# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 16:18:27 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: (~{E})-2-cyano-3-[4-(dimethylamino)phenyl]-~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ccc(cc1)/C=C(C#N)/C(=O)N[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O
#
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
 I0F  I0F  "2-cyano-3-[4-(dimethylamino)phenyl]-~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]propanamide"
  ligand  50  27  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_I0F
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
 I0F  N1   N  NH1   0  -0.731  34.3484  23.6285  28.6522
 I0F  C4   C  CH1   0   0.026  32.5636  20.9186  26.0226
 I0F  C5   C  CH1   0  -0.012  32.3344  20.8807  27.5407
 I0F  C6   C  CH2   0  -0.195  32.2825  19.4826  28.1182
 I0F  C7   C  C     0   0.618  34.0940  24.1205  29.8906
 I0F  C8   C  C     0  -0.180  35.2591  24.7092  30.6115
 I0F  C10  C  CR6   0   0.121  35.9659  25.6645  32.8758
 I0F  C13  C  CR6   0   0.414  37.5455  26.7628  34.9799
 I0F  C15  C  CR16  0  -0.287  37.3404  25.9214  32.7066
 I0F  C17  C  CH3   0  -0.543  39.7135  27.5118  35.7705
 I0F  C16  C  CH3   0  -0.543  37.7023  27.5886  37.2534
 I0F  N13  N  NT    0  -0.489  38.2986  27.2782  35.9710
 I0F  C14  C  CR16  0  -0.327  38.1050  26.4486  33.7149
 I0F  C12  C  CR16  0  -0.344  36.1644  26.5084  35.1553
 I0F  C11  C  CR16  0  -0.276  35.4176  25.9776  34.1348
 I0F  C9   C  C1    0  -0.223  35.0837  25.1034  31.9042
 I0F  C88  C  CSP   0  -0.014  36.4818  24.8436  29.9107
 I0F  N88  N  NS    0  -0.254  37.4534  24.9405  29.2923
 I0F  O7   O  O     0  -0.466  32.9831  24.0975  30.3913
 I0F  C1   C  CH1   0   0.211  33.3507  22.9693  27.8747
 I0F  O5   O  O2    0  -0.489  33.3567  21.6000  28.2024
 I0F  O4   O  OH1   0  -0.667  31.5193  20.2696  25.3399
 I0F  C3   C  CH1   0   0.018  32.6005  22.3688  25.5644
 I0F  O3   O  OH1   0  -0.662  32.9088  22.4006  24.1960
 I0F  C2   C  CH1   0  -0.037  33.6237  23.1531  26.3805
 I0F  O2   O  OH1   0  -0.660  33.5134  24.5015  26.0008
 I0F  H13  H  HNH1  0   0.413  35.3050  23.5403  28.3390
 I0F  H41  H  HCH1  0   0.224  33.5355  20.4615  25.7953
 I0F  H5   H  HCH1  0   0.224  31.3544  21.3409  27.7500
 I0F  H62  H  HCH2  0   0.208  31.3877  18.9846  27.7261
 I0F  H61  H  HCH2  0   0.219  32.1397  19.5646  29.2036
 I0F  H15  H  HCR6  0   0.265  37.8352  25.7022  31.7719
 I0F  H9N  H  HCH3  0   0.265  40.1461  27.8968  36.6882
 I0F  H9O  H  HCH3  0   0.247  40.2432  26.5926  35.5121
 I0F  H17  H  HCH3  0   0.246  39.8971  28.2445  34.9814
 I0F  H9M  H  HCH3  0   0.265  38.4582  28.0158  37.9052
 I0F  H16  H  HCH3  0   0.247  36.8945  28.3172  37.1572
 I0F  H9L  H  HCH3  0   0.246  37.3021  26.6972  37.7430
 I0F  H14  H  HCR6  0   0.279  39.1545  26.6196  33.5246
 I0F  H12  H  HCR6  0   0.277  35.6783  26.7205  36.0960
 I0F  H11  H  HCR6  0   0.266  34.3643  25.7906  34.3079
 I0F  H9   H  H     0   0.282  34.0705  24.9533  32.2642
 I0F  H1   H  HCH1  0   0.230  32.3756  23.4130  28.1135
 I0F  H63  H  HOH1  0   0.457  33.3703  17.8801  28.0979
 I0F  H42  H  HOH1  0   0.456  31.6946  19.3241  25.3354
