# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 19:16:00 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] 2-phenylethanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OC(=O)Cc4ccccc4)[C@@H](O)[C@H]3O
#
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
 DLL  DLL  '[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] 2-phenylethanoate'  ligand  52  32  .  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_DLL
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
 DLL  O     O  O     0  -0.395  -3.5011   0.9104   0.9253
 DLL  CB    C  CH2   0  -0.694  -4.7581  -0.0372  -0.9088
 DLL  CG    C  CR6   0   0.136  -5.7449   1.0851  -0.7859
 DLL  CD2   C  CR16  0  -0.297  -5.6006   2.2398  -1.5479
 DLL  CD1   C  CR16  0  -0.292  -6.8115   0.9922   0.1033
 DLL  CE2   C  CR16  0  -0.241  -6.5055   3.2859  -1.4242
 DLL  CE1   C  CR16  0  -0.242  -7.7177   2.0358   0.2298
 DLL  CZ    C  CR16  0  -0.265  -7.5659   3.1865  -0.5333
 DLL  P     P  P     0   1.462  -1.4822  -1.1493   0.9363
 DLL  O2P   O  O     0  -0.675  -1.7689  -1.2926   2.3697
 DLL  O3P   O  OH1   0  -0.727  -0.5176   0.0769   0.6491
 DLL  O1P   O  O2    0  -0.574  -2.7802  -0.9730  -0.0421
 DLL  O5'   O  O2    0  -0.572  -0.9181  -2.4173   0.1640
 DLL  C5'   C  CH2   0  -0.195   0.2586  -3.1087   0.5998
 DLL  O4'   O  O2    0  -0.503   1.6456  -1.6003  -0.6714
 DLL  O3'   O  OH1   0  -0.663   3.2642  -4.1083  -1.2458
 DLL  C2'   C  CH1   0  -0.050   3.3959  -2.5167   0.5725
 DLL  O2'   O  OH1   0  -0.650   4.7828  -2.6522   0.5627
 DLL  C1'   C  CH1   0   0.217   2.9848  -1.3489  -0.3202
 DLL  N9    N  NR5   0  -0.550   3.0932  -0.0619   0.3051
 DLL  C8    C  CR15  0   0.114   2.5871   0.3328   1.5178
 DLL  N7    N  N     0  -0.446   2.8303   1.5760   1.7974
 DLL  C5    C  CR56  0  -0.010   3.5348   2.0400   0.7151
 DLL  C6    C  CR6   0   0.462   4.0971   3.2918   0.4040
 DLL  CAZ   C  C     0   0.623  -3.6481   0.0612   0.0982
 DLL  N6    N  NH2   0  -0.816   4.0064   4.3459   1.2150
 DLL  C4'   C  CH1   0  -0.018   1.3243  -2.9789  -0.4683
 DLL  N1    N  N     0  -0.474   4.7421   3.4151  -0.7618
 DLL  C3'   C  CH1   0  -0.039   2.6263  -3.6705  -0.0772
 DLL  C2    C  CR16  0   0.048   4.8243   2.3637  -1.5720
 DLL  C4    C  CR56  0   0.494   3.7059   1.0399  -0.2266
 DLL  N3    N  N     0  -0.458   4.3409   1.1465  -1.3898
 DLL  HB1C  H  HCH2  0   0.316  -5.2427  -1.0094  -0.7807
 DLL  HB2C  H  HCH2  0   0.317  -4.3057  -0.0611  -1.9044
 DLL  HD2   H  HCR6  0   0.255  -4.7772   2.3226  -2.2474
 DLL  HD1   H  HCR6  0   0.255  -6.9378   0.0956   0.6991
 DLL  HE2   H  HCR6  0   0.257  -6.3827   4.1776  -2.0254
