# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 09:13:28 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 4-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]ethylamino]-1-(methoxymethyl)pyrimidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCN1C=CC(=NC1=O)NCCNC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34
#
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
 78V  78V  4-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]ethylamino]-1-(methoxymethyl)pyrimidin-2-one  ligand  57  32  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_78V
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
 78V  N    N  NR6   0  -0.536   7.3783  -1.0842   0.0908
 78V  N1   N  N     0  -0.553   5.1204  -0.5703  -0.3829
 78V  C6   C  CH2   0  -0.266   2.7400   0.7122   0.2038
 78V  C5   C  CR6   0   0.596   6.2612  -1.1886  -0.7551
 78V  C4   C  CR6   0   0.565   5.0496   0.1015   0.7487
 78V  N4   N  NR5   0  -0.535  -4.1322  -0.1792  -0.2342
 78V  N3   N  NH1   0  -0.607   0.4168   1.3959   0.0381
 78V  C2   C  CR16  0   0.086   7.3012  -0.3898   1.2532
 78V  O2   O  O     0  -0.501  -2.2490   0.9727  -0.9584
 78V  C    C  CH3   0  -0.416   9.7919   0.2643  -0.9159
 78V  O    O  O2    0  -0.464   9.2821  -0.9872  -1.3225
 78V  O1   O  O     0  -0.515   6.3599  -1.8304  -1.7909
 78V  C1   C  CH2   0  -0.051   8.6355  -1.6913  -0.3182
 78V  C3   C  CR16  0  -0.476   6.1636   0.2170   1.6401
 78V  N2   N  NH1   0  -0.656   3.8962   0.6894   1.0709
 78V  C7   C  CH2   0  -0.298   1.5509   1.3121   0.9349
 78V  C8   C  CH2   0  -0.279  -0.7604   1.9491   0.6729
 78V  C9   C  CR15  0   0.027  -1.8652   2.1981  -0.3281
 78V  C12  C  CR15  0  -0.034  -3.1530   2.7379   0.2852
 78V  O4   O  OH1   0  -0.657  -3.0882   4.1313   0.3999
 78V  C11  C  CR15  0  -0.043  -4.2077   2.2460  -0.7116
 78V  O3   O  OH1   0  -0.665  -4.2237   3.0436  -1.8632
 78V  C10  C  CR15  0   0.177  -3.6327   0.8843  -1.0988
 78V  C15  C  CR56  0   0.486  -5.3720  -0.7385  -0.3258
 78V  N6   N  N     0  -0.459  -6.3516  -0.4268  -1.1730
 78V  C16  C  CR16  0   0.039  -7.4195  -1.1806  -0.9785
 78V  N7   N  N     0  -0.474  -7.5968  -2.1490  -0.0833
 78V  C17  C  CR6   0   0.458  -6.6024  -2.4504   0.7595
 78V  N8   N  NH2   0  -0.817  -6.7779  -3.4209   1.6568
 78V  C14  C  CR56  0  -0.003  -5.4063  -1.7152   0.6567
 78V  N5   N  N     0  -0.452  -4.2177  -1.7612   1.3357
 78V  C13  C  CR15  0   0.099  -3.4891  -0.8381   0.7773
 78V  H8   H  HCH2  0   0.238   2.9474   1.2926  -0.7000
 78V  H9   H  HCH2  0   0.242   2.5066  -0.3058  -0.1158
 78V  H12  H  HNH1  0   0.348   0.1998   0.4661  -0.3015
 78V  H5   H  HCR6  0   0.317   8.2006  -0.3570   1.8538
 78V  H1   H  HCH3  0   0.247  10.4011   0.6498  -1.7317
