# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 02:37:16 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-amino-9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-alpha-L-xylofuranosyl}-1,9-dihydro-6H-purin-6-one
#   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)N[P](O)(O)=O)[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
 9GM  9GM  2-amino-9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-alpha-L-xylofuranosyl}-1,9-dihydro-6H-purin-6-one  ligand  49  32  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9GM
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
 9GM  C1   C  CR6   0   0.690  16.5738  -8.2342  11.3248
 9GM  C2   C  CR56  0   0.504  17.4675  -6.5500  12.4442
 9GM  C3   C  CR56  0  -0.094  18.4525  -6.2793  11.5136
 9GM  C4   C  CR15  0   0.107  18.7324  -4.8743  13.0695
 9GM  C5   C  CR15  0   0.208  16.8897  -5.5573  14.6543
 9GM  C6   C  CR15  0   0.030  16.8905  -4.0170  16.3921
 9GM  N2   N  N     0  -0.514  16.5235  -7.5001  12.4086
 9GM  O1   O  O     0  -0.504  16.7109  -4.2062  14.9901
 9GM  O4   O  O     0  -0.676  16.3454   0.6525  16.2859
 9GM  O5   O  O2    0  -0.709  15.4274  -0.5553  18.4162
 9GM  O6   O  OH1   0  -0.731  16.4439   1.2108  19.7594
 9GM  P1   P  P     0   1.495  16.3852  -0.5593  17.1152
 9GM  O7   O  O     0  -0.670  14.0082   1.5951  18.8945
 9GM  O8   O  OH1   0  -0.731  14.5794  -1.5599  22.9221
 9GM  O9   O  O     0  -0.693  16.6270  -1.5356  21.2789
 9GM  P2   P  P     0   1.478  15.0014   0.6431  19.4162
 9GM  O10  O  OH1   0  -0.731  14.3710  -2.7630  20.7791
 9GM  O11  O  OH1   0  -0.668  15.6241  -5.9516  17.1987
 9GM  O12  O  OH1   0  -0.656  18.9409  -5.9554  15.7811
 9GM  N1   N  NH2   0  -0.831  15.6649  -9.2001  11.1266
 9GM  N3   N  N     0  -0.450  19.2282  -5.2243  11.9235
 9GM  N4   N  NR5   0  -0.533  17.6531  -5.6397  13.4374
 9GM  C7   C  CH2   0  -0.221  15.7844  -3.1458  16.9335
 9GM  O2   O  O2    0  -0.568  15.8492  -1.8359  16.3462
 9GM  O3   O  OH1   0  -0.729  17.7654  -0.9482  17.8002
 9GM  N5   N  NH1   0  -0.947  14.4289  -0.2114  20.7228
 9GM  P3   P  P     0   1.431  15.1615  -1.5424  21.4357
 9GM  C8   C  CR15  0  -0.073  16.9134  -5.4249  16.9999
 9GM  C9   C  CR15  0  -0.033  17.5684  -6.2096  15.8621
 9GM  C10  C  CR6   0   0.504  18.5154  -7.0771  10.3357
 9GM  O13  O  O     0  -0.475  19.2980  -7.0054   9.4028
 9GM  N6   N  NR16  0  -0.727  17.5031  -8.0464  10.3426
 9GM  H1   H  HCR5  0   0.288  19.0905  -4.0615  13.6803
 9GM  H2   H  HCR5  0   0.272  15.9305  -6.0465  14.4579
 9GM  H3   H  HCR5  0   0.249  17.8596  -3.5385  16.5739
 9GM  H4   H  HOH1  0   0.506  16.4376   2.0375  20.2623
 9GM  H5   H  HOH1  0   0.502  14.9964  -0.9218  23.5170
