# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:23:28 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3R,4R)-4-(2-{[2-(3-chloro-5-fluorophenyl)-2,2-difluoroethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(C[C@@H]2CNC[C@@H]2OCCNCC(F)(F)c3cc(F)cc(Cl)c3)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
 JK5  JK5  6-{[(3R,4R)-4-(2-{[2-(3-chloro-5-fluorophenyl)-2,2-difluoroethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  56  30  .  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_JK5
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
 JK5  N01   N   N     0  -0.485  -5.7887   0.6718  -1.2018
 JK5  C02   C   CR6   0   0.439  -6.8098   1.5110  -1.0744
 JK5  N02   N   NH2   0  -0.839  -7.8859   1.3082  -1.8906
 JK5  C03   C   CR16  0  -0.450  -6.7843   2.5952  -0.1792
 JK5  C04   C   CR6   0   0.205  -5.6600   2.7986   0.5934
 JK5  C05   C   CR16  0  -0.433  -4.5869   1.9119   0.4436
 JK5  C06   C   CR6   0   0.279  -4.6973   0.8686  -0.4580
 JK5  C07   C   CH3   0  -0.727  -5.5845   3.9259   1.5773
 JK5  C08   C   CH2   0  -0.486  -3.5858  -0.1268  -0.6403
 JK5  O09   O   O2    0  -0.490  -1.6823  -2.0981  -0.5764
 JK5  N1'   N   NH1   0  -0.587  -4.1056  -2.9877   1.7483
 JK5  C10   C   CH2   0  -0.163  -0.7416  -3.0229  -1.0656
 JK5  C11   C   CH2   0  -0.296   0.5333  -2.2816  -1.3946
 JK5  N12   N   NH1   0  -0.612   1.1345  -1.7041  -0.2055
 JK5  C13   C   CH2   0  -0.364   2.2788  -0.8866  -0.5252
 JK5  C14   C   CT    0   0.779   3.0707  -0.5074   0.7103
 JK5  F15   F   F     0  -0.344   2.2502   0.1175   1.6070
 JK5  F16   F   F     0  -0.337   3.5191  -1.6263   1.3444
 JK5  C2'   C   CH2   0  -0.337  -3.0640  -3.5299   0.8801
 JK5  C21   C   CR6   0  -0.086   4.2373   0.3900   0.3858
 JK5  C22   C   CR16  0  -0.450   4.0756   1.7689   0.4074
 JK5  C23   C   CR6   0   0.561   5.1484   2.5592   0.0460
 JK5  F23   F   F     0  -0.305   5.0030   3.8884   0.0663
 JK5  C24   C   CR16  0  -0.371   6.3690   2.0382  -0.3349
 JK5  C25   C   CR6   0  -0.002   6.4957   0.6588  -0.3481
 JK5  CL25  CL  CL    0  -0.105   8.0045  -0.0364  -0.8223
 JK5  C26   C   CR16  0  -0.263   5.4489  -0.1758   0.0083
 JK5  C3'   C   CH1   0   0.053  -2.9703  -2.6315  -0.3831
 JK5  C4'   C   CH1   0  -0.295  -3.9775  -1.5010  -0.1036
 JK5  C5'   C   CH2   0  -0.303  -4.1712  -1.5726   1.4145
 JK5  HN02  H   HNH2  0   0.379  -7.9705   0.3893  -2.2933
 JK5  HN0A  H   HNH2  0   0.387  -8.7623   1.7201  -1.6177
 JK5  H03   H   HCR6  0   0.254  -7.6394   3.2563  -0.1035
 JK5  H05   H   HCR6  0   0.240  -3.6839   2.0346   1.0290
 JK5  H07   H   HCH3  0   0.252  -5.5233   3.5429   2.5973
 JK5  H07A  H   HCH3  0   0.250  -4.6933   4.5320   1.4114
