# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 15:14:57 2021
#   Inital geometry file: a 125 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] 2-azanyl-6-fluoranyl-benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(F)c1C(=O)O[P](O)(=O)OC[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
 9SN  9SN  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 2-azanyl-6-fluoranyl-benzoate'  ligand  51  33  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9SN
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
 9SN  C5    C  CR15  0   0.113  38.8834  -4.3382  16.8956
 9SN  N1    N  NH2   0  -0.816  38.6276  -0.7100  19.1219
 9SN  C7    C  CH1   0   0.158  40.4702  -4.5826  14.9321
 9SN  C9    C  CH1   0   0.022  39.6798  -6.6730  14.2635
 9SN  C10   C  CH2   0  -0.206  38.3726  -7.3872  14.5055
 9SN  C3    C  CR56  0   0.015  39.3025  -2.3664  17.5134
 9SN  C2    C  CR6   0   0.465  39.3808  -1.0845  18.0840
 9SN  C16   C  CH1   0  -0.046  40.6941  -6.9099  15.3836
 9SN  C18   C  CH1   0  -0.031  41.5238  -5.6190  15.3283
 9SN  C20   C  CR56  0   0.494  40.1505  -2.6155  16.4474
 9SN  C22   C  CR16  0   0.038  41.0187  -0.6033  16.5428
 9SN  C24   C  C     0   0.629  36.9441  -3.8339  13.7562
 9SN  C25   C  CR6   0  -0.362  37.0553  -2.6165  14.5692
 9SN  C27   C  CR6   0   0.565  37.9779  -1.6369  14.1635
 9SN  C28   C  CR16  0  -0.436  38.0927  -0.4017  14.7428
 9SN  C29   C  CR16  0  -0.222  37.2370  -0.1091  15.8030
 9SN  C30   C  CR16  0  -0.346  36.3374  -1.0354  16.2668
 9SN  C31   C  CR6   0   0.389  36.2253  -2.3129  15.6823
 9SN  F33   F  F     0  -0.301  38.8286  -1.9356  13.1769
 9SN  N21   N  N     0  -0.455  41.0354  -1.7707  15.9240
 9SN  N23   N  N     0  -0.470  40.2616  -0.2217  17.5686
 9SN  N32   N  NH2   0  -0.864  35.2733  -3.1434  16.1724
 9SN  N4    N  N     0  -0.443  38.5211  -3.4591  17.7802
 9SN  N6    N  NR5   0  -0.531  39.8727  -3.8947  16.0589
 9SN  O11   O  O2    0  -0.574  37.4373  -7.0624  13.4696
 9SN  O13   O  OH1   0  -0.730  35.4010  -6.9372  15.0248
 9SN  O14   O  O2    0  -0.626  36.4417  -4.8940  14.4523
 9SN  O15   O  O     0  -0.669  35.2523  -6.2322  12.5011
 9SN  O17   O  OH1   0  -0.654  41.4327  -8.0695  15.1318
 9SN  O19   O  OH1   0  -0.662  42.4630  -5.6776  14.2915
 9SN  O26   O  O     0  -0.405  37.2208  -3.9401  12.5955
 9SN  O8    O  O2    0  -0.492  39.4655  -5.2717  14.2427
 9SN  P12   P  P     0   1.493  36.0631  -6.3104  13.7223
 9SN  HC5   H  HCR5  0   0.282  38.4542  -5.3233  16.8058
 9SN  HN1B  H  HNH2  0   0.400  38.6264   0.2527  19.4127
 9SN  HN1A  H  HNH2  0   0.407  37.8681  -1.2904  19.4324
