# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 18 13:43:15 2020
#   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  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 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  -0.475  -7.7078   1.9895   1.0190
 A0P  C2    C  CR16   0   0.036  -7.1441   1.0042   1.7135
 A0P  N3    N  N      0  -0.459  -5.9558   0.4521   1.5415
 A0P  C4    C  CR56   0   0.480  -5.2996   1.0088   0.5240
 A0P  C5    C  CR56   0  -0.005  -5.7523   2.0370  -0.2882
 A0P  C6    C  CR6    0   0.455  -7.0350   2.5375   0.0001
 A0P  N6    N  NH2    0  -0.818  -7.5988   3.5227  -0.7012
 A0P  N7    N  N      0  -0.460  -4.8139   2.3554  -1.2346
 A0P  C8    C  CR15   0   0.119  -3.8278   1.5383  -0.9989
 A0P  N9    N  NR5    0  -0.531  -4.0594   0.6996   0.0533
 A0P  PA    P  P      0   1.340   1.9969  -2.1131   0.0783
 A0P  PB    P  P      0   1.293   4.4293  -0.6453   0.7290
 A0P  PG    P  P      0   1.190   6.4697   1.4873   0.0855
 A0P  C1'   C  CR15   0   0.175  -3.1929  -0.3462   0.5899
 A0P  O1A   O  O      0  -0.818   1.8105  -2.5530   1.4999
 A0P  O1B   O  OP    -1  -0.822   4.2062   0.0603   2.0346
 A0P  O1G   O  OP    -1  -0.912   7.3791   0.6849   1.0176
 A0P  C2'   C  CR15   0  -0.032  -3.6968  -1.7373   0.2058
 A0P  O2'   O  OH1    0  -0.658  -3.2318  -2.6199   1.1905
 A0P  O2A   O  OP    -1  -0.815   2.3488  -3.1250  -0.9715
 A0P  O2B   O  O      0  -0.831   5.0255  -2.0293   0.7215
 A0P  O2G   O  OP    -1  -0.918   7.0943   1.7878  -1.2801
 A0P  C3'   C  CR15   0  -0.045  -3.0012  -1.9516  -1.1463
 A0P  O3'   O  OH1    0  -0.659  -3.7108  -1.3498  -2.1997
 A0P  O3A   O  O2     0  -0.756   2.9253  -0.7890  -0.0275
 A0P  N3B   N  NH1    0  -0.971   5.1325   0.4047  -0.3705
 A0P  O3G   O  O      0  -0.909   5.8145   2.6948   0.7487
 A0P  C4'   C  CR15   0  -0.026  -1.6830  -1.2007  -0.9658
 A0P  O4'   O  O      0  -0.495  -1.9198  -0.2229   0.0571
 A0P  C5'   C  CH2    0  -0.139  -0.5332  -2.1024  -0.5698
 A0P  O5'   O  O2     0  -0.625   0.6233  -1.3182  -0.4138
 A0P  H2    H  HCR6   0   0.250  -7.7432   0.6052   2.5252
 A0P  HN6   H  HNH2   0   0.410  -7.1084   3.9676  -1.4566
 A0P  HN6A  H  HNH2   0   0.402  -8.5117   3.8645  -0.4559
 A0P  H8    H  HCR5   0   0.293  -2.9067   1.5126  -1.5583
 A0P  H1'   H  HCR5   0   0.287  -3.1617  -0.2145   1.6751
 A0P  H2'   H  HCR5   0   0.263  -4.7894  -1.7705   0.1131
 A0P  HO2'  H  HOH1   0   0.462  -3.4633  -3.5184   0.9336
 A0P  H3'   H  HCR5   0   0.254  -2.8348  -3.0209  -1.3348
 A0P  HO3'  H  HOH1   0   0.457  -4.5718  -1.7747  -2.2716
 A0P  HN3B  H  HNH1   0   0.339   5.3201  -0.0359  -1.2627
