# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 16:45:03 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 5-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]methyl]-4-azanyl-1-(methoxymethyl)pyrimidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCN1C=C(CNC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)C(=NC1=O)N
#
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
 LHB  LHB  5-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]methyl]-4-azanyl-1-(methoxymethyl)pyrimidin-2-one  ligand  54  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LHB
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
 LHB  C1   C  CR6   0   0.461  -4.7616  -2.5814  -0.5354
 LHB  C2   C  CR56  0  -0.012  -3.8722  -1.6481   0.0283
 LHB  C3   C  CR56  0   0.494  -3.8514  -0.3905  -0.5523
 LHB  N1   N  N     0  -0.458  -4.5815   0.0148  -1.5880
 LHB  C4   C  CR16  0   0.048  -5.3737  -0.9453  -2.0329
 LHB  N2   N  N     0  -0.474  -5.5044  -2.1879  -1.5765
 LHB  N3   N  NR5   0  -0.540  -2.9349   0.3218   0.1684
 LHB  C5   C  CR15  0   0.112  -2.4517  -0.5355   1.1213
 LHB  N4   N  N     0  -0.445  -2.9861  -1.7177   1.0731
 LHB  C6   C  CH1   0   0.211  -2.5138   1.6763  -0.0841
 LHB  O1   O  O2    0  -0.494  -1.1594   1.6925  -0.4398
 LHB  C7   C  CH1   0  -0.030  -0.4588   2.7295   0.2616
 LHB  C8   C  CH1   0  -0.017  -1.5410   3.6202   0.8543
 LHB  C9   C  CH1   0  -0.057  -2.6503   2.6013   1.1272
 LHB  O2   O  OH1   0  -0.654  -3.9418   3.1296   1.1703
 LHB  O3   O  OH1   0  -0.669  -1.9422   4.5477  -0.1196
 LHB  C10  C  CH2   0  -0.282   0.4664   2.1252   1.3031
 LHB  N5   N  NH1   0  -0.587   1.4177   1.2346   0.6760
 LHB  C11  C  CH2   0  -0.361   2.3710   0.6711   1.6178
 LHB  C12  C  CR6   0  -0.117   3.2719  -0.3138   0.9383
 LHB  N6   N  NH2   0  -0.816  -4.8883  -3.8262  -0.0764
 LHB  C13  C  CR6   0   0.480   2.9110  -1.6820   0.6962
 LHB  N7   N  N     0  -0.534   3.6779  -2.5108   0.0192
 LHB  C14  C  CR6   0   0.597   4.8588  -2.1128  -0.4972
 LHB  N8   N  NR6   0  -0.532   5.2556  -0.7854  -0.2734
 LHB  C15  C  CR16  0   0.061   4.4595   0.0624   0.4166
 LHB  N9   N  NH2   0  -0.814   1.7391  -2.1509   1.1446
 LHB  C16  C  CH2   0  -0.053   6.5057  -0.3110  -0.8512
 LHB  O4   O  O2    0  -0.465   6.4245  -0.1024  -2.2192
 LHB  C17  C  CH3   0  -0.418   5.6378   1.0099  -2.5885
 LHB  O5   O  O     0  -0.516   5.5910  -2.8553  -1.1351
 LHB  H1   H  HCR6  0   0.253  -6.0020  -0.6914  -2.8803
 LHB  H2   H  HCR5  0   0.286  -1.7034  -0.2288   1.8378
 LHB  H3   H  HCH1  0   0.265  -3.1408   2.0379  -0.9058
