# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 16:09:32 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: trans-N-{2'-[(4-fluorophenyl)amino]-4,4'-bipyridin-2-yl}-4-methoxycyclohexanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1CC[C@@H](CC1)C(=O)Nc2cc(ccn2)c3ccnc(Nc4ccc(F)cc4)c3
#
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
 JNK  JNK  trans-N-{2'-[(4-fluorophenyl)amino]-4,4'-bipyridin-2-yl}-4-methoxycyclohexanecarboxamide  ligand  56  31  .  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_JNK
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
 JNK  C1    C  CR6   0   0.211    1.7269  -0.1645   0.5260
 JNK  C2    C  CR6   0   0.207    0.4876  -0.9615   0.6171
 JNK  C3    C  CR16  0  -0.499    2.9260  -0.7579   0.1886
 JNK  C4    C  CR16  0  -0.427    1.7174   1.2133   0.7817
 JNK  C5    C  CR16  0  -0.481   -0.7366  -0.4041   0.2907
 JNK  C6    C  CR16  0  -0.401    0.5052  -2.2926   1.0406
 JNK  C7    C  CR6   0   0.581    4.0878   0.0339   0.1159
 JNK  C8    C  CR16  0  -0.029    2.9074   1.8984   0.6799
 JNK  C9    C  CR6   0   0.552   -1.8920  -1.1863   0.3985
 JNK  C10   C  CR16  0  -0.053   -0.6932  -2.9734   1.1093
 JNK  N11   N  NH1   0  -0.791    5.2607  -0.5876  -0.2155
 JNK  N12   N  N     0  -0.476    4.0696   1.3372   0.3548
 JNK  N13   N  NH1   0  -0.738   -3.0964  -0.5839   0.0554
 JNK  N14   N  N     0  -0.424   -1.8732  -2.4452   0.7973
 JNK  C15   C  CR6   0   0.363    6.5539  -0.0979  -0.3545
 JNK  C16   C  C     0   0.571   -4.3749  -1.0628   0.1482
 JNK  C17   C  CR16  0  -0.351    7.5473  -1.0366  -0.6636
 JNK  C18   C  CR16  0  -0.303    6.9294   1.2412  -0.2128
 JNK  C19   C  CH1   0  -0.413   -5.4279  -0.0517  -0.2656
 JNK  O20   O  O     0  -0.443   -4.6631  -2.1708   0.5484
 JNK  C21   C  CR16  0  -0.397    8.8686  -0.6623  -0.8254
 JNK  C22   C  CR16  0  -0.398    8.2566   1.6186  -0.3753
 JNK  C23   C  CH2   0  -0.427   -6.5057  -0.6974  -1.1352
 JNK  C24   C  CH2   0  -0.425   -6.0585   0.5723   0.9864
 JNK  C25   C  CR6   0   0.498    9.2081   0.6689  -0.6767
 JNK  C26   C  CH2   0  -0.470   -7.5896   0.3107  -1.5012
 JNK  C27   C  CH2   0  -0.473   -7.1427   1.5775   0.6119
 JNK  C28   C  CH1   0   0.100   -8.2156   0.9289  -0.2602
 JNK  O29   O  O2    0  -0.498   -9.1988   1.8477  -0.6872
 JNK  C30   C  CH3   0  -0.406  -10.0993   2.2483   0.3149
 JNK  F31   F  F     0  -0.322   10.4929   1.0417  -0.8295
 JNK  H3    H  HCR6  0   0.278    2.9833  -1.8162  -0.0338
 JNK  H4    H  HCR6  0   0.266    0.8153   1.7317   1.0739
 JNK  H5    H  HCR6  0   0.282   -0.8080   0.6185  -0.0582
 JNK  H6    H  HCR6  0   0.270    1.4233  -2.7838   1.3313
 JNK  H8    H  HCR6  0   0.264    2.9362   2.9645   0.8746
 JNK  H10   H  HCR6  0   0.267   -0.7087  -4.0060   1.4390
 JNK  H11   H  HNH1  0   0.414    5.1775  -1.5818  -0.3591
 JNK  H13   H  HNH1  0   0.422   -3.0103   0.3619  -0.2837
