# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 13 11:18:28 2022
#   Inital geometry file: a 138 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]methyl ~{N}-[(3~{S})-3-azanyl-3-(3-bromophenyl)propanoyl]sulfamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)c4cccc(Br)c4
#
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
 HFR  HFR  '[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(3~{S})-3-azanyl-3-(3-bromophenyl)propanoyl]sulfamate'  ligand  57  35  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HFR
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
 HFR  C4   C   CR15  0   0.095   0.6353  -31.4665  -13.3124
 HFR  C14  C   CH2   0  -0.213   3.9200  -33.2538  -14.9580
 HFR  C5   C   CR16  0  -0.288   1.9998  -26.3336  -11.8882
 HFR  C6   C   CR16  0  -0.227   0.8961  -25.8390  -11.2114
 HFR  C11  C   CH1   0  -0.146   3.0883  -27.2524  -13.9760
 HFR  C7   C   CR16  0  -0.237  -0.3130  -25.6486  -11.8671
 HFR  C8   C   CR6   0  -0.089  -0.3901  -25.9641  -13.2133
 HFR  C9   C   CR16  0  -0.289   0.7048  -26.4606  -13.9062
 HFR  C10  C   CR6   0   0.124   1.9112  -26.6494  -13.2411
 HFR  C12  C   CH2   0  -0.576   3.1294  -28.7503  -13.6179
 HFR  C13  C   C     0   0.579   4.1791  -29.5170  -14.3809
 HFR  N1   N   N     0  -0.469  -0.8659  -28.7764  -10.1747
 HFR  N2   N   N     0  -0.457   1.1111  -30.1149  -10.1305
 HFR  C3   C   CR6   0   0.470  -1.2112  -29.1797  -11.4018
 HFR  N3   N   NH2   0  -0.791   4.3197  -26.5978  -13.5777
 HFR  O1   O   O     0  -0.416   5.3442  -29.5713  -14.0714
 HFR  N4   N   NC1   0  -0.821   3.6957  -30.1391  -15.5199
 HFR  S1   S   S     0   1.607   4.5809  -31.1987  -16.4453
 HFR  O2   O   OS    0  -0.627   3.6576  -31.6796  -17.4424
 HFR  O3   O   OS    0  -0.605   5.8457  -30.6282  -16.8113
 HFR  O4   O   OC2   0  -0.567   4.9518  -32.3603  -15.4306
 HFR  C15  C   CH1   0   0.022   3.8839  -33.2362  -13.4520
 HFR  O5   O   O2    0  -0.499   3.4860  -31.9557  -12.9927
 HFR  C16  C   CH1   0   0.000   2.8333  -34.1948  -12.8923
 HFR  O6   O   OH1   0  -0.649   3.3356  -35.4914  -12.8574
 HFR  C17  C   CH1   0  -0.060   2.5221  -33.5503  -11.5366
 HFR  O7   O   OH1   0  -0.653   3.5145  -33.9425  -10.6332
 HFR  C18  C   CH1   0   0.166   2.6464  -32.0519  -11.8736
 HFR  N5   N   NR5   0  -0.532   1.3889  -31.3976  -12.1702
 HFR  N6   N   N     0  -0.442  -0.4215  -30.7099  -13.2794
 HFR  C2   C   CR56  0  -0.002  -0.3719  -30.1048  -12.0504
 HFR  C1   C   CR56  0   0.492   0.7492  -30.5145  -11.3467
 HFR  C19  C   CR16  0   0.043   0.2487  -29.2490   -9.6255
 HFR  N7   N   NH2   0  -0.814  -2.3383  -28.7187  -11.9497
 HFR  H1   H   HCR5  0   0.301   0.9160  -32.0848  -14.1512
 HFR  H2   H   HCH2  0   0.265   2.9432  -32.9884  -15.3690
 HFR  H3   H   HCH2  0   0.282   4.1767  -34.2520  -15.3122
 HFR  H4   H   HCR6  0   0.257   2.9366  -26.4746  -11.3655