 DLL  HE1   H  HCR6  0   0.257  -8.5438   1.9499   0.9237
 DLL  HZ    H  HCR6  0   0.257  -8.2723   4.0005  -0.4357
 DLL  H3P   H  HOH1  0   0.500  -0.0582   0.0680  -0.2036
 DLL  H5'1  H  HCH2  0   0.243   0.6075  -2.7388   1.5688
 DLL  H5'2  H  HCH2  0   0.280  -0.0098  -4.1571   0.7278
 DLL  H4'   H  HCH1  0   0.281   0.9380  -3.3927  -1.4047
 DLL  H1'   H  HCH1  0   0.268   3.6246  -1.3120  -1.2077
 DLL  H3'   H  HOH1  0   0.453   4.1937  -4.2607  -1.0387
 DLL  HA    H  HCH1  0   0.262   2.4581  -4.4933   0.6298
 DLL  H2'   H  HCH1  0   0.252   3.0123  -2.3669   1.5901
 DLL  HB    H  HOH1  0   0.472   5.0528  -3.1645   1.3314
 DLL  H8    H  HCR5  0   0.294   2.0418  -0.3447   2.1572
 DLL  H61N  H  HNH2  0   0.412   3.5640   4.2732   2.1142
 DLL  H62N  H  HNH2  0   0.404   4.4687   5.2073   0.9800
 DLL  H2    H  HCR6  0   0.254   5.3590   2.5311  -2.5007

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
 DLL  O    CAZ   double    1.194  0.020  1.194
 DLL  CB   CG    single    1.500  0.020  1.500
 DLL  CB   CAZ   single    1.502  0.020  1.502
 DLL  CG   CD2   aromatic  1.391  0.020  1.391
 DLL  CG   CD1   aromatic  1.392  0.020  1.392
 DLL  CD2  CE2   aromatic  1.389  0.020  1.389
 DLL  CD1  CE1   aromatic  1.388  0.020  1.388
 DLL  CE2  CZ    aromatic  1.389  0.020  1.389
 DLL  CE1  CZ    aromatic  1.389  0.020  1.389
 DLL  P    O2P   double    1.469  0.020  1.469
 DLL  P    O3P   single    1.586  0.020  1.586
 DLL  P    O1P   single    1.635  0.020  1.635
 DLL  P    O5'   single    1.588  0.020  1.588
 DLL  O1P  CAZ   single    1.357  0.020  1.357
 DLL  O5'  C5'   single    1.433  0.020  1.433
 DLL  C5'  C4'   single    1.514  0.020  1.514
 DLL  O4'  C1'   single    1.407  0.020  1.407
 DLL  O4'  C4'   single    1.430  0.020  1.430
 DLL  O3'  C3'   single    1.401  0.020  1.401
 DLL  C2'  O2'   single    1.394  0.020  1.394
 DLL  C2'  C1'   single    1.526  0.020  1.526
 DLL  C2'  C3'   single    1.532  0.020  1.532
 DLL  C1'  N9    single    1.435  0.020  1.435
 DLL  N9   C8    aromatic  1.372  0.020  1.372
 DLL  N9   C4    aromatic  1.368  0.020  1.368
 DLL  C8   N7    aromatic  1.297  0.020  1.297
 DLL  N7   C5    aromatic  1.372  0.020  1.372
 DLL  C5   C6    aromatic  1.407  0.020  1.407
 DLL  C5   C4    aromatic  1.384  0.020  1.384
 DLL  C6   N6    single    1.333  0.020  1.333
 DLL  C6   N1    aromatic  1.338  0.020  1.338
 DLL  C4'  C3'   single    1.525  0.020  1.525
 DLL  N1   C2    aromatic  1.330  0.020  1.330
 DLL  C2   N3    aromatic  1.322  0.020  1.322
 DLL  CB   HB1C  single    0.970  0.020  1.090
 DLL  CB   HB2C  single    0.970  0.020  1.090
