# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 16 20:56:44 2020
#   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  45  32  .  2021-08-06  2021-08-06  
;
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   0.689   6.0075  -1.7455   1.3654
 9GM  C2   C  CR56   0   0.502   4.3886  -1.1256  -0.0068
 9GM  C3   C  CR56   0  -0.094   4.4332  -2.2656  -0.7879
 9GM  C4   C  CR15   0   0.106   2.9145  -1.0547  -1.6232
 9GM  C5   C  CH1    0   0.210   3.0133   0.9547  -0.0992
 9GM  C6   C  CH1    0   0.006   1.3343   2.3475  -0.8977
 9GM  N2   N  N      0  -0.513   5.1425  -0.8120   1.0561
 9GM  O1   O  O2     0  -0.504   1.6309   1.1003  -0.2630
 9GM  O4   O  O      0  -0.812  -2.8572   3.8747  -0.3450
 9GM  O5   O  O2     0  -0.753  -3.3086   1.4289  -0.8982
 9GM  O6   O  OP    -1  -0.833  -5.4242   0.8576   0.4045
 9GM  P1   P  P      0   1.340  -2.4767   2.4687   0.0176
 9GM  O7   O  O      0  -0.825  -4.6754  -0.5389  -1.6503
 9GM  O8   O  OP    -1  -0.912  -2.8506  -3.1752  -0.3653
 9GM  O9   O  O      0  -0.914  -5.0145  -2.7170   0.9211
 9GM  P2   P  P      0   1.297  -4.3283   0.1825  -0.3787
 9GM  O10  O  OP    -1  -0.920  -2.7583  -2.6717   2.1461
 9GM  O11  O  OH1    0  -0.667   2.6281   3.7434   0.5436
 9GM  O12  O  OH1    0  -0.656   3.8263   1.6824  -2.2170
 9GM  N1   N  NH2    0  -0.833   6.8074  -1.5930   2.4304
 9GM  N3   N  N      0  -0.451   3.4993  -2.2005  -1.7909
 9GM  N4   N  NR5    0  -0.528   3.4054  -0.3590  -0.5471
 9GM  C7   C  CH2    0  -0.142   0.0840   2.9493  -0.3025
 9GM  O2   O  O2     0  -0.624  -1.0065   2.1328  -0.6629
 9GM  O3   O  OP    -1  -0.808  -2.4546   2.0667   1.4641
 9GM  N5   N  NH1    0  -0.992  -3.2913  -0.7412   0.5463
 9GM  P3   P  P      0   1.186  -3.5065  -2.4772   0.8240
 9GM  C8   C  CH1    0  -0.052   2.5993   3.1793  -0.7435
 9GM  C9   C  CH1    0  -0.058   3.6721   2.0939  -0.8884
 9GM  C10  C  CR6    0   0.502   5.3726  -3.2831  -0.4568
 9GM  O13  O  O      0  -0.476   5.5690  -4.3537  -1.0079
 9GM  N6   N  NR16   0  -0.727   6.1254  -2.9119   0.6652
 9GM  H1   H  HCR5   0   0.288   2.1129  -0.6687  -2.2323
 9GM  H2   H  HCH1   0   0.268   3.2931   1.0250   0.9561
 9GM  H3   H  HCH1   0   0.238   1.1668   2.1785  -1.9685
 9GM  H7   H  HOH1   0   0.460   3.4400   4.2521   0.6363
 9GM  H8   H  HOH1   0   0.464   4.1982   2.4121  -2.7233
 9GM  H9   H  HNH2   0   0.412   6.8469  -0.6849   2.8611
 9GM  H10  H  HNH2   0   0.414   7.6027  -2.1922   2.5708
 9GM  H11  H  HCH2   0   0.209   0.1837   3.0286   0.7849
 9GM  H12  H  HCH2   0   0.210  -0.0337   3.9658  -0.6981
 9GM  H14  H  HNH1   0   0.348  -2.9563  -0.2440   1.3611
 9GM  H15  H  HCH1   0   0.261   2.6758   3.9416  -1.5287
 9GM  H16  H  HCH1   0   0.259   4.6264   2.3871  -0.4337
 9GM  H17  H  HNR6   0   0.425   6.8114  -3.5887   0.9750

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    1.401  0.020  1.401
 9GM  N6   C1   single    1.366  0.020  1.366
 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  1.383  0.020  1.383
 9GM  C3   N3   aromatic  1.372  0.020  1.372
 9GM  N2   C2   single    1.340  0.020  1.340
 9GM  C2   N4   aromatic  1.359  0.020  1.359
 9GM  N3   C4   aromatic  1.297  0.020  1.297
 9GM  N4   C4   aromatic  1.372  0.020  1.372
 9GM  N4   C5   single    1.442  0.020  1.442
 9GM  C5   O1   single    1.400  0.020  1.400
 9GM  C5   C9   single    1.535  0.020  1.535
 9GM  O1   C6   single    1.430  0.020  1.430
 9GM  O12  C9   single    1.399  0.020  1.399
 9GM  C9   C8   single    1.533  0.020  1.533
 9GM  C6   C8   single    1.522  0.020  1.522
 9GM  C6   C7   single    1.510  0.020  1.510
 9GM  O2   C7   single    1.409  0.020  1.409
 9GM  O2   P1   single    1.654  0.020  1.654
 9GM  C8   O11  single    1.406  0.020  1.406
 9GM  O4   P1   deloc     1.501  0.020  1.501
 9GM  O7   P2   deloc     1.503  0.020  1.503
 9GM  O5   P1   single    1.616  0.020  1.616
