# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 22:43:43 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{R})-2-methyl-3-oxidanyl-propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CO)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
 8LH  8LH  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{R})-2-methyl-3-oxidanyl-propanoate'  ligand  49  29  .  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_8LH
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
 8LH  C1   C  CR56  0   0.486   2.8533   1.1549  -0.2215
 8LH  C2   C  CR56  0  -0.002   3.2129   1.7778   0.9630
 8LH  C3   C  CR6   0   0.455   4.3582   2.5945   0.9138
 8LH  C4   C  CR15  0   0.091   1.4703   0.6671   1.4012
 8LH  N1   N  N     0  -0.474   4.9958   2.7095  -0.2566
 8LH  N2   N  N     0  -0.459   3.4754   1.2615  -1.3950
 8LH  C5   C  CH2   0  -0.124  -5.0741   2.1482  -0.9495
 8LH  C6   C  CH1   0  -0.419  -4.0235   1.0464  -0.8960
 8LH  C7   C  CH3   0  -0.673  -2.7115   1.4506  -1.5804
 8LH  C8   C  C     0   0.616  -3.7436   0.6698   0.5320
 8LH  O2   O  O     0  -0.401  -4.0328   1.3016   1.5069
 8LH  O3   O  O2    0  -0.581  -3.0781  -0.5099   0.6124
 8LH  P1   P  P     0   1.490  -2.5062  -1.1006   2.0303
 8LH  O4   O  OH1   0  -0.718  -3.7895  -1.5188   2.8568
 8LH  O5   O  O     0  -0.676  -1.6107  -0.2121   2.7844
 8LH  O6   O  O2    0  -0.577  -1.9100  -2.4782   1.5142
 8LH  C10  C  CH1   0   0.016  -0.0907  -2.2722  -0.0962
 8LH  O7   O  O2    0  -0.498  -0.1723  -0.8588  -0.2372
 8LH  C11  C  CH1   0  -0.041   1.3651  -2.6228  -0.3958
 8LH  O8   O  OH1   0  -0.654   1.4471  -3.9266  -0.8940
 8LH  C12  C  CH1   0  -0.046   1.7392  -1.5412  -1.4161
 8LH  O9   O  OH1   0  -0.664   1.2238  -1.8464  -2.6817
 8LH  C13  C  CH1   0   0.193   0.9554  -0.3444  -0.8795
 8LH  N3   N  NR5   0  -0.543   1.7372   0.4295   0.0792
 8LH  N4   N  N     0  -0.452   2.3350   1.4607   1.9646
 8LH  C14  C  CR16  0   0.038   4.5288   2.0558  -1.3173
 8LH  N5   N  NH2   0  -0.816   4.8172   3.2572   1.9762
 8LH  H1   H  HCR5  0   0.300   0.6077   0.2476   1.8954
 8LH  H2   H  HOH1  0   0.458  -5.9745   3.1352  -2.3506
 8LH  H4   H  HCH2  0   0.213  -5.9631   1.8354  -0.3879
 8LH  H5   H  HCH1  0   0.287  -4.4181   0.1570  -1.3990
 8LH  H6   H  HCH3  0   0.258  -1.9820   0.6442  -1.5472
 8LH  H7   H  HCH3  0   0.254  -2.8947   1.6923  -2.6249
 8LH  H8   H  HCH3  0   0.233  -2.2762   2.3283  -1.1000
 8LH  H9   H  HOH1  0   0.506  -4.4299  -2.1006   2.4245
 8LH  H10  H  HCH2  0   0.249   0.0832  -2.1945   2.0573
 8LH  H11  H  HCH2  0   0.277  -0.3569  -3.7686   1.3911
 8LH  H12  H  HCH1  0   0.261  -0.7467  -2.7493  -0.8317
 8LH  H13  H  HCH1  0   0.254   1.9808  -2.4970   0.5044
 8LH  H14  H  HOH1  0   0.471   2.3529  -4.2400  -0.8027
 8LH  H15  H  HCH1  0   0.267   2.8175  -1.3493  -1.4483
