# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 15:33:26 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]oxy}phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[P](O)(O)=O)[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
 PTJ  PTJ  5'-O-[(S)-hydroxy{[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]oxy}phosphoryl]adenosine  ligand  61  36  .  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_PTJ
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
 PTJ  O15  O  O     0  -0.692   5.7667  24.4824  64.3634
 PTJ  P1   P  P     0   1.474   5.9525  25.9344  64.5243
 PTJ  O16  O  OH1   0  -0.761   5.0042  26.6609  65.5944
 PTJ  O17  O  OH1   0  -0.738   7.3746  26.4411  65.0415
 PTJ  O14  O  O2    0  -0.588   5.6543  26.7081  63.1672
 PTJ  C16  C  CH2   0  -0.173   5.8849  28.1073  62.9557
 PTJ  C13  C  CT    0  -0.178   4.6818  28.7465  62.2633
 PTJ  C14  C  CH3   0  -0.675   5.0322  30.2243  62.0658
 PTJ  C15  C  CH3   0  -0.650   4.4637  28.0806  60.9041
 PTJ  C12  C  CH1   0  -0.030   3.4307  28.5648  63.1736
 PTJ  O13  O  OH1   0  -0.671   3.6357  29.0438  64.4720
 PTJ  C11  C  C     0   0.573   2.2434  29.2947  62.5826
 PTJ  O12  O  O     0  -0.399   1.5118  28.8647  61.7379
 PTJ  O11  O  O2    0  -0.570   2.0907  30.5306  63.1020
 PTJ  P    P  P     0   1.467   1.1685  31.6647  62.3553
 PTJ  O1P  O  OH1   0  -0.706  -0.3270  31.2901  62.6964
 PTJ  O2P  O  O     0  -0.673   1.5520  31.8785  60.9509
 PTJ  O5'  O  O2    0  -0.565   1.3925  32.8608  63.3713
 PTJ  C5'  C  CH2   0  -0.197   2.6956  33.4326  63.5397
 PTJ  C4'  C  CH1   0  -0.029   2.6232  34.9253  63.2556
 PTJ  O4'  O  O2    0  -0.490   3.8790  35.4892  63.6332
 PTJ  C3'  C  CH1   0  -0.038   2.4216  35.2875  61.7795
 PTJ  O3'  O  OH1   0  -0.667   1.8753  36.5699  61.6283
 PTJ  C2'  C  CH1   0  -0.013   3.8635  35.3381  61.2981
 PTJ  O2'  O  OH1   0  -0.647   4.0119  36.0437  60.1103
 PTJ  C1'  C  CH1   0   0.185   4.5495  35.9907  62.5054
 PTJ  N9   N  NR5   0  -0.545   5.9547  35.7033  62.6127
 PTJ  C8   C  CR15  0   0.126   6.5548  34.4754  62.7227
 PTJ  N7   N  N     0  -0.444   7.8459  34.5394  62.8361
 PTJ  C5   C  CR56  0  -0.010   8.1257  35.8817  62.8035
 PTJ  C4   C  CR56  0   0.493   6.9644  36.6242  62.6723
 PTJ  N3   N  N     0  -0.457   6.8739  37.9498  62.6148
 PTJ  C2   C  CR16  0   0.048   8.0617  38.5242  62.6997
 PTJ  N1   N  N     0  -0.474   9.2528  37.9456  62.8242
 PTJ  C6   C  CR6   0   0.463   9.3273  36.6108  62.8795
 PTJ  N6   N  NH2   0  -0.815  10.5185  36.0271  63.0047
 PTJ  H1   H  HOH1  0   0.512   4.5469  26.0564  66.1952
 PTJ  H2   H  HOH1  0   0.503   8.1265  26.1033  64.5354
 PTJ  H3   H  HCH2  0   0.264   6.7580  28.2029  62.3068
