# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 02:57:14 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: 5'-O-[(R)-{[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO)[C@@H](O)C(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 PAJ  PAJ  5'-O-[(R)-{[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]oxy}(hydroxy)phosphoryl]adenosine  ligand  56  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PAJ
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
 PAJ  P     P  P     0   1.514  33.4022  36.2164  43.6590
 PAJ  O1P   O  O     0  -0.663  34.6517  35.9984  42.9254
 PAJ  O2P   O  OH1   0  -0.718  33.1233  37.7384  43.9874
 PAJ  O5'   O  O2    0  -0.585  32.1520  35.6158  42.8944
 PAJ  C5'   C  CH2   0  -0.233  30.7785  35.8120  43.2348
 PAJ  C4'   C  CH1   0  -0.014  29.9456  34.8568  42.4108
 PAJ  O4'   O  O2    0  -0.489  30.1494  35.1118  41.0237
 PAJ  C3'   C  CH1   0  -0.037  30.2552  33.3743  42.6234
 PAJ  O3'   O  OH1   0  -0.666  29.0604  32.6568  42.4592
 PAJ  C2'   C  CH1   0  -0.055  31.2261  33.0766  41.4769
 PAJ  O2'   O  OH1   0  -0.653  31.2133  31.7491  41.0400
 PAJ  C1'   C  CH1   0   0.214  30.6676  33.9797  40.3770
 PAJ  N9    N  NR5   0  -0.549  31.6367  34.3775  39.3919
 PAJ  C8    C  CR15  0   0.113  32.8617  34.9627  39.5917
 PAJ  N7    N  N     0  -0.447  33.4912  35.2289  38.4879
 PAJ  C5    C  CR56  0  -0.011  32.6436  34.8032  37.4972
 PAJ  C6    C  CR6   0   0.461  32.7379  34.8008  36.0934
 PAJ  N6    N  NH2   0  -0.817  33.7998  35.2738  35.4411
 PAJ  N1    N  N     0  -0.475  31.7106  34.2991  35.3983
 PAJ  C2    C  CR16  0   0.046  30.6536  33.8280  36.0540
 PAJ  N3    N  N     0  -0.458  30.4531  33.7745  37.3597
 PAJ  C4    C  CR56  0   0.493  31.4830  34.2753  38.0365
 PAJ  O11   O  O     0  -0.384  33.5383  33.4537  44.4948
 PAJ  C11   C  C     0   0.564  33.4767  34.2421  45.3891
 PAJ  O12   O  O2    0  -0.593  33.3389  35.5758  45.1704
 PAJ  C12   C  CH1   0  -0.018  33.5491  33.9172  46.8642
 PAJ  O13   O  OH1   0  -0.659  34.0990  32.6321  46.9286
 PAJ  C13   C  CT    0  -0.163  32.1580  34.0102  47.5648
 PAJ  C14   C  CH3   0  -0.644  31.7348  35.4671  47.7644
 PAJ  C15   C  CH3   0  -0.676  31.0862  33.2507  46.7832
 PAJ  C16   C  CH2   0  -0.151  32.2768  33.3268  48.9311
 PAJ  O14   O  OH1   0  -0.673  33.3771  33.8544  49.6364
 PAJ  HOP2  H  HOH1  0   0.507  32.4015  37.9705  44.5877
 PAJ  H5'1  H  HCH2  0   0.250  30.5981  35.6165  44.2965
 PAJ  H5'2  H  HCH2  0   0.285  30.4896  36.8435  43.0231
 PAJ  H4'   H  HCH1  0   0.280  28.9007  35.0542  42.6721
 PAJ  H3'   H  HCH1  0   0.245  30.7073  33.1802  43.6051
 PAJ  H3T   H  HOH1  0   0.451  29.2899  31.7545  42.2055
 PAJ  H2'   H  HCH1  0   0.261  32.2330  33.3959  41.7629
 PAJ  HO'2  H  HOH1  0   0.471  31.8689  31.2486  41.5355
 PAJ  H1'   H  HCH1  0   0.263  29.8834  33.4500  39.8253
 PAJ  H8    H  HCR5  0   0.289  33.2446  35.1708  40.5787
 PAJ  H61   H  HNH2  0   0.404  33.8340  35.2459  34.4368
 PAJ  H62   H  HNH2  0   0.412  34.5858  35.6573  35.9353
 PAJ  H2    H  HCR6  0   0.253  29.8552  33.4380  35.4317
 PAJ  H12   H  HCH1  0   0.273  34.2138  34.6586  47.3255
 PAJ  H13   H  HOH1  0   0.463  34.4993  32.5317  47.7985
 PAJ  H141  H  HCH3  0   0.236  30.8445  35.5070  48.3940
