# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri May 29 00:01:37 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: (2R,3S,4S,5S,6R)-5-amino-3,4-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N)[C@@H](O)[C@@H](O)[C@@H]1N
#
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
 JB2  JB2  '(2R,3S,4S,5S,6R)-5-amino-3,4-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  62  38  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JB2
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
 JB2  O6   O  O      0  -0.469  -1.8940  -4.6331  -0.9050
 JB2  C6   C  CR6    0   0.508  -2.5088  -3.6035  -1.1246
 JB2  C5   C  CR56   0  -0.040  -2.1767  -2.2699  -0.7517
 JB2  N7   N  N      0  -0.515  -1.0946  -1.7785  -0.0696
 JB2  C8   C  CR15   0   0.104  -1.2784  -0.4914  -0.0088
 JB2  N1   N  NR16   0  -0.726  -3.7182  -3.6268  -1.8289
 JB2  C2   C  CR6    0   0.687  -4.4891  -2.5429  -2.1400
 JB2  N2   N  NH2    0  -0.832  -5.6343  -2.7827  -2.7959
 JB2  N3   N  N      0  -0.509  -4.1739  -1.3193  -1.7962
 JB2  C4   C  CR56   0   0.497  -3.0259  -1.2429  -1.1097
 JB2  N9   N  NR5    0  -0.548  -2.4426  -0.1100  -0.6290
 JB2  C1'  C  CH1    0   0.232  -2.9878   1.2228  -0.7506
 JB2  O4'  O  O2     0  -0.490  -1.9485   2.1247  -0.9783
 JB2  C2'  C  CH1    0  -0.047  -3.7058   1.7197   0.5035
 JB2  O2'  O  OH1    0  -0.652  -5.0187   1.2463   0.5260
 JB2  C3'  C  CH1    0  -0.037  -3.5657   3.2352   0.3312
 JB2  O3'  O  OH1    0  -0.669  -4.4771   3.7157  -0.6231
 JB2  C4'  C  CH1    0  -0.041  -2.1570   3.3331  -0.2375
 JB2  C5'  C  CH2    0  -0.144  -1.1144   3.4766   0.8547
 JB2  O5'  O  O2     0  -0.618   0.1653   3.4197   0.2741
 JB2  P    P  P      0   1.347   1.3835   2.7676   1.1747
 JB2  O1P  O  O      0  -0.793   1.8717   3.7886   2.1537
 JB2  O2P  O  OP    -1  -0.770   0.9758   1.4079   1.6530
 JB2  OPP  O  O2     0  -0.735   2.4092   2.6842  -0.1038
 JB2  P2   P  P      0   1.367   3.7411   1.7281  -0.1976
 JB2  O3P  O  OP    -1  -0.793   4.4709   2.1205  -1.4437
 JB2  O4P  O  O      0  -0.788   4.4332   1.7000   1.1275
 JB2  O1G  O  O2     0  -0.620   2.9413   0.3162  -0.4569
 JB2  C1G  C  CH1    0   0.241   3.5282  -0.7687  -1.1067
 JB2  O5G  O  O2     0  -0.507   4.6953  -1.2119  -0.4901
 JB2  C5G  C  CH1    0   0.037   4.5458  -1.7037   0.8394
 JB2  C6G  C  CH3    0  -0.696   5.9249  -2.1539   1.2795
 JB2  C2G  C  CH1    0  -0.025   2.4666  -1.8671  -1.1372
 JB2  O2G  O  OH1    0  -0.676   2.9045  -2.9562  -1.9145
 JB2  C3G  C  CH1    0   0.031   2.1969  -2.3557   0.2862
 JB2  O3G  O  OH1    0  -0.708   1.2393  -3.3773   0.3110
 JB2  C4G  C  CH1    0  -0.132   3.4976  -2.8283   0.9329