 78V  H    H  HCH3  0   0.218   9.0015   0.9930  -0.7094
 78V  H2   H  HCH3  0   0.214  10.4225   0.1763  -0.0240
 78V  H4   H  HCH2  0   0.238   9.2533  -1.7712   0.5830
 78V  H3   H  HCH2  0   0.262   8.4393  -2.6909  -0.6976
 78V  H6   H  HCR6  0   0.286   6.1085   0.7658   2.5683
 78V  H7   H  HNH1  0   0.408   3.8809   1.2629   1.8991
 78V  H11  H  HCH2  0   0.210   1.3422   0.7228   1.8410
 78V  H10  H  HCH2  0   0.234   1.8015   2.3240   1.2682
 78V  H13  H  HCH2  0   0.202  -1.1382   1.3289   1.5026
 78V  H14  H  HCH2  0   0.247  -0.4982   2.9170   1.1097
 78V  H15  H  HCR5  0   0.242  -1.4980   2.8896  -1.0959
 78V  H19  H  HCR5  0   0.243  -3.3314   2.2636   1.2595
 78V  H20  H  HOH1  0   0.469  -3.7466   4.4212   1.0394
 78V  H17  H  HCR5  0   0.260  -5.2049   2.1571  -0.2637
 78V  H18  H  HOH1  0   0.452  -4.1016   3.9607  -1.5880
 78V  H16  H  HCR5  0   0.283  -3.9022   0.6159  -2.1241
 78V  H22  H  HCR6  0   0.252  -8.2653  -0.9891  -1.6301
 78V  H23  H  HNH2  0   0.404  -7.6423  -3.9331   1.6895
 78V  H24  H  HNH2  0   0.412  -6.0406  -3.6870   2.2850
 78V  H21  H  HCR5  0   0.297  -2.4738  -0.6055   1.0578

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
 78V  C16  N7   aromatic  1.331  0.020  1.331
 78V  C16  N6   aromatic  1.322  0.020  1.322
 78V  N7   C17  aromatic  1.338  0.020  1.338
 78V  N6   C15  aromatic  1.332  0.020  1.332
 78V  C17  N8   single    1.333  0.020  1.333
 78V  C17  C14  aromatic  1.408  0.020  1.408
 78V  C15  C14  aromatic  1.386  0.020  1.386
 78V  C15  N4   aromatic  1.363  0.020  1.363
 78V  C14  N5   aromatic  1.370  0.020  1.370
 78V  O3   C11  single    1.401  0.020  1.401
 78V  O4   C12  single    1.400  0.020  1.400
 78V  C10  N4   single    1.459  0.020  1.459
 78V  C10  C11  single    1.528  0.020  1.528
 78V  C10  O2   single    1.394  0.020  1.394
 78V  N4   C13  aromatic  1.368  0.020  1.368
 78V  C11  C12  single    1.532  0.020  1.532
 78V  O2   C9   single    1.430  0.020  1.430
 78V  C9   C12  single    1.525  0.020  1.525
 78V  C9   C8   single    1.512  0.020  1.512
 78V  N5   C13  aromatic  1.302  0.020  1.302
 78V  C8   N3   single    1.447  0.020  1.447
 78V  N3   C7   single    1.448  0.020  1.448
 78V  C7   C6   single    1.519  0.020  1.519
 78V  C6   N2   single    1.445  0.020  1.445
 78V  N2   C4   single    1.334  0.020  1.334
 78V  N1   C4   double    1.318  0.020  1.318
 78V  N1   C5   single    1.350  0.020  1.350
 78V  C4   C3   single    1.431  0.020  1.431
 78V  O1   C5   double    1.223  0.020  1.223
 78V  C5   N    single    1.405  0.020  1.405
 78V  C3   C2   double    1.346  0.020  1.346
 78V  N    C2   single    1.356  0.020  1.356
 78V  N    C1   single    1.455  0.020  1.455
 78V  C    O    single    1.411  0.020  1.411
