# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 05:02:43 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: (2S,3aR,4R,6R,6aR)-4-(6-amino-9H-purin-9-yl)-6-(hydroxymethyl)tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-2-ol 2-sulfide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@H]4O[P@](O)(=S)O[C@@H]34
#
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
 QQX  QQX  '(2S,3aR,4R,6R,6aR)-4-(6-amino-9H-purin-9-yl)-6-(hydroxymethyl)tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-2-ol 2-sulfide'  ligand  34  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QQX
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
 QQX  OP3   O  OH1   0  -0.706   2.5512   1.6297  -1.3716
 QQX  S1P   S  S1    0  -0.451   3.8432   2.9460   0.9684
 QQX  O5'   O  OH1   0  -0.665   2.1233  -4.0084  -1.4016
 QQX  C5'   C  CH2   0  -0.168   2.4932  -3.2382  -0.2890
 QQX  C4'   C  CR15  0   0.002   1.9590  -1.8389  -0.4653
 QQX  O4'   O  O     0  -0.481   0.5401  -1.8585  -0.4577
 QQX  C3'   C  C     0  -0.045   2.3447  -0.9035   0.6903
 QQX  O3'   O  O     0  -0.566   3.3612   0.0264   0.3373
 QQX  C2'   C  C     0  -0.059   1.0567  -0.1001   0.9681
 QQX  O2'   O  O     0  -0.565   1.3724   1.2756   0.8889
 QQX  C1'   C  CR15  0   0.202   0.0995  -0.5701  -0.1410
 QQX  N9    N  NR5   0  -0.559  -1.2748  -0.6359   0.2478
 QQX  C8    C  CR15  0   0.111  -1.8299  -1.4323   1.2176
 QQX  N7    N  N     0  -0.445  -3.1137  -1.2801   1.3295
 QQX  C5    C  CR56  0  -0.007  -3.4333  -0.3351   0.3870
 QQX  C6    C  CR6   0   0.462  -4.6456   0.2711   0.0090
 QQX  N6    N  NH2   0  -0.814  -5.8142  -0.0327   0.5759
 QQX  N1    N  N     0  -0.473  -4.6113   1.1794  -0.9731
 QQX  C2    C  CR16  0   0.050  -3.4485   1.4714  -1.5476
 QQX  C4    C  CR56  0   0.493  -2.3047   0.0761  -0.3014
 QQX  N3    N  N     0  -0.456  -2.2523   0.9761  -1.2778
 QQX  P     P  P     0   1.193   2.8152   1.5350   0.1999
 QQX  HP3   H  HOH1  0   0.506   2.5093   2.5334  -1.7145
 QQX  H5'   H  HOH1  0   0.462   2.4435  -4.9048  -1.2665
 QQX  H5'1  H  HCH2  0   0.212   2.1070  -3.6523   0.6521
 QQX  H5'2  H  HCH2  0   0.217   3.5831  -3.1619  -0.1805
 QQX  H4'   H  HCR5  0   0.264   2.3249  -1.4149  -1.4110
 QQX  H3'   H  H     0   0.309   2.6826  -1.4496   1.5718
 QQX  H1'   H  HCR5  0   0.278   0.1506   0.1119  -1.0000
 QQX  H2'   H  H     0   0.325   0.6517  -0.3007   1.9607
 QQX  H8    H  HCR5  0   0.306  -1.2320  -2.1122   1.8060
 QQX  H61N  H  HNH2  0   0.411  -5.8558  -0.6338   1.3803
 QQX  H62N  H  HNH2  0   0.404  -6.6374   0.4939   0.3383
 QQX  H2    H  HCR6  0   0.255  -3.4905   2.2132  -2.3375

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
 QQX  OP3  P     single    1.596  0.020  1.596
 QQX  S1P  P     double    1.907  0.020  1.907
 QQX  O5'  C5'   single    1.403  0.020  1.403
 QQX  C5'  C4'   single    1.508  0.020  1.508
 QQX  C4'  O4'   single    1.419  0.020  1.419
 QQX  C4'  C3'   single    1.536  0.020  1.536
 QQX  O4'  C1'   single    1.398  0.020  1.398
 QQX  C3'  O3'   single    1.422  0.020  1.422
