# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon May 25 19:26:09 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: (2R,3S,5S,6R)-5-amino-3-hydroxy-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[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
 GPD  GPD  '(2R,3S,5S,6R)-5-amino-3-hydroxy-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  61  37  .  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_GPD
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
 GPD  N4A   N  NH2    0  -0.838  -4.3485   3.0995  -3.0490
 GPD  C4G   C  CH1    0  -0.021  -4.8567   2.6636  -1.7562
 GPD  C5G   C  CH1    0   0.063  -3.7182   2.6436  -0.7372
 GPD  C6G   C  CH3    0  -0.698  -3.1723   4.0225  -0.4248
 GPD  O5G   O  O2     0  -0.538  -4.1732   2.1007   0.4994
 GPD  C3G   C  CH2    0  -0.490  -5.4294   1.2563  -1.8895
 GPD  C2G   C  CH1    0   0.013  -5.8375   0.6836  -0.5435
 GPD  O2G   O  OH1    0  -0.679  -6.9563   1.4091  -0.0787
 GPD  C1G   C  CH1    0   0.207  -4.6779   0.8022   0.4502
 GPD  O1G   O  O2     0  -0.634  -3.7141  -0.1349   0.0696
 GPD  P2    P  P      0   1.335  -2.3535  -0.3350   0.9998
 GPD  O3P   O  O      0  -0.678  -2.6883  -0.0207   2.4221
 GPD  O4P   O  OP    -1  -0.855  -1.1950   0.2845   0.2948
 GPD  OPP   O  O2     0  -0.659  -2.3416  -1.9746   0.7829
 GPD  P     P  P      0   1.337  -1.1542  -2.9946   1.2350
 GPD  O1P   O  OP    -1  -0.927  -1.7966  -4.3193   1.5020
 GPD  O2P   O  O      0  -0.898  -0.2504  -2.3723   2.2564
 GPD  O5'   O  O2     0  -0.626  -0.3781  -3.0585  -0.2193
 GPD  C5'   C  CH2    0  -0.143   0.9328  -3.5615  -0.2564
 GPD  C4'   C  CH1    0  -0.014   1.6764  -2.9174  -1.4125
 GPD  O4'   O  O2     0  -0.528   1.6467  -1.4914  -1.3148
 GPD  C3'   C  CH1    0  -0.055   3.1483  -3.2983  -1.4160
 GPD  O3'   O  OH1    0  -0.699   3.6473  -3.1922  -2.7250
 GPD  C2'   C  CH1    0  -0.029   3.7288  -2.2019  -0.5195
 GPD  O2'   O  OH1    0  -0.642   5.0886  -1.9474  -0.7123
 GPD  C1'   C  CH1    0   0.236   2.8996  -0.9914  -0.9562
 GPD  N9    N  NR5    0  -0.576   2.7497   0.0096   0.0728
 GPD  C8    C  CR15   0   0.080   1.9037  -0.0135   1.1592
 GPD  N7    N  N      0  -0.357   2.0805   1.0056   1.9433
 GPD  C4    C  CR56   0   0.451   3.5065   1.1342   0.1897
 GPD  C5    C  CR56   0  -0.163   3.0802   1.7381   1.3570
 GPD  C6    C  CR6    0   0.476   3.6896   2.9618   1.7562
 GPD  O6    O  O      0  -0.295   3.4683   3.6491   2.7383
 GPD  N3    N  N      0  -0.579   4.4559   1.5477  -0.6649
 GPD  C2    C  CR6    0   0.701   5.0128   2.6741  -0.3078
 GPD  N1    N  NR16   0  -0.713   4.6678   3.3490   0.8265
 GPD  N2    N  NH2    0  -0.756   5.9487   3.2416  -1.0944
