# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 21:13:20 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 6-[2-(2,3-difluoro-5-{2-[(3S)-4-methylmorpholin-3-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCOC[C@@H]1CCc2cc(F)c(F)c(CCc3cc(C)cc(N)n3)c2
#
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
 KND  KND  6-[2-(2,3-difluoro-5-{2-[(3S)-4-methylmorpholin-3-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine  ligand  54  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KND
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
 KND  C14  C  CR16  0  -0.481   1.4969   2.3858   0.7485
 KND  C15  C  CR6   0   0.165   1.5061   0.9940   0.7011
 KND  C18  C  CH2   0  -0.454   3.6331   0.0365  -0.2184
 KND  C17  C  CH2   0  -0.534   2.7599   0.2316   1.0258
 KND  C16  C  CR16  0  -0.370   0.3512   0.3289   0.3041
 KND  C22  C  CH2   0  -0.164   4.8945  -1.8404   0.8533
 KND  C23  C  CH1   0  -0.071   5.0216  -0.5257   0.0882
 KND  C13  C  CR6   0   0.426   0.3486   3.0668   0.4072
 KND  C12  C  CR6   0   0.356  -0.7917   2.3887   0.0163
 KND  C11  C  CR6   0  -0.046  -0.8147   1.0060  -0.0467
 KND  C25  C  CH2   0  -0.303   7.0657  -1.3820  -0.8210
 KND  C26  C  CH2   0  -0.190   6.8615  -2.6688  -0.0540
 KND  C02  C  CR6   0   0.440  -6.2069  -0.4300  -0.9546
 KND  C03  C  CR16  0  -0.446  -6.6379  -1.6936  -0.5134
 KND  C04  C  CR6   0   0.205  -5.8522  -2.3963   0.3764
 KND  C05  C  CR16  0  -0.436  -4.6540  -1.8114   0.8034
 KND  C06  C  CR6   0   0.276  -4.3099  -0.5605   0.3241
 KND  C09  C  CH2   0  -0.503  -2.0639   0.2704  -0.4380
 KND  F12  F  F     0  -0.306  -1.8865   3.0975  -0.2981
 KND  F13  F  F     0  -0.310   0.3185   4.4044   0.4545
 KND  N01  N  N     0  -0.482  -5.0711   0.1172  -0.5374
 KND  N02  N  NH2   0  -0.839  -6.9339   0.2717  -1.8734
 KND  N24  N  NT    0  -0.425   5.7879  -0.7642  -1.1324
 KND  O21  O  O2    0  -0.487   6.1376  -2.4364   1.1323
 KND  H1   H  HCR6  0   0.279   2.3763   2.9400   1.0537
 KND  H2   H  HCH2  0   0.232   3.1241  -0.6247  -0.9270
 KND  H3   H  HCH2  0   0.252   3.7320   1.0059  -0.7106
 KND  H4   H  HCH2  0   0.250   3.3312   0.7669   1.7895
 KND  H5   H  HCH2  0   0.254   2.4852  -0.7328   1.4569
 KND  H6   H  HCR6  0   0.252   0.3497  -0.7547   0.2639
 KND  H7   H  HCH2  0   0.237   4.4117  -1.6717   1.8162
 KND  H8   H  HCH2  0   0.195   4.2577  -2.5254   0.2709
 KND  H9   H  HCH1  0   0.195   5.5504   0.1999   0.7374
 KND  H10  H  HCH2  0   0.194   7.7161  -0.7059  -0.2380
 KND  H11  H  HCH2  0   0.240   7.5904  -1.6063  -1.7531
 KND  H12  H  HCH2  0   0.199   6.3360  -3.3963  -0.6897
 KND  H13  H  HCH2  0   0.235   7.8238  -3.1001   0.2263
 KND  H17  H  HCR6  0   0.255  -7.5758  -2.1027  -0.8698
 KND  H18  H  HCR6  0   0.244  -4.0091  -2.3261   1.5047
 KND  H19  H  HCH3  0   0.254  -5.6671  -4.5285   0.3632
 KND  H20  H  HCH3  0   0.249  -6.0754  -3.8604   1.9331
 KND  H21  H  HCH3  0   0.247  -7.3057  -3.9591   0.6688
 KND  H24  H  HCH2  0   0.259  -2.5750   0.7821  -1.2549
 KND  H25  H  HCH2  0   0.258  -1.7891  -0.7186  -0.8098
 KND  H26  H  HNH2  0   0.388  -7.9110   0.0481  -1.9614
 KND  H27  H  HNH2  0   0.379  -6.7315   1.2558  -1.9389
 KND  C27  C  CH3   0  -0.530   5.9934   0.4314  -1.9235