 QQX  C3'  C2'   single    1.543  0.020  1.543
 QQX  O3'  P     single    1.610  0.020  1.610
 QQX  C2'  O2'   single    1.414  0.020  1.414
 QQX  C2'  C1'   single    1.539  0.020  1.539
 QQX  O2'  P     single    1.620  0.020  1.620
 QQX  C1'  N9    single    1.430  0.020  1.430
 QQX  N9   C8    aromatic  1.372  0.020  1.372
 QQX  N9   C4    aromatic  1.367  0.020  1.367
 QQX  C8   N7    aromatic  1.298  0.020  1.298
 QQX  N7   C5    aromatic  1.372  0.020  1.372
 QQX  C5   C6    aromatic  1.407  0.020  1.407
 QQX  C5   C4    aromatic  1.384  0.020  1.384
 QQX  N3   C4    aromatic  1.329  0.020  1.329
 QQX  C6   N6    single    1.334  0.020  1.334
 QQX  C6   N1    aromatic  1.338  0.020  1.338
 QQX  N1   C2    aromatic  1.329  0.020  1.329
 QQX  C2   N3    aromatic  1.323  0.020  1.323
 QQX  OP3  HP3   single    0.850  0.020  0.980
 QQX  O5'  H5'   single    0.850  0.020  0.980
 QQX  C5'  H5'1  single    0.970  0.020  1.090
 QQX  C5'  H5'2  single    0.970  0.020  1.090
 QQX  C4'  H4'   single    0.970  0.020  1.090
 QQX  C3'  H3'   single    0.970  0.020  1.090
 QQX  C1'  H1'   single    0.970  0.020  1.090
 QQX  C2'  H2'   single    0.970  0.020  1.090
 QQX  C8   H8    single    0.930  0.020  1.080
 QQX  N6   H61N  single    0.860  0.020  1.020
 QQX  N6   H62N  single    0.860  0.020  1.020
 QQX  C2   H2    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
 QQX  HP3   OP3  P     114.30  3.000
 QQX  H5'   O5'  C5'   108.22  3.000
 QQX  H5'2  C5'  H5'1  106.89  3.000
 QQX  H5'2  C5'  C4'   107.38  3.000
 QQX  H5'1  C5'  C4'   108.99  3.000
 QQX  H5'2  C5'  O5'   112.23  3.000
 QQX  H5'1  C5'  O5'   112.32  3.000
 QQX  C4'   C5'  O5'   108.86  3.000
 QQX  H4'   C4'  C3'   109.19  3.000
 QQX  H4'   C4'  O4'   110.05  3.000
 QQX  C3'   C4'  O4'   104.80  3.000
 QQX  H4'   C4'  C5'   109.91  3.000
 QQX  C3'   C4'  C5'   112.84  3.000
 QQX  O4'   C4'  C5'   109.93  3.000
 QQX  C1'   O4'  C4'   107.68  3.000
 QQX  H3'   C3'  C2'   111.95  3.000
 QQX  H3'   C3'  O3'   107.85  3.000
 QQX  C2'   C3'  O3'   107.51  3.000
 QQX  H3'   C3'  C4'   112.39  3.000
 QQX  C2'   C3'  C4'   104.06  3.000
 QQX  O3'   C3'  C4'   113.02  3.000
 QQX  P     O3'  C3'   113.04  3.000
 QQX  H2'   C2'  C1'   111.64  3.000
 QQX  H2'   C2'  O2'   108.24  3.000
 QQX  C1'   C2'  O2'   113.32  3.000
 QQX  H2'   C2'  C3'   112.21  3.000
 QQX  C1'   C2'  C3'   103.32  3.000
 QQX  O2'   C2'  C3'   108.07  3.000
 QQX  P     O2'  C2'   112.25  3.000
 QQX  H1'   C1'  N9    106.62  3.000
 QQX  H1'   C1'  C2'   110.20  3.000
 QQX  N9    C1'  C2'   114.59  3.000
 QQX  H1'   C1'  O4'   112.37  3.000
 QQX  N9    C1'  O4'   108.79  3.000
 QQX  C2'   C1'  O4'   104.40  3.000
 QQX  C4    N9   C8    106.34  3.000
 QQX  C4    N9   C1'   126.22  3.000
 QQX  C8    N9   C1'   127.43  3.000
 QQX  H8    C8   N7    125.07  3.000
 QQX  H8    C8   N9    121.78  3.000
 QQX  N7    C8   N9    113.15  3.000
 QQX  C5    N7   C8    104.59  3.000
 QQX  C4    C5   C6    116.16  3.000
 QQX  C4    C5   N7    110.87  3.000