 78V  C1   O    single    1.387  0.020  1.387
 78V  C6   H8   single    0.970  0.020  1.090
 78V  C6   H9   single    0.970  0.020  1.090
 78V  N3   H12  single    0.890  0.020  1.040
 78V  C2   H5   single    0.930  0.020  1.080
 78V  C    H1   single    0.970  0.020  1.090
 78V  C    H    single    0.970  0.020  1.090
 78V  C    H2   single    0.970  0.020  1.090
 78V  C1   H4   single    0.970  0.020  1.090
 78V  C1   H3   single    0.970  0.020  1.090
 78V  C3   H6   single    0.930  0.020  1.080
 78V  N2   H7   single    0.860  0.020  1.020
 78V  C7   H11  single    0.970  0.020  1.090
 78V  C7   H10  single    0.970  0.020  1.090
 78V  C8   H13  single    0.970  0.020  1.090
 78V  C8   H14  single    0.970  0.020  1.090
 78V  C9   H15  single    0.970  0.020  1.090
 78V  C12  H19  single    0.970  0.020  1.090
 78V  O4   H20  single    0.850  0.020  0.980
 78V  C11  H17  single    0.970  0.020  1.090
 78V  O3   H18  single    0.850  0.020  0.980
 78V  C10  H16  single    0.970  0.020  1.090
 78V  C16  H22  single    0.930  0.020  1.080
 78V  N8   H23  single    0.860  0.020  1.020
 78V  N8   H24  single    0.860  0.020  1.020
 78V  C13  H21  single    0.930  0.020  1.080

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
 78V  C1   N    C2   120.25  3.000
 78V  C1   N    C5   119.13  3.000
 78V  C2   N    C5   120.58  3.000
 78V  C4   N1   C5   121.04  3.000
 78V  H9   C6   H8   107.05  3.000
 78V  H9   C6   C7   109.98  3.000
 78V  H8   C6   C7   109.66  3.000
 78V  H9   C6   N2   109.37  3.000
 78V  H8   C6   N2   110.63  3.000
 78V  C7   C6   N2   110.09  3.000
 78V  O1   C5   N1   122.83  3.000
 78V  O1   C5   N    119.01  3.000
 78V  N1   C5   N    118.16  3.000
 78V  N2   C4   C3   119.14  3.000
 78V  C3   C4   N1   122.28  3.000
 78V  N2   C4   N1   118.59  3.000
 78V  C13  N4   C15  106.24  3.000
 78V  C13  N4   C10  128.94  3.000
 78V  C15  N4   C10  124.80  3.000
 78V  H12  N3   C8   108.88  3.000
 78V  H12  N3   C7   108.79  3.000
 78V  C8   N3   C7   112.79  3.000
 78V  H5   C2   C3   121.96  3.000
 78V  H5   C2   N    116.36  3.000
 78V  C3   C2   N    121.68  3.000
 78V  C10  O2   C9   111.42  3.000
 78V  H2   C    H    108.38  3.000
 78V  H2   C    H1   108.44  3.000
 78V  H    C    H1   108.04  3.000
 78V  H2   C    O    111.79  3.000
 78V  H    C    O    112.57  3.000
 78V  H1   C    O    107.48  3.000
 78V  C1   O    C    114.21  3.000
 78V  H3   C1   H4   108.77  3.000
 78V  H3   C1   O    107.36  3.000
 78V  H4   C1   O    111.71  3.000
 78V  H3   C1   N    109.02  3.000
 78V  H4   C1   N    106.64  3.000
 78V  O    C1   N    113.25  3.000
 78V  H6   C3   C2   121.29  3.000
 78V  H6   C3   C4   122.45  3.000
 78V  C2   C3   C4   116.25  3.000
 78V  H7   N2   C4   117.55  3.000
