# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:25:17 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3R,4R)-4-(2-{[2-(2,3-difluorophenyl)-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)c3cccc(F)c3F)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
 JK4  JK4  6-{[(3R,4R)-4-(2-{[2-(2,3-difluorophenyl)-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_JK4
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
 JK4  N01   N  N     0  -0.484  -5.3627   0.7961  -1.1715
 JK4  C02   C  CR6   0   0.438  -6.3687   1.6576  -1.0767
 JK4  N02   N  NH2   0  -0.839  -7.4059   1.5007  -1.9517
 JK4  C03   C  CR16  0  -0.450  -6.3646   2.7196  -0.1549
 JK4  C04   C  CR6   0   0.205  -5.2769   2.8789   0.6782
 JK4  C05   C  CR16  0  -0.429  -4.2176   1.9712   0.5601
 JK4  C06   C  CR6   0   0.277  -4.3066   0.9499  -0.3686
 JK4  C07   C  CH3   0  -0.728  -5.2258   3.9802   1.6923
 JK4  C08   C  CH2   0  -0.487  -3.2167  -0.0761  -0.5061
 JK4  O09   O  O2    0  -0.491  -1.4184  -2.1154  -0.5980
 JK4  N1'   N  NH1   0  -0.585  -3.7363  -2.7662   2.0329
 JK4  C10   C  CH2   0  -0.159  -0.5181  -3.1313  -0.9713
 JK4  C11   C  CH2   0  -0.299   0.7161  -2.4888  -1.5620
 JK4  N12   N  NH1   0  -0.616   1.4081  -1.6812  -0.5749
 JK4  C13   C  CH2   0  -0.381   2.5659  -1.0176  -1.1224
 JK4  C14   C  CT    0   0.771   3.3868  -0.3778  -0.0185
 JK4  F15   F  F     0  -0.355   2.5779   0.4733   0.6897
 JK4  F16   F  F     0  -0.346   3.7732  -1.3349   0.8752
 JK4  C2'   C  CH2   0  -0.350  -2.5749  -3.2210   1.2842
 JK4  C21   C  CR6   0  -0.230   4.6103   0.3835  -0.4639
 JK4  C22   C  CR6   0   0.420   5.3933   1.0412   0.4756
 JK4  F22   F  F     0  -0.294   5.0767   1.0188   1.7713
 JK4  C23   C  CR6   0   0.409   6.5259   1.7382   0.0946
 JK4  F23   F  F     0  -0.302   7.2425   2.3545   1.0381
 JK4  C24   C  CR16  0  -0.401   6.9123   1.7967  -1.2273
 JK4  C25   C  CR16  0  -0.237   6.1417   1.1412  -2.1752
 JK4  C26   C  CR16  0  -0.300   5.0053   0.4432  -1.7969
 JK4  C3'   C  CH1   0   0.070  -2.6555  -2.5870  -0.1263
 JK4  C4'   C  CH1   0  -0.304  -3.6697  -1.4285   0.0417
 JK4  C5'   C  CH2   0  -0.304  -3.9581  -1.4107   1.5513
 JK4  HN02  H  HNH2  0   0.378  -7.4916   0.5923  -2.3775
 JK4  HN0A  H  HNH2  0   0.387  -8.2857   1.9251  -1.7103
 JK4  H03   H  HCR6  0   0.254  -7.2084   3.3973  -0.1051
 JK4  H05   H  HCR6  0   0.240  -3.3433   2.0579   1.1936
 JK4  H07   H  HCH3  0   0.252  -5.2031   3.5709   2.7037
 JK4  H07A  H  HCH3  0   0.250  -4.3239   4.5819   1.5734
 JK4  H07B  H  HCH3  0   0.246  -6.0878   4.6407   1.6161
 JK4  H08   H  HCH2  0   0.245  -2.9466  -0.1679  -1.5606
