# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 07:32:33 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: N-[2-(carbamimidamidooxy)ethyl]-2-{6-cyano-3-[(2,2-difluoro-2-pyridin-2-ylethyl)amino]-2-fluorophenyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)NOCCNC(=O)Cc1c(F)c(NCC(F)(F)c2ccccn2)ccc1C#N
#
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
 DKK  DKK  N-[2-(carbamimidamidooxy)ethyl]-2-{6-cyano-3-[(2,2-difluoro-2-pyridin-2-ylethyl)amino]-2-fluorophenyl}acetamide  ligand  51  31  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DKK
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
 DKK  C1    C  C     0   0.594   7.2833  -0.2656   1.0039
 DKK  O5    O  O2    0  -0.403   7.0826   1.0152  -0.9208
 DKK  C7    C  CH2   0  -0.296   5.0097   2.0929  -1.3834
 DKK  C9    C  C     0   0.554   2.9452   1.0620  -0.5857
 DKK  C11   C  CH2   0  -0.710   2.3882   0.0129   0.3726
 DKK  C12   C  CR6   0  -0.004   1.0823  -0.5338  -0.1102
 DKK  C13   C  CR6   0  -0.034   1.0186  -1.6618  -0.9482
 DKK  C14   C  CR16  0  -0.242  -0.2117  -2.1403  -1.3918
 DKK  C15   C  CR16  0  -0.364  -1.3874  -1.5208  -1.0206
 DKK  C16   C  CR6   0   0.285  -1.3689  -0.3972  -0.1833
 DKK  C19   C  CSP   0   0.011   2.2152  -2.3088  -1.3582
 DKK  C22   C  CH2   0  -0.363  -3.8119  -0.0756  -0.1704
 DKK  C30   C  CR16  0  -0.142  -8.4601   0.5372  -0.1321
 DKK  C31   C  CR16  0  -0.331  -7.1892   0.9396   0.2575
 DKK  N2    N  N     0  -0.709   6.0397  -0.5553   0.9303
 DKK  N3    N  NH2   0  -0.834   8.2080  -0.8298   1.8355
 DKK  N4    N  NH1   0  -0.383   7.8283   0.7254   0.1961
 DKK  C6    C  CH2   0  -0.184   6.4015   2.2645  -0.8150
 DKK  N8    N  NH1   0  -0.670   4.2756   1.1207  -0.6063
 DKK  O10   O  O     0  -0.500   2.2067   1.7899  -1.2370
 DKK  C17   C  CR6   0   0.455  -0.1048   0.0610   0.2282
 DKK  F18   F  F     0  -0.310  -0.0889   1.1464   1.0239
 DKK  N20   N  NS    0  -0.259   3.1871  -2.8341  -1.6923
 DKK  N21   N  NH1   0  -0.716  -2.4799   0.2465   0.2578
 DKK  C23   C  CT    0   0.771  -4.8257   0.2778   0.9019
 DKK  F24   F  F     0  -0.339  -4.5370  -0.3904   2.0518
 DKK  F25   F  F     0  -0.340  -4.7195   1.6035   1.2078
 DKK  C26   C  CR6   0   0.082  -6.2400  -0.0439   0.4838
 DKK  N27   N  N     0  -0.414  -6.4788  -1.3406   0.3345
 DKK  C28   C  CR16  0  -0.074  -7.6935  -1.7148  -0.0373
 DKK  C29   C  CR16  0  -0.315  -8.7217  -0.8137  -0.2813
 DKK  H7    H  HCH2  0   0.247   4.5069   3.0613  -1.3574
 DKK  H7A   H  HCH2  0   0.240   5.0672   1.7967  -2.4361
 DKK  H11   H  HCH2  0   0.283   3.1089  -0.7929   0.5206
 DKK  H11A  H  HCH2  0   0.313   2.2721   0.4891   1.3486
 DKK  H14   H  HCR6  0   0.281  -0.2503  -3.0037  -2.0416
 DKK  H15   H  HCR6  0   0.290  -2.3214  -1.9137  -1.3947
 DKK  H22   H  HCH2  0   0.274  -4.0941   0.4344  -1.0991
 DKK  H22A  H  HCH2  0   0.280  -3.9057  -1.1450  -0.3552
 DKK  H31   H  HCR6  0   0.281  -6.9603   1.9885   0.3764
 DKK  HN2   H  H     0   0.339   5.7759  -1.2411   1.6269
 DKK  HN3   H  HNH2  0   0.400   7.8480  -1.2933   2.6541
 DKK  HN3A  H  HNH2  0   0.395   9.0492  -0.3069   2.0240
 DKK  HN4   H  HNH1  0   0.397   8.7904   0.5687  -0.0779
