# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 06:19:46 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (2S,3R)-3-(6-amino-9H-purin-9-yl)nonan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[C@H]([C@H](C)O)n1cnc2c(N)ncnc12
#
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
 EH9  EH9  (2S,3R)-3-(6-amino-9H-purin-9-yl)nonan-2-ol  ligand  43  20  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EH9
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
 EH9  C1    C  CR6   0   0.454   3.0255  -2.1106  -0.1392
 EH9  C2    C  CR56  0  -0.005   2.1966  -1.0787  -0.6176
 EH9  C3    C  CR56  0   0.481   1.6216  -0.2573   0.3407
 EH9  C5    C  CR16  0   0.040   2.5793  -1.3518   1.9865
 EH9  C14   C  CR15  0   0.095   1.0302   0.3229  -1.6756
 EH9  N4    N  N     0  -0.455   1.7817  -0.3513   1.6600
 EH9  N6    N  N     0  -0.476   3.1959  -2.2164   1.1830
 EH9  N13   N  NR5   0  -0.498   0.8716   0.6416  -0.3568
 EH9  N15   N  N     0  -0.451   1.8139  -0.6981  -1.8763
 EH9  C20   C  CH1   0  -0.148   0.0737   1.7236   0.2006
 EH9  C21   C  CH2   0  -0.446  -1.3892   1.5894  -0.2150
 EH9  N24   N  NH2   0  -0.818   3.6433  -2.9727  -0.9488
 EH9  C26   C  CH2   0  -0.415  -2.0171   0.2479   0.1424
 EH9  C28   C  CH2   0  -0.412  -3.5029   0.2055  -0.1939
 EH9  C30   C  CH2   0  -0.408  -4.1603  -1.1254   0.1463
 EH9  C31   C  CH2   0  -0.418  -5.6486  -1.1584  -0.1802
 EH9  C34   C  CH3   0  -0.663  -6.3010  -2.4897   0.1645
 EH9  C36   C  CH1   0   0.061   0.6935   3.0831  -0.1817
 EH9  O38   O  OH1   0  -0.666  -0.0353   4.1313   0.4180
 EH9  C40   C  CH3   0  -0.682   2.1336   3.2030   0.2816
 EH9  H5    H  HCR6  0   0.249   2.7589  -1.4936   3.0471
 EH9  H14   H  HCR5  0   0.296   0.5357   0.8812  -2.4570
 EH9  H20   H  HCH1  0   0.267   0.1459   1.6125   1.2862
 EH9  H211  H  HCH2  0   0.242  -1.9550   2.3781   0.2865
 EH9  H212  H  HCH2  0   0.230  -1.4924   1.7735  -1.2906
 EH9  H241  H  HNH2  0   0.410   3.5000  -2.9452  -1.9428
 EH9  H242  H  HNH2  0   0.403   4.1934  -3.7224  -0.5667
 EH9  H261  H  HCH2  0   0.220  -1.5063  -0.5634  -0.3851
 EH9  H262  H  HCH2  0   0.219  -1.8790   0.0530   1.2112
 EH9  H281  H  HCH2  0   0.211  -4.0173   1.0118   0.3400
 EH9  H282  H  HCH2  0   0.211  -3.6374   0.4150  -1.2610
 EH9  H301  H  HCH2  0   0.208  -3.6526  -1.9322  -0.3939
 EH9  H302  H  HCH2  0   0.208  -4.0195  -1.3401   1.2115
 EH9  H311  H  HCH2  0   0.210  -6.1531  -0.3512   0.3600
 EH9  H312  H  HCH2  0   0.210  -5.7894  -0.9436  -1.2440
 EH9  H341  H  HCH3  0   0.216  -5.8338  -3.3114  -0.3818
 EH9  H342  H  HCH3  0   0.216  -6.2080  -2.7094   1.2300
 EH9  H343  H  HCH3  0   0.226  -7.3638  -2.4925  -0.0801
 EH9  H36   H  HCH1  0   0.209   0.6668   3.1774  -1.2776
 EH9  HO38  H  HOH1  0   0.458  -0.8581   4.2575  -0.0634
 EH9  H401  H  HCH3  0   0.235   2.7718   2.4652  -0.2023
 EH9  H402  H  HCH3  0   0.246   2.5281   4.1887   0.0329
 EH9  H403  H  HCH3  0   0.230   2.2145   3.0643   1.3617

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
 EH9  C34  C31   single    1.522  0.020  1.522
 EH9  C5   N6    aromatic  1.332  0.020  1.332
 EH9  C5   N4    aromatic  1.321  0.020  1.321
 EH9  C31  C30   single    1.524  0.020  1.524
 EH9  C30  C28   single    1.523  0.020  1.523
 EH9  N6   C1    aromatic  1.337  0.020  1.337
 EH9  N4   C3    aromatic  1.332  0.020  1.332
 EH9  C40  C36   single    1.518  0.020  1.518
 EH9  C28  C26   single    1.524  0.020  1.524
 EH9  C1   N24   single    1.334  0.020  1.334