 PAJ  H142  H  HCH3  0   0.240  32.5114  36.0571  48.2520
 PAJ  H143  H  HCH3  0   0.225  31.4803  35.9603  46.8273
 PAJ  H151  H  HCH3  0   0.251  30.1800  33.1499  47.3830
 PAJ  H152  H  HCH3  0   0.224  30.7928  33.7761  45.8721
 PAJ  H153  H  HCH3  0   0.246  31.4158  32.2485  46.5067
 PAJ  H161  H  HCH2  0   0.220  31.3351  33.4931  49.4711
 PAJ  H162  H  HCH2  0   0.216  32.3707  32.2422  48.7954
 PAJ  H14   H  HOH1  0   0.461  33.4712  33.3664  50.4595

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
 PAJ  P    O1P   double    1.465  0.020  1.465
 PAJ  P    O2P   single    1.582  0.020  1.582
 PAJ  P    O5'   single    1.584  0.020  1.584
 PAJ  P    O12   single    1.643  0.020  1.643
 PAJ  O2P  HOP2  single    0.850  0.020  0.980
 PAJ  O5'  C5'   single    1.429  0.020  1.429
 PAJ  C5'  C4'   single    1.512  0.020  1.512
 PAJ  C5'  H5'1  single    0.970  0.020  1.090
 PAJ  C5'  H5'2  single    0.970  0.020  1.090
 PAJ  C4'  O4'   single    1.425  0.020  1.425
 PAJ  C4'  C3'   single    1.529  0.020  1.529
 PAJ  C4'  H4'   single    0.970  0.020  1.090
 PAJ  O4'  C1'   single    1.403  0.020  1.403
 PAJ  C3'  O3'   single    1.403  0.020  1.403
 PAJ  C3'  C2'   single    1.532  0.020  1.532
 PAJ  C3'  H3'   single    0.970  0.020  1.090
 PAJ  O3'  H3T   single    0.850  0.020  0.980
 PAJ  C2'  O2'   single    1.398  0.020  1.398
 PAJ  C2'  C1'   single    1.529  0.020  1.529
 PAJ  C2'  H2'   single    0.970  0.020  1.090
 PAJ  O2'  HO'2  single    0.850  0.020  0.980
 PAJ  C1'  N9    single    1.438  0.020  1.438
 PAJ  C1'  H1'   single    0.970  0.020  1.090
 PAJ  N9   C8    aromatic  1.372  0.020  1.372
 PAJ  N9   C4    aromatic  1.368  0.020  1.368
 PAJ  C8   N7    aromatic  1.298  0.020  1.298
 PAJ  C8   H8    single    0.930  0.020  1.080
 PAJ  N7   C5    aromatic  1.372  0.020  1.372
 PAJ  C5   C6    aromatic  1.407  0.020  1.407
 PAJ  C5   C4    aromatic  1.384  0.020  1.384
 PAJ  C6   N6    single    1.333  0.020  1.333
 PAJ  C6   N1    aromatic  1.338  0.020  1.338
 PAJ  N6   H61   single    0.860  0.020  1.020
 PAJ  N6   H62   single    0.860  0.020  1.020
 PAJ  N1   C2    aromatic  1.330  0.020  1.330
 PAJ  C2   N3    aromatic  1.322  0.020  1.322
 PAJ  C2   H2    single    0.930  0.020  1.080
 PAJ  N3   C4    aromatic  1.330  0.020  1.330
 PAJ  O11  C11   double    1.194  0.020  1.194
 PAJ  C11  O12   single    1.359  0.020  1.359
 PAJ  C11  C12   single    1.512  0.020  1.512
 PAJ  C12  O13   single    1.399  0.020  1.399
 PAJ  C12  C13   single    1.560  0.020  1.560
 PAJ  C12  H12   single    0.970  0.020  1.090
 PAJ  O13  H13   single    0.850  0.020  0.980
 PAJ  C13  C14   single    1.530  0.020  1.530
 PAJ  C13  C15   single    1.529  0.020  1.529
 PAJ  C13  C16   single    1.532  0.020  1.532
 PAJ  C14  H141  single    0.970  0.020  1.090
 PAJ  C14  H142  single    0.970  0.020  1.090
 PAJ  C14  H143  single    0.970  0.020  1.090
 PAJ  C15  H151  single    0.970  0.020  1.090
 PAJ  C15  H152  single    0.970  0.020  1.090
 PAJ  C15  H153  single    0.970  0.020  1.090
 PAJ  C16  O14   single    1.409  0.020  1.409
 PAJ  C16  H161  single    0.970  0.020  1.090
 PAJ  C16  H162  single    0.970  0.020  1.090
 PAJ  O14  H14   single    0.850  0.020  0.980

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
