# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 16:48:22 2021
#   Inital geometry file: a 135 line input string
#   Ligand name: [[(2~{R},3~{R},4~{S},5~{R})-5-[2-chloranyl-6-[(phenylmethyl)amino]purin-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](F)[C@@H](O[C@@H]1CO[P](O)(=O)C[P](O)(O)=O)n2cnc3c(NCc4ccccc4)nc(Cl)nc23
#
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
 QCQ  QCQ  '[[(2~{R},3~{R},4~{S},5~{R})-5-[2-chloranyl-6-[(phenylmethyl)amino]purin-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid'  ligand  56  35  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QCQ
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
 QCQ  O3'  O   OH1   0  -0.666  -16.7295  16.4419  -36.3659
 QCQ  C3'  C   CR15  0  -0.076  -16.2237  16.6810  -35.0796
 QCQ  C2'  C   CR15  0   0.148  -15.0757  17.6599  -35.2633
 QCQ  F04  F   F     0  -0.356  -14.2602  17.6390  -34.1448
 QCQ  C4'  C   CR15  0  -0.036  -17.2015  17.4915  -34.2135
 QCQ  C5'  C   CH2   0  -0.179  -17.0478  17.1991  -32.7369
 QCQ  O5'  O   O2    0  -0.591  -17.9396  18.0516  -32.0175
 QCQ  PA   P   P     0   1.380  -18.6155  17.5790  -30.6388
 QCQ  C3A  C   CH2   0  -1.043  -17.3849  17.8555  -29.3450
 QCQ  PB   P   P     0   1.387  -16.2971  19.2867  -29.5328
 QCQ  O1B  O   O     0  -0.686  -15.2899  19.1698  -30.6160
 QCQ  O2B  O   OH1   0  -0.734  -15.7329  19.3970  -28.0415
 QCQ  O3B  O   OH1   0  -0.737  -17.2450  20.5768  -29.6372
 QCQ  O1A  O   OH1   0  -0.727  -19.6440  18.7682  -30.3712
 QCQ  O2A  O   O     0  -0.694  -19.1559  16.2009  -30.6561
 QCQ  O4'  O   O     0  -0.493  -16.9295  18.8631  -34.4907
 QCQ  C1'  C   CR15  0   0.167  -15.8189  18.9913  -35.3340
 QCQ  N9   N   NR5   0  -0.549  -15.0336  20.1192  -34.9120
 QCQ  C8   C   CR15  0   0.101  -14.6931  20.4733  -33.6306
 QCQ  N7   N   N     0  -0.454  -13.9572  21.5413  -33.5806
 QCQ  C5   C   CR56  0  -0.019  -13.7864  21.9186  -34.8900
 QCQ  C4   C   CR56  0   0.514  -14.4593  21.0415  -35.7316
 QCQ  N3   N   N     0  -0.435  -14.5279  21.0970  -37.0603
 QCQ  C2   C   CR6   0   0.281  -13.8630  22.1306  -37.5157
 QCQ  CL1  CL  CL    0  -0.111  -13.8852  22.3201  -39.2418
 QCQ  N1   N   N     0  -0.458  -13.1806  23.0457  -36.8682
 QCQ  C6   C   CR6   0   0.513  -13.1068  22.9777  -35.5265
 QCQ  N6   N   NH1   0  -0.639  -12.3890  23.9193  -34.9161
 QCQ  C29  C   CH2   0  -0.333  -12.2245  24.0771  -33.4825
 QCQ  C30  C   CR6   0   0.073  -11.0492  24.9725  -33.2015
 QCQ  C31  C   CR16  0  -0.280   -9.7525  24.5290  -33.4552
 QCQ  C32  C   CR16  0  -0.241   -8.6657  25.3539  -33.2072
 QCQ  C33  C   CR16  0  -0.264   -8.8628  26.6347  -32.7031
 QCQ  C34  C   CR16  0  -0.240  -10.1506  27.0839  -32.4496
 QCQ  C35  C   CR16  0  -0.299  -11.2380  26.2554  -32.7013
 QCQ  H1   H   HOH1  0   0.465  -17.5187  15.8950  -36.2950