 9GM  O5   P2   single    1.692  0.020  1.692
 9GM  P1   O3   deloc     1.502  0.020  1.502
 9GM  P2   O6   deloc     1.507  0.020  1.507
 9GM  P2   N5   single    1.669  0.020  1.669
 9GM  N5   P3   single    1.771  0.020  1.771
 9GM  O9   P3   deloc     1.530  0.020  1.530
 9GM  P3   O10  deloc     1.532  0.020  1.532
 9GM  P3   O8   deloc     1.527  0.020  1.527
 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  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  N5   H14  single    0.890  0.020  1.040
 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   116.94  3.000
 9GM  N1   C1   N2   120.03  3.000
 9GM  N6   C1   N2   123.01  3.000
 9GM  N4   C2   N2   126.19  3.000
 9GM  N4   C2   C3   105.30  3.000
 9GM  N2   C2   C3   128.52  3.000
 9GM  C10  C3   N3   130.76  3.000
 9GM  N3   C3   C2   110.61  3.000
 9GM  C10  C3   C2   118.63  3.000
 9GM  H1   C4   N4   121.84  3.000
 9GM  H1   C4   N3   125.33  3.000
 9GM  N4   C4   N3   112.82  3.000
 9GM  H2   C5   C9   109.79  3.000
 9GM  H2   C5   N4   106.77  3.000
 9GM  C9   C5   N4   113.57  3.000
 9GM  H2   C5   O1   111.03  3.000
 9GM  C9   C5   O1   106.65  3.000
 9GM  N4   C5   O1   109.08  3.000
 9GM  H3   C6   C8   108.06  3.000
 9GM  H3   C6   C7   108.65  3.000
 9GM  C8   C6   C7   115.50  3.000
 9GM  H3   C6   O1   109.30  3.000
 9GM  C7   C6   O1   110.14  3.000
 9GM  C8   C6   O1   105.03  3.000
 9GM  C2   N2   C1   113.08  3.000
 9GM  C6   O1   C5   110.33  3.000
 9GM  P2   O5   P1   127.60  3.000
 9GM  O3   P1   O2   109.20  3.000
 9GM  O3   P1   O5   112.41  3.000
 9GM  O2   P1   O5    95.38  3.000
 9GM  O3   P1   O4   119.16  3.000
 9GM  O5   P1   O4   109.59  3.000
 9GM  O2   P1   O4   108.42  3.000
 9GM  N5   P2   O7   110.30  3.000
 9GM  N5   P2   O6   114.33  3.000
 9GM  O7   P2   O6   119.14  3.000
 9GM  N5   P2   O5   101.73  3.000
 9GM  O6   P2   O5   105.54  3.000
 9GM  O7   P2   O5   103.47  3.000
 9GM  H7   O11  C8   108.52  3.000
 9GM  H8   O12  C9   108.60  3.000
 9GM  H10  N1   H9   116.56  3.000
 9GM  H10  N1   C1   120.99  3.000
 9GM  H9   N1   C1   117.80  3.000
 9GM  C4   N3   C3   104.73  3.000
 9GM  C5   N4   C4   127.45  3.000
 9GM  C5   N4   C2   125.95  3.000
 9GM  C4   N4   C2   106.54  3.000
 9GM  H12  C7   H11  107.51  3.000
 9GM  H12  C7   O2   111.20  3.000
 9GM  H11  C7   O2   111.50  3.000
 9GM  H12  C7   C6   108.42  3.000
 9GM  H11  C7   C6   110.18  3.000
 9GM  O2   C7   C6   108.00  3.000
 9GM  C7   O2   P1   117.70  3.000
 9GM  H14  N5   P3   113.31  3.000
 9GM  H14  N5   P2   112.35  3.000
 9GM  P3   N5   P2   123.64  3.000
 9GM  N5   P3   O10  101.56  3.000
 9GM  O10  P3   O9   114.00  3.000
 9GM  N5   P3   O9   106.46  3.000
 9GM  O10  P3   O8   113.86  3.000
 9GM  O9   P3   O8   113.65  3.000
 9GM  N5   P3   O8   105.89  3.000
 9GM  H15  C8   C9   112.06  3.000
 9GM  H15  C8   O11  112.03  3.000
 9GM  C9   C8   O11  110.88  3.000
 9GM  H15  C8   C6   111.42  3.000
 9GM  O11  C8   C6   109.22  3.000
 9GM  C9   C8   C6   100.67  3.000
 9GM  H16  C9   C8   112.36  3.000
 9GM  H16  C9   O12  112.10  3.000
 9GM  C8   C9   O12  112.03  3.000
 9GM  H16  C9   C5   111.02  3.000
 9GM  C8   C9   C5   100.17  3.000
 9GM  O12  C9   C5   108.50  3.000
 9GM  N6   C10  O13  120.50  3.000
 9GM  N6   C10  C3   110.57  3.000
 9GM  O13  C10  C3   128.92  3.000
 9GM  H17  N6   C10  115.60  3.000
 9GM  H17  N6   C1   118.21  3.000
 9GM  C10  N6   C1   126.19  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  CONST_18  H10  N1   C1   N2   180.00   0.0  0
 9GM  Var_01    P3   N5   P2   O5  -153.68  30.0  3
 9GM  Var_02    O7   P2   O5   P1  -173.25  30.0  3
 9GM  Var_03    P2   N5   P3   O8    85.46  30.0  2
 9GM  Var_04    O2   P1   O5   P2   125.23  30.0  3
 9GM  Var_05    H11  C7   O2   P1    51.52  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

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

