# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Sep 30 08:45:05 2022
#   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,4R,5S,6S)-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
 GDC  GDC  "GUANOSINE-5'-DIPHOSPHATE-BETA-L-GALACTOSE"  ligand  64  39  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GDC
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
 GDC  O3P   O  OH1   0  -0.711  14.4510  40.9350   6.7558
 GDC  P     P  P     0   1.492  15.5854  41.7807   6.0496
 GDC  O1P   O  O     0  -0.675  15.7530  41.4903   4.6188
 GDC  O2P   O  O2    0  -0.715  16.9192  41.4433   6.9155
 GDC  O5'   O  O2    0  -0.571  15.2359  43.2629   6.4747
 GDC  C5'   C  CH2   0  -0.225  16.0559  44.3880   6.1263
 GDC  C4'   C  CH1   0   0.017  16.2222  45.2958   7.3201
 GDC  O4'   O  O2    0  -0.491  14.9743  45.9007   7.6610
 GDC  C3'   C  CH1   0  -0.067  16.7398  44.6125   8.5923
 GDC  O3'   O  OH1   0  -0.663  17.6553  45.4830   9.2078
 GDC  C2'   C  CH1   0  -0.039  15.4595  44.4818   9.4287
 GDC  O2'   O  OH1   0  -0.654  15.6692  44.4437  10.8098
 GDC  C1'   C  CH1   0   0.233  14.7567  45.7769   9.0389
 GDC  N9    N  NR5   0  -0.552  13.3524  45.8490   9.3259
 GDC  C8    C  CR15  0   0.095  12.7730  46.8559  10.0624
 GDC  N7    N  N     0  -0.441  11.4920  46.7282  10.1859
 GDC  C6    C  CR6   0   0.501   9.9359  44.9522   9.2673
 GDC  O6    O  O     0  -0.463   8.8327  45.2937   9.6560
 GDC  C5    C  CR56  0  -0.091  11.1943  45.5836   9.4917
 GDC  N1    N  NR16  0  -0.726  10.0934  43.8019   8.4856
 GDC  C2    C  CR6   0   0.690  11.2732  43.3248   7.9895
 GDC  N2    N  NH2   0  -0.837  11.2147  42.2266   7.2272
 GDC  N3    N  N     0  -0.508  12.4269  43.9079   8.2071
 GDC  C4    C  CR56  0   0.500  12.3335  45.0204   8.9468
 GDC  C1    C  CH1   0   0.299  18.7301  39.8420   8.6722
 GDC  C2A   C  CH1   0  -0.001  19.0359  40.4011  10.0553
 GDC  C3    C  CH1   0  -0.002  18.7302  39.3149  11.0853
 GDC  C4A   C  CH1   0  -0.019  19.4765  38.0219  10.7477
 GDC  C5A   C  CH1   0  -0.037  19.0988  37.6272   9.3192
 GDC  C6A   C  CH2   0  -0.173  19.7918  36.3729   8.8203
 GDC  O1    O  O2    0  -0.581  19.1644  40.7825   7.7141
 GDC  O2    O  OH1   0  -0.665  18.2314  41.5369  10.2326
 GDC  O3    O  OH1   0  -0.664  19.0558  39.8345  12.3478
 GDC  O4    O  OH1   0  -0.665  20.8567  38.2427  10.8972
 GDC  O5    O  O2    0  -0.486  19.4383  38.6779   8.4242
 GDC  O6A   O  OH1   0  -0.657  19.3233  35.9578   7.5617
 GDC  P1    P  P     0   1.492  18.4152  41.1274   6.3620
 GDC  O1X   O  OH1   0  -0.726  18.2981  39.7243   5.6332
 GDC  O2X   O  O     0  -0.655  19.0322  42.2432   5.6340
 GDC  H3P   H  HOH1  0   0.511  14.3541  41.0441   7.7144
 GDC  H5'1  H  HCH2  0   0.278  15.5741  44.9185   5.3039
 GDC  H5'2  H  HCH2  0   0.254  17.0476  44.0771   5.7891
 GDC  H4'   H  HCH1  0   0.265  16.9324  46.0727   7.0127
 GDC  H3'   H  HCH1  0   0.253  17.1988  43.6391   8.3885
 GDC  HA    H  HOH1  0   0.447  17.7497  45.2099  10.1280
