# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 18:16:21 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: (2~{S},3~{R},4~{S},5~{S},6~{R})-2-[(1~{S},2~{S},3~{R},4~{S},6~{R})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)[C@H](N)[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
 CK0  CK0  (2~{S},3~{R},4~{S},5~{S},6~{R})-2-[(1~{S},2~{S},3~{R},4~{S},6~{R})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol  ligand  69  33  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CK0
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
 CK0  C4   C  CH1   0   0.033  48.0760  3.6332   1.2114
 CK0  C5   C  CH1   0  -0.016  48.9856  3.6699  -0.0158
 CK0  C6   C  CH2   0  -0.181  50.1252  2.6754   0.0199
 CK0  C3   C  CH1   0  -0.030  46.9494  4.6454   1.0190
 CK0  O2   O  OH1   0  -0.663  45.1997  5.2669  -0.5540
 CK0  C2   C  CH1   0   0.013  46.2156  4.3393  -0.2789
 CK0  O3   O  OH1   0  -0.675  46.0043  4.5766   2.0687
 CK0  O4   O  OH1   0  -0.671  48.8642  3.9331   2.3381
 CK0  O6   O  OH1   0  -0.668  49.6180  1.3694   0.1477
 CK0  O5   O  O2    0  -0.496  48.2300  3.4121  -1.1879
 CK0  C1   C  CH1   0   0.245  47.1892  4.3064  -1.4564
 CK0  O1   O  O2    0  -0.519  47.6474  5.5958  -1.7120
 CK0  CBG  C  CH1   0   0.056  47.9971  5.9020  -3.0545
 CK0  CBA  C  CH1   0   0.016  49.4052  6.4985  -3.0792
 CK0  OAK  O  OH1   0  -0.665  50.3541  5.5804  -2.5903
 CK0  CAT  C  CH1   0  -0.091  46.9792  6.8693  -3.6464
 CK0  NAC  N  NH2   0  -0.818  45.6616  6.2547  -3.6675
 CK0  CAN  C  CH2   0  -0.452  47.3989  7.2276  -5.0636
 CK0  CAS  C  CH1   0  -0.121  48.7883  7.8499  -5.1231
 CK0  NAB  N  NH2   0  -0.794  49.0795  8.2488  -6.4879
 CK0  CBF  C  CH1   0   0.045  49.8024  6.8791  -4.5060
 CK0  OAQ  O  O2    0  -0.516  51.0856  7.4771  -4.4977
 CK0  CBD  C  CH1   0   0.274  52.1589  6.6751  -4.8897
 CK0  OAO  O  O2    0  -0.498  52.3166  6.6434  -6.2818
 CK0  CBB  C  CH1   0   0.018  52.7156  7.8543  -6.9046
 CK0  CAL  C  CH2   0  -0.326  52.7388  7.6173  -8.4071
 CK0  NAA  N  NH2   0  -0.804  53.7737  6.6806  -8.8145
 CK0  CAX  C  CH1   0   0.031  54.0477  8.3285  -6.3281
 CK0  OAH  O  OH1   0  -0.672  54.3930  9.5277  -6.9792
 CK0  CAV  C  CH1   0   0.044  53.8870  8.5049  -4.8278
 CK0  OAF  O  OH1   0  -0.679  55.1109  8.9121  -4.2675
 CK0  CAU  C  CH1   0  -0.192  53.4358  7.1828  -4.2129
 CK0  NAD  N  NH2   0  -0.799  53.3807  7.3275  -2.7717
 CK0  H1   H  HCH1  0   0.214  47.6307  2.6318   1.2970
 CK0  H2   H  HCH1  0   0.215  49.4456  4.6672  -0.0596
 CK0  H3   H  HCH2  0   0.208  50.7878  2.9442   0.8498
 CK0  H4   H  HCH2  0   0.210  50.7109  2.7967  -0.9018