 HFR  H5   H   HCR6  0   0.263   0.9700  -25.6006  -10.1584
 HFR  H6   H   HCH1  0   0.247   2.8860  -27.1728  -15.0542
 HFR  H7   H   HCR6  0   0.276  -1.1699  -25.2633  -11.3311
 HFR  H8   H   HCR6  0   0.272   0.6283  -26.7023  -14.9596
 HFR  H9   H   HCH2  0   0.286   3.3413  -28.8538  -12.5522
 HFR  H10  H   HCH2  0   0.285   2.1400  -29.1674  -13.8077
 HFR  H11  H   HNH2  0   0.357   5.1067  -26.9878  -14.0802
 HFR  H12  H   HNH2  0   0.354   4.2780  -25.6210  -13.8412
 HFR  H14  H   HNC1  0   0.453   2.7019  -30.1244  -15.7190
 HFR  H15  H   HCH1  0   0.262   4.8723  -33.4921  -13.0504
 HFR  H16  H   HCH1  0   0.243   1.9259  -34.1325  -13.5110
 HFR  H17  H   HOH1  0   0.462   2.6089  -36.1058  -12.7140
 HFR  H18  H   HCH1  0   0.268   1.5153  -33.7906  -11.1756
 HFR  H19  H   HOH1  0   0.461   3.3022  -33.5832   -9.7654
 HFR  H20  H   HCH1  0   0.280   3.0690  -31.5053  -11.0256
 HFR  H21  H   HCR6  0   0.250   0.4748  -28.8738   -8.6330
 HFR  H22  H   HNH2  0   0.400  -2.8298  -27.9610  -11.5064
 HFR  H23  H   HNH2  0   0.407  -2.5430  -28.9004  -12.9171
 HFR  BR   BR  BR    0  -0.055  -2.0226  -25.7077  -14.1323

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
 HFR  O2   S1   deloc     1.442  0.020  1.442
 HFR  N3   C11  single    1.450  0.020  1.450
 HFR  C11  C10  single    1.513  0.020  1.513
 HFR  C11  C12  single    1.541  0.020  1.541
 HFR  S1   N4   single    1.662  0.020  1.662
 HFR  S1   O3   deloc     1.435  0.020  1.435
 HFR  S1   O4   single    1.586  0.020  1.586
 HFR  C5   C6   aromatic  1.386  0.020  1.386
 HFR  C5   C10  aromatic  1.392  0.020  1.392
 HFR  N4   C13  single    1.385  0.020  1.385
 HFR  C6   C7   aromatic  1.389  0.020  1.389
 HFR  C10  C9   aromatic  1.390  0.020  1.390
 HFR  O6   C16  single    1.391  0.020  1.391
 HFR  C7   C8   aromatic  1.385  0.020  1.385
 HFR  C9   C8   aromatic  1.388  0.020  1.388
 HFR  C8   BR   single    1.891  0.020  1.891
 HFR  C14  O4   single    1.444  0.020  1.444
 HFR  C14  C15  single    1.507  0.020  1.507
 HFR  C12  C13  single    1.507  0.020  1.507
 HFR  C13  O1   double    1.207  0.020  1.207
 HFR  C16  C15  single    1.528  0.020  1.528
 HFR  C16  C17  single    1.533  0.020  1.533
 HFR  C15  O5   single    1.417  0.020  1.417
 HFR  C17  O7   single    1.398  0.020  1.398
 HFR  C17  C18  single    1.541  0.020  1.541
 HFR  O5   C18  single    1.402  0.020  1.402
 HFR  C4   N5   aromatic  1.370  0.020  1.370
 HFR  C4   N6   aromatic  1.300  0.020  1.300
 HFR  C18  N5   single    1.448  0.020  1.448
 HFR  N5   C1   aromatic  1.367  0.020  1.367
 HFR  N6   C2   aromatic  1.371  0.020  1.371
 HFR  C2   C1   aromatic  1.386  0.020  1.386
 HFR  C2   C3   aromatic  1.407  0.020  1.407
 HFR  C1   N2   aromatic  1.330  0.020  1.330
 HFR  N7   C3   single    1.335  0.020  1.335