 QCQ  H2   H   HCR5  0   0.274  -15.8969  15.7588  -34.5843
 QCQ  H3   H   HCR5  0   0.274  -14.4638  17.4647  -36.1438
 QCQ  H4   H   HCR5  0   0.271  -18.2349  17.2763  -34.5059
 QCQ  H5   H   HCH2  0   0.250  -17.2909  16.1466  -32.5695
 QCQ  H6   H   HCH2  0   0.250  -16.0305  17.3775  -32.3863
 QCQ  H7   H   HCH2  0   0.340  -17.9121  17.9033  -28.3888
 QCQ  H8   H   HCH2  0   0.339  -16.7506  16.9657  -29.3072
 QCQ  H9   H   HOH1  0   0.500  -14.9829  20.0006  -27.9443
 QCQ  H10  H   HOH1  0   0.493  -17.3900  20.8976  -30.5366
 QCQ  H11  H   HOH1  0   0.502  -20.4479  18.7297  -30.9089
 QCQ  H12  H   HCR5  0   0.283  -16.1182  19.1826  -36.3698
 QCQ  H13  H   HCR5  0   0.317  -15.0317  19.9193  -32.7674
 QCQ  H14  H   HNH1  0   0.402  -12.0371  24.6546  -35.5111
 QCQ  H15  H   HCH2  0   0.258  -13.1308  24.4916  -33.0319
 QCQ  H16  H   HCH2  0   0.272  -12.0650  23.0977  -33.0325
 QCQ  H17  H   HCR6  0   0.256   -9.5907  23.5299  -33.8428
 QCQ  H18  H   HCR6  0   0.259   -7.6632  24.9965  -33.4031
 QCQ  H19  H   HCR6  0   0.258   -8.0139  27.2771  -32.5080
 QCQ  H20  H   HCR6  0   0.258  -10.3129  28.0793  -32.0568
 QCQ  H21  H   HCR6  0   0.256  -12.2423  26.6109  -32.5039

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
 QCQ  CL1  C2   single    1.737  0.020  1.737
 QCQ  C2   N3   aromatic  1.311  0.020  1.311
 QCQ  C2   N1   aromatic  1.312  0.020  1.312
 QCQ  N3   C4   aromatic  1.332  0.020  1.332
 QCQ  N1   C6   aromatic  1.345  0.020  1.345
 QCQ  O3'  C3'  single    1.403  0.020  1.403
 QCQ  C4   C5   aromatic  1.389  0.020  1.389
 QCQ  C4   N9   aromatic  1.361  0.020  1.361
 QCQ  C6   N6   single    1.332  0.020  1.332
 QCQ  C6   C5   aromatic  1.410  0.020  1.410
 QCQ  C1'  C2'  single    1.526  0.020  1.526
 QCQ  C1'  N9   single    1.438  0.020  1.438
 QCQ  C1'  O4'  single    1.400  0.020  1.400
 QCQ  C2'  C3'  single    1.520  0.020  1.520
 QCQ  C2'  F04  single    1.384  0.020  1.384
 QCQ  N6   C29  single    1.452  0.020  1.452
 QCQ  C3'  C4'  single    1.537  0.020  1.537
 QCQ  C5   N7   aromatic  1.373  0.020  1.373
 QCQ  N9   C8   aromatic  1.372  0.020  1.372
 QCQ  O4'  C4'  single    1.426  0.020  1.426
 QCQ  C4'  C5'  single    1.513  0.020  1.513
 QCQ  C29  C30  single    1.504  0.020  1.504
 QCQ  C8   N7   aromatic  1.298  0.020  1.298
 QCQ  C31  C30  aromatic  1.394  0.020  1.394
 QCQ  C31  C32  aromatic  1.387  0.020  1.387
 QCQ  C30  C35  aromatic  1.390  0.020  1.390
 QCQ  C32  C33  aromatic  1.390  0.020  1.390
 QCQ  C35  C34  aromatic  1.390  0.020  1.390
 QCQ  C33  C34  aromatic  1.387  0.020  1.387
 QCQ  C5'  O5'  single    1.428  0.020  1.428
 QCQ  O5'  PA   single    1.607  0.020  1.607
 QCQ  O2A  PA   double    1.480  0.020  1.480
 QCQ  PA   O1A  single    1.595  0.020  1.595