 DLL  CD2  HD2   single    0.930  0.020  1.080
 DLL  CD1  HD1   single    0.930  0.020  1.080
 DLL  CE2  HE2   single    0.930  0.020  1.080
 DLL  CE1  HE1   single    0.930  0.020  1.080
 DLL  CZ   HZ    single    0.930  0.020  1.080
 DLL  O3P  H3P   single    0.850  0.020  0.980
 DLL  C5'  H5'1  single    0.970  0.020  1.090
 DLL  C5'  H5'2  single    0.970  0.020  1.090
 DLL  C4'  H4'   single    0.970  0.020  1.090
 DLL  C1'  H1'   single    0.970  0.020  1.090
 DLL  O3'  H3'   single    0.850  0.020  0.980
 DLL  C3'  HA    single    0.970  0.020  1.090
 DLL  C2'  H2'   single    0.970  0.020  1.090
 DLL  O2'  HB    single    0.850  0.020  0.980
 DLL  C8   H8    single    0.930  0.020  1.080
 DLL  N6   H61N  single    0.860  0.020  1.020
 DLL  N6   H62N  single    0.860  0.020  1.020
 DLL  C2   H2    single    0.930  0.020  1.080
 DLL  C4   N3    aromatic  1.330  0.020  1.330

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
 DLL  HB2C  CB   HB1C  105.69  3.000
 DLL  HB2C  CB   CAZ   107.82  3.000
 DLL  HB1C  CB   CAZ   107.89  3.000
 DLL  HB2C  CB   CG    111.29  3.000
 DLL  HB1C  CB   CG    111.35  3.000
 DLL  CAZ   CB   CG    112.48  3.000
 DLL  CD1   CG   CD2   119.01  3.000
 DLL  CD1   CG   CB    120.45  3.000
 DLL  CD2   CG   CB    120.54  3.000
 DLL  HD2   CD2  CE2   119.68  3.000
 DLL  HD2   CD2  CG    119.73  3.000
 DLL  CE2   CD2  CG    120.59  3.000
 DLL  HD1   CD1  CE1   119.72  3.000
 DLL  HD1   CD1  CG    119.72  3.000
 DLL  CE1   CD1  CG    120.56  3.000
 DLL  HE2   CE2  CZ    120.13  3.000
 DLL  HE2   CE2  CD2   119.81  3.000
 DLL  CZ    CE2  CD2   120.06  3.000
 DLL  HE1   CE1  CZ    120.10  3.000
 DLL  HE1   CE1  CD1   119.81  3.000
 DLL  CZ    CE1  CD1   120.09  3.000
 DLL  HZ    CZ   CE1   120.14  3.000
 DLL  HZ    CZ   CE2   120.17  3.000
 DLL  CE1   CZ   CE2   119.68  3.000
 DLL  O5'   P    O1P    94.42  3.000
 DLL  O5'   P    O3P   108.25  3.000
 DLL  O1P   P    O3P   106.92  3.000
 DLL  O5'   P    O2P   117.78  3.000
 DLL  O1P   P    O2P   116.07  3.000
 DLL  O3P   P    O2P   111.76  3.000
 DLL  H3P   O3P  P     116.15  3.000
 DLL  CAZ   O1P  P     121.87  3.000
 DLL  C5'   O5'  P     121.95  3.000
 DLL  H5'2  C5'  H5'1  107.44  3.000
 DLL  H5'2  C5'  C4'   109.80  3.000
 DLL  H5'1  C5'  C4'   111.79  3.000
 DLL  H5'2  C5'  O5'   107.32  3.000
 DLL  H5'1  C5'  O5'   111.60  3.000
 DLL  C4'   C5'  O5'   108.79  3.000
 DLL  C4'   O4'  C1'   110.53  3.000
 DLL  H3'   O3'  C3'   108.00  3.000
 DLL  H2'   C2'  C3'   108.69  3.000
 DLL  H2'   C2'  C1'   110.10  3.000
 DLL  C3'   C2'  C1'   101.12  3.000
 DLL  H2'   C2'  O2'   111.56  3.000
 DLL  C3'   C2'  O2'   115.08  3.000