 DKK  H6    H  HCH2  0   0.234   6.3509   2.5813   0.2289
 DKK  H6A   H  HCH2  0   0.239   6.9381   3.0341  -1.3785
 DKK  HN8   H  HNH1  0   0.450   4.8319   0.4336  -0.0734
 DKK  HN21  H  HNH1  0   0.402  -2.3430   1.1781   0.6165
 DKK  H28   H  HCR6  0   0.274  -7.8596  -2.7799  -0.1485
 DKK  H29   H  HCR6  0   0.279  -9.6966  -1.1690  -0.5839
 DKK  H30   H  HCR6  0   0.283  -9.2305   1.2736  -0.3165

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
 DKK  C1   N2    double    1.279  0.020  1.279
 DKK  C1   N3    single    1.366  0.020  1.366
 DKK  C1   N4    single    1.390  0.020  1.390
 DKK  O5   N4    single    1.374  0.020  1.374
 DKK  O5   C6    single    1.427  0.020  1.427
 DKK  C7   C6    single    1.513  0.020  1.513
 DKK  C7   N8    single    1.445  0.020  1.445
 DKK  C9   C11   single    1.526  0.020  1.526
 DKK  C9   N8    single    1.332  0.020  1.332
 DKK  C9   O10   double    1.225  0.020  1.225
 DKK  C11  C12   single    1.496  0.020  1.496
 DKK  C12  C13   aromatic  1.407  0.020  1.407
 DKK  C12  C17   aromatic  1.370  0.020  1.370
 DKK  C13  C14   aromatic  1.393  0.020  1.393
 DKK  C13  C19   single    1.421  0.020  1.421
 DKK  C14  C15   aromatic  1.380  0.020  1.380
 DKK  C15  C16   aromatic  1.401  0.020  1.401
 DKK  C16  C17   aromatic  1.406  0.020  1.406
 DKK  C16  N21   single    1.358  0.020  1.358
 DKK  C19  N20   triple    1.154  0.020  1.154
 DKK  C22  N21   single    1.436  0.020  1.436
 DKK  C22  C23   single    1.517  0.020  1.517
 DKK  C30  C31   aromatic  1.389  0.020  1.389
 DKK  C30  C29   aromatic  1.384  0.020  1.384
 DKK  C31  C26   aromatic  1.385  0.020  1.385
 DKK  C17  F18   single    1.346  0.020  1.346
 DKK  C23  F24   single    1.361  0.020  1.361
 DKK  C23  F25   single    1.365  0.020  1.365
 DKK  C23  C26   single    1.510  0.020  1.510
 DKK  C26  N27   aromatic  1.327  0.020  1.327
 DKK  N27  C28   aromatic  1.324  0.020  1.324
 DKK  C28  C29   aromatic  1.389  0.020  1.389
 DKK  C7   H7    single    0.970  0.020  1.090
 DKK  C7   H7A   single    0.970  0.020  1.090
 DKK  C11  H11   single    0.970  0.020  1.090
 DKK  C11  H11A  single    0.970  0.020  1.090
 DKK  C14  H14   single    0.930  0.020  1.080
 DKK  C15  H15   single    0.930  0.020  1.080
 DKK  C22  H22   single    0.970  0.020  1.090
 DKK  C22  H22A  single    0.970  0.020  1.090
 DKK  C30  H30   single    0.930  0.020  1.080
 DKK  C31  H31   single    0.930  0.020  1.080
 DKK  N2   HN2   single    0.890  0.020  1.040
 DKK  N3   HN3   single    0.890  0.020  1.040
 DKK  N3   HN3A  single    0.890  0.020  1.040
 DKK  N4   HN4   single    0.890  0.020  1.040
 DKK  C6   H6    single    0.970  0.020  1.090
 DKK  C6   H6A   single    0.970  0.020  1.090
 DKK  N8   HN8   single    0.860  0.020  1.020
 DKK  N21  HN21  single    0.890  0.020  1.040
 DKK  C28  H28   single    0.930  0.020  1.080
 DKK  C29  H29   single    0.930  0.020  1.080

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
 DKK  N4    C1   N3   112.52  3.000
 DKK  N4    C1   N2   120.62  3.000
 DKK  N3    C1   N2   126.86  3.000
 DKK  C6    O5   N4   112.55  3.000
 DKK  H7A   C7   H7   106.68  3.000
