# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat May 23 20:43:47 2020
#   Inital geometry file: a 152 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,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
#
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
 GDD  GDD  '[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  62  39  .  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_GDD
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
 GDD  N2    N  NH2    0  -0.833   5.5784  -1.7931   3.7383
 GDD  C2    C  C      0   0.692   4.4884  -1.7425   2.9623
 GDD  N1    N  NH1    0  -0.728   3.7354  -2.8792   2.8756
 GDD  N3    N  N      0  -0.511   4.2046  -0.6452   2.3050
 GDD  C4    C  CR5    0   0.498   3.1060  -0.7534   1.5473
 GDD  C5    C  CR5    0  -0.039   2.2748  -1.8450   1.3999
 GDD  C6    C  C      0   0.509   2.5752  -3.0428   2.1091
 GDD  O6    O  O      0  -0.470   1.9706  -4.1014   2.1103
 GDD  N7    N  N      0  -0.518   1.2446  -1.5474   0.5456
 GDD  C8    C  CR15   0   0.106   1.4439  -0.3149   0.1779
 GDD  N9    N  NR5    0  -0.548   2.5669   0.2186   0.7604
 GDD  C1'   C  CR15   0   0.232   3.1189   1.5416   0.5777
 GDD  C2'   C  CR15   0  -0.050   3.9081   1.7139  -0.7193
 GDD  O2'   O  OH1    0  -0.651   5.2183   1.2647  -0.5484
 GDD  C3'   C  CR15   0  -0.034   3.7652   3.2227  -0.9464
 GDD  O3'   O  OH1    0  -0.669   4.6282   3.9419  -0.1050
 GDD  C4'   C  CR15   0  -0.042   2.3277   3.4456  -0.4982
 GDD  O4'   O  O      0  -0.491   2.0793   2.4694   0.5198
 GDD  C5'   C  CH2    0  -0.147   1.3595   3.2790  -1.6535
 GDD  O5'   O  O2     0  -0.618   0.0424   3.2869  -1.1611
 GDD  PA    P  P      0   1.349  -1.0760   2.4484  -2.0396
 GDD  O1A   O  O      0  -0.771  -0.6518   1.0144  -2.1343
 GDD  O2A   O  OP    -1  -0.793  -1.3963   3.2181  -3.2823
 GDD  O3A   O  O2     0  -0.736  -2.2555   2.6631  -0.9200
 GDD  PB    P  P      0   1.369  -3.6140   1.7433  -0.8064
 GDD  O2B   O  OP    -1  -0.793  -4.5158   2.4188   0.1782
 GDD  O3B   O  O      0  -0.782  -4.0858   1.3855  -2.1774
 GDD  O1B   O  O2     0  -0.621  -2.8980   0.4496  -0.0882
 GDD  C11   C  CH1    0   0.240  -3.5855  -0.4558   0.7157
 GDD  O51   O  O2     0  -0.503  -4.6198  -1.1107   0.0505
 GDD  C51   C  CH1    0  -0.003  -4.2331  -1.8904  -1.0706
 GDD  C61   C  CH2    0  -0.164  -5.4803  -2.5830  -1.5761
 GDD  O6A   O  OH1    0  -0.666  -6.4097  -1.6264  -2.0245
 GDD  C21   C  CH1    0  -0.029  -2.5347  -1.4500   1.2091
 GDD  O21   O  OH1    0  -0.674  -3.0946  -2.3518   2.1326
 GDD  C31   C  CH1    0  -0.003  -1.9949  -2.2392   0.0168
 GDD  O31   O  OH1    0  -0.712  -1.0540  -3.2006   0.4079
 GDD  C41   C  CH1    0   0.011  -3.1435  -2.9183  -0.7167
