# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 15:30:03 2022
#   Inital geometry file: a 157 line input string
#   Ligand name: [[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[2-(methylamino)phenyl]carbonyloxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ccccc1C(=O)O[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO[P](O)(=O)O[P](O)(=O)O[P](O)(S)=O)n3cnc4c(N)ncnc34
#
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
 TGB  TGB  '[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[2-(methylamino)phenyl]carbonyloxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphinic acid'  ligand  61  41  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TGB
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
 TGB  C13  C  CH1    0  -0.050   0.6025  -30.6794   5.2733
 TGB  C15  C  CH1    0   0.215  -0.2984  -31.9063   5.4022
 TGB  C17  C  CR15   0   0.106  -1.7310  -31.7813   3.3276
 TGB  C20  C  CR6    0   0.170  -1.2116  -34.8437   1.6925
 TGB  C01  C  CH3    0  -0.554   6.7185  -29.5281   8.8452
 TGB  C03  C  C      0   0.183   4.8173  -31.0914   8.7817
 TGB  C04  C  C1     0  -0.260   5.5557  -32.0644   9.4919
 TGB  C05  C  C1     0  -0.290   5.0168  -33.2950   9.7921
 TGB  C06  C  C1     0  -0.211   3.7176  -33.6270   9.4078
 TGB  C07  C  C1     0  -0.287   2.9741  -32.6897   8.7253
 TGB  C08  C  C      0  -0.098   3.4843  -31.4237   8.4053
 TGB  C12  C  CH1    0  -0.093   0.5149  -30.1194   6.7004
 TGB  C19  C  CR56   0   0.218  -1.3159  -33.6618   2.4493
 TGB  C23  C  CR16   0   0.052   0.2632  -35.6206   3.2794
 TGB  C25  C  CR56   0   0.540  -0.5588  -33.6127   3.6088
 TGB  C27  C  CH1    0  -0.016  -0.9185  -30.4723   7.1130
 TGB  N16  N  NR5    0  -0.492  -0.8343  -32.3955   4.1634
 TGB  N18  N  N      0  -0.491  -2.0402  -32.5067   2.2932
 TGB  N21  N  NH2    0  -0.803  -1.8911  -35.0425   0.5614
 TGB  N22  N  N      0  -0.409  -0.4043  -35.8103   2.1454
 TGB  N24  N  N      0  -0.519   0.2496  -34.5632   4.0722
 TGB  O11  O  O2     0  -0.449   1.3898  -30.8628   7.5413
 TGB  O14  O  OH1    0  -0.633   1.8643  -31.0798   4.8451
 TGB  O26  O  O2     0  -0.540  -1.3484  -31.5131   6.2328
 TGB  O31  O  O      0  -0.806  -2.0757  -26.6081   4.3741
 TGB  O32  O  OP    -1  -0.780  -2.7767  -26.5180   6.8866
 TGB  O33  O  O2     0  -0.651  -4.1124  -27.9251   5.3090
 TGB  O39  O  OP    -1  -0.790  -6.7509  -28.2508   1.3817
 TGB  O40  O  O      0  -0.908  -7.0438  -25.7644   2.1107
 TGB  P34  P  P      0   1.305  -4.7243  -28.6257   3.9575
 TGB  P38  P  P      0   1.080  -6.7910  -27.1985   2.4406
 TGB  S41  S  S2     0  -0.361  -8.2535  -27.7614   3.9348
 TGB  H1   H  HCH1   0   0.263   0.1406  -29.9544   4.5935
 TGB  H2   H  HCH1   0   0.285   0.2747  -32.7383   5.8311
 TGB  H3   H  HCR5   0   0.351  -2.1267  -30.7949   3.5339
 TGB  H4   H  HCH2   0   0.232  -1.6774  -28.6627   7.9146
 TGB  H5   H  HCH2   0   0.281  -2.9025  -29.6947   7.1772
 TGB  H6   H  HCH3   0   0.198   6.9032  -28.5247   8.4716
