# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 17:00:11 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (2~{S},3~{R},4~{R},5~{S},6~{R})-2-[5-(9~{H}-fluoren-2-yl)-4~{H}-1,2,4-triazol-3-yl]-6-(hydroxymethyl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2[nH]c(nn2)c3ccc4c(Cc5ccccc45)c3
#
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
 CKZ  CKZ  (2~{S},3~{R},4~{R},5~{S},6~{R})-2-[5-(9~{H}-fluoren-2-yl)-4~{H}-1,2,4-triazol-3-yl]-6-(hydroxymethyl)oxane-3,4,5-triol  ligand  50  29  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CKZ
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
 CKZ  O5'  O  O2    0  -0.491  -3.8742  -0.9331  -0.4028
 CKZ  C5'  C  CH1   0  -0.017  -5.1732  -1.1507   0.1138
 CKZ  C4'  C  CH1   0   0.038  -6.0063   0.1261  -0.0165
 CKZ  C3'  C  CH1   0  -0.029  -5.2868   1.2836   0.6678
 CKZ  C2'  C  CH1   0   0.020  -3.8663   1.4148   0.1301
 CKZ  C1'  C  CH1   0  -0.055  -3.1629   0.0661   0.2801
 CKZ  C1   C  CR5   0   0.428  -1.7850   0.1161  -0.2857
 CKZ  O2'  O  OH1   0  -0.669  -3.1072   2.3586   0.8418
 CKZ  O3'  O  OH1   0  -0.675  -6.0387   2.4563   0.4398
 CKZ  O4'  O  OH1   0  -0.673  -7.2636  -0.1093   0.5651
 CKZ  C6'  C  CH2   0  -0.157  -5.7833  -2.3042  -0.6534
 CKZ  O6'  O  OH1   0  -0.671  -5.0220  -3.4631  -0.4116
 CKZ  N5   N  NR15  0  -0.680  -0.6580   0.0043   0.4479
 CKZ  C4   C  CR5   0   0.446   0.3675   0.1142  -0.4305
 CKZ  N3   N  N     0  -0.335  -0.1247   0.2817  -1.6320
 CKZ  N2   N  N     0  -0.317  -1.4724   0.2850  -1.5391
 CKZ  C6   C  CR6   0   0.017   1.7839   0.0577  -0.0896
 CKZ  C11  C  CR16  0  -0.304   2.2080   0.0038   1.2410
 CKZ  C10  C  CR16  0  -0.331   3.5566  -0.0438   1.5590
 CKZ  C9   C  CR56  0   0.114   4.4885  -0.0366   0.5310
 CKZ  C8   C  CR56  0   0.070   4.0696   0.0168  -0.8048
 CKZ  C7   C  CR16  0  -0.359   2.7292   0.0642  -1.1208
 CKZ  C14  C  CR56  0   0.133   5.9466  -0.0769   0.5580
 CKZ  C13  C  CR56  0   0.039   6.4131  -0.0491  -0.7620
 CKZ  C12  C  CH2   0  -0.525   5.2590   0.0087  -1.7235
 CKZ  C18  C  CR16  0  -0.346   6.8337  -0.1331   1.6256
 CKZ  C17  C  CR16  0  -0.257   8.1956  -0.1607   1.3564
 CKZ  C16  C  CR16  0  -0.260   8.6608  -0.1325   0.0436
 CKZ  C15  C  CR16  0  -0.319   7.7713  -0.0766  -1.0251
 CKZ  H1   H  HCH1  0   0.224  -5.1096  -1.4205   1.1809
 CKZ  H2   H  HCH1  0   0.212  -6.1053   0.3645  -1.0882
 CKZ  H3   H  HCH1  0   0.225  -5.2284   1.0629   1.7444
 CKZ  H4   H  HCH1  0   0.228  -3.9088   1.6604  -0.9404
 CKZ  H5   H  HCH1  0   0.254  -3.0896  -0.1696   1.3540