 GDD  O41   O  OH1    0  -0.674  -2.6293  -3.4942  -1.8994
 GDD  H2N1  H  HNH2   0   0.414   6.0688  -0.9339   3.9188
 GDD  H2N2  H  HNH2   0   0.416   5.7279  -2.5464   4.3871
 GDD  H1    H  HNH1   0   0.426   4.0236  -3.6878   3.4123
 GDD  H8    H  HCR5   0   0.329   0.8050   0.2471  -0.4935
 GDD  H1'   H  HCR5   0   0.257   3.7759   1.7161   1.4378
 GDD  H2'   H  HCR5   0   0.248   3.3996   1.1767  -1.5299
 GDD  HA    H  HOH1   0   0.469   5.6050   1.0994  -1.4142
 GDD  H3'   H  HCR5   0   0.252   3.9093   3.4918  -2.0016
 GDD  HB    H  HOH1   0   0.449   5.5007   3.5337  -0.1571
 GDD  H4'   H  HCR5   0   0.261   2.2008   4.4376  -0.0548
 GDD  H5'1  H  HCH2   0   0.225   1.5252   4.1026  -2.3582
 GDD  H5'2  H  HCH2   0   0.204   1.5797   2.3487  -2.1909
 GDD  H11   H  HCH1   0   0.227  -4.0668   0.0561   1.5594
 GDD  H51   H  HCH1   0   0.227  -3.8400  -1.2377  -1.8591
 GDD  H611  H  HCH2   0   0.192  -5.1937  -3.2650  -2.3857
 GDD  H612  H  HCH2   0   0.190  -5.8948  -3.2028  -0.7678
 GDD  H6A   H  HOH1   0   0.452  -7.1629  -2.0989  -2.3898
 GDD  H21   H  HCH1   0   0.220  -1.7085  -0.8831   1.6606
 GDD  HC    H  HOH1   0   0.450  -3.3240  -1.8653   2.9303
 GDD  H31   H  HCH1   0   0.234  -1.5429  -1.5094  -0.6710
 GDD  HD    H  HOH1   0   0.464  -0.1994  -2.7327   0.4765
 GDD  H41   H  HCH1   0   0.211  -3.5726  -3.6911  -0.0643
 GDD  HE    H  HOH1   0   0.452  -3.1121  -4.3014  -2.0916

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
 GDD  N2   C2    single    1.339  0.020  1.339
 GDD  N2   H2N1  single    0.890  0.020  1.040
 GDD  N2   H2N2  single    0.890  0.020  1.040
 GDD  C2   N1    single    1.366  0.020  1.366
 GDD  C2   N3    double    1.310  0.020  1.310
 GDD  N1   C6    single    1.400  0.020  1.400
 GDD  N1   H1    single    0.860  0.020  1.020
 GDD  N3   C4    single    1.339  0.020  1.339
 GDD  C4   C5    aromatic  1.380  0.020  1.380
 GDD  C4   N9    aromatic  1.362  0.020  1.362
 GDD  C5   C6    single    1.424  0.020  1.424
 GDD  C5   N7    aromatic  1.371  0.020  1.371
 GDD  C6   O6    double    1.219  0.020  1.219
 GDD  N7   C8    aromatic  1.302  0.020  1.302
 GDD  C8   N9    aromatic  1.373  0.020  1.373
 GDD  C8   H8    single    0.930  0.020  1.080
 GDD  N9   C1'   single    1.445  0.020  1.445
 GDD  C1'  C2'   single    1.528  0.020  1.528
 GDD  C1'  O4'   single    1.395  0.020  1.395
 GDD  C1'  H1'   single    0.970  0.020  1.090
 GDD  C2'  O2'   single    1.396  0.020  1.396
 GDD  C2'  C3'   single    1.532  0.020  1.532
 GDD  C2'  H2'   single    0.970  0.020  1.090
 GDD  O2'  HA    single    0.850  0.020  0.980
 GDD  C3'  O3'   single    1.404  0.020  1.404
 GDD  C3'  C4'   single    1.522  0.020  1.522
 GDD  C3'  H3'   single    0.970  0.020  1.090