 CK0  H5   H  HCH1  0   0.224  47.3858  5.6519   0.9592
 CK0  H6   H  HOH1  0   0.452  44.5915  5.2668   0.1930
 CK0  H7   H  HCH1  0   0.219  45.8011  3.3222  -0.1991
 CK0  H8   H  HOH1  0   0.458  46.2271  5.2307   2.7367
 CK0  H9   H  HOH1  0   0.451  48.3459  3.7520   3.1280
 CK0  H10  H  HOH1  0   0.455  50.3610  0.7686   0.2511
 CK0  H11  H  HCH1  0   0.241  46.6811  3.8992  -2.3385
 CK0  H12  H  HCH1  0   0.218  47.9953  4.9866  -3.6636
 CK0  H13  H  HCH1  0   0.215  49.4045  7.4172  -2.4738
 CK0  H14  H  HOH1  0   0.461  50.4195  5.6786  -1.6375
 CK0  H15  H  HCH1  0   0.202  47.0070  7.7931  -3.0439
 CK0  H16  H  HNH2  0   0.350  45.3219  6.1355  -2.7210
 CK0  H17  H  HNH2  0   0.343  45.0097  6.8887  -4.1138
 CK0  H19  H  HCH2  0   0.245  46.6807  7.9294  -5.4946
 CK0  H20  H  HCH2  0   0.223  47.3733  6.3246  -5.6852
 CK0  H21  H  HCH1  0   0.228  48.7815  8.7623  -4.5146
 CK0  H22  H  HNH2  0   0.359  49.9332  8.7897  -6.5178
 CK0  H23  H  HNH2  0   0.338  49.2453  7.4279  -7.0600
 CK0  H25  H  HCH1  0   0.217  49.8099  5.9678  -5.1243
 CK0  H26  H  HCH1  0   0.229  51.9849  5.6330  -4.6055
 CK0  H27  H  HCH1  0   0.212  51.9743  8.6439  -6.7171
 CK0  H28  H  HCH2  0   0.211  52.8020  8.5926  -8.9039
 CK0  H29  H  HCH2  0   0.235  51.7667  7.2024  -8.6845
 CK0  H30  H  HNH2  0   0.351  53.5769  6.3517  -9.7502
 CK0  H31  H  HNH2  0   0.344  54.6626  7.1603  -8.8773
 CK0  H33  H  HCH1  0   0.205  54.8077  7.5502  -6.5014
 CK0  H34  H  HOH1  0   0.451  55.2447  9.8201  -6.6398
 CK0  H35  H  HCH1  0   0.193  53.1107  9.2686  -4.6514
 CK0  H36  H  HOH1  0   0.441  55.0404  8.7105  -3.3234
 CK0  H37  H  HCH1  0   0.248  54.2122  6.4411  -4.4331
 CK0  H38  H  HNH2  0   0.348  52.5371  7.8195  -2.5025
 CK0  H39  H  HNH2  0   0.357  53.3369  6.4203  -2.3266

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
 CK0  NAA  CAL  single  1.454  0.020  1.454
 CK0  CAL  CBB  single  1.521  0.020  1.521
 CK0  OAH  CAX  single  1.408  0.020  1.408
 CK0  CBB  CAX  single  1.527  0.020  1.527
 CK0  CBB  OAO  single  1.419  0.020  1.419
 CK0  CAX  CAV  single  1.519  0.020  1.519
 CK0  NAB  CAS  single  1.451  0.020  1.451
 CK0  OAO  CBD  single  1.401  0.020  1.401
 CK0  CAV  OAF  single  1.406  0.020  1.406
 CK0  CAV  CAU  single  1.526  0.020  1.526
 CK0  CAN  CAS  single  1.524  0.020  1.524
 CK0  CAN  CAT  single  1.521  0.020  1.521
 CK0  CAS  CBF  single  1.534  0.020  1.534
 CK0  CBD  OAQ  single  1.396  0.020  1.396
 CK0  CBD  CAU  single  1.532  0.020  1.532
 CK0  CBF  OAQ  single  1.416  0.020  1.416
 CK0  CBF  CBA  single  1.529  0.020  1.529