 JK4  H08A  H  HCH2  0   0.238  -2.3269   0.2629   0.0275
 JK4  HN1'  H  HNH1  0   0.345  -4.5341  -3.3350   1.7746
 JK4  H10   H  HCH2  0   0.204  -0.2334  -3.7512  -0.1109
 JK4  H10A  H  HCH2  0   0.208  -0.9725  -3.7982  -1.7173
 JK4  H11   H  HCH2  0   0.234   1.3820  -3.2883  -1.8975
 JK4  H11A  H  HCH2  0   0.203   0.4317  -1.9195  -2.4606
 JK4  HN12  H  HNH1  0   0.350   0.7623  -0.9889  -0.2167
 JK4  H13   H  HCH2  0   0.260   3.1925  -1.7560  -1.6292
 JK4  H13A  H  HCH2  0   0.237   2.3209  -0.2472  -1.8678
 JK4  H2'   H  HCH2  0   0.225  -1.6645  -2.8558   1.7739
 JK4  H2'A  H  HCH2  0   0.243  -2.5270  -4.3101   1.2719
 JK4  H24   H  HCR6  0   0.300   7.8021   2.3454  -1.5057
 JK4  H25   H  HCR6  0   0.282   6.4303   1.1752  -3.2161
 JK4  H26   H  HCR6  0   0.284   4.4261  -0.0567  -2.5598
 JK4  H3'   H  HCH1  0   0.209  -3.0547  -3.3190  -0.8420
 JK4  H4'   H  HCH1  0   0.249  -4.5895  -1.7107  -0.4780
 JK4  H5'   H  HCH2  0   0.241  -4.9656  -1.0715   1.7919
 JK4  H5'A  H  HCH2  0   0.217  -3.2590  -0.7335   2.0563

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
 JK4  N01  C02   aromatic  1.328  0.020  1.328
 JK4  N01  C06   aromatic  1.336  0.020  1.336
 JK4  C02  N02   single    1.366  0.020  1.366
 JK4  C02  C03   aromatic  1.406  0.020  1.406
 JK4  C03  C04   aromatic  1.379  0.020  1.379
 JK4  C04  C05   aromatic  1.400  0.020  1.400
 JK4  C04  C07   single    1.498  0.020  1.498
 JK4  C05  C06   aromatic  1.383  0.020  1.383
 JK4  C06  C08   single    1.503  0.020  1.503
 JK4  C08  C4'   single    1.528  0.020  1.528
 JK4  O09  C10   single    1.408  0.020  1.408
 JK4  O09  C3'   single    1.406  0.020  1.406
 JK4  N1'  C2'   single    1.455  0.020  1.455
 JK4  N1'  C5'   single    1.456  0.020  1.456
 JK4  C10  C11   single    1.512  0.020  1.512
 JK4  C11  N12   single    1.451  0.020  1.451
 JK4  N12  C13   single    1.442  0.020  1.442
 JK4  C13  C14   single    1.517  0.020  1.517
 JK4  C14  F15   single    1.371  0.020  1.371
 JK4  C14  F16   single    1.365  0.020  1.365
 JK4  C14  C21   single    1.508  0.020  1.508
 JK4  C2'  C3'   single    1.549  0.020  1.549
 JK4  C21  C22   aromatic  1.389  0.020  1.389
 JK4  C21  C26   aromatic  1.392  0.020  1.392
 JK4  C22  F22   single    1.334  0.020  1.334
 JK4  C22  C23   aromatic  1.383  0.020  1.383
 JK4  C23  F23   single    1.335  0.020  1.335
 JK4  C23  C24   aromatic  1.378  0.020  1.378
 JK4  C24  C25   aromatic  1.386  0.020  1.386
 JK4  C25  C26   aromatic  1.386  0.020  1.386
 JK4  C3'  C4'   single    1.549  0.020  1.549
 JK4  C4'  C5'   single    1.537  0.020  1.537
 JK4  N02  HN02  single    0.890  0.020  1.040
 JK4  N02  HN0A  single    0.890  0.020  1.040