 9GM  H6   H  HOH1  0   0.500  14.6955  -3.6350  21.0433
 9GM  H7   H  HOH1  0   0.465  15.3500  -5.7942  18.1064
 9GM  H8   H  HOH1  0   0.467  19.3753  -6.3656  16.5360
 9GM  H9   H  HNH2  0   0.412  15.0831  -9.4556  11.9065
 9GM  H10  H  HNH2  0   0.414  15.8140  -9.9116  10.4316
 9GM  H11  H  HCH2  0   0.271  14.8062  -3.5454  16.6721
 9GM  H12  H  HCH2  0   0.247  15.8492  -3.1007  18.0245
 9GM  H13  H  HOH1  0   0.508  18.5420  -0.7924  17.2442
 9GM  H14  H  HNH1  0   0.447  13.4632  -0.0175  20.9649
 9GM  H15  H  HCR5  0   0.281  17.5121  -5.4526  17.9163
 9GM  H16  H  HCR5  0   0.263  17.3405  -7.2795  15.9206
 9GM  H17  H  HNR6  0   0.425  17.4734  -8.6523   9.5320

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
 9GM  O13  C10  double    1.220  0.020  1.220
 9GM  N6   C10  single    1.402  0.020  1.402
 9GM  N6   C1   single    1.365  0.020  1.365
 9GM  N1   C1   single    1.341  0.020  1.341
 9GM  C10  C3   single    1.424  0.020  1.424
 9GM  C1   N2   double    1.310  0.020  1.310
 9GM  C3   C2   aromatic  1.382  0.020  1.382
 9GM  C3   N3   aromatic  1.372  0.020  1.372
 9GM  N2   C2   single    1.340  0.020  1.340
 9GM  C2   N4   aromatic  1.360  0.020  1.360
 9GM  N3   C4   aromatic  1.297  0.020  1.297
 9GM  N4   C4   aromatic  1.373  0.020  1.373
 9GM  N4   C5   single    1.439  0.020  1.439
 9GM  C5   O1   single    1.404  0.020  1.404
 9GM  C5   C9   single    1.531  0.020  1.531
 9GM  O1   C6   single    1.426  0.020  1.426
 9GM  O12  C9   single    1.398  0.020  1.398
 9GM  C9   C8   single    1.530  0.020  1.530
 9GM  C6   C8   single    1.534  0.020  1.534
 9GM  C6   C7   single    1.508  0.020  1.508
 9GM  O2   C7   single    1.437  0.020  1.437
 9GM  O2   P1   single    1.584  0.020  1.584
 9GM  C8   O11  single    1.407  0.020  1.407
 9GM  O4   P1   double    1.469  0.020  1.469
 9GM  O7   P2   double    1.471  0.020  1.471
 9GM  O5   P1   single    1.616  0.020  1.616
 9GM  O5   P2   single    1.618  0.020  1.618
 9GM  P1   O3   single    1.589  0.020  1.589
 9GM  P2   O6   single    1.588  0.020  1.588
 9GM  P2   N5   single    1.663  0.020  1.663
 9GM  N5   P3   single    1.678  0.020  1.678
 9GM  O9   P3   double    1.474  0.020  1.474
 9GM  P3   O10  single    1.596  0.020  1.596
 9GM  P3   O8   single    1.596  0.020  1.596
 9GM  C4   H1   single    0.930  0.020  1.080
 9GM  C5   H2   single    0.970  0.020  1.090
 9GM  C6   H3   single    0.970  0.020  1.090
 9GM  O6   H4   single    0.850  0.020  0.980
 9GM  O8   H5   single    0.850  0.020  0.980
 9GM  O10  H6   single    0.850  0.020  0.980
 9GM  O11  H7   single    0.850  0.020  0.980
 9GM  O12  H8   single    0.850  0.020  0.980
