# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 00:46:56 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 6-[2-(5-{2-[(2S,4R)-4-ethoxy-1-methylpyrrolidin-2-yl]ethyl}-2,3-difluorophenyl)ethyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[C@@H]1C[C@H](CCc2cc(F)c(F)c(CCc3cc(C)cc(N)n3)c2)N(C)C1
#
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
 KNS  KNS  6-[2-(5-{2-[(2S,4R)-4-ethoxy-1-methylpyrrolidin-2-yl]ethyl}-2,3-difluorophenyl)ethyl]-4-methylpyridin-2-amine  ligand  60  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KNS
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
 KNS  C12  C  CR6   0   0.353  -1.9638   2.9036   0.2251
 KNS  C13  C  CR6   0   0.424  -0.9251   3.7971   0.4209
 KNS  C11  C  CR6   0  -0.049  -1.7551   1.7019  -0.4279
 KNS  C14  C  CR16  0  -0.481   0.3500   3.5110  -0.0138
 KNS  C23  C  CH1   0   0.062   5.8188  -0.7984   0.2080
 KNS  C15  C  CR6   0   0.163   0.5965   2.3055  -0.6680
 KNS  C17  C  CH2   0  -0.518   1.9912   1.9399  -1.0888
 KNS  C21  C  CH3   0  -0.535   4.7960   0.3785  -2.6396
 KNS  C18  C  CH2   0  -0.401   2.7591   1.2668   0.0484
 KNS  C02  C  CR6   0   0.441  -6.2671  -1.6835   0.3566
 KNS  C03  C  CR16  0  -0.446  -6.0709  -3.0349   0.0222
 KNS  C04  C  CR6   0   0.205  -4.7838  -3.5074  -0.1330
 KNS  C05  C  CR16  0  -0.433  -3.7259  -2.6115   0.0585
 KNS  C06  C  CR6   0   0.274  -4.0095  -1.2979   0.3857
 KNS  C08  C  CH2   0  -0.490  -2.9102  -0.2905   0.5640
 KNS  C09  C  CH2   0  -0.506  -2.8622   0.7035  -0.6058
 KNS  C16  C  CR16  0  -0.368  -0.4611   1.4259  -0.8667
 KNS  C22  C  CH2   0  -0.322   4.8856  -1.3129  -0.8923
 KNS  C24  C  CH2   0  -0.502   4.9446   0.2624   0.8544
 KNS  C25  C  CH1   0  -0.064   4.1829   0.8784  -0.3271
 KNS  C27  C  CH2   0  -0.150   7.1281  -2.7154   0.6421
 KNS  C28  C  CH3   0  -0.687   7.7024  -3.5123   1.7920
 KNS  F12  F  F     0  -0.307  -3.1838   3.2275   0.6799
 KNS  F13  F  F     0  -0.310  -1.1796   4.9521   1.0493
 KNS  N01  N  N     0  -0.482  -5.2545  -0.8406   0.5301
 KNS  N02  N  NH2   0  -0.839  -7.5244  -1.1939   0.5651
 KNS  N21  N  NT    0  -0.427   4.2190  -0.1245  -1.4093
 KNS  O26  O  O2    0  -0.492   6.2334  -1.7488   1.1517
 KNS  H1   H  HCR6  0   0.278   1.1447   4.2270   0.1581
 KNS  H2   H  HCH1  0   0.202   6.6973  -0.3257  -0.2599
 KNS  H3   H  HCH2  0   0.247   1.9505   1.2636  -1.9452
 KNS  H4   H  HCH2  0   0.240   2.5301   2.8347  -1.4127
 KNS  H5   H  HCH3  0   0.233   4.7390  -0.3830  -3.4181
 KNS  H6   H  HCH3  0   0.233   4.2289   1.2407  -2.9918
 KNS  H7   H  HCH3  0   0.198   5.8471   0.6910  -2.5507
 KNS  H8   H  HCH2  0   0.227   2.7925   1.9412   0.9102
 KNS  H9   H  HCH2  0   0.223   2.2187   0.3713   0.3730
 KNS  H10  H  HCR6  0   0.255  -6.9235  -3.6909  -0.1083