 KND  C08  C  CH2   0  -0.487  -3.0339   0.1148   0.7416
 KND  C07  C  CH3   0  -0.726  -6.2538  -3.7554   0.8629
 KND  H14  H  HCH3  0   0.237   6.6411   0.1957  -2.7685
 KND  H15  H  HCH3  0   0.240   5.0564   0.8066  -2.3323
 KND  H16  H  HCH3  0   0.194   6.4679   1.2472  -1.3565
 KND  H22  H  HCH2  0   0.251  -3.2722   1.1000   1.1503
 KND  H23  H  HCH2  0   0.250  -2.5512  -0.4553   1.5373

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
 KND  C26  O21  single    1.409  0.020  1.409
 KND  C26  C25  single    1.512  0.020  1.512
 KND  O21  C22  single    1.407  0.020  1.407
 KND  C25  N24  single    1.453  0.020  1.453
 KND  C22  C23  single    1.526  0.020  1.526
 KND  N24  C23  single    1.461  0.020  1.461
 KND  N24  C27  single    1.448  0.020  1.448
 KND  C23  C18  single    1.529  0.020  1.529
 KND  C17  C18  single    1.533  0.020  1.533
 KND  C17  C15  single    1.503  0.020  1.503
 KND  C15  C16  aromatic  1.391  0.020  1.391
 KND  C15  C14  aromatic  1.393  0.020  1.393
 KND  C16  C11  aromatic  1.393  0.020  1.393
 KND  C14  C13  aromatic  1.378  0.020  1.378
 KND  C08  C06  single    1.503  0.020  1.503
 KND  C08  C09  single    1.535  0.020  1.535
 KND  N02  C02  single    1.366  0.020  1.366
 KND  N01  C06  aromatic  1.335  0.020  1.335
 KND  N01  C02  aromatic  1.328  0.020  1.328
 KND  C11  C09  single    1.502  0.020  1.502
 KND  C11  C12  aromatic  1.384  0.020  1.384
 KND  C06  C05  aromatic  1.383  0.020  1.383
 KND  C02  C03  aromatic  1.406  0.020  1.406
 KND  C13  C12  aromatic  1.383  0.020  1.383
 KND  C13  F13  single    1.339  0.020  1.339
 KND  C12  F12  single    1.342  0.020  1.342
 KND  C05  C04  aromatic  1.400  0.020  1.400
 KND  C03  C04  aromatic  1.379  0.020  1.379
 KND  C04  C07  single    1.498  0.020  1.498
 KND  C14  H1   single    0.930  0.020  1.080
 KND  C18  H2   single    0.970  0.020  1.090
 KND  C18  H3   single    0.970  0.020  1.090
 KND  C17  H4   single    0.970  0.020  1.090
 KND  C17  H5   single    0.970  0.020  1.090
 KND  C16  H6   single    0.930  0.020  1.080
 KND  C22  H7   single    0.970  0.020  1.090
 KND  C22  H8   single    0.970  0.020  1.090
 KND  C23  H9   single    0.970  0.020  1.090
 KND  C25  H10  single    0.970  0.020  1.090
 KND  C25  H11  single    0.970  0.020  1.090
 KND  C26  H12  single    0.970  0.020  1.090
 KND  C26  H13  single    0.970  0.020  1.090
 KND  C27  H14  single    0.970  0.020  1.090
 KND  C27  H15  single    0.970  0.020  1.090
 KND  C27  H16  single    0.970  0.020  1.090
 KND  C03  H17  single    0.930  0.020  1.080
 KND  C05  H18  single    0.930  0.020  1.080
 KND  C07  H19  single    0.970  0.020  1.090
 KND  C07  H20  single    0.970  0.020  1.090
 KND  C07  H21  single    0.970  0.020  1.090
 KND  C08  H22  single    0.970  0.020  1.090
 KND  C08  H23  single    0.970  0.020  1.090
 KND  C09  H24  single    0.970  0.020  1.090
 KND  C09  H25  single    0.970  0.020  1.090
 KND  N02  H26  single    0.890  0.020  1.040
 KND  N02  H27  single    0.890  0.020  1.040

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
 KND  H1   C14  C13  119.56  3.000
 KND  H1   C14  C15  121.03  3.000
 KND  C13  C14  C15  119.41  3.000
 KND  C16  C15  C17  120.79  3.000