 QCQ  PA   C3A  single    1.807  0.020  1.807
 QCQ  O1B  PB   double    1.484  0.020  1.484
 QCQ  C3A  PB   single    1.807  0.020  1.807
 QCQ  PB   O3B  single    1.604  0.020  1.604
 QCQ  PB   O2B  single    1.598  0.020  1.598
 QCQ  O3'  H1   single    0.850  0.020  0.980
 QCQ  C3'  H2   single    0.970  0.020  1.090
 QCQ  C2'  H3   single    0.970  0.020  1.090
 QCQ  C4'  H4   single    0.970  0.020  1.090
 QCQ  C5'  H5   single    0.970  0.020  1.090
 QCQ  C5'  H6   single    0.970  0.020  1.090
 QCQ  C3A  H7   single    0.970  0.020  1.090
 QCQ  C3A  H8   single    0.970  0.020  1.090
 QCQ  O2B  H9   single    0.850  0.020  0.980
 QCQ  O3B  H10  single    0.850  0.020  0.980
 QCQ  O1A  H11  single    0.850  0.020  0.980
 QCQ  C1'  H12  single    0.970  0.020  1.090
 QCQ  C8   H13  single    0.930  0.020  1.080
 QCQ  N6   H14  single    0.860  0.020  1.020
 QCQ  C29  H15  single    0.970  0.020  1.090
 QCQ  C29  H16  single    0.970  0.020  1.090
 QCQ  C31  H17  single    0.930  0.020  1.080
 QCQ  C32  H18  single    0.930  0.020  1.080
 QCQ  C33  H19  single    0.930  0.020  1.080
 QCQ  C34  H20  single    0.930  0.020  1.080
 QCQ  C35  H21  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
 QCQ  H1   O3'  C3'  108.96  3.000
 QCQ  H2   C3'  C4'  112.24  3.000
 QCQ  H2   C3'  C2'  111.79  3.000
 QCQ  C4'  C3'  C2'  102.06  3.000
 QCQ  H2   C3'  O3'  112.23  3.000
 QCQ  C4'  C3'  O3'  112.16  3.000
 QCQ  C2'  C3'  O3'  105.74  3.000
 QCQ  H3   C2'  C1'  113.09  3.000
 QCQ  H3   C2'  F04  108.62  3.000
 QCQ  C1'  C2'  F04  109.72  3.000
 QCQ  H3   C2'  C3'  113.98  3.000
 QCQ  F04  C2'  C3'  109.73  3.000
 QCQ  C1'  C2'  C3'  101.52  3.000
 QCQ  H4   C4'  O4'  108.49  3.000
 QCQ  H4   C4'  C5'  108.57  3.000
 QCQ  O4'  C4'  C5'  110.88  3.000
 QCQ  H4   C4'  C3'  110.25  3.000
 QCQ  C5'  C4'  C3'  112.54  3.000
 QCQ  O4'  C4'  C3'  106.04  3.000
 QCQ  H6   C5'  H5   108.40  3.000
 QCQ  H6   C5'  O5'  108.84  3.000
 QCQ  H5   C5'  O5'  111.02  3.000
 QCQ  H6   C5'  C4'  112.14  3.000
 QCQ  H5   C5'  C4'  108.23  3.000
 QCQ  O5'  C5'  C4'  108.23  3.000
 QCQ  PA   O5'  C5'  121.29  3.000
 QCQ  O2A  PA   O1A  117.44  3.000
 QCQ  O1A  PA   C3A  101.83  3.000
 QCQ  O2A  PA   C3A  113.54  3.000
 QCQ  C3A  PA   O5'  106.43  3.000
 QCQ  O1A  PA   O5'  101.30  3.000
 QCQ  O2A  PA   O5'  114.67  3.000
 QCQ  H8   C3A  H7   106.57  3.000
 QCQ  H8   C3A  PB   107.39  3.000
 QCQ  H7   C3A  PB   110.27  3.000
 QCQ  H8   C3A  PA   107.18  3.000
 QCQ  H7   C3A  PA   107.73  3.000
 QCQ  PB   C3A  PA   117.17  3.000
 QCQ  O3B  PB   O2B  102.34  3.000
 QCQ  O2B  PB   O1B  116.55  3.000
 QCQ  O3B  PB   O1B  114.64  3.000
 QCQ  O2B  PB   C3A   99.79  3.000
 QCQ  O3B  PB   C3A  106.73  3.000
 QCQ  O1B  PB   C3A  114.96  3.000
 QCQ  H9   O2B  PB   114.22  3.000