 GPD  HN4A  H  HNH2   0   0.344  -5.0748   2.9895  -3.7464
 GPD  HN4B  H  HNH2   0   0.349  -4.1515   4.0919  -3.0252
 GPD  H4G   H  HCH1   0   0.153  -5.6444   3.3271  -1.3672
 GPD  H5G   H  HCH1   0   0.254  -2.9079   2.0252  -1.1435
 GPD  H6G   H  HCH3   0   0.246  -3.9566   4.6852  -0.0527
 GPD  H6GA  H  HCH3   0   0.275  -2.3849   3.9654   0.3274
 GPD  H6GB  H  HCH3   0   0.184  -2.7363   4.4796  -1.3127
 GPD  H3G   H  HCH2   0   0.231  -6.2916   1.2545  -2.5633
 GPD  H3GA  H  HCH2   0   0.250  -4.6754   0.6072  -2.3428
 GPD  H2G   H  HCH1   0   0.268  -6.0851  -0.3799  -0.6561
 GPD  HO2G  H  HOH1   0   0.447  -7.2771   0.9930   0.7272
 GPD  H1G   H  HCH1   0   0.279  -5.0301   0.5953   1.4686
 GPD  H5'   H  HCH2   0   0.242   1.4606  -3.3709   0.6849
 GPD  H5'A  H  HCH2   0   0.231   0.9375  -4.6477  -0.4131
 GPD  H4'   H  HCH1   0   0.284   1.1951  -3.2015  -2.3537
 GPD  H3'   H  HCH1   0   0.300   3.3148  -4.3010  -0.9994
 GPD  HO3'  H  HOH1   0   0.438   4.6010  -3.0605  -2.6656
 GPD  H2'   H  HCH1   0   0.255   3.5065  -2.4368   0.5286
 GPD  HO2'  H  HOH1   0   0.412   5.5995  -2.5422  -0.1551
 GPD  H1'   H  HCH1   0   0.237   3.3899  -0.4910  -1.7996
 GPD  H8    H  HCR5   0   0.256   1.1566  -0.7828   1.2983
 GPD  HN1   H  HNR6   0   0.407   5.1357   4.2219   1.0313
 GPD  HN2   H  HNH2   0   0.437   6.3337   2.6627  -1.8215
 GPD  HN2A  H  HNH2   0   0.414   6.5753   3.9315  -0.7157

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
 GPD  C4G  N4A   single    1.456  0.020  1.456
 GPD  N4A  HN4A  single    0.890  0.020  1.040
 GPD  N4A  HN4B  single    0.890  0.020  1.040
 GPD  C3G  C4G   single    1.525  0.020  1.525
 GPD  C4G  C5G   single    1.528  0.020  1.528
 GPD  C4G  H4G   single    0.970  0.020  1.090
 GPD  O5G  C5G   single    1.425  0.020  1.425
 GPD  C5G  C6G   single    1.516  0.020  1.516
 GPD  C5G  H5G   single    0.970  0.020  1.090
 GPD  C6G  H6G   single    0.970  0.020  1.090
 GPD  C6G  H6GA  single    0.970  0.020  1.090
 GPD  C6G  H6GB  single    0.970  0.020  1.090
 GPD  C1G  O5G   single    1.394  0.020  1.394
 GPD  C2G  C3G   single    1.519  0.020  1.519
 GPD  C3G  H3G   single    0.970  0.020  1.090
 GPD  C3G  H3GA  single    0.970  0.020  1.090
 GPD  O2G  C2G   single    1.412  0.020  1.412
 GPD  C1G  C2G   single    1.532  0.020  1.532
 GPD  C2G  H2G   single    0.970  0.020  1.090
 GPD  O2G  HO2G  single    0.850  0.020  0.980
 GPD  C1G  O1G   single    1.397  0.020  1.397
 GPD  C1G  H1G   single    0.970  0.020  1.090
 GPD  P2   O1G   single    1.660  0.020  1.660
 GPD  OPP  P2    single    1.654  0.020  1.654
 GPD  O3P  P2    deloc     1.495  0.020  1.495
 GPD  P2   O4P   deloc     1.491  0.020  1.491