 KND  C16  C15  C14  118.83  3.000
 KND  C17  C15  C14  120.34  3.000
 KND  H3   C18  H2   106.66  3.000
 KND  H3   C18  C23  109.55  3.000
 KND  H2   C18  C23  109.27  3.000
 KND  H3   C18  C17  107.73  3.000
 KND  H2   C18  C17  109.72  3.000
 KND  C23  C18  C17  113.66  3.000
 KND  H5   C17  H4   106.74  3.000
 KND  H5   C17  C18  110.59  3.000
 KND  H4   C17  C18  109.36  3.000
 KND  H5   C17  C15  108.89  3.000
 KND  H4   C17  C15  109.77  3.000
 KND  C18  C17  C15  111.38  3.000
 KND  H6   C16  C11  118.37  3.000
 KND  H6   C16  C15  119.32  3.000
 KND  C11  C16  C15  122.31  3.000
 KND  H8   C22  H7   107.88  3.000
 KND  H8   C22  O21  110.62  3.000
 KND  H7   C22  O21  106.36  3.000
 KND  H8   C22  C23  108.58  3.000
 KND  H7   C22  C23  110.26  3.000
 KND  O21  C22  C23  113.00  3.000
 KND  H9   C23  N24  110.26  3.000
 KND  H9   C23  C22  108.07  3.000
 KND  N24  C23  C22  108.78  3.000
 KND  H9   C23  C18  108.06  3.000
 KND  N24  C23  C18  111.64  3.000
 KND  C22  C23  C18  109.97  3.000
 KND  F13  C13  C12  118.77  3.000
 KND  F13  C13  C14  120.25  3.000
 KND  C12  C13  C14  120.98  3.000
 KND  F12  C12  C11  120.23  3.000
 KND  F12  C12  C13  118.69  3.000
 KND  C11  C12  C13  121.08  3.000
 KND  C09  C11  C12  121.00  3.000
 KND  C12  C11  C16  117.39  3.000
 KND  C09  C11  C16  121.59  3.000
 KND  H11  C25  H10  107.04  3.000
 KND  H11  C25  N24  109.07  3.000
 KND  H10  C25  N24  111.76  3.000
 KND  H11  C25  C26  108.83  3.000
 KND  H10  C25  C26  109.44  3.000
 KND  N24  C25  C26  110.59  3.000
 KND  H13  C26  H12  107.97  3.000
 KND  H13  C26  O21  107.58  3.000
 KND  H12  C26  O21  110.51  3.000
 KND  H13  C26  C25  110.34  3.000
 KND  H12  C26  C25  109.53  3.000
 KND  O21  C26  C25  110.86  3.000
 KND  N02  C02  N01  117.06  3.000
 KND  N01  C02  C03  122.27  3.000
 KND  N02  C02  C03  120.64  3.000
 KND  H17  C03  C04  120.85  3.000
 KND  H17  C03  C02  120.09  3.000
 KND  C04  C03  C02  119.06  3.000
 KND  C07  C04  C05  120.62  3.000
 KND  C07  C04  C03  121.26  3.000
 KND  C05  C04  C03  118.12  3.000
 KND  H18  C05  C06  120.41  3.000
 KND  H18  C05  C04  120.57  3.000
 KND  C06  C05  C04  119.02  3.000
 KND  N01  C06  C08  115.81  3.000
 KND  N01  C06  C05  122.76  3.000
 KND  C08  C06  C05  121.42  3.000
 KND  H25  C09  H24  106.72  3.000
 KND  H25  C09  C08  109.20  3.000
 KND  H24  C09  C08  109.08  3.000
 KND  H25  C09  C11  108.85  3.000
 KND  H24  C09  C11  110.80  3.000
 KND  C08  C09  C11  112.03  3.000
 KND  C06  N01  C02  118.77  3.000
 KND  H27  N02  H26  114.00  3.000
 KND  H27  N02  C02  116.04  3.000
 KND  H26  N02  C02  117.49  3.000
 KND  C27  N24  C25  110.08  3.000
 KND  C27  N24  C23  113.33  3.000
 KND  C25  N24  C23  110.59  3.000
 KND  C26  O21  C22  110.91  3.000
 KND  H16  C27  H15  108.00  3.000
 KND  H16  C27  H14  107.65  3.000
 KND  H15  C27  H14  107.14  3.000
 KND  H16  C27  N24  113.05  3.000
 KND  H15  C27  N24  111.55  3.000
 KND  H14  C27  N24  109.21  3.000
 KND  H23  C08  H22  107.13  3.000
 KND  H23  C08  C09  109.50  3.000
 KND  H22  C08  C09  109.50  3.000
 KND  H23  C08  C06  110.08  3.000
 KND  H22  C08  C06  108.89  3.000
 KND  C09  C08  C06  111.63  3.000
 KND  H21  C07  H20  108.36  3.000