 I0F  H31  H  HCH1  0   0.208  31.6076  22.8105  25.7577
 I0F  H32  H  HOH1  0   0.448  32.9162  23.3211  23.9126
 I0F  H21  H  HCH1  0   0.228  34.6248  22.7510  26.1583
 I0F  H22  H  HOH1  0   0.457  34.3032  24.9736  26.2818
 I0F  O6   O  OH1   0  -0.667  33.4617  18.7873  27.7934

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
 I0F  O3   C3   single    1.403  0.020  1.403
 I0F  O4   C4   single    1.406  0.020  1.406
 I0F  C3   C4   single    1.521  0.020  1.521
 I0F  C3   C2   single    1.526  0.020  1.526
 I0F  C4   C5   single    1.536  0.020  1.536
 I0F  O2   C2   single    1.405  0.020  1.405
 I0F  C2   C1   single    1.530  0.020  1.530
 I0F  O6   C6   single    1.407  0.020  1.407
 I0F  C5   C6   single    1.514  0.020  1.514
 I0F  C5   O5   single    1.414  0.020  1.414
 I0F  C1   O5   single    1.408  0.020  1.408
 I0F  C1   N1   single    1.426  0.020  1.426
 I0F  N1   C7   single    1.357  0.020  1.357
 I0F  N88  C88  triple    1.156  0.020  1.156
 I0F  C7   O7   double    1.219  0.020  1.219
 I0F  C7   C8   single    1.491  0.020  1.491
 I0F  C88  C8   single    1.416  0.020  1.416
 I0F  C8   C9   double    1.363  0.020  1.363
 I0F  C9   C10  single    1.427  0.020  1.427
 I0F  C15  C10  aromatic  1.409  0.020  1.409
 I0F  C15  C14  aromatic  1.371  0.020  1.371
 I0F  C10  C11  aromatic  1.408  0.020  1.408
 I0F  C14  C13  aromatic  1.419  0.020  1.419
 I0F  C11  C12  aromatic  1.372  0.020  1.372
 I0F  C13  C12  aromatic  1.415  0.020  1.415
 I0F  C13  N13  single    1.347  0.020  1.347
 I0F  C17  N13  single    1.448  0.020  1.448
 I0F  N13  C16  single    1.448  0.020  1.448
 I0F  N1   H13  single    0.860  0.020  1.020
 I0F  C4   H41  single    0.970  0.020  1.090
 I0F  C5   H5   single    0.970  0.020  1.090
 I0F  C6   H62  single    0.970  0.020  1.090
 I0F  C6   H61  single    0.970  0.020  1.090
 I0F  C15  H15  single    0.930  0.020  1.080
 I0F  C17  H9N  single    0.970  0.020  1.090
 I0F  C17  H9O  single    0.970  0.020  1.090
 I0F  C17  H17  single    0.970  0.020  1.090
 I0F  C16  H9M  single    0.970  0.020  1.090
 I0F  C16  H16  single    0.970  0.020  1.090
 I0F  C16  H9L  single    0.970  0.020  1.090
 I0F  C14  H14  single    0.930  0.020  1.080
 I0F  C12  H12  single    0.930  0.020  1.080
 I0F  C11  H11  single    0.930  0.020  1.080
 I0F  C9   H9   single    0.930  0.020  1.080
 I0F  C1   H1   single    0.970  0.020  1.090
 I0F  O6   H63  single    0.850  0.020  0.980
 I0F  O4   H42  single    0.850  0.020  0.980
 I0F  C3   H31  single    0.970  0.020  1.090
 I0F  O3   H32  single    0.850  0.020  0.980
 I0F  C2   H21  single    0.970  0.020  1.090
 I0F  O2   H22  single    0.850  0.020  0.980

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
 I0F  H13  N1   C1   116.93  3.000
 I0F  H13  N1   C7   119.48  3.000
 I0F  C1   N1   C7   122.28  3.000
 I0F  H41  C4   C3   108.25  3.000
 I0F  H41  C4   O4   111.39  3.000
 I0F  C3   C4   O4   108.16  3.000
 I0F  H41  C4   C5   109.06  3.000
 I0F  C3   C4   C5   108.96  3.000
 I0F  O4   C4   C5   110.96  3.000
 I0F  H5   C5   O5   109.96  3.000
 I0F  H5   C5   C6   106.42  3.000
 I0F  O5   C5   C6   108.43  3.000
 I0F  H5   C5   C4   108.06  3.000