 DKK  H7A   C7   N8   111.20  3.000
 DKK  H7    C7   N8   110.49  3.000
 DKK  H7A   C7   C6   110.09  3.000
 DKK  H7    C7   C6   108.31  3.000
 DKK  N8    C7   C6   109.98  3.000
 DKK  O10   C9   N8   124.61  3.000
 DKK  O10   C9   C11  121.49  3.000
 DKK  N8    C9   C11  113.87  3.000
 DKK  H11A  C11  H11  105.72  3.000
 DKK  H11A  C11  C12  110.80  3.000
 DKK  H11   C11  C12  110.51  3.000
 DKK  H11A  C11  C9   107.47  3.000
 DKK  H11   C11  C9   110.59  3.000
 DKK  C12   C11  C9   111.55  3.000
 DKK  C17   C12  C13  117.13  3.000
 DKK  C17   C12  C11  121.19  3.000
 DKK  C13   C12  C11  121.66  3.000
 DKK  C19   C13  C14  119.72  3.000
 DKK  C19   C13  C12  119.93  3.000
 DKK  C14   C13  C12  120.34  3.000
 DKK  H14   C14  C15  119.33  3.000
 DKK  H14   C14  C13  119.82  3.000
 DKK  C15   C14  C13  120.85  3.000
 DKK  H15   C15  C16  120.66  3.000
 DKK  H15   C15  C14  118.70  3.000
 DKK  C16   C15  C14  120.63  3.000
 DKK  N21   C16  C17  119.08  3.000
 DKK  N21   C16  C15  124.30  3.000
 DKK  C17   C16  C15  116.61  3.000
 DKK  N20   C19  C13  180.00  3.000
 DKK  H22A  C22  H22  106.91  3.000
 DKK  H22A  C22  C23  106.92  3.000
 DKK  H22   C22  C23  108.56  3.000
 DKK  H22A  C22  N21  110.53  3.000
 DKK  H22   C22  N21  112.77  3.000
 DKK  C23   C22  N21  110.90  3.000
 DKK  H30   C30  C29  120.76  3.000
 DKK  H30   C30  C31  120.16  3.000
 DKK  C29   C30  C31  119.08  3.000
 DKK  H31   C31  C26  121.75  3.000
 DKK  H31   C31  C30  120.41  3.000
 DKK  C26   C31  C30  117.84  3.000
 DKK  HN2   N2   C1   111.54  3.000
 DKK  HN3A  N3   HN3  112.64  3.000
 DKK  HN3A  N3   C1   117.68  3.000
 DKK  HN3   N3   C1   116.29  3.000
 DKK  HN4   N4   O5   109.17  3.000
 DKK  HN4   N4   C1   114.80  3.000
 DKK  O5    N4   C1   114.21  3.000
 DKK  H6A   C6   H6   108.11  3.000
 DKK  H6A   C6   C7   109.72  3.000
 DKK  H6    C6   C7   110.45  3.000
 DKK  H6A   C6   O5   110.09  3.000
 DKK  H6    C6   O5   110.30  3.000
 DKK  C7    C6   O5   108.18  3.000
 DKK  HN8   N8   C9   120.07  3.000
 DKK  HN8   N8   C7   116.85  3.000
 DKK  C9    N8   C7   123.06  3.000
 DKK  F18   C17  C16  116.51  3.000
 DKK  F18   C17  C12  119.07  3.000
 DKK  C16   C17  C12  124.41  3.000
 DKK  HN21  N21  C22  116.08  3.000
 DKK  HN21  N21  C16  116.29  3.000
 DKK  C22   N21  C16  123.77  3.000
 DKK  C26   C23  F25  110.00  3.000
 DKK  C26   C23  F24  109.16  3.000
 DKK  F25   C23  F24  105.73  3.000
 DKK  C26   C23  C22  112.37  3.000
 DKK  F25   C23  C22  109.43  3.000
 DKK  F24   C23  C22  109.94  3.000
 DKK  N27   C26  C23  114.08  3.000
 DKK  N27   C26  C31  123.51  3.000
 DKK  C23   C26  C31  122.41  3.000
 DKK  C28   N27  C26  118.21  3.000
 DKK  H28   C28  C29  120.41  3.000
 DKK  H28   C28  N27  116.56  3.000
 DKK  C29   C28  N27  123.03  3.000
 DKK  H29   C29  C28  120.24  3.000
 DKK  H29   C29  C30  121.44  3.000
 DKK  C28   C29  C30  118.32  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
 DKK  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 DKK  CONST_02  C15  C16  C17  C12     0.00   0.0  0
 DKK  CONST_03  C16  C17  C12  C13     0.00   0.0  0
 DKK  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 DKK  CONST_05  C17  C12  C13  C14     0.00   0.0  0