 A0P  H4'   H  HCR5   0   0.257  -1.4180  -0.6776  -1.8909
 A0P  H5'   H  HCH2   0   0.207  -0.7824  -2.6420   0.3505
 A0P  H5'A  H  HCH2   0   0.207  -0.4065  -2.8497  -1.3630

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  1.331  0.020  1.331
 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  1.333  0.020  1.333
 A0P  N9   C4    aromatic  1.362  0.020  1.362
 A0P  C4   C5    aromatic  1.386  0.020  1.386
 A0P  N7   C5    aromatic  1.370  0.020  1.370
 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  1.302  0.020  1.302
 A0P  N9   C8    aromatic  1.365  0.020  1.365
 A0P  C8   H8    single    0.930  0.020  1.080
 A0P  C1'  N9    single    1.460  0.020  1.460
 A0P  O3A  PA    single    1.621  0.020  1.621
 A0P  O5'  PA    single    1.662  0.020  1.662
 A0P  PA   O1A   deloc     1.500  0.020  1.500
 A0P  PA   O2A   deloc     1.500  0.020  1.500
 A0P  O2B  PB    deloc     1.507  0.020  1.507
 A0P  PB   N3B   single    1.675  0.020  1.675
 A0P  PB   O1B   deloc     1.501  0.020  1.501
 A0P  PB   O3A   single    1.690  0.020  1.690
 A0P  O3G  PG    deloc     1.525  0.020  1.525
 A0P  PG   O2G   deloc     1.531  0.020  1.531
 A0P  PG   O1G   deloc     1.530  0.020  1.530
 A0P  PG   N3B   single    1.780  0.020  1.780
 A0P  O4'  C1'   single    1.386  0.020  1.386
 A0P  C1'  C2'   single    1.529  0.020  1.529
 A0P  C1'  H1'   single    0.970  0.020  1.090
 A0P  C3'  C2'   single    1.536  0.020  1.536
 A0P  O2'  C2'   single    1.402  0.020  1.402
 A0P  C2'  H2'   single    0.970  0.020  1.090
 A0P  O2'  HO2'  single    0.850  0.020  0.980
 A0P  C4'  C3'   single    1.528  0.020  1.528
 A0P  C3'  O3'   single    1.405  0.020  1.405
 A0P  C3'  H3'   single    0.970  0.020  1.090
 A0P  O3'  HO3'  single    0.850  0.020  0.980
 A0P  N3B  HN3B  single    0.890  0.020  1.040
 A0P  C5'  C4'   single    1.514  0.020  1.514
 A0P  C4'  O4'   single    1.435  0.020  1.435
 A0P  C4'  H4'   single    0.970  0.020  1.090
 A0P  C5'  O5'   single    1.406  0.020  1.406
 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   119.18  3.000
 A0P  H2    C2   N3   116.12  3.000
 A0P  H2    C2   N1   115.40  3.000
 A0P  N3    C2   N1   128.48  3.000
 A0P  C4    N3   C2   111.57  3.000
 A0P  N9    C4   C5   105.27  3.000
 A0P  C5    C4   N3   126.61  3.000
 A0P  N9    C4   N3   128.12  3.000
 A0P  N7    C5   C6   133.10  3.000
 A0P  C6    C5   C4   116.21  3.000
 A0P  N7    C5   C4   110.69  3.000
 A0P  N6    C6   C5   122.70  3.000
 A0P  N6    C6   N1   119.34  3.000
 A0P  C5    C6   N1   117.95  3.000
 A0P  HN6A  N6   HN6  118.44  3.000
 A0P  HN6A  N6   C6   120.44  3.000
 A0P  HN6   N6   C6   121.06  3.000
 A0P  C8    N7   C5   104.35  3.000
