# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 13:37:29 2022
#   Inital geometry file: a 146 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-[6-chloranyl-4-[[(1~{S})-1-(4-fluorophenyl)ethyl]amino]pyrazolo[3,4-b]pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1cc(Cl)nc2n(ncc12)[C@@H]3O[C@H](CO[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O)c4ccc(F)cc4
#
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
 O1T  O1T  '[[(2~{R},3~{S},4~{R},5~{R})-5-[6-chloranyl-4-[[(1~{S})-1-(4-fluorophenyl)ethyl]amino]pyrazolo[3,4-b]pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid'  ligand  58  37  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O1T
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
 O1T  N1   N   N      0  -0.249  -13.5657  19.4197  -34.8714
 O1T  N3   N   NH1    0  -0.685  -12.2014  23.4010  -33.6043
 O1T  C4   C   CH2    0  -1.008  -17.0913  16.7963  -29.9224
 O1T  C5   C   CH1    0   0.143  -15.7413  19.1614  -35.9583
 O1T  C6   C   CR15   0  -0.075  -12.8661  20.4023  -34.3676
 O1T  C7   C   CR56   0  -0.247  -13.4991  21.6455  -34.6131
 O1T  C8   C   CR56   0   0.593  -14.6561  21.3086  -35.3182
 O1T  C10  C   CR16   0  -0.384  -14.2602  23.8932  -34.7658
 O1T  C13  C   CR6    0   0.116  -11.5348  25.6972  -34.2297
 O1T  C15  C   CR16   0  -0.398  -11.5360  27.9243  -35.1798
 O1T  C17  C   CR16   0  -0.395  -10.1570  26.1956  -36.1531
 O1T  C18  C   CR16   0  -0.278  -10.6210  25.2999  -35.2004
 O1T  C16  C   CR6    0   0.513  -10.6196  27.4975  -36.1203
 O1T  C14  C   CR16   0  -0.282  -11.9884  27.0115  -34.2367
 O1T  C12  C   CH1    0  -0.166  -11.9784  24.7514  -33.1320
 O1T  C19  C   CH3    0  -0.669  -10.9478  24.7132  -32.0096
 O1T  C11  C   CR6    0   0.468  -13.2750  23.0088  -34.3042
 O1T  C9   C   CR6    0   0.142  -15.3566  23.3852  -35.4603
 O1T  CL   CL  CL     0  -0.114  -16.5465  24.5331  -35.9958
 O1T  N2   N   N      0  -0.459  -15.6047  22.1362  -35.7583
 O1T  N    N   NR5    0  -0.414  -14.6428  19.9621  -35.4651
 O1T  C1   C   CH1    0  -0.009  -15.3021  17.7838  -36.4455
 O1T  O1   O   OH1    0  -0.667  -16.2478  17.3796  -37.4005
 O1T  O8   O   O2     0  -0.483  -16.6941  18.9344  -34.9620
 O1T  C2   C   CH1    0  -0.003  -16.5255  17.6437  -34.3736
 O1T  C    C   CH1    0  -0.032  -15.4071  16.9455  -35.1687
 O1T  O    O   OH1    0  -0.670  -15.6773  15.6124  -35.5152
 O1T  C3   C   CH2    0  -0.152  -16.1686  17.7589  -32.9054
 O1T  O2   O   O2     0  -0.625  -17.1617  18.4108  -32.1615
 O1T  P    P   P      0   1.240  -18.1806  17.4994  -31.2037
 O1T  O7   O   O      0  -0.829  -18.7206  16.3715  -32.0572
 O1T  O6   O   OP    -1  -0.813  -19.1491  18.5086  -30.6416
 O1T  P1   P   P      0   1.162  -15.8159  17.8094  -28.9637
 O1T  O5   O   O      0  -0.892  -14.7380  18.2058  -29.9832
 O1T  O4   O   OP    -1  -0.905  -16.5686  19.0038  -28.3622
 O1T  O3   O   OP    -1  -0.912  -15.3174  16.8034  -27.9132