 JK5  H07B  H   HCH3  0   0.246  -6.4545   4.5771   1.5138
 JK5  H08   H   HCH2  0   0.245  -3.3497  -0.2000  -1.7052
 JK5  H08A  H   HCH2  0   0.240  -2.6864   0.2303  -0.1366
 JK5  HN1'  H   HNH1  0   0.345  -4.9900  -3.4125   1.4970
 JK5  H10   H   HCH2  0   0.203  -0.5355  -3.8133  -0.3313
 JK5  H10A  H   HCH2  0   0.208  -1.1147  -3.5137  -1.9755
 JK5  H11   H   HCH2  0   0.234   1.2361  -2.9925  -1.8374
 JK5  H11A  H   HCH2  0   0.202   0.3193  -1.5300  -2.1704
 JK5  HN12  H   HNH1  0   0.350   0.4385  -1.1375   0.2635
 JK5  H13   H   HCH2  0   0.261   2.9504  -1.4462  -1.1825
 JK5  H13A  H   HCH2  0   0.240   2.0271   0.0384  -1.0657
 JK5  H2'   H   HCH2  0   0.226  -2.1011  -3.4980   1.4010
 JK5  H2'A  H   HCH2  0   0.240  -3.2711  -4.5744   0.6468
 JK5  H22   H   HCR6  0   0.293   3.1410   2.2318   0.6932
 JK5  H24   H   HCR6  0   0.308   7.1879   2.6878  -0.6132
 JK5  H26   H   HCR6  0   0.292   5.5830  -1.2481  -0.0197
 JK5  H3'   H   HCH1  0   0.214  -3.2648  -3.1853  -1.2849
 JK5  H4'   H   HCH1  0   0.247  -4.9242  -1.7901  -0.5718
 JK5  H5'   H   HCH2  0   0.241  -5.1116  -1.1368   1.7526
 JK5  H5'A  H   HCH2  0   0.215  -3.3612  -1.0371   1.9239

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
 JK5  N01  C02   aromatic  1.328  0.020  1.328
 JK5  N01  C06   aromatic  1.335  0.020  1.335
 JK5  C02  N02   single    1.366  0.020  1.366
 JK5  C02  C03   aromatic  1.406  0.020  1.406
 JK5  C03  C04   aromatic  1.379  0.020  1.379
 JK5  C04  C05   aromatic  1.400  0.020  1.400
 JK5  C04  C07   single    1.498  0.020  1.498
 JK5  C05  C06   aromatic  1.383  0.020  1.383
 JK5  C06  C08   single    1.503  0.020  1.503
 JK5  C08  C4'   single    1.526  0.020  1.526
 JK5  O09  C10   single    1.407  0.020  1.407
 JK5  O09  C3'   single    1.407  0.020  1.407
 JK5  N1'  C2'   single    1.460  0.020  1.460
 JK5  N1'  C5'   single    1.455  0.020  1.455
 JK5  C10  C11   single    1.511  0.020  1.511
 JK5  C11  N12   single    1.452  0.020  1.452
 JK5  N12  C13   single    1.442  0.020  1.442
 JK5  C13  C14   single    1.516  0.020  1.516
 JK5  C14  F15   single    1.367  0.020  1.367
 JK5  C14  F16   single    1.362  0.020  1.362
 JK5  C14  C21   single    1.507  0.020  1.507
 JK5  C2'  C3'   single    1.553  0.020  1.553
 JK5  C21  C22   aromatic  1.389  0.020  1.389
 JK5  C21  C26   aromatic  1.389  0.020  1.389
 JK5  C22  C23   aromatic  1.381  0.020  1.381
 JK5  C23  F23   single    1.337  0.020  1.337
 JK5  C23  C24   aromatic  1.381  0.020  1.381
 JK5  C24  C25   aromatic  1.385  0.020  1.385
 JK5  C25  CL25  single    1.728  0.020  1.728
 JK5  C25  C26   aromatic  1.385  0.020  1.385
 JK5  C3'  C4'   single    1.540  0.020  1.540
 JK5  C4'  C5'   single    1.532  0.020  1.532