 KND  H21  C07  H19  107.76  3.000
 KND  H20  C07  H19  107.05  3.000
 KND  H21  C07  C04  111.76  3.000
 KND  H20  C07  C04  111.24  3.000
 KND  H19  C07  C04  110.47  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
 KND  CONST_01  C11  C16  C15  C14     0.00   0.0  0
 KND  CONST_02  C11  C12  C13  C14     0.00   0.0  0
 KND  CONST_03  C12  C11  C16  C15     0.00   0.0  0
 KND  CONST_04  C12  C13  C14  C15     0.00   0.0  0
 KND  CONST_05  C13  C14  C15  C16     0.00   0.0  0
 KND  CONST_06  C13  C12  C11  C16     0.00   0.0  0
 KND  CONST_07  C05  C06  N01  C02     0.00   0.0  0
 KND  CONST_08  C05  C04  C03  C02     0.00   0.0  0
 KND  CONST_09  C06  N01  C02  C03     0.00   0.0  0
 KND  CONST_10  C06  C05  C04  C03     0.00   0.0  0
 KND  CONST_11  N01  C06  C05  C04     0.00   0.0  0
 KND  CONST_12  N01  C02  C03  C04     0.00   0.0  0
 KND  CONST_13  F12  C12  C13  C14   180.00   0.0  0
 KND  CONST_14  C09  C11  C16  C15   180.00   0.0  0
 KND  CONST_15  F13  C13  C14  C15   180.00   0.0  0
 KND  CONST_16  C11  C16  C15  C17   180.00   0.0  0
 KND  CONST_17  C13  C14  C15  C17   180.00   0.0  0
 KND  CONST_18  F12  C12  C11  C16   180.00   0.0  0
 KND  CONST_19  C09  C11  C12  C13   180.00   0.0  0
 KND  CONST_20  F13  C13  C12  C11   180.00   0.0  0
 KND  CONST_21  C08  C06  N01  C02   180.00   0.0  0
 KND  CONST_22  C07  C04  C03  C02   180.00   0.0  0
 KND  CONST_23  C08  C06  C05  C04   180.00   0.0  0
 KND  CONST_24  N02  C02  C03  C04   180.00   0.0  0
 KND  CONST_25  N02  C02  N01  C06   180.00   0.0  0
 KND  CONST_26  C07  C04  C05  C06   180.00   0.0  0
 KND  CONST_27  H6   C16  C15  C14   180.00   0.0  0
 KND  CONST_28  H1   C14  C15  C16   180.00   0.0  0
 KND  CONST_29  H18  C05  C04  C03   180.00   0.0  0
 KND  CONST_30  H17  C03  C04  C05   180.00   0.0  0
 KND  Var_01    C25  C26  O21  C22    57.50  30.0  1
 KND  Var_02    C26  C25  N24  C23    56.83  30.0  1
 KND  Var_03    O21  C26  C25  N24   -57.75  30.0  1
 KND  Var_04    H7   C22  O21  C26  -178.60  30.0  1
 KND  Var_05    C18  C17  C15  C14   -88.18  30.0  3
 KND  Var_06    C23  C18  C17  C15   170.46  30.0  3
 KND  Var_07    C08  C09  C11  C16    96.51  30.0  2
 KND  Var_08    C06  C08  C09  C11   177.11  30.0  1
 KND  Var_09    C09  C08  C06  C05   114.02  30.0  2
 KND  Var_10    H14  C27  N24  C23   175.18  30.0  3
 KND  Var_11    H19  C07  C04  C03   103.74  30.0  2

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
 KND  chir_01  C23  C22  N24  C18  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
 KND  plan-1  C14  0.020
 KND  plan-1  C15  0.020
 KND  plan-1  C17  0.020
 KND  plan-1  C16  0.020
 KND  plan-1  C13  0.020
 KND  plan-1  C12  0.020
 KND  plan-1  C11  0.020
 KND  plan-1  C09  0.020
 KND  plan-1  F12  0.020
 KND  plan-1  F13  0.020
 KND  plan-1  H1   0.020
 KND  plan-1  H6   0.020
 KND  plan-2  C02  0.020
 KND  plan-2  C03  0.020
 KND  plan-2  C04  0.020
 KND  plan-2  C05  0.020
 KND  plan-2  C06  0.020
 KND  plan-2  N01  0.020
 KND  plan-2  N02  0.020
 KND  plan-2  H17  0.020
 KND  plan-2  H18  0.020
 KND  plan-2  C08  0.020
 KND  plan-2  C07  0.020
 KND  plan-3  C02  0.020
 KND  plan-3  N02  0.020
 KND  plan-3  H26  0.020
 KND  plan-3  H27  0.020

