# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 17:09:25 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: a 2 line input string
#   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)=O)[C@@H](O[P](O)(O)=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
 PAP  PAP  'adenosine 3'-(dihydrogen phosphate) 5'-(trihydrogen diphosphate)'  ligand  47  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_PAP
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
 PAP  PB    P  P     0   1.401   8.8343   6.6810   2.0259
 PAP  O1B   O  O     0  -0.686  10.1813   6.0960   2.0272
 PAP  O2B   O  OH1   0  -0.602   8.0259   6.3434   3.3445
 PAP  O3B   O  OH1   0  -0.612   7.9844   6.2801   0.7541
 PAP  PA    P  P     0   1.429   9.8991   9.3009   2.6569
 PAP  O1A   O  O     0  -0.761  10.0696   9.0528   4.0944
 PAP  O2A   O  OH1   0  -0.581   9.3680  10.7187   2.1852
 PAP  O3A   O  O2    0  -0.750   8.8434   8.3090   1.9248
 PAP  O5'   O  O2    0  -0.587  11.2490   9.1598   1.8425
 PAP  C5'   C  CH2   0  -0.337  11.3051   9.0366   0.4168
 PAP  C4'   C  CH1   0   0.062  12.4839   9.8614  -0.0778
 PAP  O4'   O  O2    0  -0.476  12.6636   9.5925  -1.4641
 PAP  C3'   C  CH1   0  -0.086  12.2594  11.3644   0.0322
 PAP  O3'   O  O2    0  -0.641  13.5306  12.0027   0.0661
 PAP  P     P  P     0   1.369  13.7797  13.4217   0.7931
 PAP  O1    O  O     0  -0.747  15.1000  13.9427   0.3952
 PAP  O2    O  OH1   0  -0.594  12.4882  14.2861   0.4829
 PAP  O3    O  OH1   0  -0.636  13.5598  13.1979   2.3573
 PAP  C2'   C  CH1   0  -0.044  11.5672  11.6630  -1.2976
 PAP  O2'   O  OH1   0  -0.615  11.6904  13.0030  -1.6980
 PAP  C1'   C  CH1   0   0.203  12.3052  10.7046  -2.2428
 PAP  N9    N  NR5   0  -0.559  11.5305  10.2781  -3.3744
 PAP  C8    C  CR15  0   0.146  11.9364  10.3271  -4.6827
 PAP  N7    N  N     0  -0.461  11.0747   9.8257  -5.5124
 PAP  C5    C  CR56  0  -0.108  10.0407   9.4054  -4.7143
 PAP  C6    C  CR6   0   0.410   8.8170   8.7682  -4.9965
 PAP  N6    N  NH2   0  -0.716   8.4381   8.4551  -6.2342
 PAP  N1    N  N     0  -0.429   8.0112   8.4753  -3.9686
 PAP  C2    C  CR16  0   0.033   8.3904   8.7964  -2.7364
 PAP  N3    N  N     0  -0.502   9.5062   9.3920  -2.3511
 PAP  C4    C  CR56  0   0.488  10.3013   9.6743  -3.3812
 PAP  HOB2  H  HOH1  0   0.514   7.1397   6.7214   3.4361
 PAP  HOB3  H  HOH1  0   0.523   7.0514   6.5357   0.7353
 PAP  HOA2  H  HOH1  0   0.526   8.6020  11.0628   2.6661
 PAP  H5'1  H  HCH2  0   0.271  11.4652   7.9874   0.1658
 PAP  H5'2  H  HCH2  0   0.260  10.3780   9.3548  -0.0643
 PAP  H4'   H  HCH1  0   0.251  13.3853   9.5619   0.4628
 PAP  H3'   H  HCH1  0   0.259  11.6469  11.6324   0.8966
 PAP  HO2   H  HOH1  0   0.530  12.0777  14.0376  -0.3801
 PAP  HO3   H  HOH1  0   0.511  14.3616  12.9256   2.8226
 PAP  H2'   H  HCH1  0   0.292  10.5156  11.3776  -1.2083
 PAP  HO2'  H  HOH1  0   0.468  10.8970  13.2689  -2.1747
 PAP  H1'   H  HCH1  0   0.287  13.1947  11.1998  -2.6463
 PAP  H8    H  HCR5  0   0.259  12.8907  10.7571  -4.9505
 PAP  HN61  H  HNH2  0   0.384   7.5743   7.9661  -6.3928
 PAP  HN62  H  HNH2  0   0.427   9.0347   8.6357  -7.0224
 PAP  H2    H  HCR6  0   0.226   7.6949   8.5311  -1.9473

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
 PAP  PB   O1B   double    1.469  0.020  1.469
 PAP  PB   O2B   single    1.583  0.020  1.583
 PAP  PB   O3B   single    1.581  0.020  1.581
 PAP  PB   O3A   single    1.631  0.020  1.631
 PAP  O2B  HOB2  single    0.850  0.020  0.980
 PAP  O3B  HOB3  single    0.850  0.020  0.980
 PAP  PA   O1A   double    1.469  0.020  1.469
 PAP  PA   O2A   single    1.586  0.020  1.586
 PAP  PA   O3A   single    1.623  0.020  1.623
 PAP  PA   O5'   single    1.583  0.020  1.583