 CKZ  H6   H  HOH1  0   0.460  -3.3700   3.2414   0.5645
 CKZ  H7   H  HOH1  0   0.462  -5.9655   3.0325   1.2055
 CKZ  H8   H  HOH1  0   0.453  -7.7556   0.7191   0.5527
 CKZ  H9   H  HCH2  0   0.213  -6.8214  -2.4260  -0.3263
 CKZ  H10  H  HCH2  0   0.200  -5.8084  -2.0471  -1.7213
 CKZ  H11  H  HOH1  0   0.457  -5.3997  -4.1791  -0.9297
 CKZ  H12  H  HNR5  0   0.437  -0.6072  -0.1499   1.4432
 CKZ  H13  H  HCR6  0   0.248   1.4887   0.0038   2.0501
 CKZ  H14  H  HCR6  0   0.254   3.8636  -0.0838   2.5966
 CKZ  H15  H  HCR6  0   0.253   2.4031   0.1050  -2.1526
 CKZ  H16  H  HCH2  0   0.282   5.2452  -0.8524  -2.3977
 CKZ  H17  H  HCH2  0   0.282   5.2937   0.8987  -2.3580
 CKZ  H18  H  HCR6  0   0.248   6.4778  -0.1545   2.6486
 CKZ  H19  H  HCR6  0   0.258   8.9039  -0.2043   2.1733
 CKZ  H20  H  HCR6  0   0.257   9.7263  -0.1540  -0.1454
 CKZ  H21  H  HCR6  0   0.254   8.1406  -0.0553  -2.0433

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
 CKZ  O3'  C3'  single    1.412  0.020  1.412
 CKZ  O4'  C4'  single    1.405  0.020  1.405
 CKZ  C3'  C4'  single    1.525  0.020  1.525
 CKZ  C3'  C2'  single    1.525  0.020  1.525
 CKZ  C4'  C5'  single    1.530  0.020  1.530
 CKZ  O2'  C2'  single    1.405  0.020  1.405
 CKZ  C2'  C1'  single    1.528  0.020  1.528
 CKZ  O6'  C6'  single    1.408  0.020  1.408
 CKZ  C5'  C6'  single    1.514  0.020  1.514
 CKZ  C5'  O5'  single    1.415  0.020  1.415
 CKZ  C1'  O5'  single    1.404  0.020  1.404
 CKZ  C1'  C1   single    1.490  0.020  1.490
 CKZ  N2   C1   aromatic  1.303  0.020  1.303
 CKZ  N2   N3   aromatic  1.351  0.020  1.351
 CKZ  C1   N5   aromatic  1.349  0.020  1.349
 CKZ  N3   C4   aromatic  1.309  0.020  1.309
 CKZ  N5   C4   aromatic  1.355  0.020  1.355
 CKZ  C4   C6   single    1.458  0.020  1.458
 CKZ  C6   C7   aromatic  1.399  0.020  1.399
 CKZ  C6   C11  aromatic  1.398  0.020  1.398
 CKZ  C7   C8   aromatic  1.378  0.020  1.378
 CKZ  C11  C10  aromatic  1.386  0.020  1.386
 CKZ  C8   C12  single    1.503  0.020  1.503
 CKZ  C8   C9   aromatic  1.401  0.020  1.401
 CKZ  C10  C9   aromatic  1.388  0.020  1.388
 CKZ  C12  C13  single    1.503  0.020  1.503
 CKZ  C9   C14  aromatic  1.459  0.020  1.459
 CKZ  C13  C14  aromatic  1.400  0.020  1.400
 CKZ  C13  C15  aromatic  1.384  0.020  1.384
 CKZ  C14  C18  aromatic  1.389  0.020  1.389
 CKZ  C15  C16  aromatic  1.391  0.020  1.391
 CKZ  C18  C17  aromatic  1.389  0.020  1.389
 CKZ  C16  C17  aromatic  1.393  0.020  1.393
 CKZ  C5'  H1   single    0.970  0.020  1.090