 GPD  P    OPP   single    1.629  0.020  1.629
 GPD  O5'  P     single    1.650  0.020  1.650
 GPD  O2P  P     deloc     1.499  0.020  1.499
 GPD  P    O1P   deloc     1.496  0.020  1.496
 GPD  O5'  C5'   single    1.405  0.020  1.405
 GPD  C4'  C5'   single    1.518  0.020  1.518
 GPD  C5'  H5'   single    0.970  0.020  1.090
 GPD  C5'  H5'A  single    0.970  0.020  1.090
 GPD  O4'  C4'   single    1.430  0.020  1.430
 GPD  C3'  C4'   single    1.520  0.020  1.520
 GPD  C4'  H4'   single    0.970  0.020  1.090
 GPD  C1'  O4'   single    1.396  0.020  1.396
 GPD  C2'  C3'   single    1.531  0.020  1.531
 GPD  O3'  C3'   single    1.405  0.020  1.405
 GPD  C3'  H3'   single    0.970  0.020  1.090
 GPD  O3'  HO3'  single    0.850  0.020  0.980
 GPD  O2'  C2'   single    1.397  0.020  1.397
 GPD  C1'  C2'   single    1.531  0.020  1.531
 GPD  C2'  H2'   single    0.970  0.020  1.090
 GPD  O2'  HO2'  single    0.850  0.020  0.980
 GPD  N9   C1'   single    1.443  0.020  1.443
 GPD  C1'  H1'   single    0.970  0.020  1.090
 GPD  C4   N9    aromatic  1.361  0.020  1.361
 GPD  N9   C8    aromatic  1.377  0.020  1.377
 GPD  N7   C8    aromatic  1.298  0.020  1.298
 GPD  C8   H8    single    0.930  0.020  1.080
 GPD  C5   N7    aromatic  1.371  0.020  1.371
 GPD  N3   C4    single    1.343  0.020  1.343
 GPD  C5   C4    aromatic  1.382  0.020  1.382
 GPD  C6   C5    single    1.424  0.020  1.424
 GPD  N1   C6    single    1.404  0.020  1.404
 GPD  O6   C6    double    1.219  0.020  1.219
 GPD  C2   N3    double    1.306  0.020  1.306
 GPD  N2   C2    single    1.348  0.020  1.348
 GPD  N1   C2    single    1.364  0.020  1.364
 GPD  N1   HN1   single    0.860  0.020  1.020
 GPD  N2   HN2   single    0.890  0.020  1.040
 GPD  N2   HN2A  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
 GPD  HN4B  N4A  HN4A  105.20  3.000
 GPD  HN4B  N4A  C4G   109.91  3.000
 GPD  HN4A  N4A  C4G   109.18  3.000
 GPD  H4G   C4G  C3G   108.56  3.000
 GPD  H4G   C4G  C5G   107.78  3.000
 GPD  C3G   C4G  C5G   109.02  3.000
 GPD  H4G   C4G  N4A   112.52  3.000
 GPD  C5G   C4G  N4A   109.63  3.000
 GPD  C3G   C4G  N4A   109.25  3.000
 GPD  H5G   C5G  O5G   110.02  3.000
 GPD  H5G   C5G  C6G   108.85  3.000
 GPD  O5G   C5G  C6G   106.43  3.000
 GPD  H5G   C5G  C4G   108.10  3.000
 GPD  C6G   C5G  C4G   113.20  3.000
 GPD  O5G   C5G  C4G   110.23  3.000
 GPD  H6GB  C6G  H6GA  107.16  3.000
 GPD  H6GB  C6G  H6G   108.08  3.000
 GPD  H6GA  C6G  H6G   108.38  3.000
 GPD  H6GB  C6G  C5G   110.97  3.000
 GPD  H6GA  C6G  C5G   110.77  3.000
 GPD  H6G   C6G  C5G   111.32  3.000
 GPD  C1G   O5G  C5G   116.09  3.000
 GPD  H3GA  C3G  H3G   106.69  3.000