 PAJ  O12   P    O5'   105.42  3.000
 PAJ  O12   P    O2P   100.22  3.000
 PAJ  O5'   P    O2P   109.02  3.000
 PAJ  O12   P    O1P   115.82  3.000
 PAJ  O5'   P    O1P   112.03  3.000
 PAJ  O2P   P    O1P   113.42  3.000
 PAJ  HOP2  O2P  P     119.43  3.000
 PAJ  C5'   O5'  P     126.29  3.000
 PAJ  H5'2  C5'  H5'1  108.25  3.000
 PAJ  H5'2  C5'  C4'   110.21  3.000
 PAJ  H5'1  C5'  C4'   108.97  3.000
 PAJ  H5'2  C5'  O5'   109.75  3.000
 PAJ  H5'1  C5'  O5'   111.42  3.000
 PAJ  C4'   C5'  O5'   108.25  3.000
 PAJ  H4'   C4'  C3'   109.56  3.000
 PAJ  H4'   C4'  O4'   109.66  3.000
 PAJ  C3'   C4'  O4'   106.25  3.000
 PAJ  H4'   C4'  C5'   106.37  3.000
 PAJ  C3'   C4'  C5'   115.17  3.000
 PAJ  O4'   C4'  C5'   109.80  3.000
 PAJ  C1'   O4'  C4'   110.92  3.000
 PAJ  H3'   C3'  C2'   111.96  3.000
 PAJ  H3'   C3'  O3'   111.39  3.000
 PAJ  C2'   C3'  O3'   110.66  3.000
 PAJ  H3'   C3'  C4'   112.26  3.000
 PAJ  C2'   C3'  C4'   102.28  3.000
 PAJ  O3'   C3'  C4'   107.88  3.000
 PAJ  H3T   O3'  C3'   107.84  3.000
 PAJ  H2'   C2'  C1'   110.60  3.000
 PAJ  H2'   C2'  O2'   111.54  3.000
 PAJ  C1'   C2'  O2'   109.44  3.000
 PAJ  H2'   C2'  C3'   109.33  3.000
 PAJ  C1'   C2'  C3'   101.08  3.000
 PAJ  O2'   C2'  C3'   114.38  3.000
 PAJ  HO'2  O2'  C2'   109.08  3.000
 PAJ  H1'   C1'  N9    105.74  3.000
 PAJ  H1'   C1'  C2'   109.77  3.000
 PAJ  N9    C1'  C2'   114.21  3.000
 PAJ  H1'   C1'  O4'   110.97  3.000
 PAJ  N9    C1'  O4'   109.96  3.000
 PAJ  C2'   C1'  O4'   106.26  3.000
 PAJ  C4    N9   C8    106.04  3.000
 PAJ  C4    N9   C1'   125.62  3.000
 PAJ  C8    N9   C1'   128.31  3.000
 PAJ  H8    C8   N7    124.48  3.000
 PAJ  H8    C8   N9    122.15  3.000
 PAJ  N7    C8   N9    113.37  3.000
 PAJ  C5    N7   C8    104.53  3.000
 PAJ  C4    C5   C6    116.38  3.000
 PAJ  C4    C5   N7    110.80  3.000
 PAJ  C6    C5   N7    132.83  3.000
 PAJ  N1    C6   N6    119.37  3.000
 PAJ  N1    C6   C5    117.87  3.000
 PAJ  N6    C6   C5    122.76  3.000
 PAJ  H62   N6   H61   118.39  3.000
 PAJ  H62   N6   C6    121.20  3.000
 PAJ  H61   N6   C6    120.41  3.000
 PAJ  C2    N1   C6    119.13  3.000
 PAJ  H2    C2   N3    116.13  3.000
 PAJ  H2    C2   N1    115.42  3.000
 PAJ  N3    C2   N1    128.45  3.000
 PAJ  C4    N3   C2    111.70  3.000
 PAJ  N3    C4   C5    126.47  3.000
 PAJ  N3    C4   N9    128.26  3.000
 PAJ  C5    C4   N9    105.27  3.000
 PAJ  C12   C11  O12   111.89  3.000
 PAJ  C12   C11  O11   125.90  3.000
 PAJ  O12   C11  O11   122.21  3.000
 PAJ  C11   O12  P     121.80  3.000
 PAJ  H12   C12  C13   108.12  3.000
 PAJ  H12   C12  O13   111.29  3.000
 PAJ  C13   C12  O13   112.61  3.000
 PAJ  H12   C12  C11   107.09  3.000
 PAJ  C13   C12  C11   112.49  3.000
 PAJ  O13   C12  C11   105.13  3.000
 PAJ  H13   O13  C12   107.50  3.000
 PAJ  C16   C13  C15   106.78  3.000
 PAJ  C16   C13  C14   109.25  3.000
 PAJ  C15   C13  C14   110.24  3.000
 PAJ  C16   C13  C12   107.74  3.000
 PAJ  C15   C13  C12   111.46  3.000
 PAJ  C14   C13  C12   111.22  3.000
 PAJ  H143  C14  H142  107.83  3.000
 PAJ  H143  C14  H141  106.81  3.000
 PAJ  H142  C14  H141  107.66  3.000
 PAJ  H143  C14  C13   112.55  3.000
 PAJ  H142  C14  C13   112.12  3.000
 PAJ  H141  C14  C13   109.62  3.000
 PAJ  H153  C15  H152  108.17  3.000