 EH9  C1   C2    aromatic  1.407  0.020  1.407
 EH9  C26  C21   single    1.524  0.020  1.524
 EH9  C3   C2    aromatic  1.387  0.020  1.387
 EH9  C3   N13   aromatic  1.363  0.020  1.363
 EH9  C2   N15   aromatic  1.370  0.020  1.370
 EH9  C36  C20   single    1.542  0.020  1.542
 EH9  C36  O38   single    1.411  0.020  1.411
 EH9  C21  C20   single    1.527  0.020  1.527
 EH9  N13  C20   single    1.455  0.020  1.455
 EH9  N13  C14   aromatic  1.366  0.020  1.366
 EH9  N15  C14   aromatic  1.303  0.020  1.303
 EH9  C5   H5    single    0.930  0.020  1.080
 EH9  C14  H14   single    0.930  0.020  1.080
 EH9  C20  H20   single    0.970  0.020  1.090
 EH9  C21  H211  single    0.970  0.020  1.090
 EH9  C21  H212  single    0.970  0.020  1.090
 EH9  N24  H241  single    0.860  0.020  1.020
 EH9  N24  H242  single    0.860  0.020  1.020
 EH9  C26  H261  single    0.970  0.020  1.090
 EH9  C26  H262  single    0.970  0.020  1.090
 EH9  C28  H281  single    0.970  0.020  1.090
 EH9  C28  H282  single    0.970  0.020  1.090
 EH9  C30  H301  single    0.970  0.020  1.090
 EH9  C30  H302  single    0.970  0.020  1.090
 EH9  C31  H311  single    0.970  0.020  1.090
 EH9  C31  H312  single    0.970  0.020  1.090
 EH9  C34  H341  single    0.970  0.020  1.090
 EH9  C34  H342  single    0.970  0.020  1.090
 EH9  C34  H343  single    0.970  0.020  1.090
 EH9  C36  H36   single    0.970  0.020  1.090
 EH9  O38  HO38  single    0.850  0.020  0.980
 EH9  C40  H401  single    0.970  0.020  1.090
 EH9  C40  H402  single    0.970  0.020  1.090
 EH9  C40  H403  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
 EH9  N24   C1   N6    119.33  3.000
 EH9  N24   C1   C2    122.69  3.000
 EH9  N6    C1   C2    117.98  3.000
 EH9  N15   C2   C3    110.77  3.000
 EH9  N15   C2   C1    132.90  3.000
 EH9  C3    C2   C1    116.33  3.000
 EH9  N13   C3   N4    128.28  3.000
 EH9  N13   C3   C2    105.38  3.000
 EH9  N4    C3   C2    126.34  3.000
 EH9  H5    C5   N6    115.36  3.000
 EH9  H5    C5   N4    116.15  3.000
 EH9  N6    C5   N4    128.49  3.000
 EH9  H14   C14  N15   124.69  3.000
 EH9  H14   C14  N13   121.64  3.000
 EH9  N15   C14  N13   113.67  3.000
 EH9  C5    N4   C3    111.77  3.000
 EH9  C5    N6   C1    119.09  3.000
 EH9  C20   N13  C14   127.36  3.000
 EH9  C14   N13  C3    106.04  3.000
 EH9  C20   N13  C3    126.59  3.000
 EH9  C14   N15  C2    104.14  3.000
 EH9  H20   C20  C36   108.00  3.000
 EH9  H20   C20  C21   108.94  3.000
 EH9  C36   C20  C21   113.27  3.000
 EH9  H20   C20  N13   105.57  3.000
 EH9  C21   C20  N13   110.84  3.000
 EH9  C36   C20  N13   109.88  3.000
 EH9  H212  C21  H211  106.29  3.000
 EH9  H212  C21  C26   109.83  3.000
 EH9  H211  C21  C26   108.33  3.000
 EH9  H212  C21  C20   110.03  3.000
 EH9  H211  C21  C20   107.93  3.000
 EH9  C26   C21  C20   114.10  3.000
 EH9  H242  N24  H241  118.32  3.000
 EH9  H242  N24  C1    120.30  3.000
 EH9  H241  N24  C1    121.11  3.000
 EH9  H262  C26  H261  106.24  3.000
 EH9  H262  C26  C28   109.47  3.000
 EH9  H261  C26  C28   109.16  3.000
 EH9  H262  C26  C21   109.49  3.000
 EH9  H261  C26  C21   110.32  3.000
 EH9  C28   C26  C21   111.99  3.000
 EH9  H282  C28  H281  106.04  3.000
 EH9  H282  C28  C30   109.37  3.000
 EH9  H281  C28  C30   109.37  3.000
 EH9  H282  C28  C26   109.23  3.000
 EH9  H281  C28  C26   109.26  3.000
 EH9  C30   C28  C26   113.32  3.000
 EH9  H302  C30  H301  105.99  3.000
 EH9  H302  C30  C31   109.24  3.000