 GDD  O3'  HB    single    0.850  0.020  0.980
 GDD  C4'  O4'   single    1.432  0.020  1.432
 GDD  C4'  C5'   single    1.517  0.020  1.517
 GDD  C4'  H4'   single    0.970  0.020  1.090
 GDD  C5'  O5'   single    1.406  0.020  1.406
 GDD  C5'  H5'1  single    0.970  0.020  1.090
 GDD  C5'  H5'2  single    0.970  0.020  1.090
 GDD  O5'  PA    single    1.651  0.020  1.651
 GDD  PA   O1A   deloc     1.498  0.020  1.498
 GDD  PA   O2A   deloc     1.496  0.020  1.496
 GDD  PA   O3A   single    1.640  0.020  1.640
 GDD  O3A  PB    single    1.645  0.020  1.645
 GDD  PB   O2B   deloc     1.496  0.020  1.496
 GDD  PB   O3B   deloc     1.493  0.020  1.493
 GDD  PB   O1B   single    1.644  0.020  1.644
 GDD  O1B  C11   single    1.392  0.020  1.392
 GDD  C11  O51   single    1.393  0.020  1.393
 GDD  C11  C21   single    1.528  0.020  1.528
 GDD  C11  H11   single    0.970  0.020  1.090
 GDD  O51  C51   single    1.419  0.020  1.419
 GDD  C51  C61   single    1.513  0.020  1.513
 GDD  C51  C41   single    1.539  0.020  1.539
 GDD  C51  H51   single    0.970  0.020  1.090
 GDD  C61  O6A   single    1.407  0.020  1.407
 GDD  C61  H611  single    0.970  0.020  1.090
 GDD  C61  H612  single    0.970  0.020  1.090
 GDD  O6A  H6A   single    0.850  0.020  0.980
 GDD  C21  O21   single    1.407  0.020  1.407
 GDD  C21  C31   single    1.528  0.020  1.528
 GDD  C21  H21   single    0.970  0.020  1.090
 GDD  O21  HC    single    0.850  0.020  0.980
 GDD  C31  O31   single    1.401  0.020  1.401
 GDD  C31  C41   single    1.523  0.020  1.523
 GDD  C31  H31   single    0.970  0.020  1.090
 GDD  O31  HD    single    0.850  0.020  0.980
 GDD  C41  O41   single    1.412  0.020  1.412
 GDD  C41  H41   single    0.970  0.020  1.090
 GDD  O41  HE    single    0.850  0.020  0.980

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
 GDD  H2N2  N2   H2N1  116.86  3.000
 GDD  H2N2  N2   C2    121.56  3.000
 GDD  H2N1  N2   C2    117.95  3.000
 GDD  N3    C2   N1    123.06  3.000
 GDD  N3    C2   N2    119.92  3.000
 GDD  N1    C2   N2    117.01  3.000
 GDD  H1    N1   C6    115.64  3.000
 GDD  H1    N1   C2    118.29  3.000
 GDD  C6    N1   C2    126.07  3.000
 GDD  C4    N3   C2    113.20  3.000
 GDD  N9    C4   C5    105.33  3.000
 GDD  N9    C4   N3    126.45  3.000
 GDD  C5    C4   N3    128.21  3.000
 GDD  N7    C5   C6    130.64  3.000
 GDD  N7    C5   C4    110.34  3.000
 GDD  C6    C5   C4    119.02  3.000
 GDD  O6    C6   C5    128.77  3.000
 GDD  O6    C6   N1    120.79  3.000
 GDD  C5    C6   N1    110.43  3.000
 GDD  C8    N7   C5    105.46  3.000
 GDD  H8    C8   N9    122.92  3.000
 GDD  H8    C8   N7    125.15  3.000
 GDD  N9    C8   N7    111.92  3.000
 GDD  C1'   N9   C8    127.91  3.000
