# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri May 22 22:45:28 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl 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]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
 GFB  GFB  '[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  61  38  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GFB
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
 GFB  O1P   O  OP    -1  -0.785  -0.1250   0.0475   1.9924
 GFB  P     P  P      0   1.363   0.9432   0.2223   0.9528
 GFB  O3P   O  O      0  -0.778   2.1974   0.9641   1.2901
 GFB  O2P   O  O2     0  -0.745   1.2719  -1.2156   0.2325
 GFB  O5'   O  O2     0  -0.613   0.2753   0.8621  -0.4100
 GFB  P1    P  P      0   1.364   2.1063  -2.4595   0.9115
 GFB  C5'   C  CH2    0  -0.152  -0.4958   2.0306  -0.2727
 GFB  C4'   C  CH1    0  -0.043  -1.5357   2.0727  -1.3778
 GFB  O4'   O  O2     0  -0.488  -2.2802   0.8531  -1.4285
 GFB  C3'   C  CH1    0  -0.032  -2.5591   3.1730  -1.1359
 GFB  C1'   C  CH1    0   0.222  -3.5896   1.0499  -0.9839
 GFB  O3'   O  OH1    0  -0.669  -3.0971   3.5803  -2.3668
 GFB  C2'   C  CH1    0  -0.052  -3.6016   2.4190  -0.3034
 GFB  O2'   O  OH1    0  -0.653  -4.8892   2.9574  -0.3406
 GFB  N9    N  NR5    0  -0.540  -3.9658  -0.0394  -0.1167
 GFB  C8    C  CR15   0   0.059  -3.2279  -0.5825   0.9102
 GFB  C4    C  CR5    0   0.506  -5.1383  -0.7273  -0.1602
 GFB  N7    N  N      0  -0.449  -3.8494  -1.5518   1.5096
 GFB  C5    C  CR5    0  -0.098  -5.0514  -1.6584   0.8580
 GFB  C6    C  C      0   0.501  -6.1427  -2.5491   1.0651
 GFB  O6    O  O      0  -0.476  -6.2614  -3.4341   1.8965
 GFB  N1    N  NH1    0  -0.727  -7.1667  -2.2972   0.1424
 GFB  C2    C  C      0   0.689  -7.1513  -1.3459  -0.8372
 GFB  N2    N  NH2    0  -0.832  -8.2474  -1.2410  -1.6034
 GFB  N3    N  N      0  -0.512  -6.1434  -0.5311  -1.0243
 GFB  C1    C  CH1    0   0.258   4.3932  -1.4546   0.0024
 GFB  C2A   C  CH1    0  -0.019   4.7012  -0.9704  -1.4146
 GFB  O1    O  O2     0  -0.637   3.4340  -2.4592  -0.0752
 GFB  O5    O  O2     0  -0.491   5.5324  -2.0217   0.5855
 GFB  C3    C  CH1    0   0.018   5.8546   0.0242  -1.3606
 GFB  O2    O  OH1    0  -0.673   3.6003  -0.3036  -1.9829
 GFB  C4A   C  CH1    0   0.002   7.0525  -0.5939  -0.6561
 GFB  O3    O  OH1    0  -0.672   6.2459   0.4661  -2.6355
 GFB  C5A   C  CH1    0   0.014   6.6014  -1.1022   0.7178
 GFB  O4    O  OH1    0  -0.671   7.5692  -1.6187  -1.4692
 GFB  C6A   C  CH3    0  -0.705   7.7088  -1.7882   1.4917
 GFB  O1X   O  O      0  -0.793   2.4973  -2.1034   2.3070
 GFB  O2X   O  OP    -1  -0.771   1.3873  -3.7213   0.5727