 8LH  H16  H  HOH1  0   0.453   1.3182  -2.7974  -2.8179
 8LH  H17  H  HCH1  0   0.285   0.6540   0.3303  -1.6858
 8LH  H18  H  HCR6  0   0.252   5.0907   2.1955  -2.2346
 8LH  H19  H  HNH2  0   0.411   4.3915   3.1459   2.8794
 8LH  H20  H  HNH2  0   0.403   5.6678   3.7893   1.9127
 8LH  C9   C  CH2   0  -0.195  -0.5114  -2.6948   1.2891
 8LH  H3   H  HCH2  0   0.204  -4.6847   3.0510  -0.4635
 8LH  O1   O  OH1   0  -0.669  -5.3818   2.3800  -2.3038

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
 8LH  O5   P1   double    1.470  0.020  1.470
 8LH  O4   P1   single    1.583  0.020  1.583
 8LH  P1   O3   single    1.639  0.020  1.639
 8LH  P1   O6   single    1.587  0.020  1.587
 8LH  O3   C8   single    1.357  0.020  1.357
 8LH  C7   C6   single    1.534  0.020  1.534
 8LH  O6   C9   single    1.433  0.020  1.433
 8LH  C8   C6   single    1.503  0.020  1.503
 8LH  C8   O2   double    1.197  0.020  1.197
 8LH  C9   C10  single    1.508  0.020  1.508
 8LH  C6   C5   single    1.523  0.020  1.523
 8LH  C10  C11  single    1.527  0.020  1.527
 8LH  C10  O7   single    1.423  0.020  1.423
 8LH  O8   C11  single    1.398  0.020  1.398
 8LH  C11  C12  single    1.533  0.020  1.533
 8LH  C5   O1   single    1.408  0.020  1.408
 8LH  O7   C13  single    1.396  0.020  1.396
 8LH  O9   C12  single    1.400  0.020  1.400
 8LH  C12  C13  single    1.528  0.020  1.528
 8LH  C13  N3   single    1.459  0.020  1.459
 8LH  C4   N3   aromatic  1.369  0.020  1.369
 8LH  C4   N4   aromatic  1.302  0.020  1.302
 8LH  N3   C1   aromatic  1.365  0.020  1.365
 8LH  N4   C2   aromatic  1.369  0.020  1.369
 8LH  C1   C2   aromatic  1.386  0.020  1.386
 8LH  C1   N2   aromatic  1.333  0.020  1.333
 8LH  C2   C3   aromatic  1.407  0.020  1.407
 8LH  N2   C14  aromatic  1.322  0.020  1.322
 8LH  C3   N5   single    1.334  0.020  1.334
 8LH  C3   N1   aromatic  1.338  0.020  1.338
 8LH  C14  N1   aromatic  1.331  0.020  1.331
 8LH  C4   H1   single    0.930  0.020  1.080
 8LH  O1   H2   single    0.850  0.020  0.980
 8LH  C5   H3   single    0.970  0.020  1.090
 8LH  C5   H4   single    0.970  0.020  1.090
 8LH  C6   H5   single    0.970  0.020  1.090
 8LH  C7   H6   single    0.970  0.020  1.090
 8LH  C7   H7   single    0.970  0.020  1.090
 8LH  C7   H8   single    0.970  0.020  1.090
 8LH  O4   H9   single    0.850  0.020  0.980
 8LH  C9   H10  single    0.970  0.020  1.090
 8LH  C9   H11  single    0.970  0.020  1.090
 8LH  C10  H12  single    0.970  0.020  1.090
 8LH  C11  H13  single    0.970  0.020  1.090
 8LH  O8   H14  single    0.850  0.020  0.980
 8LH  C12  H15  single    0.970  0.020  1.090
 8LH  O9   H16  single    0.850  0.020  0.980
 8LH  C13  H17  single    0.970  0.020  1.090
 8LH  C14  H18  single    0.930  0.020  1.080
