# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 17:16:22 2022
#   Inital geometry file: a 148 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-[(4~{E})-4-[(4-chlorophenyl)methoxyimino]-3-methyl-2-oxidanylidene-pyrimidin-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: CN/1C(=O)N(C=CC/1=N/OCc2ccc(Cl)cc2)[C@@H]3O[C@H](CO[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 BOI  BOI  "[[(2~{R},3~{S},4~{R},5~{R})-5-[(4~{E})-4-[(4-chlorophenyl)methoxyimino]-3-methyl-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid"  ligand  56  35  .  2022-09-16  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BOI
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
 BOI  O8   O   O      0  -0.494  13.6938  15.3422  34.0908
 BOI  C15  C   CR6    0   0.757  12.5562  15.7607  33.9670
 BOI  N2   N   NR6    0  -0.589  12.2357  16.7869  33.1112
 BOI  C14  C   CH3    0  -0.531  13.2980  17.3994  32.3299
 BOI  C6   C   CR6    0   0.508  10.9545  17.3212  32.9831
 BOI  N1   N   N      0  -0.235  10.8434  18.3503  32.2215
 BOI  O7   O   O2     0  -0.400   9.5411  18.8265  32.2221
 BOI  C7   C   CH2    0  -0.197   9.3363  19.6336  31.0930
 BOI  C8   C   CR6    0   0.063   9.2605  18.8608  29.8017
 BOI  C13  C   CR16   0  -0.293   8.7259  17.5763  29.7569
 BOI  C12  C   CR16   0  -0.198   8.6066  16.8956  28.5548
 BOI  C11  C   CR6    0  -0.052   9.0218  17.5108  27.3834
 BOI  CL   CL  CL     0  -0.134   8.8603  16.6707  25.8741
 BOI  C10  C   CR16   0  -0.197   9.5626  18.7858  27.4010
 BOI  C9   C   CR16   0  -0.302   9.6825  19.4483  28.6144
 BOI  C5   C   CR16   0  -0.475   9.9165  16.6462  33.7077
 BOI  C4   C   CR16   0   0.035  10.2291  15.6287  34.5224
 BOI  N    N   NR6    0  -0.580  11.5201  15.2139  34.6938
 BOI  C3   C   CR15   0   0.195  11.8868  14.1420  35.6434
 BOI  O6   O   O      0  -0.493  10.7399  13.4683  36.0538
 BOI  C16  C   CR15   0  -0.043  12.5489  14.7058  36.9043
 BOI  O9   O   OH1    0  -0.662  13.4339  13.7273  37.3809
 BOI  C17  C   CR15   0  -0.016  11.3415  14.8735  37.8217
 BOI  O10  O   OH1    0  -0.661  11.7565  14.9273  39.1559
 BOI  C2   C   CR15   0  -0.013  10.4958  13.6542  37.4515
 BOI  C1   C   CH2    0  -0.149   9.0249  13.8446  37.7329
 BOI  O5   O   O2     0  -0.629   8.3124  12.6966  37.3545
 BOI  P1   P   P      0   1.248   6.7307  12.5023  37.8520
 BOI  O3   O   O      0  -0.829   6.6906  12.7539  39.3437
 BOI  O4   O   OP    -1  -0.814   6.3573  11.1366  37.3350
 BOI  C    C   CH2    0  -1.014   5.7891  13.8099  36.9991
 BOI  P    P   P      0   1.181   6.0926  14.2998  35.2048
 BOI  O    O   O      0  -0.849   7.3802  15.1547  35.2329
 BOI  O2   O   OP    -1  -0.894   6.2289  13.0051  34.3986
 BOI  O1   O   OP    -1  -0.902   4.8494  15.1274  34.8553
 BOI  H19  H   HCH3   0   0.268  14.2215  16.8564  32.4836
 BOI  H17  H   HCH3   0   0.251  13.0398  17.3774  31.2729
 BOI  H18  H   HCH3   0   0.250  13.4373  18.4379  32.6277
 BOI  H12  H   HCH2   0   0.227  10.1065  20.4096  31.0196
 BOI  H11  H   HCH2   0   0.255   8.3834  20.1377  31.2748