 GFB  H5'   H  HCH2   0   0.206  -0.9828   2.0711   0.7083
 GFB  H5'A  H  HCH2   0   0.227   0.1266   2.9296  -0.3563
 GFB  H4'   H  HCH1   0   0.260  -1.0367   2.2025  -2.3426
 GFB  H3'   H  HCH1   0   0.251  -2.1276   4.0176  -0.5814
 GFB  H1'   H  HCH1   0   0.258  -4.3050   1.0401  -1.8140
 GFB  HO3'  H  HOH1   0   0.449  -3.9513   3.9935  -2.1942
 GFB  H2'   H  HCH1   0   0.249  -3.2375   2.3184   0.7269
 GFB  HO2'  H  HOH1   0   0.469  -4.9531   3.6577   0.3165
 GFB  H8    H  HCR5   0   0.315  -2.2304  -0.2383   1.1549
 GFB  HN1   H  HNH1   0   0.424  -7.9875  -2.8830   0.2293
 GFB  H1    H  HCH1   0   0.208   4.0426  -0.5996   0.6037
 GFB  H2A   H  HCH1   0   0.211   4.9986  -1.8404  -2.0195
 GFB  H3    H  HCH1   0   0.212   5.5290   0.8742  -0.7389
 GFB  HO2   H  HOH1   0   0.450   2.8209  -0.8643  -1.9097
 GFB  H4A   H  HCH1   0   0.230   7.8011   0.1940  -0.4878
 GFB  HO3   H  HOH1   0   0.450   5.4876   0.8906  -3.0492
 GFB  H5A   H  HCH1   0   0.212   6.2659  -0.2217   1.2889
 GFB  HO4   H  HOH1   0   0.456   8.4160  -1.8992  -1.1100
 GFB  H6A   H  HCH3   0   0.251   7.3741  -2.0501   2.4949
 GFB  H6AA  H  HCH3   0   0.230   8.0368  -2.7051   1.0001
 GFB  H6AB  H  HCH3   0   0.237   8.5691  -1.1261   1.5911
 GFB  HN2   H  HNH2   0   0.411  -8.1860  -0.6605  -2.4226
 GFB  HN2A  H  HNH2   0   0.414  -8.9355  -1.9739  -1.6285

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
 GFB  P     O1P   deloc     1.501  0.020  1.501
 GFB  O3P   P     deloc     1.496  0.020  1.496
 GFB  P     O5'   single    1.647  0.020  1.647
 GFB  P     O2P   single    1.641  0.020  1.641
 GFB  O2P   P1    single    1.645  0.020  1.645
 GFB  O5'   C5'   single    1.407  0.020  1.407
 GFB  O1    P1    single    1.654  0.020  1.654
 GFB  O1X   P1    deloc     1.492  0.020  1.492
 GFB  P1    O2X   deloc     1.491  0.020  1.491
 GFB  C4'   C5'   single    1.518  0.020  1.518
 GFB  C5'   H5'A  single    0.970  0.020  1.090
 GFB  C5'   H5'   single    0.970  0.020  1.090
 GFB  H4'   C4'   single    0.970  0.020  1.090
 GFB  C3'   C4'   single    1.522  0.020  1.522
 GFB  C4'   O4'   single    1.430  0.020  1.430
 GFB  O4'   C1'   single    1.397  0.020  1.397
 GFB  O3'   C3'   single    1.404  0.020  1.404
 GFB  C3'   C2'   single    1.532  0.020  1.532
 GFB  C3'   H3'   single    0.970  0.020  1.090
 GFB  C2'   C1'   single    1.529  0.020  1.529
 GFB  H1'   C1'   single    0.970  0.020  1.090
 GFB  C1'   N9    single    1.442  0.020  1.442
 GFB  HO3'  O3'   single    0.850  0.020  0.980
 GFB  O2'   C2'   single    1.396  0.020  1.396
 GFB  C2'   H2'   single    0.970  0.020  1.090
 GFB  O2'   HO2'  single    0.850  0.020  0.980
 GFB  N9    C4    aromatic  1.360  0.020  1.360