 JB2  N4A  N  NH2    0  -0.788   3.2423  -3.2424   2.3022
 JB2  H1   H  HCR5   0   0.330  -0.5974   0.2141   0.4530
 JB2  H2   H  HNR6   0   0.425  -4.0420  -4.5427  -2.1121
 JB2  H3   H  HNH2   0   0.415  -5.7784  -3.6527  -3.2802
 JB2  H4   H  HNH2   0   0.412  -6.1437  -1.9887  -3.1453
 JB2  H5   H  HCH1   0   0.256  -3.6903   1.1871  -1.5912
 JB2  H6   H  HCH1   0   0.249  -3.1478   1.4011   1.3928
 JB2  H7   H  HOH1   0   0.469  -5.3488   1.2931   1.4286
 JB2  H8   H  HCH1   0   0.252  -3.6588   3.7696   1.2860
 JB2  H9   H  HOH1   0   0.449  -5.3472   3.3600  -0.4081
 JB2  H10  H  HCH1   0   0.260  -2.0725   4.1753  -0.9312
 JB2  H11  H  HCH2   0   0.223  -1.2757   4.4370   1.3582
 JB2  H12  H  HCH2   0   0.206  -1.2487   2.6906   1.6068
 JB2  H15  H  HCH1   0   0.223   3.8303  -0.4915  -2.1253
 JB2  H16  H  HCH1   0   0.213   4.2168  -0.8851   1.4926
 JB2  H17  H  HCH3   0   0.240   6.6436  -1.3381   1.1988
 JB2  H18  H  HCH3   0   0.222   5.9169  -2.4739   2.3209
 JB2  H19  H  HCH3   0   0.224   6.2805  -2.9893   0.6728
 JB2  H20  H  HCH1   0   0.218   1.5403  -1.4398  -1.5459
 JB2  H21  H  HOH1   0   0.449   2.9442  -2.6749  -2.8337
 JB2  H22  H  HCH1   0   0.218   1.8438  -1.4832   0.8582
 JB2  H23  H  HOH1   0   0.462   0.3764  -2.9404   0.1831
 JB2  H24  H  HCH1   0   0.221   3.8709  -3.7029   0.3871
 JB2  H25  H  HNH2   0   0.346   4.0899  -3.5970   2.7258
 JB2  H26  H  HNH2   0   0.333   2.9652  -2.4402   2.8582

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
 JB2  O3'  C3'  single    1.404  0.020  1.404
 JB2  O2'  C2'  single    1.396  0.020  1.396
 JB2  C3'  C2'  single    1.532  0.020  1.532
 JB2  C3'  C4'  single    1.522  0.020  1.522
 JB2  O1P  P    deloc     1.496  0.020  1.496
 JB2  C2'  C1'  single    1.528  0.020  1.528
 JB2  C4'  O4'  single    1.433  0.020  1.433
 JB2  C4'  C5'  single    1.517  0.020  1.517
 JB2  O5'  P    single    1.649  0.020  1.649
 JB2  O5'  C5'  single    1.406  0.020  1.406
 JB2  C1'  O4'  single    1.395  0.020  1.395
 JB2  C1'  N9   single    1.445  0.020  1.445
 JB2  N2   C2   single    1.341  0.020  1.341
 JB2  P    O2P  deloc     1.498  0.020  1.498
 JB2  P    OPP  single    1.641  0.020  1.641
 JB2  O4P  P2   deloc     1.495  0.020  1.495
 JB2  N3   C2   double    1.310  0.020  1.310
 JB2  N3   C4   single    1.340  0.020  1.340
 JB2  C2   N1   single    1.366  0.020  1.366
 JB2  N9   C4   aromatic  1.362  0.020  1.362
 JB2  N9   C8   aromatic  1.373  0.020  1.373
 JB2  C4   C5   aromatic  1.380  0.020  1.380
 JB2  OPP  P2   single    1.642  0.020  1.642
 JB2  P2   O1G  single    1.643  0.020  1.643