 HFR  N2   C19  aromatic  1.322  0.020  1.322
 HFR  C3   N1   aromatic  1.337  0.020  1.337
 HFR  N1   C19  aromatic  1.329  0.020  1.329
 HFR  C4   H1   single    0.930  0.020  1.080
 HFR  C14  H2   single    0.970  0.020  1.090
 HFR  C14  H3   single    0.970  0.020  1.090
 HFR  C5   H4   single    0.930  0.020  1.080
 HFR  C6   H5   single    0.930  0.020  1.080
 HFR  C11  H6   single    0.970  0.020  1.090
 HFR  C7   H7   single    0.930  0.020  1.080
 HFR  C9   H8   single    0.930  0.020  1.080
 HFR  C12  H9   single    0.970  0.020  1.090
 HFR  C12  H10  single    0.970  0.020  1.090
 HFR  N3   H11  single    0.890  0.020  1.040
 HFR  N3   H12  single    0.890  0.020  1.040
 HFR  N4   H14  single    0.860  0.020  1.020
 HFR  C15  H15  single    0.970  0.020  1.090
 HFR  C16  H16  single    0.970  0.020  1.090
 HFR  O6   H17  single    0.850  0.020  0.980
 HFR  C17  H18  single    0.970  0.020  1.090
 HFR  O7   H19  single    0.850  0.020  0.980
 HFR  C18  H20  single    0.970  0.020  1.090
 HFR  C19  H21  single    0.930  0.020  1.080
 HFR  N7   H22  single    0.860  0.020  1.020
 HFR  N7   H23  single    0.860  0.020  1.020

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
 HFR  H1   C4   N6   124.37  3.000
 HFR  H1   C4   N5   122.26  3.000
 HFR  N6   C4   N5   113.37  3.000
 HFR  H3   C14  H2   108.11  3.000
 HFR  H3   C14  C15  109.95  3.000
 HFR  H2   C14  C15  110.60  3.000
 HFR  H3   C14  O4   106.98  3.000
 HFR  H2   C14  O4   111.43  3.000
 HFR  C15  C14  O4   109.69  3.000
 HFR  H4   C5   C10  119.67  3.000
 HFR  H4   C5   C6   120.01  3.000
 HFR  C10  C5   C6   120.32  3.000
 HFR  H5   C6   C7   119.26  3.000
 HFR  H5   C6   C5   119.96  3.000
 HFR  C7   C6   C5   120.79  3.000
 HFR  H6   C11  N3   113.12  3.000
 HFR  H6   C11  C12  107.64  3.000
 HFR  N3   C11  C12  110.63  3.000
 HFR  H6   C11  C10  107.71  3.000
 HFR  C12  C11  C10  107.18  3.000
 HFR  N3   C11  C10  110.32  3.000
 HFR  H7   C7   C8   121.25  3.000
 HFR  H7   C7   C6   120.31  3.000
 HFR  C8   C7   C6   118.44  3.000
 HFR  BR   C8   C9   119.15  3.000
 HFR  BR   C8   C7   119.32  3.000
 HFR  C9   C8   C7   121.54  3.000
 HFR  H8   C9   C10  119.73  3.000
 HFR  H8   C9   C8   120.64  3.000
 HFR  C10  C9   C8   119.63  3.000
 HFR  C9   C10  C11  119.79  3.000
 HFR  C9   C10  C5   119.29  3.000
 HFR  C11  C10  C5   120.86  3.000
 HFR  H10  C12  H9   108.05  3.000
 HFR  H10  C12  C13  110.44  3.000
 HFR  H9   C12  C13  108.11  3.000
 HFR  H10  C12  C11  107.90  3.000
 HFR  H9   C12  C11  108.92  3.000
 HFR  C13  C12  C11  113.29  3.000
 HFR  N4   C13  O1   121.85  3.000
 HFR  O1   C13  C12  124.43  3.000
 HFR  N4   C13  C12  113.69  3.000
 HFR  C19  N1   C3   119.24  3.000
 HFR  C19  N2   C1   111.61  3.000
 HFR  N7   C3   C2   122.76  3.000
 HFR  N7   C3   N1   119.37  3.000
 HFR  C2   C3   N1   117.85  3.000