 PTJ  H4   H  HCH2  0   0.255   6.1161  28.6263  63.8890
 PTJ  H5   H  HCH3  0   0.245   5.0838  30.7656  63.0119
 PTJ  H6   H  HCH3  0   0.250   6.0042  30.3180  61.5787
 PTJ  H7   H  HCH3  0   0.236   4.3121  30.7262  61.4169
 PTJ  H8   H  HCH3  0   0.242   4.1723  27.0344  60.9998
 PTJ  H9   H  HCH3  0   0.242   3.6955  28.5870  60.3207
 PTJ  H10  H  HCH3  0   0.239   5.3852  28.1197  60.3211
 PTJ  H11  H  HCH1  0   0.278   3.1591  27.5023  63.1677
 PTJ  H12  H  HOH1  0   0.466   3.9540  28.3172  65.0215
 PTJ  H13  H  HOH1  0   0.515  -0.8603  31.0282  61.9328
 PTJ  H14  H  HCH2  0   0.289   3.0041  33.2620  64.5710
 PTJ  H15  H  HCH2  0   0.214   3.4346  32.9475  62.8934
 PTJ  H16  H  HCH1  0   0.278   1.8333  35.3628  63.8745
 PTJ  H17  H  HCH1  0   0.264   1.8378  34.5316  61.2433
 PTJ  H18  H  HOH1  0   0.462   0.9552  36.5444  61.9093
 PTJ  H19  H  HCH1  0   0.237   4.2182  34.3026  61.1941
 PTJ  H20  H  HOH1  0   0.464   4.8544  35.8066  59.7115
 PTJ  H21  H  HCH1  0   0.269   4.4666  37.0804  62.4407
 PTJ  H22  H  HCR5  0   0.275   5.9864  33.5570  62.7218
 PTJ  H23  H  HCR6  0   0.254   8.0716  39.6082  62.6628
 PTJ  H24  H  HNH2  0   0.405  11.3554  36.5829  63.0456
 PTJ  H25  H  HNH2  0   0.413  10.6082  35.0266  63.0317

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
 PTJ  O2'  C2'  single    1.390  0.020  1.390
 PTJ  O2P  P    double    1.471  0.020  1.471
 PTJ  C2'  C3'  single    1.521  0.020  1.521
 PTJ  C2'  C1'  single    1.534  0.020  1.534
 PTJ  C8   N7   aromatic  1.298  0.020  1.298
 PTJ  C8   N9   aromatic  1.371  0.020  1.371
 PTJ  N7   C5   aromatic  1.372  0.020  1.372
 PTJ  C15  C13  single    1.529  0.020  1.529
 PTJ  C3'  O3'  single    1.402  0.020  1.402
 PTJ  C3'  C4'  single    1.533  0.020  1.533
 PTJ  N9   C1'  single    1.438  0.020  1.438
 PTJ  N9   C4   aromatic  1.368  0.020  1.368
 PTJ  O12  C11  double    1.197  0.020  1.197
 PTJ  P    O1P  single    1.579  0.020  1.579
 PTJ  P    O5'  single    1.585  0.020  1.585
 PTJ  P    O11  single    1.641  0.020  1.641
 PTJ  N6   C6   single    1.332  0.020  1.332
 PTJ  C5   C4   aromatic  1.385  0.020  1.385
 PTJ  C5   C6   aromatic  1.408  0.020  1.408
 PTJ  C1'  O4'  single    1.405  0.020  1.405
 PTJ  C11  O11  single    1.349  0.020  1.349
 PTJ  C11  C12  single    1.514  0.020  1.514
 PTJ  C14  C13  single    1.532  0.020  1.532
 PTJ  O5'  C5'  single    1.433  0.020  1.433
 PTJ  C4   N3   aromatic  1.330  0.020  1.330
 PTJ  C5'  C4'  single    1.521  0.020  1.521
 PTJ  C6   N1   aromatic  1.338  0.020  1.338
 PTJ  C13  C12  single    1.558  0.020  1.558
 PTJ  C13  C16  single    1.528  0.020  1.528
 PTJ  C4'  O4'  single    1.427  0.020  1.427