 O1T  H1   H   HNH1   0   0.409  -11.5520  22.6929  -33.3008
 O1T  H2   H   HCH2   0   0.204  -17.7766  16.3446  -29.1937
 O1T  H3   H   HCH2   0   0.200  -16.5613  15.9488  -30.3708
 O1T  H4   H   HCH1   0   0.272  -16.2021  19.7413  -36.7600
 O1T  H5   H   HCR5   0   0.274  -11.9400  20.2016  -33.8496
 O1T  H6   H   HCR6   0   0.295  -14.1895  24.9565  -34.5962
 O1T  H7   H   HCR6   0   0.277  -11.8936  28.9458  -35.1815
 O1T  H8   H   HCR6   0   0.277   -9.4445  25.8854  -36.9064
 O1T  H9   H   HCR6   0   0.260  -10.2618  24.2783  -35.2216
 O1T  H10  H   HCR6   0   0.263  -12.7091  27.3347  -33.4944
 O1T  H11  H   HCH1   0   0.265  -12.9171  25.1300  -32.7118
 O1T  H12  H   HCH3   0   0.253  -10.7857  25.7154  -31.6171
 O1T  H13  H   HCH3   0   0.249  -11.2885  24.0776  -31.1915
 O1T  H14  H   HCH3   0   0.238   -9.9910  24.3334  -32.3720
 O1T  H15  H   HCH1   0   0.244  -14.2867  17.7890  -36.8574
 O1T  H16  H   HOH1   0   0.452  -16.3107  16.4180  -37.3672
 O1T  H17  H   HCH1   0   0.231  -17.4677  17.0957  -34.4793
 O1T  H18  H   HCH1   0   0.238  -14.4615  17.0195  -34.6187
 O1T  H19  H   HOH1   0   0.464  -15.7412  15.0823  -34.7143
 O1T  H20  H   HCH2   0   0.191  -15.9599  16.7462  -32.5368
 O1T  H21  H   HCH2   0   0.202  -15.2327  18.3163  -32.8043
 O1T  F    F   F      0  -0.316  -10.1654  28.3736  -37.0326

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
 O1T  CL   C9   single    1.738  0.020  1.738
 O1T  C9   C10  aromatic  1.394  0.020  1.394
 O1T  C9   N2   aromatic  1.308  0.020  1.308
 O1T  C10  C11  aromatic  1.402  0.020  1.402
 O1T  N2   C8   aromatic  1.334  0.020  1.334
 O1T  O1   C1   single    1.403  0.020  1.403
 O1T  C11  N3   single    1.340  0.020  1.340
 O1T  C11  C7   aromatic  1.416  0.020  1.416
 O1T  C8   C7   aromatic  1.396  0.020  1.396
 O1T  C8   N    aromatic  1.355  0.020  1.355
 O1T  C1   C5   single    1.526  0.020  1.526
 O1T  C1   C    single    1.531  0.020  1.531
 O1T  N3   C12  single    1.448  0.020  1.448
 O1T  C5   N    single    1.446  0.020  1.446
 O1T  C5   O8   single    1.397  0.020  1.397
 O1T  C7   C6   aromatic  1.417  0.020  1.417
 O1T  N    N1   aromatic  1.344  0.020  1.344
 O1T  O    C    single    1.404  0.020  1.404
 O1T  C18  C17  aromatic  1.388  0.020  1.388
 O1T  C18  C13  aromatic  1.391  0.020  1.391
 O1T  C    C2   single    1.540  0.020  1.540
 O1T  O8   C2   single    1.429  0.020  1.429
 O1T  C12  C19  single    1.524  0.020  1.524
 O1T  C12  C13  single    1.515  0.020  1.515
 O1T  C17  C16  aromatic  1.382  0.020  1.382
 O1T  C2   C3   single    1.515  0.020  1.515
 O1T  C6   N1   aromatic  1.307  0.020  1.307
 O1T  C13  C14  aromatic  1.390  0.020  1.390
 O1T  C16  F    single    1.344  0.020  1.344
 O1T  C16  C15  aromatic  1.381  0.020  1.381
 O1T  C14  C15  aromatic  1.388  0.020  1.388
 O1T  C3   O2   single    1.402  0.020  1.402
 O1T  O2   P    single    1.669  0.020  1.669
