# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:45:41 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 6-{[(3R,4R)-4-(2-{[(2R)-1-(3-fluorophenyl)propan-2-yl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Cc1cccc(F)c1)NCCO[C@H]2CNC[C@H]2Cc3cc(C)cc(N)n3
#
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
 X2E  X2E  6-{[(3R,4R)-4-(2-{[(2R)-1-(3-fluorophenyl)propan-2-yl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  59  28  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X2E
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
 X2E  N01   N  N     0  -0.482   3.3404   0.1421   1.3515
 X2E  C02   C  CR6   0   0.450   4.4332   0.8976   1.3082
 X2E  N02   N  NH2   0  -0.817   5.3132   0.7750   2.3471
 X2E  C03   C  CR16  0  -0.426   4.6679   1.8234   0.2779
 X2E  C04   C  CR6   0   0.212   3.7354   1.9508  -0.7320
 X2E  C05   C  CR16  0  -0.413   2.5891   1.1533  -0.6724
 X2E  C06   C  CR6   0   0.282   2.4329   0.2691   0.3810
 X2E  C07   C  CH3   0  -0.703   3.9469   2.8987  -1.8727
 X2E  C08   C  CH2   0  -0.487   1.2294  -0.6265   0.4677
 X2E  O09   O  O2    0  -0.480  -0.7934  -2.4265   0.4288
 X2E  N1'   N  NH1   0  -0.536   1.6912  -3.4821  -1.9017
 X2E  C10   C  CH2   0  -0.146  -1.8862  -3.2879   0.6386
 X2E  C11   C  CH2   0  -0.282  -3.0443  -2.4654   1.1616
 X2E  N11   N  NH1   0  -0.583  -3.4187  -1.4370   0.2108
 X2E  C13   C  CH1   0  -0.056  -4.3779  -0.4736   0.7252
 X2E  C14   C  CH2   0  -0.491  -4.4205   0.7468  -0.2020
 X2E  C15   C  CH3   0  -0.641  -5.7656  -1.0895   0.8396
 X2E  C2'   C  CH2   0  -0.344   0.4069  -3.7563  -1.2756
 X2E  C21   C  CR6   0   0.128  -3.0964   1.4536  -0.3027
 X2E  C22   C  CR16  0  -0.297  -2.3257   1.3918  -1.4610
 X2E  C23   C  CR16  0  -0.204  -1.0929   2.0294  -1.5271
 X2E  C24   C  CR16  0  -0.399  -0.6028   2.7380  -0.4407
 X2E  C25   C  CR6   0   0.562  -1.3777   2.7845   0.7025
 X2E  F25   F  F     0  -0.309  -0.9186   3.4653   1.7673
 X2E  C26   C  CR16  0  -0.441  -2.6062   2.1641   0.7929
 X2E  C3'   C  CH1   0   0.082   0.4139  -3.0702   0.1126
 X2E  C4'   C  CH1   0  -0.302   1.5736  -2.0464   0.0165
 X2E  C5'   C  CH2   0  -0.297   2.0146  -2.1360  -1.4535
 X2E  HN02  H  HNH2  0   0.362   5.2513  -0.0783   2.8783
 X2E  HN0A  H  HNH2  0   0.364   6.2565   1.0896   2.1925
 X2E  H03   H  HCR6  0   0.224   5.5687   2.4258   0.2840
 X2E  H05   H  HCR6  0   0.221   1.8344   1.2195  -1.4456
 X2E  H07   H  HCH3  0   0.246   4.2814   2.3592  -2.7608
 X2E  H07A  H  HCH3  0   0.232   3.0225   3.4116  -2.1392
 X2E  H07B  H  HCH3  0   0.236   4.7003   3.6501  -1.6410
 X2E  H08   H  HCH2  0   0.246   0.8681  -0.6368   1.4980