 PTJ  C12  O13  single    1.399  0.020  1.399
 PTJ  C16  O14  single    1.434  0.020  1.434
 PTJ  N3   C2   aromatic  1.322  0.020  1.322
 PTJ  O14  P1   single    1.590  0.020  1.590
 PTJ  N1   C2   aromatic  1.330  0.020  1.330
 PTJ  O15  P1   double    1.473  0.020  1.473
 PTJ  O17  P1   single    1.596  0.020  1.596
 PTJ  P1   O16  single    1.604  0.020  1.604
 PTJ  O16  H1   single    0.850  0.020  0.980
 PTJ  O17  H2   single    0.850  0.020  0.980
 PTJ  C16  H3   single    0.970  0.020  1.090
 PTJ  C16  H4   single    0.970  0.020  1.090
 PTJ  C14  H5   single    0.970  0.020  1.090
 PTJ  C14  H6   single    0.970  0.020  1.090
 PTJ  C14  H7   single    0.970  0.020  1.090
 PTJ  C15  H8   single    0.970  0.020  1.090
 PTJ  C15  H9   single    0.970  0.020  1.090
 PTJ  C15  H10  single    0.970  0.020  1.090
 PTJ  C12  H11  single    0.970  0.020  1.090
 PTJ  O13  H12  single    0.850  0.020  0.980
 PTJ  O1P  H13  single    0.850  0.020  0.980
 PTJ  C5'  H14  single    0.970  0.020  1.090
 PTJ  C5'  H15  single    0.970  0.020  1.090
 PTJ  C4'  H16  single    0.970  0.020  1.090
 PTJ  C3'  H17  single    0.970  0.020  1.090
 PTJ  O3'  H18  single    0.850  0.020  0.980
 PTJ  C2'  H19  single    0.970  0.020  1.090
 PTJ  O2'  H20  single    0.850  0.020  0.980
 PTJ  C1'  H21  single    0.970  0.020  1.090
 PTJ  C8   H22  single    0.930  0.020  1.080
 PTJ  C2   H23  single    0.930  0.020  1.080
 PTJ  N6   H24  single    0.860  0.020  1.020
 PTJ  N6   H25  single    0.860  0.020  1.020

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
 PTJ  O14  P1   O17  106.81  3.000
 PTJ  O17  P1   O16   99.61  3.000
 PTJ  O14  P1   O16  103.77  3.000
 PTJ  O16  P1   O15  116.42  3.000
 PTJ  O17  P1   O15  117.45  3.000
 PTJ  O14  P1   O15  111.27  3.000
 PTJ  H1   O16  P1   114.26  3.000
 PTJ  H2   O17  P1   114.34  3.000
 PTJ  C16  O14  P1   124.78  3.000
 PTJ  H4   C16  H3   107.26  3.000
 PTJ  H4   C16  C13  110.79  3.000
 PTJ  H3   C16  C13  108.88  3.000
 PTJ  H4   C16  O14  111.81  3.000
 PTJ  H3   C16  O14  107.56  3.000
 PTJ  C13  C16  O14  110.39  3.000
 PTJ  C12  C13  C15  110.74  3.000
 PTJ  C12  C13  C14  111.82  3.000
 PTJ  C15  C13  C14  109.77  3.000
 PTJ  C12  C13  C16  108.58  3.000
 PTJ  C14  C13  C16  106.37  3.000
 PTJ  C15  C13  C16  109.44  3.000
 PTJ  H7   C14  H6   106.42  3.000
 PTJ  H7   C14  H5   108.57  3.000
 PTJ  H6   C14  H5   107.60  3.000
 PTJ  H7   C14  C13  111.68  3.000
 PTJ  H6   C14  C13  110.14  3.000
 PTJ  H5   C14  C13  112.19  3.000
 PTJ  H10  C15  H9   107.02  3.000
 PTJ  H10  C15  H8   107.88  3.000
 PTJ  H9   C15  H8   107.73  3.000
 PTJ  H10  C15  C13  109.81  3.000
 PTJ  H9   C15  C13  111.97  3.000