 9SN  HC7   H  HCH1  0   0.282  40.9157  -3.8071  14.3040
 9SN  HC9   H  HCH1  0   0.263  40.1032  -6.9968  13.3049
 9SN  H10B  H  HCH2  0   0.277  38.5386  -8.4645  14.4733
 9SN  H10A  H  HCH2  0   0.240  37.9753  -7.1470  15.4946
 9SN  HC16  H  HCH1  0   0.251  40.1820  -6.9668  16.3533
 9SN  HC18  H  HCH1  0   0.263  41.9870  -5.3756  16.2920
 9SN  HC22  H  HCR6  0   0.250  41.7115   0.1446  16.1715
 9SN  HC28  H  HCR6  0   0.273  38.8348   0.3023  14.3944
 9SN  HC29  H  HCR6  0   0.273  37.2989   0.8578  16.2843
 9SN  HC30  H  HCR6  0   0.267  35.6989  -0.7946  17.1074
 9SN  H32B  H  HNH2  0   0.396  34.8558  -2.8830  17.0497
 9SN  H32A  H  HNH2  0   0.401  35.3296  -4.1324  16.0173
 9SN  HO13  H  HOH1  0   0.511  34.9206  -7.7630  14.8711
 9SN  HO17  H  HOH1  0   0.472  41.8015  -8.3926  15.9602
 9SN  HO19  H  HOH1  0   0.454  42.8256  -6.5722  14.2712

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
 9SN  C5   N4    aromatic  1.299  0.020  1.299
 9SN  C5   N6    aromatic  1.370  0.020  1.370
 9SN  N1   C2    single    1.336  0.020  1.336
 9SN  C7   C18   single    1.530  0.020  1.530
 9SN  C7   N6    single    1.449  0.020  1.449
 9SN  C7   O8    single    1.400  0.020  1.400
 9SN  C9   C10   single    1.509  0.020  1.509
 9SN  C9   C16   single    1.530  0.020  1.530
 9SN  C9   O8    single    1.418  0.020  1.418
 9SN  C10  O11   single    1.433  0.020  1.433
 9SN  C3   C2    aromatic  1.405  0.020  1.405
 9SN  C3   C20   aromatic  1.385  0.020  1.385
 9SN  C3   N4    aromatic  1.370  0.020  1.370
 9SN  C2   N23   aromatic  1.336  0.020  1.336
 9SN  C16  C18   single    1.535  0.020  1.535
 9SN  C16  O17   single    1.398  0.020  1.398
 9SN  C18  O19   single    1.400  0.020  1.400
 9SN  C20  N21   aromatic  1.331  0.020  1.331
 9SN  C20  N6    aromatic  1.365  0.020  1.365
 9SN  C22  N21   aromatic  1.321  0.020  1.321
 9SN  C22  N23   aromatic  1.331  0.020  1.331
 9SN  C24  C25   single    1.468  0.020  1.468
 9SN  C24  O14   single    1.364  0.020  1.364
 9SN  C24  O26   double    1.198  0.020  1.198
 9SN  C25  C27   aromatic  1.405  0.020  1.405
 9SN  C25  C31   aromatic  1.421  0.020  1.421
 9SN  C27  C28   aromatic  1.369  0.020  1.369
 9SN  C27  F33   single    1.337  0.020  1.337
 9SN  C28  C29   aromatic  1.393  0.020  1.393
 9SN  C29  C30   aromatic  1.372  0.020  1.372
 9SN  C30  C31   aromatic  1.409  0.020  1.409
 9SN  C31  N32   single    1.355  0.020  1.355
 9SN  O11  P12   single    1.587  0.020  1.587
 9SN  O13  P12   single    1.590  0.020  1.590
 9SN  O14  P12   single    1.638  0.020  1.638
 9SN  O15  P12   double    1.468  0.020  1.468
 9SN  C5   HC5   single    0.930  0.020  1.080