 X2E  H08A  H  HCH2  0   0.251   0.4269  -0.2174  -0.1500
 X2E  HN1'  H  HNH1  0   0.316   2.3822  -4.1224  -1.5281
 X2E  H10   H  HCH2  0   0.200  -2.1814  -3.7921  -0.2912
 X2E  H10A  H  HCH2  0   0.186  -1.6372  -4.0694   1.3699
 X2E  H11   H  HCH2  0   0.210  -3.8821  -3.1471   1.3294
 X2E  H11A  H  HCH2  0   0.187  -2.7755  -2.0517   2.1473
 X2E  HN11  H  HNH1  0   0.353  -2.5723  -0.9431  -0.0473
 X2E  H13   H  HCH1  0   0.183  -4.0838  -0.1189   1.7293
 X2E  H14   H  HCH2  0   0.237  -4.7481   0.4277  -1.1949
 X2E  H14A  H  HCH2  0   0.236  -5.1765   1.4386   0.1771
 X2E  H15   H  HCH3  0   0.213  -6.4797  -0.3559   1.2159
 X2E  H15A  H  HCH3  0   0.221  -6.1138  -1.4385  -0.1344
 X2E  H15B  H  HCH3  0   0.224  -5.7805  -1.9372   1.5250
 X2E  H2'   H  HCH2  0   0.231  -0.3858  -3.3023  -1.8814
 X2E  H2'A  H  HCH2  0   0.225   0.2174  -4.8291  -1.2319
 X2E  H22   H  HCR6  0   0.231  -2.6944   0.8460  -2.3207
 X2E  H23   H  HCR6  0   0.229  -0.5063   1.9757  -2.4354
 X2E  H24   H  HCR6  0   0.249   0.3561   3.2378  -0.4775
 X2E  H26   H  HCR6  0   0.242  -3.1805   2.2318   1.7094
 X2E  H3'   H  HCH1  0   0.188   0.6359  -3.8116   0.8935
 X2E  H4'   H  HCH1  0   0.235   2.3965  -2.4092   0.6399
 X2E  H5'   H  HCH2  0   0.232   3.0725  -1.9178  -1.5996
 X2E  H5'A  H  HCH2  0   0.214   1.4477  -1.4171  -2.0574

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
 X2E  N01  C06   aromatic  1.335  0.020  1.335
 X2E  N01  C02   aromatic  1.329  0.020  1.329
 X2E  N02  C02   single    1.367  0.020  1.367
 X2E  C02  C03   aromatic  1.405  0.020  1.405
 X2E  N02  HN02  single    0.890  0.020  1.040
 X2E  N02  HN0A  single    0.890  0.020  1.040
 X2E  C03  C04   aromatic  1.380  0.020  1.380
 X2E  C03  H03   single    0.930  0.020  1.080
 X2E  C05  C04   aromatic  1.398  0.020  1.398
 X2E  C04  C07   single    1.498  0.020  1.498
 X2E  C06  C05   aromatic  1.384  0.020  1.384
 X2E  C05  H05   single    0.930  0.020  1.080
 X2E  C08  C06   single    1.503  0.020  1.503
 X2E  C07  H07   single    0.970  0.020  1.090
 X2E  C07  H07A  single    0.970  0.020  1.090
 X2E  C07  H07B  single    0.970  0.020  1.090
 X2E  C08  C4'   single    1.529  0.020  1.529
 X2E  C08  H08   single    0.970  0.020  1.090
 X2E  C08  H08A  single    0.970  0.020  1.090
 X2E  C10  O09   single    1.407  0.020  1.407
 X2E  O09  C3'   single    1.404  0.020  1.404
 X2E  C2'  N1'   single    1.455  0.020  1.455
 X2E  C5'  N1'   single    1.455  0.020  1.455
 X2E  N1'  HN1'  single    0.890  0.020  1.040
 X2E  C11  C10   single    1.514  0.020  1.514
 X2E  C10  H10   single    0.970  0.020  1.090
 X2E  C10  H10A  single    0.970  0.020  1.090