 9GM  N1   H9   single    0.890  0.020  1.040
 9GM  N1   H10  single    0.890  0.020  1.040
 9GM  C7   H11  single    0.970  0.020  1.090
 9GM  C7   H12  single    0.970  0.020  1.090
 9GM  O3   H13  single    0.850  0.020  0.980
 9GM  N5   H14  single    0.860  0.020  1.020
 9GM  C8   H15  single    0.970  0.020  1.090
 9GM  C9   H16  single    0.970  0.020  1.090
 9GM  N6   H17  single    0.860  0.020  1.020

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
 9GM  N6   C1   N1   117.01  3.000
 9GM  N1   C1   N2   119.99  3.000
 9GM  N6   C1   N2   122.98  3.000
 9GM  N4   C2   N2   126.17  3.000
 9GM  N4   C2   C3   105.27  3.000
 9GM  N2   C2   C3   128.56  3.000
 9GM  C10  C3   N3   130.76  3.000
 9GM  N3   C3   C2   110.64  3.000
 9GM  C10  C3   C2   118.60  3.000
 9GM  H1   C4   N4   121.97  3.000
 9GM  H1   C4   N3   125.25  3.000
 9GM  N4   C4   N3   112.76  3.000
 9GM  H2   C5   C9   109.85  3.000
 9GM  H2   C5   N4   106.72  3.000
 9GM  C9   C5   N4   114.05  3.000
 9GM  H2   C5   O1   111.19  3.000
 9GM  C9   C5   O1   106.13  3.000
 9GM  N4   C5   O1   108.96  3.000
 9GM  H3   C6   C8   108.77  3.000
 9GM  H3   C6   C7   109.67  3.000
 9GM  C8   C6   C7   113.51  3.000
 9GM  H3   C6   O1   109.41  3.000
 9GM  C7   C6   O1   109.70  3.000
 9GM  C8   C6   O1   105.65  3.000
 9GM  C2   N2   C1   113.09  3.000
 9GM  C6   O1   C5   110.30  3.000
 9GM  P2   O5   P1   130.97  3.000
 9GM  H4   O6   P2   114.33  3.000
 9GM  O3   P1   O2   107.82  3.000
 9GM  O3   P1   O5    99.70  3.000
 9GM  O2   P1   O5   101.09  3.000
 9GM  O3   P1   O4   117.95  3.000
 9GM  O5   P1   O4   115.88  3.000
 9GM  O2   P1   O4   112.44  3.000
 9GM  H5   O8   P3   114.10  3.000
 9GM  N5   P2   O7   112.25  3.000
 9GM  N5   P2   O6   109.07  3.000
 9GM  O7   P2   O6   117.29  3.000
 9GM  N5   P2   O5   101.29  3.000
 9GM  O6   P2   O5    99.16  3.000
 9GM  O7   P2   O5   115.97  3.000
 9GM  H6   O10  P3   114.27  3.000
 9GM  H7   O11  C8   109.48  3.000
 9GM  H8   O12  C9   108.66  3.000
 9GM  H10  N1   H9   116.22  3.000
 9GM  H10  N1   C1   120.75  3.000
 9GM  H9   N1   C1   117.41  3.000
 9GM  C4   N3   C3   104.79  3.000
 9GM  C5   N4   C4   127.71  3.000
 9GM  C5   N4   C2   125.70  3.000
 9GM  C4   N4   C2   106.54  3.000
 9GM  H12  C7   H11  107.93  3.000
 9GM  H12  C7   O2   111.56  3.000
 9GM  H11  C7   O2   106.08  3.000
 9GM  H12  C7   C6   109.78  3.000
 9GM  H11  C7   C6   111.15  3.000
 9GM  O2   C7   C6   110.29  3.000
 9GM  C7   O2   P1   123.48  3.000
 9GM  H13  O3   P1   114.20  3.000
 9GM  H14  N5   P3   117.77  3.000
 9GM  H14  N5   P2   114.65  3.000
 9GM  P3   N5   P2   126.23  3.000
 9GM  N5   P3   O10  102.45  3.000
 9GM  O10  P3   O9   116.89  3.000