 JNK  H17   H  HCR6  0   0.276    7.2835  -2.0811  -0.7797
 JNK  H18   H  HCR6  0   0.294    6.1923   1.9900   0.0231
 JNK  H19   H  HCH1  0   0.255   -4.9579   0.7522  -0.8437
 JNK  H21   H  HCR6  0   0.280    9.6211  -1.4029  -1.0628
 JNK  H22   H  HCR6  0   0.277    8.5361   2.6583  -0.2638
 JNK  H231  H  HCH2  0   0.228   -6.9493  -1.5399  -0.5984
 JNK  H232  H  HCH2  0   0.247   -6.0617  -1.1037  -2.0466
 JNK  H241  H  HCH2  0   0.232   -6.4893  -0.2210   1.6055
 JNK  H242  H  HCH2  0   0.248   -5.2946   1.0643   1.5927
 JNK  H261  H  HCH2  0   0.241   -8.3603  -0.1799  -2.1003
 JNK  H262  H  HCH2  0   0.222   -7.1591   1.1048  -2.1213
 JNK  H271  H  HCH2  0   0.222   -6.6993   2.4179   0.0670
 JNK  H272  H  HCH2  0   0.244   -7.5794   1.9853   1.5267
 JNK  H28   H  HCH1  0   0.190   -8.6948   0.1258   0.3253
 JNK  H301  H  HCH3  0   0.202  -10.5776   1.3895   0.8014
 JNK  H302  H  HCH3  0   0.205   -9.6323   2.8582   1.0956
 JNK  H303  H  HCH3  0   0.233  -10.8763   2.8488  -0.1578

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
 JNK  C1   C2    single    1.476  0.020  1.476
 JNK  C1   C3    aromatic  1.380  0.020  1.380
 JNK  C1   C4    aromatic  1.401  0.020  1.401
 JNK  C2   C5    aromatic  1.384  0.020  1.384
 JNK  C2   C6    aromatic  1.397  0.020  1.397
 JNK  C3   C7    aromatic  1.408  0.020  1.408
 JNK  C3   H3    single    0.930  0.020  1.080
 JNK  C4   C8    aromatic  1.377  0.020  1.377
 JNK  C4   H4    single    0.930  0.020  1.080
 JNK  C5   C9    aromatic  1.399  0.020  1.399
 JNK  C5   H5    single    0.930  0.020  1.080
 JNK  C6   C10   aromatic  1.380  0.020  1.380
 JNK  C6   H6    single    0.930  0.020  1.080
 JNK  C7   N11   single    1.368  0.020  1.368
 JNK  C7   N12   aromatic  1.325  0.020  1.325
 JNK  C8   N12   aromatic  1.331  0.020  1.331
 JNK  C8   H8    single    0.930  0.020  1.080
 JNK  C9   N13   single    1.390  0.020  1.390
 JNK  C9   N14   aromatic  1.321  0.020  1.321
 JNK  C10  N14   aromatic  1.330  0.020  1.330
 JNK  C10  H10   single    0.930  0.020  1.080
 JNK  N11  C15   single    1.390  0.020  1.390
 JNK  N11  H11   single    0.860  0.020  1.020
 JNK  N13  C16   single    1.368  0.020  1.368
 JNK  N13  H13   single    0.860  0.020  1.020
 JNK  C15  C17   aromatic  1.401  0.020  1.401
 JNK  C15  C18   aromatic  1.398  0.020  1.398
 JNK  C16  C19   single    1.517  0.020  1.517
 JNK  C16  O20   double    1.213  0.020  1.213
 JNK  C17  C21   aromatic  1.383  0.020  1.383
 JNK  C17  H17   single    0.930  0.020  1.080
 JNK  C18  C22   aromatic  1.389  0.020  1.389
 JNK  C18  H18   single    0.930  0.020  1.080
 JNK  C19  C23   single    1.528  0.020  1.528
 JNK  C19  C24   single    1.534  0.020  1.534
 JNK  C19  H19   single    0.970  0.020  1.090
 JNK  C21  C25   aromatic  1.382  0.020  1.382
 JNK  C21  H21   single    0.930  0.020  1.080
 JNK  C22  C25   aromatic  1.378  0.020  1.378