 LHB  H4   H  HCH1  0   0.261   0.1474   3.2783  -0.4649
 LHB  H5   H  HCH1  0   0.251  -1.2024   4.1132   1.7751
 LHB  H6   H  HCH1  0   0.251  -2.4106   2.0565   2.0482
 LHB  H7   H  HOH1  0   0.470  -4.1285   3.4270   2.0663
 LHB  H8   H  HOH1  0   0.450  -2.8228   4.8640   0.1142
 LHB  H10  H  HCH2  0   0.249   1.0148   2.9419   1.7809
 LHB  H9   H  HCH2  0   0.199  -0.1165   1.6408   2.1063
 LHB  H11  H  HNH1  0   0.342   0.9224   0.4881   0.2028
 LHB  H12  H  HCH2  0   0.260   2.9751   1.4863   2.0237
 LHB  H13  H  HCH2  0   0.213   1.8872   0.2096   2.4942
 LHB  H14  H  HNH2  0   0.412  -4.3516  -4.1497   0.7089
 LHB  H15  H  HNH2  0   0.404  -5.5494  -4.4571  -0.4954
 LHB  H16  H  HCR6  0   0.313   4.8296   1.0729   0.5361
 LHB  H18  H  HNH2  0   0.406   1.2132  -1.6554   1.8433
 LHB  H17  H  HNH2  0   0.405   1.5530  -3.1372   1.0643
 LHB  H20  H  HCH2  0   0.241   6.7723   0.6062  -0.3144
 LHB  H19  H  HCH2  0   0.265   7.2784  -1.0559  -0.6791
 LHB  H22  H  HCH3  0   0.219   4.5761   0.8684  -2.3621
 LHB  H23  H  HCH3  0   0.216   5.9757   1.9271  -2.0939
 LHB  H21  H  HCH3  0   0.249   5.7390   1.1386  -3.6645

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
 LHB  C4   N2   aromatic  1.330  0.020  1.330
 LHB  C4   N1   aromatic  1.322  0.020  1.322
 LHB  N2   C1   aromatic  1.338  0.020  1.338
 LHB  N1   C3   aromatic  1.330  0.020  1.330
 LHB  C1   N6   single    1.333  0.020  1.333
 LHB  C1   C2   aromatic  1.407  0.020  1.407
 LHB  C3   C2   aromatic  1.385  0.020  1.385
 LHB  C3   N3   aromatic  1.366  0.020  1.366
 LHB  O2   C9   single    1.396  0.020  1.396
 LHB  C2   N4   aromatic  1.372  0.020  1.372
 LHB  C6   N3   single    1.441  0.020  1.441
 LHB  C6   C9   single    1.530  0.020  1.530
 LHB  C6   O1   single    1.400  0.020  1.400
 LHB  O3   C8   single    1.403  0.020  1.403
 LHB  N3   C5   aromatic  1.370  0.020  1.370
 LHB  C9   C8   single    1.531  0.020  1.531
 LHB  O1   C7   single    1.435  0.020  1.435
 LHB  C8   C7   single    1.522  0.020  1.522
 LHB  C7   C10  single    1.519  0.020  1.519
 LHB  N4   C5   aromatic  1.298  0.020  1.298
 LHB  C10  N5   single    1.446  0.020  1.446
 LHB  N5   C11  single    1.454  0.020  1.454
 LHB  N9   C13  single    1.340  0.020  1.340
 LHB  C11  C12  single    1.498  0.020  1.498
 LHB  C13  C12  single    1.436  0.020  1.436
 LHB  C13  N7   double    1.317  0.020  1.317
 LHB  C12  C15  double    1.351  0.020  1.351
 LHB  N7   C14  single    1.349  0.020  1.349
 LHB  C15  N8   single    1.352  0.020  1.352
 LHB  C14  N8   single    1.403  0.020  1.403
 LHB  C14  O5   double    1.222  0.020  1.222