 KNS  H11  H  HCR6  0   0.243  -2.6993  -2.9380  -0.0506
 KNS  H12  H  HCH3  0   0.255  -4.2725  -5.0013  -1.5777
 KNS  H13  H  HCH3  0   0.248  -3.6695  -5.3356   0.0358
 KNS  H14  H  HCH3  0   0.247  -5.3819  -5.5674  -0.3340
 KNS  H15  H  HCH2  0   0.251  -3.0653   0.2568   1.4971
 KNS  H16  H  HCH2  0   0.251  -1.9476  -0.7994   0.6442
 KNS  H17  H  HCH2  0   0.259  -3.8297   1.1979  -0.6991
 KNS  H18  H  HCH2  0   0.259  -2.6981   0.1537  -1.5348
 KNS  H19  H  HCR6  0   0.251  -0.2804   0.4883  -1.3812
 KNS  H20  H  HCH2  0   0.237   5.3960  -1.8502  -1.6935
 KNS  H21  H  HCH2  0   0.223   4.1617  -2.0061  -0.4447
 KNS  H22  H  HCH2  0   0.228   4.2504  -0.2248   1.5477
 KNS  H23  H  HCH2  0   0.251   5.5073   1.0079   1.4168
 KNS  H24  H  HCH1  0   0.223   4.7104   1.7825  -0.6587
 KNS  H25  H  HCH2  0   0.197   7.9377  -2.2277   0.0824
 KNS  H26  H  HCH2  0   0.202   6.6185  -3.3880  -0.0598
 KNS  H27  H  HCH3  0   0.228   8.2558  -2.8727   2.4802
 KNS  H28  H  HCH3  0   0.229   6.9201  -4.0250   2.3526
 KNS  H29  H  HCH3  0   0.230   8.3885  -4.2682   1.4101
 KNS  H30  H  HNH2  0   0.388  -8.2947  -1.7035   0.1663
 KNS  H31  H  HNH2  0   0.379  -7.6251  -0.1931   0.5204
 KNS  C07  C  CH3   0  -0.726  -4.5175  -4.9309  -0.5162

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
 KNS  C27  O26  single    1.412  0.020  1.412
 KNS  C27  C28  single    1.512  0.020  1.512
 KNS  O26  C23  single    1.402  0.020  1.402
 KNS  C22  N21  single    1.457  0.020  1.457
 KNS  C22  C23  single    1.532  0.020  1.532
 KNS  N21  C21  single    1.449  0.020  1.449
 KNS  N21  C25  single    1.476  0.020  1.476
 KNS  C23  C24  single    1.519  0.020  1.519
 KNS  C18  C25  single    1.523  0.020  1.523
 KNS  C18  C17  single    1.528  0.020  1.528
 KNS  C24  C25  single    1.535  0.020  1.535
 KNS  C17  C15  single    1.502  0.020  1.502
 KNS  C15  C14  aromatic  1.394  0.020  1.394
 KNS  C15  C16  aromatic  1.390  0.020  1.390
 KNS  C14  C13  aromatic  1.377  0.020  1.377
 KNS  C16  C11  aromatic  1.394  0.020  1.394
 KNS  C13  F13  single    1.339  0.020  1.339
 KNS  C13  C12  aromatic  1.384  0.020  1.384
 KNS  C11  C12  aromatic  1.383  0.020  1.383
 KNS  C11  C09  single    1.501  0.020  1.501
 KNS  C08  C09  single    1.536  0.020  1.536
 KNS  C08  C06  single    1.502  0.020  1.502
 KNS  N01  C06  aromatic  1.334  0.020  1.334
 KNS  N01  C02  aromatic  1.329  0.020  1.329
 KNS  C12  F12  single    1.342  0.020  1.342
 KNS  N02  C02  single    1.365  0.020  1.365
 KNS  C06  C05  aromatic  1.383  0.020  1.383
 KNS  C02  C03  aromatic  1.406  0.020  1.406
 KNS  C05  C04  aromatic  1.399  0.020  1.399
 KNS  C03  C04  aromatic  1.380  0.020  1.380
 KNS  C04  C07  single    1.498  0.020  1.498
 KNS  C14  H1   single    0.930  0.020  1.080
 KNS  C23  H2   single    0.970  0.020  1.090
