# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 22 03:00:01 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 9-{5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-beta-L-ribofuranosyl}-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[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
 ANK  ANK  9-{5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-beta-L-ribofuranosyl}-9H-purin-6-amine  ligand  44  31  .  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_ANK
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
 ANK  N1    N  N      0  -0.452  -7.1554   2.0298   0.8450
 ANK  C2    C  CR16   0   0.048  -7.1360   1.2263  -0.2156
 ANK  N3    N  N      0  -0.499  -6.1120   0.5698  -0.7312
 ANK  C4    C  CR56   0   0.415  -4.9874   0.7931  -0.0505
 ANK  C5    C  CR56   0  -0.016  -4.8502   1.6089   1.0620
 ANK  C6    C  CR6    0   0.461  -6.0193   2.2452   1.5177
 ANK  N6    N  NH2    0  -0.782  -6.0345   3.0422   2.5885
 ANK  N7    N  N      0  -0.358  -3.5494   1.6361   1.4869
 ANK  C8    C  CR15   0   0.068  -2.9155   0.8569   0.6559
 ANK  N9    N  NR5    0  -0.546  -3.7376   0.2995  -0.2890
 ANK  PA    P  P      0   1.344   1.1436  -0.5471   0.9715
 ANK  PB    P  P      0   1.247   3.5555   0.8798   0.1171
 ANK  PG    P  P      0   1.135   6.3561   0.7605  -1.0273
 ANK  C1'   C  CH1    0   0.183  -3.3538  -0.5576  -1.4134
 ANK  O1A   O  O      0  -0.787   0.3177   0.7092   0.9875
 ANK  O1B   O  O      0  -0.716   3.2134   1.8182  -1.0029
 ANK  O1G   O  OP    -1  -0.949   6.0556   0.7709  -2.5232
 ANK  C2'   C  CH1    0   0.043  -4.0865  -1.8957  -1.3718
 ANK  O2'   O  OH1    0  -0.643  -4.0731  -2.4191  -2.6722
 ANK  O2A   O  OP    -1  -0.967   1.4550  -1.2355   2.2671
 ANK  O2B   O  OP    -1  -0.955   3.5146   1.3739   1.5399
 ANK  O2G   O  O      0  -0.938   6.4985   2.1541  -0.4132
 ANK  C3'   C  CH1    0  -0.009  -3.1677  -2.6989  -0.4461
 ANK  O3'   O  OH1    0  -0.703  -3.2276  -4.0832  -0.6557
 ANK  O3A   O  O2     0  -0.666   2.4556  -0.4007   0.0385
 ANK  N3B   N  NH1    0  -0.935   4.9360   0.0115  -0.2604
 ANK  O3G   O  OP    -1  -0.961   7.4665  -0.2121  -0.6199
 ANK  C4'   C  CH1    0  -0.055  -1.7830  -2.1693  -0.8193
 ANK  O4'   O  O2     0  -0.480  -1.9982  -0.8506  -1.3266
 ANK  C5'   C  CH2    0  -0.143  -0.8339  -2.1501   0.3576
 ANK  O5'   O  O2     0  -0.545   0.4167  -1.6446  -0.0392
 ANK  H2    H  HCR6   0   0.269  -8.0884   1.0960  -0.7187
 ANK  HN6   H  HNH2   0   0.392  -6.8729   3.5365   2.8401
 ANK  HN6A  H  HNH2   0   0.423  -5.1879   3.2574   3.0848
 ANK  H8    H  HCR5   0   0.274  -1.8474   0.6735   0.6787
 ANK  H1'   H  HCH1   0   0.242  -3.5581  -0.0085  -2.3363
 ANK  H2'   H  HCH1   0   0.252  -5.1053  -1.8056  -0.9812
 ANK  HO2'  H  HOH1   0   0.465  -4.0344  -3.3809  -2.5992
 ANK  H3'   H  HCH1   0   0.246  -3.4004  -2.4438   0.5959
 ANK  HO3'  H  HOH1   0   0.434  -3.9692  -4.4402  -0.1565
 ANK  HN3B  H  HNH1   0   0.344   5.2173  -0.6139   0.4847
 ANK  H4'   H  HCH1   0   0.283  -1.3584  -2.7810  -1.6244
 ANK  H5'   H  HCH2   0   0.250  -1.2852  -1.5675   1.1705
 ANK  H5'A  H  HCH2   0   0.286  -0.7350  -3.1782   0.7268

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
 ANK  N1   C2    aromatic  1.331  0.020  1.331
 ANK  N1   C6    aromatic  1.338  0.020  1.338
 ANK  C2   N3    aromatic  1.321  0.020  1.321
 ANK  N3   C4    aromatic  1.333  0.020  1.333
 ANK  C4   C5    aromatic  1.386  0.020  1.386
 ANK  C4   N9    aromatic  1.365  0.020  1.365
 ANK  C5   C6    aromatic  1.407  0.020  1.407
 ANK  C5   N7    aromatic  1.369  0.020  1.369
 ANK  C6   N6    single    1.335  0.020  1.335