 X2E  C11  N11   single    1.450  0.020  1.450
 X2E  C11  H11   single    0.970  0.020  1.090
 X2E  C11  H11A  single    0.970  0.020  1.090
 X2E  C13  N11   single    1.454  0.020  1.454
 X2E  N11  HN11  single    0.890  0.020  1.040
 X2E  C15  C13   single    1.522  0.020  1.522
 X2E  C13  C14   single    1.533  0.020  1.533
 X2E  C13  H13   single    0.970  0.020  1.090
 X2E  C21  C14   single    1.504  0.020  1.504
 X2E  C14  H14   single    0.970  0.020  1.090
 X2E  C14  H14A  single    0.970  0.020  1.090
 X2E  C15  H15   single    0.970  0.020  1.090
 X2E  C15  H15A  single    0.970  0.020  1.090
 X2E  C15  H15B  single    0.970  0.020  1.090
 X2E  C3'  C2'   single    1.549  0.020  1.549
 X2E  C2'  H2'   single    0.970  0.020  1.090
 X2E  C2'  H2'A  single    0.970  0.020  1.090
 X2E  C26  C21   aromatic  1.395  0.020  1.395
 X2E  C21  C22   aromatic  1.393  0.020  1.393
 X2E  C23  C22   aromatic  1.390  0.020  1.390
 X2E  C22  H22   single    0.930  0.020  1.080
 X2E  C24  C23   aromatic  1.387  0.020  1.387
 X2E  C23  H23   single    0.930  0.020  1.080
 X2E  C25  C24   aromatic  1.382  0.020  1.382
 X2E  C24  H24   single    0.930  0.020  1.080
 X2E  F25  C25   single    1.345  0.020  1.345
 X2E  C25  C26   aromatic  1.379  0.020  1.379
 X2E  C26  H26   single    0.930  0.020  1.080
 X2E  C3'  C4'   single    1.550  0.020  1.550
 X2E  C3'  H3'   single    0.970  0.020  1.090
 X2E  C4'  C5'   single    1.537  0.020  1.537
 X2E  C4'  H4'   single    0.970  0.020  1.090
 X2E  C5'  H5'   single    0.970  0.020  1.090
 X2E  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
 X2E  C06   N01  C02   118.77  3.000
 X2E  C03   C02  N02   120.59  3.000
 X2E  C03   C02  N01   122.39  3.000
 X2E  N02   C02  N01   116.97  3.000
 X2E  HN0A  N02  HN02  113.80  3.000
 X2E  HN0A  N02  C02   117.30  3.000
 X2E  HN02  N02  C02   115.93  3.000
 X2E  H03   C03  C04   120.96  3.000
 X2E  H03   C03  C02   120.07  3.000
 X2E  C04   C03  C02   118.98  3.000
 X2E  C07   C04  C05   120.62  3.000
 X2E  C07   C04  C03   121.33  3.000
 X2E  C05   C04  C03   118.05  3.000
 X2E  H05   C05  C06   120.26  3.000
 X2E  H05   C05  C04   120.43  3.000
 X2E  C06   C05  C04   119.31  3.000
 X2E  C08   C06  C05   121.00  3.000
 X2E  C08   C06  N01   116.48  3.000
 X2E  C05   C06  N01   122.50  3.000
 X2E  H07B  C07  H07A  108.31  3.000
 X2E  H07B  C07  H07   107.59  3.000
 X2E  H07A  C07  H07   107.06  3.000
 X2E  H07B  C07  C04   111.85  3.000
 X2E  H07A  C07  C04   111.35  3.000
 X2E  H07   C07  C04   110.49  3.000
 X2E  H08A  C08  H08   107.10  3.000
 X2E  H08A  C08  C4'   110.26  3.000
 X2E  H08   C08  C4'   110.13  3.000