 GFB  N9    C8    aromatic  1.376  0.020  1.376
 GFB  H8    C8    single    0.930  0.020  1.080
 GFB  C8    N7    aromatic  1.298  0.020  1.298
 GFB  N3    C4    single    1.340  0.020  1.340
 GFB  C4    C5    aromatic  1.382  0.020  1.382
 GFB  C5    N7    aromatic  1.371  0.020  1.371
 GFB  C5    C6    single    1.424  0.020  1.424
 GFB  N1    C6    single    1.401  0.020  1.401
 GFB  C6    O6    double    1.220  0.020  1.220
 GFB  C2    N1    single    1.366  0.020  1.366
 GFB  N1    HN1   single    0.860  0.020  1.020
 GFB  N3    C2    double    1.310  0.020  1.310
 GFB  N2    C2    single    1.341  0.020  1.341
 GFB  HN2   N2    single    0.890  0.020  1.040
 GFB  N2    HN2A  single    0.890  0.020  1.040
 GFB  C2A   C1    single    1.529  0.020  1.529
 GFB  C1    O5    single    1.400  0.020  1.400
 GFB  C1    H1    single    0.970  0.020  1.090
 GFB  C1    O1    single    1.391  0.020  1.391
 GFB  C3    C2A   single    1.524  0.020  1.524
 GFB  O2    C2A   single    1.407  0.020  1.407
 GFB  H2A   C2A   single    0.970  0.020  1.090
 GFB  C5A   O5    single    1.416  0.020  1.416
 GFB  O3    C3    single    1.405  0.020  1.405
 GFB  C3    H3    single    0.970  0.020  1.090
 GFB  C3    C4A   single    1.521  0.020  1.521
 GFB  HO2   O2    single    0.850  0.020  0.980
 GFB  H4A   C4A   single    0.970  0.020  1.090
 GFB  O4    C4A   single    1.407  0.020  1.407
 GFB  C4A   C5A   single    1.533  0.020  1.533
 GFB  HO3   O3    single    0.850  0.020  0.980
 GFB  C5A   H5A   single    0.970  0.020  1.090
 GFB  C5A   C6A   single    1.515  0.020  1.515
 GFB  O4    HO4   single    0.850  0.020  0.980
 GFB  H6A   C6A   single    0.970  0.020  1.090
 GFB  H6AA  C6A   single    0.970  0.020  1.090
 GFB  C6A   H6AB  single    0.970  0.020  1.090

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
 GFB  O5'   P    O2P    93.35  3.000
 GFB  O2P   P    O3P   111.44  3.000
 GFB  O5'   P    O3P   109.51  3.000
 GFB  O2P   P    O1P   110.15  3.000
 GFB  O5'   P    O1P   109.25  3.000
 GFB  O3P   P    O1P   119.89  3.000
 GFB  P1    O2P  P     125.66  3.000
 GFB  C5'   O5'  P     117.66  3.000
 GFB  O2X   P1   O1X   122.73  3.000
 GFB  O2X   P1   O1    104.58  3.000
 GFB  O1X   P1   O1    110.33  3.000
 GFB  O2X   P1   O2P   107.55  3.000
 GFB  O1X   P1   O2P   109.79  3.000
 GFB  O1    P1   O2P    99.26  3.000
 GFB  H5'A  C5'  H5'   106.86  3.000
 GFB  H5'   C5'  C4'   110.25  3.000
 GFB  H5'A  C5'  C4'   108.09  3.000
 GFB  H5'   C5'  O5'   111.20  3.000
 GFB  H5'A  C5'  O5'   111.26  3.000
 GFB  C4'   C5'  O5'   109.12  3.000
 GFB  H4'   C4'  C3'   111.17  3.000
 GFB  C3'   C4'  O4'   105.80  3.000
 GFB  H4'   C4'  O4'   107.90  3.000
