# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 02:49:17 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-amino-9-[(2S,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-3,9-dihydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2ncn([C@@H]3O[C@H](CO)[C@H]4O[P](O)(=O)O[C@@H]34)c2N1
#
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
 9K9  9K9  2-amino-9-[(2S,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-3,9-dihydro-6H-purin-6-one  ligand  35  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9K9
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
 9K9  O    O  O     0  -0.491  -5.3984   1.0623  -1.1033
 9K9  C2   C  CR6   0   0.420  -4.5037   0.5078  -0.4769
 9K9  C    C  CR56  0  -0.113  -3.1015   0.8363  -0.6176
 9K9  N3   N  N     0  -0.432  -2.4688   1.7646  -1.4042
 9K9  C4   C  CR15  0   0.096  -1.2089   1.6404  -1.1377
 9K9  N1   N  N     0  -0.537  -4.7779  -0.4887   0.4279
 9K9  C3   C  CR6   0   0.676  -3.8484  -1.1008   1.1102
 9K9  N4   N  NH2   0  -0.826  -4.1788  -2.0816   1.9577
 9K9  N    N  NR16  0  -0.737  -2.5119  -0.8225   1.0007
 9K9  C1   C  CR56  0   0.646  -2.1762   0.1584   0.1268
 9K9  N2   N  NR5   0  -0.534  -0.9611   0.6610  -0.1981
 9K9  C5   C  CR15  0   0.176   0.3348   0.2753   0.2944
 9K9  C6   C  CR15  0  -0.061   1.2385  -0.3395  -0.7935
 9K9  O3   O  O2    0  -0.583   1.7390  -1.6003  -0.3808
 9K9  O1   O  O     0  -0.476   0.9758   1.4327   0.7442
 9K9  C8   C  CR15  0  -0.007   2.3693   1.3393   0.4998
 9K9  C9   C  CH2   0  -0.155   2.9772   2.7183   0.4523
 9K9  O2   O  OH1   0  -0.664   2.8911   3.2999   1.7259
 9K9  C7   C  CR15  0  -0.037   2.4514   0.6011  -0.8378
 9K9  O4   O  O2    0  -0.581   3.6122  -0.1989  -0.9628
 9K9  P    P  P     0   1.458   3.3347  -1.7420  -0.5879
 9K9  O6   O  OH1   0  -0.715   3.5426  -2.4757  -1.9785
 9K9  O5   O  O     0  -0.666   4.0549  -2.3164   0.5570
 9K9  H1   H  HCR5  0   0.299  -0.4108   2.2235  -1.5716
 9K9  H2   H  HNH2  0   0.414  -5.1545  -2.2305   2.1480
 9K9  H3   H  HNH2  0   0.416  -3.5186  -2.4670   2.6106
 9K9  H4   H  HNR6  0   0.441  -1.8305  -1.3197   1.5563
 9K9  H5   H  HCR5  0   0.280   0.1918  -0.4541   1.0996
 9K9  H6   H  HCR5  0   0.320   0.7235  -0.4447  -1.7499
 9K9  H7   H  HCR5  0   0.263   2.8584   0.7448   1.2850
 9K9  H8   H  HCH2  0   0.219   4.0161   2.6056   0.1171
 9K9  H9   H  HCH2  0   0.208   2.4547   3.3093  -0.3125
 9K9  H10  H  HOH1  0   0.463   3.3329   4.1536   1.6965
 9K9  H11  H  HCR5  0   0.309   2.4067   1.2883  -1.6847
 9K9  H12  H  HOH1  0   0.509   3.9948  -3.3284  -1.9153

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
 9K9  O   C2   double    1.225  0.020  1.225
 9K9  N3  C    aromatic  1.372  0.020  1.372