 QQX  C6    C5   N7    132.98  3.000
 QQX  N1    C6   N6    119.28  3.000
 QQX  N1    C6   C5    117.87  3.000
 QQX  N6    C6   C5    122.85  3.000
 QQX  H62N  N6   H61N  117.93  3.000
 QQX  H62N  N6   C6    119.83  3.000
 QQX  H61N  N6   C6    120.84  3.000
 QQX  C2    N1   C6    119.26  3.000
 QQX  H2    C2   N3    116.10  3.000
 QQX  H2    C2   N1    115.54  3.000
 QQX  N3    C2   N1    128.36  3.000
 QQX  N3    C4   C5    126.77  3.000
 QQX  N3    C4   N9    128.18  3.000
 QQX  C5    C4   N9    105.05  3.000
 QQX  C4    N3   C2    111.59  3.000
 QQX  O2'   P    O3'    96.64  3.000
 QQX  O2'   P    S1P   115.29  3.000
 QQX  O3'   P    S1P   118.42  3.000
 QQX  O2'   P    OP3   106.32  3.000
 QQX  O3'   P    OP3   101.28  3.000
 QQX  S1P   P    OP3   116.22  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
 QQX  CONST_01  C5    N7  C8   N9     0.00   0.0  0
 QQX  CONST_02  N7    C5  C4   N9     0.00   0.0  0
 QQX  CONST_03  C6    C5  C4   N9   180.00   0.0  0
 QQX  CONST_04  C2    N3  C4   N9   180.00   0.0  0
 QQX  CONST_05  C5    C4  N9   C8     0.00   0.0  0
 QQX  CONST_06  N3    C4  N9   C8   180.00   0.0  0
 QQX  CONST_07  C6    C5  N7   C8   180.00   0.0  0
 QQX  CONST_08  C4    C5  N7   C8     0.00   0.0  0
 QQX  CONST_09  C4    N9  C8   N7     0.00   0.0  0
 QQX  CONST_10  N1    C6  C5   N7   180.00   0.0  0
 QQX  CONST_11  N3    C4  C5   N7   180.00   0.0  0
 QQX  CONST_12  C2    N1  C6   C5     0.00   0.0  0
 QQX  CONST_13  C2    N3  C4   C5     0.00   0.0  0
 QQX  CONST_14  N3    C4  C5   C6     0.00   0.0  0
 QQX  CONST_15  N3    C2  N1   C6     0.00   0.0  0
 QQX  CONST_16  C4    C5  C6   N1     0.00   0.0  0
 QQX  CONST_17  C4    N3  C2   N1     0.00   0.0  0
 QQX  CONST_18  N7    C8  N9   C1'  180.00   0.0  0
 QQX  CONST_19  C5    C4  N9   C1'  180.00   0.0  0
 QQX  CONST_20  N3    C4  N9   C1'    0.00   0.0  0
 QQX  CONST_21  N6    C6  C5   N7     0.00   0.0  0
 QQX  CONST_22  C4    C5  C6   N6   180.00   0.0  0
 QQX  CONST_23  C2    N1  C6   N6   180.00   0.0  0
 QQX  CONST_24  H8    C8  N9   C1'    0.00   0.0  0
 QQX  CONST_25  H2    C2  N1   C6   180.00   0.0  0
 QQX  CONST_26  H61N  N6  C6   C5     0.00   0.0  0
 QQX  CONST_27  H62N  N6  C6   C5   180.00   0.0  0
 QQX  Var_01    O2'   P   O3'  C3'   12.54  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
 QQX  chir_01  C4'  C5'  O4'  C3'  negativ
 QQX  chir_02  C3'  O3'  C2'  C4'  negativ
 QQX  chir_03  C2'  O2'  C1'  C3'  negativ
 QQX  chir_04  C1'  O4'  N9   C2'  negativ
 QQX  chir_05  P    S1P  O3'  O2'  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
 QQX  plan-1  C1'   0.020
 QQX  plan-1  N9    0.020
 QQX  plan-1  C8    0.020
 QQX  plan-1  N7    0.020
 QQX  plan-1  C5    0.020
 QQX  plan-1  C6    0.020
 QQX  plan-1  N6    0.020
 QQX  plan-1  N1    0.020
 QQX  plan-1  C2    0.020
 QQX  plan-1  C4    0.020
 QQX  plan-1  N3    0.020
 QQX  plan-1  H8    0.020
 QQX  plan-1  H2    0.020
 QQX  plan-2  C6    0.020
 QQX  plan-2  N6    0.020
 QQX  plan-2  H61N  0.020
 QQX  plan-2  H62N  0.020

