# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 19:43:03 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)-5-[(2-hydroxyethoxy)methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCOCc1cc(C(=O)NOCCO)c(Nc2ccc(I)cc2F)c(F)c1F
#
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
 MEK  MEK  3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)-5-[(2-hydroxyethoxy)methyl]benzamide  ligand  47  29  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MEK
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
 MEK  N1    N  NH1   0  -0.347  -1.4932   1.6838   0.0779
 MEK  C4    C  CR6   0  -0.234   3.1454   0.8673   0.3803
 MEK  C5    C  CR16  0  -0.376   3.1198   0.3272   1.6596
 MEK  C6    C  CR6   0   0.495   2.0841  -0.5166   1.9925
 MEK  C7    C  CR6   0  -0.086  -1.9350  -0.5706   0.6697
 MEK  C8    C  CR16  0  -0.332  -3.2064  -0.6594   0.1112
 MEK  C10   C  CR6   0   0.419  -3.1065  -3.0162   0.1963
 MEK  C13   C  C     0   0.493  -1.4111   0.7739   1.0658
 MEK  C15   C  CH2   0  -0.193  -1.4014   5.1867   0.9088
 MEK  F3    F  F     0  -0.296  -3.6439  -4.2215  -0.0119
 MEK  C9    C  CR6   0  -0.186  -3.8221  -1.8793  -0.1327
 MEK  C16   C  CH2   0  -0.125  -5.2090  -2.0050  -0.6989
 MEK  O4    O  O2    0  -0.487  -5.6888  -0.7367  -1.0312
 MEK  C18   C  CH2   0  -0.185  -7.4419   0.6273  -1.8992
 MEK  O5    O  OH1   0  -0.671  -6.6528   1.1101  -2.9615
 MEK  C11   C  CR6   0   0.359  -1.8303  -2.9495   0.7146
 MEK  F2    F  F     0  -0.298  -1.1745  -4.0853   0.9721
 MEK  C12   C  CR6   0   0.168  -1.2100  -1.7315   0.9727
 MEK  N2    N  NH1   0  -0.778   0.0663  -1.7256   1.5009
 MEK  C1    C  CR6   0   0.177   1.0750  -0.8696   1.0989
 MEK  C2    C  CR16  0  -0.293   1.1486  -0.3309  -0.1836
 MEK  C3    C  CR16  0  -0.222   2.1637   0.5431  -0.5420
 MEK  I1    I  I     0   0.062   4.6928   2.1826  -0.1525
 MEK  O1    O  O     0  -0.444  -1.0032   1.0184   2.1845
 MEK  O2    O  O2    0  -0.380  -1.0012   2.9317   0.2738
 MEK  C14   C  CH2   0  -0.173  -2.0332   3.8436   0.6580
 MEK  O3    O  OH1   0  -0.670  -0.8955   5.7026  -0.2995
 MEK  HN1   H  HNH1  0   0.421  -1.6768   1.4358  -0.8852
 MEK  H5    H  HCR6  0   0.300   3.8711   0.5619   2.4022
 MEK  H8    H  HCR6  0   0.279  -3.7486   0.2517  -0.0994
 MEK  H15   H  HCH2  0   0.213  -2.1800   5.8283   1.3397
 MEK  H15A  H  HCH2  0   0.211  -0.6188   5.0823   1.6709
 MEK  H17   H  HCH2  0   0.209  -7.0595  -1.4200  -2.4242
 MEK  H17A  H  HCH2  0   0.212  -7.6999  -1.1737  -0.7970
 MEK  H16   H  HCH2  0   0.230  -5.1931  -2.6613  -1.5809
 MEK  H16A  H  HCH2  0   0.231  -5.8637  -2.4933   0.0382
 MEK  H18   H  HCH2  0   0.205  -8.5044   0.5734  -2.1677
 MEK  H18A  H  HCH2  0   0.203  -7.3704   1.2696  -1.0120
 MEK  HO5   H  HOH1  0   0.456  -6.9491   1.9993  -3.1739
 MEK  HN2   H  HNH1  0   0.408   0.3075  -2.4652   2.1410
 MEK  H2    H  HCR6  0   0.295   0.4082  -0.6029  -0.9248