 TGB  H7   H  HCH3   0   0.240   6.8756  -29.5164   9.9267
 TGB  H8   H  HCH3   0   0.271   7.4654  -30.1940   8.4043
 TGB  H9   H  H      0   0.262   6.5678  -31.8460   9.8029
 TGB  H10  H  H      0   0.250   5.6204  -34.0123  10.3342
 TGB  H11  H  H      0   0.257   3.2998  -34.5972   9.6377
 TGB  H12  H  H      0   0.251   1.9668  -32.9430   8.4270
 TGB  H13  H  HCH1   0   0.319   0.7220  -29.0514   6.7719
 TGB  H14  H  HCR6   0   0.268   0.8984  -36.4434   3.5904
 TGB  H15  H  HCH1   0   0.307  -0.9264  -30.8492   8.1411
 TGB  H16  H  HNH1   0   0.356   4.8262  -29.2556   7.9472
 TGB  H17  H  HNH2   0   0.383  -1.7496  -35.8838   0.0292
 TGB  H18  H  HNH2   0   0.392  -2.4629  -34.3178   0.1645
 TGB  H19  H  HOH1   0   0.480   2.3282  -30.3225   4.4752
 TGB  H23  H  HSH1   0   0.281  -9.1738  -26.8949   3.4933
 TGB  C28  C  CH2    0  -0.182  -1.8831  -29.3100   7.0561
 TGB  C09  C  C      0   0.518   2.6526  -30.4579   7.6771
 TGB  O29  O  O2     0  -0.586  -1.7377  -28.6140   5.8420
 TGB  O10  O  O      0  -0.362   3.0382  -29.3875   7.2520
 TGB  P30  P  P      0   1.371  -2.6364  -27.2547   5.5939
 TGB  N02  N  NH1    0  -0.637   5.3753  -29.8992   8.4922
 TGB  O35  O  OP    -1  -0.804  -5.7999  -29.5635   4.4035
 TGB  O36  O  O      0  -0.862  -3.6412  -29.0926   3.0367
 TGB  O37  O  O2     0  -0.758  -5.4286  -27.2572   3.3497

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
 TGB  N21  C20  single    1.334  0.020  1.334
 TGB  O40  P38  deloc     1.493  0.020  1.493
 TGB  N18  C17  aromatic  1.301  0.020  1.301
 TGB  N18  C19  aromatic  1.372  0.020  1.372
 TGB  O31  P30  deloc     1.490  0.020  1.490
 TGB  C17  N16  aromatic  1.371  0.020  1.371
 TGB  C20  C19  aromatic  1.407  0.020  1.407
 TGB  C20  N22  aromatic  1.338  0.020  1.338
 TGB  C19  C25  aromatic  1.386  0.020  1.386
 TGB  P38  O37  single    1.639  0.020  1.639
 TGB  P38  S41  single    2.165  0.020  2.165
 TGB  P38  O39  deloc     1.493  0.020  1.493
 TGB  O37  P34  single    1.655  0.020  1.655
 TGB  O36  P34  deloc     1.496  0.020  1.496
 TGB  N22  C23  aromatic  1.330  0.020  1.330
 TGB  N16  C25  aromatic  1.366  0.020  1.366
 TGB  N16  C15  single    1.436  0.020  1.436
 TGB  P34  O33  single    1.641  0.020  1.641
 TGB  P34  O35  deloc     1.495  0.020  1.495
 TGB  C25  N24  aromatic  1.331  0.020  1.331
 TGB  P30  O32  deloc     1.494  0.020  1.494
 TGB  P30  O33  single    1.646  0.020  1.646
 TGB  P30  O29  single    1.648  0.020  1.648
 TGB  O14  C13  single    1.391  0.020  1.391
 TGB  O29  C28  single    1.407  0.020  1.407
 TGB  C13  C15  single    1.528  0.020  1.528
 TGB  C13  C12  single    1.536  0.020  1.536
 TGB  C15  O26  single    1.395  0.020  1.395
 TGB  C23  N24  aromatic  1.322  0.020  1.322
 TGB  C06  C07  aromatic  1.377  0.020  1.377
 TGB  C06  C05  aromatic  1.395  0.020  1.395
 TGB  O26  C27  single    1.429  0.020  1.429
 TGB  C07  C08  aromatic  1.402  0.020  1.402
 TGB  C28  C27  single    1.511  0.020  1.511
 TGB  C05  C04  aromatic  1.376  0.020  1.376