 QCQ  H10  O3B  PB   114.61  3.000
 QCQ  H11  O1A  PA   114.37  3.000
 QCQ  C1'  O4'  C4'  110.89  3.000
 QCQ  H12  C1'  N9   106.85  3.000
 QCQ  H12  C1'  O4'  111.65  3.000
 QCQ  N9   C1'  O4'  109.17  3.000
 QCQ  H12  C1'  C2'  109.22  3.000
 QCQ  O4'  C1'  C2'  106.17  3.000
 QCQ  N9   C1'  C2'  113.87  3.000
 QCQ  C4   N9   C8   106.43  3.000
 QCQ  C8   N9   C1'  127.74  3.000
 QCQ  C4   N9   C1'  125.83  3.000
 QCQ  H13  C8   N7   124.68  3.000
 QCQ  H13  C8   N9   122.41  3.000
 QCQ  N7   C8   N9   112.89  3.000
 QCQ  C5   N7   C8   105.06  3.000
 QCQ  C6   C5   C4   115.73  3.000
 QCQ  C6   C5   N7   134.16  3.000
 QCQ  C4   C5   N7   110.11  3.000
 QCQ  N3   C4   C5   127.09  3.000
 QCQ  C5   C4   N9   105.51  3.000
 QCQ  N3   C4   N9   127.40  3.000
 QCQ  C2   N3   C4   110.70  3.000
 QCQ  N1   C2   CL1  114.90  3.000
 QCQ  N1   C2   N3   129.96  3.000
 QCQ  CL1  C2   N3   115.15  3.000
 QCQ  C6   N1   C2   119.03  3.000
 QCQ  N6   C6   N1   116.80  3.000
 QCQ  N6   C6   C5   125.71  3.000
 QCQ  N1   C6   C5   117.49  3.000
 QCQ  H14  N6   C29  117.61  3.000
 QCQ  H14  N6   C6   115.64  3.000
 QCQ  C29  N6   C6   126.19  3.000
 QCQ  H16  C29  H15  106.96  3.000
 QCQ  H16  C29  C30  110.10  3.000
 QCQ  H15  C29  C30  110.18  3.000
 QCQ  H16  C29  N6   109.07  3.000
 QCQ  H15  C29  N6   110.75  3.000
 QCQ  C30  C29  N6   109.74  3.000
 QCQ  C35  C30  C31  119.05  3.000
 QCQ  C35  C30  C29  120.70  3.000
 QCQ  C31  C30  C29  120.24  3.000
 QCQ  H17  C31  C32  119.69  3.000
 QCQ  H17  C31  C30  119.82  3.000
 QCQ  C32  C31  C30  120.49  3.000
 QCQ  H18  C32  C33  120.08  3.000
 QCQ  H18  C32  C31  119.82  3.000
 QCQ  C33  C32  C31  120.11  3.000
 QCQ  H19  C33  C34  120.19  3.000
 QCQ  H19  C33  C32  120.06  3.000
 QCQ  C34  C33  C32  119.74  3.000
 QCQ  H20  C34  C35  119.77  3.000
 QCQ  H20  C34  C33  120.22  3.000
 QCQ  C35  C34  C33  120.01  3.000
 QCQ  H21  C35  C34  119.78  3.000
 QCQ  H21  C35  C30  119.63  3.000
 QCQ  C34  C35  C30  120.60  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
 QCQ  CONST_01  C2   N3   C4   N9   180.00   0.0  0
 QCQ  CONST_02  C6   C5   C4   N9   180.00   0.0  0
 QCQ  CONST_03  N7   C5   C4   N9     0.00   0.0  0
 QCQ  CONST_04  C5   N7   C8   N9     0.00   0.0  0
 QCQ  CONST_05  N3   C4   N9   C8   180.00   0.0  0
 QCQ  CONST_06  C5   C4   N9   C8     0.00   0.0  0
 QCQ  CONST_07  C4   C5   N7   C8     0.00   0.0  0
 QCQ  CONST_08  C6   C5   N7   C8   180.00   0.0  0
 QCQ  CONST_09  N3   C4   C5   N7   180.00   0.0  0
 QCQ  CONST_10  N1   C6   C5   N7   180.00   0.0  0
 QCQ  CONST_11  C4   N9   C8   N7     0.00   0.0  0
 QCQ  CONST_12  C2   N3   C4   C5     0.00   0.0  0
 QCQ  CONST_13  C2   N1   C6   C5     0.00   0.0  0
 QCQ  CONST_14  N1   C2   N3   C4     0.00   0.0  0