 KNS  C17  H3   single    0.970  0.020  1.090
 KNS  C17  H4   single    0.970  0.020  1.090
 KNS  C21  H5   single    0.970  0.020  1.090
 KNS  C21  H6   single    0.970  0.020  1.090
 KNS  C21  H7   single    0.970  0.020  1.090
 KNS  C18  H8   single    0.970  0.020  1.090
 KNS  C18  H9   single    0.970  0.020  1.090
 KNS  C03  H10  single    0.930  0.020  1.080
 KNS  C05  H11  single    0.930  0.020  1.080
 KNS  C07  H12  single    0.970  0.020  1.090
 KNS  C07  H13  single    0.970  0.020  1.090
 KNS  C07  H14  single    0.970  0.020  1.090
 KNS  C08  H15  single    0.970  0.020  1.090
 KNS  C08  H16  single    0.970  0.020  1.090
 KNS  C09  H17  single    0.970  0.020  1.090
 KNS  C09  H18  single    0.970  0.020  1.090
 KNS  C16  H19  single    0.930  0.020  1.080
 KNS  C22  H20  single    0.970  0.020  1.090
 KNS  C22  H21  single    0.970  0.020  1.090
 KNS  C24  H22  single    0.970  0.020  1.090
 KNS  C24  H23  single    0.970  0.020  1.090
 KNS  C25  H24  single    0.970  0.020  1.090
 KNS  C27  H25  single    0.970  0.020  1.090
 KNS  C27  H26  single    0.970  0.020  1.090
 KNS  C28  H27  single    0.970  0.020  1.090
 KNS  C28  H28  single    0.970  0.020  1.090
 KNS  C28  H29  single    0.970  0.020  1.090
 KNS  N02  H30  single    0.890  0.020  1.040
 KNS  N02  H31  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
 KNS  F12  C12  C11  120.46  3.000
 KNS  F12  C12  C13  118.60  3.000
 KNS  C11  C12  C13  120.95  3.000
 KNS  F13  C13  C14  120.21  3.000
 KNS  F13  C13  C12  118.72  3.000
 KNS  C14  C13  C12  121.07  3.000
 KNS  C16  C11  C09  121.03  3.000
 KNS  C09  C11  C12  121.48  3.000
 KNS  C16  C11  C12  117.43  3.000
 KNS  H1   C14  C15  121.09  3.000
 KNS  H1   C14  C13  119.46  3.000
 KNS  C15  C14  C13  119.45  3.000
 KNS  H2   C23  O26  109.93  3.000
 KNS  H2   C23  C24  109.88  3.000
 KNS  O26  C23  C24  110.92  3.000
 KNS  H2   C23  C22  108.96  3.000
 KNS  C24  C23  C22  100.93  3.000
 KNS  O26  C23  C22  115.84  3.000
 KNS  C16  C15  C17  120.83  3.000
 KNS  C16  C15  C14  118.68  3.000
 KNS  C17  C15  C14  120.42  3.000
 KNS  H4   C17  H3   107.03  3.000
 KNS  H4   C17  C18  109.46  3.000
 KNS  H3   C17  C18  109.23  3.000
 KNS  H4   C17  C15  109.96  3.000
 KNS  H3   C17  C15  109.63  3.000
 KNS  C18  C17  C15  111.43  3.000
 KNS  H7   C21  H6   107.36  3.000
 KNS  H7   C21  H5   107.82  3.000
 KNS  H6   C21  H5   107.12  3.000
 KNS  H7   C21  N21  114.23  3.000
 KNS  H6   C21  N21  109.98  3.000
 KNS  H5   C21  N21  110.05  3.000
 KNS  H9   C18  H8   106.58  3.000
 KNS  H9   C18  C25  109.02  3.000
 KNS  H8   C18  C25  108.82  3.000
 KNS  H9   C18  C17  109.43  3.000
 KNS  H8   C18  C17  109.25  3.000
 KNS  C25  C18  C17  113.49  3.000
 KNS  N02  C02  N01  117.02  3.000