 TGB  C12  C27  single    1.533  0.020  1.533
 TGB  C12  O11  single    1.423  0.020  1.423
 TGB  C08  C09  single    1.468  0.020  1.468
 TGB  C08  C03  aromatic  1.424  0.020  1.424
 TGB  C09  O11  single    1.333  0.020  1.333
 TGB  C09  O10  double    1.215  0.020  1.215
 TGB  C04  C03  aromatic  1.413  0.020  1.413
 TGB  C03  N02  single    1.348  0.020  1.348
 TGB  N02  C01  single    1.438  0.020  1.438
 TGB  C13  H1   single    0.970  0.020  1.090
 TGB  C15  H2   single    0.970  0.020  1.090
 TGB  C17  H3   single    0.930  0.020  1.080
 TGB  C28  H4   single    0.970  0.020  1.090
 TGB  C28  H5   single    0.970  0.020  1.090
 TGB  C01  H6   single    0.970  0.020  1.090
 TGB  C01  H7   single    0.970  0.020  1.090
 TGB  C01  H8   single    0.970  0.020  1.090
 TGB  C04  H9   single    0.930  0.020  1.080
 TGB  C05  H10  single    0.930  0.020  1.080
 TGB  C06  H11  single    0.930  0.020  1.080
 TGB  C07  H12  single    0.930  0.020  1.080
 TGB  C12  H13  single    0.970  0.020  1.090
 TGB  C23  H14  single    0.930  0.020  1.080
 TGB  C27  H15  single    0.970  0.020  1.090
 TGB  N02  H16  single    0.860  0.020  1.020
 TGB  N21  H17  single    0.860  0.020  1.020
 TGB  N21  H18  single    0.860  0.020  1.020
 TGB  O14  H19  single    0.850  0.020  0.980
 TGB  S41  H23  single    1.200  0.020  1.300

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
 TGB  H1   C13  O14  112.43  3.000
 TGB  H1   C13  C12  108.13  3.000
 TGB  O14  C13  C12  116.28  3.000
 TGB  H1   C13  C15  109.58  3.000
 TGB  C12  C13  C15  100.42  3.000
 TGB  O14  C13  C15  109.25  3.000
 TGB  H2   C15  O26  111.96  3.000
 TGB  H2   C15  N16  105.89  3.000
 TGB  O26  C15  N16  109.19  3.000
 TGB  H2   C15  C13  109.50  3.000
 TGB  O26  C15  C13  105.53  3.000
 TGB  N16  C15  C13  114.90  3.000
 TGB  H3   C17  N18  124.94  3.000
 TGB  H3   C17  N16  122.07  3.000
 TGB  N18  C17  N16  112.98  3.000
 TGB  N22  C20  N21  119.11  3.000
 TGB  N22  C20  C19  117.98  3.000
 TGB  N21  C20  C19  122.90  3.000
 TGB  H8   C01  H7   107.90  3.000
 TGB  H8   C01  H6   107.92  3.000
 TGB  H7   C01  H6   107.81  3.000
 TGB  H8   C01  N02  112.46  3.000
 TGB  H7   C01  N02  112.34  3.000
 TGB  H6   C01  N02  108.22  3.000
 TGB  N02  C03  C08  122.48  3.000
 TGB  N02  C03  C04  120.05  3.000
 TGB  C08  C03  C04  117.46  3.000
 TGB  H9   C04  C05  118.97  3.000
 TGB  H9   C04  C03  119.65  3.000
 TGB  C05  C04  C03  121.38  3.000
 TGB  H10  C05  C06  119.96  3.000
 TGB  H10  C05  C04  118.89  3.000
 TGB  C06  C05  C04  121.15  3.000
 TGB  H11  C06  C07  120.49  3.000
 TGB  H11  C06  C05  121.00  3.000
 TGB  C07  C06  C05  118.51  3.000
 TGB  H12  C07  C08  119.20  3.000
 TGB  H12  C07  C06  118.71  3.000
 TGB  C08  C07  C06  122.09  3.000
 TGB  C09  C08  C07  120.08  3.000
 TGB  C09  C08  C03  120.52  3.000
 TGB  C07  C08  C03  119.40  3.000
 TGB  H13  C12  O11  110.87  3.000
 TGB  H13  C12  C27  112.68  3.000
 TGB  O11  C12  C27  107.19  3.000
 TGB  H13  C12  C13  114.04  3.000
 TGB  O11  C12  C13  108.88  3.000
