H22  H  HCR6  0   0.234  -26.6072   -7.4298  -56.1361
 GKC  H23  H  HCH2  0   0.215  -22.9745   -8.4089  -55.9522
 GKC  H24  H  HCH2  0   0.200  -23.9527   -7.5790  -54.7445
 GKC  H25  H  HCH1  0   0.232  -24.6326  -10.4640  -58.4142
 GKC  H26  H  HCH1  0   0.222  -26.1960  -11.1636  -60.9418
 GKC  H27  H  HCH1  0   0.222  -23.8731  -10.4412  -61.3761
 GKC  H28  H  HOH1  0   0.453  -21.8910   -7.8616  -60.3819
 GKC  H29  H  HOH1  0   0.453  -27.1342   -6.0162  -60.3244
 GKC  H30  H  HOH1  0   0.447  -27.5880   -4.7164  -56.9619
 GKC  H31  H  HOH1  0   0.460  -26.0145   -5.9657  -54.6568
 GKC  H32  H  HOH1  0   0.458  -24.4610   -9.8692  -54.9618
 GKC  H33  H  HOH1  0   0.460  -27.6705  -10.5005  -59.4413
 GKC  H34  H  HOH1  0   0.450  -27.1935  -13.5425  -59.8024
 GKC  O10  O  OH1   0  -0.663  -22.5666   -8.4667  -60.6991
 GKC  C13  C  CH2   0  -0.131  -22.5704  -14.5123  -61.1772

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
 GKC  C16  C19  single  1.525  0.020  1.525
 GKC  C16  C14  single  1.529  0.020  1.529
 GKC  C19  C18  single  1.525  0.020  1.525
 GKC  C13  C14  single  1.518  0.020  1.518
 GKC  C13  O11  single  1.419  0.020  1.419
 GKC  C14  C15  single  1.528  0.020  1.528
 GKC  C18  C17  single  1.525  0.020  1.525
 GKC  O9   C11  single  1.403  0.020  1.403
 GKC  O11  C12  single  1.371  0.020  1.371
 GKC  C12  C11  single  1.524  0.020  1.524
 GKC  C12  O7   single  1.407  0.020  1.407
 GKC  C15  C17  single  1.525  0.020  1.525
 GKC  C11  C8   single  1.524  0.020  1.524
 GKC  O2   C2   single  1.404  0.020  1.404
 GKC  C8   O8   single  1.408  0.020  1.408
 GKC  C8   C7   single  1.528  0.020  1.528
 GKC  O7   C9   single  1.415  0.020  1.415
 GKC  C9   C7   single  1.532  0.020  1.532
 GKC  C9   C10  single  1.523  0.020  1.523
 GKC  O10  C10  single  1.406  0.020  1.406
 GKC  C7   O5   single  1.415  0.020  1.415
 GKC  O5   C1   single  1.377  0.020  1.377
 GKC  C2   C1   single  1.533  0.020  1.533
 GKC  C2   C4   single  1.534  0.020  1.534
 GKC  O3   C4   single  1.405  0.020  1.405
 GKC  C1   O1   single  1.409  0.020  1.409
 GKC  C4   C5   single  1.527  0.020  1.527
 GKC  O1   C3   single  1.420  0.020  1.420
 GKC  C5   C3   single  1.539  0.020  1.539
 GKC  C5   O4   single  1.409  0.020  1.409
 GKC  C3   C6   single  1.516  0.020  1.516
 GKC  C6   O6   single  1.408  0.020  1.408
 GKC  C1   H1   single  0.970  0.020  1.090
 GKC  C10  H2   single  0.970  0.020  1.090
 GKC  C10  H3   single  0.970  0.020  1.090
 GKC  C11  H4   single  0.970  0.020  1.090
 GKC  C12  H5   single  0.970  0.020  1.090
 GKC  C13  H6   single  0.970  0.020  1.090
 GKC  C13  H7   single  0.970  0.020  1.090
 GKC  C14  H8   single  0.970  0.020  1.090
 GKC  C15  H9   single  0.970  0.020  1.090
 GKC  C15  H10  single  0.970  0.020  1.090
 GKC  C16  H11  single  0.970  0.020  1.090
 GKC  C16  H12  single  0.970  0.020  1.090
 GKC  C17  H13  single  0.970  0.020  1.090
 GKC  C17  H14  single  0.970  0.020  1.090
 GKC  C18  H15  single  0.970  0.020  1.090