 GDC  H2'   H  HCH1  0   0.262  14.8779  43.6252   9.0750
 GDC  HB    H  HOH1  0   0.466  15.7920  43.5284  11.0809
 GDC  H1'   H  HCH1  0   0.252  15.2099  46.6095   9.5930
 GDC  H8    H  HCR5  0   0.294  13.3726  47.6521  10.4796
 GDC  H1    H  HNR6  0   0.424   9.2389  43.3032   8.2691
 GDC  H2N1  H  HNH2  0   0.416  10.3850  41.6623   7.1642
 GDC  H2N2  H  HNH2  0   0.406  12.0768  41.8172   6.9116
 GDC  HC    H  HCH1  0   0.226  17.6454  39.6652   8.5879
 GDC  H2A   H  HCH1  0   0.233  20.1056  40.6528  10.1003
 GDC  H3    H  HCH1  0   0.227  17.6552  39.0885  11.0182
 GDC  H4A   H  HCH1  0   0.241  19.1200  37.2311  11.4225
 GDC  H5A   H  HCH1  0   0.230  18.0110  37.4541   9.2914
 GDC  H6A1  H  HCH2  0   0.232  19.5803  35.5649   9.5239
 GDC  H6A2  H  HCH2  0   0.206  20.8780  36.5270   8.8174
 GDC  H2    H  HOH1  0   0.456  18.3741  41.8704  11.1247
 GDC  HD    H  HOH1  0   0.457  18.6015  39.3194  13.0218
 GDC  H4    H  HOH1  0   0.458  21.2927  37.4054  11.0776
 GDC  H6A   H  HOH1  0   0.446  19.5598  36.6291   6.9139
 GDC  H1PA  H  HOH1  0   0.505  18.0189  39.7581   4.7065

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
 GDC  O3P  P     single    1.581  0.020  1.581
 GDC  O3P  H3P   single    0.850  0.020  0.980
 GDC  P    O1P   double    1.470  0.020  1.470
 GDC  P    O2P   single    1.626  0.020  1.626
 GDC  P    O5'   single    1.581  0.020  1.581
 GDC  O2P  P1    single    1.626  0.020  1.626
 GDC  O5'  C5'   single    1.435  0.020  1.435
 GDC  C5'  C4'   single    1.509  0.020  1.509
 GDC  C5'  H5'1  single    0.970  0.020  1.090
 GDC  C5'  H5'2  single    0.970  0.020  1.090
 GDC  C4'  O4'   single    1.428  0.020  1.428
 GDC  C4'  C3'   single    1.534  0.020  1.534
 GDC  C4'  H4'   single    0.970  0.020  1.090
 GDC  O4'  C1'   single    1.401  0.020  1.401
 GDC  C3'  O3'   single    1.405  0.020  1.405
 GDC  C3'  C2'   single    1.535  0.020  1.535
 GDC  C3'  H3'   single    0.970  0.020  1.090
 GDC  O3'  HA    single    0.850  0.020  0.980
 GDC  C2'  O2'   single    1.397  0.020  1.397
 GDC  C2'  C1'   single    1.524  0.020  1.524
 GDC  C2'  H2'   single    0.970  0.020  1.090
 GDC  O2'  HB    single    0.850  0.020  0.980
 GDC  C1'  N9    single    1.435  0.020  1.435
 GDC  C1'  H1'   single    0.970  0.020  1.090
 GDC  N9   C8    aromatic  1.376  0.020  1.376
 GDC  N9   C4    aromatic  1.367  0.020  1.367
 GDC  C8   N7    aromatic  1.293  0.020  1.293
 GDC  C8   H8    single    0.930  0.020  1.080
 GDC  N7   C5    aromatic  1.371  0.020  1.371
 GDC  C6   O6    double    1.218  0.020  1.218
 GDC  C6   C5    single    1.426  0.020  1.426
 GDC  C6   N1    single    1.400  0.020  1.400
 GDC  C5   C4    aromatic  1.383  0.020  1.383
 GDC  N1   C2    single    1.366  0.020  1.366
 GDC  N1   H1    single    0.860  0.020  1.020
 GDC  C2   N2    single    1.338  0.020  1.338
 GDC  C2   N3    double    1.311  0.020  1.311
 GDC  N2   H2N1  single    0.860  0.020  1.020
