# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 01:16:15 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: [[[[(2S,3R,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]amino]phosphonic acid
#   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
 A0P  A0P  '[[[[(2S,3R,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]amino]phosphonic acid'  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_A0P
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
 A0P  N1    N  N     0  -0.474  62.6422  -33.0954  12.7667
 A0P  C2    C  CR16  0   0.047  62.6972  -33.4498  11.4860
 A0P  N3    N  N     0  -0.457  61.6962  -33.6812  10.6541
 A0P  C4    C  CR56  0   0.493  60.5169  -33.5158  11.2464
 A0P  C5    C  CR56  0  -0.011  60.2997  -33.1489  12.5641
 A0P  C6    C  CR6   0   0.461  61.4480  -32.9334  13.3483
 A0P  N6    N  NH2   0  -0.816  61.3908  -32.5865  14.6346
 A0P  N7    N  N     0  -0.448  58.9565  -33.0643  12.8320
 A0P  C8    C  CR15  0   0.112  58.3820  -33.3748  11.7098
 A0P  N9    N  NR5   0  -0.542  59.2698  -33.6660  10.7072
 A0P  PA    P  P     0   1.473  55.6778  -30.7618   6.4852
 A0P  PB    P  P     0   1.475  53.9034  -31.8608   4.4139
 A0P  PG    P  P     0   1.455  53.4740  -34.7433   4.9217
 A0P  C1'   C  CR15  0   0.199  58.9684  -33.9973   9.3434
 A0P  O1A   O  O     0  -0.692  54.6839  -31.2215   7.4744
 A0P  O1B   O  OH1   0  -0.722  52.7467  -30.8501   4.8141
 A0P  O1G   O  OH1   0  -0.730  53.0375  -35.4796   6.2652
 A0P  C2'   C  CR15  0  -0.031  58.0579  -35.2060   9.1745
 A0P  O2'   O  OH1   0  -0.652  58.8005  -36.3761   9.3112
 A0P  O2A   O  OH1   0  -0.701  55.9864  -29.2162   6.3989
 A0P  O2B   O  O     0  -0.665  54.0824  -32.2264   3.0020
 A0P  O2G   O  OH1   0  -0.745  55.0101  -35.1844   4.7994
 A0P  C3'   C  CR15  0  -0.032  57.4717  -34.9322   7.7981
 A0P  O3'   O  OH1   0  -0.663  56.2982  -35.6625   7.6033
 A0P  O3A   O  O2    0  -0.694  55.2644  -31.1526   4.9665
 A0P  N3B   N  NH1   0  -0.981  53.6078  -33.1437   5.4239
 A0P  O3G   O  O     0  -0.683  52.6477  -34.9670   3.7237
 A0P  C4'   C  CR15  0  -0.017  57.2745  -33.4108   7.8671
 A0P  O4'   O  O     0  -0.488  58.2954  -32.9235   8.7348
 A0P  C5'   C  CH2   0  -0.222  57.3956  -32.7518   6.5135
 A0P  O5'   O  O2    0  -0.562  57.1509  -31.3389   6.5784
 A0P  H2    H  HCR6  0   0.253  63.6952  -33.5618  11.0760
 A0P  HN6   H  HNH2  0   0.404  62.2357  -32.3819  15.1400
 A0P  HN6A  H  HNH2  0   0.412  60.5119  -32.3945  15.0821
 A0P  H8    H  HCR5  0   0.302  57.3145  -33.4061  11.5496
 A0P  H1'   H  HCR5  0   0.268  59.9321  -34.1893   8.8575
 A0P  HO1B  H  HOH1  0   0.509  52.7665  -29.9985   4.3536
 A0P  HO1G  H  HOH1  0   0.506  52.0858  -35.4628   6.4379
 A0P  H2'   H  HCR5  0   0.246  57.2357  -35.1554   9.9053
 A0P  HO2'  H  HOH1  0   0.465  58.1969  -37.1249   9.3393