 GKC  C18  H16  single  0.970  0.020  1.090
 GKC  C19  H17  single  0.970  0.020  1.090
 GKC  C19  H18  single  0.970  0.020  1.090
 GKC  C2   H19  single  0.970  0.020  1.090
 GKC  C3   H20  single  0.970  0.020  1.090
 GKC  C4   H21  single  0.970  0.020  1.090
 GKC  C5   H22  single  0.970  0.020  1.090
 GKC  C6   H23  single  0.970  0.020  1.090
 GKC  C6   H24  single  0.970  0.020  1.090
 GKC  C7   H25  single  0.970  0.020  1.090
 GKC  C8   H26  single  0.970  0.020  1.090
 GKC  C9   H27  single  0.970  0.020  1.090
 GKC  O10  H28  single  0.850  0.020  0.980
 GKC  O2   H29  single  0.850  0.020  0.980
 GKC  O3   H30  single  0.850  0.020  0.980
 GKC  O4   H31  single  0.850  0.020  0.980
 GKC  O6   H32  single  0.850  0.020  0.980
 GKC  O8   H33  single  0.850  0.020  0.980
 GKC  O9   H34  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
 GKC  C3   O1   C1   114.54  3.000
 GKC  H1   C1   O5   110.30  3.000
 GKC  H1   C1   C2   107.34  3.000
 GKC  O5   C1   C2   110.25  3.000
 GKC  H1   C1   O1   109.68  3.000
 GKC  C2   C1   O1   111.04  3.000
 GKC  O5   C1   O1   108.24  3.000
 GKC  H3   C10  H2   107.09  3.000
 GKC  H3   C10  O10  111.20  3.000
 GKC  H2   C10  O10  112.16  3.000
 GKC  H3   C10  C9   107.38  3.000
 GKC  H2   C10  C9   109.86  3.000
 GKC  O10  C10  C9   109.03  3.000
 GKC  H4   C11  O9   111.54  3.000
 GKC  H4   C11  C8   108.46  3.000
 GKC  O9   C11  C8   111.85  3.000
 GKC  H4   C11  C12  108.07  3.000
 GKC  C8   C11  C12  108.56  3.000
 GKC  O9   C11  C12  108.25  3.000
 GKC  H5   C12  O7   109.08  3.000
 GKC  H5   C12  O11  110.94  3.000
 GKC  O7   C12  O11  108.43  3.000
 GKC  H5   C12  C11  109.16  3.000
 GKC  O7   C12  C11  109.89  3.000
 GKC  O11  C12  C11  109.32  3.000
 GKC  H8   C14  C16  107.72  3.000
 GKC  H8   C14  C15  108.48  3.000
 GKC  C16  C14  C15  110.53  3.000
 GKC  H8   C14  C13  108.40  3.000
 GKC  C15  C14  C13  112.13  3.000
 GKC  C16  C14  C13  109.45  3.000
 GKC  H10  C15  H9   106.56  3.000
 GKC  H10  C15  C17  109.01  3.000
 GKC  H9   C15  C17  110.11  3.000
 GKC  H10  C15  C14  108.84  3.000
 GKC  H9   C15  C14  110.40  3.000
 GKC  C17  C15  C14  111.76  3.000
 GKC  H12  C16  H11  106.42  3.000
 GKC  H12  C16  C19  109.39  3.000
 GKC  H11  C16  C19  110.05  3.000
 GKC  H12  C16  C14  109.00  3.000
 GKC  H11  C16  C14  109.87  3.000
 GKC  C19  C16  C14  111.95  3.000
 GKC  H14  C17  H13  106.28  3.000
 GKC  H14  C17  C18  109.29  3.000
 GKC  H13  C17  C18  110.26  3.000
 GKC  H14  C17  C15  109.53  3.000
 GKC  H13  C17  C15  109.88  3.000
 GKC  C18  C17  C15  111.46  3.000
 GKC  H16  C18  H15  106.48  3.000
 GKC  H16  C18  C19  110.31  3.000
 GKC  H15  C18  C19  109.30  3.000
 GKC  H16  C18  C17  110.38  3.000
 GKC  H15  C18  C17  109.23  3.000
 GKC  C19  C18  C17  111.04  3.000
 GKC  H18  C19  H17  106.51  3.000
 GKC  H18  C19  C18  109.27  3.000
 GKC  H17  C19  C18  110.40  3.000
 GKC  H18  C19  C16  109.14  3.000
 GKC  H17  C19  C16  109.98  3.000
 GKC  C18  C19  C16  111.40  3.000