 BOI  H16  H   HCR6   0   0.263   8.3926  17.0905  30.6654
 BOI  H15  H   HCR6   0   0.276   8.1902  15.8974  28.5334
 BOI  H14  H   HCR6   0   0.276   9.8929  19.2579  26.4856
 BOI  H13  H   HCR6   0   0.260  10.1132  20.4427  28.6283
 BOI  H10  H   HCR6   0   0.270   8.8843  16.9335  33.6036
 BOI  H9   H   HCR6   0   0.347   9.4277  15.1082  35.0374
 BOI  H1   H   HCR5   0   0.272  12.5575  13.4580  35.1189
 BOI  H20  H   HCR5   0   0.255  13.0582  15.6579  36.7198
 BOI  H21  H   HOH1   0   0.453  13.6252  13.9149  38.3065
 BOI  H22  H   HCR5   0   0.230  10.8055  15.7894  37.5306
 BOI  H23  H   HOH1   0   0.463  10.9988  15.1117  39.7197
 BOI  H    H   HCR5   0   0.227  10.8610  12.7742  37.9964
 BOI  H7   H   HCH2   0   0.214   8.6539  14.7249  37.1979
 BOI  H8   H   HCH2   0   0.190   8.9310  14.0410  38.8097
 BOI  H4   H   HCH2   0   0.202   5.8480  14.7211  37.6035
 BOI  H5   H   HCH2   0   0.209   4.7449  13.4837  37.0785

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
 BOI  CL   C11  single    1.735  0.020  1.735
 BOI  C10  C11  aromatic  1.385  0.020  1.385
 BOI  C10  C9   aromatic  1.388  0.020  1.388
 BOI  C11  C12  aromatic  1.387  0.020  1.387
 BOI  C9   C8   aromatic  1.390  0.020  1.390
 BOI  C12  C13  aromatic  1.387  0.020  1.387
 BOI  C8   C13  aromatic  1.392  0.020  1.392
 BOI  C8   C7   single    1.507  0.020  1.507
 BOI  C7   O7   single    1.403  0.020  1.403
 BOI  O7   N1   single    1.387  0.020  1.387
 BOI  N1   C6   double    1.285  0.020  1.285
 BOI  C14  N2   single    1.454  0.020  1.454
 BOI  C6   N2   single    1.394  0.020  1.394
 BOI  C6   C5   single    1.435  0.020  1.435
 BOI  N2   C15  single    1.374  0.020  1.374
 BOI  C5   C4   double    1.340  0.020  1.340
 BOI  C15  O8   double    1.218  0.020  1.218
 BOI  C15  N    single    1.379  0.020  1.379
 BOI  C4   N    single    1.367  0.020  1.367
 BOI  N    C3   single    1.478  0.020  1.478
 BOI  O2   P    deloc     1.531  0.020  1.531
 BOI  O1   P    deloc     1.534  0.020  1.534
 BOI  C3   O6   single    1.392  0.020  1.392
 BOI  C3   C16  single    1.532  0.020  1.532
 BOI  O6   C2   single    1.431  0.020  1.431
 BOI  P    O    deloc     1.546  0.020  1.546
 BOI  P    C    single    1.885  0.020  1.885
 BOI  C16  O9   single    1.403  0.020  1.403
 BOI  C16  C17  single    1.526  0.020  1.526
 BOI  O5   C1   single    1.403  0.020  1.403
 BOI  O5   P1   single    1.669  0.020  1.669
 BOI  O4   P1   deloc     1.507  0.020  1.507
 BOI  C2   C1   single    1.510  0.020  1.510
 BOI  C2   C17  single    1.529  0.020  1.529
 BOI  C    P1   single    1.823  0.020  1.823
 BOI  P1   O3   deloc     1.513  0.020  1.513
 BOI  C17  O10  single    1.398  0.020  1.398
 BOI  C14  H19  single    0.970  0.020  1.090
 BOI  C14  H17  single    0.970  0.020  1.090
 BOI  C14  H18  single    0.970  0.020  1.090
 BOI  C7   H12  single    0.970  0.020  1.090
 BOI  C7   H11  single    0.970  0.020  1.090
 BOI  C13  H16  single    0.930  0.020  1.080
 BOI  C12  H15  single    0.930  0.020  1.080
 BOI  C10  H14  single    0.930  0.020  1.080
