# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 12:27:13 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (1~{S},2~{S},3~{S},6~{R})-2-[[2-[5,7-bis(fluoranyl)-1~{H}-indol-3-yl]-5-fluoranyl-pyrimidin-4-yl]amino]-3,6-dimethyl-cyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CC[C@@H](C)[C@@H]([C@H]1Nc2nc(ncc2F)c3c[nH]c4c(F)cc(F)cc34)C(O)=O
#
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
 KWN  KWN  '(1~{S},2~{S},3~{S},6~{R})-2-[[2-[5,7-bis(fluoranyl)-1~{H}-indol-3-yl]-5-fluoranyl-pyrimidin-4-yl]amino]-3,6-dimethyl-cyclohexane-1-carboxylic acid'  ligand  50  30  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KWN
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
 KWN  C10   C  CR15   0  -0.011   1.7350   1.5160  -0.1026
 KWN  C15   C  CR16   0  -0.183   0.5966  -3.1122  -0.1657
 KWN  C20   C  CH1    0  -0.014  -2.8903   0.2544  -0.2371
 KWN  C21   C  CH1    0  -0.362  -4.3472   0.2734   0.2404
 KWN  C22   C  C      0   0.417  -4.4528  -0.5259   1.5556
 KWN  C26   C  CH2    0  -0.418  -4.6231   2.5000  -0.9105
 KWN  C28   C  CH1    0  -0.244  -2.6937   0.9934  -1.5696
 KWN  C02   C  CR6    0   0.553   5.3022   1.7129   0.0467
 KWN  C03   C  CR16   0  -0.601   6.2168   0.6910   0.0904
 KWN  C04   C  CR6    0   0.558   5.7370  -0.6221   0.0782
 KWN  C06   C  CR16   0  -0.568   4.4075  -0.9551   0.0248
 KWN  C07   C  CR56   0   0.060   3.4841   0.0995  -0.0194
 KWN  C08   C  CR56   0   0.181   3.9450   1.4322  -0.0074
 KWN  C11   C  CR5    0  -0.072   2.0530   0.1773  -0.0807
 KWN  C12   C  CR6    0   0.326   1.0806  -0.9045  -0.1247
 KWN  C16   C  CR6    0   0.344  -0.7310  -2.8248  -0.2261
 KWN  C18   C  CR6    0   0.431  -1.1388  -1.4723  -0.2333
 KWN  C25   C  CH1    0  -0.216  -4.8341   1.7192   0.3856
 KWN  C27   C  CH2    0  -0.432  -3.1791   2.4332  -1.3918
 KWN  C29   C  CH3    0  -0.669  -3.3575   0.3002  -2.7542
 KWN  C30   C  CH3    0  -0.661  -6.2955   1.7776   0.8133
 KWN  F01   F  F      0  -0.306   5.7094   2.9882   0.0551
 KWN  F05   F  F      0  -0.323   6.6537  -1.6064   0.1210
 KWN  F17   F  F      0  -0.307  -1.6622  -3.7934  -0.2745
 KWN  N09   N  NR15   0  -0.673   2.8598   2.2618  -0.0585
 KWN  N13   N  N      0  -0.489  -0.1995  -0.5364  -0.1766
 KWN  N14   N  N      0  -0.463   1.5298  -2.1509  -0.1164
 KWN  N19   N  NH1    0  -0.689  -2.4269  -1.1227  -0.2893
 KWN  O23   O  O      0  -0.605  -3.9738   0.0056   2.5769
 KWN  O24   O  OC    -1  -0.611  -4.9782  -1.6578   1.4871
 KWN  H101  H  HCR5   0   0.294   0.7637   1.9806  -0.1488
 KWN  H151  H  HCR6   0   0.281   0.9352  -4.1431  -0.1568
 KWN  H201  H  HCH1   0   0.236  -2.2865   0.7741   0.5149
 KWN  H211  H  HCH1   0   0.207  -4.9723  -0.2237  -0.5128