 CKZ  C4'  H2   single    0.970  0.020  1.090
 CKZ  C3'  H3   single    0.970  0.020  1.090
 CKZ  C2'  H4   single    0.970  0.020  1.090
 CKZ  C1'  H5   single    0.970  0.020  1.090
 CKZ  O2'  H6   single    0.850  0.020  0.980
 CKZ  O3'  H7   single    0.850  0.020  0.980
 CKZ  O4'  H8   single    0.850  0.020  0.980
 CKZ  C6'  H9   single    0.970  0.020  1.090
 CKZ  C6'  H10  single    0.970  0.020  1.090
 CKZ  O6'  H11  single    0.850  0.020  0.980
 CKZ  N5   H12  single    0.860  0.020  1.020
 CKZ  C11  H13  single    0.930  0.020  1.080
 CKZ  C10  H14  single    0.930  0.020  1.080
 CKZ  C7   H15  single    0.930  0.020  1.080
 CKZ  C12  H16  single    0.970  0.020  1.090
 CKZ  C12  H17  single    0.970  0.020  1.090
 CKZ  C18  H18  single    0.930  0.020  1.080
 CKZ  C17  H19  single    0.930  0.020  1.080
 CKZ  C16  H20  single    0.930  0.020  1.080
 CKZ  C15  H21  single    0.930  0.020  1.080

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
 CKZ  C1'  O5'  C5'  113.39  3.000
 CKZ  H1   C5'  C6'  109.11  3.000
 CKZ  H1   C5'  C4'  108.54  3.000
 CKZ  C6'  C5'  C4'  111.92  3.000
 CKZ  H1   C5'  O5'  109.77  3.000
 CKZ  C6'  C5'  O5'  107.59  3.000
 CKZ  C4'  C5'  O5'  109.90  3.000
 CKZ  H2   C4'  O4'  110.99  3.000
 CKZ  H2   C4'  C3'  108.33  3.000
 CKZ  O4'  C4'  C3'  111.32  3.000
 CKZ  H2   C4'  C5'  108.19  3.000
 CKZ  C3'  C4'  C5'  109.77  3.000
 CKZ  O4'  C4'  C5'  108.18  3.000
 CKZ  H3   C3'  O3'  110.67  3.000
 CKZ  H3   C3'  C2'  108.23  3.000
 CKZ  O3'  C3'  C2'  111.58  3.000
 CKZ  H3   C3'  C4'  108.16  3.000
 CKZ  C2'  C3'  C4'  110.28  3.000
 CKZ  O3'  C3'  C4'  107.86  3.000
 CKZ  H4   C2'  O2'  111.36  3.000
 CKZ  H4   C2'  C1'  108.09  3.000
 CKZ  O2'  C2'  C1'  107.12  3.000
 CKZ  H4   C2'  C3'  109.07  3.000
 CKZ  C1'  C2'  C3'  108.56  3.000
 CKZ  O2'  C2'  C3'  112.49  3.000
 CKZ  H5   C1'  C1   108.40  3.000
 CKZ  H5   C1'  C2'  108.36  3.000
 CKZ  C1   C1'  C2'  111.02  3.000
 CKZ  H5   C1'  O5'  110.83  3.000
 CKZ  C1   C1'  O5'  107.91  3.000
 CKZ  C2'  C1'  O5'  110.31  3.000
 CKZ  N2   C1   N5   109.48  3.000
 CKZ  N5   C1   C1'  124.26  3.000
 CKZ  N2   C1   C1'  126.26  3.000
 CKZ  H6   O2'  C2'  108.84  3.000
 CKZ  H7   O3'  C3'  109.19  3.000
 CKZ  H8   O4'  C4'  107.91  3.000
 CKZ  H10  C6'  H9   107.14  3.000
 CKZ  H10  C6'  O6'  111.84  3.000
 CKZ  H9   C6'  O6'  111.70  3.000
 CKZ  H10  C6'  C5'  108.87  3.000
 CKZ  H9   C6'  C5'  108.39  3.000
 CKZ  O6'  C6'  C5'  108.80  3.000
 CKZ  H11  O6'  C6'  107.95  3.000
 CKZ  H12  N5   C4   127.89  3.000