 EH9  H301  C30  C31   109.32  3.000
 EH9  H302  C30  C28   109.45  3.000
 EH9  H301  C30  C28   109.47  3.000
 EH9  C31   C30  C28   113.12  3.000
 EH9  H312  C31  H311  106.00  3.000
 EH9  H312  C31  C34   109.68  3.000
 EH9  H311  C31  C34   109.62  3.000
 EH9  H312  C31  C30   109.25  3.000
 EH9  H311  C31  C30   109.17  3.000
 EH9  C34   C31  C30   112.89  3.000
 EH9  H343  C34  H342  107.54  3.000
 EH9  H343  C34  H341  107.63  3.000
 EH9  H342  C34  H341  107.49  3.000
 EH9  H343  C34  C31   111.66  3.000
 EH9  H342  C34  C31   111.13  3.000
 EH9  H341  C34  C31   111.20  3.000
 EH9  H36   C36  C40   108.68  3.000
 EH9  H36   C36  O38   110.32  3.000
 EH9  C40   C36  O38   107.56  3.000
 EH9  H36   C36  C20   108.22  3.000
 EH9  O38   C36  C20   110.00  3.000
 EH9  C40   C36  C20   112.04  3.000
 EH9  HO38  O38  C36   109.07  3.000
 EH9  H403  C40  H402  108.28  3.000
 EH9  H403  C40  H401  108.06  3.000
 EH9  H402  C40  H401  107.40  3.000
 EH9  H403  C40  C36   111.24  3.000
 EH9  H402  C40  C36   110.19  3.000
 EH9  H401  C40  C36   111.53  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
 EH9  CONST_01  N4    C5   N6   C1      0.00   0.0  0
 EH9  CONST_02  N4    C3   C2   C1      0.00   0.0  0
 EH9  CONST_03  N13   C3   C2   C1    180.00   0.0  0
 EH9  CONST_04  C14   N15  C2   C1    180.00   0.0  0
 EH9  CONST_05  C5    N6   C1   C2      0.00   0.0  0
 EH9  CONST_06  C5    N4   C3   C2      0.00   0.0  0
 EH9  CONST_07  C14   N13  C3   C2      0.00   0.0  0
 EH9  CONST_08  N13   C14  N15  C2      0.00   0.0  0
 EH9  CONST_09  N6    C5   N4   C3      0.00   0.0  0
 EH9  CONST_10  N6    C1   C2   C3      0.00   0.0  0
 EH9  CONST_11  C14   N15  C2   C3      0.00   0.0  0
 EH9  CONST_12  N15   C14  N13  C3      0.00   0.0  0
 EH9  CONST_13  N13   C3   N4   C5    180.00   0.0  0
 EH9  CONST_14  N4    C3   N13  C14   180.00   0.0  0
 EH9  CONST_15  N15   C2   C3   N4    180.00   0.0  0
 EH9  CONST_16  N15   C2   C1   N6    180.00   0.0  0
 EH9  CONST_17  N15   C2   C3   N13     0.00   0.0  0
 EH9  CONST_18  C20   N13  C3   C2    180.00   0.0  0
 EH9  CONST_19  N24   C1   C2   C3    180.00   0.0  0
 EH9  CONST_20  N24   C1   N6   C5    180.00   0.0  0
 EH9  CONST_21  C20   N13  C3   N4      0.00   0.0  0
 EH9  CONST_22  N24   C1   C2   N15     0.00   0.0  0
 EH9  CONST_23  C20   N13  C14  N15   180.00   0.0  0
 EH9  CONST_24  H5    C5   N6   C1    180.00   0.0  0
 EH9  CONST_25  H14   C14  N15  C2    180.00   0.0  0
 EH9  CONST_26  H241  N24  C1   C2      0.00   0.0  0
 EH9  CONST_27  H242  N24  C1   C2    180.00   0.0  0
 EH9  Var_01    C28   C26  C21  C20   175.51  30.0  1
 EH9  Var_02    C30   C28  C26  C21   179.77  30.0  2
 EH9  Var_03    C31   C30  C28  C26   179.48  30.0  1
 EH9  Var_04    C34   C31  C30  C28  -179.88  30.0  2
 EH9  Var_05    H341  C34  C31  C30   -59.58  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
 EH9  chir_01  C20  C36  C21  N13  negativ
 EH9  chir_02  C36  O38  C20  C40  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
 EH9  plan-1  C1    0.020
 EH9  plan-1  C2    0.020
 EH9  plan-1  C3    0.020
 EH9  plan-1  C5    0.020
 EH9  plan-1  C14   0.020
 EH9  plan-1  N4    0.020
 EH9  plan-1  N6    0.020
 EH9  plan-1  N13   0.020
 EH9  plan-1  N15   0.020
 EH9  plan-1  C20   0.020
 EH9  plan-1  N24   0.020
 EH9  plan-1  H5    0.020
 EH9  plan-1  H14   0.020
 EH9  plan-2  C1    0.020
 EH9  plan-2  N24   0.020
 EH9  plan-2  H241  0.020
 EH9  plan-2  H242  0.020