 9GM  N5   P3   O9   112.66  3.000
 9GM  O10  P3   O8   101.19  3.000
 9GM  O9   P3   O8   117.49  3.000
 9GM  N5   P3   O8   104.18  3.000
 9GM  H15  C8   C9   112.05  3.000
 9GM  H15  C8   O11  111.92  3.000
 9GM  C9   C8   O11  107.79  3.000
 9GM  H15  C8   C6   111.29  3.000
 9GM  O11  C8   C6   112.71  3.000
 9GM  C9   C8   C6   100.52  3.000
 9GM  H16  C9   C8   111.86  3.000
 9GM  H16  C9   O12  112.64  3.000
 9GM  C8   C9   O12  111.73  3.000
 9GM  H16  C9   C5   111.47  3.000
 9GM  C8   C9   C5   100.27  3.000
 9GM  O12  C9   C5   108.18  3.000
 9GM  N6   C10  O13  120.52  3.000
 9GM  N6   C10  C3   110.58  3.000
 9GM  O13  C10  C3   128.90  3.000
 9GM  H17  N6   C10  115.54  3.000
 9GM  H17  N6   C1   118.28  3.000
 9GM  C10  N6   C1   126.18  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
 9GM  CONST_01  C4   N3   C3   C2     0.00   0.0  0
 9GM  CONST_02  N3   C4   N4   C2     0.00   0.0  0
 9GM  CONST_03  C4   N4   C2   C3     0.00   0.0  0
 9GM  CONST_04  N4   C4   N3   C3     0.00   0.0  0
 9GM  CONST_05  N4   C2   C3   N3     0.00   0.0  0
 9GM  CONST_06  C5   N4   C2   C3   180.00   0.0  0
 9GM  CONST_07  N2   C2   N4   C5     0.00   0.0  0
 9GM  CONST_08  N3   C4   N4   C5   180.00   0.0  0
 9GM  CONST_09  C3   C10  N6   C1     0.00   0.0  0
 9GM  CONST_10  N6   C1   N2   C2     0.00   0.0  0
 9GM  CONST_11  C10  N6   C1   N2     0.00   0.0  0
 9GM  CONST_12  O13  C10  N6   C1   180.00   0.0  0
 9GM  CONST_13  N1   C1   N2   C2   180.00   0.0  0
 9GM  CONST_14  C10  N6   C1   N1   180.00   0.0  0
 9GM  CONST_15  H1   C4   N4   C2   180.00   0.0  0
 9GM  CONST_16  H17  N6   C10  C3   180.00   0.0  0
 9GM  CONST_17  H9   N1   C1   N2     0.00   0.0  0
 9GM  Var_01    P3   N5   P2   O5    45.40  30.0  3
 9GM  Var_02    O7   P2   O5   P1    75.43  30.0  3
 9GM  Var_03    P2   N5   P3   O8   156.64  30.0  1
 9GM  Var_04    O2   P1   O5   P2  -156.98  30.0  3
 9GM  Var_05    H11  C7   O2   P1   134.71  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
 9GM  chir_01  C5  N4   O1  C9   positiv
 9GM  chir_02  C6  O1   C7  C8   negativ
 9GM  chir_05  C8  C9   C6  O11  negativ
 9GM  chir_06  C9  O12  C5  C8   positiv
 9GM  chir_07  P1  O4   O5  O3   both
 9GM  chir_08  P2  O5   O7  N5   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
 9GM  plan-1  C1   0.020
 9GM  plan-1  C2   0.020
 9GM  plan-1  C3   0.020
 9GM  plan-1  C4   0.020
 9GM  plan-1  C5   0.020
 9GM  plan-1  N2   0.020
 9GM  plan-1  N1   0.020
 9GM  plan-1  N3   0.020
 9GM  plan-1  N4   0.020
 9GM  plan-1  C10  0.020
 9GM  plan-1  O13  0.020
 9GM  plan-1  N6   0.020
 9GM  plan-1  H1   0.020
 9GM  plan-1  H9   0.020
 9GM  plan-1  H10  0.020
 9GM  plan-1  H17  0.020