 BOI  C9   H13  single    0.930  0.020  1.080
 BOI  C5   H10  single    0.930  0.020  1.080
 BOI  C4   H9   single    0.930  0.020  1.080
 BOI  C3   H1   single    0.970  0.020  1.090
 BOI  C16  H20  single    0.970  0.020  1.090
 BOI  O9   H21  single    0.850  0.020  0.980
 BOI  C17  H22  single    0.970  0.020  1.090
 BOI  O10  H23  single    0.850  0.020  0.980
 BOI  C2   H    single    0.970  0.020  1.090
 BOI  C1   H7   single    0.970  0.020  1.090
 BOI  C1   H8   single    0.970  0.020  1.090
 BOI  C    H4   single    0.970  0.020  1.090
 BOI  C    H5   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
 BOI  N    C15  N2   116.69  3.000
 BOI  N    C15  O8   120.79  3.000
 BOI  N2   C15  O8   122.52  3.000
 BOI  C6   N2   C14  117.42  3.000
 BOI  C6   N2   C15  123.91  3.000
 BOI  C14  N2   C15  118.61  3.000
 BOI  H18  C14  H17  108.37  3.000
 BOI  H18  C14  H19  109.29  3.000
 BOI  H17  C14  H19  109.28  3.000
 BOI  H18  C14  N2   110.37  3.000
 BOI  H17  C14  N2   109.88  3.000
 BOI  H19  C14  N2   109.62  3.000
 BOI  C5   C6   N1   127.85  3.000
 BOI  C5   C6   N2   115.99  3.000
 BOI  N1   C6   N2   116.16  3.000
 BOI  O7   N1   C6   110.85  3.000
 BOI  C7   O7   N1   109.53  3.000
 BOI  H11  C7   H12  107.29  3.000
 BOI  H11  C7   C8   109.58  3.000
 BOI  H12  C7   C8   109.95  3.000
 BOI  H11  C7   O7   104.99  3.000
 BOI  H12  C7   O7   111.02  3.000
 BOI  C8   C7   O7   113.70  3.000
 BOI  C9   C8   C13  118.62  3.000
 BOI  C13  C8   C7   121.34  3.000
 BOI  C9   C8   C7   119.99  3.000
 BOI  H16  C13  C12  118.73  3.000
 BOI  H16  C13  C8   120.34  3.000
 BOI  C12  C13  C8   120.93  3.000
 BOI  H15  C12  C11  120.52  3.000
 BOI  H15  C12  C13  120.21  3.000
 BOI  C11  C12  C13  119.26  3.000
 BOI  C10  C11  CL   119.55  3.000
 BOI  C10  C11  C12  120.96  3.000
 BOI  CL   C11  C12  119.49  3.000
 BOI  H14  C10  C9   120.35  3.000
 BOI  H14  C10  C11  120.67  3.000
 BOI  C9   C10  C11  118.97  3.000
 BOI  H13  C9   C10  118.93  3.000
 BOI  H13  C9   C8   119.83  3.000
 BOI  C10  C9   C8   121.25  3.000
 BOI  H10  C5   C4   119.01  3.000
 BOI  H10  C5   C6   121.29  3.000
 BOI  C4   C5   C6   119.70  3.000
 BOI  H9   C4   N    119.49  3.000
 BOI  H9   C4   C5   118.70  3.000
 BOI  N    C4   C5   121.79  3.000
 BOI  C3   N    C4   122.34  3.000
 BOI  C3   N    C15  116.09  3.000
 BOI  C4   N    C15  121.56  3.000
 BOI  H1   C3   C16  111.13  3.000
 BOI  H1   C3   O6   110.15  3.000
 BOI  C16  C3   O6   106.95  3.000
 BOI  H1   C3   N    107.33  3.000
 BOI  C16  C3   N    111.66  3.000
 BOI  O6   C3   N    109.63  3.000
 BOI  C2   O6   C3   111.45  3.000
 BOI  H20  C16  C17  111.94  3.000
 BOI  H20  C16  O9   111.73  3.000
 BOI  C17  C16  O9   111.82  3.000
 BOI  H20  C16  C3   112.47  3.000
 BOI  C17  C16  C3   101.15  3.000
 BOI  O9   C16  C3   107.19  3.000
 BOI  H21  O9   C16  108.40  3.000
 BOI  H22  C17  C2   109.28  3.000
 BOI  H22  C17  O10  111.41  3.000
 BOI  C2   C17  O10  115.20  3.000
 BOI  H22  C17  C16  108.54  3.000
 BOI  O10  C17  C16  110.07  3.000
 BOI  C2   C17  C16  101.80  3.000
