# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 23:51:13 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(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
 6R9  6R9  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate'  ligand  42  26  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6R9
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
 6R9  C01  C  CH3   0  -0.766  -5.8888  -1.7527   1.8702
 6R9  C02  C  C     0   0.579  -4.8072  -1.9165   0.8574
 6R9  C09  C  CH2   0  -0.213  -1.7357   1.5983  -1.0567
 6R9  C10  C  CH1   0   0.025  -0.7025   1.9830  -0.0275
 6R9  C11  C  CH1   0  -0.037   0.5110   2.6902  -0.6260
 6R9  C12  C  CH1   0  -0.043   1.5896   2.3669   0.4156
 6R9  C13  C  CH1   0   0.183   1.2156   0.9386   0.8098
 6R9  C16  C  CR15  0   0.108   1.5358  -0.6590  -1.1530
 6R9  C18  C  CR56  0  -0.004   3.4395  -1.4501  -0.6971
 6R9  C19  C  CR56  0   0.492   3.1446  -0.5620   0.3238
 6R9  C21  C  CR16  0   0.044   5.0461  -0.9469   1.3469
 6R9  C23  C  CR6   0   0.460   4.6802  -2.1097  -0.6066
 6R9  N15  N  NR5   0  -0.537   1.9126  -0.0594   0.0191
 6R9  N17  N  N     0  -0.447   2.4185  -1.4968  -1.6094
 6R9  N20  N  N     0  -0.459   3.9118  -0.2679   1.3709
 6R9  N22  N  N     0  -0.473   5.4631  -1.8272   0.4412
 6R9  N24  N  NH2   0  -0.815   5.0975  -2.9900  -1.5155
 6R9  O03  O  O     0  -0.409  -4.4367  -2.9388   0.3577
 6R9  O04  O  O2    0  -0.568  -4.2448  -0.7206   0.5336
 6R9  O06  O  O     0  -0.673  -3.5069  -1.0690  -1.9600
 6R9  O07  O  OH1   0  -0.742  -1.8156  -1.3896  -0.0917
 6R9  O08  O  O2    0  -0.574  -2.8373   0.9399  -0.4171
 6R9  O14  O  O2    0  -0.529  -0.1666   0.8154   0.5957
 6R9  O25  O  OH1   0  -0.660   1.4386   3.1661   1.5547
 6R9  O26  O  OH1   0  -0.652   0.2506   4.0542  -0.7715
 6R9  P05  P  P     0   1.455  -3.0950  -0.6182  -0.6239
 6R9  H1   H  HCH3  0   0.286  -6.6911  -1.1373   1.4611
 6R9  H2   H  HCH3  0   0.273  -6.2901  -2.7212   2.1526
 6R9  H3   H  HCH3  0   0.284  -5.5095  -1.2423   2.7553
 6R9  H4   H  HCH2  0   0.288  -2.1240   2.5011  -1.5274
 6R9  H5   H  HCH2  0   0.248  -1.3010   0.9803  -1.8480
 6R9  H6   H  HCH1  0   0.272  -1.1683   2.6199   0.7330
 6R9  H7   H  HCH1  0   0.254   0.7819   2.2251  -1.5831
 6R9  H8   H  HCH1  0   0.270   2.6045   2.4216   0.0040
 6R9  H9   H  HCH1  0   0.294   1.4621   0.7413   1.8558
 6R9  H10  H  HCR5  0   0.286   0.5900  -0.4539  -1.6284
 6R9  H11  H  HCR6  0   0.254   5.7300  -0.7652   2.1692
 6R9  H12  H  HNH2  0   0.412   4.5269  -3.2336  -2.3059
 6R9  H13  H  HNH2  0   0.405   5.9902  -3.4412  -1.4138
 6R9  H14  H  HOH1  0   0.501  -1.2623  -0.8977   0.5394
 6R9  H15  H  HOH1  0   0.455   1.2681   4.0705   1.2642
 6R9  H16  H  HOH1  0   0.473   0.8500   4.4186  -1.4307

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
 6R9  C01  C02  single    1.491  0.020  1.491
 6R9  O03  C02  double    1.197  0.020  1.197
 6R9  O06  P05  double    1.469  0.020  1.469
 6R9  C02  O04  single    1.361  0.020  1.361
 6R9  O04  P05  single    1.635  0.020  1.635
 6R9  N24  C23  single    1.332  0.020  1.332
 6R9  P05  O08  single    1.593  0.020  1.593
 6R9  P05  O07  single    1.586  0.020  1.586
 6R9  N17  C16  aromatic  1.300  0.020  1.300
 6R9  N17  C18  aromatic  1.370  0.020  1.370
 6R9  C16  N15  aromatic  1.369  0.020  1.369
