# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 12:06:13 2021
#   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  48  31  .  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_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  -0.473  -28.9957  24.7614  22.0742
 ANK  C2    C  CR16  0   0.045  -27.7649  24.2926  21.8888
 ANK  N3    N  N     0  -0.457  -27.3925  23.0655  21.5708
 ANK  C4    C  CR56  0   0.501  -28.4350  22.2476  21.4365
 ANK  C5    C  CR56  0  -0.005  -29.7678  22.5901  21.6023
 ANK  C6    C  CR6   0   0.459  -30.0345  23.9301  21.9395
 ANK  N6    N  NH2   0  -0.816  -31.2710  24.3894  22.1374
 ANK  N7    N  N     0  -0.453  -30.5847  21.5085  21.3918
 ANK  C8    C  CR15  0   0.115  -29.7661  20.5433  21.1050
 ANK  N9    N  NR5   0  -0.545  -28.4486  20.9154  21.1210
 ANK  PA    P  P     0   1.449  -24.3196  22.5044  17.2352
 ANK  PB    P  P     0   1.476  -21.6575  23.7504  16.8109
 ANK  PG    P  P     0   1.452  -22.3803  23.8029  13.8691
 ANK  C1'   C  CR15  0   0.218  -27.3402  20.0555  20.8003
 ANK  O1A   O  O     0  -0.680  -24.0075  21.1905  16.6504
 ANK  O1B   O  O     0  -0.662  -20.8060  24.6220  17.6335
 ANK  O1G   O  OH1   0  -0.760  -23.8833  23.2371  13.9453
 ANK  C2'   C  CR15  0  -0.029  -26.2351  20.0332  21.8568
 ANK  O2'   O  OH1   0  -0.656  -26.5874  19.1560  22.8789
 ANK  O2A   O  OH1   0  -0.734  -25.1985  23.5055  16.3843
 ANK  O2B   O  OH1   0  -0.727  -21.1321  22.3203  16.3827
 ANK  O2G   O  O     0  -0.683  -21.3534  22.8227  13.4738
 ANK  C3'   C  CR15  0  -0.039  -25.0250  19.6406  21.0087
 ANK  O3'   O  OH1   0  -0.665  -25.0663  18.2524  20.8141
 ANK  O3A   O  O2    0  -0.694  -22.9794  23.3396  17.6409
 ANK  N3B   N  NH1   0  -0.974  -22.1802  24.4701  15.3953
 ANK  O3G   O  OH1   0  -0.724  -22.5816  25.0806  12.9436
 ANK  C4'   C  CR15  0  -0.045  -25.3158  20.4122  19.7179
 ANK  O4'   O  O     0  -0.486  -26.7355  20.4812  19.6108
 ANK  C5'   C  CH2   0  -0.208  -24.7110  21.8030  19.7412
 ANK  O5'   O  O2    0  -0.562  -25.1224  22.5640  18.5962
 ANK  H2    H  HCR6  0   0.253  -26.9658  25.0149  22.0154
 ANK  HN6   H  HNH2  0   0.404  -31.4255  25.3677  22.3106
 ANK  HN6A  H  HNH2  0   0.411  -32.0716  23.8048  21.9733
 ANK  H8    H  HCR5  0   0.302  -30.0514  19.5275  20.8725
 ANK  H1'   H  HCR5  0   0.261  -27.7648  19.0509  20.6869
 ANK  HO1G  H  HOH1  0   0.515  -24.1055  22.5732  13.2757
 ANK  H2'   H  HCR5  0   0.262  -26.0732  21.0495  22.2336
 ANK  HO2'  H  HOH1  0   0.464  -26.0049  19.3074  23.6294
 ANK  HO2A  H  HOH1  0   0.512  -24.9941  23.4702  15.4296
 ANK  HO2B  H  HOH1  0   0.505  -20.3352  22.3139  15.8330
 ANK  H3'   H  HCR5  0   0.256  -24.0788  19.9583  21.4659
 ANK  HO3'  H  HOH1  0   0.458  -24.3473  18.0063  20.2233
 ANK  HN3B  H  HNH1  0   0.454  -22.4156  25.4538  15.4856
 ANK  HO3G  H  HOH1  0   0.508  -21.7584  25.4813  12.6306