 GPD  H3GA  C3G  C2G   109.20  3.000
 GPD  H3G   C3G  C2G   109.48  3.000
 GPD  H3GA  C3G  C4G   108.97  3.000
 GPD  H3G   C3G  C4G   110.56  3.000
 GPD  C2G   C3G  C4G   111.80  3.000
 GPD  H2G   C2G  C1G   108.19  3.000
 GPD  H2G   C2G  O2G   110.66  3.000
 GPD  C1G   C2G  O2G   110.27  3.000
 GPD  H2G   C2G  C3G   109.58  3.000
 GPD  C1G   C2G  C3G   110.02  3.000
 GPD  O2G   C2G  C3G   108.12  3.000
 GPD  HO2G  O2G  C2G   108.53  3.000
 GPD  H1G   C1G  O1G   110.35  3.000
 GPD  H1G   C1G  C2G   110.15  3.000
 GPD  O1G   C1G  C2G   107.07  3.000
 GPD  H1G   C1G  O5G   105.02  3.000
 GPD  O1G   C1G  O5G   112.62  3.000
 GPD  C2G   C1G  O5G   111.66  3.000
 GPD  P2    O1G  C1G   119.57  3.000
 GPD  OPP   P2   O4P   110.14  3.000
 GPD  O4P   P2   O3P   122.46  3.000
 GPD  OPP   P2   O3P   109.56  3.000
 GPD  O4P   P2   O1G   108.77  3.000
 GPD  O3P   P2   O1G   108.92  3.000
 GPD  OPP   P2   O1G    92.97  3.000
 GPD  P     OPP  P2    126.12  3.000
 GPD  O5'   P    O2P   109.46  3.000
 GPD  O2P   P    O1P   120.32  3.000
 GPD  O5'   P    O1P   108.96  3.000
 GPD  O1P   P    OPP   106.91  3.000
 GPD  O2P   P    OPP   111.63  3.000
 GPD  O5'   P    OPP    97.03  3.000
 GPD  C5'   O5'  P     118.44  3.000
 GPD  H5'A  C5'  H5'   107.03  3.000
 GPD  H5'A  C5'  C4'   108.00  3.000
 GPD  H5'   C5'  C4'   110.15  3.000
 GPD  H5'A  C5'  O5'   111.24  3.000
 GPD  H5'   C5'  O5'   111.38  3.000
 GPD  C4'   C5'  O5'   108.98  3.000
 GPD  H4'   C4'  C3'   111.02  3.000
 GPD  H4'   C4'  O4'   107.97  3.000
 GPD  C3'   C4'  O4'   105.67  3.000
 GPD  H4'   C4'  C5'   109.23  3.000
 GPD  C3'   C4'  C5'   111.69  3.000
 GPD  O4'   C4'  C5'   111.16  3.000
 GPD  C1'   O4'  C4'   110.87  3.000
 GPD  H3'   C3'  C2'   111.98  3.000
 GPD  H3'   C3'  O3'   111.62  3.000
 GPD  C2'   C3'  O3'   110.91  3.000
 GPD  H3'   C3'  C4'   112.00  3.000
 GPD  O3'   C3'  C4'   109.09  3.000
 GPD  C2'   C3'  C4'   100.74  3.000
 GPD  HO3'  O3'  C3'   107.71  3.000
 GPD  H2'   C2'  C1'   109.40  3.000
 GPD  H2'   C2'  O2'   111.61  3.000
 GPD  C1'   C2'  O2'   110.11  3.000
 GPD  H2'   C2'  C3'   109.23  3.000
 GPD  C1'   C2'  C3'   101.18  3.000
 GPD  O2'   C2'  C3'   114.77  3.000
 GPD  HO2'  O2'  C2'   108.93  3.000
 GPD  H1'   C1'  N9    106.16  3.000
 GPD  H1'   C1'  C2'   109.76  3.000
 GPD  N9    C1'  C2'   113.66  3.000
 GPD  H1'   C1'  O4'   111.55  3.000
 GPD  N9    C1'  O4'   109.77  3.000
 GPD  C2'   C1'  O4'   106.03  3.000
 GPD  C4    N9   C8    106.72  3.000
 GPD  C8    N9   C1'   127.93  3.000
 GPD  C4    N9   C1'   125.22  3.000
 GPD  H8    C8   N7    125.10  3.000
 GPD  H8    C8   N9    122.53  3.000
 GPD  N7    C8   N9    112.32  3.000
 GPD  C5    N7   C8    105.10  3.000