 QCQ  CONST_15  N1   C6   C5   C4     0.00   0.0  0
 QCQ  CONST_16  C6   N1   C2   N3     0.00   0.0  0
 QCQ  CONST_17  C6   C5   C4   N3     0.00   0.0  0
 QCQ  CONST_18  C33  C32  C31  C30    0.00   0.0  0
 QCQ  CONST_19  C33  C34  C35  C30    0.00   0.0  0
 QCQ  CONST_20  C34  C35  C30  C31    0.00   0.0  0
 QCQ  CONST_21  C34  C33  C32  C31    0.00   0.0  0
 QCQ  CONST_22  C35  C30  C31  C32    0.00   0.0  0
 QCQ  CONST_23  C35  C34  C33  C32    0.00   0.0  0
 QCQ  CONST_24  N3   C4   N9   C1'    0.00   0.0  0
 QCQ  CONST_25  C5   C4   N9   C1'  180.00   0.0  0
 QCQ  CONST_26  N7   C8   N9   C1'  180.00   0.0  0
 QCQ  CONST_27  N6   C6   C5   N7     0.00   0.0  0
 QCQ  CONST_28  CL1  C2   N3   C4   180.00   0.0  0
 QCQ  CONST_29  N6   C6   C5   C4   180.00   0.0  0
 QCQ  CONST_30  N6   C6   N1   C2   180.00   0.0  0
 QCQ  CONST_31  C6   N1   C2   CL1  180.00   0.0  0
 QCQ  CONST_32  C32  C31  C30  C29  180.00   0.0  0
 QCQ  CONST_33  C34  C35  C30  C29  180.00   0.0  0
 QCQ  CONST_34  H13  C8   N9   C1'    0.00   0.0  0
 QCQ  CONST_35  H18  C32  C31  C30  180.00   0.0  0
 QCQ  CONST_36  H20  C34  C35  C30  180.00   0.0  0
 QCQ  CONST_37  H21  C35  C30  C31  180.00   0.0  0
 QCQ  CONST_38  H19  C33  C32  C31  180.00   0.0  0
 QCQ  CONST_39  H17  C31  C32  C33  180.00   0.0  0
 QCQ  CONST_40  C29  N6   C6   C5     0.00   0.0  0
 QCQ  CONST_41  C29  N6   C6   N1   180.00   0.0  0
 QCQ  CONST_42  H14  N6   C6   C5   180.00   0.0  0
 QCQ  Var_01    C30  C29  N6   C6   163.43  30.0  3
 QCQ  Var_02    C31  C30  C29  N6   -69.93  30.0  2
 QCQ  Var_03    O2A  PA   O5'  C5'  -44.85  30.0  3
 QCQ  Var_04    PB   C3A  PA   O5'   34.35  30.0  3
 QCQ  Var_05    O1B  PB   C3A  PA   -70.80  30.0  3
 QCQ  Var_06    H5   C5'  O5'  PA    29.45  30.0  2

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
 QCQ  chir_01  C3'  O3'  C2'  C4'  negativ
 QCQ  chir_02  C2'  F04  C1'  C3'  positiv
 QCQ  chir_03  C4'  O4'  C3'  C5'  negativ
 QCQ  chir_05  C1'  C2'  N9   O4'  positiv
 QCQ  chir_06  PA   O2A  O1A  C3A  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
 QCQ  plan-1  C29  0.020
 QCQ  plan-1  C30  0.020
 QCQ  plan-1  C31  0.020
 QCQ  plan-1  C32  0.020
 QCQ  plan-1  C33  0.020
 QCQ  plan-1  C34  0.020
 QCQ  plan-1  C35  0.020
 QCQ  plan-1  H17  0.020
 QCQ  plan-1  H18  0.020
 QCQ  plan-1  H19  0.020
 QCQ  plan-1  H20  0.020
 QCQ  plan-1  H21  0.020
 QCQ  plan-2  C1'  0.020
 QCQ  plan-2  N9   0.020
 QCQ  plan-2  C8   0.020
 QCQ  plan-2  N7   0.020
 QCQ  plan-2  C5   0.020
 QCQ  plan-2  C4   0.020
 QCQ  plan-2  N3   0.020
 QCQ  plan-2  C2   0.020
 QCQ  plan-2  CL1  0.020
 QCQ  plan-2  N1   0.020
 QCQ  plan-2  C6   0.020
 QCQ  plan-2  N6   0.020
 QCQ  plan-2  H13  0.020
 QCQ  plan-3  C6   0.020
 QCQ  plan-3  N6   0.020
 QCQ  plan-3  C29  0.020
 QCQ  plan-3  H14  0.020