 6R9  O08  C09  single    1.434  0.020  1.434
 6R9  C23  C18  aromatic  1.408  0.020  1.408
 6R9  C23  N22  aromatic  1.338  0.020  1.338
 6R9  C18  C19  aromatic  1.385  0.020  1.385
 6R9  O14  C13  single    1.404  0.020  1.404
 6R9  O14  C10  single    1.428  0.020  1.428
 6R9  N15  C19  aromatic  1.365  0.020  1.365
 6R9  N15  C13  single    1.452  0.020  1.452
 6R9  N22  C21  aromatic  1.330  0.020  1.330
 6R9  C19  N20  aromatic  1.331  0.020  1.331
 6R9  C09  C10  single    1.508  0.020  1.508
 6R9  C13  C12  single    1.528  0.020  1.528
 6R9  C21  N20  aromatic  1.322  0.020  1.322
 6R9  C10  C11  single    1.527  0.020  1.527
 6R9  C12  C11  single    1.534  0.020  1.534
 6R9  C12  O25  single    1.400  0.020  1.400
 6R9  C11  O26  single    1.396  0.020  1.396
 6R9  C01  H1   single    0.970  0.020  1.090
 6R9  C01  H2   single    0.970  0.020  1.090
 6R9  C01  H3   single    0.970  0.020  1.090
 6R9  C09  H4   single    0.970  0.020  1.090
 6R9  C09  H5   single    0.970  0.020  1.090
 6R9  C10  H6   single    0.970  0.020  1.090
 6R9  C11  H7   single    0.970  0.020  1.090
 6R9  C12  H8   single    0.970  0.020  1.090
 6R9  C13  H9   single    0.970  0.020  1.090
 6R9  C16  H10  single    0.930  0.020  1.080
 6R9  C21  H11  single    0.930  0.020  1.080
 6R9  N24  H12  single    0.860  0.020  1.020
 6R9  N24  H13  single    0.860  0.020  1.020
 6R9  O07  H14  single    0.850  0.020  0.980
 6R9  O25  H15  single    0.850  0.020  0.980
 6R9  O26  H16  single    0.850  0.020  0.980

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
 6R9  H3   C01  H2   109.58  3.000
 6R9  H3   C01  H1   107.23  3.000
 6R9  H2   C01  H1   109.20  3.000
 6R9  H3   C01  C02  110.53  3.000
 6R9  H2   C01  C02  110.30  3.000
 6R9  H1   C01  C02  109.93  3.000
 6R9  O04  C02  O03  121.57  3.000
 6R9  O04  C02  C01  111.41  3.000
 6R9  O03  C02  C01  127.02  3.000
 6R9  H5   C09  H4   107.29  3.000
 6R9  H5   C09  O08  111.63  3.000
 6R9  H4   C09  O08  107.41  3.000
 6R9  H5   C09  C10  111.43  3.000
 6R9  H4   C09  C10  109.12  3.000
 6R9  O08  C09  C10  109.81  3.000
 6R9  H6   C10  O14  109.38  3.000
 6R9  H6   C10  C11  109.92  3.000
 6R9  O14  C10  C11  104.57  3.000
 6R9  H6   C10  C09  109.31  3.000
 6R9  C11  C10  C09  113.28  3.000
 6R9  O14  C10  C09  110.26  3.000
 6R9  H7   C11  O26  111.65  3.000
 6R9  H7   C11  C12  109.22  3.000
 6R9  O26  C11  C12  114.07  3.000
 6R9  H7   C11  C10  109.98  3.000
 6R9  O26  C11  C10  110.18  3.000
 6R9  C12  C11  C10  101.25  3.000
 6R9  H8   C12  O25  112.14  3.000
 6R9  H8   C12  C13  111.71  3.000
 6R9  O25  C12  C13  107.30  3.000
 6R9  H8   C12  C11  112.67  3.000
 6R9  O25  C12  C11  110.88  3.000
 6R9  C13  C12  C11  101.54  3.000
 6R9  H9   C13  O14  110.62  3.000
 6R9  H9   C13  N15  106.80  3.000
 6R9  O14  C13  N15  109.22  3.000
 6R9  H9   C13  C12  111.13  3.000
 6R9  N15  C13  C12  112.62  3.000
 6R9  O14  C13  C12  106.47  3.000
 6R9  H10  C16  N17  124.30  3.000
 6R9  H10  C16  N15  122.37  3.000
 6R9  N17  C16  N15  113.33  3.000
 6R9  N17  C18  C23  133.12  3.000
 6R9  C23  C18  C19  116.14  3.000
 6R9  N17  C18  C19  110.73  3.000
 6R9  N20  C19  N15  127.92  3.000
 6R9  N20  C19  C18  126.79  3.000
 6R9  N15  C19  C18  105.29  3.000
 6R9  H11  C21  N22  115.43  3.000
 6R9  H11  C21  N20  116.17  3.000