 8LH  N5   H19  single    0.860  0.020  1.020
 8LH  N5   H20  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
 8LH  N3   C1   N2   128.20  3.000
 8LH  N2   C1   C2   126.56  3.000
 8LH  N3   C1   C2   105.24  3.000
 8LH  N4   C2   C3   132.97  3.000
 8LH  C3   C2   C1   116.24  3.000
 8LH  N4   C2   C1   110.78  3.000
 8LH  N5   C3   N1   119.35  3.000
 8LH  N1   C3   C2   117.92  3.000
 8LH  N5   C3   C2   122.72  3.000
 8LH  H1   C4   N4   124.73  3.000
 8LH  H1   C4   N3   122.04  3.000
 8LH  N4   C4   N3   113.21  3.000
 8LH  C14  N1   C3   119.21  3.000
 8LH  C14  N2   C1   111.62  3.000
 8LH  H4   C5   H3   107.19  3.000
 8LH  H4   C5   C6   109.55  3.000
 8LH  H3   C5   C6   109.57  3.000
 8LH  H4   C5   O1   111.24  3.000
 8LH  H3   C5   O1   111.61  3.000
 8LH  C6   C5   O1   107.67  3.000
 8LH  H5   C6   C8   107.45  3.000
 8LH  H5   C6   C7   108.49  3.000
 8LH  C8   C6   C7   109.30  3.000
 8LH  H5   C6   C5   108.83  3.000
 8LH  C8   C6   C5   110.06  3.000
 8LH  C7   C6   C5   112.56  3.000
 8LH  H8   C7   H7   108.13  3.000
 8LH  H8   C7   H6   108.38  3.000
 8LH  H7   C7   H6   107.88  3.000
 8LH  H8   C7   C6   110.90  3.000
 8LH  H7   C7   C6   110.05  3.000
 8LH  H6   C7   C6   111.39  3.000
 8LH  O3   C8   O2   121.94  3.000
 8LH  O2   C8   C6   126.61  3.000
 8LH  O3   C8   C6   111.44  3.000
 8LH  P1   O3   C8   122.40  3.000
 8LH  O6   P1   O5   117.56  3.000
 8LH  O6   P1   O4   104.18  3.000
 8LH  O5   P1   O4   112.70  3.000
 8LH  O6   P1   O3    99.36  3.000
 8LH  O4   P1   O3   105.31  3.000
 8LH  O5   P1   O3   116.01  3.000
 8LH  H9   O4   P1   117.54  3.000
 8LH  C9   O6   P1   123.29  3.000
 8LH  H12  C10  C11  109.84  3.000
 8LH  H12  C10  O7   109.39  3.000
 8LH  C11  C10  O7   105.26  3.000
 8LH  H12  C10  C9   109.14  3.000
 8LH  O7   C10  C9   110.69  3.000
 8LH  C11  C10  C9   112.44  3.000
 8LH  C13  O7   C10  111.43  3.000
 8LH  H13  C11  C12  109.15  3.000
 8LH  H13  C11  O8   111.47  3.000
 8LH  C12  C11  O8   113.98  3.000
 8LH  H13  C11  C10  110.33  3.000
 8LH  C12  C11  C10  101.61  3.000
 8LH  O8   C11  C10  109.87  3.000
 8LH  H14  O8   C11  108.97  3.000
 8LH  H15  C12  C13  112.21  3.000
 8LH  H15  C12  O9   111.95  3.000
 8LH  C13  C12  O9   107.42  3.000
 8LH  H15  C12  C11  112.53  3.000
 8LH  C13  C12  C11  101.17  3.000
 8LH  O9   C12  C11  110.97  3.000
 8LH  H16  O9   C12  107.83  3.000
 8LH  H17  C13  N3   107.75  3.000
 8LH  H17  C13  C12  111.45  3.000
 8LH  N3   C13  C12  111.80  3.000
 8LH  H17  C13  O7   110.12  3.000
 8LH  N3   C13  O7   109.02  3.000
 8LH  C12  C13  O7   106.70  3.000
 8LH  C13  N3   C4   128.45  3.000
 8LH  C4   N3   C1   106.25  3.000
 8LH  C13  N3   C1   125.13  3.000
 8LH  C4   N4   C2   104.50  3.000
 8LH  H18  C14  N2   116.14  3.000
 8LH  H18  C14  N1   115.41  3.000