 TGB  C27  C12  C13  102.68  3.000
 TGB  N18  C19  C25  110.72  3.000
 TGB  C25  C19  C20  116.06  3.000
 TGB  N18  C19  C20  133.22  3.000
 TGB  H14  C23  N24  116.15  3.000
 TGB  H14  C23  N22  115.48  3.000
 TGB  N24  C23  N22  128.37  3.000
 TGB  N24  C25  N16  128.14  3.000
 TGB  N24  C25  C19  126.72  3.000
 TGB  N16  C25  C19  105.14  3.000
 TGB  H15  C27  O26  108.98  3.000
 TGB  H15  C27  C12  109.80  3.000
 TGB  O26  C27  C12  106.45  3.000
 TGB  H15  C27  C28  107.18  3.000
 TGB  C12  C27  C28  114.18  3.000
 TGB  O26  C27  C28  110.17  3.000
 TGB  C25  N16  C17  106.47  3.000
 TGB  C25  N16  C15  125.37  3.000
 TGB  C17  N16  C15  128.14  3.000
 TGB  C19  N18  C17  104.68  3.000
 TGB  H18  N21  H17  118.32  3.000
 TGB  H18  N21  C20  121.15  3.000
 TGB  H17  N21  C20  120.10  3.000
 TGB  C23  N22  C20  119.24  3.000
 TGB  C25  N24  C23  111.63  3.000
 TGB  C12  O11  C09  118.94  3.000
 TGB  H19  O14  C13  109.22  3.000
 TGB  C27  O26  C15  110.21  3.000
 TGB  P34  O33  P30  130.62  3.000
 TGB  O37  P34  O36  109.88  3.000
 TGB  O36  P34  O35  120.57  3.000
 TGB  O37  P34  O35  108.79  3.000
 TGB  O35  P34  O33  106.88  3.000
 TGB  O36  P34  O33  111.73  3.000
 TGB  O37  P34  O33   96.21  3.000
 TGB  S41  P38  O40  106.73  3.000
 TGB  S41  P38  O39  108.92  3.000
 TGB  O40  P38  O39  121.64  3.000
 TGB  O39  P38  O37  110.23  3.000
 TGB  S41  P38  O37   99.75  3.000
 TGB  O40  P38  O37  107.32  3.000
 TGB  H23  S41  P38   93.92  3.000
 TGB  H5   C28  H4   107.19  3.000
 TGB  H5   C28  O29  111.41  3.000
 TGB  H4   C28  O29  111.39  3.000
 TGB  H5   C28  C27  108.63  3.000
 TGB  H4   C28  C27  107.78  3.000
 TGB  O29  C28  C27  110.30  3.000
 TGB  O11  C09  O10  122.19  3.000
 TGB  O10  C09  C08  125.00  3.000
 TGB  O11  C09  C08  112.80  3.000
 TGB  P30  O29  C28  118.78  3.000
 TGB  O33  P30  O32  105.45  3.000
 TGB  O33  P30  O31  111.87  3.000
 TGB  O32  P30  O31  121.97  3.000
 TGB  O33  P30  O29  100.32  3.000
 TGB  O32  P30  O29  109.12  3.000
 TGB  O31  P30  O29  106.01  3.000
 TGB  H16  N02  C03  117.14  3.000
 TGB  H16  N02  C01  118.54  3.000
 TGB  C03  N02  C01  124.22  3.000
 TGB  P38  O37  P34  125.96  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
 TGB  CONST_01  C20  C19  N18  C17   180.00   0.0  0
 TGB  CONST_02  C25  C19  N18  C17     0.00   0.0  0
 TGB  CONST_03  C19  C25  N16  C17     0.00   0.0  0
 TGB  CONST_04  N24  C25  N16  C17   180.00   0.0  0
 TGB  CONST_05  N16  C25  C19  C20   180.00   0.0  0
 TGB  CONST_06  N24  C25  C19  C20     0.00   0.0  0
 TGB  CONST_07  N24  C23  N22  C20     0.00   0.0  0
 TGB  CONST_08  C06  C07  C08  C03     0.00   0.0  0
 TGB  CONST_09  C06  C05  C04  C03     0.00   0.0  0
 TGB  CONST_10  C07  C06  C05  C04     0.00   0.0  0
 TGB  CONST_11  C07  C08  C03  C04     0.00   0.0  0
 TGB  CONST_12  C08  C07  C06  C05     0.00   0.0  0
 TGB  CONST_13  C08  C03  C04  C05     0.00   0.0  0
 TGB  CONST_14  N16  C17  N18  C19     0.00   0.0  0
 TGB  CONST_15  C23  N22  C20  C19     0.00   0.0  0