 A0P  HO2A  H  HOH1  0   0.516  55.4420  -28.6679   6.9818
 A0P  HO2G  H  HOH1  0   0.508  55.1538  -35.9587   4.2361
 A0P  H3'   H  HCR5  0   0.240  58.2315  -35.1720   7.0388
 A0P  HO3'  H  HOH1  0   0.458  56.0696  -35.6685   6.6676
 A0P  HN3B  H  HNH1  0   0.447  53.5219  -32.9541   6.4184
 A0P  H4'   H  HCR5  0   0.258  56.2930  -33.1991   8.3068
 A0P  H5'   H  HCH2  0   0.280  58.4088  -32.8631   6.1274
 A0P  H5'A  H  HCH2  0   0.242  56.7214  -33.2344   5.8001

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
 A0P  C2   N1    aromatic  1.330  0.020  1.330
 A0P  C6   N1    aromatic  1.338  0.020  1.338
 A0P  N3   C2    aromatic  1.322  0.020  1.322
 A0P  C2   H2    single    0.930  0.020  1.080
 A0P  C4   N3    aromatic  1.330  0.020  1.330
 A0P  N9   C4    aromatic  1.367  0.020  1.367
 A0P  C4   C5    aromatic  1.385  0.020  1.385
 A0P  N7   C5    aromatic  1.372  0.020  1.372
 A0P  C5   C6    aromatic  1.407  0.020  1.407
 A0P  C6   N6    single    1.334  0.020  1.334
 A0P  N6   HN6   single    0.860  0.020  1.020
 A0P  N6   HN6A  single    0.860  0.020  1.020
 A0P  C8   N7    aromatic  1.298  0.020  1.298
 A0P  N9   C8    aromatic  1.370  0.020  1.370
 A0P  C8   H8    single    0.930  0.020  1.080
 A0P  C1'  N9    single    1.435  0.020  1.435
 A0P  O3A  PA    single    1.622  0.020  1.622
 A0P  O5'  PA    single    1.585  0.020  1.585
 A0P  PA   O1A   double    1.476  0.020  1.476
 A0P  PA   O2A   single    1.578  0.020  1.578
 A0P  O2B  PB    double    1.469  0.020  1.469
 A0P  PB   N3B   single    1.659  0.020  1.659
 A0P  PB   O1B   single    1.587  0.020  1.587
 A0P  PB   O3A   single    1.631  0.020  1.631
 A0P  O3G  PG    double    1.472  0.020  1.472
 A0P  PG   O2G   single    1.603  0.020  1.603
 A0P  PG   O1G   single    1.593  0.020  1.593
 A0P  PG   N3B   single    1.682  0.020  1.682
 A0P  O4'  C1'   single    1.406  0.020  1.406
 A0P  C1'  C2'   single    1.523  0.020  1.523
 A0P  C1'  H1'   single    0.970  0.020  1.090
 A0P  O1B  HO1B  single    0.850  0.020  0.980
 A0P  O1G  HO1G  single    0.850  0.020  0.980
 A0P  C3'  C2'   single    1.521  0.020  1.521
 A0P  O2'  C2'   single    1.393  0.020  1.393
 A0P  C2'  H2'   single    0.970  0.020  1.090
 A0P  O2'  HO2'  single    0.850  0.020  0.980
 A0P  O2A  HO2A  single    0.850  0.020  0.980
 A0P  O2G  HO2G  single    0.850  0.020  0.980
 A0P  C4'  C3'   single    1.536  0.020  1.536
 A0P  C3'  O3'   single    1.396  0.020  1.396
 A0P  C3'  H3'   single    0.970  0.020  1.090
 A0P  O3'  HO3'  single    0.850  0.020  0.980
 A0P  N3B  HN3B  single    0.860  0.020  1.020
 A0P  C5'  C4'   single    1.510  0.020  1.510
 A0P  C4'  O4'   single    1.426  0.020  1.426
 A0P  C4'  H4'   single    0.970  0.020  1.090
 A0P  C5'  O5'   single    1.435  0.020  1.435
 A0P  C5'  H5'   single    0.970  0.020  1.090