 MEK  H3    H  HCR6  0   0.282   2.1805   0.9454  -1.5451
 MEK  H14   H  HCH2  0   0.231  -2.5188   3.5052   1.5775
 MEK  H14A  H  HCH2  0   0.229  -2.7932   3.9109  -0.1278
 MEK  HO3   H  HOH1  0   0.458  -0.4779   6.5475  -0.1113
 MEK  F1    F  F     0  -0.307   2.0394  -1.0309   3.2308
 MEK  C17   C  CH2   0  -0.162  -7.0016  -0.7680  -1.5414

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
 MEK  N1   O2    single    1.356  0.020  1.356
 MEK  N1   C13   single    1.346  0.020  1.346
 MEK  N1   HN1   single    0.860  0.020  1.020
 MEK  C3   C4    aromatic  1.385  0.020  1.385
 MEK  C4   I1    single    2.100  0.020  2.100
 MEK  C4   C5    aromatic  1.389  0.020  1.389
 MEK  C6   C5    aromatic  1.377  0.020  1.377
 MEK  C5   H5    single    0.930  0.020  1.080
 MEK  C1   C6    aromatic  1.393  0.020  1.393
 MEK  C6   F1    single    1.342  0.020  1.342
 MEK  C8   C7    aromatic  1.391  0.020  1.391
 MEK  C7   C13   single    1.496  0.020  1.496
 MEK  C7   C12   aromatic  1.402  0.020  1.402
 MEK  C9   C8    aromatic  1.388  0.020  1.388
 MEK  C8   H8    single    0.930  0.020  1.080
 MEK  C9   C10   aromatic  1.383  0.020  1.383
 MEK  F3   C10   single    1.336  0.020  1.336
 MEK  C10  C11   aromatic  1.379  0.020  1.379
 MEK  C13  O1    double    1.216  0.020  1.216
 MEK  C14  C15   single    1.505  0.020  1.505
 MEK  C15  O3    single    1.408  0.020  1.408
 MEK  C15  H15   single    0.970  0.020  1.090
 MEK  C15  H15A  single    0.970  0.020  1.090
 MEK  C18  C17   single    1.506  0.020  1.506
 MEK  C17  O4    single    1.409  0.020  1.409
 MEK  C17  H17   single    0.970  0.020  1.090
 MEK  C17  H17A  single    0.970  0.020  1.090
 MEK  C16  C9    single    1.503  0.020  1.503
 MEK  O4   C16   single    1.396  0.020  1.396
 MEK  C16  H16   single    0.970  0.020  1.090
 MEK  C16  H16A  single    0.970  0.020  1.090
 MEK  O5   C18   single    1.409  0.020  1.409
 MEK  C18  H18   single    0.970  0.020  1.090
 MEK  C18  H18A  single    0.970  0.020  1.090
 MEK  O5   HO5   single    0.850  0.020  0.980
 MEK  C11  C12   aromatic  1.391  0.020  1.391
 MEK  C11  F2    single    1.337  0.020  1.337
 MEK  C12  N2    single    1.381  0.020  1.381
 MEK  N2   C1    single    1.383  0.020  1.383
 MEK  N2   HN2   single    0.860  0.020  1.020
 MEK  C2   C1    aromatic  1.393  0.020  1.393
 MEK  C2   C3    aromatic  1.387  0.020  1.387
 MEK  C2   H2    single    0.930  0.020  1.080
 MEK  C3   H3    single    0.930  0.020  1.080
 MEK  C14  O2    single    1.430  0.020  1.430
 MEK  C14  H14   single    0.970  0.020  1.090
 MEK  C14  H14A  single    0.970  0.020  1.090
 MEK  O3   HO3   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
 MEK  HN1   N1   O2   115.42  3.000
 MEK  HN1   N1   C13  122.99  3.000
 MEK  O2    N1   C13  119.62  3.000
 MEK  I1    C4   C3   119.99  3.000
 MEK  I1    C4   C5   119.40  3.000
 MEK  C3    C4   C5   120.61  3.000
 MEK  H5    C5   C6   119.29  3.000