 9SN  N1   HN1B  single    0.860  0.020  1.020
 9SN  N1   HN1A  single    0.860  0.020  1.020
 9SN  C7   HC7   single    0.970  0.020  1.090
 9SN  C9   HC9   single    0.970  0.020  1.090
 9SN  C10  H10B  single    0.970  0.020  1.090
 9SN  C10  H10A  single    0.970  0.020  1.090
 9SN  C16  HC16  single    0.970  0.020  1.090
 9SN  C18  HC18  single    0.970  0.020  1.090
 9SN  C22  HC22  single    0.930  0.020  1.080
 9SN  C28  HC28  single    0.930  0.020  1.080
 9SN  C29  HC29  single    0.930  0.020  1.080
 9SN  C30  HC30  single    0.930  0.020  1.080
 9SN  N32  H32B  single    0.890  0.020  1.040
 9SN  N32  H32A  single    0.890  0.020  1.040
 9SN  O13  HO13  single    0.850  0.020  0.980
 9SN  O17  HO17  single    0.850  0.020  0.980
 9SN  O19  HO19  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
 9SN  HC5   C5   N6    122.17  3.000
 9SN  HC5   C5   N4    124.34  3.000
 9SN  N6    C5   N4    113.48  3.000
 9SN  HN1A  N1   HN1B  117.55  3.000
 9SN  HN1A  N1   C2    120.27  3.000
 9SN  HN1B  N1   C2    119.58  3.000
 9SN  HC7   C7   O8    111.02  3.000
 9SN  HC7   C7   N6    106.14  3.000
 9SN  O8    C7   N6    108.71  3.000
 9SN  HC7   C7   C18   110.42  3.000
 9SN  O8    C7   C18   106.76  3.000
 9SN  N6    C7   C18   113.84  3.000
 9SN  HC9   C9   O8    109.71  3.000
 9SN  HC9   C9   C16   109.77  3.000
 9SN  O8    C9   C16   105.31  3.000
 9SN  HC9   C9   C10   109.56  3.000
 9SN  O8    C9   C10   109.83  3.000
 9SN  C16   C9   C10   112.56  3.000
 9SN  H10A  C10  H10B  107.41  3.000
 9SN  H10A  C10  O11   111.55  3.000
 9SN  H10B  C10  O11   107.57  3.000
 9SN  H10A  C10  C9    110.86  3.000
 9SN  H10B  C10  C9    109.33  3.000
 9SN  O11   C10  C9    110.01  3.000
 9SN  N4    C3   C20   110.85  3.000
 9SN  N4    C3   C2    132.88  3.000
 9SN  C20   C3   C2    116.26  3.000
 9SN  N23   C2   C3    117.98  3.000
 9SN  N23   C2   N1    119.35  3.000
 9SN  C3    C2   N1    122.66  3.000
 9SN  HC16  C16  O17   111.25  3.000
 9SN  HC16  C16  C18   109.11  3.000
 9SN  O17   C16  C18   113.92  3.000
 9SN  HC16  C16  C9    110.21  3.000
 9SN  O17   C16  C9    110.30  3.000
 9SN  C18   C16  C9    101.64  3.000
 9SN  HC18  C18  O19   112.13  3.000
 9SN  HC18  C18  C16   112.53  3.000
 9SN  O19   C18  C16   110.73  3.000
 9SN  HC18  C18  C7    111.60  3.000
 9SN  O19   C18  C7    107.37  3.000
 9SN  C16   C18  C7    101.93  3.000
 9SN  N6    C20  N21   128.18  3.000
 9SN  N6    C20  C3    105.24  3.000
 9SN  N21   C20  C3    126.58  3.000
 9SN  HC22  C22  N23   115.43  3.000
 9SN  HC22  C22  N21   116.14  3.000
 9SN  N23   C22  N21   128.43  3.000
 9SN  O26   C24  O14   120.71  3.000
 9SN  O26   C24  C25   126.34  3.000