 GDC  N2   H2N2  single    0.860  0.020  1.020
 GDC  N3   C4    single    1.339  0.020  1.339
 GDC  C1   C2A   single    1.523  0.020  1.523
 GDC  C1   O1    single    1.411  0.020  1.411
 GDC  C1   O5    single    1.385  0.020  1.385
 GDC  C1   HC    single    0.970  0.020  1.090
 GDC  C2A  C3    single    1.528  0.020  1.528
 GDC  C2A  O2    single    1.403  0.020  1.403
 GDC  C2A  H2A   single    0.970  0.020  1.090
 GDC  C3   C4A   single    1.531  0.020  1.531
 GDC  C3   O3    single    1.403  0.020  1.403
 GDC  C3   H3    single    0.970  0.020  1.090
 GDC  C4A  C5A   single    1.529  0.020  1.529
 GDC  C4A  O4    single    1.406  0.020  1.406
 GDC  C4A  H4A   single    0.970  0.020  1.090
 GDC  C5A  C6A   single    1.517  0.020  1.517
 GDC  C5A  O5    single    1.421  0.020  1.421
 GDC  C5A  H5A   single    0.970  0.020  1.090
 GDC  C6A  O6A   single    1.406  0.020  1.406
 GDC  C6A  H6A1  single    0.970  0.020  1.090
 GDC  C6A  H6A2  single    0.970  0.020  1.090
 GDC  O1   P1    single    1.584  0.020  1.584
 GDC  O2   H2    single    0.850  0.020  0.980
 GDC  O3   HD    single    0.850  0.020  0.980
 GDC  O4   H4    single    0.850  0.020  0.980
 GDC  O6A  H6A   single    0.850  0.020  0.980
 GDC  P1   O1X   single    1.585  0.020  1.585
 GDC  P1   O2X   double    1.468  0.020  1.468
 GDC  O1X  H1PA  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
 GDC  H3P   O3P  P     116.94  3.000
 GDC  O5'   P    O2P   103.46  3.000
 GDC  O5'   P    O1P   118.18  3.000
 GDC  O2P   P    O1P   112.59  3.000
 GDC  O5'   P    O3P   102.86  3.000
 GDC  O2P   P    O3P   103.87  3.000
 GDC  O1P   P    O3P   114.27  3.000
 GDC  P1    O2P  P     127.87  3.000
 GDC  C5'   O5'  P     122.91  3.000
 GDC  H5'2  C5'  H5'1  107.86  3.000
 GDC  H5'2  C5'  C4'   108.37  3.000
 GDC  H5'1  C5'  C4'   110.65  3.000
 GDC  H5'2  C5'  O5'   111.74  3.000
 GDC  H5'1  C5'  O5'   108.17  3.000
 GDC  C4'   C5'  O5'   110.03  3.000
 GDC  H4'   C4'  C3'   109.24  3.000
 GDC  H4'   C4'  O4'   109.44  3.000
 GDC  C3'   C4'  O4'   106.59  3.000
 GDC  H4'   C4'  C5'   106.01  3.000
 GDC  C3'   C4'  C5'   115.17  3.000
 GDC  O4'   C4'  C5'   110.32  3.000
 GDC  C1'   O4'  C4'   109.46  3.000
 GDC  H3'   C3'  C2'   112.04  3.000
 GDC  H3'   C3'  O3'   111.04  3.000
 GDC  C2'   C3'  O3'   110.95  3.000
 GDC  H3'   C3'  C4'   112.51  3.000
 GDC  C2'   C3'  C4'   102.03  3.000
 GDC  O3'   C3'  C4'   107.89  3.000
 GDC  HA    O3'  C3'   107.83  3.000
 GDC  H2'   C2'  C1'   109.72  3.000
 GDC  H2'   C2'  O2'   112.20  3.000
 GDC  C1'   C2'  O2'   110.19  3.000
 GDC  H2'   C2'  C3'   109.50  3.000
 GDC  C1'   C2'  C3'    99.96  3.000
 GDC  O2'   C2'  C3'   114.57  3.000
 GDC  HB    O2'  C2'   108.87  3.000
 GDC  H1'   C1'  N9    105.36  3.000
 GDC  H1'   C1'  C2'   108.96  3.000
 GDC  N9    C1'  C2'   116.28  3.000
 GDC  H1'   C1'  O4'   111.43  3.000
 GDC  N9    C1'  O4'   110.14  3.000
 GDC  C2'   C1'  O4'   104.78  3.000
 GDC  C4    N9   C8    106.16  3.000