 CK0  CAU  NAD  single  1.450  0.020  1.450
 CK0  CAT  NAC  single  1.454  0.020  1.454
 CK0  CAT  CBG  single  1.524  0.020  1.524
 CK0  CBG  CBA  single  1.529  0.020  1.529
 CK0  CBG  O1   single  1.421  0.020  1.421
 CK0  CBA  OAK  single  1.408  0.020  1.408
 CK0  O1   C1   single  1.392  0.020  1.392
 CK0  C1   O5   single  1.398  0.020  1.398
 CK0  C1   C2   single  1.528  0.020  1.528
 CK0  O5   C5   single  1.418  0.020  1.418
 CK0  O2   C2   single  1.403  0.020  1.403
 CK0  C2   C3   single  1.522  0.020  1.522
 CK0  C6   O6   single  1.407  0.020  1.407
 CK0  C6   C5   single  1.513  0.020  1.513
 CK0  C5   C4   single  1.528  0.020  1.528
 CK0  C3   C4   single  1.527  0.020  1.527
 CK0  C3   O3   single  1.414  0.020  1.414
 CK0  C4   O4   single  1.407  0.020  1.407
 CK0  C4   H1   single  0.970  0.020  1.090
 CK0  C5   H2   single  0.970  0.020  1.090
 CK0  C6   H3   single  0.970  0.020  1.090
 CK0  C6   H4   single  0.970  0.020  1.090
 CK0  C3   H5   single  0.970  0.020  1.090
 CK0  O2   H6   single  0.850  0.020  0.980
 CK0  C2   H7   single  0.970  0.020  1.090
 CK0  O3   H8   single  0.850  0.020  0.980
 CK0  O4   H9   single  0.850  0.020  0.980
 CK0  O6   H10  single  0.850  0.020  0.980
 CK0  C1   H11  single  0.970  0.020  1.090
 CK0  CBG  H12  single  0.970  0.020  1.090
 CK0  CBA  H13  single  0.970  0.020  1.090
 CK0  OAK  H14  single  0.850  0.020  0.980
 CK0  CAT  H15  single  0.970  0.020  1.090
 CK0  NAC  H16  single  0.890  0.020  1.040
 CK0  NAC  H17  single  0.890  0.020  1.040
 CK0  CAN  H19  single  0.970  0.020  1.090
 CK0  CAN  H20  single  0.970  0.020  1.090
 CK0  CAS  H21  single  0.970  0.020  1.090
 CK0  NAB  H22  single  0.890  0.020  1.040
 CK0  NAB  H23  single  0.890  0.020  1.040
 CK0  CBF  H25  single  0.970  0.020  1.090
 CK0  CBD  H26  single  0.970  0.020  1.090
 CK0  CBB  H27  single  0.970  0.020  1.090
 CK0  CAL  H28  single  0.970  0.020  1.090
 CK0  CAL  H29  single  0.970  0.020  1.090
 CK0  NAA  H30  single  0.890  0.020  1.040
 CK0  NAA  H31  single  0.890  0.020  1.040
 CK0  CAX  H33  single  0.970  0.020  1.090
 CK0  OAH  H34  single  0.850  0.020  0.980
 CK0  CAV  H35  single  0.970  0.020  1.090
 CK0  OAF  H36  single  0.850  0.020  0.980
 CK0  CAU  H37  single  0.970  0.020  1.090
 CK0  NAD  H38  single  0.890  0.020  1.040
 CK0  NAD  H39  single  0.890  0.020  1.040

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
 CK0  H1   C4   O4   111.02  3.000
 CK0  H1   C4   C3   108.35  3.000
 CK0  O4   C4   C3   111.89  3.000
 CK0  H1   C4   C5   109.00  3.000
 CK0  O4   C4   C5   107.72  3.000