 BOI  H23  O10  C17  109.44  3.000
 BOI  H    C2   C1   109.44  3.000
 BOI  H    C2   C17  109.57  3.000
 BOI  C1   C2   C17  113.15  3.000
 BOI  H    C2   O6   108.90  3.000
 BOI  C17  C2   O6   104.22  3.000
 BOI  C1   C2   O6   111.39  3.000
 BOI  H8   C1   H7   107.84  3.000
 BOI  H8   C1   O5   111.55  3.000
 BOI  H7   C1   O5   110.73  3.000
 BOI  H8   C1   C2   106.77  3.000
 BOI  H7   C1   C2   109.91  3.000
 BOI  O5   C1   C2   109.95  3.000
 BOI  P1   O5   C1   119.73  3.000
 BOI  C    P1   O4   111.19  3.000
 BOI  C    P1   O3   109.16  3.000
 BOI  O4   P1   O3   118.83  3.000
 BOI  O3   P1   O5   107.43  3.000
 BOI  C    P1   O5   105.45  3.000
 BOI  O4   P1   O5   103.77  3.000
 BOI  H5   C    H4   104.99  3.000
 BOI  H5   C    P    107.43  3.000
 BOI  H4   C    P    107.49  3.000
 BOI  H5   C    P1   104.15  3.000
 BOI  H4   C    P1   108.11  3.000
 BOI  P    C    P1   123.28  3.000
 BOI  O1   P    O2   114.11  3.000
 BOI  O1   P    O    112.38  3.000
 BOI  O2   P    O    113.77  3.000
 BOI  O    P    C    105.11  3.000
 BOI  O1   P    C    103.10  3.000
 BOI  O2   P    C    107.21  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
 BOI  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 BOI  CONST_02  C11  C12  C13  C8      0.00   0.0  0
 BOI  CONST_03  C10  C11  C12  C13     0.00   0.0  0
 BOI  CONST_04  C10  C9   C8   C13     0.00   0.0  0
 BOI  CONST_05  C9   C10  C11  C12     0.00   0.0  0
 BOI  CONST_06  C9   C8   C13  C12     0.00   0.0  0
 BOI  CONST_07  C5   C6   N2   C15     0.00   0.0  0
 BOI  CONST_08  C4   N    C15  N2      0.00   0.0  0
 BOI  CONST_09  C3   N    C15  N2    180.00   0.0  0
 BOI  CONST_10  N    C15  N2   C6      0.00   0.0  0
 BOI  CONST_11  C10  C9   C8   C7    180.00   0.0  0
 BOI  CONST_12  C12  C13  C8   C7    180.00   0.0  0
 BOI  CONST_13  CL   C11  C12  C13   180.00   0.0  0
 BOI  CONST_14  C9   C10  C11  CL    180.00   0.0  0
 BOI  CONST_15  C6   N2   C15  O8    180.00   0.0  0
 BOI  CONST_16  C4   N    C15  O8    180.00   0.0  0
 BOI  CONST_17  C3   N    C15  O8      0.00   0.0  0
 BOI  CONST_18  N1   C6   N2   C15   180.00   0.0  0
 BOI  CONST_19  C5   C6   N2   C14   180.00   0.0  0
 BOI  CONST_20  N    C15  N2   C14   180.00   0.0  0
 BOI  CONST_21  H14  C10  C9   C8    180.00   0.0  0
 BOI  CONST_22  H15  C12  C13  C8    180.00   0.0  0
 BOI  CONST_23  H13  C9   C8   C13   180.00   0.0  0
 BOI  CONST_24  H14  C10  C11  C12   180.00   0.0  0
 BOI  CONST_25  H13  C9   C10  C11   180.00   0.0  0
 BOI  CONST_26  H16  C13  C12  C11   180.00   0.0  0
 BOI  CONST_27  H15  C12  C11  C10   180.00   0.0  0
 BOI  CONST_28  H16  C13  C8   C9    180.00   0.0  0
 BOI  CONST_29  C14  N2   C15  O8      0.00   0.0  0
 BOI  CONST_30  O7   N1   C6   N2    180.00   0.0  0
 BOI  CONST_31  N1   C6   N2   C14     0.00   0.0  0
 BOI  CONST_32  C5   C6   N1   O7      0.00   0.0  0
 BOI  Var_01    H9   C4   N    C15   173.85  30.0  1
 BOI  Var_02    H10  C5   C6   N2   -174.69  30.0  1
 BOI  Var_03    H9   C4   C5   C6   -178.00  30.0  1
 BOI  Var_04    H10  C5   C4   N     179.79  30.0  1