 9SN  O14   C24  C25   112.94  3.000
 9SN  C31   C25  C27   117.42  3.000
 9SN  C31   C25  C24   124.51  3.000
 9SN  C27   C25  C24   117.89  3.000
 9SN  F33   C27  C28   117.42  3.000
 9SN  F33   C27  C25   118.37  3.000
 9SN  C28   C27  C25   124.17  3.000
 9SN  HC28  C28  C29   122.02  3.000
 9SN  HC28  C28  C27   120.59  3.000
 9SN  C29   C28  C27   117.38  3.000
 9SN  HC29  C29  C30   119.37  3.000
 9SN  HC29  C29  C28   119.40  3.000
 9SN  C30   C29  C28   121.21  3.000
 9SN  HC30  C30  C31   118.47  3.000
 9SN  HC30  C30  C29   119.94  3.000
 9SN  C31   C30  C29   121.59  3.000
 9SN  N32   C31  C30   117.48  3.000
 9SN  N32   C31  C25   124.24  3.000
 9SN  C30   C31  C25   118.16  3.000
 9SN  C22   N21  C20   111.61  3.000
 9SN  C22   N23  C2    119.15  3.000
 9SN  H32A  N32  H32B  114.43  3.000
 9SN  H32A  N32  C31   120.61  3.000
 9SN  H32B  N32  C31   116.64  3.000
 9SN  C3    N4   C5    104.37  3.000
 9SN  C20   N6   C7    125.60  3.000
 9SN  C20   N6   C5    106.05  3.000
 9SN  C7    N6   C5    128.26  3.000
 9SN  P12   O11  C10   123.88  3.000
 9SN  HO13  O13  P12   114.40  3.000
 9SN  P12   O14  C24   121.99  3.000
 9SN  HO17  O17  C16   109.02  3.000
 9SN  HO19  O19  C18   107.84  3.000
 9SN  C9    O8   C7    111.77  3.000
 9SN  O15   P12  O14   116.90  3.000
 9SN  O15   P12  O13   118.19  3.000
 9SN  O14   P12  O13    94.13  3.000
 9SN  O15   P12  O11   111.78  3.000
 9SN  O14   P12  O11   106.30  3.000
 9SN  O13   P12  O11   107.72  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
 9SN  CONST_01  C2    C3   N4   C5   180.00   0.0  0
 9SN  CONST_02  C20   C3   N4   C5     0.00   0.0  0
 9SN  CONST_03  C3    C20  N6   C5     0.00   0.0  0
 9SN  CONST_04  N21   C20  N6   C5   180.00   0.0  0
 9SN  CONST_05  C22   N23  C2   C3     0.00   0.0  0
 9SN  CONST_06  C22   N21  C20  C3     0.00   0.0  0
 9SN  CONST_07  N6    C5   N4   C3     0.00   0.0  0
 9SN  CONST_08  N21   C20  C3   C2     0.00   0.0  0
 9SN  CONST_09  N6    C20  C3   C2   180.00   0.0  0
 9SN  CONST_10  N21   C22  N23  C2     0.00   0.0  0
 9SN  CONST_11  N23   C2   C3   C20    0.00   0.0  0
 9SN  CONST_12  N23   C22  N21  C20    0.00   0.0  0
 9SN  CONST_13  N4    C5   N6   C20    0.00   0.0  0
 9SN  CONST_14  N6    C20  N21  C22  180.00   0.0  0
 9SN  CONST_15  C29   C28  C27  C25    0.00   0.0  0
 9SN  CONST_16  C29   C30  C31  C25    0.00   0.0  0
 9SN  CONST_17  C30   C31  C25  C27    0.00   0.0  0
 9SN  CONST_18  C30   C29  C28  C27    0.00   0.0  0
 9SN  CONST_19  C31   C25  C27  C28    0.00   0.0  0
 9SN  CONST_20  C31   C30  C29  C28    0.00   0.0  0
 9SN  CONST_21  N4    C3   C20  N21  180.00   0.0  0