 9K9  N3  C4   aromatic  1.294  0.020  1.294
 9K9  C2  C    single    1.447  0.020  1.447
 9K9  C2  N1   single    1.374  0.020  1.374
 9K9  C   C1   aromatic  1.367  0.020  1.367
 9K9  N1  C3   double    1.306  0.020  1.306
 9K9  C4  N2   aromatic  1.380  0.020  1.380
 9K9  C1  N2   aromatic  1.355  0.020  1.355
 9K9  C1  N    single    1.356  0.020  1.356
 9K9  N2  C5   single    1.439  0.020  1.439
 9K9  C3  N    single    1.370  0.020  1.370
 9K9  C3  N4   single    1.338  0.020  1.338
 9K9  O1  C5   single    1.397  0.020  1.397
 9K9  O1  C8   single    1.418  0.020  1.418
 9K9  C5  C6   single    1.542  0.020  1.542
 9K9  O2  C9   single    1.403  0.020  1.403
 9K9  C9  C8   single    1.508  0.020  1.508
 9K9  C8  C7   single    1.530  0.020  1.530
 9K9  C6  O3   single    1.418  0.020  1.418
 9K9  C6  C7   single    1.535  0.020  1.535
 9K9  O3  P    single    1.615  0.020  1.615
 9K9  C7  O4   single    1.415  0.020  1.415
 9K9  O4  P    single    1.612  0.020  1.612
 9K9  P   O5   double    1.469  0.020  1.469
 9K9  P   O6   single    1.586  0.020  1.586
 9K9  C4  H1   single    0.930  0.020  1.080
 9K9  N4  H2   single    0.860  0.020  1.020
 9K9  N4  H3   single    0.860  0.020  1.020
 9K9  N   H4   single    0.860  0.020  1.020
 9K9  C5  H5   single    0.970  0.020  1.090
 9K9  C6  H6   single    0.970  0.020  1.090
 9K9  C8  H7   single    0.970  0.020  1.090
 9K9  C9  H8   single    0.970  0.020  1.090
 9K9  C9  H9   single    0.970  0.020  1.090
 9K9  O2  H10  single    0.850  0.020  0.980
 9K9  C7  H11  single    0.970  0.020  1.090
 9K9  O6  H12  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
 9K9  N1   C2  C   114.97  3.000
 9K9  N1   C2  O   121.29  3.000
 9K9  C    C2  O   123.73  3.000
 9K9  C1   C   N3  109.61  3.000
 9K9  C1   C   C2  119.35  3.000
 9K9  N3   C   C2  131.03  3.000
 9K9  C4   N3  C   105.43  3.000
 9K9  H1   C4  N2  121.63  3.000
 9K9  H1   C4  N3  125.83  3.000
 9K9  N2   C4  N3  112.54  3.000
 9K9  C3   N1  C2  122.84  3.000
 9K9  N    C3  N4  116.15  3.000
 9K9  N4   C3  N1  119.94  3.000
 9K9  N    C3  N1  123.90  3.000
 9K9  H3   N4  H2  117.23  3.000
 9K9  H3   N4  C3  122.03  3.000
 9K9  H2   N4  C3  117.93  3.000
 9K9  H4   N   C1  122.92  3.000
 9K9  H4   N   C3  120.96  3.000
 9K9  C1   N   C3  116.11  3.000
 9K9  N2   C1  N   130.17  3.000
 9K9  N    C1  C   122.82  3.000
 9K9  N2   C1  C   107.01  3.000
 9K9  C5   N2  C1  128.78  3.000
 9K9  C5   N2  C4  125.81  3.000
 9K9  C1   N2  C4  105.40  3.000
 9K9  H5   C5  O1  112.00  3.000
 9K9  H5   C5  C6  109.23  3.000
 9K9  O1   C5  C6  106.76  3.000
 9K9  H5   C5  N2  108.21  3.000
 9K9  C6   C5  N2  113.15  3.000
 9K9  O1   C5  N2  107.54  3.000