 CKZ  H12  N5   C1   126.25  3.000
 CKZ  C4   N5   C1   105.85  3.000
 CKZ  C6   C4   N3   125.79  3.000
 CKZ  C6   C4   N5   125.50  3.000
 CKZ  N3   C4   N5   108.71  3.000
 CKZ  N2   N3   C4   108.20  3.000
 CKZ  N3   N2   C1   107.77  3.000
 CKZ  C7   C6   C11  119.80  3.000
 CKZ  C11  C6   C4   121.26  3.000
 CKZ  C7   C6   C4   118.94  3.000
 CKZ  H13  C11  C10  118.35  3.000
 CKZ  H13  C11  C6   120.66  3.000
 CKZ  C10  C11  C6   120.99  3.000
 CKZ  H14  C10  C9   121.31  3.000
 CKZ  H14  C10  C11  119.80  3.000
 CKZ  C9   C10  C11  118.90  3.000
 CKZ  C14  C9   C8   108.51  3.000
 CKZ  C14  C9   C10  131.11  3.000
 CKZ  C8   C9   C10  120.38  3.000
 CKZ  C12  C8   C7   129.04  3.000
 CKZ  C12  C8   C9   110.24  3.000
 CKZ  C7   C8   C9   120.72  3.000
 CKZ  H15  C7   C8   120.85  3.000
 CKZ  H15  C7   C6   119.94  3.000
 CKZ  C8   C7   C6   119.21  3.000
 CKZ  C18  C14  C13  120.83  3.000
 CKZ  C18  C14  C9   130.81  3.000
 CKZ  C13  C14  C9   108.36  3.000
 CKZ  C15  C13  C12  129.26  3.000
 CKZ  C15  C13  C14  120.38  3.000
 CKZ  C12  C13  C14  110.36  3.000
 CKZ  H17  C12  H16  106.47  3.000
 CKZ  H17  C12  C13  112.21  3.000
 CKZ  H16  C12  C13  111.94  3.000
 CKZ  H17  C12  C8   112.05  3.000
 CKZ  H16  C12  C8   111.79  3.000
 CKZ  C13  C12  C8   102.53  3.000
 CKZ  H18  C18  C17  120.33  3.000
 CKZ  H18  C18  C14  121.11  3.000
 CKZ  C17  C18  C14  118.56  3.000
 CKZ  H19  C17  C16  119.58  3.000
 CKZ  H19  C17  C18  119.76  3.000
 CKZ  C16  C17  C18  120.65  3.000
 CKZ  H20  C16  C15  119.73  3.000
 CKZ  H20  C16  C17  119.53  3.000
 CKZ  C15  C16  C17  120.74  3.000
 CKZ  H21  C15  C16  120.32  3.000
 CKZ  H21  C15  C13  120.85  3.000
 CKZ  C16  C15  C13  118.83  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
 CKZ  CONST_01  C4   N3   N2   C1     0.00   0.0  0
 CKZ  CONST_02  N3   C4   N5   C1     0.00   0.0  0
 CKZ  CONST_03  C6   C4   N5   C1   180.00   0.0  0
 CKZ  CONST_04  N3   N2   C1   N5     0.00   0.0  0
 CKZ  CONST_05  N2   N3   C4   N5     0.00   0.0  0
 CKZ  CONST_06  C7   C6   C4   N5   180.00   0.0  0
 CKZ  CONST_07  C11  C6   C4   N5     0.00   0.0  0
 CKZ  CONST_08  N2   C1   N5   C4     0.00   0.0  0
 CKZ  CONST_09  C8   C7   C6   C4   180.00   0.0  0
 CKZ  CONST_10  C10  C11  C6   C4   180.00   0.0  0
 CKZ  CONST_11  C7   C6   C4   N3     0.00   0.0  0
 CKZ  CONST_12  C11  C6   C4   N3   180.00   0.0  0
 CKZ  CONST_13  C6   C4   N3   N2   180.00   0.0  0
 CKZ  CONST_14  C9   C8   C7   C6     0.00   0.0  0
 CKZ  CONST_15  C9   C10  C11  C6     0.00   0.0  0