 A0P  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
 A0P  C6    N1   C2   119.19  3.000
 A0P  H2    C2   N3   116.15  3.000
 A0P  H2    C2   N1   115.44  3.000
 A0P  N3    C2   N1   128.42  3.000
 A0P  C4    N3   C2   111.67  3.000
 A0P  N9    C4   C5   105.15  3.000
 A0P  C5    C4   N3   126.56  3.000
 A0P  N9    C4   N3   128.29  3.000
 A0P  N7    C5   C6   132.89  3.000
 A0P  C6    C5   C4   116.29  3.000
 A0P  N7    C5   C4   110.83  3.000
 A0P  N6    C6   C5   122.85  3.000
 A0P  N6    C6   N1   119.27  3.000
 A0P  C5    C6   N1   117.88  3.000
 A0P  HN6A  N6   HN6  118.18  3.000
 A0P  HN6A  N6   C6   121.12  3.000
 A0P  HN6   N6   C6   120.12  3.000
 A0P  C8    N7   C5   104.46  3.000
 A0P  H8    C8   N9   121.71  3.000
 A0P  H8    C8   N7   124.93  3.000
 A0P  N9    C8   N7   113.36  3.000
 A0P  C1'   N9   C8   127.45  3.000
 A0P  C1'   N9   C4   126.28  3.000
 A0P  C8    N9   C4   106.21  3.000
 A0P  O5'   PA   O3A  101.78  3.000
 A0P  O5'   PA   O2A  100.26  3.000
 A0P  O3A   PA   O2A  103.56  3.000
 A0P  O2A   PA   O1A  118.25  3.000
 A0P  O5'   PA   O1A  118.24  3.000
 A0P  O3A   PA   O1A  112.39  3.000
 A0P  N3B   PB   O3A  106.15  3.000
 A0P  O3A   PB   O2B  109.39  3.000
 A0P  N3B   PB   O2B  114.47  3.000
 A0P  O3A   PB   O1B  104.25  3.000
 A0P  N3B   PB   O1B  102.06  3.000
 A0P  O2B   PB   O1B  119.31  3.000
 A0P  O3G   PG   N3B  115.60  3.000
 A0P  N3B   PG   O2G  102.02  3.000
 A0P  O3G   PG   O2G  115.72  3.000
 A0P  N3B   PG   O1G  102.10  3.000
 A0P  O2G   PG   O1G  101.52  3.000
 A0P  O3G   PG   O1G  117.53  3.000
 A0P  H1'   C1'  O4'  111.27  3.000
 A0P  H1'   C1'  C2'  109.73  3.000
 A0P  O4'   C1'  C2'  105.78  3.000
 A0P  H1'   C1'  N9   106.08  3.000
 A0P  C2'   C1'  N9   114.46  3.000
 A0P  O4'   C1'  N9   109.60  3.000
 A0P  HO1B  O1B  PB   115.16  3.000
 A0P  HO1G  O1G  PG   114.34  3.000
 A0P  H2'   C2'  C3'  107.73  3.000
 A0P  H2'   C2'  O2'  111.81  3.000
 A0P  C3'   C2'  O2'  116.46  3.000
 A0P  H2'   C2'  C1'  109.66  3.000
 A0P  O2'   C2'  C1'  109.71  3.000
 A0P  C3'   C2'  C1'  100.83  3.000
 A0P  HO2'  O2'  C2'  108.80  3.000
 A0P  HO2A  O2A  PA   114.32  3.000
 A0P  HO2G  O2G  PG   114.00  3.000
 A0P  H3'   C3'  C4'  109.61  3.000
 A0P  H3'   C3'  O3'  111.72  3.000
 A0P  C4'   C3'  O3'  114.62  3.000
 A0P  H3'   C3'  C2'  108.60  3.000
 A0P  O3'   C3'  C2'  110.86  3.000
 A0P  C4'   C3'  C2'  100.79  3.000
 A0P  HO3'  O3'  C3'  109.77  3.000
 A0P  PB    O3A  PA   129.40  3.000
 A0P  HN3B  N3B  PG   117.59  3.000
 A0P  HN3B  N3B  PB   117.81  3.000
 A0P  PG    N3B  PB   124.59  3.000
 A0P  H4'   C4'  C5'  110.30  3.000
 A0P  H4'   C4'  O4'  109.33  3.000
 A0P  C5'   C4'  O4'  109.81  3.000
 A0P  H4'   C4'  C3'  108.93  3.000
 A0P  O4'   C4'  C3'  105.91  3.000
 A0P  C5'   C4'  C3'  112.44  3.000
 A0P  C4'   O4'  C1'  110.19  3.000