 CK0  C3   C4   C5   108.80  3.000
 CK0  H2   C5   O5   110.79  3.000
 CK0  H2   C5   C6   106.39  3.000
 CK0  O5   C5   C6   107.54  3.000
 CK0  H2   C5   C4   107.63  3.000
 CK0  C6   C5   C4   114.44  3.000
 CK0  O5   C5   C4   110.01  3.000
 CK0  H4   C6   H3   106.61  3.000
 CK0  H4   C6   O6   111.77  3.000
 CK0  H3   C6   O6   112.15  3.000
 CK0  H4   C6   C5   108.01  3.000
 CK0  H3   C6   C5   108.19  3.000
 CK0  O6   C6   C5   109.93  3.000
 CK0  H5   C3   O3   110.52  3.000
 CK0  H5   C3   C2   109.23  3.000
 CK0  O3   C3   C2   107.52  3.000
 CK0  H5   C3   C4   108.73  3.000
 CK0  O3   C3   C4   111.55  3.000
 CK0  C2   C3   C4   109.26  3.000
 CK0  H6   O2   C2   107.77  3.000
 CK0  H7   C2   C1   106.01  3.000
 CK0  H7   C2   O2   110.63  3.000
 CK0  C1   C2   O2   108.93  3.000
 CK0  H7   C2   C3   107.78  3.000
 CK0  O2   C2   C3   112.54  3.000
 CK0  C1   C2   C3   110.75  3.000
 CK0  H8   O3   C3   109.14  3.000
 CK0  H9   O4   C4   108.40  3.000
 CK0  H10  O6   C6   108.15  3.000
 CK0  C1   O5   C5   116.05  3.000
 CK0  H11  C1   O1   110.42  3.000
 CK0  H11  C1   O5   105.19  3.000
 CK0  O1   C1   O5   112.49  3.000
 CK0  H11  C1   C2   109.43  3.000
 CK0  O5   C1   C2   109.88  3.000
 CK0  O1   C1   C2   109.34  3.000
 CK0  CBG  O1   C1   117.01  3.000
 CK0  H12  CBG  CAT  108.18  3.000
 CK0  H12  CBG  CBA  108.50  3.000
 CK0  CAT  CBG  CBA  111.17  3.000
 CK0  H12  CBG  O1   110.10  3.000
 CK0  CBA  CBG  O1   109.03  3.000
 CK0  CAT  CBG  O1   109.84  3.000
 CK0  H13  CBA  CBF  107.81  3.000
 CK0  H13  CBA  OAK  110.72  3.000
 CK0  CBF  CBA  OAK  108.13  3.000
 CK0  H13  CBA  CBG  108.43  3.000
 CK0  OAK  CBA  CBG  111.13  3.000
 CK0  CBF  CBA  CBG  110.57  3.000
 CK0  H14  OAK  CBA  108.90  3.000
 CK0  H15  CAT  CAN  107.74  3.000
 CK0  H15  CAT  NAC  112.62  3.000
 CK0  CAN  CAT  NAC  109.64  3.000
 CK0  H15  CAT  CBG  107.61  3.000
 CK0  NAC  CAT  CBG  110.04  3.000
 CK0  CAN  CAT  CBG  109.10  3.000
 CK0  H17  NAC  H16  105.65  3.000
 CK0  H17  NAC  CAT  108.97  3.000
 CK0  H16  NAC  CAT  109.89  3.000
 CK0  H20  CAN  H19  106.86  3.000
 CK0  H20  CAN  CAS  109.60  3.000
 CK0  H19  CAN  CAS  108.77  3.000
 CK0  H20  CAN  CAT  109.13  3.000
 CK0  H19  CAN  CAT  109.72  3.000
 CK0  CAS  CAN  CAT  112.60  3.000
 CK0  H21  CAS  CBF  107.91  3.000
 CK0  H21  CAS  NAB  107.11  3.000
 CK0  CBF  CAS  NAB  114.81  3.000
 CK0  H21  CAS  CAN  108.21  3.000
 CK0  CBF  CAS  CAN  109.20  3.000
 CK0  NAB  CAS  CAN  109.39  3.000
 CK0  H23  NAB  H22  106.17  3.000
 CK0  H23  NAB  CAS  109.92  3.000
 CK0  H22  NAB  CAS  110.14  3.000