 JB2  P2   O3P  deloc     1.496  0.020  1.496
 JB2  N1   C6   single    1.400  0.020  1.400
 JB2  O1G  C1G  single    1.394  0.020  1.394
 JB2  C8   N7   aromatic  1.302  0.020  1.302
 JB2  O3G  C3G  single    1.400  0.020  1.400
 JB2  C3G  C2G  single    1.529  0.020  1.529
 JB2  C3G  C4G  single    1.528  0.020  1.528
 JB2  N4A  C4G  single    1.453  0.020  1.453
 JB2  C5   C6   single    1.424  0.020  1.424
 JB2  C5   N7   aromatic  1.370  0.020  1.370
 JB2  C6   O6   double    1.219  0.020  1.219
 JB2  C2G  C1G  single    1.528  0.020  1.528
 JB2  C2G  O2G  single    1.408  0.020  1.408
 JB2  C4G  C5G  single    1.540  0.020  1.540
 JB2  C1G  O5G  single    1.392  0.020  1.392
 JB2  C5G  O5G  single    1.425  0.020  1.425
 JB2  C5G  C6G  single    1.516  0.020  1.516
 JB2  C8   H1   single    0.930  0.020  1.080
 JB2  N1   H2   single    0.860  0.020  1.020
 JB2  N2   H3   single    0.890  0.020  1.040
 JB2  N2   H4   single    0.890  0.020  1.040
 JB2  C1'  H5   single    0.970  0.020  1.090
 JB2  C2'  H6   single    0.970  0.020  1.090
 JB2  O2'  H7   single    0.850  0.020  0.980
 JB2  C3'  H8   single    0.970  0.020  1.090
 JB2  O3'  H9   single    0.850  0.020  0.980
 JB2  C4'  H10  single    0.970  0.020  1.090
 JB2  C5'  H11  single    0.970  0.020  1.090
 JB2  C5'  H12  single    0.970  0.020  1.090
 JB2  C1G  H15  single    0.970  0.020  1.090
 JB2  C5G  H16  single    0.970  0.020  1.090
 JB2  C6G  H17  single    0.970  0.020  1.090
 JB2  C6G  H18  single    0.970  0.020  1.090
 JB2  C6G  H19  single    0.970  0.020  1.090
 JB2  C2G  H20  single    0.970  0.020  1.090
 JB2  O2G  H21  single    0.850  0.020  0.980
 JB2  C3G  H22  single    0.970  0.020  1.090
 JB2  O3G  H23  single    0.850  0.020  0.980
 JB2  C4G  H24  single    0.970  0.020  1.090
 JB2  N4A  H25  single    0.890  0.020  1.040
 JB2  N4A  H26  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
 JB2  N1   C6   C5   110.42  3.000
 JB2  C5   C6   O6   128.77  3.000
 JB2  N1   C6   O6   120.82  3.000
 JB2  C4   C5   N7   110.38  3.000
 JB2  N7   C5   C6   130.57  3.000
 JB2  C4   C5   C6   119.05  3.000
 JB2  C8   N7   C5   105.45  3.000
 JB2  H1   C8   N9   122.98  3.000
 JB2  H1   C8   N7   125.09  3.000
 JB2  N9   C8   N7   111.92  3.000
 JB2  H2   N1   C2   118.29  3.000
 JB2  H2   N1   C6   115.62  3.000
 JB2  C2   N1   C6   126.09  3.000
 JB2  N3   C2   N2   120.06  3.000
 JB2  N3   C2   N1   123.08  3.000
 JB2  N2   C2   N1   116.83  3.000
 JB2  H4   N2   H3   116.28  3.000
 JB2  H4   N2   C2   117.45  3.000
 JB2  H3   N2   C2   120.82  3.000
 JB2  C4   N3   C2   113.20  3.000
 JB2  N9   C4   N3   126.53  3.000