 6R9  N22  C21  N20  128.40  3.000
 6R9  N24  C23  N22  119.37  3.000
 6R9  N22  C23  C18  117.84  3.000
 6R9  N24  C23  C18  122.79  3.000
 6R9  C19  N15  C16  106.15  3.000
 6R9  C19  N15  C13  124.39  3.000
 6R9  C16  N15  C13  129.44  3.000
 6R9  C18  N17  C16  104.50  3.000
 6R9  C21  N20  C19  111.52  3.000
 6R9  C23  N22  C21  119.31  3.000
 6R9  H13  N24  H12  118.35  3.000
 6R9  H13  N24  C23  120.37  3.000
 6R9  H12  N24  C23  121.26  3.000
 6R9  P05  O04  C02  120.95  3.000
 6R9  H14  O07  P05  115.51  3.000
 6R9  P05  O08  C09  121.03  3.000
 6R9  C13  O14  C10  111.36  3.000
 6R9  H15  O25  C12  108.01  3.000
 6R9  H16  O26  C11  108.97  3.000
 6R9  O08  P05  O07  107.56  3.000
 6R9  O07  P05  O06  112.46  3.000
 6R9  O08  P05  O06  117.63  3.000
 6R9  O07  P05  O04  107.42  3.000
 6R9  O08  P05  O04   94.77  3.000
 6R9  O06  P05  O04  115.31  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
 6R9  CONST_01  C23  C18  N17  C16   180.00   0.0  0
 6R9  CONST_02  C19  C18  N17  C16     0.00   0.0  0
 6R9  CONST_03  C18  C19  N15  C16     0.00   0.0  0
 6R9  CONST_04  N20  C19  N15  C16   180.00   0.0  0
 6R9  CONST_05  N15  C16  N17  C18     0.00   0.0  0
 6R9  CONST_06  C21  N22  C23  C18     0.00   0.0  0
 6R9  CONST_07  C21  N20  C19  C18     0.00   0.0  0
 6R9  CONST_08  N22  C23  C18  C19     0.00   0.0  0
 6R9  CONST_09  N17  C16  N15  C19     0.00   0.0  0
 6R9  CONST_10  N22  C21  N20  C19     0.00   0.0  0
 6R9  CONST_11  N15  C19  N20  C21   180.00   0.0  0
 6R9  CONST_12  N15  C19  C18  C23   180.00   0.0  0
 6R9  CONST_13  N20  C19  C18  C23     0.00   0.0  0
 6R9  CONST_14  N20  C21  N22  C23     0.00   0.0  0
 6R9  CONST_15  N17  C18  C19  N15     0.00   0.0  0
 6R9  CONST_16  N22  C23  C18  N17   180.00   0.0  0
 6R9  CONST_17  N20  C19  C18  N17   180.00   0.0  0
 6R9  CONST_18  N17  C16  N15  C13   180.00   0.0  0
 6R9  CONST_19  C18  C19  N15  C13   180.00   0.0  0
 6R9  CONST_20  N20  C19  N15  C13     0.00   0.0  0
 6R9  CONST_21  N24  C23  C18  C19   180.00   0.0  0
 6R9  CONST_22  N24  C23  N22  C21   180.00   0.0  0
 6R9  CONST_23  N24  C23  C18  N17     0.00   0.0  0
 6R9  CONST_24  H10  C16  N15  C13     0.00   0.0  0
 6R9  CONST_25  H11  C21  N20  C19   180.00   0.0  0
 6R9  CONST_26  H12  N24  C23  C18     0.00   0.0  0
 6R9  CONST_27  H13  N24  C23  C18   180.00   0.0  0
 6R9  Var_01    O06  P05  O04  C02    59.87  30.0  3
 6R9  Var_02    H1   C01  C02  O03  -117.61  30.0  3
 6R9  Var_03    H4   C09  O08  P05   131.56  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
 6R9  chir_01  C10  O14  C09  C11  positiv
 6R9  chir_02  C11  O26  C10  C12  positiv
 6R9  chir_03  C12  O25  C11  C13  positiv
 6R9  chir_04  C13  O14  N15  C12  negativ
 6R9  chir_05  P05  O04  O08  O07  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
 6R9  plan-1  C13  0.020
 6R9  plan-1  C16  0.020
 6R9  plan-1  C18  0.020
 6R9  plan-1  C19  0.020
 6R9  plan-1  C21  0.020
 6R9  plan-1  C23  0.020
 6R9  plan-1  N15  0.020
 6R9  plan-1  N17  0.020
 6R9  plan-1  N20  0.020
 6R9  plan-1  N22  0.020
 6R9  plan-1  N24  0.020
 6R9  plan-1  H10  0.020
 6R9  plan-1  H11  0.020
 6R9  plan-2  C23  0.020
 6R9  plan-2  N24  0.020
 6R9  plan-2  H12  0.020
 6R9  plan-2  H13  0.020
 6R9  plan-3  C01  0.020
 6R9  plan-3  C02  0.020
 6R9  plan-3  O03  0.020
 6R9  plan-3  O04  0.020