 JNK  C22  H22   single    0.930  0.020  1.080
 JNK  C23  C26   single    1.525  0.020  1.525
 JNK  C23  H231  single    0.970  0.020  1.090
 JNK  C23  H232  single    0.970  0.020  1.090
 JNK  C24  C27   single    1.525  0.020  1.525
 JNK  C24  H241  single    0.970  0.020  1.090
 JNK  C24  H242  single    0.970  0.020  1.090
 JNK  C25  F31   single    1.347  0.020  1.347
 JNK  C26  C28   single    1.521  0.020  1.521
 JNK  C26  H261  single    0.970  0.020  1.090
 JNK  C26  H262  single    0.970  0.020  1.090
 JNK  C27  C28   single    1.527  0.020  1.527
 JNK  C27  H271  single    0.970  0.020  1.090
 JNK  C27  H272  single    0.970  0.020  1.090
 JNK  C28  O29   single    1.412  0.020  1.412
 JNK  C28  H28   single    0.970  0.020  1.090
 JNK  O29  C30   single    1.405  0.020  1.405
 JNK  C30  H301  single    0.970  0.020  1.090
 JNK  C30  H302  single    0.970  0.020  1.090
 JNK  C30  H303  single    0.970  0.020  1.090

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
 JNK  C4    C1   C3    118.25  3.000
 JNK  C4    C1   C2    120.92  3.000
 JNK  C3    C1   C2    120.83  3.000
 JNK  C6    C2   C5    117.80  3.000
 JNK  C6    C2   C1    121.50  3.000
 JNK  C5    C2   C1    120.70  3.000
 JNK  H3    C3   C7    119.69  3.000
 JNK  H3    C3   C1    121.10  3.000
 JNK  C7    C3   C1    119.21  3.000
 JNK  H4    C4   C8    120.18  3.000
 JNK  H4    C4   C1    121.78  3.000
 JNK  C8    C4   C1    118.03  3.000
 JNK  H5    C5   C9    119.88  3.000
 JNK  H5    C5   C2    120.97  3.000
 JNK  C9    C5   C2    119.14  3.000
 JNK  H6    C6   C10   120.00  3.000
 JNK  H6    C6   C2    121.68  3.000
 JNK  C10   C6   C2    118.31  3.000
 JNK  N12   C7   N11   120.15  3.000
 JNK  N12   C7   C3    122.17  3.000
 JNK  N11   C7   C3    117.68  3.000
 JNK  H8    C8   N12   115.80  3.000
 JNK  H8    C8   C4    119.94  3.000
 JNK  N12   C8   C4    124.26  3.000
 JNK  N14   C9   N13   120.01  3.000
 JNK  N14   C9   C5    122.98  3.000
 JNK  N13   C9   C5    117.01  3.000
 JNK  H10   C10  N14   115.91  3.000
 JNK  H10   C10  C6    119.83  3.000
 JNK  N14   C10  C6    124.26  3.000
 JNK  H11   N11  C15   114.21  3.000
 JNK  H11   N11  C7    114.32  3.000
 JNK  C15   N11  C7    131.45  3.000
 JNK  C8    N12  C7    118.08  3.000
 JNK  H13   N13  C16   115.52  3.000
 JNK  H13   N13  C9    114.56  3.000
 JNK  C16   N13  C9    129.89  3.000
 JNK  C10   N14  C9    117.52  3.000
 JNK  C18   C15  C17   118.27  3.000
 JNK  C18   C15  N11   125.26  3.000
 JNK  C17   C15  N11   116.47  3.000
 JNK  O20   C16  C19   122.27  3.000
 JNK  O20   C16  N13   124.34  3.000
 JNK  C19   C16  N13   113.37  3.000
 JNK  H17   C17  C21   118.75  3.000
 JNK  H17   C17  C15   119.79  3.000
 JNK  C21   C17  C15   121.46  3.000
 JNK  H18   C18  C22   119.38  3.000
 JNK  H18   C18  C15   120.30  3.000
 JNK  C22   C18  C15   120.33  3.000
 JNK  H19   C19  C24   107.96  3.000
 JNK  H19   C19  C23   108.19  3.000