 MEK  H5    C5   C4   122.34  3.000
 MEK  C6    C5   C4   118.35  3.000
 MEK  F1    C6   C1   118.08  3.000
 MEK  F1    C6   C5   118.90  3.000
 MEK  C1    C6   C5   123.02  3.000
 MEK  C12   C7   C13  120.39  3.000
 MEK  C12   C7   C8   120.42  3.000
 MEK  C13   C7   C8   118.92  3.000
 MEK  H8    C8   C9   118.95  3.000
 MEK  H8    C8   C7   118.86  3.000
 MEK  C9    C8   C7   122.14  3.000
 MEK  C11   C10  C9   121.90  3.000
 MEK  C11   C10  F3   118.32  3.000
 MEK  C9    C10  F3   119.76  3.000
 MEK  O1    C13  C7   122.81  3.000
 MEK  O1    C13  N1   124.07  3.000
 MEK  C7    C13  N1   113.07  3.000
 MEK  H15A  C15  H15  106.80  3.000
 MEK  H15A  C15  O3   112.00  3.000
 MEK  H15   C15  O3   112.19  3.000
 MEK  H15A  C15  C14  109.28  3.000
 MEK  H15   C15  C14  106.82  3.000
 MEK  O3    C15  C14  109.56  3.000
 MEK  C16   C9   C10  119.88  3.000
 MEK  C16   C9   C8   123.29  3.000
 MEK  C10   C9   C8   116.82  3.000
 MEK  H16A  C16  H16  106.33  3.000
 MEK  H16A  C16  O4   110.98  3.000
 MEK  H16   C16  O4   110.87  3.000
 MEK  H16A  C16  C9   109.50  3.000
 MEK  H16   C16  C9   109.80  3.000
 MEK  O4    C16  C9   109.31  3.000
 MEK  C16   O4   C17  112.72  3.000
 MEK  H18A  C18  H18  106.84  3.000
 MEK  H18A  C18  O5   111.87  3.000
 MEK  H18   C18  O5   112.01  3.000
 MEK  H18A  C18  C17  109.33  3.000
 MEK  H18   C18  C17  107.20  3.000
 MEK  O5    C18  C17  109.44  3.000
 MEK  HO5   O5   C18  108.13  3.000
 MEK  C12   C11  F2   119.31  3.000
 MEK  F2    C11  C10  119.04  3.000
 MEK  C12   C11  C10  121.65  3.000
 MEK  N2    C12  C11  119.13  3.000
 MEK  N2    C12  C7   123.84  3.000
 MEK  C11   C12  C7   117.03  3.000
 MEK  HN2   N2   C1   117.68  3.000
 MEK  HN2   N2   C12  117.45  3.000
 MEK  C1    N2   C12  124.44  3.000
 MEK  C2    C1   N2   123.07  3.000
 MEK  C2    C1   C6   117.02  3.000
 MEK  N2    C1   C6   119.91  3.000
 MEK  H2    C2   C3   118.83  3.000
 MEK  H2    C2   C1   119.81  3.000
 MEK  C3    C2   C1   121.36  3.000
 MEK  H3    C3   C2   119.06  3.000
 MEK  H3    C3   C4   121.31  3.000
 MEK  C2    C3   C4   119.61  3.000
 MEK  C14   O2   N1   111.35  3.000
 MEK  H14A  C14  H14  108.31  3.000
 MEK  H14A  C14  O2   110.32  3.000
 MEK  H14   C14  O2   110.44  3.000
 MEK  H14A  C14  C15  110.85  3.000
 MEK  H14   C14  C15  108.81  3.000
 MEK  O2    C14  C15  108.11  3.000
 MEK  HO3   O3   C15  108.08  3.000
 MEK  H17A  C17  H17  106.96  3.000
 MEK  H17A  C17  C18  108.50  3.000
 MEK  H17   C17  C18  110.08  3.000
 MEK  H17A  C17  O4   110.80  3.000
 MEK  H17   C17  O4   110.68  3.000
 MEK  C18   C17  O4   109.75  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
 MEK  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 MEK  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 MEK  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 MEK  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 MEK  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 MEK  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 MEK  CONST_07  C10  C9   C8   C7      0.00   0.0  0