 ANK  N7   C8    aromatic  1.304  0.020  1.304
 ANK  C8   N9    aromatic  1.371  0.020  1.371
 ANK  N9   C1'   single    1.465  0.020  1.465
 ANK  PA   O1A   deloc     1.504  0.020  1.504
 ANK  PA   O2A   deloc     1.500  0.020  1.500
 ANK  PA   O3A   single    1.617  0.020  1.617
 ANK  PA   O5'   single    1.660  0.020  1.660
 ANK  PB   O1B   deloc     1.501  0.020  1.501
 ANK  PB   O2B   deloc     1.507  0.020  1.507
 ANK  PB   O3A   single    1.690  0.020  1.690
 ANK  PB   N3B   single    1.674  0.020  1.674
 ANK  PG   O1G   deloc     1.526  0.020  1.526
 ANK  PG   O2G   deloc     1.530  0.020  1.530
 ANK  PG   N3B   single    1.779  0.020  1.779
 ANK  PG   O3G   deloc     1.531  0.020  1.531
 ANK  C1'  C2'   single    1.526  0.020  1.526
 ANK  C1'  O4'   single    1.390  0.020  1.390
 ANK  C2'  O2'   single    1.402  0.020  1.402
 ANK  C2'  C3'   single    1.532  0.020  1.532
 ANK  C3'  O3'   single    1.401  0.020  1.401
 ANK  C3'  C4'   single    1.529  0.020  1.529
 ANK  C4'  O4'   single    1.429  0.020  1.429
 ANK  C4'  C5'   single    1.512  0.020  1.512
 ANK  C5'  O5'   single    1.406  0.020  1.406
 ANK  C2   H2    single    0.930  0.020  1.080
 ANK  N6   HN6   single    0.860  0.020  1.020
 ANK  N6   HN6A  single    0.860  0.020  1.020
 ANK  C8   H8    single    0.930  0.020  1.080
 ANK  C1'  H1'   single    0.970  0.020  1.090
 ANK  C2'  H2'   single    0.970  0.020  1.090
 ANK  O2'  HO2'  single    0.850  0.020  0.980
 ANK  C3'  H3'   single    0.970  0.020  1.090
 ANK  O3'  HO3'  single    0.850  0.020  0.980
 ANK  N3B  HN3B  single    0.890  0.020  1.040
 ANK  C4'  H4'   single    0.970  0.020  1.090
 ANK  C5'  H5'   single    0.970  0.020  1.090
 ANK  C5'  H5'A  single    0.970  0.020  1.090

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
 ANK  C6    N1   C2   119.05  3.000
 ANK  H2    C2   N3   116.09  3.000
 ANK  H2    C2   N1   115.42  3.000
 ANK  N3    C2   N1   128.49  3.000
 ANK  C4    N3   C2   111.79  3.000
 ANK  N9    C4   C5   105.21  3.000
 ANK  N9    C4   N3   128.51  3.000
 ANK  C5    C4   N3   126.27  3.000
 ANK  N7    C5   C6   132.86  3.000
 ANK  N7    C5   C4   110.79  3.000
 ANK  C6    C5   C4   116.35  3.000
 ANK  N6    C6   C5   122.64  3.000
 ANK  N6    C6   N1   119.32  3.000
 ANK  C5    C6   N1   118.04  3.000
 ANK  HN6A  N6   HN6  118.28  3.000
 ANK  HN6A  N6   C6   120.96  3.000
 ANK  HN6   N6   C6   120.25  3.000
 ANK  C8    N7   C5   104.61  3.000
 ANK  H8    C8   N9   122.45  3.000
 ANK  H8    C8   N7   124.53  3.000
 ANK  N9    C8   N7   113.01  3.000
 ANK  C1'   N9   C8   127.58  3.000
 ANK  C1'   N9   C4   125.85  3.000
 ANK  C8    N9   C4   106.36  3.000
 ANK  O5'   PA   O3A   93.66  3.000
 ANK  O5'   PA   O2A  108.27  3.000
 ANK  O3A   PA   O2A  111.81  3.000
 ANK  O5'   PA   O1A  108.57  3.000
 ANK  O3A   PA   O1A  112.10  3.000
 ANK  O2A   PA   O1A  119.23  3.000
 ANK  N3B   PB   O3A   97.65  3.000
 ANK  N3B   PB   O2B  113.92  3.000
 ANK  O3A   PB   O2B  105.95  3.000
 ANK  N3B   PB   O1B  110.12  3.000
 ANK  O3A   PB   O1B  106.90  3.000
 ANK  O2B   PB   O1B  119.58  3.000
 ANK  O3G   PG   N3B  101.35  3.000
 ANK  O3G   PG   O2G  113.85  3.000
 ANK  N3B   PG   O2G  106.54  3.000
 ANK  O3G   PG   O1G  114.08  3.000
 ANK  N3B   PG   O1G  105.56  3.000
 ANK  O2G   PG   O1G  113.94  3.000
 ANK  H1'   C1'  O4'  109.94  3.000
 ANK  H1'   C1'  C2'  111.95  3.000
 ANK  O4'   C1'  C2'  106.37  3.000
 ANK  H1'   C1'  N9   107.76  3.000
 ANK  O4'   C1'  N9   109.32  3.000
 ANK  C2'   C1'  N9   111.49  3.000
 ANK  H2'   C2'  C3'  112.69  3.000
 ANK  H2'   C2'  O2'  111.75  3.000