 GFB  O4'   C4'  C5'   111.03  3.000
 GFB  C3'   C4'  C5'   111.41  3.000
 GFB  H4'   C4'  C5'   109.44  3.000
 GFB  C1'   O4'  C4'   110.89  3.000
 GFB  H3'   C3'  C2'   111.80  3.000
 GFB  H3'   C3'  O3'   111.72  3.000
 GFB  C2'   C3'  O3'   111.00  3.000
 GFB  H3'   C3'  C4'   111.83  3.000
 GFB  C2'   C3'  C4'   100.84  3.000
 GFB  O3'   C3'  C4'   109.15  3.000
 GFB  H1'   C1'  N9    106.17  3.000
 GFB  N9    C1'  C2'   113.99  3.000
 GFB  H1'   C1'  C2'   109.88  3.000
 GFB  N9    C1'  O4'   109.24  3.000
 GFB  H1'   C1'  O4'   111.70  3.000
 GFB  C2'   C1'  O4'   105.97  3.000
 GFB  HO3'  O3'  C3'   107.87  3.000
 GFB  H2'   C2'  O2'   111.49  3.000
 GFB  H2'   C2'  C1'   109.46  3.000
 GFB  O2'   C2'  C1'   109.92  3.000
 GFB  H2'   C2'  C3'   109.23  3.000
 GFB  O2'   C2'  C3'   115.03  3.000
 GFB  C1'   C2'  C3'   101.16  3.000
 GFB  HO2'  O2'  C2'   108.89  3.000
 GFB  C4    N9   C8    106.65  3.000
 GFB  C8    N9   C1'   127.36  3.000
 GFB  C4    N9   C1'   125.99  3.000
 GFB  H8    C8   N7    125.01  3.000
 GFB  N7    C8   N9    112.49  3.000
 GFB  H8    C8   N9    122.48  3.000
 GFB  N3    C4   C5    128.37  3.000
 GFB  C5    C4   N9    105.24  3.000
 GFB  N3    C4   N9    126.38  3.000
 GFB  C5    N7   C8    104.97  3.000
 GFB  C6    C5   N7    130.64  3.000
 GFB  C6    C5   C4    118.71  3.000
 GFB  N7    C5   C4    110.65  3.000
 GFB  N1    C6   O6    120.54  3.000
 GFB  O6    C6   C5    128.86  3.000
 GFB  N1    C6   C5    110.60  3.000
 GFB  HN1   N1   C2    118.29  3.000
 GFB  HN1   N1   C6    115.59  3.000
 GFB  C2    N1   C6    126.12  3.000
 GFB  N3    C2   N2    119.91  3.000
 GFB  N2    C2   N1    117.07  3.000
 GFB  N3    C2   N1    123.00  3.000
 GFB  HN2A  N2   HN2   116.23  3.000
 GFB  HN2A  N2   C2    121.09  3.000
 GFB  HN2   N2   C2    117.42  3.000
 GFB  C2    N3   C4    113.21  3.000
 GFB  H1    C1   O5    110.23  3.000
 GFB  H1    C1   O1    111.79  3.000
 GFB  O5    C1   O1    106.97  3.000
 GFB  O1    C1   C2A   108.42  3.000
 GFB  H1    C1   C2A   108.90  3.000
 GFB  O5    C1   C2A   110.52  3.000
 GFB  H2A   C2A  O2    111.35  3.000
 GFB  H2A   C2A  C3    109.32  3.000
 GFB  O2    C2A  C3    107.29  3.000
 GFB  H2A   C2A  C1    108.27  3.000
 GFB  O2    C2A  C1    111.52  3.000
 GFB  C3    C2A  C1    109.05  3.000
 GFB  C1    O1   P1    121.35  3.000
 GFB  C5A   O5   C1    112.97  3.000
 GFB  H3    C3   O3    110.58  3.000
 GFB  H3    C3   C4A   106.55  3.000
 GFB  O3    C3   C4A   109.20  3.000
 GFB  C4A   C3   C2A   110.32  3.000
 GFB  H3    C3   C2A   107.44  3.000
 GFB  O3    C3   C2A   112.58  3.000
 GFB  HO2   O2   C2A   109.07  3.000
 GFB  H4A   C4A  O4    111.13  3.000
 GFB  O4    C4A  C5A   112.62  3.000