 JK5  N02  HN02  single    0.890  0.020  1.040
 JK5  N02  HN0A  single    0.890  0.020  1.040
 JK5  C03  H03   single    0.930  0.020  1.080
 JK5  C05  H05   single    0.930  0.020  1.080
 JK5  C07  H07   single    0.970  0.020  1.090
 JK5  C07  H07A  single    0.970  0.020  1.090
 JK5  C07  H07B  single    0.970  0.020  1.090
 JK5  C08  H08   single    0.970  0.020  1.090
 JK5  C08  H08A  single    0.970  0.020  1.090
 JK5  N1'  HN1'  single    0.890  0.020  1.040
 JK5  C10  H10   single    0.970  0.020  1.090
 JK5  C10  H10A  single    0.970  0.020  1.090
 JK5  C11  H11   single    0.970  0.020  1.090
 JK5  C11  H11A  single    0.970  0.020  1.090
 JK5  N12  HN12  single    0.890  0.020  1.040
 JK5  C13  H13   single    0.970  0.020  1.090
 JK5  C13  H13A  single    0.970  0.020  1.090
 JK5  C2'  H2'   single    0.970  0.020  1.090
 JK5  C2'  H2'A  single    0.970  0.020  1.090
 JK5  C22  H22   single    0.930  0.020  1.080
 JK5  C24  H24   single    0.930  0.020  1.080
 JK5  C26  H26   single    0.930  0.020  1.080
 JK5  C3'  H3'   single    0.970  0.020  1.090
 JK5  C4'  H4'   single    0.970  0.020  1.090
 JK5  C5'  H5'   single    0.970  0.020  1.090
 JK5  C5'  H5'A  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
 JK5  C06   N01  C02   118.81  3.000
 JK5  C03   C02  N02   120.61  3.000
 JK5  C03   C02  N01   122.30  3.000
 JK5  N02   C02  N01   117.05  3.000
 JK5  HN0A  N02  HN02  114.14  3.000
 JK5  HN0A  N02  C02   117.61  3.000
 JK5  HN02  N02  C02   116.15  3.000
 JK5  H03   C03  C04   120.94  3.000
 JK5  H03   C03  C02   120.04  3.000
 JK5  C04   C03  C02   119.02  3.000
 JK5  C07   C04  C05   120.55  3.000
 JK5  C07   C04  C03   121.32  3.000
 JK5  C05   C04  C03   118.13  3.000
 JK5  H05   C05  C06   120.28  3.000
 JK5  H05   C05  C04   120.63  3.000
 JK5  C06   C05  C04   119.09  3.000
 JK5  C08   C06  C05   121.30  3.000
 JK5  C08   C06  N01   116.05  3.000
 JK5  C05   C06  N01   122.65  3.000
 JK5  H07B  C07  H07A  108.16  3.000
 JK5  H07B  C07  H07   108.02  3.000
 JK5  H07A  C07  H07   106.94  3.000
 JK5  H07B  C07  C04   111.81  3.000
 JK5  H07A  C07  C04   111.07  3.000
 JK5  H07   C07  C04   110.65  3.000
 JK5  H08A  C08  H08   107.08  3.000
 JK5  H08A  C08  C4'   110.11  3.000
 JK5  H08   C08  C4'   109.74  3.000
 JK5  H08A  C08  C06   109.69  3.000
 JK5  H08   C08  C06   108.79  3.000
 JK5  C4'   C08  C06   111.33  3.000
 JK5  C3'   O09  C10   114.24  3.000
 JK5  HN1'  N1'  C5'   108.15  3.000
 JK5  HN1'  N1'  C2'   108.64  3.000
 JK5  C5'   N1'  C2'   104.88  3.000
 JK5  H10A  C10  H10   107.20  3.000
 JK5  H10A  C10  C11   108.98  3.000
 JK5  H10   C10  C11   109.90  3.000
 JK5  H10A  C10  O09   110.76  3.000