 KWN  H262  H  HCH2   0   0.207  -5.2951   2.1091  -1.6830
 KWN  H261  H  HCH2   0   0.224  -4.9128   3.5440  -0.7581
 KWN  H281  H  HCH1   0   0.237  -1.6178   1.0243  -1.7651
 KWN  H031  H  HCR6   0   0.299   7.2785   0.8951   0.1320
 KWN  H061  H  HCR6   0   0.270   4.0850  -1.9858   0.0161
 KWN  H251  H  HCH1   0   0.204  -4.2272   2.1900   1.1679
 KWN  H272  H  HCH2   0   0.225  -3.0638   2.9832  -2.3296
 KWN  H271  H  HCH2   0   0.217  -2.5361   2.9370  -0.6613
 KWN  H1    H  HCH3   0   0.220  -4.4432   0.2554  -2.6633
 KWN  H291  H  HCH3   0   0.227  -3.1310   0.8354  -3.6781
 KWN  H292  H  HCH3   0   0.227  -2.9951  -0.7215  -2.8762
 KWN  H2    H  HCH3   0   0.227  -6.4587   1.3069   1.7836
 KWN  H301  H  HCH3   0   0.222  -6.6368   2.8120   0.8921
 KWN  H302  H  HCH3   0   0.210  -6.9377   1.2751   0.0855
 KWN  H091  H  HNR5   0   0.423   2.8828   3.2682  -0.0650
 KWN  H191  H  HNH1   0   0.391  -3.1233  -1.8511  -0.2750

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
 KWN  C10  C11   aromatic  1.376  0.020  1.376
 KWN  C10  N09   aromatic  1.350  0.020  1.350
 KWN  C15  C16   aromatic  1.360  0.020  1.360
 KWN  C15  N14   aromatic  1.341  0.020  1.341
 KWN  C20  C21   single    1.533  0.020  1.533
 KWN  C20  C28   single    1.536  0.020  1.536
 KWN  C20  N19   single    1.454  0.020  1.454
 KWN  C21  C22   single    1.543  0.020  1.543
 KWN  C21  C25   single    1.533  0.020  1.533
 KWN  C22  O23   deloc     1.247  0.020  1.247
 KWN  C22  O24   deloc     1.250  0.020  1.250
 KWN  C26  C25   single    1.528  0.020  1.528
 KWN  C26  C27   single    1.524  0.020  1.524
 KWN  C28  C27   single    1.530  0.020  1.530
 KWN  C28  C29   single    1.525  0.020  1.525
 KWN  C02  C03   aromatic  1.372  0.020  1.372
 KWN  C02  C08   aromatic  1.387  0.020  1.387
 KWN  C02  F01   single    1.339  0.020  1.339
 KWN  C03  C04   aromatic  1.398  0.020  1.398
 KWN  C04  C06   aromatic  1.372  0.020  1.372
 KWN  C04  F05   single    1.346  0.020  1.346
 KWN  C06  C07   aromatic  1.402  0.020  1.402
 KWN  C07  C08   aromatic  1.410  0.020  1.410
 KWN  C07  C11   aromatic  1.435  0.020  1.435
 KWN  C08  N09   aromatic  1.367  0.020  1.367
 KWN  C11  C12   single    1.455  0.020  1.455
 KWN  C12  N13   aromatic  1.333  0.020  1.333
 KWN  C12  N14   aromatic  1.325  0.020  1.325
 KWN  C16  C18   aromatic  1.413  0.020  1.413
 KWN  C16  F17   single    1.344  0.020  1.344
 KWN  C18  N13   aromatic  1.327  0.020  1.327
 KWN  C18  N19   single    1.336  0.020  1.336
 KWN  C25  C30   single    1.524  0.020  1.524
 KWN  C10  H101  single    0.930  0.020  1.080
 KWN  C15  H151  single    0.930  0.020  1.080
 KWN  C20  H201  single    0.970  0.020  1.090
 KWN  C21  H211  single    0.970  0.020  1.090