 8LH  N2   C14  N1   128.45  3.000
 8LH  H20  N5   H19  118.30  3.000
 8LH  H20  N5   C3   120.25  3.000
 8LH  H19  N5   C3   121.01  3.000
 8LH  H11  C9   H10  107.96  3.000
 8LH  H11  C9   C10  108.81  3.000
 8LH  H10  C9   C10  111.45  3.000
 8LH  H11  C9   O6   105.82  3.000
 8LH  H10  C9   O6   110.58  3.000
 8LH  C10  C9   O6   111.97  3.000
 8LH  H2   O1   C5   108.12  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
 8LH  CONST_01  N4   C4   N3  C1     0.00   0.0  0
 8LH  CONST_02  C4   N4   C2  C1     0.00   0.0  0
 8LH  CONST_03  N1   C3   C2  C1     0.00   0.0  0
 8LH  CONST_04  N1   C14  N2  C1     0.00   0.0  0
 8LH  CONST_05  N3   C4   N4  C2     0.00   0.0  0
 8LH  CONST_06  C4   N3   C1  C2     0.00   0.0  0
 8LH  CONST_07  C14  N2   C1  C2     0.00   0.0  0
 8LH  CONST_08  C14  N1   C3  C2     0.00   0.0  0
 8LH  CONST_09  C4   N4   C2  C3   180.00   0.0  0
 8LH  CONST_10  N3   C1   C2  C3   180.00   0.0  0
 8LH  CONST_11  N2   C1   C2  C3     0.00   0.0  0
 8LH  CONST_12  N2   C14  N1  C3     0.00   0.0  0
 8LH  CONST_13  N2   C1   N3  C4   180.00   0.0  0
 8LH  CONST_14  N4   C2   C3  N1   180.00   0.0  0
 8LH  CONST_15  N4   C2   C1  N2   180.00   0.0  0
 8LH  CONST_16  N4   C2   C1  N3     0.00   0.0  0
 8LH  CONST_17  C14  N2   C1  N3   180.00   0.0  0
 8LH  CONST_18  C13  N3   C1  C2   180.00   0.0  0
 8LH  CONST_19  C13  N3   C1  N2     0.00   0.0  0
 8LH  CONST_20  N4   C4   N3  C13  180.00   0.0  0
 8LH  CONST_21  N5   C3   C2  C1   180.00   0.0  0
 8LH  CONST_22  N5   C3   C2  N4     0.00   0.0  0
 8LH  CONST_23  N5   C3   N1  C14  180.00   0.0  0
 8LH  CONST_24  H1   C4   N3  C1   180.00   0.0  0
 8LH  CONST_25  H18  C14  N2  C1   180.00   0.0  0
 8LH  CONST_26  H19  N5   C3  C2     0.00   0.0  0
 8LH  CONST_27  H20  N5   C3  C2   180.00   0.0  0
 8LH  Var_01    C10  C9   O6  P1   -86.67  30.0  3
 8LH  Var_02    O5   P1   O3  C8   -55.36  30.0  2

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
 8LH  chir_01  C6   C7  C8   C5   negativ
 8LH  chir_03  C10  O7  C9   C11  positiv
 8LH  chir_04  C11  O8  C10  C12  positiv
 8LH  chir_05  C12  O9  C11  C13  positiv
 8LH  chir_06  C13  O7  N3   C12  negativ
 8LH  chir_07  P1   O4  O3   O6   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
 8LH  plan-1  C1   0.020
 8LH  plan-1  C2   0.020
 8LH  plan-1  C3   0.020
 8LH  plan-1  C4   0.020
 8LH  plan-1  N1   0.020
 8LH  plan-1  N2   0.020
 8LH  plan-1  C13  0.020
 8LH  plan-1  N3   0.020
 8LH  plan-1  N4   0.020
 8LH  plan-1  C14  0.020
 8LH  plan-1  N5   0.020
 8LH  plan-1  H1   0.020
 8LH  plan-1  H18  0.020
 8LH  plan-2  C3   0.020
 8LH  plan-2  N5   0.020
 8LH  plan-2  H19  0.020
 8LH  plan-2  H20  0.020
 8LH  plan-3  C6   0.020
 8LH  plan-3  C8   0.020
 8LH  plan-3  O2   0.020
 8LH  plan-3  O3   0.020