 KNS  N02  C02  C03  120.63  3.000
 KNS  N01  C02  C03  122.30  3.000
 KNS  H10  C03  C04  120.86  3.000
 KNS  H10  C03  C02  120.05  3.000
 KNS  C04  C03  C02  119.09  3.000
 KNS  C07  C04  C05  120.59  3.000
 KNS  C07  C04  C03  121.34  3.000
 KNS  C05  C04  C03  118.06  3.000
 KNS  H11  C05  C06  120.31  3.000
 KNS  H11  C05  C04  120.66  3.000
 KNS  C06  C05  C04  119.04  3.000
 KNS  N01  C06  C08  116.12  3.000
 KNS  N01  C06  C05  122.85  3.000
 KNS  C08  C06  C05  121.01  3.000
 KNS  H16  C08  H15  107.21  3.000
 KNS  H16  C08  C09  109.27  3.000
 KNS  H15  C08  C09  109.31  3.000
 KNS  H16  C08  C06  109.96  3.000
 KNS  H15  C08  C06  109.48  3.000
 KNS  C09  C08  C06  111.51  3.000
 KNS  H18  C09  H17  106.79  3.000
 KNS  H18  C09  C08  109.08  3.000
 KNS  H17  C09  C08  109.32  3.000
 KNS  H18  C09  C11  108.95  3.000
 KNS  H17  C09  C11  111.28  3.000
 KNS  C08  C09  C11  111.30  3.000
 KNS  H19  C16  C15  119.21  3.000
 KNS  H19  C16  C11  118.37  3.000
 KNS  C15  C16  C11  122.42  3.000
 KNS  H21  C22  H20  107.27  3.000
 KNS  H21  C22  N21  110.98  3.000
 KNS  H20  C22  N21  110.79  3.000
 KNS  H21  C22  C23  108.73  3.000
 KNS  H20  C22  C23  114.06  3.000
 KNS  N21  C22  C23  105.04  3.000
 KNS  H23  C24  H22  107.75  3.000
 KNS  H23  C24  C25  112.26  3.000
 KNS  H22  C24  C25  110.56  3.000
 KNS  H23  C24  C23  113.58  3.000
 KNS  H22  C24  C23  108.87  3.000
 KNS  C25  C24  C23  103.78  3.000
 KNS  H24  C25  N21  109.05  3.000
 KNS  H24  C25  C24  108.93  3.000
 KNS  N21  C25  C24  106.24  3.000
 KNS  H24  C25  C18  108.28  3.000
 KNS  C24  C25  C18  112.12  3.000
 KNS  N21  C25  C18  112.15  3.000
 KNS  H26  C27  H25  106.76  3.000
 KNS  H26  C27  O26  110.86  3.000
 KNS  H25  C27  O26  110.30  3.000
 KNS  H26  C27  C28  109.85  3.000
 KNS  H25  C27  C28  109.97  3.000
 KNS  O26  C27  C28  109.08  3.000
 KNS  H29  C28  H28  107.79  3.000
 KNS  H29  C28  H27  107.97  3.000
 KNS  H28  C28  H27  108.39  3.000
 KNS  H29  C28  C27  109.76  3.000
 KNS  H28  C28  C27  111.48  3.000
 KNS  H27  C28  C27  111.31  3.000
 KNS  C06  N01  C02  118.65  3.000
 KNS  H31  N02  H30  114.16  3.000
 KNS  H31  N02  C02  116.22  3.000
 KNS  H30  N02  C02  117.58  3.000
 KNS  C25  N21  C22  107.77  3.000
 KNS  C25  N21  C21  113.35  3.000
 KNS  C22  N21  C21  113.71  3.000
 KNS  C27  O26  C23  114.10  3.000
 KNS  H14  C07  H13  108.41  3.000
 KNS  H14  C07  H12  107.65  3.000
 KNS  H13  C07  H12  107.09  3.000
 KNS  H14  C07  C04  111.81  3.000
 KNS  H13  C07  C04  111.20  3.000
 KNS  H12  C07  C04  110.49  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
 KNS  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 KNS  CONST_02  C15  C16  C11  C12     0.00   0.0  0
 KNS  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 KNS  CONST_04  C16  C11  C12  C13     0.00   0.0  0