 KWN  C26  H262  single    0.970  0.020  1.090
 KWN  C26  H261  single    0.970  0.020  1.090
 KWN  C28  H281  single    0.970  0.020  1.090
 KWN  C03  H031  single    0.930  0.020  1.080
 KWN  C06  H061  single    0.930  0.020  1.080
 KWN  C25  H251  single    0.970  0.020  1.090
 KWN  C27  H272  single    0.970  0.020  1.090
 KWN  C27  H271  single    0.970  0.020  1.090
 KWN  C29  H1    single    0.970  0.020  1.090
 KWN  C29  H291  single    0.970  0.020  1.090
 KWN  C29  H292  single    0.970  0.020  1.090
 KWN  C30  H2    single    0.970  0.020  1.090
 KWN  C30  H301  single    0.970  0.020  1.090
 KWN  C30  H302  single    0.970  0.020  1.090
 KWN  N09  H091  single    0.860  0.020  1.020
 KWN  N19  H191  single    0.860  0.020  1.020

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
 KWN  H101  C10  N09   120.93  3.000
 KWN  H101  C10  C11   128.93  3.000
 KWN  N09   C10  C11   110.14  3.000
 KWN  H151  C15  N14   117.63  3.000
 KWN  H151  C15  C16   120.39  3.000
 KWN  N14   C15  C16   121.98  3.000
 KWN  H201  C20  N19   107.35  3.000
 KWN  H201  C20  C28   107.26  3.000
 KWN  N19   C20  C28   112.56  3.000
 KWN  H201  C20  C21   107.70  3.000
 KWN  N19   C20  C21   109.01  3.000
 KWN  C28   C20  C21   112.69  3.000
 KWN  H211  C21  C25   108.14  3.000
 KWN  H211  C21  C22   108.15  3.000
 KWN  C25   C21  C22   112.72  3.000
 KWN  H211  C21  C20   108.77  3.000
 KWN  C25   C21  C20   110.06  3.000
 KWN  C22   C21  C20   108.91  3.000
 KWN  O24   C22  O23   126.33  3.000
 KWN  O24   C22  C21   116.83  3.000
 KWN  O23   C22  C21   116.81  3.000
 KWN  H261  C26  H262  106.03  3.000
 KWN  H261  C26  C27   109.68  3.000
 KWN  H262  C26  C27   110.04  3.000
 KWN  H261  C26  C25   109.45  3.000
 KWN  H262  C26  C25   109.33  3.000
 KWN  C27   C26  C25   112.11  3.000
 KWN  H281  C28  C29   107.59  3.000
 KWN  H281  C28  C27   107.84  3.000
 KWN  C29   C28  C27   112.33  3.000
 KWN  H281  C28  C20   107.13  3.000
 KWN  C29   C28  C20   113.55  3.000
 KWN  C27   C28  C20   108.14  3.000
 KWN  F01   C02  C08   119.39  3.000
 KWN  F01   C02  C03   120.43  3.000
 KWN  C08   C02  C03   120.18  3.000
 KWN  H031  C03  C04   120.95  3.000
 KWN  H031  C03  C02   120.99  3.000
 KWN  C04   C03  C02   118.07  3.000
 KWN  F05   C04  C06   118.94  3.000
 KWN  F05   C04  C03   116.93  3.000
 KWN  C06   C04  C03   124.13  3.000
 KWN  H061  C06  C07   121.38  3.000
 KWN  H061  C06  C04   121.43  3.000
 KWN  C07   C06  C04   117.19  3.000
 KWN  C11   C07  C08   105.97  3.000
 KWN  C11   C07  C06   134.35  3.000
 KWN  C08   C07  C06   119.68  3.000
 KWN  N09   C08  C07   108.29  3.000
 KWN  N09   C08  C02   130.95  3.000
 KWN  C07   C08  C02   120.76  3.000
 KWN  C12   C11  C07   128.87  3.000