 GDD  C1'   N9   C4    125.12  3.000
 GDD  C8    N9   C4    106.96  3.000
 GDD  H1'   C1'  O4'   111.93  3.000
 GDD  H1'   C1'  C2'   109.79  3.000
 GDD  O4'   C1'  C2'   105.95  3.000
 GDD  H1'   C1'  N9    105.99  3.000
 GDD  O4'   C1'  N9    109.24  3.000
 GDD  C2'   C1'  N9    114.07  3.000
 GDD  H2'   C2'  C3'   109.23  3.000
 GDD  H2'   C2'  O2'   111.59  3.000
 GDD  C3'   C2'  O2'   115.00  3.000
 GDD  H2'   C2'  C1'   109.42  3.000
 GDD  C3'   C2'  C1'   100.87  3.000
 GDD  O2'   C2'  C1'   110.16  3.000
 GDD  HA    O2'  C2'   108.80  3.000
 GDD  H3'   C3'  C4'   111.77  3.000
 GDD  H3'   C3'  O3'   111.69  3.000
 GDD  C4'   C3'  O3'   109.22  3.000
 GDD  H3'   C3'  C2'   111.80  3.000
 GDD  C4'   C3'  C2'   100.87  3.000
 GDD  O3'   C3'  C2'   111.00  3.000
 GDD  HB    O3'  C3'   107.88  3.000
 GDD  H4'   C4'  C5'   109.53  3.000
 GDD  H4'   C4'  O4'   108.05  3.000
 GDD  C5'   C4'  O4'   110.85  3.000
 GDD  H4'   C4'  C3'   111.20  3.000
 GDD  C5'   C4'  C3'   111.25  3.000
 GDD  O4'   C4'  C3'   105.86  3.000
 GDD  C4'   O4'  C1'   110.71  3.000
 GDD  H5'2  C5'  H5'1  106.97  3.000
 GDD  H5'2  C5'  O5'   111.37  3.000
 GDD  H5'1  C5'  O5'   111.24  3.000
 GDD  H5'2  C5'  C4'   109.78  3.000
 GDD  H5'1  C5'  C4'   108.10  3.000
 GDD  O5'   C5'  C4'   109.31  3.000
 GDD  PA    O5'  C5'   116.45  3.000
 GDD  O3A   PA   O2A   110.21  3.000
 GDD  O3A   PA   O1A   111.84  3.000
 GDD  O2A   PA   O1A   120.03  3.000
 GDD  O3A   PA   O5'    93.29  3.000
 GDD  O2A   PA   O5'   109.01  3.000
 GDD  O1A   PA   O5'   109.14  3.000
 GDD  PB    O3A  PA    124.60  3.000
 GDD  O1B   PB   O3B   110.50  3.000
 GDD  O1B   PB   O2B   109.29  3.000
 GDD  O3B   PB   O2B   121.46  3.000
 GDD  O1B   PB   O3A    96.34  3.000
 GDD  O3B   PB   O3A   109.36  3.000
 GDD  O2B   PB   O3A   106.90  3.000
 GDD  C11   O1B  PB    123.29  3.000
 GDD  H11   C11  C21   110.89  3.000
 GDD  H11   C11  O51   105.10  3.000
 GDD  C21   C11  O51   111.02  3.000
 GDD  H11   C11  O1B   110.92  3.000
 GDD  C21   C11  O1B   105.66  3.000
 GDD  O51   C11  O1B   113.36  3.000
 GDD  C51   O51  C11   115.66  3.000
 GDD  H51   C51  C41   108.00  3.000
 GDD  H51   C51  C61   109.13  3.000
 GDD  C41   C51  C61   110.76  3.000
 GDD  H51   C51  O51   109.80  3.000
 GDD  C41   C51  O51   112.22  3.000
 GDD  C61   C51  O51   106.90  3.000
 GDD  H612  C61  H611  106.90  3.000
 GDD  H612  C61  O6A   111.62  3.000
 GDD  H611  C61  O6A   111.11  3.000
 GDD  H612  C61  C51   108.85  3.000
 GDD  H611  C61  C51   108.41  3.000
 GDD  O6A   C61  C51   109.85  3.000
 GDD  H6A   O6A  C61   107.73  3.000
 GDD  H21   C21  C31   108.74  3.000
 GDD  H21   C21  O21   111.11  3.000
 GDD  C31   C21  O21   108.76  3.000
 GDD  H21   C21  C11   108.30  3.000