 ANK  H4'   H  HCR5  0   0.268  -24.9304  19.8689  18.8498
 ANK  H5'   H  HCH2  0   0.275  -25.0554  22.3724  20.6025
 ANK  H5'A  H  HCH2  0   0.256  -23.6219  21.7254  19.7970

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  1.330  0.020  1.330
 ANK  N1   C6    aromatic  1.337  0.020  1.337
 ANK  C2   N3    aromatic  1.321  0.020  1.321
 ANK  N3   C4    aromatic  1.332  0.020  1.332
 ANK  C4   C5    aromatic  1.386  0.020  1.386
 ANK  C4   N9    aromatic  1.369  0.020  1.369
 ANK  C5   C6    aromatic  1.407  0.020  1.407
 ANK  C5   N7    aromatic  1.372  0.020  1.372
 ANK  C6   N6    single    1.334  0.020  1.334
 ANK  N7   C8    aromatic  1.298  0.020  1.298
 ANK  C8   N9    aromatic  1.369  0.020  1.369
 ANK  N9   C1'   single    1.439  0.020  1.439
 ANK  PA   O1A   double    1.472  0.020  1.472
 ANK  PA   O2A   single    1.581  0.020  1.581
 ANK  PA   O3A   single    1.630  0.020  1.630
 ANK  PA   O5'   single    1.581  0.020  1.581
 ANK  PB   O1B   double    1.470  0.020  1.470
 ANK  PB   O2B   single    1.583  0.020  1.583
 ANK  PB   O3A   single    1.614  0.020  1.614
 ANK  PB   N3B   single    1.672  0.020  1.672
 ANK  PG   O1G   single    1.608  0.020  1.608
 ANK  PG   O2G   double    1.474  0.020  1.474
 ANK  PG   N3B   single    1.678  0.020  1.678
 ANK  PG   O3G   single    1.590  0.020  1.590
 ANK  C1'  C2'   single    1.529  0.020  1.529
 ANK  C1'  O4'   single    1.401  0.020  1.401
 ANK  C2'  O2'   single    1.392  0.020  1.392
 ANK  C2'  C3'   single    1.529  0.020  1.529
 ANK  C3'  O3'   single    1.402  0.020  1.402
 ANK  C3'  C4'   single    1.532  0.020  1.532
 ANK  C4'  O4'   single    1.425  0.020  1.425
 ANK  C4'  C5'   single    1.517  0.020  1.517
 ANK  C5'  O5'   single    1.435  0.020  1.435
 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  O1G  HO1G  single    0.850  0.020  0.980
 ANK  C2'  H2'   single    0.970  0.020  1.090
 ANK  O2'  HO2'  single    0.850  0.020  0.980
 ANK  O2A  HO2A  single    0.850  0.020  0.980
 ANK  O2B  HO2B  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    0.860  0.020  1.020
 ANK  O3G  HO3G  single    0.850  0.020  0.980
 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   119.06  3.000
 ANK  H2    C2   N3   116.04  3.000
 ANK  H2    C2   N1   115.52  3.000
 ANK  N3    C2   N1   128.44  3.000
 ANK  C4    N3   C2   111.97  3.000
 ANK  N9    C4   C5   104.97  3.000
 ANK  N9    C4   N3   128.95  3.000
 ANK  C5    C4   N3   126.07  3.000
 ANK  N7    C5   C6   132.43  3.000
 ANK  N7    C5   C4   111.07  3.000
 ANK  C6    C5   C4   116.50  3.000
 ANK  N6    C6   C5   122.63  3.000
 ANK  N6    C6   N1   119.42  3.000
 ANK  C5    C6   N1   117.95  3.000
 ANK  HN6A  N6   HN6  118.15  3.000
 ANK  HN6A  N6   C6   120.93  3.000
 ANK  HN6   N6   C6   120.20  3.000
 ANK  C8    N7   C5   104.17  3.000
 ANK  H8    C8   N9   120.81  3.000