 DLL  C1'   C2'  O2'   109.77  3.000
 DLL  HB    O2'  C2'   108.99  3.000
 DLL  H1'   C1'  N9    106.20  3.000
 DLL  H1'   C1'  C2'   110.03  3.000
 DLL  N9    C1'  C2'   114.26  3.000
 DLL  H1'   C1'  O4'   111.10  3.000
 DLL  N9    C1'  O4'   109.93  3.000
 DLL  C2'   C1'  O4'   105.40  3.000
 DLL  C4    N9   C8    106.08  3.000
 DLL  C4    N9   C1'   125.92  3.000
 DLL  C8    N9   C1'   127.98  3.000
 DLL  H8    C8   N7    124.65  3.000
 DLL  H8    C8   N9    121.96  3.000
 DLL  N7    C8   N9    113.39  3.000
 DLL  C5    N7   C8    104.49  3.000
 DLL  C4    C5   C6    116.29  3.000
 DLL  C4    C5   N7    110.84  3.000
 DLL  C6    C5   N7    132.87  3.000
 DLL  N1    C6   N6    119.34  3.000
 DLL  N1    C6   C5    117.85  3.000
 DLL  N6    C6   C5    122.80  3.000
 DLL  O1P   CAZ  CB    110.69  3.000
 DLL  O1P   CAZ  O     122.31  3.000
 DLL  CB    CAZ  O     127.00  3.000
 DLL  H62N  N6   H61N  118.27  3.000
 DLL  H62N  N6   C6    120.26  3.000
 DLL  H61N  N6   C6    121.14  3.000
 DLL  H4'   C4'  C3'   110.44  3.000
 DLL  H4'   C4'  O4'   108.81  3.000
 DLL  C3'   C4'  O4'   106.37  3.000
 DLL  H4'   C4'  C5'   108.83  3.000
 DLL  C3'   C4'  C5'   112.39  3.000
 DLL  O4'   C4'  C5'   109.93  3.000
 DLL  C2    N1   C6    119.20  3.000
 DLL  HA    C3'  C4'   111.98  3.000
 DLL  HA    C3'  C2'   111.61  3.000
 DLL  C4'   C3'  C2'   101.31  3.000
 DLL  HA    C3'  O3'   111.88  3.000
 DLL  C4'   C3'  O3'   108.44  3.000
 DLL  C2'   C3'  O3'   111.12  3.000
 DLL  H2    C2   N3    116.12  3.000
 DLL  H2    C2   N1    115.47  3.000
 DLL  N3    C2   N1    128.41  3.000
 DLL  N3    C4   C5    126.60  3.000
 DLL  N3    C4   N9    128.20  3.000
 DLL  C5    C4   N9    105.20  3.000
 DLL  C4    N3   C2    111.65  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
 DLL  CONST_01  CZ    CE2  CD2  CG      0.00   0.0  0
 DLL  CONST_02  CZ    CE1  CD1  CG      0.00   0.0  0
 DLL  CONST_03  CE1   CD1  CG   CD2     0.00   0.0  0
 DLL  CONST_04  CE1   CZ   CE2  CD2     0.00   0.0  0
 DLL  CONST_05  CE2   CD2  CG   CD1     0.00   0.0  0
 DLL  CONST_06  CE2   CZ   CE1  CD1     0.00   0.0  0
 DLL  CONST_07  C5    N7   C8   N9      0.00   0.0  0
 DLL  CONST_08  N7    C5   C4   N9      0.00   0.0  0
 DLL  CONST_09  C6    C5   C4   N9    180.00   0.0  0
 DLL  CONST_10  C2    N3   C4   N9    180.00   0.0  0
 DLL  CONST_11  C5    C4   N9   C8      0.00   0.0  0
 DLL  CONST_12  N3    C4   N9   C8    180.00   0.0  0
 DLL  CONST_13  C6    C5   N7   C8    180.00   0.0  0
 DLL  CONST_14  C4    C5   N7   C8      0.00   0.0  0
 DLL  CONST_15  C4    N9   C8   N7      0.00   0.0  0
 DLL  CONST_16  N1    C6   C5   N7    180.00   0.0  0