 CKZ  CONST_16  C8   C7   C6   C11    0.00   0.0  0
 CKZ  CONST_17  C8   C9   C10  C11    0.00   0.0  0
 CKZ  CONST_18  C14  C9   C10  C11  180.00   0.0  0
 CKZ  CONST_19  C7   C6   C11  C10    0.00   0.0  0
 CKZ  CONST_20  C7   C8   C9   C10    0.00   0.0  0
 CKZ  CONST_21  C13  C14  C9   C10  180.00   0.0  0
 CKZ  CONST_22  C18  C14  C9   C10    0.00   0.0  0
 CKZ  CONST_23  C15  C13  C14  C9   180.00   0.0  0
 CKZ  CONST_24  C17  C18  C14  C9   180.00   0.0  0
 CKZ  CONST_25  C13  C14  C9   C8     0.00   0.0  0
 CKZ  CONST_26  C18  C14  C9   C8   180.00   0.0  0
 CKZ  CONST_27  C14  C9   C8   C7   180.00   0.0  0
 CKZ  CONST_28  C16  C15  C13  C14    0.00   0.0  0
 CKZ  CONST_29  C16  C17  C18  C14    0.00   0.0  0
 CKZ  CONST_30  C17  C18  C14  C13    0.00   0.0  0
 CKZ  CONST_31  C17  C16  C15  C13    0.00   0.0  0
 CKZ  CONST_32  C15  C13  C14  C18    0.00   0.0  0
 CKZ  CONST_33  C15  C16  C17  C18    0.00   0.0  0
 CKZ  CONST_34  N3   N2   C1   C1'  180.00   0.0  0
 CKZ  CONST_35  C4   N5   C1   C1'  180.00   0.0  0
 CKZ  CONST_36  H12  N5   C1   C1'    0.00   0.0  0
 CKZ  CONST_37  H15  C7   C6   C4     0.00   0.0  0
 CKZ  CONST_38  H13  C11  C6   C4     0.00   0.0  0
 CKZ  CONST_39  H14  C10  C11  C6   180.00   0.0  0
 CKZ  CONST_40  H18  C18  C14  C9     0.00   0.0  0
 CKZ  CONST_41  H21  C15  C13  C14  180.00   0.0  0
 CKZ  CONST_42  H19  C17  C18  C14  180.00   0.0  0
 CKZ  CONST_43  H20  C16  C15  C13  180.00   0.0  0
 CKZ  Var_01    H16  C12  C8   C9   119.81  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
 CKZ  chir_01  C5'  C4'  C6'  O5'  negativ
 CKZ  chir_02  C4'  O4'  C5'  C3'  positiv
 CKZ  chir_03  C3'  O3'  C4'  C2'  negativ
 CKZ  chir_04  C2'  O2'  C3'  C1'  positiv
 CKZ  chir_05  C1'  O5'  C2'  C1   positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 CKZ  plan-1  C1'  0.020
 CKZ  plan-1  C1   0.020
 CKZ  plan-1  N5   0.020
 CKZ  plan-1  C4   0.020
 CKZ  plan-1  N3   0.020
 CKZ  plan-1  N2   0.020
 CKZ  plan-1  C6   0.020
 CKZ  plan-1  H12  0.020
 CKZ  plan-2  C4   0.020
 CKZ  plan-2  C6   0.020
 CKZ  plan-2  C11  0.020
 CKZ  plan-2  C10  0.020
 CKZ  plan-2  C9   0.020
 CKZ  plan-2  C8   0.020
 CKZ  plan-2  C7   0.020
 CKZ  plan-2  C14  0.020
 CKZ  plan-2  C13  0.020
 CKZ  plan-2  C12  0.020
 CKZ  plan-2  C18  0.020
 CKZ  plan-2  C17  0.020
 CKZ  plan-2  C16  0.020
 CKZ  plan-2  C15  0.020
 CKZ  plan-2  H13  0.020
 CKZ  plan-2  H14  0.020
 CKZ  plan-2  H15  0.020
 CKZ  plan-2  H18  0.020
 CKZ  plan-2  H19  0.020
 CKZ  plan-2  H20  0.020
 CKZ  plan-2  H21  0.020