 JB2  N9   C4   C5   105.31  3.000
 JB2  N3   C4   C5   128.16  3.000
 JB2  C1'  N9   C4   125.16  3.000
 JB2  C4   N9   C8   106.95  3.000
 JB2  C1'  N9   C8   127.88  3.000
 JB2  H5   C1'  C2'  109.81  3.000
 JB2  H5   C1'  O4'  111.92  3.000
 JB2  C2'  C1'  O4'  105.89  3.000
 JB2  H5   C1'  N9   106.04  3.000
 JB2  O4'  C1'  N9   109.20  3.000
 JB2  C2'  C1'  N9   114.09  3.000
 JB2  C4'  O4'  C1'  110.64  3.000
 JB2  H6   C2'  C3'  109.39  3.000
 JB2  H6   C2'  O2'  111.52  3.000
 JB2  C3'  C2'  O2'  115.05  3.000
 JB2  H6   C2'  C1'  109.38  3.000
 JB2  C3'  C2'  C1'  100.75  3.000
 JB2  O2'  C2'  C1'  110.17  3.000
 JB2  H7   O2'  C2'  108.74  3.000
 JB2  H8   C3'  C4'  111.84  3.000
 JB2  H8   C3'  O3'  111.68  3.000
 JB2  C4'  C3'  O3'  108.95  3.000
 JB2  H8   C3'  C2'  112.08  3.000
 JB2  C4'  C3'  C2'  100.97  3.000
 JB2  O3'  C3'  C2'  110.83  3.000
 JB2  H9   O3'  C3'  107.93  3.000
 JB2  H10  C4'  C5'  109.30  3.000
 JB2  H10  C4'  C3'  110.96  3.000
 JB2  C5'  C4'  C3'  111.91  3.000
 JB2  H10  C4'  O4'  108.07  3.000
 JB2  C5'  C4'  O4'  110.62  3.000
 JB2  C3'  C4'  O4'  105.88  3.000
 JB2  H12  C5'  H11  107.16  3.000
 JB2  H12  C5'  O5'  111.45  3.000
 JB2  H11  C5'  O5'  111.04  3.000
 JB2  H12  C5'  C4'  110.00  3.000
 JB2  H11  C5'  C4'  108.21  3.000
 JB2  O5'  C5'  C4'  108.93  3.000
 JB2  P    O5'  C5'  117.56  3.000
 JB2  OPP  P    O2P  111.88  3.000
 JB2  OPP  P    O1P  109.91  3.000
 JB2  O2P  P    O1P  119.95  3.000
 JB2  OPP  P    O5'   93.23  3.000
 JB2  O2P  P    O5'  109.40  3.000
 JB2  O1P  P    O5'  109.17  3.000
 JB2  P2   OPP  P    125.51  3.000
 JB2  O1G  P2   O4P  110.43  3.000
 JB2  O1G  P2   O3P  109.34  3.000
 JB2  O4P  P2   O3P  121.15  3.000
 JB2  O3P  P2   OPP  106.88  3.000
 JB2  O1G  P2   OPP   96.57  3.000
 JB2  O4P  P2   OPP  109.62  3.000
 JB2  C1G  O1G  P2   122.49  3.000
 JB2  H15  C1G  C2G  110.74  3.000
 JB2  H15  C1G  O5G  105.10  3.000
 JB2  C2G  C1G  O5G  111.25  3.000
 JB2  H15  C1G  O1G  110.59  3.000
 JB2  O5G  C1G  O1G  113.21  3.000
 JB2  C2G  C1G  O1G  106.03  3.000
 JB2  C5G  O5G  C1G  115.78  3.000
 JB2  H16  C5G  C4G  107.72  3.000
 JB2  H16  C5G  C6G  108.75  3.000
 JB2  C4G  C5G  C6G  112.62  3.000
 JB2  H16  C5G  O5G  109.22  3.000
 JB2  C6G  C5G  O5G  106.13  3.000
 JB2  C4G  C5G  O5G  112.33  3.000
 JB2  H19  C6G  H18  107.99  3.000
 JB2  H19  C6G  H17  108.46  3.000
 JB2  H18  C6G  H17  107.18  3.000
 JB2  H19  C6G  C5G  111.23  3.000
 JB2  H18  C6G  C5G  110.98  3.000
 JB2  H17  C6G  C5G  110.85  3.000
 JB2  H20  C2G  C3G  108.77  3.000
 JB2  H20  C2G  O2G  110.95  3.000
 JB2  C3G  C2G  O2G  108.77  3.000
 JB2  H20  C2G  C1G  108.28  3.000