 9SN  CONST_22  N4    C3   C2   N23  180.00   0.0  0
 9SN  CONST_23  N6    C20  C3   N4     0.00   0.0  0
 9SN  CONST_24  N4    C5   N6   C7   180.00   0.0  0
 9SN  CONST_25  C3    C20  N6   C7   180.00   0.0  0
 9SN  CONST_26  N21   C20  N6   C7     0.00   0.0  0
 9SN  CONST_27  C20   C3   C2   N1   180.00   0.0  0
 9SN  CONST_28  N4    C3   C2   N1     0.00   0.0  0
 9SN  CONST_29  C22   N23  C2   N1   180.00   0.0  0
 9SN  CONST_30  C28   C27  C25  C24  180.00   0.0  0
 9SN  CONST_31  C30   C31  C25  C24  180.00   0.0  0
 9SN  CONST_32  N32   C31  C25  C27  180.00   0.0  0
 9SN  CONST_33  F33   C27  C28  C29  180.00   0.0  0
 9SN  CONST_34  N32   C31  C30  C29  180.00   0.0  0
 9SN  CONST_35  F33   C27  C25  C31  180.00   0.0  0
 9SN  CONST_36  HC5   C5   N6   C7     0.00   0.0  0
 9SN  CONST_37  HC22  C22  N23  C2   180.00   0.0  0
 9SN  CONST_38  HC28  C28  C27  C25  180.00   0.0  0
 9SN  CONST_39  HC30  C30  C31  C25  180.00   0.0  0
 9SN  CONST_40  HC29  C29  C28  C27  180.00   0.0  0
 9SN  CONST_41  HN1B  N1   C2   C3   180.00   0.0  0
 9SN  CONST_42  HN1A  N1   C2   C3     0.00   0.0  0
 9SN  CONST_43  H32B  N32  C31  C25  180.00   0.0  0
 9SN  Var_01    O14   C24  C25  C27  156.84  30.0  2
 9SN  Var_02    O13   P12  O11  C10  -42.88  30.0  3
 9SN  Var_03    O11   P12  O14  C24   77.18  30.0  3
 9SN  Var_04    H10B  C10  O11  P12  123.46  30.0  1

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
 9SN  chir_01  C7   C18  N6   O8   positiv
 9SN  chir_02  C9   O8   C10  C16  positiv
 9SN  chir_03  C16  O17  C9   C18  positiv
 9SN  chir_04  C18  O19  C16  C7   positiv
 9SN  chir_05  P12  O13  O14  O15  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
 9SN  plan-1  C24   0.020
 9SN  plan-1  C25   0.020
 9SN  plan-1  C27   0.020
 9SN  plan-1  C28   0.020
 9SN  plan-1  C29   0.020
 9SN  plan-1  C30   0.020
 9SN  plan-1  C31   0.020
 9SN  plan-1  F33   0.020
 9SN  plan-1  N32   0.020
 9SN  plan-1  HC28  0.020
 9SN  plan-1  HC29  0.020
 9SN  plan-1  HC30  0.020
 9SN  plan-2  C5    0.020
 9SN  plan-2  N1    0.020
 9SN  plan-2  C7    0.020
 9SN  plan-2  C3    0.020
 9SN  plan-2  C2    0.020
 9SN  plan-2  C20   0.020
 9SN  plan-2  C22   0.020
 9SN  plan-2  N21   0.020
 9SN  plan-2  N23   0.020
 9SN  plan-2  N4    0.020
 9SN  plan-2  N6    0.020
 9SN  plan-2  HC5   0.020
 9SN  plan-2  HC22  0.020
 9SN  plan-3  N1    0.020
 9SN  plan-3  C2    0.020
 9SN  plan-3  HN1B  0.020
 9SN  plan-3  HN1A  0.020
 9SN  plan-4  C31   0.020
 9SN  plan-4  N32   0.020
 9SN  plan-4  H32B  0.020
 9SN  plan-4  H32A  0.020
 9SN  plan-5  C24   0.020
 9SN  plan-5  C25   0.020
 9SN  plan-5  O14   0.020
 9SN  plan-5  O26   0.020