 DLL  CONST_17  N3    C4   C5   N7    180.00   0.0  0
 DLL  CONST_18  C2    N1   C6   C5      0.00   0.0  0
 DLL  CONST_19  C2    N3   C4   C5      0.00   0.0  0
 DLL  CONST_20  N3    C4   C5   C6      0.00   0.0  0
 DLL  CONST_21  N3    C2   N1   C6      0.00   0.0  0
 DLL  CONST_22  C4    C5   C6   N1      0.00   0.0  0
 DLL  CONST_23  C4    N3   C2   N1      0.00   0.0  0
 DLL  CONST_24  N7    C8   N9   C1'   180.00   0.0  0
 DLL  CONST_25  C5    C4   N9   C1'   180.00   0.0  0
 DLL  CONST_26  N3    C4   N9   C1'     0.00   0.0  0
 DLL  CONST_27  CE2   CD2  CG   CB    180.00   0.0  0
 DLL  CONST_28  CE1   CD1  CG   CB    180.00   0.0  0
 DLL  CONST_29  N6    C6   C5   N7      0.00   0.0  0
 DLL  CONST_30  C4    C5   C6   N6    180.00   0.0  0
 DLL  CONST_31  C2    N1   C6   N6    180.00   0.0  0
 DLL  CONST_32  HE2   CE2  CD2  CG    180.00   0.0  0
 DLL  CONST_33  HE1   CE1  CD1  CG    180.00   0.0  0
 DLL  CONST_34  HD1   CD1  CG   CD2   180.00   0.0  0
 DLL  CONST_35  HZ    CZ   CE2  CD2   180.00   0.0  0
 DLL  CONST_36  HD2   CD2  CG   CD1   180.00   0.0  0
 DLL  CONST_37  H8    C8   N9   C1'     0.00   0.0  0
 DLL  CONST_38  H2    C2   N1   C6    180.00   0.0  0
 DLL  CONST_39  H61N  N6   C6   C5      0.00   0.0  0
 DLL  CONST_40  H62N  N6   C6   C5    180.00   0.0  0
 DLL  Var_01    CAZ   CB   CG   CD2    93.02  30.0  2
 DLL  Var_02    CG    CB   CAZ  O      -0.38  30.0  1
 DLL  Var_03    C4'   C5'  O5'  P    -116.15  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
 DLL  chir_02  C2'  O2'  C1'  C3'  negativ
 DLL  chir_03  C1'  O4'  N9   C2'  negativ
 DLL  chir_04  C4'  O4'  C3'  C5'  negativ
 DLL  chir_05  C3'  O3'  C4'  C2'  positiv
 DLL  chir_06  P    O3P  O1P  O5'  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
 DLL  plan-1  CB    0.020
 DLL  plan-1  CG    0.020
 DLL  plan-1  CD2   0.020
 DLL  plan-1  CD1   0.020
 DLL  plan-1  CE2   0.020
 DLL  plan-1  CE1   0.020
 DLL  plan-1  CZ    0.020
 DLL  plan-1  HD2   0.020
 DLL  plan-1  HD1   0.020
 DLL  plan-1  HE2   0.020
 DLL  plan-1  HE1   0.020
 DLL  plan-1  HZ    0.020
 DLL  plan-2  C1'   0.020
 DLL  plan-2  N9    0.020
 DLL  plan-2  C8    0.020
 DLL  plan-2  N7    0.020
 DLL  plan-2  C5    0.020
 DLL  plan-2  C6    0.020
 DLL  plan-2  N6    0.020
 DLL  plan-2  N1    0.020
 DLL  plan-2  C2    0.020
 DLL  plan-2  C4    0.020
 DLL  plan-2  N3    0.020
 DLL  plan-2  H8    0.020
 DLL  plan-2  H2    0.020
 DLL  plan-3  C6    0.020
 DLL  plan-3  N6    0.020
 DLL  plan-3  H61N  0.020
 DLL  plan-3  H62N  0.020
 DLL  plan-4  O     0.020
 DLL  plan-4  CB    0.020
 DLL  plan-4  O1P   0.020
 DLL  plan-4  CAZ   0.020