 JK4  C03  H03   single    0.930  0.020  1.080
 JK4  C05  H05   single    0.930  0.020  1.080
 JK4  C07  H07   single    0.970  0.020  1.090
 JK4  C07  H07A  single    0.970  0.020  1.090
 JK4  C07  H07B  single    0.970  0.020  1.090
 JK4  C08  H08   single    0.970  0.020  1.090
 JK4  C08  H08A  single    0.970  0.020  1.090
 JK4  N1'  HN1'  single    0.890  0.020  1.040
 JK4  C10  H10   single    0.970  0.020  1.090
 JK4  C10  H10A  single    0.970  0.020  1.090
 JK4  C11  H11   single    0.970  0.020  1.090
 JK4  C11  H11A  single    0.970  0.020  1.090
 JK4  N12  HN12  single    0.890  0.020  1.040
 JK4  C13  H13   single    0.970  0.020  1.090
 JK4  C13  H13A  single    0.970  0.020  1.090
 JK4  C2'  H2'   single    0.970  0.020  1.090
 JK4  C2'  H2'A  single    0.970  0.020  1.090
 JK4  C24  H24   single    0.930  0.020  1.080
 JK4  C25  H25   single    0.930  0.020  1.080
 JK4  C26  H26   single    0.930  0.020  1.080
 JK4  C3'  H3'   single    0.970  0.020  1.090
 JK4  C4'  H4'   single    0.970  0.020  1.090
 JK4  C5'  H5'   single    0.970  0.020  1.090
 JK4  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
 JK4  C06   N01  C02   118.78  3.000
 JK4  C03   C02  N02   120.59  3.000
 JK4  C03   C02  N01   122.31  3.000
 JK4  N02   C02  N01   117.06  3.000
 JK4  HN0A  N02  HN02  114.05  3.000
 JK4  HN0A  N02  C02   117.50  3.000
 JK4  HN02  N02  C02   116.04  3.000
 JK4  H03   C03  C04   120.94  3.000
 JK4  H03   C03  C02   120.02  3.000
 JK4  C04   C03  C02   119.04  3.000
 JK4  C07   C04  C05   120.53  3.000
 JK4  C07   C04  C03   121.38  3.000
 JK4  C05   C04  C03   118.09  3.000
 JK4  H05   C05  C06   120.24  3.000
 JK4  H05   C05  C04   120.63  3.000
 JK4  C06   C05  C04   119.12  3.000
 JK4  C08   C06  C05   121.25  3.000
 JK4  C08   C06  N01   116.09  3.000
 JK4  C05   C06  N01   122.65  3.000
 JK4  H07B  C07  H07A  108.21  3.000
 JK4  H07B  C07  H07   108.00  3.000
 JK4  H07A  C07  H07   106.90  3.000
 JK4  H07B  C07  C04   111.82  3.000
 JK4  H07A  C07  C04   111.10  3.000
 JK4  H07   C07  C04   110.63  3.000
 JK4  H08A  C08  H08   107.24  3.000
 JK4  H08A  C08  C4'   109.96  3.000
 JK4  H08   C08  C4'   110.18  3.000
 JK4  H08A  C08  C06   109.54  3.000
 JK4  H08   C08  C06   108.96  3.000
 JK4  C4'   C08  C06   110.88  3.000
 JK4  C3'   O09  C10   114.19  3.000
 JK4  HN1'  N1'  C5'   108.57  3.000
 JK4  HN1'  N1'  C2'   108.78  3.000
 JK4  C5'   N1'  C2'   104.04  3.000
 JK4  H10A  C10  H10   107.24  3.000
 JK4  H10A  C10  C11   109.29  3.000
 JK4  H10   C10  C11   109.55  3.000
 JK4  H10A  C10  O09   110.70  3.000
 JK4  H10   C10  O09   111.43  3.000
 JK4  C11   C10  O09   108.60  3.000