 GPD  N3    C4   C5    128.41  3.000
 GPD  C5    C4   N9    105.20  3.000
 GPD  N3    C4   N9    126.38  3.000
 GPD  C6    C5   C4    118.71  3.000
 GPD  C6    C5   N7    130.63  3.000
 GPD  C4    C5   N7    110.66  3.000
 GPD  N1    C6   O6    120.31  3.000
 GPD  O6    C6   C5    129.24  3.000
 GPD  N1    C6   C5    110.45  3.000
 GPD  C2    N3   C4    113.14  3.000
 GPD  N2    C2   N1    116.91  3.000
 GPD  N1    C2   N3    123.10  3.000
 GPD  N2    C2   N3    119.97  3.000
 GPD  HN1   N1   C2    118.58  3.000
 GPD  HN1   N1   C6    115.23  3.000
 GPD  C2    N1   C6    126.18  3.000
 GPD  HN2A  N2   HN2   115.36  3.000
 GPD  HN2A  N2   C2    120.10  3.000
 GPD  HN2   N2   C2    116.44  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
 GPD  CONST_01  N7   C5   C4   N9      0.00   0.0  0
 GPD  CONST_02  C5   N7   C8   N9      0.00   0.0  0
 GPD  CONST_03  C5   C4   N9   C8      0.00   0.0  0
 GPD  CONST_04  C4   C5   N7   C8      0.00   0.0  0
 GPD  CONST_05  C4   N9   C8   N7      0.00   0.0  0
 GPD  CONST_06  N3   C4   N9   C1'     0.00   0.0  0
 GPD  CONST_07  C5   C4   N9   C1'   180.00   0.0  0
 GPD  CONST_08  N7   C8   N9   C1'   180.00   0.0  0
 GPD  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 GPD  CONST_10  C2   N1   C6   C5      0.00   0.0  0
 GPD  CONST_11  N3   C2   N1   C6      0.00   0.0  0
 GPD  CONST_12  N2   C2   N3   C4    180.00   0.0  0
 GPD  CONST_13  N2   C2   N1   C6    180.00   0.0  0
 GPD  CONST_14  C2   N1   C6   O6    180.00   0.0  0
 GPD  CONST_15  H8   C8   N9   C1'     0.00   0.0  0
 GPD  CONST_16  HN1  N1   C6   C5    180.00   0.0  0
 GPD  CONST_17  HN2  N2   C2   N3      0.00   0.0  0
 GPD  Var_01    OPP  P2   O1G  C1G   141.53  30.0  2
 GPD  Var_02    C4'  C5'  O5'  P    -151.46  30.0  3
 GPD  Var_03    O5'  P    OPP  P2    -96.10  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
 GPD  chir_01  C4G  N4A  C3G  C5G  negativ
 GPD  chir_02  C5G  O5G  C4G  C6G  negativ
 GPD  chir_03  C2G  O2G  C3G  C1G  negativ
 GPD  chir_04  C1G  O5G  O1G  C2G  positiv
 GPD  chir_07  C4'  C5'  O4'  C3'  negativ
 GPD  chir_08  C3'  O3'  C4'  C2'  positiv
 GPD  chir_09  C2'  O2'  C3'  C1'  positiv
 GPD  chir_10  C1'  O4'  N9   C2'  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
 GPD  plan-1  C1'   0.020
 GPD  plan-1  N9    0.020
 GPD  plan-1  C8    0.020
 GPD  plan-1  N7    0.020
 GPD  plan-1  C4    0.020
 GPD  plan-1  C5    0.020
 GPD  plan-1  C6    0.020
 GPD  plan-1  O6    0.020
 GPD  plan-1  N3    0.020
 GPD  plan-1  C2    0.020
 GPD  plan-1  N1    0.020
 GPD  plan-1  N2    0.020
 GPD  plan-1  H8    0.020
 GPD  plan-1  HN1   0.020
 GPD  plan-1  HN2   0.020
 GPD  plan-1  HN2A  0.020