 O1T  O7   P    deloc     1.514  0.020  1.514
 O1T  P    O6   deloc     1.507  0.020  1.507
 O1T  P    C4   single    1.823  0.020  1.823
 O1T  O5   P1   deloc     1.536  0.020  1.536
 O1T  C4   P1   single    1.890  0.020  1.890
 O1T  P1   O4   deloc     1.535  0.020  1.535
 O1T  P1   O3   deloc     1.538  0.020  1.538
 O1T  N3   H1   single    0.860  0.020  1.020
 O1T  C4   H2   single    0.970  0.020  1.090
 O1T  C4   H3   single    0.970  0.020  1.090
 O1T  C5   H4   single    0.970  0.020  1.090
 O1T  C6   H5   single    0.930  0.020  1.080
 O1T  C10  H6   single    0.930  0.020  1.080
 O1T  C15  H7   single    0.930  0.020  1.080
 O1T  C17  H8   single    0.930  0.020  1.080
 O1T  C18  H9   single    0.930  0.020  1.080
 O1T  C14  H10  single    0.930  0.020  1.080
 O1T  C12  H11  single    0.970  0.020  1.090
 O1T  C19  H12  single    0.970  0.020  1.090
 O1T  C19  H13  single    0.970  0.020  1.090
 O1T  C19  H14  single    0.970  0.020  1.090
 O1T  C1   H15  single    0.970  0.020  1.090
 O1T  O1   H16  single    0.850  0.020  0.980
 O1T  C2   H17  single    0.970  0.020  1.090
 O1T  C    H18  single    0.970  0.020  1.090
 O1T  O    H19  single    0.850  0.020  0.980
 O1T  C3   H20  single    0.970  0.020  1.090
 O1T  C3   H21  single    0.970  0.020  1.090

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
 O1T  N    N1   C6   107.20  3.000
 O1T  H1   N3   C11  117.90  3.000
 O1T  H1   N3   C12  117.25  3.000
 O1T  C11  N3   C12  124.51  3.000
 O1T  H3   C4   H2   104.80  3.000
 O1T  H3   C4   P1   107.20  3.000
 O1T  H2   C4   P1   107.77  3.000
 O1T  H3   C4   P    107.44  3.000
 O1T  H2   C4   P    104.61  3.000
 O1T  P1   C4   P    123.58  3.000
 O1T  H4   C5   O8   108.79  3.000
 O1T  H4   C5   C1   111.51  3.000
 O1T  O8   C5   C1   106.10  3.000
 O1T  H4   C5   N    106.09  3.000
 O1T  O8   C5   N    111.40  3.000
 O1T  C1   C5   N    112.97  3.000
 O1T  H5   C6   C7   129.01  3.000
 O1T  H5   C6   N1   120.28  3.000
 O1T  C7   C6   N1   110.72  3.000
 O1T  C11  C7   C8   118.28  3.000
 O1T  C8   C7   C6   104.24  3.000
 O1T  C11  C7   C6   137.44  3.000
 O1T  N    C8   N2   126.02  3.000
 O1T  N    C8   C7   106.65  3.000
 O1T  N2   C8   C7   127.33  3.000
 O1T  H6   C10  C9   119.27  3.000
 O1T  H6   C10  C11  121.59  3.000
 O1T  C9   C10  C11  119.14  3.000
 O1T  C12  C13  C14  119.88  3.000
 O1T  C14  C13  C18  118.73  3.000
 O1T  C12  C13  C18  121.30  3.000
 O1T  H7   C15  C14  120.93  3.000
 O1T  H7   C15  C16  120.66  3.000
 O1T  C14  C15  C16  118.41  3.000
 O1T  H8   C17  C16  120.46  3.000
 O1T  H8   C17  C18  120.86  3.000
 O1T  C16  C17  C18  118.68  3.000
 O1T  H9   C18  C17  118.98  3.000
 O1T  H9   C18  C13  120.06  3.000
 O1T  C17  C18  C13  120.96  3.000
 O1T  F    C16  C17  119.00  3.000
 O1T  F    C16  C15  119.03  3.000
 O1T  C17  C16  C15  121.97  3.000
 O1T  H10  C14  C15  119.07  3.000