 KWN  C12   C11  C10   124.63  3.000
 KWN  C07   C11  C10   106.50  3.000
 KWN  N14   C12  N13   125.85  3.000
 KWN  N14   C12  C11   118.20  3.000
 KWN  N13   C12  C11   115.95  3.000
 KWN  F17   C16  C18   119.32  3.000
 KWN  F17   C16  C15   121.71  3.000
 KWN  C18   C16  C15   118.98  3.000
 KWN  N19   C18  N13   119.98  3.000
 KWN  N19   C18  C16   121.94  3.000
 KWN  N13   C18  C16   118.08  3.000
 KWN  H251  C25  C30   108.31  3.000
 KWN  H251  C25  C26   108.03  3.000
 KWN  C30   C25  C26   110.54  3.000
 KWN  H251  C25  C21   107.27  3.000
 KWN  C30   C25  C21   111.56  3.000
 KWN  C26   C25  C21   110.97  3.000
 KWN  H271  C27  H272  106.17  3.000
 KWN  H271  C27  C28   108.90  3.000
 KWN  H272  C27  C28   109.90  3.000
 KWN  H271  C27  C26   108.99  3.000
 KWN  H272  C27  C26   110.42  3.000
 KWN  C28   C27  C26   112.26  3.000
 KWN  H292  C29  H291  107.20  3.000
 KWN  H292  C29  H1    107.56  3.000
 KWN  H291  C29  H1    107.30  3.000
 KWN  H292  C29  C28   111.59  3.000
 KWN  H291  C29  C28   110.14  3.000
 KWN  H1    C29  C28   112.79  3.000
 KWN  H302  C30  H301  107.45  3.000
 KWN  H302  C30  H2    107.82  3.000
 KWN  H301  C30  H2    107.33  3.000
 KWN  H302  C30  C25   111.04  3.000
 KWN  H301  C30  C25   110.87  3.000
 KWN  H2    C30  C25   112.12  3.000
 KWN  H091  N09  C08   126.08  3.000
 KWN  H091  N09  C10   124.82  3.000
 KWN  C08   N09  C10   109.10  3.000
 KWN  C18   N13  C12   119.12  3.000
 KWN  C12   N14  C15   116.00  3.000
 KWN  H191  N19  C18   118.46  3.000
 KWN  H191  N19  C20   117.64  3.000
 KWN  C18   N19  C20   123.62  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
 KWN  CONST_01  C06   C07  C11  C10  180.00   0.0  0
 KWN  CONST_02  C08   C07  C11  C10    0.00   0.0  0
 KWN  CONST_03  N13   C12  C11  C10    0.00   0.0  0
 KWN  CONST_04  N14   C12  C11  C10  180.00   0.0  0
 KWN  CONST_05  C02   C08  N09  C10  180.00   0.0  0
 KWN  CONST_06  C07   C08  N09  C10    0.00   0.0  0
 KWN  CONST_07  N13   C18  C16  C15    0.00   0.0  0
 KWN  CONST_08  C11   C12  N14  C15  180.00   0.0  0
 KWN  CONST_09  N13   C12  N14  C15    0.00   0.0  0
 KWN  CONST_10  C06   C04  C03  C02    0.00   0.0  0
 KWN  CONST_11  C06   C07  C08  C02    0.00   0.0  0
 KWN  CONST_12  C11   C07  C08  C02  180.00   0.0  0
 KWN  CONST_13  C07   C08  C02  C03    0.00   0.0  0
 KWN  CONST_14  N09   C08  C02  C03  180.00   0.0  0
 KWN  CONST_15  C07   C06  C04  C03    0.00   0.0  0
 KWN  CONST_16  C08   C02  C03  C04    0.00   0.0  0
 KWN  CONST_17  C08   C07  C06  C04    0.00   0.0  0
 KWN  CONST_18  C11   C07  C06  C04  180.00   0.0  0
 KWN  CONST_19  N09   C08  C07  C06  180.00   0.0  0
 KWN  CONST_20  C12   C11  C07  C06    0.00   0.0  0