 A0P  H5'A  C5'  H5'  107.27  3.000
 A0P  H5'A  C5'  O5'  111.02  3.000
 A0P  H5'   C5'  O5'  105.96  3.000
 A0P  H5'A  C5'  C4'  110.03  3.000
 A0P  H5'   C5'  C4'  110.34  3.000
 A0P  O5'   C5'  C4'  112.05  3.000
 A0P  C5'   O5'  PA   120.95  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
 A0P  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 A0P  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 A0P  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 A0P  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 A0P  CONST_05  N9    C4   N3   C2   180.00   0.0  0
 A0P  CONST_06  C5    C4   N3   C2     0.00   0.0  0
 A0P  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 A0P  CONST_08  C8    N9   C4   N3   180.00   0.0  0
 A0P  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 A0P  CONST_10  C6    C5   C4   N3     0.00   0.0  0
 A0P  CONST_11  N7    C8   N9   C4     0.00   0.0  0
 A0P  CONST_12  C8    N7   C5   C4     0.00   0.0  0
 A0P  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 A0P  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 A0P  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 A0P  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 A0P  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 A0P  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 A0P  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 A0P  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 A0P  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 A0P  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 A0P  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 A0P  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 A0P  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 A0P  CONST_26  HN6   N6   C6   N1     0.00   0.0  0
 A0P  CONST_27  HN6A  N6   C6   N1   180.00   0.0  0
 A0P  Var_01    C4'   C5'  O5'  PA   -85.96  30.0  1
 A0P  Var_02    O2B   PB   O3A  PA  -170.07  30.0  1
 A0P  Var_03    O3G   PG   N3B  PB   -45.20  30.0  3
 A0P  Var_04    O5'   PA   O3A  PB   132.18  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
 A0P  chir_03  C1'  N9   O4'  C2'  positiv
 A0P  chir_04  C2'  O2'  C1'  C3'  negativ
 A0P  chir_05  C3'  O3'  C4'  C2'  negativ
 A0P  chir_06  C4'  O4'  C3'  C5'  positiv
 A0P  chir_07  PA   O5'  O1A  O2A  both
 A0P  chir_08  PB   O1B  O2B  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
 A0P  plan-1  N1    0.020
 A0P  plan-1  C2    0.020
 A0P  plan-1  N3    0.020
 A0P  plan-1  C4    0.020
 A0P  plan-1  C5    0.020
 A0P  plan-1  C6    0.020
 A0P  plan-1  N6    0.020
 A0P  plan-1  N7    0.020
 A0P  plan-1  C8    0.020
 A0P  plan-1  N9    0.020
 A0P  plan-1  C1'   0.020
 A0P  plan-1  H2    0.020
 A0P  plan-1  H8    0.020
 A0P  plan-2  C6    0.020
 A0P  plan-2  N6    0.020
 A0P  plan-2  HN6   0.020
 A0P  plan-2  HN6A  0.020