 GDC  C4    N9   C1'   130.05  3.000
 GDC  C8    N9   C1'   123.78  3.000
 GDC  H8    C8   N7    125.84  3.000
 GDC  H8    C8   N9    120.83  3.000
 GDC  N7    C8   N9    113.33  3.000
 GDC  C5    N7   C8    104.43  3.000
 GDC  N1    C6   C5    110.64  3.000
 GDC  N1    C6   O6    120.69  3.000
 GDC  C5    C6   O6    128.66  3.000
 GDC  C4    C5   C6    119.00  3.000
 GDC  C4    C5   N7    111.14  3.000
 GDC  C6    C5   N7    129.86  3.000
 GDC  H1    N1   C2    118.62  3.000
 GDC  H1    N1   C6    115.42  3.000
 GDC  C2    N1   C6    125.95  3.000
 GDC  N3    C2   N2    119.88  3.000
 GDC  N3    C2   N1    122.99  3.000
 GDC  N2    C2   N1    117.11  3.000
 GDC  H2N2  N2   H2N1  117.35  3.000
 GDC  H2N2  N2   C2    118.40  3.000
 GDC  H2N1  N2   C2    122.17  3.000
 GDC  C4    N3   C2    113.57  3.000
 GDC  N3    C4   C5    127.84  3.000
 GDC  N3    C4   N9    127.21  3.000
 GDC  C5    C4   N9    104.95  3.000
 GDC  HC    C1   O5    110.78  3.000
 GDC  HC    C1   O1    110.96  3.000
 GDC  O5    C1   O1    106.33  3.000
 GDC  HC    C1   C2A   109.02  3.000
 GDC  O5    C1   C2A   111.63  3.000
 GDC  O1    C1   C2A   108.07  3.000
 GDC  H2A   C2A  O2    111.54  3.000
 GDC  H2A   C2A  C3    109.25  3.000
 GDC  O2    C2A  C3    112.06  3.000
 GDC  H2A   C2A  C1    108.44  3.000
 GDC  O2    C2A  C1    107.27  3.000
 GDC  C3    C2A  C1    108.13  3.000
 GDC  H3    C3   O3    110.95  3.000
 GDC  H3    C3   C4A   106.80  3.000
 GDC  O3    C3   C4A   113.46  3.000
 GDC  H3    C3   C2A   107.49  3.000
 GDC  O3    C3   C2A   107.27  3.000
 GDC  C4A   C3   C2A   110.75  3.000
 GDC  H4A   C4A  O4    111.48  3.000
 GDC  H4A   C4A  C5A   107.91  3.000
 GDC  O4    C4A  C5A   112.48  3.000
 GDC  H4A   C4A  C3    108.32  3.000
 GDC  O4    C4A  C3    108.82  3.000
 GDC  C5A   C4A  C3    107.68  3.000
 GDC  H5A   C5A  O5    109.64  3.000
 GDC  H5A   C5A  C6A   108.22  3.000
 GDC  O5    C5A  C6A   107.15  3.000
 GDC  H5A   C5A  C4A   107.94  3.000
 GDC  O5    C5A  C4A   109.77  3.000
 GDC  C6A   C5A  C4A   114.06  3.000
 GDC  H6A2  C6A  H6A1  107.30  3.000
 GDC  H6A2  C6A  O6A   111.66  3.000
 GDC  H6A1  C6A  O6A   107.09  3.000
 GDC  H6A2  C6A  C5A   109.69  3.000
 GDC  H6A1  C6A  C5A   108.14  3.000
 GDC  O6A   C6A  C5A   112.72  3.000
 GDC  P1    O1   C1    125.39  3.000
 GDC  H2    O2   C2A   108.21  3.000
 GDC  HD    O3   C3    108.81  3.000
 GDC  H4    O4   C4A   109.18  3.000
 GDC  C5A   O5   C1    112.73  3.000
 GDC  H6A   O6A  C6A   108.35  3.000
 GDC  O2X   P1   O1X   118.40  3.000
 GDC  O2X   P1   O1    112.95  3.000
 GDC  O1X   P1   O1    103.57  3.000
 GDC  O2X   P1   O2P   114.06  3.000
 GDC  O1X   P1   O2P   105.10  3.000
 GDC  O1    P1   O2P   100.78  3.000
 GDC  H1PA  O1X  P1    115.49  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
 GDC  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 GDC  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 GDC  CONST_03  C5    C4   N9   C8      0.00   0.0  0