 KWN  CONST_21  N09   C10  C11  C07    0.00   0.0  0
 KWN  CONST_22  N13   C12  C11  C07  180.00   0.0  0
 KWN  CONST_23  N14   C12  C11  C07    0.00   0.0  0
 KWN  CONST_24  C12   C11  C07  C08  180.00   0.0  0
 KWN  CONST_25  C11   C10  N09  C08    0.00   0.0  0
 KWN  CONST_26  N09   C08  C07  C11    0.00   0.0  0
 KWN  CONST_27  C18   N13  C12  C11  180.00   0.0  0
 KWN  CONST_28  N09   C10  C11  C12  180.00   0.0  0
 KWN  CONST_29  C16   C18  N13  C12    0.00   0.0  0
 KWN  CONST_30  C16   C15  N14  C12    0.00   0.0  0
 KWN  CONST_31  N14   C15  C16  C18    0.00   0.0  0
 KWN  CONST_32  N14   C12  N13  C18    0.00   0.0  0
 KWN  CONST_33  N19   C18  C16  C15  180.00   0.0  0
 KWN  CONST_34  F05   C04  C03  C02  180.00   0.0  0
 KWN  CONST_35  F01   C02  C03  C04  180.00   0.0  0
 KWN  CONST_36  F05   C04  C06  C07  180.00   0.0  0
 KWN  CONST_37  F01   C02  C08  C07  180.00   0.0  0
 KWN  CONST_38  N19   C18  N13  C12  180.00   0.0  0
 KWN  CONST_39  N09   C08  C02  F01    0.00   0.0  0
 KWN  CONST_40  N14   C15  C16  F17  180.00   0.0  0
 KWN  CONST_41  N13   C18  C16  F17  180.00   0.0  0
 KWN  CONST_42  C16   C18  N19  C20  180.00   0.0  0
 KWN  CONST_43  N13   C18  N19  C20    0.00   0.0  0
 KWN  CONST_44  H091  N09  C08  C02    0.00   0.0  0
 KWN  CONST_45  H061  C06  C04  C03  180.00   0.0  0
 KWN  CONST_46  H031  C03  C04  C06  180.00   0.0  0
 KWN  CONST_47  H101  C10  C11  C07  180.00   0.0  0
 KWN  CONST_48  H151  C15  N14  C12  180.00   0.0  0
 KWN  CONST_49  H191  N19  C18  C16    0.00   0.0  0
 KWN  Var_01    C25   C26  C27  C28   55.86  30.0  1

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
 KWN  chir_01  C20  C21  C28  N19  positiv
 KWN  chir_02  C21  C20  C22  C25  negativ
 KWN  chir_03  C28  C29  C27  C20  negativ
 KWN  chir_04  C25  C21  C26  C30  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
 KWN  plan-1  C15   0.020
 KWN  plan-1  C11   0.020
 KWN  plan-1  C12   0.020
 KWN  plan-1  C16   0.020
 KWN  plan-1  C18   0.020
 KWN  plan-1  F17   0.020
 KWN  plan-1  N13   0.020
 KWN  plan-1  N14   0.020
 KWN  plan-1  N19   0.020
 KWN  plan-1  H151  0.020
 KWN  plan-2  C10   0.020
 KWN  plan-2  C02   0.020
 KWN  plan-2  C03   0.020
 KWN  plan-2  C04   0.020
 KWN  plan-2  C06   0.020
 KWN  plan-2  C07   0.020
 KWN  plan-2  C08   0.020
 KWN  plan-2  C11   0.020
 KWN  plan-2  C12   0.020
 KWN  plan-2  F01   0.020
 KWN  plan-2  F05   0.020
 KWN  plan-2  N09   0.020
 KWN  plan-2  H101  0.020
 KWN  plan-2  H031  0.020
 KWN  plan-2  H061  0.020
 KWN  plan-2  H091  0.020
 KWN  plan-3  C20   0.020
 KWN  plan-3  C18   0.020
 KWN  plan-3  N19   0.020
 KWN  plan-3  H191  0.020
 KWN  plan-4  C21   0.020
 KWN  plan-4  C22   0.020
 KWN  plan-4  O23   0.020
 KWN  plan-4  O24   0.020