 I0F  O5   C5   C4   110.00  3.000
 I0F  C6   C5   C4   113.89  3.000
 I0F  H61  C6   H62  106.34  3.000
 I0F  H61  C6   O6   111.97  3.000
 I0F  H62  C6   O6   112.14  3.000
 I0F  H61  C6   C5   108.22  3.000
 I0F  H62  C6   C5   108.13  3.000
 I0F  O6   C6   C5   109.86  3.000
 I0F  O7   C7   C8   121.39  3.000
 I0F  C8   C7   N1   115.98  3.000
 I0F  O7   C7   N1   122.63  3.000
 I0F  C88  C8   C9   123.59  3.000
 I0F  C9   C8   C7   118.18  3.000
 I0F  C88  C8   C7   118.22  3.000
 I0F  C9   C10  C11  117.08  3.000
 I0F  C11  C10  C15  116.54  3.000
 I0F  C9   C10  C15  126.38  3.000
 I0F  C12  C13  C14  117.11  3.000
 I0F  C12  C13  N13  121.54  3.000
 I0F  C14  C13  N13  121.35  3.000
 I0F  H15  C15  C14  117.33  3.000
 I0F  H15  C15  C10  120.93  3.000
 I0F  C14  C15  C10  121.74  3.000
 I0F  H17  C17  H9O  108.19  3.000
 I0F  H17  C17  H9N  107.82  3.000
 I0F  H9O  C17  H9N  107.78  3.000
 I0F  H17  C17  N13  111.87  3.000
 I0F  H9O  C17  N13  111.78  3.000
 I0F  H9N  C17  N13  109.24  3.000
 I0F  H9L  C16  H16  108.23  3.000
 I0F  H9L  C16  H9M  107.87  3.000
 I0F  H16  C16  H9M  107.78  3.000
 I0F  H9L  C16  N13  111.88  3.000
 I0F  H16  C16  N13  111.69  3.000
 I0F  H9M  C16  N13  109.23  3.000
 I0F  C16  N13  C17  119.38  3.000
 I0F  C16  N13  C13  120.22  3.000
 I0F  C17  N13  C13  120.40  3.000
 I0F  H14  C14  C15  118.24  3.000
 I0F  H14  C14  C13  120.35  3.000
 I0F  C15  C14  C13  121.41  3.000
 I0F  H12  C12  C11  118.63  3.000
 I0F  H12  C12  C13  120.79  3.000
 I0F  C11  C12  C13  120.58  3.000
 I0F  H11  C11  C12  118.50  3.000
 I0F  H11  C11  C10  118.87  3.000
 I0F  C12  C11  C10  122.63  3.000
 I0F  H9   C9   C10  113.92  3.000
 I0F  H9   C9   C8   113.24  3.000
 I0F  C10  C9   C8   132.83  3.000
 I0F  N88  C88  C8   180.00  3.000
 I0F  H1   C1   C2   108.81  3.000
 I0F  H1   C1   O5   110.26  3.000
 I0F  C2   C1   O5   110.08  3.000
 I0F  H1   C1   N1   108.42  3.000
 I0F  O5   C1   N1   108.64  3.000
 I0F  C2   C1   N1   110.61  3.000
 I0F  C1   O5   C5   112.50  3.000
 I0F  H42  O4   C4   108.70  3.000
 I0F  H31  C3   C2   107.69  3.000
 I0F  H31  C3   O3   111.06  3.000
 I0F  C2   C3   O3   111.26  3.000
 I0F  H31  C3   C4   107.87  3.000
 I0F  C2   C3   C4   110.19  3.000
 I0F  O3   C3   C4   108.70  3.000
 I0F  H32  O3   C3   108.07  3.000
 I0F  H21  C2   O2   111.54  3.000
 I0F  H21  C2   C3   108.30  3.000
 I0F  O2   C2   C3   107.22  3.000
 I0F  H21  C2   C1   108.38  3.000
 I0F  O2   C2   C1   111.42  3.000
 I0F  C3   C2   C1   109.93  3.000
 I0F  H22  O2   C2   109.12  3.000
 I0F  H63  O6   C6   108.27  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
 I0F  CONST_01  C13  C14  C15  C10     0.00   0.0  0
 I0F  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 I0F  CONST_03  C12  C11  C10  C15     0.00   0.0  0
 I0F  CONST_04  C12  C13  C14  C15     0.00   0.0  0
 I0F  CONST_05  C11  C10  C15  C14     0.00   0.0  0
 I0F  CONST_06  C11  C12  C13  C14     0.00   0.0  0
 I0F  CONST_07  N13  C13  C14  C15   180.00   0.0  0
 I0F  CONST_08  C11  C12  C13  N13   180.00   0.0  0
 I0F  CONST_09  C9   C10  C15  C14   180.00   0.0  0
 I0F  CONST_10  C9   C10  C11  C12   180.00   0.0  0