 9K9  H6   C6  C7  113.99  3.000
 9K9  H6   C6  O3  109.63  3.000
 9K9  C7   C6  O3  105.91  3.000
 9K9  H6   C6  C5  112.34  3.000
 9K9  C7   C6  C5  103.83  3.000
 9K9  O3   C6  C5  110.86  3.000
 9K9  P    O3  C6  112.92  3.000
 9K9  C8   O1  C5  109.93  3.000
 9K9  H7   C8  C7  109.85  3.000
 9K9  H7   C8  C9  109.74  3.000
 9K9  C7   C8  C9  113.09  3.000
 9K9  H7   C8  O1  110.46  3.000
 9K9  C7   C8  O1  103.60  3.000
 9K9  C9   C8  O1  109.97  3.000
 9K9  H9   C9  H8  107.03  3.000
 9K9  H9   C9  O2  112.32  3.000
 9K9  H8   C9  O2  112.21  3.000
 9K9  H9   C9  C8  108.79  3.000
 9K9  H8   C9  C8  107.30  3.000
 9K9  O2   C9  C8  109.02  3.000
 9K9  H10  O2  C9  108.19  3.000
 9K9  H11  C7  O4  108.72  3.000
 9K9  H11  C7  C8  111.86  3.000
 9K9  O4   C7  C8  113.20  3.000
 9K9  H11  C7  C6  112.06  3.000
 9K9  O4   C7  C6  107.71  3.000
 9K9  C8   C7  C6  103.18  3.000
 9K9  P    O4  C7  112.29  3.000
 9K9  O5   P   O6  115.98  3.000
 9K9  O6   P   O4  102.50  3.000
 9K9  O5   P   O4  118.10  3.000
 9K9  O6   P   O3  106.41  3.000
 9K9  O5   P   O3  114.74  3.000
 9K9  O4   P   O3   96.65  3.000
 9K9  H12  O6  P   114.31  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
 9K9  CONST_01  N2  C4  N3  C     0.00   0.0  0
 9K9  CONST_02  C4  N2  C1  C     0.00   0.0  0
 9K9  CONST_03  N2  C1  C   N3    0.00   0.0  0
 9K9  CONST_04  C1  N2  C4  N3    0.00   0.0  0
 9K9  CONST_05  C1  C   N3  C4    0.00   0.0  0
 9K9  CONST_06  C5  N2  C1  C   180.00   0.0  0
 9K9  CONST_07  C5  N2  C4  N3  180.00   0.0  0
 9K9  CONST_08  C5  N2  C1  N     0.00   0.0  0
 9K9  CONST_09  N   C3  N1  C2    0.00   0.0  0
 9K9  CONST_10  C1  N   C3  N1    0.00   0.0  0
 9K9  CONST_11  N4  C3  N1  C2  180.00   0.0  0
 9K9  CONST_12  C1  N   C3  N4  180.00   0.0  0
 9K9  CONST_13  H1  C4  N3  C   180.00   0.0  0
 9K9  CONST_14  H4  N   C3  N1  180.00   0.0  0
 9K9  CONST_15  H2  N4  C3  N1    0.00   0.0  0
 9K9  CONST_16  H3  N4  C3  N1  180.00   0.0  0
 9K9  Var_01    O4  P   O3  C6    9.15  30.0  1

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
 9K9  chir_01  C5  N2  O1  C6  positiv
 9K9  chir_02  C6  O3  C7  C5  positiv
 9K9  chir_03  C8  O1  C9  C7  positiv
 9K9  chir_04  C7  O4  C6  C8  negativ
 9K9  chir_05  P   O4  O5  O6  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
 9K9  plan-1  O   0.020
 9K9  plan-1  C2  0.020
 9K9  plan-1  C   0.020
 9K9  plan-1  N3  0.020
 9K9  plan-1  C4  0.020
 9K9  plan-1  N1  0.020
 9K9  plan-1  C3  0.020
 9K9  plan-1  N4  0.020
 9K9  plan-1  N   0.020
 9K9  plan-1  C1  0.020
 9K9  plan-1  N2  0.020
 9K9  plan-1  C5  0.020
 9K9  plan-1  H1  0.020
 9K9  plan-1  H2  0.020
 9K9  plan-1  H3  0.020
 9K9  plan-1  H4  0.020