 KNS  CONST_05  C14  C15  C16  C11     0.00   0.0  0
 KNS  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 KNS  CONST_07  C05  C06  N01  C02     0.00   0.0  0
 KNS  CONST_08  C05  C04  C03  C02     0.00   0.0  0
 KNS  CONST_09  C06  N01  C02  C03     0.00   0.0  0
 KNS  CONST_10  C06  C05  C04  C03     0.00   0.0  0
 KNS  CONST_11  N01  C06  C05  C04     0.00   0.0  0
 KNS  CONST_12  N01  C02  C03  C04     0.00   0.0  0
 KNS  CONST_13  C17  C15  C14  C13   180.00   0.0  0
 KNS  CONST_14  C09  C11  C12  C13   180.00   0.0  0
 KNS  CONST_15  C17  C15  C16  C11   180.00   0.0  0
 KNS  CONST_16  F13  C13  C12  C11   180.00   0.0  0
 KNS  CONST_17  F12  C12  C13  C14   180.00   0.0  0
 KNS  CONST_18  F13  C13  C14  C15   180.00   0.0  0
 KNS  CONST_19  C09  C11  C16  C15   180.00   0.0  0
 KNS  CONST_20  C08  C06  N01  C02   180.00   0.0  0
 KNS  CONST_21  C07  C04  C03  C02   180.00   0.0  0
 KNS  CONST_22  C08  C06  C05  C04   180.00   0.0  0
 KNS  CONST_23  N02  C02  C03  C04   180.00   0.0  0
 KNS  CONST_24  N02  C02  N01  C06   180.00   0.0  0
 KNS  CONST_25  C07  C04  C05  C06   180.00   0.0  0
 KNS  CONST_26  F12  C12  C11  C16   180.00   0.0  0
 KNS  CONST_27  H1   C14  C13  C12   180.00   0.0  0
 KNS  CONST_28  H19  C16  C11  C12   180.00   0.0  0
 KNS  CONST_29  H11  C05  C04  C03   180.00   0.0  0
 KNS  CONST_30  H10  C03  C04  C05   180.00   0.0  0
 KNS  Var_01    C25  N21  C22  C23   -27.02  30.0  1
 KNS  Var_02    C08  C09  C11  C12   -90.59  30.0  2
 KNS  Var_03    C06  C08  C09  C11  -179.56  30.0  1
 KNS  Var_04    C18  C17  C15  C14    85.40  30.0  2
 KNS  Var_05    C25  C18  C17  C15  -179.87  30.0  1
 KNS  Var_06    C09  C08  C06  C05   107.46  30.0  2
 KNS  Var_07    H12  C07  C04  C03   101.45  30.0  2
 KNS  Var_08    H5   C21  N21  C22    59.99  30.0  3
 KNS  Var_09    C28  C27  O26  C23   169.34  30.0  2
 KNS  Var_10    H27  C28  C27  O26   -61.02  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
 KNS  chir_01  C23  O26  C22  C24  negativ
 KNS  chir_02  C25  N21  C18  C24  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
 KNS  plan-1  C12  0.020
 KNS  plan-1  C13  0.020
 KNS  plan-1  C11  0.020
 KNS  plan-1  C14  0.020
 KNS  plan-1  C15  0.020
 KNS  plan-1  C17  0.020
 KNS  plan-1  C09  0.020
 KNS  plan-1  C16  0.020
 KNS  plan-1  F12  0.020
 KNS  plan-1  F13  0.020
 KNS  plan-1  H1   0.020
 KNS  plan-1  H19  0.020
 KNS  plan-2  C02  0.020
 KNS  plan-2  C03  0.020
 KNS  plan-2  C04  0.020
 KNS  plan-2  C05  0.020
 KNS  plan-2  C06  0.020
 KNS  plan-2  C08  0.020
 KNS  plan-2  N01  0.020
 KNS  plan-2  N02  0.020
 KNS  plan-2  H10  0.020
 KNS  plan-2  H11  0.020
 KNS  plan-2  C07  0.020
 KNS  plan-3  C02  0.020
 KNS  plan-3  N02  0.020
 KNS  plan-3  H30  0.020
 KNS  plan-3  H31  0.020