 GDD  C31   C21  C11   109.08  3.000
 GDD  O21   C21  C11   110.81  3.000
 GDD  HC    O21  C21   108.36  3.000
 GDD  H31   C31  C41   107.74  3.000
 GDD  H31   C31  O31   110.73  3.000
 GDD  C41   C31  O31   109.58  3.000
 GDD  H31   C31  C21   106.88  3.000
 GDD  C41   C31  C21   109.85  3.000
 GDD  O31   C31  C21   111.95  3.000
 GDD  HD    O31  C31   106.17  3.000
 GDD  H41   C41  O41   110.65  3.000
 GDD  H41   C41  C31   108.80  3.000
 GDD  O41   C41  C31   108.09  3.000
 GDD  H41   C41  C51   109.26  3.000
 GDD  O41   C41  C51   109.72  3.000
 GDD  C31   C41  C51   110.30  3.000
 GDD  HE    O41  C41   109.11  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
 GDD  CONST_01  C8    N7   C5   C4      0.00   0.0  0
 GDD  CONST_02  N7    C8   N9   C4      0.00   0.0  0
 GDD  CONST_03  C8    N9   C4   C5      0.00   0.0  0
 GDD  CONST_04  N9    C8   N7   C5      0.00   0.0  0
 GDD  CONST_05  N9    C4   C5   N7      0.00   0.0  0
 GDD  CONST_06  C1'   N9   C4   N3      0.00   0.0  0
 GDD  CONST_07  C1'   N9   C4   C5    180.00   0.0  0
 GDD  CONST_08  C1'   N9   C8   N7    180.00   0.0  0
 GDD  CONST_09  C5    C6   N1   C2      0.00   0.0  0
 GDD  CONST_10  C4    N3   C2   N1      0.00   0.0  0
 GDD  CONST_11  C6    N1   C2   N3      0.00   0.0  0
 GDD  CONST_12  C6    N1   C2   N2    180.00   0.0  0
 GDD  CONST_13  C4    N3   C2   N2    180.00   0.0  0
 GDD  CONST_14  O6    C6   N1   C2    180.00   0.0  0
 GDD  CONST_15  H8    C8   N9   C4    180.00   0.0  0
 GDD  CONST_16  H1    N1   C2   N3    180.00   0.0  0
 GDD  CONST_17  H2N1  N2   C2   N1    180.00   0.0  0
 GDD  CONST_18  H2N2  N2   C2   N1      0.00   0.0  0
 GDD  Var_01    O1A   PA   O5'  C5'    58.76  30.0  3
 GDD  Var_02    O2B   PB   O3A  PA   -170.36  30.0  3
 GDD  Var_03    H5'1  C5'  O5'  PA     88.66  30.0  2

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
 GDD  chir_01  C1'  N9   C2'  O4'  negativ
 GDD  chir_02  C2'  O2'  C3'  C1'  positiv
 GDD  chir_03  C3'  O3'  C4'  C2'  positiv
 GDD  chir_04  C4'  O4'  C3'  C5'  negativ
 GDD  chir_07  C11  O1B  O51  C21  negativ
 GDD  chir_08  C51  O51  C61  C41  positiv
 GDD  chir_09  C21  O21  C11  C31  positiv
 GDD  chir_10  C31  O31  C21  C41  positiv
 GDD  chir_11  C41  O41  C31  C51  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
 GDD  plan-1  N2    0.020
 GDD  plan-1  C2    0.020
 GDD  plan-1  N1    0.020
 GDD  plan-1  N3    0.020
 GDD  plan-1  C4    0.020
 GDD  plan-1  C5    0.020
 GDD  plan-1  C6    0.020
 GDD  plan-1  O6    0.020
 GDD  plan-1  N7    0.020
 GDD  plan-1  C8    0.020
 GDD  plan-1  N9    0.020
 GDD  plan-1  C1'   0.020
 GDD  plan-1  H2N1  0.020
 GDD  plan-1  H2N2  0.020
 GDD  plan-1  H1    0.020
 GDD  plan-1  H8    0.020