 78V  H7   N2   C6   118.17  3.000
 78V  C4   N2   C6   123.62  3.000
 78V  H10  C7   H11  106.72  3.000
 78V  H10  C7   N3   108.32  3.000
 78V  H11  C7   N3   113.08  3.000
 78V  H10  C7   C6   109.42  3.000
 78V  H11  C7   C6   109.46  3.000
 78V  N3   C7   C6   109.74  3.000
 78V  H14  C8   H13  106.22  3.000
 78V  H14  C8   C9   107.09  3.000
 78V  H13  C8   C9   109.91  3.000
 78V  H14  C8   N3   108.57  3.000
 78V  H13  C8   N3   113.19  3.000
 78V  C9   C8   N3   111.53  3.000
 78V  H15  C9   C12  109.94  3.000
 78V  H15  C9   C8   108.84  3.000
 78V  C12  C9   C8   114.15  3.000
 78V  H15  C9   O2   108.76  3.000
 78V  C8   C9   O2   110.29  3.000
 78V  C12  C9   O2   104.71  3.000
 78V  H19  C12  C11  109.06  3.000
 78V  H19  C12  O4   111.40  3.000
 78V  C11  C12  O4   113.88  3.000
 78V  H19  C12  C9   109.94  3.000
 78V  C11  C12  C9   101.89  3.000
 78V  O4   C12  C9   110.26  3.000
 78V  H20  O4   C12  108.81  3.000
 78V  H17  C11  C10  111.93  3.000
 78V  H17  C11  O3   111.81  3.000
 78V  C10  C11  O3   107.66  3.000
 78V  H17  C11  C12  112.72  3.000
 78V  C10  C11  C12  101.06  3.000
 78V  O3   C11  C12  111.09  3.000
 78V  H18  O3   C11  107.77  3.000
 78V  H16  C10  C11  111.32  3.000
 78V  H16  C10  O2   110.78  3.000
 78V  C11  C10  O2   106.95  3.000
 78V  H16  C10  N4   107.00  3.000
 78V  O2   C10  N4   109.06  3.000
 78V  C11  C10  N4   111.75  3.000
 78V  C14  C15  N6   126.70  3.000
 78V  C14  C15  N4   105.31  3.000
 78V  N6   C15  N4   127.99  3.000
 78V  C16  N6   C15  111.54  3.000
 78V  H22  C16  N7   115.39  3.000
 78V  H22  C16  N6   116.16  3.000
 78V  N7   C16  N6   128.45  3.000
 78V  C17  N7   C16  119.26  3.000
 78V  C14  C17  N8   122.76  3.000
 78V  C14  C17  N7   117.90  3.000
 78V  N8   C17  N7   119.34  3.000
 78V  H24  N8   H23  118.41  3.000
 78V  H24  N8   C17  121.14  3.000
 78V  H23  N8   C17  120.39  3.000
 78V  N5   C14  C17  133.12  3.000
 78V  N5   C14  C15  110.72  3.000
 78V  C17  C14  C15  116.16  3.000
 78V  C13  N5   C14  104.43  3.000
 78V  H21  C13  N5   124.61  3.000
 78V  H21  C13  N4   122.07  3.000
 78V  N5   C13  N4   113.31  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
 78V  CONST_01  C16  N6   C15  N4   180.00   0.0  0
 78V  CONST_02  C17  C14  C15  N4   180.00   0.0  0
 78V  CONST_03  N5   C14  C15  N4     0.00   0.0  0
 78V  CONST_04  C14  N5   C13  N4     0.00   0.0  0
 78V  CONST_05  N7   C16  N6   C15    0.00   0.0  0
 78V  CONST_06  N7   C17  C14  C15    0.00   0.0  0
 78V  CONST_07  C13  N5   C14  C15    0.00   0.0  0
 78V  CONST_08  N5   C13  N4   C15    0.00   0.0  0
 78V  CONST_09  C17  N7   C16  N6     0.00   0.0  0
 78V  CONST_10  C17  C14  C15  N6     0.00   0.0  0
 78V  CONST_11  N5   C14  C15  N6   180.00   0.0  0