 HFR  H12  N3   H11  105.94  3.000
 HFR  H12  N3   C11  109.21  3.000
 HFR  H11  N3   C11  110.49  3.000
 HFR  H14  N4   S1   114.96  3.000
 HFR  H14  N4   C13  119.81  3.000
 HFR  S1   N4   C13  123.94  3.000
 HFR  O4   S1   O3   104.37  3.000
 HFR  O4   S1   O2   110.36  3.000
 HFR  O3   S1   O2   121.39  3.000
 HFR  O4   S1   N4   103.60  3.000
 HFR  O3   S1   N4   110.98  3.000
 HFR  O2   S1   N4   104.87  3.000
 HFR  S1   O4   C14  119.68  3.000
 HFR  H15  C15  C16  109.82  3.000
 HFR  H15  C15  O5   110.18  3.000
 HFR  C16  C15  O5   104.77  3.000
 HFR  H15  C15  C14  109.98  3.000
 HFR  O5   C15  C14  109.95  3.000
 HFR  C16  C15  C14  112.04  3.000
 HFR  C18  O5   C15  111.39  3.000
 HFR  H16  C16  C17  107.83  3.000
 HFR  H16  C16  O6   111.39  3.000
 HFR  C17  C16  O6   116.29  3.000
 HFR  H16  C16  C15  109.00  3.000
 HFR  C17  C16  C15  101.52  3.000
 HFR  O6   C16  C15  110.22  3.000
 HFR  H17  O6   C16  109.04  3.000
 HFR  H18  C17  C18  111.05  3.000
 HFR  H18  C17  O7   112.18  3.000
 HFR  C18  C17  O7   110.91  3.000
 HFR  H18  C17  C16  112.68  3.000
 HFR  C18  C17  C16  101.48  3.000
 HFR  O7   C17  C16  108.02  3.000
 HFR  H19  O7   C17  108.73  3.000
 HFR  H20  C18  N5   105.58  3.000
 HFR  H20  C18  C17  110.34  3.000
 HFR  N5   C18  C17  114.46  3.000
 HFR  H20  C18  O5   110.67  3.000
 HFR  N5   C18  O5   108.99  3.000
 HFR  C17  C18  O5   106.83  3.000
 HFR  C1   N5   C18  125.10  3.000
 HFR  C1   N5   C4   106.11  3.000
 HFR  C18  N5   C4   128.73  3.000
 HFR  C2   N6   C4   104.49  3.000
 HFR  C1   C2   N6   110.74  3.000
 HFR  C1   C2   C3   116.28  3.000
 HFR  N6   C2   C3   132.98  3.000
 HFR  C2   C1   N5   105.30  3.000
 HFR  C2   C1   N2   126.55  3.000
 HFR  N5   C1   N2   128.15  3.000
 HFR  H21  C19  N2   116.09  3.000
 HFR  H21  C19  N1   115.45  3.000
 HFR  N2   C19  N1   128.45  3.000
 HFR  H23  N7   H22  117.43  3.000
 HFR  H23  N7   C3   120.28  3.000
 HFR  H22  N7   C3   119.44  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
 HFR  CONST_01  C2   C1   N5   C4      0.00   0.0  0
 HFR  CONST_02  N2   C1   N5   C4    180.00   0.0  0
 HFR  CONST_03  C1   C2   N6   C4      0.00   0.0  0
 HFR  CONST_04  C3   C2   N6   C4    180.00   0.0  0
 HFR  CONST_05  C8   C7   C6   C5      0.00   0.0  0
 HFR  CONST_06  C8   C9   C10  C5      0.00   0.0  0
 HFR  CONST_07  C9   C10  C5   C6      0.00   0.0  0
 HFR  CONST_08  C9   C8   C7   C6      0.00   0.0  0
 HFR  CONST_09  C10  C5   C6   C7      0.00   0.0  0
 HFR  CONST_10  C10  C9   C8   C7      0.00   0.0  0
 HFR  CONST_11  N6   C2   C3   N1    180.00   0.0  0
 HFR  CONST_12  C1   C2   C3   N1      0.00   0.0  0
 HFR  CONST_13  C1   N2   C19  N1      0.00   0.0  0
 HFR  CONST_14  N6   C2   C1   N2    180.00   0.0  0
 HFR  CONST_15  C3   C2   C1   N2      0.00   0.0  0
 HFR  CONST_16  C3   N1   C19  N2      0.00   0.0  0