 ANK  H8    C8   N7   125.47  3.000
 ANK  N9    C8   N7   113.72  3.000
 ANK  C1'   N9   C8   125.18  3.000
 ANK  C1'   N9   C4   128.69  3.000
 ANK  C8    N9   C4   106.07  3.000
 ANK  O5'   PA   O3A  100.59  3.000
 ANK  O5'   PA   O2A   99.04  3.000
 ANK  O3A   PA   O2A  105.46  3.000
 ANK  O5'   PA   O1A  118.91  3.000
 ANK  O3A   PA   O1A  112.46  3.000
 ANK  O2A   PA   O1A  118.00  3.000
 ANK  N3B   PB   O3A  106.79  3.000
 ANK  N3B   PB   O2B  105.29  3.000
 ANK  O3A   PB   O2B  100.43  3.000
 ANK  N3B   PB   O1B  113.56  3.000
 ANK  O3A   PB   O1B  109.73  3.000
 ANK  O2B   PB   O1B  119.66  3.000
 ANK  O3G   PG   N3B  103.00  3.000
 ANK  O3G   PG   O2G  117.80  3.000
 ANK  N3B   PG   O2G  115.18  3.000
 ANK  O3G   PG   O1G  101.07  3.000
 ANK  N3B   PG   O1G  102.02  3.000
 ANK  O2G   PG   O1G  115.47  3.000
 ANK  H1'   C1'  O4'  110.97  3.000
 ANK  H1'   C1'  C2'  109.75  3.000
 ANK  O4'   C1'  C2'  106.21  3.000
 ANK  H1'   C1'  N9   105.80  3.000
 ANK  O4'   C1'  N9   109.89  3.000
 ANK  C2'   C1'  N9   114.29  3.000
 ANK  HO1G  O1G  PG   115.01  3.000
 ANK  H2'   C2'  C3'  108.17  3.000
 ANK  H2'   C2'  O2'  111.68  3.000
 ANK  C3'   C2'  O2'  116.47  3.000
 ANK  H2'   C2'  C1'  109.32  3.000
 ANK  C3'   C2'  C1'  101.10  3.000
 ANK  O2'   C2'  C1'  109.49  3.000
 ANK  HO2'  O2'  C2'  108.68  3.000
 ANK  HO2A  O2A  PA   112.75  3.000
 ANK  HO2B  O2B  PB   115.65  3.000
 ANK  H3'   C3'  C4'  111.64  3.000
 ANK  H3'   C3'  O3'  111.69  3.000
 ANK  C4'   C3'  O3'  112.10  3.000
 ANK  H3'   C3'  C2'  112.14  3.000
 ANK  C4'   C3'  C2'  100.83  3.000
 ANK  O3'   C3'  C2'  107.93  3.000
 ANK  HO3'  O3'  C3'  108.44  3.000
 ANK  PB    O3A  PA   132.50  3.000
 ANK  HN3B  N3B  PG   116.01  3.000
 ANK  HN3B  N3B  PB   114.46  3.000
 ANK  PG    N3B  PB   129.52  3.000
 ANK  HO3G  O3G  PG   114.42  3.000
 ANK  H4'   C4'  C5'  109.09  3.000
 ANK  H4'   C4'  O4'  108.37  3.000
 ANK  C5'   C4'  O4'  110.73  3.000
 ANK  H4'   C4'  C3'  110.58  3.000
 ANK  C5'   C4'  C3'  111.92  3.000
 ANK  O4'   C4'  C3'  106.07  3.000
 ANK  C4'   O4'  C1'  110.58  3.000
 ANK  H5'A  C5'  H5'  108.18  3.000
 ANK  H5'A  C5'  O5'  111.35  3.000
 ANK  H5'   C5'  O5'  105.27  3.000
 ANK  H5'A  C5'  C4'  109.44  3.000
 ANK  H5'   C5'  C4'  111.45  3.000
 ANK  O5'   C5'  C4'  111.08  3.000
 ANK  C5'   O5'  PA   121.41  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  -87.64  30.0  2
 ANK  Var_02    O1B   PB   O3A  PA  174.67  30.0  2
 ANK  Var_03    O1A   PA   O3A  PB   53.12  30.0  2
 ANK  Var_04    O1G   PG   N3B  PB   87.58  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
 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
 ANK  chir_07  PA   O2A  O3A  O5'  both
 ANK  chir_08  PB   O2B  O1B  N3B  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
 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