 PAP  O2A  HOA2  single    0.850  0.020  0.980
 PAP  O5'  C5'   single    1.432  0.020  1.432
 PAP  C5'  C4'   single    1.521  0.020  1.521
 PAP  C5'  H5'1  single    0.970  0.020  1.090
 PAP  C5'  H5'2  single    0.970  0.020  1.090
 PAP  C4'  O4'   single    1.424  0.020  1.424
 PAP  C4'  C3'   single    1.524  0.020  1.524
 PAP  C4'  H4'   single    0.970  0.020  1.090
 PAP  O4'  C1'   single    1.404  0.020  1.404
 PAP  C3'  O3'   single    1.423  0.020  1.423
 PAP  C3'  C2'   single    1.529  0.020  1.529
 PAP  C3'  H3'   single    0.970  0.020  1.090
 PAP  O3'  P     single    1.614  0.020  1.614
 PAP  P    O1    double    1.474  0.020  1.474
 PAP  P    O2    single    1.585  0.020  1.585
 PAP  P    O3    single    1.595  0.020  1.595
 PAP  O2   HO2   single    0.850  0.020  0.980
 PAP  O3   HO3   single    0.850  0.020  0.980
 PAP  C2'  O2'   single    1.404  0.020  1.404
 PAP  C2'  C1'   single    1.535  0.020  1.535
 PAP  C2'  H2'   single    0.970  0.020  1.090
 PAP  O2'  HO2'  single    0.850  0.020  0.980
 PAP  C1'  N9    single    1.436  0.020  1.436
 PAP  C1'  H1'   single    0.970  0.020  1.090
 PAP  N9   C8    aromatic  1.371  0.020  1.371
 PAP  N9   C4    aromatic  1.369  0.020  1.369
 PAP  C8   N7    aromatic  1.297  0.020  1.297
 PAP  C8   H8    single    0.930  0.020  1.080
 PAP  N7   C5    aromatic  1.372  0.020  1.372
 PAP  C5   C6    aromatic  1.408  0.020  1.408
 PAP  C5   C4    aromatic  1.385  0.020  1.385
 PAP  C6   N6    single    1.332  0.020  1.332
 PAP  C6   N1    aromatic  1.339  0.020  1.339
 PAP  N6   HN61  single    0.860  0.020  1.020
 PAP  N6   HN62  single    0.860  0.020  1.020
 PAP  N1   C2    aromatic  1.329  0.020  1.329
 PAP  C2   N3    aromatic  1.322  0.020  1.322
 PAP  C2   H2    single    0.930  0.020  1.080
 PAP  N3   C4    aromatic  1.332  0.020  1.332

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
 PAP  O3A   PB   O3B   101.90  3.000
 PAP  O3A   PB   O2B   105.51  3.000
 PAP  O3B   PB   O2B   109.96  3.000
 PAP  O3A   PB   O1B   113.11  3.000
 PAP  O3B   PB   O1B   113.12  3.000
 PAP  O2B   PB   O1B   112.50  3.000
 PAP  HOB2  O2B  PB    117.59  3.000
 PAP  HOB3  O3B  PB    117.83  3.000
 PAP  O5'   PA   O3A   105.56  3.000
 PAP  O5'   PA   O2A   102.25  3.000
 PAP  O3A   PA   O2A   101.20  3.000
 PAP  O5'   PA   O1A   112.93  3.000
 PAP  O3A   PA   O1A   114.44  3.000
 PAP  O2A   PA   O1A   118.75  3.000
 PAP  HOA2  O2A  PA    115.80  3.000
 PAP  PA    O3A  PB    125.84  3.000
 PAP  C5'   O5'  PA    123.60  3.000
 PAP  H5'2  C5'  H5'1  107.67  3.000
 PAP  H5'2  C5'  C4'   110.90  3.000
 PAP  H5'1  C5'  C4'   109.45  3.000
 PAP  H5'2  C5'  O5'   112.35  3.000
 PAP  H5'1  C5'  O5'   108.52  3.000
 PAP  C4'   C5'  O5'   107.90  3.000
 PAP  H4'   C4'  C3'   110.86  3.000
 PAP  H4'   C4'  O4'   109.02  3.000
 PAP  C3'   C4'  O4'   105.98  3.000
 PAP  H4'   C4'  C5'   109.25  3.000
 PAP  C3'   C4'  C5'   113.40  3.000
 PAP  O4'   C4'  C5'   108.18  3.000
 PAP  C1'   O4'  C4'   110.99  3.000
 PAP  H3'   C3'  C2'   112.73  3.000
 PAP  H3'   C3'  O3'   111.83  3.000
 PAP  C2'   C3'  O3'   109.73  3.000
 PAP  H3'   C3'  C4'   112.43  3.000
 PAP  C2'   C3'  C4'   101.34  3.000
 PAP  O3'   C3'  C4'   108.21  3.000
 PAP  P     O3'  C3'   122.90  3.000
 PAP  O3    P    O2     98.98  3.000
 PAP  O3    P    O1    115.96  3.000
 PAP  O2    P    O1    118.97  3.000
 PAP  O3    P    O3'   107.28  3.000
 PAP  O2    P    O3'   105.40  3.000
 PAP  O1    P    O3'   109.12  3.000
 PAP  HO2   O2   P     111.88  3.000
 PAP  HO3   O3   P     113.41  3.000
 PAP  H2'   C2'  C1'   110.47  3.000
 PAP  H2'   C2'  O2'   110.91  3.000
 PAP  C1'   C2'  O2'   112.21  3.000
 PAP  H2'   C2'  C3'   108.28  3.000
 PAP  C1'   C2'  C3'   101.30  3.000