 I0F  CONST_11  H14  C14  C15  C10   180.00   0.0  0
 I0F  CONST_12  H12  C12  C11  C10   180.00   0.0  0
 I0F  CONST_13  H15  C15  C14  C13   180.00   0.0  0
 I0F  CONST_14  H11  C11  C12  C13   180.00   0.0  0
 I0F  CONST_15  H11  C11  C10  C15   180.00   0.0  0
 I0F  CONST_16  H12  C12  C13  C14   180.00   0.0  0
 I0F  CONST_17  H14  C14  C13  C12   180.00   0.0  0
 I0F  CONST_18  H15  C15  C10  C11   180.00   0.0  0
 I0F  CONST_19  C14  C13  N13  C17     0.00   0.0  0
 I0F  CONST_20  C12  C13  N13  C17   180.00   0.0  0
 I0F  CONST_21  C14  C13  N13  C16   180.00   0.0  0
 I0F  CONST_22  C12  C13  N13  C16     0.00   0.0  0
 I0F  CONST_23  C1   N1   C7   C8    180.00   0.0  0
 I0F  CONST_24  C1   N1   C7   O7      0.00   0.0  0
 I0F  CONST_25  H13  N1   C7   C8      0.00   0.0  0
 I0F  CONST_26  H13  N1   C7   O7    180.00   0.0  0
 I0F  Var_01    C15  C10  C9   C8     -2.06  30.0  2
 I0F  Var_02    C11  C10  C9   C8    178.84  30.0  2
 I0F  Var_03    H9   C9   C10  C15   177.51  30.0  2
 I0F  Var_04    H9   C9   C10  C11    -1.60  30.0  2
 I0F  Var_05    C10  C9   C8   C7    178.43   0.0  2
 I0F  Var_06    C88  C8   C9   C10    -2.40   0.0  2
 I0F  Var_07    H9N  C17  N13  C13  -178.18  30.0  3
 I0F  Var_08    H9O  C17  N13  C13   -58.99  30.0  3
 I0F  Var_09    H17  C17  N13  C13    62.52  30.0  3
 I0F  Var_10    H9M  C16  N13  C13  -178.50  30.0  3
 I0F  Var_11    H16  C16  N13  C13   -59.37  30.0  3
 I0F  Var_12    H9L  C16  N13  C13    62.14  30.0  3
 I0F  Var_13    C88  C8   C7   N1      6.77  30.0  2
 I0F  Var_14    C9   C8   C7   N1   -174.02  30.0  2
 I0F  Var_15    N88  C88  C8   C7     10.11  30.0  2
 I0F  Var_16    O7   C7   C8   C9      6.48  30.0  1
 I0F  Var_17    N88  C88  C8   C9   -169.06  30.0  2
 I0F  Var_18    O7   C7   C8   C88  -172.73  30.0  1
 I0F  Var_19    H9   C9   C8   C7     -1.14   0.0  2
 I0F  Var_20    H9   C9   C8   C88   178.03   0.0  2
 I0F  Var_21    H9M  C16  N13  C17     2.25  30.0  3
 I0F  Var_22    H16  C16  N13  C17   121.38  30.0  3
 I0F  Var_23    H9L  C16  N13  C17  -117.12  30.0  3
 I0F  Var_24    H9N  C17  N13  C16     1.07  30.0  3
 I0F  Var_25    H9O  C17  N13  C16   120.27  30.0  3
 I0F  Var_26    H17  C17  N13  C16  -118.23  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
 I0F  chir_01  C4  O4  C3  C5  negativ
 I0F  chir_02  C5  O5  C4  C6  negativ
 I0F  chir_03  C1  O5  N1  C2  negativ
 I0F  chir_04  C3  O3  C2  C4  positiv
 I0F  chir_05  C2  O2  C3  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
 I0F  plan-1  C10  0.020
 I0F  plan-1  C13  0.020
 I0F  plan-1  C15  0.020
 I0F  plan-1  N13  0.020
 I0F  plan-1  C14  0.020
 I0F  plan-1  C12  0.020
 I0F  plan-1  C11  0.020
 I0F  plan-1  C9   0.020
 I0F  plan-1  H15  0.020
 I0F  plan-1  H14  0.020
 I0F  plan-1  H12  0.020
 I0F  plan-1  H11  0.020
 I0F  plan-2  N1   0.020
 I0F  plan-2  C7   0.020
 I0F  plan-2  C8   0.020
 I0F  plan-2  O7   0.020
 I0F  plan-2  C1   0.020
 I0F  plan-2  H13  0.020
 I0F  plan-3  C13  0.020
 I0F  plan-3  C17  0.020
 I0F  plan-3  C16  0.020
 I0F  plan-3  N13  0.020
 I0F  plan-4  C7   0.020
 I0F  plan-4  C8   0.020
 I0F  plan-4  C10  0.020
 I0F  plan-4  C9   0.020
 I0F  plan-4  C88  0.020
 I0F  plan-4  H9   0.020