 PTJ  H8   C15  C13  112.21  3.000
 PTJ  H11  C12  C11  105.71  3.000
 PTJ  H11  C12  O13  111.90  3.000
 PTJ  C11  C12  O13  108.19  3.000
 PTJ  H11  C12  C13  107.99  3.000
 PTJ  O13  C12  C13  112.62  3.000
 PTJ  C11  C12  C13  110.21  3.000
 PTJ  H12  O13  C12  108.60  3.000
 PTJ  O11  C11  O12  122.10  3.000
 PTJ  O11  C11  C12  112.34  3.000
 PTJ  O12  C11  C12  125.55  3.000
 PTJ  P    O11  C11  121.42  3.000
 PTJ  O5'  P    O2P  117.72  3.000
 PTJ  O5'  P    O1P  100.04  3.000
 PTJ  O2P  P    O1P  119.18  3.000
 PTJ  O5'  P    O11   98.65  3.000
 PTJ  O1P  P    O11  105.66  3.000
 PTJ  O2P  P    O11  112.84  3.000
 PTJ  H13  O1P  P    114.58  3.000
 PTJ  C5'  O5'  P    120.33  3.000
 PTJ  H15  C5'  H14  107.34  3.000
 PTJ  H15  C5'  C4'  110.89  3.000
 PTJ  H14  C5'  C4'  110.11  3.000
 PTJ  H15  C5'  O5'  111.56  3.000
 PTJ  H14  C5'  O5'  107.83  3.000
 PTJ  C4'  C5'  O5'  109.05  3.000
 PTJ  H16  C4'  C3'  110.80  3.000
 PTJ  H16  C4'  O4'  109.11  3.000
 PTJ  C3'  C4'  O4'  106.08  3.000
 PTJ  H16  C4'  C5'  108.71  3.000
 PTJ  O4'  C4'  C5'  107.24  3.000
 PTJ  C3'  C4'  C5'  114.70  3.000
 PTJ  C1'  O4'  C4'  110.40  3.000
 PTJ  H17  C3'  C2'  111.92  3.000
 PTJ  H17  C3'  O3'  111.76  3.000
 PTJ  C2'  C3'  O3'  107.75  3.000
 PTJ  H17  C3'  C4'  112.23  3.000
 PTJ  O3'  C3'  C4'  111.78  3.000
 PTJ  C2'  C3'  C4'  100.83  3.000
 PTJ  H18  O3'  C3'  108.47  3.000
 PTJ  H19  C2'  C1'  109.32  3.000
 PTJ  H19  C2'  O2'  111.28  3.000
 PTJ  C1'  C2'  O2'  114.13  3.000
 PTJ  H19  C2'  C3'  107.73  3.000
 PTJ  C1'  C2'  C3'  100.89  3.000
 PTJ  O2'  C2'  C3'  112.87  3.000
 PTJ  H20  O2'  C2'  108.82  3.000
 PTJ  H21  C1'  N9   106.10  3.000
 PTJ  H21  C1'  C2'  110.06  3.000
 PTJ  N9   C1'  C2'  114.23  3.000
 PTJ  H21  C1'  O4'  111.51  3.000
 PTJ  N9   C1'  O4'  109.58  3.000
 PTJ  C2'  C1'  O4'  105.46  3.000
 PTJ  C4   N9   C8   106.04  3.000
 PTJ  C4   N9   C1'  126.15  3.000
 PTJ  C8   N9   C1'  127.78  3.000
 PTJ  H22  C8   N7   124.45  3.000
 PTJ  H22  C8   N9   122.08  3.000
 PTJ  N7   C8   N9   113.47  3.000
 PTJ  C5   N7   C8   104.43  3.000
 PTJ  C6   C5   C4   116.32  3.000
 PTJ  C6   C5   N7   132.84  3.000
 PTJ  C4   C5   N7   110.85  3.000
 PTJ  N3   C4   C5   126.56  3.000
 PTJ  N3   C4   N9   128.24  3.000
 PTJ  C5   C4   N9   105.20  3.000
 PTJ  C2   N3   C4   111.66  3.000
 PTJ  H23  C2   N1   115.45  3.000
 PTJ  H23  C2   N3   116.12  3.000
 PTJ  N1   C2   N3   128.43  3.000
 PTJ  C6   N1   C2   119.19  3.000
 PTJ  N6   C6   N1   119.39  3.000
 PTJ  N1   C6   C5   117.84  3.000
 PTJ  N6   C6   C5   122.77  3.000
 PTJ  H25  N6   H24  118.36  3.000
 PTJ  H25  N6   C6   121.23  3.000
 PTJ  H24  N6   C6   120.38  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