 ANK  C3'   C2'  O2'  111.05  3.000
 ANK  H2'   C2'  C1'  112.60  3.000
 ANK  C3'   C2'  C1'  100.85  3.000
 ANK  O2'   C2'  C1'  107.31  3.000
 ANK  HO2'  O2'  C2'  107.59  3.000
 ANK  H3'   C3'  C4'  110.08  3.000
 ANK  H3'   C3'  O3'  111.25  3.000
 ANK  C4'   C3'  O3'  110.15  3.000
 ANK  H3'   C3'  C2'  108.95  3.000
 ANK  C4'   C3'  C2'  102.36  3.000
 ANK  O3'   C3'  C2'  113.70  3.000
 ANK  HO3'  O3'  C3'  108.77  3.000
 ANK  PB    O3A  PA   124.75  3.000
 ANK  HN3B  N3B  PG   110.82  3.000
 ANK  HN3B  N3B  PB   112.56  3.000
 ANK  PG    N3B  PB   122.48  3.000
 ANK  H4'   C4'  C5'  109.60  3.000
 ANK  H4'   C4'  O4'  108.21  3.000
 ANK  C5'   C4'  O4'  111.05  3.000
 ANK  H4'   C4'  C3'  109.67  3.000
 ANK  C5'   C4'  C3'  112.51  3.000
 ANK  O4'   C4'  C3'  105.66  3.000
 ANK  C4'   O4'  C1'  111.32  3.000
 ANK  H5'A  C5'  H5'  106.58  3.000
 ANK  H5'A  C5'  O5'  110.60  3.000
 ANK  H5'   C5'  O5'  112.58  3.000
 ANK  H5'A  C5'  C4'  107.86  3.000
 ANK  H5'   C5'  C4'  108.98  3.000
 ANK  O5'   C5'  C4'  110.07  3.000
 ANK  C5'   O5'  PA   117.10  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
 ANK  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 ANK  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 ANK  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 ANK  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 ANK  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 ANK  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 ANK  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 ANK  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 ANK  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 ANK  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 ANK  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 ANK  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 ANK  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 ANK  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 ANK  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 ANK  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 ANK  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 ANK  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 ANK  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 ANK  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 ANK  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 ANK  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 ANK  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 ANK  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 ANK  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 ANK  CONST_26  HN6   N6   C6   N1     0.00   0.0  0
 ANK  CONST_27  HN6A  N6   C6   N1   180.00   0.0  0
 ANK  Var_01    C4'   C5'  O5'  PA   135.95  30.0  1
 ANK  Var_02    O1B   PB   O3A  PA  -100.01  30.0  1
 ANK  Var_03    O1A   PA   O3A  PB    49.87  30.0  1
 ANK  Var_04    O1G   PG   N3B  PB   -83.71  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
 ANK  chir_03  C1'  N9   C2'  O4'  positiv
 ANK  chir_04  C2'  O2'  C3'  C1'  negativ
 ANK  chir_05  C3'  O3'  C4'  C2'  negativ
 ANK  chir_06  C4'  O4'  C3'  C5'  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
 ANK  plan-1  N1    0.020
 ANK  plan-1  C2    0.020
 ANK  plan-1  N3    0.020
 ANK  plan-1  C4    0.020
 ANK  plan-1  C5    0.020
 ANK  plan-1  C6    0.020
 ANK  plan-1  N6    0.020
 ANK  plan-1  N7    0.020
 ANK  plan-1  C8    0.020
 ANK  plan-1  N9    0.020
 ANK  plan-1  C1'   0.020
 ANK  plan-1  H2    0.020
 ANK  plan-1  H8    0.020
 ANK  plan-2  C6    0.020
 ANK  plan-2  N6    0.020
 ANK  plan-2  HN6   0.020
 ANK  plan-2  HN6A  0.020