 O1T  H10  C14  C13  119.69  3.000
 O1T  C15  C14  C13  121.24  3.000
 O1T  H11  C12  C19  107.79  3.000
 O1T  H11  C12  C13  108.23  3.000
 O1T  C19  C12  C13  110.56  3.000
 O1T  H11  C12  N3   108.38  3.000
 O1T  C13  C12  N3   113.01  3.000
 O1T  C19  C12  N3   108.72  3.000
 O1T  H14  C19  H13  108.67  3.000
 O1T  H14  C19  H12  108.03  3.000
 O1T  H13  C19  H12  108.22  3.000
 O1T  H14  C19  C12  110.91  3.000
 O1T  H13  C19  C12  110.84  3.000
 O1T  H12  C19  C12  110.07  3.000
 O1T  C10  C11  C7   115.11  3.000
 O1T  C7   C11  N3   121.50  3.000
 O1T  C10  C11  N3   123.38  3.000
 O1T  N2   C9   CL   115.51  3.000
 O1T  N2   C9   C10  127.65  3.000
 O1T  CL   C9   C10  116.84  3.000
 O1T  C9   N2   C8   112.49  3.000
 O1T  C8   N    C5   125.45  3.000
 O1T  C5   N    N1   122.41  3.000
 O1T  C8   N    N1   111.17  3.000
 O1T  H15  C1   C    112.31  3.000
 O1T  H15  C1   O1   111.72  3.000
 O1T  C    C1   O1   111.32  3.000
 O1T  H15  C1   C5   112.48  3.000
 O1T  C    C1   C5   102.02  3.000
 O1T  O1   C1   C5   106.46  3.000
 O1T  H16  O1   C1   107.92  3.000
 O1T  C2   O8   C5   111.10  3.000
 O1T  H17  C2   C3   109.52  3.000
 O1T  H17  C2   C    110.38  3.000
 O1T  C3   C2   C    111.33  3.000
 O1T  H17  C2   O8   108.11  3.000
 O1T  C3   C2   O8   110.99  3.000
 O1T  C    C2   O8   106.42  3.000
 O1T  H18  C    O    110.73  3.000
 O1T  H18  C    C2   109.68  3.000
 O1T  O    C    C2   114.73  3.000
 O1T  H18  C    C1   108.80  3.000
 O1T  C2   C    C1   103.43  3.000
 O1T  O    C    C1   109.11  3.000
 O1T  H19  O    C    109.30  3.000
 O1T  H21  C3   H20  106.04  3.000
 O1T  H21  C3   O2   108.67  3.000
 O1T  H20  C3   O2   112.68  3.000
 O1T  H21  C3   C2   109.25  3.000
 O1T  H20  C3   C2   107.45  3.000
 O1T  O2   C3   C2   112.50  3.000
 O1T  P    O2   C3   118.89  3.000
 O1T  O6   P    O7   118.67  3.000
 O1T  O6   P    O2   103.92  3.000
 O1T  O7   P    O2   107.51  3.000
 O1T  O6   P    C4   112.34  3.000
 O1T  O7   P    C4   108.79  3.000
 O1T  O2   P    C4   104.43  3.000
 O1T  O3   P1   O4   113.61  3.000
 O1T  O3   P1   O5   113.26  3.000
 O1T  O4   P1   O5   113.80  3.000
 O1T  O3   P1   C4   102.39  3.000
 O1T  O4   P1   C4   106.56  3.000
 O1T  O5   P1   C4   105.98  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
 O1T  CONST_01  N2   C8   N    N1   180.00   0.0  0
 O1T  CONST_02  C7   C8   N    N1     0.00   0.0  0
 O1T  CONST_03  C11  C7   C6   N1   180.00   0.0  0
 O1T  CONST_04  C8   C7   C6   N1     0.00   0.0  0
 O1T  CONST_05  C10  C11  C7   C6   180.00   0.0  0
 O1T  CONST_06  N2   C8   C7   C6   180.00   0.0  0
 O1T  CONST_07  N    C8   C7   C6     0.00   0.0  0
 O1T  CONST_08  C8   N    N1   C6     0.00   0.0  0
 O1T  CONST_09  C9   C10  C11  C7     0.00   0.0  0
 O1T  CONST_10  C9   N2   C8   C7     0.00   0.0  0
 O1T  CONST_11  N    N1   C6   C7     0.00   0.0  0
 O1T  CONST_12  C10  C9   N2   C8     0.00   0.0  0