 A0P  H8    C8   N9   122.02  3.000
 A0P  H8    C8   N7   124.61  3.000
 A0P  N9    C8   N7   113.36  3.000
 A0P  C1'   N9   C8   128.49  3.000
 A0P  C1'   N9   C4   125.16  3.000
 A0P  C8    N9   C4   106.34  3.000
 A0P  O5'   PA   O3A   93.63  3.000
 A0P  O5'   PA   O2A  108.03  3.000
 A0P  O3A   PA   O2A  111.79  3.000
 A0P  O2A   PA   O1A  119.65  3.000
 A0P  O5'   PA   O1A  108.56  3.000
 A0P  O3A   PA   O1A  111.89  3.000
 A0P  N3B   PB   O3A   97.65  3.000
 A0P  O3A   PB   O2B  105.77  3.000
 A0P  N3B   PB   O2B  113.97  3.000
 A0P  O3A   PB   O1B  107.29  3.000
 A0P  N3B   PB   O1B  109.80  3.000
 A0P  O2B   PB   O1B  119.67  3.000
 A0P  O3G   PG   N3B  105.67  3.000
 A0P  N3B   PG   O2G  101.38  3.000
 A0P  O3G   PG   O2G  114.05  3.000
 A0P  N3B   PG   O1G  106.48  3.000
 A0P  O2G   PG   O1G  113.82  3.000
 A0P  O3G   PG   O1G  113.93  3.000
 A0P  H1'   C1'  O4'  110.16  3.000
 A0P  H1'   C1'  C2'  111.61  3.000
 A0P  O4'   C1'  C2'  106.69  3.000
 A0P  H1'   C1'  N9   107.18  3.000
 A0P  C2'   C1'  N9   111.34  3.000
 A0P  O4'   C1'  N9   109.88  3.000
 A0P  H2'   C2'  C3'  111.87  3.000
 A0P  H2'   C2'  O2'  111.76  3.000
 A0P  C3'   C2'  O2'  112.36  3.000
 A0P  H2'   C2'  C1'  112.16  3.000
 A0P  O2'   C2'  C1'  106.69  3.000
 A0P  C3'   C2'  C1'  101.48  3.000
 A0P  HO2'  O2'  C2'  108.69  3.000
 A0P  H3'   C3'  C4'  111.59  3.000
 A0P  H3'   C3'  O3'  111.39  3.000
 A0P  C4'   C3'  O3'  108.28  3.000
 A0P  H3'   C3'  C2'  110.83  3.000
 A0P  O3'   C3'  C2'  111.81  3.000
 A0P  C4'   C3'  C2'  102.60  3.000
 A0P  HO3'  O3'  C3'  108.57  3.000
 A0P  PB    O3A  PA   123.38  3.000
 A0P  HN3B  N3B  PG   110.56  3.000
 A0P  HN3B  N3B  PB   112.54  3.000
 A0P  PG    N3B  PB   121.90  3.000
 A0P  H4'   C4'  C5'  108.77  3.000
 A0P  H4'   C4'  O4'  108.45  3.000
 A0P  C5'   C4'  O4'  110.17  3.000
 A0P  H4'   C4'  C3'  110.10  3.000
 A0P  O4'   C4'  C3'  106.07  3.000
 A0P  C5'   C4'  C3'  113.17  3.000
 A0P  C4'   O4'  C1'  111.42  3.000
 A0P  H5'A  C5'  H5'  107.35  3.000
 A0P  H5'A  C5'  O5'  111.41  3.000
 A0P  H5'   C5'  O5'  111.63  3.000
 A0P  H5'A  C5'  C4'  107.71  3.000
 A0P  H5'   C5'  C4'  109.90  3.000
 A0P  O5'   C5'  C4'  108.75  3.000
 A0P  C5'   O5'  PA   116.48  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  180.00   0.0  0
 A0P  CONST_27  HN6A  N6   C6   N1    0.00   0.0  0
 A0P  Var_01    C4'   C5'  O5'  PA  177.79  30.0  1
 A0P  Var_02    O2B   PB   O3A  PA   33.14  30.0  1
 A0P  Var_03    O3G   PG   N3B  PB  -82.10  30.0  3
 A0P  Var_04    O5'   PA   O3A  PB  162.07  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

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