 JNK  C24   C19  C23   110.26  3.000
 JNK  H19   C19  C16   109.57  3.000
 JNK  C24   C19  C16   109.49  3.000
 JNK  C23   C19  C16   111.29  3.000
 JNK  H21   C21  C25   120.79  3.000
 JNK  H21   C21  C17   120.33  3.000
 JNK  C25   C21  C17   118.88  3.000
 JNK  H22   C22  C25   120.42  3.000
 JNK  H22   C22  C18   119.71  3.000
 JNK  C25   C22  C18   119.87  3.000
 JNK  H232  C23  H231  106.74  3.000
 JNK  H232  C23  C26   109.55  3.000
 JNK  H231  C23  C26   109.82  3.000
 JNK  H232  C23  C19   110.20  3.000
 JNK  H231  C23  C19   109.42  3.000
 JNK  C26   C23  C19   111.02  3.000
 JNK  H242  C24  H241  106.73  3.000
 JNK  H242  C24  C27   109.66  3.000
 JNK  H241  C24  C27   109.68  3.000
 JNK  H242  C24  C19   110.41  3.000
 JNK  H241  C24  C19   109.18  3.000
 JNK  C27   C24  C19   111.09  3.000
 JNK  F31   C25  C22   119.54  3.000
 JNK  F31   C25  C21   119.27  3.000
 JNK  C22   C25  C21   121.19  3.000
 JNK  H262  C26  H261  107.00  3.000
 JNK  H262  C26  C28   109.20  3.000
 JNK  H261  C26  C28   109.85  3.000
 JNK  H262  C26  C23   109.62  3.000
 JNK  H261  C26  C23   109.64  3.000
 JNK  C28   C26  C23   111.43  3.000
 JNK  H272  C27  H271  106.97  3.000
 JNK  H272  C27  C28   110.85  3.000
 JNK  H271  C27  C28   109.04  3.000
 JNK  H272  C27  C24   108.93  3.000
 JNK  H271  C27  C24   109.88  3.000
 JNK  C28   C27  C24   111.08  3.000
 JNK  H28   C28  O29   109.38  3.000
 JNK  H28   C28  C27   108.13  3.000
 JNK  O29   C28  C27   112.68  3.000
 JNK  H28   C28  C26   108.41  3.000
 JNK  O29   C28  C26   107.72  3.000
 JNK  C27   C28  C26   110.44  3.000
 JNK  C30   O29  C28   114.58  3.000
 JNK  H303  C30  H302  107.84  3.000
 JNK  H303  C30  H301  108.24  3.000
 JNK  H302  C30  H301  107.80  3.000
 JNK  H303  C30  O29   107.73  3.000
 JNK  H302  C30  O29   113.19  3.000
 JNK  H301  C30  O29   111.87  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
 JNK  CONST_01  C9    C5   C2   C1    180.00   0.0  0
 JNK  CONST_02  C10   C6   C2   C1    180.00   0.0  0
 JNK  CONST_03  N12   C7   C3   C1      0.00   0.0  0
 JNK  CONST_04  N12   C8   C4   C1      0.00   0.0  0
 JNK  CONST_05  C7    C3   C1   C2    180.00   0.0  0
 JNK  CONST_06  C8    C4   C1   C2    180.00   0.0  0
 JNK  CONST_07  N14   C9   C5   C2      0.00   0.0  0
 JNK  CONST_08  N14   C10  C6   C2      0.00   0.0  0
 JNK  CONST_11  C8    C4   C1   C3      0.00   0.0  0
 JNK  CONST_12  C8    N12  C7   C3      0.00   0.0  0
 JNK  CONST_15  C7    C3   C1   C4      0.00   0.0  0
 JNK  CONST_16  C7    N12  C8   C4      0.00   0.0  0
 JNK  CONST_17  C10   C6   C2   C5      0.00   0.0  0
 JNK  CONST_18  C10   N14  C9   C5      0.00   0.0  0
 JNK  CONST_19  C9    C5   C2   C6      0.00   0.0  0
 JNK  CONST_20  C9    N14  C10  C6      0.00   0.0  0
 JNK  CONST_21  C25   C21  C17  C15     0.00   0.0  0
 JNK  CONST_22  C25   C22  C18  C15     0.00   0.0  0