 GFB  H4A   C4A  C5A   107.50  3.000
 GFB  C5A   C4A  C3    108.55  3.000
 GFB  O4    C4A  C3    108.52  3.000
 GFB  H4A   C4A  C3    108.41  3.000
 GFB  HO3   O3   C3    108.02  3.000
 GFB  H5A   C5A  C6A   108.64  3.000
 GFB  C6A   C5A  C4A   113.13  3.000
 GFB  H5A   C5A  C4A   106.81  3.000
 GFB  C6A   C5A  O5    107.79  3.000
 GFB  H5A   C5A  O5    109.72  3.000
 GFB  C4A   C5A  O5    110.72  3.000
 GFB  HO4   O4   C4A   108.66  3.000
 GFB  H6AB  C6A  H6AA  108.32  3.000
 GFB  H6AB  C6A  H6A   107.72  3.000
 GFB  H6AA  C6A  H6A   107.77  3.000
 GFB  H6AB  C6A  C5A   110.39  3.000
 GFB  H6AA  C6A  C5A   111.72  3.000
 GFB  H6A   C6A  C5A   110.77  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
 GFB  CONST_01  N7   C5   C4   N9      0.00   0.0  0
 GFB  CONST_02  C5   N7   C8   N9      0.00   0.0  0
 GFB  CONST_03  C5   C4   N9   C8      0.00   0.0  0
 GFB  CONST_04  C4   C5   N7   C8      0.00   0.0  0
 GFB  CONST_05  N7   C8   N9   C4      0.00   0.0  0
 GFB  CONST_06  N3   C4   N9   C1'     0.00   0.0  0
 GFB  CONST_07  C5   C4   N9   C1'   180.00   0.0  0
 GFB  CONST_08  N7   C8   N9   C1'   180.00   0.0  0
 GFB  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 GFB  CONST_10  C2   N1   C6   C5      0.00   0.0  0
 GFB  CONST_11  N3   C2   N1   C6      0.00   0.0  0
 GFB  CONST_12  N2   C2   N3   C4    180.00   0.0  0
 GFB  CONST_13  N2   C2   N1   C6    180.00   0.0  0
 GFB  CONST_14  C2   N1   C6   O6    180.00   0.0  0
 GFB  CONST_15  H8   C8   N9   C1'     0.00   0.0  0
 GFB  CONST_16  HN1  N1   C6   C5    180.00   0.0  0
 GFB  CONST_17  HN2  N2   C2   N1    180.00   0.0  0
 GFB  Var_01    C4'  C5'  O5'  P    -152.00  30.0  3
 GFB  Var_02    O1X  P1   O1   C1    -42.98  30.0  3
 GFB  Var_03    O1   P1   O2P  P    -114.18  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
 GFB  chir_03  C4'  C5'  C3'  O4'  positiv
 GFB  chir_04  C3'  O3'  C2'  C4'  negativ
 GFB  chir_05  C1'  O4'  N9   C2'  negativ
 GFB  chir_06  C2'  O2'  C1'  C3'  negativ
 GFB  chir_07  C1   C2A  O5   O1   positiv
 GFB  chir_08  C2A  O2   C1   C3   positiv
 GFB  chir_09  C3   O3   C2A  C4A  negativ
 GFB  chir_10  C4A  O4   C5A  C3   positiv
 GFB  chir_11  C5A  O5   C4A  C6A  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
 GFB  plan-1  C1'   0.020
 GFB  plan-1  N9    0.020
 GFB  plan-1  C8    0.020
 GFB  plan-1  C4    0.020
 GFB  plan-1  N7    0.020
 GFB  plan-1  C5    0.020
 GFB  plan-1  C6    0.020
 GFB  plan-1  O6    0.020
 GFB  plan-1  N1    0.020
 GFB  plan-1  C2    0.020
 GFB  plan-1  N2    0.020
 GFB  plan-1  N3    0.020
 GFB  plan-1  H8    0.020
 GFB  plan-1  HN1   0.020
 GFB  plan-1  HN2   0.020
 GFB  plan-1  HN2A  0.020