 O1T  CONST_13  C10  C11  C7   C8     0.00   0.0  0
 O1T  CONST_14  C16  C17  C18  C13    0.00   0.0  0
 O1T  CONST_15  C16  C15  C14  C13    0.00   0.0  0
 O1T  CONST_16  C18  C17  C16  C15    0.00   0.0  0
 O1T  CONST_17  C18  C13  C14  C15    0.00   0.0  0
 O1T  CONST_18  C14  C13  C18  C17    0.00   0.0  0
 O1T  CONST_19  C14  C15  C16  C17    0.00   0.0  0
 O1T  CONST_20  N2   C9   C10  C11    0.00   0.0  0
 O1T  CONST_21  N2   C8   C7   C11    0.00   0.0  0
 O1T  CONST_22  N    C8   C7   C11  180.00   0.0  0
 O1T  CONST_23  N    C8   N2   C9   180.00   0.0  0
 O1T  CONST_24  N2   C8   N    C5     0.00   0.0  0
 O1T  CONST_25  C7   C8   N    C5   180.00   0.0  0
 O1T  CONST_26  C6   N1   N    C5   180.00   0.0  0
 O1T  CONST_27  C9   C10  C11  N3   180.00   0.0  0
 O1T  CONST_28  C8   C7   C11  N3   180.00   0.0  0
 O1T  CONST_29  C6   C7   C11  N3     0.00   0.0  0
 O1T  CONST_30  CL   C9   N2   C8   180.00   0.0  0
 O1T  CONST_31  C12  C13  C14  C15  180.00   0.0  0
 O1T  CONST_32  C12  C13  C18  C17  180.00   0.0  0
 O1T  CONST_33  C18  C17  C16  F    180.00   0.0  0
 O1T  CONST_34  C14  C15  C16  F    180.00   0.0  0
 O1T  CONST_35  CL   C9   C10  C11  180.00   0.0  0
 O1T  CONST_36  H6   C10  C11  C7   180.00   0.0  0
 O1T  CONST_37  H5   C6   C7   C8   180.00   0.0  0
 O1T  CONST_38  H8   C17  C18  C13  180.00   0.0  0
 O1T  CONST_39  H7   C15  C14  C13  180.00   0.0  0
 O1T  CONST_40  H10  C14  C13  C18  180.00   0.0  0
 O1T  CONST_41  H9   C18  C17  C16  180.00   0.0  0
 O1T  CONST_42  C12  N3   C11  C7   180.00   0.0  0
 O1T  CONST_43  C12  N3   C11  C10    0.00   0.0  0
 O1T  CONST_44  H1   N3   C11  C7     0.00   0.0  0
 O1T  Var_01    O7   P    O2   C3   -49.85  30.0  3
 O1T  Var_02    P1   C4   P    O2    46.90  30.0  3
 O1T  Var_03    O5   P1   C4   P    -68.08  30.0  3
 O1T  Var_04    H20  C3   O2   P    -18.39  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
 O1T  chir_01  C5   C1  N    O8   positiv
 O1T  chir_02  C12  N3  C13  C19  positiv
 O1T  chir_03  C1   O1  C5   C    negativ
 O1T  chir_04  C2   O8  C    C3   negativ
 O1T  chir_05  C    O   C2   C1   positiv

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
 O1T  plan-1  C13  0.020
 O1T  plan-1  C15  0.020
 O1T  plan-1  C17  0.020
 O1T  plan-1  C18  0.020
 O1T  plan-1  C16  0.020
 O1T  plan-1  C14  0.020
 O1T  plan-1  C12  0.020
 O1T  plan-1  H7   0.020
 O1T  plan-1  H8   0.020
 O1T  plan-1  H9   0.020
 O1T  plan-1  H10  0.020
 O1T  plan-1  F    0.020
 O1T  plan-2  N1   0.020
 O1T  plan-2  N3   0.020
 O1T  plan-2  C5   0.020
 O1T  plan-2  C6   0.020
 O1T  plan-2  C7   0.020
 O1T  plan-2  C8   0.020
 O1T  plan-2  C10  0.020
 O1T  plan-2  C11  0.020
 O1T  plan-2  C9   0.020
 O1T  plan-2  CL   0.020
 O1T  plan-2  N2   0.020
 O1T  plan-2  N    0.020
 O1T  plan-2  H5   0.020
 O1T  plan-2  H6   0.020
 O1T  plan-3  N3   0.020
 O1T  plan-3  C12  0.020
 O1T  plan-3  C11  0.020
 O1T  plan-3  H1   0.020