 PAJ  H153  C15  H151  107.78  3.000
 PAJ  H152  C15  H151  106.25  3.000
 PAJ  H153  C15  C13   111.98  3.000
 PAJ  H152  C15  C13   112.08  3.000
 PAJ  H151  C15  C13   110.31  3.000
 PAJ  H162  C16  H161  106.50  3.000
 PAJ  H162  C16  O14   111.42  3.000
 PAJ  H161  C16  O14   111.51  3.000
 PAJ  H162  C16  C13   109.71  3.000
 PAJ  H161  C16  C13   107.72  3.000
 PAJ  O14   C16  C13   109.86  3.000
 PAJ  H14   O14  C16   108.35  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
 PAJ  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 PAJ  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 PAJ  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 PAJ  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 PAJ  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 PAJ  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 PAJ  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 PAJ  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 PAJ  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 PAJ  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 PAJ  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 PAJ  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 PAJ  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 PAJ  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 PAJ  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 PAJ  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 PAJ  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 PAJ  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 PAJ  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 PAJ  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 PAJ  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 PAJ  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 PAJ  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 PAJ  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 PAJ  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 PAJ  CONST_26  H61   N6   C6   C5    180.00   0.0  0
 PAJ  CONST_27  H62   N6   C6   C5      0.00   0.0  0
 PAJ  Var_01    C4'   C5'  O5'  P    -169.38  30.0  3
 PAJ  Var_02    O11   C11  O12  P      -6.42  30.0  1
 PAJ  Var_03    O12   P    O5'  C5'    62.39  30.0  2
 PAJ  Var_04    O14   C16  C13  C12    51.92  30.0  3
 PAJ  Var_05    H141  C14  C13  C12  -170.95  30.0  3
 PAJ  Var_06    H151  C15  C13  C12   168.25  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
 PAJ  chir_02  C4'  C5'  O4'  C3'  negativ
 PAJ  chir_03  C3'  O3'  C4'  C2'  positiv
 PAJ  chir_04  C2'  O2'  C3'  C1'  positiv
 PAJ  chir_05  C1'  O4'  N9   C2'  negativ
 PAJ  chir_06  C12  O13  C11  C13  negativ
 PAJ  chir_07  P    O2P  O5'  O12  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
 PAJ  plan-1  C1'  0.020
 PAJ  plan-1  N9   0.020
 PAJ  plan-1  C8   0.020
 PAJ  plan-1  N7   0.020
 PAJ  plan-1  C5   0.020
 PAJ  plan-1  C6   0.020
 PAJ  plan-1  N6   0.020
 PAJ  plan-1  N1   0.020
 PAJ  plan-1  C2   0.020
 PAJ  plan-1  N3   0.020
 PAJ  plan-1  C4   0.020
 PAJ  plan-1  H8   0.020
 PAJ  plan-1  H2   0.020
 PAJ  plan-2  C6   0.020
 PAJ  plan-2  N6   0.020
 PAJ  plan-2  H61  0.020
 PAJ  plan-2  H62  0.020
 PAJ  plan-3  O11  0.020
 PAJ  plan-3  C11  0.020
 PAJ  plan-3  O12  0.020
 PAJ  plan-3  C12  0.020