 MEK  CONST_08  C10  C11  C12  C7      0.00   0.0  0
 MEK  CONST_09  C11  C12  C7   C8      0.00   0.0  0
 MEK  CONST_10  C11  C10  C9   C8      0.00   0.0  0
 MEK  CONST_11  C12  C7   C8   C9      0.00   0.0  0
 MEK  CONST_12  C12  C11  C10  C9      0.00   0.0  0
 MEK  CONST_13  F1   C6   C5   C4    180.00   0.0  0
 MEK  CONST_14  N2   C1   C6   C5    180.00   0.0  0
 MEK  CONST_15  I1   C4   C5   C6    180.00   0.0  0
 MEK  CONST_16  C16  C9   C8   C7    180.00   0.0  0
 MEK  CONST_17  F2   C11  C12  C7    180.00   0.0  0
 MEK  CONST_18  N2   C12  C7   C8    180.00   0.0  0
 MEK  CONST_19  F3   C10  C9   C8    180.00   0.0  0
 MEK  CONST_20  N2   C12  C11  C10   180.00   0.0  0
 MEK  CONST_21  C9   C8   C7   C13   180.00   0.0  0
 MEK  CONST_22  C11  C12  C7   C13   180.00   0.0  0
 MEK  CONST_23  C12  C11  C10  F3    180.00   0.0  0
 MEK  CONST_24  F2   C11  C10  C9    180.00   0.0  0
 MEK  CONST_25  C11  C10  C9   C16   180.00   0.0  0
 MEK  CONST_26  C3   C2   C1   N2    180.00   0.0  0
 MEK  CONST_27  C2   C1   C6   F1    180.00   0.0  0
 MEK  CONST_28  I1   C4   C3   C2    180.00   0.0  0
 MEK  CONST_29  H2   C2   C3   C4    180.00   0.0  0
 MEK  CONST_30  H3   C3   C4   C5    180.00   0.0  0
 MEK  CONST_31  H8   C8   C9   C10   180.00   0.0  0
 MEK  CONST_32  H5   C5   C6   C1    180.00   0.0  0
 MEK  CONST_33  O2   N1   C13  C7    180.00   0.0  0
 MEK  CONST_34  HN1  N1   C13  C7      0.00   0.0  0
 MEK  CONST_35  O2   N1   C13  O1      0.00   0.0  0
 MEK  Var_01    C12  N2   C1   C6    152.40  30.0  2
 MEK  Var_02    C1   N2   C12  C7    -41.48  30.0  2
 MEK  Var_03    C8   C7   C13  N1    -51.92  30.0  2
 MEK  Var_04    O4   C16  C9   C8      5.16  30.0  1
 MEK  Var_05    C9   C16  O4   C17  -178.59  30.0  3
 MEK  Var_06    C15  C14  O2   N1    177.78  30.0  1
 MEK  Var_07    C18  C17  O4   C16  -179.01  30.0  1
 MEK  Var_08    O5   C18  C17  O4     65.44  30.0  1
 MEK  Var_09    O3   C15  C14  O2     66.27  30.0  3

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
 MEK  plan-1  C7   0.020
 MEK  plan-1  C8   0.020
 MEK  plan-1  C10  0.020
 MEK  plan-1  C13  0.020
 MEK  plan-1  F3   0.020
 MEK  plan-1  C9   0.020
 MEK  plan-1  C16  0.020
 MEK  plan-1  C11  0.020
 MEK  plan-1  F2   0.020
 MEK  plan-1  C12  0.020
 MEK  plan-1  N2   0.020
 MEK  plan-1  H8   0.020
 MEK  plan-2  C4   0.020
 MEK  plan-2  C5   0.020
 MEK  plan-2  C6   0.020
 MEK  plan-2  N2   0.020
 MEK  plan-2  C1   0.020
 MEK  plan-2  C2   0.020
 MEK  plan-2  C3   0.020
 MEK  plan-2  I1   0.020
 MEK  plan-2  H5   0.020
 MEK  plan-2  H2   0.020
 MEK  plan-2  H3   0.020
 MEK  plan-2  F1   0.020
 MEK  plan-3  N1   0.020
 MEK  plan-3  C7   0.020
 MEK  plan-3  C13  0.020
 MEK  plan-3  O1   0.020
 MEK  plan-3  O2   0.020
 MEK  plan-3  HN1  0.020