 LHB  N8   C16  single    1.457  0.020  1.457
 LHB  C16  O4   single    1.386  0.020  1.386
 LHB  O4   C17  single    1.412  0.020  1.412
 LHB  C4   H1   single    0.930  0.020  1.080
 LHB  C5   H2   single    0.930  0.020  1.080
 LHB  C6   H3   single    0.970  0.020  1.090
 LHB  C7   H4   single    0.970  0.020  1.090
 LHB  C8   H5   single    0.970  0.020  1.090
 LHB  C9   H6   single    0.970  0.020  1.090
 LHB  O2   H7   single    0.850  0.020  0.980
 LHB  O3   H8   single    0.850  0.020  0.980
 LHB  C10  H10  single    0.970  0.020  1.090
 LHB  C10  H9   single    0.970  0.020  1.090
 LHB  N5   H11  single    0.890  0.020  1.040
 LHB  C11  H12  single    0.970  0.020  1.090
 LHB  C11  H13  single    0.970  0.020  1.090
 LHB  N6   H14  single    0.860  0.020  1.020
 LHB  N6   H15  single    0.860  0.020  1.020
 LHB  C15  H16  single    0.930  0.020  1.080
 LHB  N9   H18  single    0.890  0.020  1.040
 LHB  N9   H17  single    0.890  0.020  1.040
 LHB  C16  H20  single    0.970  0.020  1.090
 LHB  C16  H19  single    0.970  0.020  1.090
 LHB  C17  H22  single    0.970  0.020  1.090
 LHB  C17  H23  single    0.970  0.020  1.090
 LHB  C17  H21  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
 LHB  N6   C1   N2   119.33  3.000
 LHB  N6   C1   C2   122.80  3.000
 LHB  N2   C1   C2   117.87  3.000
 LHB  N4   C2   C3   110.83  3.000
 LHB  N4   C2   C1   132.83  3.000
 LHB  C3   C2   C1   116.34  3.000
 LHB  N3   C3   N1   128.31  3.000
 LHB  N3   C3   C2   105.20  3.000
 LHB  N1   C3   C2   126.48  3.000
 LHB  C4   N1   C3   111.69  3.000
 LHB  H1   C4   N2   115.45  3.000
 LHB  H1   C4   N1   116.10  3.000
 LHB  N2   C4   N1   128.45  3.000
 LHB  C4   N2   C1   119.16  3.000
 LHB  C6   N3   C5   127.38  3.000
 LHB  C5   N3   C3   106.10  3.000
 LHB  C6   N3   C3   126.42  3.000
 LHB  H2   C5   N4   124.63  3.000
 LHB  H2   C5   N3   121.86  3.000
 LHB  N4   C5   N3   113.50  3.000
 LHB  C5   N4   C2   104.36  3.000
 LHB  H3   C6   C9   110.08  3.000
 LHB  H3   C6   O1   111.06  3.000
 LHB  C9   C6   O1   106.28  3.000
 LHB  H3   C6   N3   105.94  3.000
 LHB  O1   C6   N3   109.76  3.000
 LHB  C9   C6   N3   113.80  3.000
 LHB  C7   O1   C6   110.89  3.000
 LHB  H4   C7   C10  108.52  3.000
 LHB  H4   C7   C8   111.05  3.000
 LHB  C10  C7   C8   113.52  3.000
 LHB  H4   C7   O1   107.98  3.000
 LHB  C10  C7   O1   110.20  3.000
 LHB  C8   C7   O1   105.44  3.000
 LHB  H5   C8   O3   111.92  3.000
 LHB  H5   C8   C9   111.89  3.000
 LHB  O3   C8   C9   110.88  3.000
 LHB  H5   C8   C7   111.73  3.000
 LHB  C9   C8   C7   101.26  3.000
 LHB  O3   C8   C7   108.65  3.000