 PAP  O2'   C2'  C3'   113.25  3.000
 PAP  HO2'  O2'  C2'   109.41  3.000
 PAP  H1'   C1'  N9    106.39  3.000
 PAP  H1'   C1'  C2'   109.58  3.000
 PAP  N9    C1'  C2'   114.28  3.000
 PAP  H1'   C1'  O4'   110.80  3.000
 PAP  N9    C1'  O4'   109.84  3.000
 PAP  C2'   C1'  O4'   106.00  3.000
 PAP  C4    N9   C8    106.07  3.000
 PAP  C4    N9   C1'   128.24  3.000
 PAP  C8    N9   C1'   125.57  3.000
 PAP  H8    C8   N7    125.60  3.000
 PAP  H8    C8   N9    120.82  3.000
 PAP  N7    C8   N9    113.57  3.000
 PAP  C5    N7   C8    104.30  3.000
 PAP  C4    C5   C6    116.38  3.000
 PAP  C4    C5   N7    111.02  3.000
 PAP  C6    C5   N7    132.60  3.000
 PAP  N1    C6   N6    119.40  3.000
 PAP  N1    C6   C5    117.92  3.000
 PAP  N6    C6   C5    122.67  3.000
 PAP  HN62  N6   HN61  118.29  3.000
 PAP  HN62  N6   C6    121.18  3.000
 PAP  HN61  N6   C6    120.37  3.000
 PAP  C2    N1   C6    119.18  3.000
 PAP  H2    C2   N3    116.05  3.000
 PAP  H2    C2   N1    115.63  3.000
 PAP  N3    C2   N1    128.32  3.000
 PAP  C4    N3   C2    111.96  3.000
 PAP  N3    C4   C5    126.25  3.000
 PAP  N3    C4   N9    128.73  3.000
 PAP  C5    C4   N9    105.03  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
 PAP  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 PAP  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 PAP  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 PAP  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 PAP  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 PAP  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 PAP  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 PAP  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 PAP  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 PAP  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 PAP  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 PAP  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 PAP  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 PAP  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 PAP  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 PAP  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 PAP  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 PAP  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 PAP  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 PAP  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 PAP  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 PAP  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 PAP  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 PAP  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 PAP  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 PAP  CONST_26  HN61  N6   C6   C5    180.00   0.0  0
 PAP  CONST_27  HN62  N6   C6   C5      0.00   0.0  0
 PAP  Var_01    C4'   C5'  O5'  PA    140.28  30.0  3
 PAP  Var_02    O1    P    O3'  C3'  -167.47  30.0  3
 PAP  Var_03    O1A   PA   O3A  PB    -50.35  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
 PAP  chir_02  C4'  C5'  O4'  C3'  negativ
 PAP  chir_03  C3'  O3'  C2'  C4'  negativ
 PAP  chir_04  C2'  O2'  C1'  C3'  negativ
 PAP  chir_05  C1'  O4'  N9   C2'  negativ
 PAP  chir_06  PA   O2A  O3A  O5'  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
 PAP  plan-1  C1'   0.020
 PAP  plan-1  N9    0.020
 PAP  plan-1  C8    0.020
 PAP  plan-1  N7    0.020
 PAP  plan-1  C5    0.020
 PAP  plan-1  C6    0.020
 PAP  plan-1  N6    0.020
 PAP  plan-1  N1    0.020
 PAP  plan-1  C2    0.020
 PAP  plan-1  N3    0.020
 PAP  plan-1  C4    0.020
 PAP  plan-1  H8    0.020
 PAP  plan-1  H2    0.020
 PAP  plan-2  C6    0.020
 PAP  plan-2  N6    0.020
 PAP  plan-2  HN61  0.020
 PAP  plan-2  HN62  0.020