 HFR  CONST_17  N5   C1   C2   C3    180.00   0.0  0
 HFR  CONST_18  C2   N6   C4   N5      0.00   0.0  0
 HFR  CONST_19  N6   C2   C1   N5      0.00   0.0  0
 HFR  CONST_20  C19  N2   C1   N5    180.00   0.0  0
 HFR  CONST_21  C1   N5   C4   N6      0.00   0.0  0
 HFR  CONST_22  C19  N2   C1   C2      0.00   0.0  0
 HFR  CONST_23  C19  N1   C3   C2      0.00   0.0  0
 HFR  CONST_24  C18  N5   C1   N2      0.00   0.0  0
 HFR  CONST_25  N6   C4   N5   C18   180.00   0.0  0
 HFR  CONST_26  C2   C1   N5   C18   180.00   0.0  0
 HFR  CONST_27  C11  C10  C5   C6    180.00   0.0  0
 HFR  CONST_28  BR   C8   C7   C6    180.00   0.0  0
 HFR  CONST_29  C8   C9   C10  C11   180.00   0.0  0
 HFR  CONST_30  BR   C8   C9   C10   180.00   0.0  0
 HFR  CONST_31  N7   C3   C2   N6      0.00   0.0  0
 HFR  CONST_32  N7   C3   C2   C1    180.00   0.0  0
 HFR  CONST_33  N7   C3   N1   C19   180.00   0.0  0
 HFR  CONST_34  H7   C7   C6   C5    180.00   0.0  0
 HFR  CONST_35  H8   C9   C10  C5    180.00   0.0  0
 HFR  CONST_36  H4   C5   C6   C7    180.00   0.0  0
 HFR  CONST_37  H5   C6   C7   C8    180.00   0.0  0
 HFR  CONST_38  H21  C19  N1   C3    180.00   0.0  0
 HFR  CONST_39  H1   C4   N5   C18     0.00   0.0  0
 HFR  CONST_40  H22  N7   C3   N1      0.00   0.0  0
 HFR  CONST_41  H23  N7   C3   N1    180.00   0.0  0
 HFR  CONST_42  S1   N4   C13  C12   180.00   0.0  0
 HFR  CONST_43  S1   N4   C13  O1      0.00   0.0  0
 HFR  CONST_44  H14  N4   C13  C12     0.00   0.0  0
 HFR  Var_01    C15  C14  O4   S1   -124.09  30.0  2
 HFR  Var_02    O2   S1   O4   C14   -41.52  30.0  2
 HFR  Var_03    N4   C13  C12  C11   -95.28  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
 HFR  chir_01  C11  N3   C10  C12  positiv
 HFR  chir_02  C15  C14  C16  O5   positiv
 HFR  chir_03  C16  O6   C17  C15  negativ
 HFR  chir_04  C17  O7   C18  C16  negativ
 HFR  chir_05  C18  O5   N5   C17  negativ

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
 HFR  plan-1  C5   0.020
 HFR  plan-1  C6   0.020
 HFR  plan-1  C11  0.020
 HFR  plan-1  C7   0.020
 HFR  plan-1  C8   0.020
 HFR  plan-1  C9   0.020
 HFR  plan-1  C10  0.020
 HFR  plan-1  H4   0.020
 HFR  plan-1  H5   0.020
 HFR  plan-1  H7   0.020
 HFR  plan-1  H8   0.020
 HFR  plan-1  BR   0.020
 HFR  plan-2  C4   0.020
 HFR  plan-2  N1   0.020
 HFR  plan-2  N2   0.020
 HFR  plan-2  C3   0.020
 HFR  plan-2  C18  0.020
 HFR  plan-2  N5   0.020
 HFR  plan-2  N6   0.020
 HFR  plan-2  C2   0.020
 HFR  plan-2  C1   0.020
 HFR  plan-2  C19  0.020
 HFR  plan-2  N7   0.020
 HFR  plan-2  H1   0.020
 HFR  plan-2  H21  0.020
 HFR  plan-3  C3   0.020
 HFR  plan-3  N7   0.020
 HFR  plan-3  H22  0.020
 HFR  plan-3  H23  0.020
 HFR  plan-4  C12  0.020
 HFR  plan-4  C13  0.020
 HFR  plan-4  O1   0.020
 HFR  plan-4  N4   0.020
 HFR  plan-4  S1   0.020
 HFR  plan-4  H14  0.020