 LHB  H6   C9   O2   111.36  3.000
 LHB  H6   C9   C8   108.78  3.000
 LHB  O2   C9   C8   115.09  3.000
 LHB  H6   C9   C6   110.18  3.000
 LHB  C8   C9   C6   101.34  3.000
 LHB  O2   C9   C6   109.62  3.000
 LHB  H7   O2   C9   108.98  3.000
 LHB  H8   O3   C8   108.03  3.000
 LHB  H9   C10  H10  105.94  3.000
 LHB  H9   C10  N5   113.11  3.000
 LHB  H10  C10  N5   108.63  3.000
 LHB  H9   C10  C7   110.60  3.000
 LHB  H10  C10  C7   107.94  3.000
 LHB  N5   C10  C7   110.39  3.000
 LHB  H11  N5   C11  109.72  3.000
 LHB  H11  N5   C10  109.55  3.000
 LHB  C11  N5   C10  112.90  3.000
 LHB  H13  C11  H12  105.05  3.000
 LHB  H13  C11  C12  110.45  3.000
 LHB  H12  C11  C12  109.06  3.000
 LHB  H13  C11  N5   112.93  3.000
 LHB  H12  C11  N5   108.29  3.000
 LHB  C12  C11  N5   110.82  3.000
 LHB  C15  C12  C13  114.92  3.000
 LHB  C15  C12  C11  121.40  3.000
 LHB  C13  C12  C11  123.51  3.000
 LHB  H15  N6   H14  118.36  3.000
 LHB  H15  N6   C1   120.34  3.000
 LHB  H14  N6   C1   121.28  3.000
 LHB  N9   C13  N7   117.48  3.000
 LHB  N7   C13  C12  122.70  3.000
 LHB  N9   C13  C12  119.81  3.000
 LHB  C14  N7   C13  121.41  3.000
 LHB  O5   C14  N8   119.23  3.000
 LHB  O5   C14  N7   123.02  3.000
 LHB  N8   C14  N7   117.75  3.000
 LHB  C16  N8   C15  120.23  3.000
 LHB  C16  N8   C14  119.18  3.000
 LHB  C15  N8   C14  120.52  3.000
 LHB  H16  C15  N8   116.11  3.000
 LHB  H16  C15  C12  121.19  3.000
 LHB  N8   C15  C12  122.70  3.000
 LHB  H17  N9   H18  116.21  3.000
 LHB  H17  N9   C13  118.55  3.000
 LHB  H18  N9   C13  121.19  3.000
 LHB  H19  C16  H20  108.86  3.000
 LHB  H19  C16  O4   107.52  3.000
 LHB  H20  C16  O4   111.83  3.000
 LHB  H19  C16  N8   108.90  3.000
 LHB  H20  C16  N8   106.68  3.000
 LHB  O4   C16  N8   112.97  3.000
 LHB  C17  O4   C16  114.17  3.000
 LHB  H21  C17  H23  108.58  3.000
 LHB  H21  C17  H22  108.06  3.000
 LHB  H23  C17  H22  108.30  3.000
 LHB  H21  C17  O4   107.46  3.000
 LHB  H23  C17  O4   111.70  3.000
 LHB  H22  C17  O4   112.61  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
 LHB  CONST_01  N1   C4   N2   C1     0.00   0.0  0
 LHB  CONST_02  N1   C3   C2   C1     0.00   0.0  0
 LHB  CONST_03  N3   C3   C2   C1   180.00   0.0  0
 LHB  CONST_04  C5   N4   C2   C1   180.00   0.0  0
 LHB  CONST_05  C4   N2   C1   C2     0.00   0.0  0
 LHB  CONST_06  C4   N1   C3   C2     0.00   0.0  0
 LHB  CONST_07  C5   N3   C3   C2     0.00   0.0  0
 LHB  CONST_08  N3   C5   N4   C2     0.00   0.0  0
 LHB  CONST_09  N2   C4   N1   C3     0.00   0.0  0
 LHB  CONST_10  N2   C1   C2   C3     0.00   0.0  0