 JNK  CONST_23  C22   C18  C15  C17     0.00   0.0  0
 JNK  CONST_24  C22   C25  C21  C17     0.00   0.0  0
 JNK  CONST_25  C21   C17  C15  C18     0.00   0.0  0
 JNK  CONST_26  C21   C25  C22  C18     0.00   0.0  0
 JNK  CONST_27  N11   C7   C3   C1    180.00   0.0  0
 JNK  CONST_28  N13   C9   C5   C2    180.00   0.0  0
 JNK  CONST_29  N11   C7   N12  C8    180.00   0.0  0
 JNK  CONST_30  N13   C9   N14  C10   180.00   0.0  0
 JNK  CONST_31  C21   C17  C15  N11   180.00   0.0  0
 JNK  CONST_32  C22   C18  C15  N11   180.00   0.0  0
 JNK  CONST_33  F31   C25  C21  C17   180.00   0.0  0
 JNK  CONST_34  F31   C25  C22  C18   180.00   0.0  0
 JNK  CONST_35  H5    C5   C2   C1      0.00   0.0  0
 JNK  CONST_36  H6    C6   C2   C1      0.00   0.0  0
 JNK  CONST_37  H8    C8   C4   C1    180.00   0.0  0
 JNK  CONST_38  H3    C3   C1   C2      0.00   0.0  0
 JNK  CONST_39  H4    C4   C1   C2      0.00   0.0  0
 JNK  CONST_40  H10   C10  C6   C2    180.00   0.0  0
 JNK  CONST_41  H21   C21  C17  C15   180.00   0.0  0
 JNK  CONST_42  H22   C22  C18  C15   180.00   0.0  0
 JNK  CONST_43  H18   C18  C15  C17   180.00   0.0  0
 JNK  CONST_44  H17   C17  C15  C18   180.00   0.0  0
 JNK  CONST_45  C19   C16  N13  C9    180.00   0.0  0
 JNK  CONST_46  C16   N13  C9   C5    180.00   0.0  0
 JNK  CONST_47  C16   N13  C9   N14     0.00   0.0  0
 JNK  CONST_48  H13   N13  C9   C5      0.00   0.0  0
 JNK  CONST_49  O20   C16  N13  C9      0.00   0.0  0
 JNK  Var_01    C28   C26  C23  C19   -56.73  30.0  1
 JNK  Var_02    C28   C27  C24  C19    56.59  30.0  1
 JNK  Var_03    C15   N11  C7   C3   -179.30  30.0  2
 JNK  Var_04    C17   C15  N11  C7    177.74  30.0  2
 JNK  Var_05    H301  C30  O29  C28   -54.09  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
 JNK  chir_01  C19  C16  C23  C24  negativ
 JNK  chir_02  C28  O29  C26  C27  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
 JNK  plan-1  C1   0.020
 JNK  plan-1  C2   0.020
 JNK  plan-1  C3   0.020
 JNK  plan-1  C4   0.020
 JNK  plan-1  C7   0.020
 JNK  plan-1  C8   0.020
 JNK  plan-1  N11  0.020
 JNK  plan-1  N12  0.020
 JNK  plan-1  H3   0.020
 JNK  plan-1  H4   0.020
 JNK  plan-1  H8   0.020
 JNK  plan-2  C1   0.020
 JNK  plan-2  C2   0.020
 JNK  plan-2  C5   0.020
 JNK  plan-2  C6   0.020
 JNK  plan-2  C9   0.020
 JNK  plan-2  C10  0.020
 JNK  plan-2  N13  0.020
 JNK  plan-2  N14  0.020
 JNK  plan-2  H5   0.020
 JNK  plan-2  H6   0.020
 JNK  plan-2  H10  0.020
 JNK  plan-3  N11  0.020
 JNK  plan-3  C15  0.020
 JNK  plan-3  C17  0.020
 JNK  plan-3  C18  0.020
 JNK  plan-3  C21  0.020
 JNK  plan-3  C22  0.020
 JNK  plan-3  C25  0.020
 JNK  plan-3  F31  0.020
 JNK  plan-3  H17  0.020
 JNK  plan-3  H18  0.020
 JNK  plan-3  H21  0.020
 JNK  plan-3  H22  0.020
 JNK  plan-4  C9   0.020
 JNK  plan-4  N13  0.020
 JNK  plan-4  C16  0.020
 JNK  plan-4  C19  0.020
 JNK  plan-4  O20  0.020
 JNK  plan-4  H13  0.020

