# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 11:35:50 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (2~{S})-~{N}-[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-2-azanyl-4-methyl-pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C(=O)N[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n2cnc3c(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
 9YN  9YN  (2~{S})-~{N}-[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-2-azanyl-4-methyl-pentanamide  ligand  52  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9YN
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
 9YN  O    O  O     0  -0.494  -2.2990   0.6942   2.0352
 9YN  C    C  C     0   0.584  -2.0740  -0.0273   1.0750
 9YN  CA   C  CH1   0  -0.251  -2.9011  -1.2700   0.7856
 9YN  CB   C  CH2   0  -0.407  -4.1429  -0.8324  -0.0097
 9YN  CG1  C  CH1   0  -0.245  -5.0725  -1.9739  -0.4258
 9YN  CD1  C  CH3   0  -0.647  -6.3089  -1.4059  -1.1165
 9YN  CD2  C  CH3   0  -0.660  -4.3707  -2.9856  -1.3268
 9YN  N    N  NH2   0  -0.786  -3.1683  -1.9546   2.0365
 9YN  NAI  N  NH1   0  -0.661  -1.1195   0.2432   0.1702
 9YN  CAJ  C  CR15  0  -0.140  -0.2730   1.3970   0.2630
 9YN  CAK  C  CR15  0   0.005  -0.9488   2.7568   0.0767
 9YN  OAL  O  OH1   0  -0.664  -1.8878   2.6338  -0.9542
 9YN  CAM  C  CR15  0  -0.055   0.2590   3.6085  -0.3195
 9YN  CAN  C  CH2   0  -0.164   1.0038   4.1474   0.8883
 9YN  OAO  O  OH1   0  -0.665   2.1875   4.7628   0.4470
 9YN  OAP  O  O     0  -0.491   1.0887   2.7418  -1.0970
 9YN  CAQ  C  CR15  0   0.226   0.7654   1.4116  -0.8673
 9YN  N9   N  NR5   0  -0.538   1.9691   0.6757  -0.5316
 9YN  C8   C  CR15  0   0.106   3.1569   1.1542  -0.0508
 9YN  N7   N  N     0  -0.453   4.0277   0.2144   0.1820
 9YN  C5   C  CR56  0  -0.000   3.3805  -0.9455  -0.1551
 9YN  C4   C  CR56  0   0.498   2.0964  -0.6781  -0.5998
 9YN  C6   C  CR6   0   0.462   3.7558  -2.3024  -0.1313
 9YN  N6   N  NH2   0  -0.816   4.9587  -2.7109   0.2708
 9YN  N1   N  N     0  -0.476   2.8551  -3.2086  -0.5308
 9YN  C2   C  CR16  0   0.052   1.6534  -2.8026  -0.9304
 9YN  N3   N  N     0  -0.475   1.1864  -1.5675  -0.9973
 9YN  H1   H  HCH1  0   0.246  -2.3060  -1.9463   0.1634
 9YN  H2   H  HCH2  0   0.230  -4.7054  -0.1164   0.5997
 9YN  H3   H  HCH2  0   0.221  -3.8210  -0.2925  -0.9081
 9YN  H4   H  HCH1  0   0.212  -5.4103  -2.4921   0.4795
 9YN  H5   H  HCH3  0   0.214  -6.0368  -0.8848  -2.0376
 9YN  H6   H  HCH3  0   0.226  -7.0129  -2.1973  -1.3790
 9YN  H7   H  HCH3  0   0.225  -6.8325  -0.6957  -0.4744
 9YN  H8   H  HCH3  0   0.227  -3.5500  -3.4981  -0.8219
 9YN  H9   H  HCH3  0   0.230  -5.0658  -3.7547  -1.6671
 9YN  H10  H  HCH3  0   0.216  -3.9598  -2.4940  -2.2121
 9YN  H11  H  HNH2  0   0.343  -3.7622  -1.3777   2.6207
 9YN  H12  H  HNH2  0   0.354  -3.6918  -2.8005   1.8506
 9YN  H14  H  HNH1  0   0.406  -0.9109  -0.4460  -0.5382
 9YN  H15  H  HCR5  0   0.292   0.2463   1.4041   1.2276
 9YN  H16  H  HCR5  0   0.259  -1.4024   3.1139   1.0072
 9YN  H17  H  HOH1  0   0.459  -2.3494   3.4727  -1.0510