 LHB  CONST_11  C5   N4   C2   C3     0.00   0.0  0
 LHB  CONST_12  N4   C5   N3   C3     0.00   0.0  0
 LHB  CONST_13  N4   C2   C3   N1   180.00   0.0  0
 LHB  CONST_14  C5   N3   C3   N1   180.00   0.0  0
 LHB  CONST_15  N3   C3   N1   C4   180.00   0.0  0
 LHB  CONST_16  N4   C2   C1   N2   180.00   0.0  0
 LHB  CONST_17  N4   C2   C3   N3     0.00   0.0  0
 LHB  CONST_18  C6   N3   C3   C2   180.00   0.0  0
 LHB  CONST_19  C6   N3   C3   N1     0.00   0.0  0
 LHB  CONST_20  C6   N3   C5   N4   180.00   0.0  0
 LHB  CONST_21  C14  N7   C13  C12    0.00   0.0  0
 LHB  CONST_22  N8   C14  N7   C13    0.00   0.0  0
 LHB  CONST_23  C15  N8   C14  N7     0.00   0.0  0
 LHB  CONST_24  N6   C1   C2   C3   180.00   0.0  0
 LHB  CONST_25  N6   C1   N2   C4   180.00   0.0  0
 LHB  CONST_26  N6   C1   C2   N4     0.00   0.0  0
 LHB  CONST_27  O5   C14  N7   C13  180.00   0.0  0
 LHB  CONST_28  C16  N8   C14  N7   180.00   0.0  0
 LHB  CONST_29  N9   C13  N7   C14  180.00   0.0  0
 LHB  CONST_30  O5   C14  N8   C15  180.00   0.0  0
 LHB  CONST_31  H1   C4   N2   C1   180.00   0.0  0
 LHB  CONST_32  H2   C5   N4   C2   180.00   0.0  0
 LHB  CONST_33  O5   C14  N8   C16    0.00   0.0  0
 LHB  CONST_34  H14  N6   C1   C2     0.00   0.0  0
 LHB  CONST_35  H15  N6   C1   C2   180.00   0.0  0
 LHB  CONST_37  H17  N9   C13  C12  180.00   0.0  0
 LHB  Var_01    C13  C12  C11  N5   -82.56  30.0  3
 LHB  Var_02    O4   C16  N8   C14   73.98  30.0  3
 LHB  Var_03    C11  N5   C10  C7   177.39  30.0  3
 LHB  Var_04    C12  C11  N5   C10  176.09  30.0  3
 LHB  Var_05    H22  C17  O4   C16  -67.36  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
 LHB  chir_01  C6  N3  C9  O1   negativ
 LHB  chir_02  C7  O1  C8  C10  negativ
 LHB  chir_03  C8  O3  C7  C9   positiv
 LHB  chir_04  C9  O2  C8  C6   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
 LHB  plan-1  C11  0.020
 LHB  plan-1  C12  0.020
 LHB  plan-1  C13  0.020
 LHB  plan-1  N7   0.020
 LHB  plan-1  C14  0.020
 LHB  plan-1  N8   0.020
 LHB  plan-1  C15  0.020
 LHB  plan-1  N9   0.020
 LHB  plan-1  C16  0.020
 LHB  plan-1  O5   0.020
 LHB  plan-1  H16  0.020
 LHB  plan-1  H18  0.020
 LHB  plan-1  H17  0.020
 LHB  plan-2  C1   0.020
 LHB  plan-2  C2   0.020
 LHB  plan-2  C3   0.020
 LHB  plan-2  N1   0.020
 LHB  plan-2  C4   0.020
 LHB  plan-2  N2   0.020
 LHB  plan-2  N3   0.020
 LHB  plan-2  C5   0.020
 LHB  plan-2  N4   0.020
 LHB  plan-2  C6   0.020
 LHB  plan-2  N6   0.020
 LHB  plan-2  H1   0.020
 LHB  plan-2  H2   0.020
 LHB  plan-3  C1   0.020
 LHB  plan-3  N6   0.020
 LHB  plan-3  H14  0.020
 LHB  plan-3  H15  0.020