 JK5  H10   C10  O09   111.47  3.000
 JK5  C11   C10  O09   108.51  3.000
 JK5  H11A  C11  H11   106.46  3.000
 JK5  H11A  C11  N12   112.70  3.000
 JK5  H11   C11  N12   108.92  3.000
 JK5  H11A  C11  C10   108.92  3.000
 JK5  H11   C11  C10   108.15  3.000
 JK5  N12   C11  C10   111.48  3.000
 JK5  HN12  N12  C13   109.32  3.000
 JK5  HN12  N12  C11   108.50  3.000
 JK5  C13   N12  C11   111.86  3.000
 JK5  H13A  C13  H13   105.99  3.000
 JK5  H13A  C13  C14   108.03  3.000
 JK5  H13   C13  C14   107.28  3.000
 JK5  H13A  C13  N12   113.82  3.000
 JK5  H13   C13  N12   109.29  3.000
 JK5  C14   C13  N12   112.06  3.000
 JK5  C21   C14  F16   109.55  3.000
 JK5  C21   C14  F15   109.50  3.000
 JK5  F16   C14  F15   105.54  3.000
 JK5  C21   C14  C13   112.20  3.000
 JK5  F16   C14  C13   110.24  3.000
 JK5  F15   C14  C13   109.60  3.000
 JK5  H2'A  C2'  H2'   107.26  3.000
 JK5  H2'A  C2'  C3'   113.06  3.000
 JK5  H2'   C2'  C3'   108.48  3.000
 JK5  H2'A  C2'  N1'   110.34  3.000
 JK5  H2'   C2'  N1'   109.48  3.000
 JK5  C3'   C2'  N1'   108.17  3.000
 JK5  C26   C21  C22   120.67  3.000
 JK5  C26   C21  C14   119.41  3.000
 JK5  C22   C21  C14   119.85  3.000
 JK5  H22   C22  C23   119.72  3.000
 JK5  H22   C22  C21   121.99  3.000
 JK5  C23   C22  C21   118.29  3.000
 JK5  C24   C23  F23   118.38  3.000
 JK5  C24   C23  C22   122.90  3.000
 JK5  F23   C23  C22   118.72  3.000
 JK5  H24   C24  C25   121.75  3.000
 JK5  H24   C24  C23   120.91  3.000
 JK5  C25   C24  C23   117.34  3.000
 JK5  C26   C25  CL25  119.21  3.000
 JK5  C26   C25  C24   121.89  3.000
 JK5  CL25  C25  C24   118.90  3.000
 JK5  H26   C26  C25   119.82  3.000
 JK5  H26   C26  C21   121.27  3.000
 JK5  C25   C26  C21   118.91  3.000
 JK5  H3'   C3'  C4'   110.11  3.000
 JK5  H3'   C3'  C2'   111.10  3.000
 JK5  C4'   C3'  C2'   103.75  3.000
 JK5  H3'   C3'  O09   108.88  3.000
 JK5  C4'   C3'  O09   110.20  3.000
 JK5  C2'   C3'  O09   112.72  3.000
 JK5  H4'   C4'  C5'   107.58  3.000
 JK5  H4'   C4'  C3'   107.11  3.000
 JK5  C5'   C4'  C3'   103.20  3.000
 JK5  H4'   C4'  C08   108.01  3.000
 JK5  C5'   C4'  C08   115.02  3.000
 JK5  C3'   C4'  C08   115.43  3.000
 JK5  H5'A  C5'  H5'   107.33  3.000
 JK5  H5'A  C5'  C4'   110.13  3.000
 JK5  H5'   C5'  C4'   113.43  3.000
 JK5  H5'A  C5'  N1'   109.57  3.000
 JK5  H5'   C5'  N1'   110.88  3.000
 JK5  C4'   C5'  N1'   105.48  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
 JK5  CONST_01  C04   C03  C02  N01     0.00   0.0  0
 JK5  CONST_02  C04   C05  C06  N01     0.00   0.0  0
 JK5  CONST_03  C05   C06  N01  C02     0.00   0.0  0
 JK5  CONST_04  C05   C04  C03  C02     0.00   0.0  0
 JK5  CONST_05  C06   N01  C02  C03     0.00   0.0  0