 9YN  H18  H  HCR5  0   0.267  -0.0332   4.4450  -0.9619
 9YN  H19  H  HCH2  0   0.223   0.3368   4.8540   1.3991
 9YN  H20  H  HCH2  0   0.206   1.2137   3.3395   1.6028
 9YN  H21  H  HOH1  0   0.461   2.6758   5.0597   1.2202
 9YN  H22  H  HCR5  0   0.272   0.3603   0.9481  -1.7755
 9YN  H23  H  HCR5  0   0.294   3.3268   2.2105   0.0932
 9YN  H24  H  HNH2  0   0.413   5.6543  -2.0547   0.5789
 9YN  H25  H  HNH2  0   0.405   5.1870  -3.6899   0.2803
 9YN  H26  H  HCR6  0   0.254   0.9724  -3.5886  -1.2379

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
 9YN  CD2  CG1  single    1.526  0.020  1.526
 9YN  CG1  CB   single    1.530  0.020  1.530
 9YN  CG1  CD1  single    1.526  0.020  1.526
 9YN  CB   CA   single    1.538  0.020  1.538
 9YN  O    C    double    1.222  0.020  1.222
 9YN  CA   N    single    1.451  0.020  1.451
 9YN  CA   C    single    1.521  0.020  1.521
 9YN  OAL  CAK  single    1.400  0.020  1.400
 9YN  C    NAI  single    1.343  0.020  1.343
 9YN  CAK  CAJ  single    1.530  0.020  1.530
 9YN  CAK  CAM  single    1.530  0.020  1.530
 9YN  NAI  CAJ  single    1.434  0.020  1.434
 9YN  CAJ  CAQ  single    1.535  0.020  1.535
 9YN  CAM  CAN  single    1.518  0.020  1.518
 9YN  CAM  OAP  single    1.430  0.020  1.430
 9YN  CAN  OAO  single    1.405  0.020  1.405
 9YN  CAQ  OAP  single    1.388  0.020  1.388
 9YN  CAQ  N9   single    1.450  0.020  1.450
 9YN  C8   N9   aromatic  1.368  0.020  1.368
 9YN  C8   N7   aromatic  1.302  0.020  1.302
 9YN  N9   C4   aromatic  1.362  0.020  1.362
 9YN  N7   C5   aromatic  1.370  0.020  1.370
 9YN  C4   C5   aromatic  1.385  0.020  1.385
 9YN  C4   N3   aromatic  1.333  0.020  1.333
 9YN  C5   C6   aromatic  1.408  0.020  1.408
 9YN  N3   C2   aromatic  1.322  0.020  1.322
 9YN  C6   N6   single    1.332  0.020  1.332
 9YN  C6   N1   aromatic  1.339  0.020  1.339
 9YN  C2   N1   aromatic  1.330  0.020  1.330
 9YN  CA   H1   single    0.970  0.020  1.090
 9YN  CB   H2   single    0.970  0.020  1.090
 9YN  CB   H3   single    0.970  0.020  1.090
 9YN  CG1  H4   single    0.970  0.020  1.090
 9YN  CD1  H5   single    0.970  0.020  1.090
 9YN  CD1  H6   single    0.970  0.020  1.090
 9YN  CD1  H7   single    0.970  0.020  1.090
 9YN  CD2  H8   single    0.970  0.020  1.090
 9YN  CD2  H9   single    0.970  0.020  1.090
 9YN  CD2  H10  single    0.970  0.020  1.090
 9YN  N    H11  single    0.890  0.020  1.040
 9YN  N    H12  single    0.890  0.020  1.040
 9YN  NAI  H14  single    0.860  0.020  1.020
 9YN  CAJ  H15  single    0.970  0.020  1.090
 9YN  CAK  H16  single    0.970  0.020  1.090
 9YN  OAL  H17  single    0.850  0.020  0.980
 9YN  CAM  H18  single    0.970  0.020  1.090
 9YN  CAN  H19  single    0.970  0.020  1.090
 9YN  CAN  H20  single    0.970  0.020  1.090
 9YN  OAO  H21  single    0.850  0.020  0.980
 9YN  CAQ  H22  single    0.970  0.020  1.090
 9YN  C8   H23  single    0.930  0.020  1.080
 9YN  N6   H24  single    0.860  0.020  1.020
 9YN  N6   H25  single    0.860  0.020  1.020