 JK4  H11A  C11  H11   106.56  3.000
 JK4  H11A  C11  N12   112.99  3.000
 JK4  H11   C11  N12   108.98  3.000
 JK4  H11A  C11  C10   109.14  3.000
 JK4  H11   C11  C10   107.84  3.000
 JK4  N12   C11  C10   111.11  3.000
 JK4  HN12  N12  C13   109.38  3.000
 JK4  HN12  N12  C11   108.49  3.000
 JK4  C13   N12  C11   112.37  3.000
 JK4  H13A  C13  H13   106.66  3.000
 JK4  H13A  C13  C14   108.56  3.000
 JK4  H13   C13  C14   108.18  3.000
 JK4  H13A  C13  N12   113.63  3.000
 JK4  H13   C13  N12   108.99  3.000
 JK4  C14   C13  N12   110.62  3.000
 JK4  C21   C14  F16   108.52  3.000
 JK4  C21   C14  F15   108.53  3.000
 JK4  F16   C14  F15   105.31  3.000
 JK4  C21   C14  C13   115.91  3.000
 JK4  F16   C14  C13   109.50  3.000
 JK4  F15   C14  C13   108.56  3.000
 JK4  H2'A  C2'  H2'   107.54  3.000
 JK4  H2'A  C2'  C3'   113.64  3.000
 JK4  H2'   C2'  C3'   108.28  3.000
 JK4  H2'A  C2'  N1'   110.68  3.000
 JK4  H2'   C2'  N1'   109.21  3.000
 JK4  C3'   C2'  N1'   107.41  3.000
 JK4  C26   C21  C22   117.88  3.000
 JK4  C26   C21  C14   122.33  3.000
 JK4  C22   C21  C14   119.78  3.000
 JK4  C23   C22  F22   118.05  3.000
 JK4  C23   C22  C21   120.93  3.000
 JK4  F22   C22  C21   121.02  3.000
 JK4  C24   C23  F23   120.50  3.000
 JK4  C24   C23  C22   121.00  3.000
 JK4  F23   C23  C22   118.50  3.000
 JK4  H24   C24  C25   121.40  3.000
 JK4  H24   C24  C23   119.93  3.000
 JK4  C25   C24  C23   118.68  3.000
 JK4  H25   C25  C26   119.84  3.000
 JK4  H25   C25  C24   119.69  3.000
 JK4  C26   C25  C24   120.47  3.000
 JK4  H26   C26  C25   118.67  3.000
 JK4  H26   C26  C21   120.28  3.000
 JK4  C25   C26  C21   121.05  3.000
 JK4  H3'   C3'  C4'   109.33  3.000
 JK4  H3'   C3'  C2'   109.85  3.000
 JK4  C4'   C3'  C2'   103.98  3.000
 JK4  H3'   C3'  O09   108.94  3.000
 JK4  C4'   C3'  O09   111.21  3.000
 JK4  C2'   C3'  O09   113.41  3.000
 JK4  H4'   C4'  C5'   108.18  3.000
 JK4  H4'   C4'  C3'   107.83  3.000
 JK4  C5'   C4'  C3'   103.77  3.000
 JK4  H4'   C4'  C08   107.90  3.000
 JK4  C5'   C4'  C08   113.42  3.000
 JK4  C3'   C4'  C08   115.41  3.000
 JK4  H5'A  C5'  H5'   107.19  3.000
 JK4  H5'A  C5'  C4'   109.87  3.000
 JK4  H5'   C5'  C4'   113.19  3.000
 JK4  H5'A  C5'  N1'   109.00  3.000
 JK4  H5'   C5'  N1'   110.96  3.000
 JK4  C4'   C5'  N1'   106.59  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
 JK4  CONST_01  C04  C03  C02  N01     0.00   0.0  0
 JK4  CONST_02  C04  C05  C06  N01     0.00   0.0  0
 JK4  CONST_03  C05  C06  N01  C02     0.00   0.0  0
 JK4  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 JK4  CONST_05  C06  N01  C02  C03     0.00   0.0  0