 CK0  H25  CBF  OAQ  110.28  3.000
 CK0  H25  CBF  CAS  107.60  3.000
 CK0  OAQ  CBF  CAS  109.53  3.000
 CK0  H25  CBF  CBA  108.64  3.000
 CK0  OAQ  CBF  CBA  109.58  3.000
 CK0  CAS  CBF  CBA  111.17  3.000
 CK0  CBD  OAQ  CBF  116.91  3.000
 CK0  H26  CBD  CAU  109.48  3.000
 CK0  H26  CBD  OAO  104.74  3.000
 CK0  CAU  CBD  OAO  110.65  3.000
 CK0  H26  CBD  OAQ  110.61  3.000
 CK0  CAU  CBD  OAQ  109.05  3.000
 CK0  OAO  CBD  OAQ  112.24  3.000
 CK0  CBB  OAO  CBD  116.64  3.000
 CK0  H27  CBB  CAX  107.50  3.000
 CK0  H27  CBB  CAL  106.90  3.000
 CK0  CAX  CBB  CAL  114.07  3.000
 CK0  H27  CBB  OAO  110.40  3.000
 CK0  CAX  CBB  OAO  110.16  3.000
 CK0  CAL  CBB  OAO  107.75  3.000
 CK0  H29  CAL  H28  105.90  3.000
 CK0  H29  CAL  NAA  108.51  3.000
 CK0  H28  CAL  NAA  113.90  3.000
 CK0  H29  CAL  CBB  107.23  3.000
 CK0  H28  CAL  CBB  108.05  3.000
 CK0  NAA  CAL  CBB  112.83  3.000
 CK0  H31  NAA  H30  105.53  3.000
 CK0  H31  NAA  CAL  109.71  3.000
 CK0  H30  NAA  CAL  109.28  3.000
 CK0  H33  CAX  CAV  108.09  3.000
 CK0  H33  CAX  OAH  111.09  3.000
 CK0  CAV  CAX  OAH  112.58  3.000
 CK0  H33  CAX  CBB  108.84  3.000
 CK0  CAV  CAX  CBB  108.46  3.000
 CK0  OAH  CAX  CBB  107.70  3.000
 CK0  H34  OAH  CAX  108.23  3.000
 CK0  H35  CAV  CAU  109.10  3.000
 CK0  H35  CAV  OAF  110.38  3.000
 CK0  CAU  CAV  OAF  110.34  3.000
 CK0  H35  CAV  CAX  108.22  3.000
 CK0  CAU  CAV  CAX  109.18  3.000
 CK0  OAF  CAV  CAX  109.58  3.000
 CK0  H36  OAF  CAV  105.36  3.000
 CK0  H37  CAU  NAD  107.11  3.000
 CK0  H37  CAU  CAV  107.21  3.000
 CK0  NAD  CAU  CAV  108.98  3.000
 CK0  H37  CAU  CBD  106.11  3.000
 CK0  NAD  CAU  CBD  116.15  3.000
 CK0  CAV  CAU  CBD  110.82  3.000
 CK0  H39  NAD  H38  106.41  3.000
 CK0  H39  NAD  CAU  110.46  3.000
 CK0  H38  NAD  CAU  110.14  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
 CK0  Var_01  H30  NAA  CAL  CBB  163.36  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
 CK0  chir_01  C4   C5   C3   O4   positiv
 CK0  chir_02  C5   O5   C4   C6   negativ
 CK0  chir_03  C3   O3   C4   C2   negativ
 CK0  chir_04  C2   O2   C3   C1   positiv
 CK0  chir_05  C1   O1   O5   C2   negativ
 CK0  chir_06  CBG  O1   CAT  CBA  negativ
 CK0  chir_07  CBA  OAK  CBG  CBF  positiv
 CK0  chir_08  CAT  NAC  CAN  CBG  positiv
 CK0  chir_09  CAS  NAB  CBF  CAN  positiv
 CK0  chir_10  CBF  OAQ  CBA  CAS  negativ
 CK0  chir_11  CBD  OAQ  OAO  CAU  negativ
 CK0  chir_12  CBB  OAO  CAL  CAX  positiv
 CK0  chir_13  CAX  OAH  CBB  CAV  positiv
 CK0  chir_14  CAV  OAF  CAX  CAU  negativ
 CK0  chir_15  CAU  NAD  CAV  CBD  positiv