 TGB  CONST_16  C23  N24  C25  C19     0.00   0.0  0
 TGB  CONST_17  N16  C25  N24  C23   180.00   0.0  0
 TGB  CONST_18  N22  C20  C19  C25     0.00   0.0  0
 TGB  CONST_19  N18  C17  N16  C25     0.00   0.0  0
 TGB  CONST_20  N22  C23  N24  C25     0.00   0.0  0
 TGB  CONST_21  N18  C19  C25  N16     0.00   0.0  0
 TGB  CONST_22  N22  C20  C19  N18   180.00   0.0  0
 TGB  CONST_23  N24  C25  C19  N18   180.00   0.0  0
 TGB  CONST_24  N18  C17  N16  C15   180.00   0.0  0
 TGB  CONST_25  C19  C25  N16  C15   180.00   0.0  0
 TGB  CONST_26  N24  C25  N16  C15     0.00   0.0  0
 TGB  CONST_27  C09  C08  C03  C04   180.00   0.0  0
 TGB  CONST_28  N02  C03  C04  C05   180.00   0.0  0
 TGB  CONST_29  C09  C08  C07  C06   180.00   0.0  0
 TGB  CONST_30  N02  C03  C08  C07   180.00   0.0  0
 TGB  CONST_31  N21  C20  N22  C23   180.00   0.0  0
 TGB  CONST_32  N21  C20  C19  C25   180.00   0.0  0
 TGB  CONST_33  N21  C20  C19  N18     0.00   0.0  0
 TGB  CONST_34  H3   C17  N16  C15     0.00   0.0  0
 TGB  CONST_35  H14  C23  N22  C20   180.00   0.0  0
 TGB  CONST_36  H12  C07  C08  C03   180.00   0.0  0
 TGB  CONST_37  H10  C05  C04  C03   180.00   0.0  0
 TGB  CONST_38  H11  C06  C05  C04   180.00   0.0  0
 TGB  CONST_39  H9   C04  C05  C06   180.00   0.0  0
 TGB  CONST_40  C08  C03  N02  C01   180.00   0.0  0
 TGB  CONST_41  C04  C03  N02  C01     0.00   0.0  0
 TGB  CONST_42  H16  N02  C03  C04   180.00   0.0  0
 TGB  CONST_43  H17  N21  C20  C19   180.00   0.0  0
 TGB  CONST_44  H18  N21  C20  C19     0.00   0.0  0
 TGB  Var_01    O11  C09  C08  C03  -172.57  30.0  2
 TGB  Var_02    H6   C01  N02  C03   178.94  30.0  3
 TGB  Var_03    O31  P30  O29  C28   169.05  30.0  2
 TGB  Var_04    S41  P38  O37  P34    69.42  30.0  3
 TGB  Var_05    H4   C28  O29  P30   -57.14  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
 TGB  chir_01  C13  O14  C15  C12  negativ
 TGB  chir_02  C15  O26  N16  C13  negativ
 TGB  chir_03  C12  O11  C13  C27  negativ
 TGB  chir_04  C27  O26  C12  C28  negativ

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
 TGB  plan-1  C03  0.020
 TGB  plan-1  C04  0.020
 TGB  plan-1  C05  0.020
 TGB  plan-1  C06  0.020
 TGB  plan-1  C07  0.020
 TGB  plan-1  C08  0.020
 TGB  plan-1  H9   0.020
 TGB  plan-1  H10  0.020
 TGB  plan-1  H11  0.020
 TGB  plan-1  H12  0.020
 TGB  plan-1  C09  0.020
 TGB  plan-1  N02  0.020
 TGB  plan-2  C15  0.020
 TGB  plan-2  C17  0.020
 TGB  plan-2  C20  0.020
 TGB  plan-2  C19  0.020
 TGB  plan-2  C23  0.020
 TGB  plan-2  C25  0.020
 TGB  plan-2  N16  0.020
 TGB  plan-2  N18  0.020
 TGB  plan-2  N21  0.020
 TGB  plan-2  N22  0.020
 TGB  plan-2  N24  0.020
 TGB  plan-2  H3   0.020
 TGB  plan-2  H14  0.020
 TGB  plan-3  C20  0.020
 TGB  plan-3  N21  0.020
 TGB  plan-3  H17  0.020
 TGB  plan-3  H18  0.020
 TGB  plan-4  C01  0.020
 TGB  plan-4  C03  0.020
 TGB  plan-4  H16  0.020
 TGB  plan-4  N02  0.020
 TGB  plan-5  C08  0.020
 TGB  plan-5  O11  0.020
 TGB  plan-5  C09  0.020
 TGB  plan-5  O10  0.020