 JK4  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 JK4  CONST_07  C24  C23  C22  C21     0.00   0.0  0
 JK4  CONST_08  C24  C25  C26  C21     0.00   0.0  0
 JK4  CONST_09  C25  C26  C21  C22     0.00   0.0  0
 JK4  CONST_10  C25  C24  C23  C22     0.00   0.0  0
 JK4  CONST_11  C26  C21  C22  C23     0.00   0.0  0
 JK4  CONST_12  C26  C25  C24  C23     0.00   0.0  0
 JK4  CONST_13  C08  C06  N01  C02   180.00   0.0  0
 JK4  CONST_14  C07  C04  C03  C02   180.00   0.0  0
 JK4  CONST_15  C06  N01  C02  N02   180.00   0.0  0
 JK4  CONST_16  C04  C03  C02  N02   180.00   0.0  0
 JK4  CONST_17  C08  C06  C05  C04   180.00   0.0  0
 JK4  CONST_18  C07  C04  C05  C06   180.00   0.0  0
 JK4  CONST_19  C23  C22  C21  C14   180.00   0.0  0
 JK4  CONST_20  C25  C26  C21  C14   180.00   0.0  0
 JK4  CONST_21  F23  C23  C22  C21   180.00   0.0  0
 JK4  CONST_22  C26  C21  C22  F22   180.00   0.0  0
 JK4  CONST_23  C24  C23  C22  F22   180.00   0.0  0
 JK4  CONST_24  C25  C24  C23  F23   180.00   0.0  0
 JK4  CONST_25  H03  C03  C02  N01   180.00   0.0  0
 JK4  CONST_26  H05  C05  C06  N01   180.00   0.0  0
 JK4  CONST_27  H25  C25  C26  C21   180.00   0.0  0
 JK4  CONST_28  H26  C26  C21  C22   180.00   0.0  0
 JK4  CONST_29  H24  C24  C23  C22   180.00   0.0  0
 JK4  Var_01    C4'  C5'  N1'  C2'    38.45  30.0  1
 JK4  Var_02    C5'  N1'  C2'  C3'   -34.47  30.0  1
 JK4  Var_03    C4'  C08  C06  N01   -70.69  30.0  2
 JK4  Var_04    C22  C21  C14  C13   177.71  30.0  2
 JK4  Var_05    H07  C07  C04  C03   115.93  30.0  2
 JK4  Var_06    C21  C14  C13  N12  -178.40  30.0  3
 JK4  Var_07    H10  C10  O09  C3'   -63.87  30.0  3
 JK4  Var_08    N12  C11  C10  O09    63.69  30.0  3
 JK4  Var_09    C13  N12  C11  C10  -178.00  30.0  3
 JK4  Var_10    C14  C13  N12  C11  -170.53  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
 JK4  chir_01  C3'  O09  C2'  C4'  negativ
 JK4  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
 JK4  plan-1  N01   0.020
 JK4  plan-1  C02   0.020
 JK4  plan-1  N02   0.020
 JK4  plan-1  C03   0.020
 JK4  plan-1  C04   0.020
 JK4  plan-1  C05   0.020
 JK4  plan-1  C06   0.020
 JK4  plan-1  C07   0.020
 JK4  plan-1  C08   0.020
 JK4  plan-1  H03   0.020
 JK4  plan-1  H05   0.020
 JK4  plan-2  C14   0.020
 JK4  plan-2  C21   0.020
 JK4  plan-2  C22   0.020
 JK4  plan-2  F22   0.020
 JK4  plan-2  C23   0.020
 JK4  plan-2  F23   0.020
 JK4  plan-2  C24   0.020
 JK4  plan-2  C25   0.020
 JK4  plan-2  C26   0.020
 JK4  plan-2  H24   0.020
 JK4  plan-2  H25   0.020
 JK4  plan-2  H26   0.020
 JK4  plan-3  C02   0.020
 JK4  plan-3  N02   0.020
 JK4  plan-3  HN02  0.020
 JK4  plan-3  HN0A  0.020