 9YN  C2   H26  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
 9YN  NAI  C    CA   115.03  3.000
 9YN  NAI  C    O    122.79  3.000
 9YN  CA   C    O    122.13  3.000
 9YN  H1   CA   N    107.37  3.000
 9YN  H1   CA   CB   108.71  3.000
 9YN  N    CA   CB   115.55  3.000
 9YN  H1   CA   C    108.50  3.000
 9YN  N    CA   C    108.77  3.000
 9YN  CB   CA   C    107.76  3.000
 9YN  H3   CB   H2   106.54  3.000
 9YN  H3   CB   CG1  108.84  3.000
 9YN  H2   CB   CG1  109.08  3.000
 9YN  H3   CB   CA   109.07  3.000
 9YN  H2   CB   CA   108.23  3.000
 9YN  CG1  CB   CA   114.77  3.000
 9YN  H4   CG1  CD2  108.42  3.000
 9YN  H4   CG1  CD1  107.46  3.000
 9YN  CD2  CG1  CD1  110.63  3.000
 9YN  H4   CG1  CB   108.37  3.000
 9YN  CD1  CG1  CB   109.74  3.000
 9YN  CD2  CG1  CB   112.08  3.000
 9YN  H7   CD1  H6   107.69  3.000
 9YN  H7   CD1  H5   107.76  3.000
 9YN  H6   CD1  H5   107.68  3.000
 9YN  H7   CD1  CG1  111.39  3.000
 9YN  H6   CD1  CG1  111.20  3.000
 9YN  H5   CD1  CG1  110.94  3.000
 9YN  H10  CD2  H9   107.69  3.000
 9YN  H10  CD2  H8   107.66  3.000
 9YN  H9   CD2  H8   107.00  3.000
 9YN  H10  CD2  CG1  110.68  3.000
 9YN  H9   CD2  CG1  111.01  3.000
 9YN  H8   CD2  CG1  112.59  3.000
 9YN  H12  N    H11  106.18  3.000
 9YN  H12  N    CA   109.35  3.000
 9YN  H11  N    CA   109.65  3.000
 9YN  H14  NAI  CAJ  118.19  3.000
 9YN  H14  NAI  C    118.81  3.000
 9YN  CAJ  NAI  C    122.55  3.000
 9YN  H15  CAJ  CAQ  109.12  3.000
 9YN  H15  CAJ  CAK  108.11  3.000
 9YN  CAQ  CAJ  CAK  101.58  3.000
 9YN  H15  CAJ  NAI  110.00  3.000
 9YN  CAQ  CAJ  NAI  111.06  3.000
 9YN  CAK  CAJ  NAI  116.52  3.000
 9YN  H16  CAK  CAM  111.44  3.000
 9YN  H16  CAK  OAL  112.12  3.000
 9YN  CAM  CAK  OAL  112.82  3.000
 9YN  H16  CAK  CAJ  111.67  3.000
 9YN  CAM  CAK  CAJ  100.23  3.000
 9YN  OAL  CAK  CAJ  107.93  3.000
 9YN  H17  OAL  CAK  108.61  3.000
 9YN  H18  CAM  OAP  107.40  3.000
 9YN  H18  CAM  CAN  109.08  3.000
 9YN  OAP  CAM  CAN  111.29  3.000
 9YN  H18  CAM  CAK  111.51  3.000
 9YN  OAP  CAM  CAK  105.16  3.000
 9YN  CAN  CAM  CAK  112.27  3.000
 9YN  H20  CAN  H19  106.67  3.000
 9YN  H20  CAN  OAO  111.43  3.000
 9YN  H19  CAN  OAO  112.09  3.000
 9YN  H20  CAN  CAM  110.50  3.000
 9YN  H19  CAN  CAM  107.49  3.000
 9YN  OAO  CAN  CAM  108.60  3.000
 9YN  H21  OAO  CAN  108.09  3.000
 9YN  CAQ  OAP  CAM  110.84  3.000
 9YN  H22  CAQ  N9   106.48  3.000
 9YN  H22  CAQ  OAP  110.72  3.000
 9YN  N9   CAQ  OAP  109.34  3.000
 9YN  H22  CAQ  CAJ  110.84  3.000
 9YN  N9   CAQ  CAJ  112.72  3.000
 9YN  OAP  CAQ  CAJ  106.77  3.000
 9YN  C4   N9   C8   106.52  3.000
 9YN  C4   N9   CAQ  124.79  3.000
 9YN  C8   N9   CAQ  128.66  3.000
 9YN  H23  C8   N7   125.25  3.000
 9YN  H23  C8   N9   121.72  3.000
 9YN  N7   C8   N9   113.02  3.000
 9YN  C5   N7   C8   104.54  3.000
 9YN  C6   C5   C4   116.01  3.000
 9YN  C6   C5   N7   133.29  3.000
 9YN  C4   C5   N7   110.70  3.000
 9YN  N3   C4   C5   126.86  3.000
 9YN  N3   C4   N9   127.92  3.000
 9YN  C5   C4   N9   105.22  3.000