 DKK  CONST_06  C17  C16  C15  C14     0.00   0.0  0
 DKK  CONST_07  N27  C26  C31  C30     0.00   0.0  0
 DKK  CONST_08  N27  C28  C29  C30     0.00   0.0  0
 DKK  CONST_09  C28  C29  C30  C31     0.00   0.0  0
 DKK  CONST_10  C28  N27  C26  C31     0.00   0.0  0
 DKK  CONST_11  C29  C30  C31  C26     0.00   0.0  0
 DKK  CONST_12  C29  C28  N27  C26     0.00   0.0  0
 DKK  CONST_13  C14  C13  C12  C11   180.00   0.0  0
 DKK  CONST_14  C16  C17  C12  C11   180.00   0.0  0
 DKK  CONST_15  N21  C16  C17  C12   180.00   0.0  0
 DKK  CONST_16  F18  C17  C12  C13   180.00   0.0  0
 DKK  CONST_17  N21  C16  C15  C14   180.00   0.0  0
 DKK  CONST_18  C19  C13  C14  C15   180.00   0.0  0
 DKK  CONST_19  F18  C17  C16  C15   180.00   0.0  0
 DKK  CONST_20  C17  C12  C13  C19   180.00   0.0  0
 DKK  CONST_21  C23  C26  C31  C30   180.00   0.0  0
 DKK  CONST_22  C28  N27  C26  C23   180.00   0.0  0
 DKK  CONST_23  H14  C14  C13  C12   180.00   0.0  0
 DKK  CONST_24  H15  C15  C14  C13   180.00   0.0  0
 DKK  CONST_25  H28  C28  C29  C30   180.00   0.0  0
 DKK  CONST_26  H29  C29  C30  C31   180.00   0.0  0
 DKK  CONST_27  H30  C30  C31  C26   180.00   0.0  0
 DKK  CONST_28  H31  C31  C26  N27   180.00   0.0  0
 DKK  CONST_29  C22  N21  C16  C15     0.00   0.0  0
 DKK  CONST_30  C17  C16  N21  C22   180.00   0.0  0
 DKK  CONST_32  C11  C9   N8   C7    180.00   0.0  0
 DKK  CONST_33  O10  C9   N8   C7      0.00   0.0  0
 DKK  CONST_36  HN8  N8   C9   C11     0.00   0.0  0
 DKK  CONST_40  HN2  N2   C1   N3      0.00   0.0  0
 DKK  Var_01    C13  C12  C11  C9     90.06  30.0  2
 DKK  Var_02    C31  C26  C23  C22  -112.89  30.0  2
 DKK  Var_03    N8   C9   C11  C12  -149.73  30.0  2
 DKK  Var_04    C23  C22  N21  C16   152.43  30.0  2
 DKK  Var_05    C26  C23  C22  N21   179.82  30.0  3
 DKK  Var_06    N8   C7   C6   O5     62.43  30.0  2
 DKK  Var_07    C6   C7   N8   C9    158.25  30.0  2
 DKK  Var_08    H6   C6   O5   N4    -17.98  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
 DKK  plan-1  C11   0.020
 DKK  plan-1  C12   0.020
 DKK  plan-1  C13   0.020
 DKK  plan-1  C14   0.020
 DKK  plan-1  C15   0.020
 DKK  plan-1  C16   0.020
 DKK  plan-1  C19   0.020
 DKK  plan-1  C17   0.020
 DKK  plan-1  F18   0.020
 DKK  plan-1  N20   0.020
 DKK  plan-1  N21   0.020
 DKK  plan-1  H14   0.020
 DKK  plan-1  H15   0.020
 DKK  plan-2  C30   0.020
 DKK  plan-2  C31   0.020
 DKK  plan-2  C23   0.020
 DKK  plan-2  C26   0.020
 DKK  plan-2  N27   0.020
 DKK  plan-2  C28   0.020
 DKK  plan-2  C29   0.020
 DKK  plan-2  H31   0.020
 DKK  plan-2  H28   0.020
 DKK  plan-2  H29   0.020
 DKK  plan-2  H30   0.020
 DKK  plan-3  C7    0.020
 DKK  plan-3  C9    0.020
 DKK  plan-3  C11   0.020
 DKK  plan-3  N8    0.020
 DKK  plan-3  O10   0.020
 DKK  plan-3  HN8   0.020
 DKK  plan-4  C16   0.020
 DKK  plan-4  C22   0.020
 DKK  plan-4  N21   0.020
 DKK  plan-4  HN21  0.020
 DKK  plan-5  C1    0.020
 DKK  plan-5  O5    0.020
 DKK  plan-5  N2    0.020
 DKK  plan-5  N3    0.020
 DKK  plan-5  N4    0.020
 DKK  plan-5  HN2   0.020
 DKK  plan-5  HN3   0.020
 DKK  plan-5  HN3A  0.020
 DKK  plan-5  HN4   0.020