 PTJ  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 PTJ  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 PTJ  CONST_03  C6   C5   C4   N9    180.00   0.0  0
 PTJ  CONST_04  C2   N3   C4   N9    180.00   0.0  0
 PTJ  CONST_05  C4   C5   N7   C8      0.00   0.0  0
 PTJ  CONST_06  C6   C5   N7   C8    180.00   0.0  0
 PTJ  CONST_07  C5   C4   N9   C8      0.00   0.0  0
 PTJ  CONST_08  N3   C4   N9   C8    180.00   0.0  0
 PTJ  CONST_09  C4   N9   C8   N7      0.00   0.0  0
 PTJ  CONST_10  N3   C4   C5   N7    180.00   0.0  0
 PTJ  CONST_11  N1   C6   C5   N7    180.00   0.0  0
 PTJ  CONST_12  C2   N3   C4   C5      0.00   0.0  0
 PTJ  CONST_13  C2   N1   C6   C5      0.00   0.0  0
 PTJ  CONST_14  N1   C6   C5   C4      0.00   0.0  0
 PTJ  CONST_15  N1   C2   N3   C4      0.00   0.0  0
 PTJ  CONST_16  C6   C5   C4   N3      0.00   0.0  0
 PTJ  CONST_17  C6   N1   C2   N3      0.00   0.0  0
 PTJ  CONST_18  N7   C8   N9   C1'   180.00   0.0  0
 PTJ  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 PTJ  CONST_20  N3   C4   N9   C1'     0.00   0.0  0
 PTJ  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 PTJ  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 PTJ  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 PTJ  CONST_24  H22  C8   N9   C1'     0.00   0.0  0
 PTJ  CONST_25  H23  C2   N3   C4    180.00   0.0  0
 PTJ  CONST_26  H24  N6   C6   C5    180.00   0.0  0
 PTJ  CONST_27  H25  N6   C6   C5      0.00   0.0  0
 PTJ  Var_01    C4'  C5'  O5'  P     123.40  30.0  3
 PTJ  Var_02    C13  C16  O14  P1   -134.44  30.0  2
 PTJ  Var_03    C15  C13  C16  O14   -60.68  30.0  1
 PTJ  Var_04    O2P  P    O11  C11   -53.65  30.0  2
 PTJ  Var_05    H8   C15  C13  C16    65.90  30.0  3
 PTJ  Var_06    H5   C14  C13  C16   -68.26  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
 PTJ  chir_01  C12  C11  C13  O13  negativ
 PTJ  chir_03  C4'  C3'  C5'  O4'  negativ
 PTJ  chir_04  C3'  O3'  C2'  C4'  negativ
 PTJ  chir_05  C2'  O2'  C1'  C3'  negativ
 PTJ  chir_06  C1'  O4'  N9   C2'  negativ
 PTJ  chir_07  P    O1P  O5'  O11  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
 PTJ  plan-1  C1'  0.020
 PTJ  plan-1  N9   0.020
 PTJ  plan-1  C8   0.020
 PTJ  plan-1  N7   0.020
 PTJ  plan-1  C5   0.020
 PTJ  plan-1  C4   0.020
 PTJ  plan-1  N3   0.020
 PTJ  plan-1  C2   0.020
 PTJ  plan-1  N1   0.020
 PTJ  plan-1  C6   0.020
 PTJ  plan-1  N6   0.020
 PTJ  plan-1  H22  0.020
 PTJ  plan-1  H23  0.020
 PTJ  plan-2  C6   0.020
 PTJ  plan-2  N6   0.020
 PTJ  plan-2  H24  0.020
 PTJ  plan-2  H25  0.020
 PTJ  plan-3  C12  0.020
 PTJ  plan-3  C11  0.020
 PTJ  plan-3  O12  0.020
 PTJ  plan-3  O11  0.020