 BOI  Var_05    H9   C4   N    C3     -4.96  30.0  1
 BOI  Var_06    C9   C8   C7   O7   -149.76  30.0  2
 BOI  Var_07    C13  C8   C7   O7     32.71  30.0  2
 BOI  Var_08    H19  C14  N2   C15     5.63  30.0  3
 BOI  Var_09    H17  C14  N2   C15   125.74  30.0  3
 BOI  Var_10    H18  C14  N2   C15  -114.80  30.0  3
 BOI  Var_11    H19  C14  N2   C6   -176.98  30.0  3
 BOI  Var_12    H17  C14  N2   C6    -56.87  30.0  3
 BOI  Var_13    H18  C14  N2   C6     62.59  30.0  3
 BOI  Var_14    H10  C5   C6   N1      4.62  30.0  1
 BOI  Var_15    H12  C7   C8   C13   157.89  30.0  2
 BOI  Var_16    H11  C7   C8   C13   -84.42  30.0  2
 BOI  Var_17    H12  C7   C8   C9    -24.59  30.0  2
 BOI  Var_18    H11  C7   C8   C9     93.10  30.0  2
 BOI  Var_19    C7   O7   N1   C6   -160.71  30.0  2
 BOI  Var_20    C8   C7   O7   N1     72.21  30.0  2
 BOI  Var_21    P1   O5   C1   C2    166.83  30.0  2
 BOI  Var_22    O4   P1   O5   C1   -176.27  30.0  3
 BOI  Var_23    C    P1   O5   C1     66.74  30.0  3
 BOI  Var_24    O3   P1   O5   C1    -49.59  30.0  3
 BOI  Var_25    P    C    P1   O5     40.50  30.0  1
 BOI  Var_26    O2   P    C    P1     44.63  30.0  3
 BOI  Var_27    O1   P    C    P1    165.36  30.0  3
 BOI  Var_28    O    P    C    P1    -76.75  30.0  3
 BOI  Var_29    P    C    P1   O3    155.65  30.0  1
 BOI  Var_30    P    C    P1   O4    -71.34  30.0  1
 BOI  Var_31    H12  C7   O7   N1    -52.39  30.0  2
 BOI  Var_32    H11  C7   O7   N1   -168.02  30.0  2
 BOI  Var_33    H4   C    P1   O5    -85.86  30.0  1
 BOI  Var_34    H5   C    P1   O5    162.84  30.0  1
 BOI  Var_35    H7   C1   O5   P1    -71.53  30.0  3
 BOI  Var_36    H8   C1   O5   P1     48.57  30.0  3
 BOI  Var_37    H4   C    P1   O3     29.29  30.0  1
 BOI  Var_38    H5   C    P1   O3    -82.00  30.0  1
 BOI  Var_39    H4   C    P1   O4    162.31  30.0  1
 BOI  Var_40    H5   C    P1   O4     51.01  30.0  1
 BOI  Var_41    H4   C    P    O      49.88  30.0  3
 BOI  Var_42    H5   C    P    O     162.41  30.0  3
 BOI  Var_43    H4   C    P    O2    171.26  30.0  3
 BOI  Var_44    H5   C    P    O2    -76.21  30.0  3
 BOI  Var_45    H4   C    P    O1    -68.01  30.0  3
 BOI  Var_46    H5   C    P    O1     44.52  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
 BOI  chir_01  C3   N    O6   C16  positiv
 BOI  chir_02  C16  O9   C3   C17  negativ
 BOI  chir_03  C17  O10  C2   C16  positiv
 BOI  chir_04  C2   O6   C17  C1   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
 BOI  plan-1  C7   0.020
 BOI  plan-1  C8   0.020
 BOI  plan-1  C13  0.020
 BOI  plan-1  C12  0.020
 BOI  plan-1  C11  0.020
 BOI  plan-1  CL   0.020
 BOI  plan-1  C10  0.020
 BOI  plan-1  C9   0.020
 BOI  plan-1  H16  0.020
 BOI  plan-1  H15  0.020
 BOI  plan-1  H14  0.020
 BOI  plan-1  H13  0.020
 BOI  plan-2  O8   0.020
 BOI  plan-2  C15  0.020
 BOI  plan-2  N2   0.020
 BOI  plan-2  C14  0.020
 BOI  plan-2  C6   0.020
 BOI  plan-2  N1   0.020
 BOI  plan-2  O7   0.020
 BOI  plan-2  C5   0.020
 BOI  plan-2  C4   0.020
 BOI  plan-2  N    0.020
 BOI  plan-2  C3   0.020