 9YN  N1   C6   N6   119.33  3.000
 9YN  N1   C6   C5   117.90  3.000
 9YN  N6   C6   C5   122.76  3.000
 9YN  H25  N6   H24  118.41  3.000
 9YN  H25  N6   C6   120.43  3.000
 9YN  H24  N6   C6   121.16  3.000
 9YN  C2   N1   C6   119.40  3.000
 9YN  H26  C2   N3   116.16  3.000
 9YN  H26  C2   N1   115.55  3.000
 9YN  N3   C2   N1   128.29  3.000
 9YN  C2   N3   C4   111.54  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
 9YN  CONST_01  C5   N7   C8   N9     0.00   0.0  0
 9YN  CONST_02  N7   C5   C4   N9     0.00   0.0  0
 9YN  CONST_03  C6   C5   C4   N9   180.00   0.0  0
 9YN  CONST_04  C2   N3   C4   N9   180.00   0.0  0
 9YN  CONST_05  C5   C4   N9   C8     0.00   0.0  0
 9YN  CONST_06  N3   C4   N9   C8   180.00   0.0  0
 9YN  CONST_07  C4   C5   N7   C8     0.00   0.0  0
 9YN  CONST_08  C6   C5   N7   C8   180.00   0.0  0
 9YN  CONST_09  C4   N9   C8   N7     0.00   0.0  0
 9YN  CONST_10  N3   C4   C5   N7   180.00   0.0  0
 9YN  CONST_11  N1   C6   C5   N7   180.00   0.0  0
 9YN  CONST_12  C2   N3   C4   C5     0.00   0.0  0
 9YN  CONST_13  C2   N1   C6   C5     0.00   0.0  0
 9YN  CONST_14  N1   C6   C5   C4     0.00   0.0  0
 9YN  CONST_15  N1   C2   N3   C4     0.00   0.0  0
 9YN  CONST_16  N3   C4   C5   C6     0.00   0.0  0
 9YN  CONST_17  N3   C2   N1   C6     0.00   0.0  0
 9YN  CONST_18  N7   C8   N9   CAQ  180.00   0.0  0
 9YN  CONST_19  C5   C4   N9   CAQ  180.00   0.0  0
 9YN  CONST_20  N3   C4   N9   CAQ    0.00   0.0  0
 9YN  CONST_21  N6   C6   C5   N7     0.00   0.0  0
 9YN  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 9YN  CONST_23  C2   N1   C6   N6   180.00   0.0  0
 9YN  CONST_24  H23  C8   N9   CAQ    0.00   0.0  0
 9YN  CONST_25  H26  C2   N3   C4   180.00   0.0  0
 9YN  CONST_26  H24  N6   C6   C5     0.00   0.0  0
 9YN  CONST_27  H25  N6   C6   C5   180.00   0.0  0
 9YN  CONST_28  CAJ  NAI  C    O      0.00   0.0  0
 9YN  CONST_29  CAJ  NAI  C    CA   180.00   0.0  0
 9YN  CONST_30  H14  NAI  C    O    180.00   0.0  0
 9YN  Var_01    CD2  CG1  CB   CA   -60.67  30.0  3
 9YN  Var_02    H8   CD2  CG1  CB    63.88  30.0  3
 9YN  Var_03    H5   CD1  CG1  CB    63.04  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
 9YN  chir_01  CA   CB   N    C    positiv
 9YN  chir_02  CAJ  NAI  CAK  CAQ  positiv
 9YN  chir_03  CAK  OAL  CAM  CAJ  positiv
 9YN  chir_04  CAM  OAP  CAK  CAN  negativ
 9YN  chir_05  CAQ  OAP  N9   CAJ  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
 9YN  plan-1  CAQ  0.020
 9YN  plan-1  N9   0.020
 9YN  plan-1  C8   0.020
 9YN  plan-1  N7   0.020
 9YN  plan-1  C5   0.020
 9YN  plan-1  C4   0.020
 9YN  plan-1  C6   0.020
 9YN  plan-1  N6   0.020
 9YN  plan-1  N1   0.020
 9YN  plan-1  C2   0.020
 9YN  plan-1  N3   0.020
 9YN  plan-1  H23  0.020
 9YN  plan-1  H26  0.020
 9YN  plan-2  C6   0.020
 9YN  plan-2  N6   0.020
 9YN  plan-2  H24  0.020
 9YN  plan-2  H25  0.020
 9YN  plan-3  O    0.020
 9YN  plan-3  C    0.020
 9YN  plan-3  CA   0.020
 9YN  plan-3  NAI  0.020
 9YN  plan-3  CAJ  0.020
 9YN  plan-3  H14  0.020