 JB2  O2G  C2G  C1G  110.54  3.000
 JB2  C3G  C2G  C1G  109.49  3.000
 JB2  H21  O2G  C2G  108.31  3.000
 JB2  H22  C3G  C4G  107.35  3.000
 JB2  H22  C3G  O3G  110.46  3.000
 JB2  C4G  C3G  O3G  110.43  3.000
 JB2  H22  C3G  C2G  106.67  3.000
 JB2  C4G  C3G  C2G  110.05  3.000
 JB2  O3G  C3G  C2G  111.73  3.000
 JB2  H23  O3G  C3G  106.01  3.000
 JB2  H24  C4G  N4A  107.56  3.000
 JB2  H24  C4G  C3G  109.02  3.000
 JB2  N4A  C4G  C3G  109.72  3.000
 JB2  H24  C4G  C5G  108.70  3.000
 JB2  N4A  C4G  C5G  112.64  3.000
 JB2  C3G  C4G  C5G  109.14  3.000
 JB2  H26  N4A  H25  106.05  3.000
 JB2  H26  N4A  C4G  109.82  3.000
 JB2  H25  N4A  C4G  110.32  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
 JB2  CONST_01  C8   N9   C4   C5     0.00   0.0  0
 JB2  CONST_02  N9   C8   N7   C5     0.00   0.0  0
 JB2  CONST_03  C4   N9   C8   N7     0.00   0.0  0
 JB2  CONST_04  N9   C4   C5   N7     0.00   0.0  0
 JB2  CONST_05  C4   C5   N7   C8     0.00   0.0  0
 JB2  CONST_06  C1'  N9   C4   C5   180.00   0.0  0
 JB2  CONST_07  C1'  N9   C8   N7   180.00   0.0  0
 JB2  CONST_08  C1'  N9   C4   N3     0.00   0.0  0
 JB2  CONST_09  N3   C2   N1   C6     0.00   0.0  0
 JB2  CONST_10  C2   N1   C6   C5     0.00   0.0  0
 JB2  CONST_11  C4   N3   C2   N1     0.00   0.0  0
 JB2  CONST_12  C2   N1   C6   O6   180.00   0.0  0
 JB2  CONST_13  N2   C2   N1   C6   180.00   0.0  0
 JB2  CONST_14  C4   N3   C2   N2   180.00   0.0  0
 JB2  CONST_15  H1   C8   N7   C5   180.00   0.0  0
 JB2  CONST_16  H2   N1   C6   C5   180.00   0.0  0
 JB2  CONST_18  H4   N2   C2   N1   180.00   0.0  0
 JB2  Var_01    O1P  P    O5'  C5'  -79.49  30.0  3
 JB2  Var_02    O4P  P2   OPP  P    -39.07  30.0  3
 JB2  Var_03    H11  C5'  O5'  P     92.64  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
 JB2  chir_01  C1'  C2'  O4'  N9   negativ
 JB2  chir_02  C2'  O2'  C3'  C1'  positiv
 JB2  chir_03  C3'  O3'  C4'  C2'  positiv
 JB2  chir_04  C4'  O4'  C3'  C5'  negativ
 JB2  chir_07  C1G  O1G  C2G  O5G  positiv
 JB2  chir_08  C5G  O5G  C6G  C4G  positiv
 JB2  chir_09  C2G  O2G  C1G  C3G  positiv
 JB2  chir_10  C3G  O3G  C2G  C4G  positiv
 JB2  chir_11  C4G  N4A  C5G  C3G  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
 JB2  plan-1  O6   0.020
 JB2  plan-1  C6   0.020
 JB2  plan-1  C5   0.020
 JB2  plan-1  N7   0.020
 JB2  plan-1  C8   0.020
 JB2  plan-1  N1   0.020
 JB2  plan-1  C2   0.020
 JB2  plan-1  N2   0.020
 JB2  plan-1  N3   0.020
 JB2  plan-1  C4   0.020
 JB2  plan-1  N9   0.020
 JB2  plan-1  C1'  0.020
 JB2  plan-1  H1   0.020
 JB2  plan-1  H2   0.020
 JB2  plan-1  H3   0.020
 JB2  plan-1  H4   0.020