 GKC  H19  C2   O2   110.98  3.000
 GKC  H19  C2   C4   107.81  3.000
 GKC  O2   C2   C4   112.22  3.000
 GKC  H19  C2   C1   106.81  3.000
 GKC  C4   C2   C1   108.56  3.000
 GKC  O2   C2   C1   110.27  3.000
 GKC  H20  C3   C6   106.73  3.000
 GKC  H20  C3   C5   106.37  3.000
 GKC  C6   C3   C5   114.35  3.000
 GKC  H20  C3   O1   106.08  3.000
 GKC  C6   C3   O1   111.38  3.000
 GKC  C5   C3   O1   111.35  3.000
 GKC  H21  C4   O3   110.53  3.000
 GKC  H21  C4   C5   107.32  3.000
 GKC  O3   C4   C5   112.41  3.000
 GKC  H21  C4   C2   107.29  3.000
 GKC  C5   C4   C2   110.85  3.000
 GKC  O3   C4   C2   108.32  3.000
 GKC  H22  C5   O4   110.06  3.000
 GKC  H22  C5   C4   109.21  3.000
 GKC  O4   C5   C4   108.27  3.000
 GKC  H22  C5   C3   110.99  3.000
 GKC  O4   C5   C3   110.34  3.000
 GKC  C4   C5   C3   107.89  3.000
 GKC  H24  C6   H23  106.69  3.000
 GKC  H24  C6   O6   112.04  3.000
 GKC  H23  C6   O6   111.58  3.000
 GKC  H24  C6   C3   108.17  3.000
 GKC  H23  C6   C3   108.29  3.000
 GKC  O6   C6   C3   109.92  3.000
 GKC  H25  C7   O5   110.69  3.000
 GKC  H25  C7   C9   108.05  3.000
 GKC  O5   C7   C9   111.18  3.000
 GKC  H25  C7   C8   109.26  3.000
 GKC  O5   C7   C8   108.78  3.000
 GKC  C9   C7   C8   108.84  3.000
 GKC  H26  C8   O8   110.52  3.000
 GKC  H26  C8   C7   108.02  3.000
 GKC  O8   C8   C7   112.37  3.000
 GKC  H26  C8   C11  108.03  3.000
 GKC  C7   C8   C11  110.34  3.000
 GKC  O8   C8   C11  107.48  3.000
 GKC  H27  C9   O7   109.99  3.000
 GKC  H27  C9   C7   109.25  3.000
 GKC  O7   C9   C7   107.34  3.000
 GKC  H27  C9   C10  108.11  3.000
 GKC  C7   C9   C10  115.40  3.000
 GKC  O7   C9   C10  106.67  3.000
 GKC  C13  O11  C12  115.98  3.000
 GKC  H29  O2   C2   108.03  3.000
 GKC  H30  O3   C4   107.75  3.000
 GKC  H31  O4   C5   109.17  3.000
 GKC  C7   O5   C1   115.28  3.000
 GKC  H32  O6   C6   108.55  3.000
 GKC  C9   O7   C12  113.94  3.000
 GKC  H33  O8   C8   108.93  3.000
 GKC  H34  O9   C11  107.93  3.000
 GKC  H28  O10  C10  108.00  3.000
 GKC  H7   C13  H6   107.17  3.000
 GKC  H7   C13  O11  110.32  3.000
 GKC  H6   C13  O11  110.03  3.000
 GKC  H7   C13  C14  109.28  3.000
 GKC  H6   C13  C14  110.03  3.000
 GKC  O11  C13  C14  109.95  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
 GKC  Var_01  C18  C19  C16  C14    55.24  30.0  1
 GKC  Var_02  C18  C17  C15  C14   -55.51  30.0  1
 GKC  Var_03  C19  C18  C17  C15    55.21  30.0  1
 GKC  Var_04  C14  C13  O11  C12  -146.43  30.0  1

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
 GKC  chir_01  C1   O5   C2   O1   positiv
 GKC  chir_02  C11  O9   C12  C8   negativ
 GKC  chir_03  C12  O11  O7   C11  positiv
 GKC  chir_04  C14  C15  C13  C16  positiv
 GKC  chir_05  C2   O2   C1   C4   negativ
 GKC  chir_06  C3   O1   C5   C6   negativ
 GKC  chir_07  C4   O3   C5   C2   negativ
 GKC  chir_08  C5   O4   C3   C4   positiv
 GKC  chir_09  C7   O5   C8   C9   negativ
 GKC  chir_10  C8   O8   C11  C7   positiv
 GKC  chir_11  C9   O7   C7   C10  negativ