 78V  CONST_12  C13  N4   C15  N6   180.00   0.0  0
 78V  CONST_13  C14  C17  N7   C16    0.00   0.0  0
 78V  CONST_14  C14  C15  N6   C16    0.00   0.0  0
 78V  CONST_15  N5   C14  C17  N7   180.00   0.0  0
 78V  CONST_16  C13  N5   C14  C17  180.00   0.0  0
 78V  CONST_17  C13  N4   C15  C14    0.00   0.0  0
 78V  CONST_18  N6   C15  N4   C10    0.00   0.0  0
 78V  CONST_19  C14  C15  N4   C10  180.00   0.0  0
 78V  CONST_20  N5   C13  N4   C10  180.00   0.0  0
 78V  CONST_21  C4   N1   C5   N      0.00   0.0  0
 78V  CONST_22  C2   N    C5   N1     0.00   0.0  0
 78V  CONST_23  C3   C4   N1   C5     0.00   0.0  0
 78V  CONST_24  N8   C17  C14  C15  180.00   0.0  0
 78V  CONST_25  N8   C17  N7   C16  180.00   0.0  0
 78V  CONST_26  N5   C14  C17  N8     0.00   0.0  0
 78V  CONST_27  C1   N    C5   N1   180.00   0.0  0
 78V  CONST_28  N2   C4   N1   C5   180.00   0.0  0
 78V  CONST_29  O1   C5   N1   C4   180.00   0.0  0
 78V  CONST_30  O1   C5   N    C2   180.00   0.0  0
 78V  CONST_31  H21  C13  N4   C10    0.00   0.0  0
 78V  CONST_32  H22  C16  N6   C15  180.00   0.0  0
 78V  CONST_33  C6   N2   C4   N1     0.00   0.0  0
 78V  CONST_34  C3   C4   N2   C6   180.00   0.0  0
 78V  CONST_35  C1   N    C5   O1     0.00   0.0  0
 78V  CONST_36  H23  N8   C17  N7     0.00   0.0  0
 78V  CONST_37  H24  N8   C17  N7   180.00   0.0  0
 78V  CONST_38  H7   N2   C4   N1   180.00   0.0  0
 78V  Var_01    O    C1   N    C5    74.11  30.0  3
 78V  Var_02    C7   C6   N2   C4   173.26  30.0  1
 78V  Var_03    C9   C8   N3   C7   172.29  30.0  1
 78V  Var_04    C8   N3   C7   C6   179.47  30.0  1
 78V  Var_05    N2   C6   C7   N3   177.03  30.0  3
 78V  Var_06    H1   C    O    C1   171.50  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
 78V  chir_01  C9   O2  C12  C8   negativ
 78V  chir_02  C12  O4  C9   C11  positiv
 78V  chir_03  C11  O3  C12  C10  positiv
 78V  chir_04  C10  O2  N4   C11  negativ

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
 78V  plan-1  N    0.020
 78V  plan-1  N1   0.020
 78V  plan-1  C6   0.020
 78V  plan-1  C5   0.020
 78V  plan-1  C4   0.020
 78V  plan-1  C2   0.020
 78V  plan-1  O1   0.020
 78V  plan-1  C1   0.020
 78V  plan-1  C3   0.020
 78V  plan-1  N2   0.020
 78V  plan-1  H5   0.020
 78V  plan-1  H6   0.020
 78V  plan-1  H7   0.020
 78V  plan-2  N4   0.020
 78V  plan-2  C10  0.020
 78V  plan-2  C15  0.020
 78V  plan-2  N6   0.020
 78V  plan-2  C16  0.020
 78V  plan-2  N7   0.020
 78V  plan-2  C17  0.020
 78V  plan-2  N8   0.020
 78V  plan-2  C14  0.020
 78V  plan-2  N5   0.020
 78V  plan-2  C13  0.020
 78V  plan-2  H22  0.020
 78V  plan-2  H21  0.020
 78V  plan-3  C17  0.020
 78V  plan-3  N8   0.020
 78V  plan-3  H23  0.020
 78V  plan-3  H24  0.020