 JK5  CONST_06  C06   C05  C04  C03     0.00   0.0  0
 JK5  CONST_07  C24   C23  C22  C21     0.00   0.0  0
 JK5  CONST_08  C24   C25  C26  C21     0.00   0.0  0
 JK5  CONST_09  C25   C26  C21  C22     0.00   0.0  0
 JK5  CONST_10  C25   C24  C23  C22     0.00   0.0  0
 JK5  CONST_11  C26   C21  C22  C23     0.00   0.0  0
 JK5  CONST_12  C26   C25  C24  C23     0.00   0.0  0
 JK5  CONST_13  C08   C06  N01  C02   180.00   0.0  0
 JK5  CONST_14  C07   C04  C03  C02   180.00   0.0  0
 JK5  CONST_15  C06   N01  C02  N02   180.00   0.0  0
 JK5  CONST_16  C04   C03  C02  N02   180.00   0.0  0
 JK5  CONST_17  C08   C06  C05  C04   180.00   0.0  0
 JK5  CONST_18  C07   C04  C05  C06   180.00   0.0  0
 JK5  CONST_19  C23   C22  C21  C14   180.00   0.0  0
 JK5  CONST_20  C25   C26  C21  C14   180.00   0.0  0
 JK5  CONST_21  F23   C23  C22  C21   180.00   0.0  0
 JK5  CONST_22  CL25  C25  C26  C21   180.00   0.0  0
 JK5  CONST_23  CL25  C25  C24  C23   180.00   0.0  0
 JK5  CONST_24  C25   C24  C23  F23   180.00   0.0  0
 JK5  CONST_25  H03   C03  C02  N01   180.00   0.0  0
 JK5  CONST_26  H05   C05  C06  N01   180.00   0.0  0
 JK5  CONST_27  H26   C26  C21  C22   180.00   0.0  0
 JK5  CONST_28  H24   C24  C23  C22   180.00   0.0  0
 JK5  CONST_29  H22   C22  C23  C24   180.00   0.0  0
 JK5  Var_01    C4'   C5'  N1'  C2'    38.34  30.0  1
 JK5  Var_02    C5'   N1'  C2'  C3'   -25.85  30.0  1
 JK5  Var_03    C4'   C08  C06  N01   -68.53  30.0  2
 JK5  Var_04    C22   C21  C14  C13    90.87  30.0  2
 JK5  Var_05    H07   C07  C04  C03   114.72  30.0  2
 JK5  Var_06    C21   C14  C13  N12  -177.83  30.0  3
 JK5  Var_07    H10   C10  O09  C3'   -66.14  30.0  3
 JK5  Var_08    N12   C11  C10  O09    64.09  30.0  3
 JK5  Var_09    C13   N12  C11  C10  -174.37  30.0  3
 JK5  Var_10    C14   C13  N12  C11  -168.66  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
 JK5  chir_01  C3'  O09  C2'  C4'  negativ
 JK5  chir_02  C4'  C08  C3'  C5'  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
 JK5  plan-1  N01   0.020
 JK5  plan-1  C02   0.020
 JK5  plan-1  N02   0.020
 JK5  plan-1  C03   0.020
 JK5  plan-1  C04   0.020
 JK5  plan-1  C05   0.020
 JK5  plan-1  C06   0.020
 JK5  plan-1  C07   0.020
 JK5  plan-1  C08   0.020
 JK5  plan-1  H03   0.020
 JK5  plan-1  H05   0.020
 JK5  plan-2  C14   0.020
 JK5  plan-2  C21   0.020
 JK5  plan-2  C22   0.020
 JK5  plan-2  C23   0.020
 JK5  plan-2  F23   0.020
 JK5  plan-2  C24   0.020
 JK5  plan-2  C25   0.020
 JK5  plan-2  CL25  0.020
 JK5  plan-2  C26   0.020
 JK5  plan-2  H22   0.020
 JK5  plan-2  H24   0.020
 JK5  plan-2  H26   0.020
 JK5  plan-3  C02   0.020
 JK5  plan-3  N02   0.020
 JK5  plan-3  HN02  0.020
 JK5  plan-3  HN0A  0.020