 GDC  CONST_04  C4    C5   N7   C8      0.00   0.0  0
 GDC  CONST_05  C4    N9   C8   N7      0.00   0.0  0
 GDC  CONST_06  N7    C8   N9   C1'   180.00   0.0  0
 GDC  CONST_07  C5    C4   N9   C1'   180.00   0.0  0
 GDC  CONST_08  N3    C4   N9   C1'     0.00   0.0  0
 GDC  CONST_09  N3    C2   N1   C6      0.00   0.0  0
 GDC  CONST_10  C2    N1   C6   C5      0.00   0.0  0
 GDC  CONST_11  C4    N3   C2   N1      0.00   0.0  0
 GDC  CONST_12  N2    C2   N1   C6    180.00   0.0  0
 GDC  CONST_13  C2    N1   C6   O6    180.00   0.0  0
 GDC  CONST_14  C4    N3   C2   N2    180.00   0.0  0
 GDC  CONST_15  H8    C8   N9   C1'     0.00   0.0  0
 GDC  CONST_16  H8    C8   N7   C5    180.00   0.0  0
 GDC  CONST_17  H8    C8   N9   C4    180.00   0.0  0
 GDC  CONST_18  H1    N1   C6   C5    180.00   0.0  0
 GDC  CONST_19  H1    N1   C2   N3    180.00   0.0  0
 GDC  CONST_20  H1    N1   C6   O6      0.00   0.0  0
 GDC  CONST_21  H2N1  N2   C2   N1      0.00   0.0  0
 GDC  CONST_22  H2N2  N2   C2   N1    180.00   0.0  0
 GDC  CONST_23  H1    N1   C2   N2      0.00   0.0  0
 GDC  CONST_24  H2N1  N2   C2   N3    180.00   0.0  0
 GDC  CONST_25  H2N2  N2   C2   N3      0.00   0.0  0
 GDC  Var_01    C4'   C5'  O5'  P    -135.88  30.0  3
 GDC  Var_02    C1    O1   P1   O2P    52.00  30.0  2
 GDC  Var_03    O1X   P1   O1   C1    -56.59  30.0  3
 GDC  Var_04    O2X   P1   O1   C1    174.09  30.0  3
 GDC  Var_05    P1    O2P  P    O3P   137.04  30.0  3
 GDC  Var_06    C5'   O5'  P    O3P   176.10  30.0  3
 GDC  Var_07    O1    P1   O2P  P    -175.69  30.0  3
 GDC  Var_08    O1X   P1   O2P  P     -68.31  30.0  3
 GDC  Var_09    O2X   P1   O2P  P      63.00  30.0  3
 GDC  Var_10    P1    O2P  P    O1P    12.91  30.0  3
 GDC  Var_11    C5'   O5'  P    O1P   -56.99  30.0  3
 GDC  Var_12    C5'   O5'  P    O2P    68.20  30.0  3
 GDC  Var_13    P1    O2P  P    O5'  -115.81  30.0  3
 GDC  Var_14    H5'1  C5'  O5'  P     103.14  30.0  3
 GDC  Var_15    H5'2  C5'  O5'  P     -15.44  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
 GDC  chir_02  C4'  C5'  O4'  C3'  negativ
 GDC  chir_03  C3'  O3'  C4'  C2'  positiv
 GDC  chir_04  C2'  O2'  C3'  C1'  positiv
 GDC  chir_05  C1'  O4'  N9   C2'  negativ
 GDC  chir_06  C1   C2A  O1   O5   negativ
 GDC  chir_07  C2A  O2   C1   C3   positiv
 GDC  chir_08  C3   O3   C2A  C4A  negativ
 GDC  chir_09  C4A  O4   C5A  C3   positiv
 GDC  chir_10  C5A  O5   C4A  C6A  positiv
 GDC  chir_11  P    O1P  O2P  O5'  both
 GDC  chir_12  P1   O1X  O1   O2P  both

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
 GDC  plan-1  C1'   0.020
 GDC  plan-1  N9    0.020
 GDC  plan-1  C8    0.020
 GDC  plan-1  N7    0.020
 GDC  plan-1  C6    0.020
 GDC  plan-1  O6    0.020
 GDC  plan-1  C5    0.020
 GDC  plan-1  N1    0.020
 GDC  plan-1  C2    0.020
 GDC  plan-1  N2    0.020
 GDC  plan-1  N3    0.020
 GDC  plan-1  C4    0.020
 GDC  plan-1  H8    0.020
 GDC  plan-1  H1    0.020
 GDC  plan-1  H2N1  0.020
 GDC  plan-1  H2N2  0.020