 X2E  H08A  C08  C06   109.43  3.000
 X2E  H08   C08  C06   108.97  3.000
 X2E  C4'   C08  C06   110.86  3.000
 X2E  C3'   O09  C10   114.88  3.000
 X2E  HN1'  N1'  C5'   108.63  3.000
 X2E  HN1'  N1'  C2'   108.92  3.000
 X2E  C5'   N1'  C2'   103.77  3.000
 X2E  H10A  C10  H10   107.33  3.000
 X2E  H10A  C10  C11   109.26  3.000
 X2E  H10   C10  C11   109.65  3.000
 X2E  H10A  C10  O09   111.02  3.000
 X2E  H10   C10  O09   111.32  3.000
 X2E  C11   C10  O09   108.24  3.000
 X2E  H11A  C11  H11   106.48  3.000
 X2E  H11A  C11  N11   112.53  3.000
 X2E  H11   C11  N11   110.19  3.000
 X2E  H11A  C11  C10   109.05  3.000
 X2E  H11   C11  C10   107.49  3.000
 X2E  N11   C11  C10   110.88  3.000
 X2E  HN11  N11  C13   108.56  3.000
 X2E  HN11  N11  C11   107.28  3.000
 X2E  C13   N11  C11   114.11  3.000
 X2E  H13   C13  C15   107.72  3.000
 X2E  H13   C13  C14   107.54  3.000
 X2E  C15   C13  C14   110.00  3.000
 X2E  H13   C13  N11   111.02  3.000
 X2E  C14   C13  N11   109.38  3.000
 X2E  C15   C13  N11   111.10  3.000
 X2E  H14A  C14  H14   107.02  3.000
 X2E  H14A  C14  C21   109.56  3.000
 X2E  H14   C14  C21   109.89  3.000
 X2E  H14A  C14  C13   108.26  3.000
 X2E  H14   C14  C13   108.98  3.000
 X2E  C21   C14  C13   112.95  3.000
 X2E  H15B  C15  H15A  107.94  3.000
 X2E  H15B  C15  H15   107.29  3.000
 X2E  H15A  C15  H15   108.30  3.000
 X2E  H15B  C15  C13   111.97  3.000
 X2E  H15A  C15  C13   110.67  3.000
 X2E  H15   C15  C13   110.52  3.000
 X2E  H2'A  C2'  H2'   107.70  3.000
 X2E  H2'A  C2'  C3'   113.63  3.000
 X2E  H2'   C2'  C3'   108.37  3.000
 X2E  H2'A  C2'  N1'   110.86  3.000
 X2E  H2'   C2'  N1'   108.82  3.000
 X2E  C3'   C2'  N1'   107.35  3.000
 X2E  C26   C21  C22   118.78  3.000
 X2E  C22   C21  C14   121.46  3.000
 X2E  C26   C21  C14   119.74  3.000
 X2E  H22   C22  C23   119.70  3.000
 X2E  H22   C22  C21   119.62  3.000
 X2E  C23   C22  C21   120.68  3.000
 X2E  H23   C23  C24   119.42  3.000
 X2E  H23   C23  C22   119.87  3.000
 X2E  C24   C23  C22   120.71  3.000
 X2E  H24   C24  C25   120.64  3.000
 X2E  H24   C24  C23   121.51  3.000
 X2E  C25   C24  C23   117.86  3.000
 X2E  C26   C25  F25   118.68  3.000
 X2E  C26   C25  C24   122.58  3.000
 X2E  F25   C25  C24   118.74  3.000
 X2E  H26   C26  C25   119.96  3.000
 X2E  H26   C26  C21   120.66  3.000
 X2E  C25   C26  C21   119.39  3.000
 X2E  H3'   C3'  C4'   109.78  3.000
 X2E  H3'   C3'  C2'   109.81  3.000
 X2E  C4'   C3'  C2'   103.91  3.000
 X2E  H3'   C3'  O09   108.83  3.000
 X2E  C4'   C3'  O09   110.77  3.000
 X2E  C2'   C3'  O09   113.64  3.000
 X2E  H4'   C4'  C5'   108.05  3.000
 X2E  H4'   C4'  C3'   107.96  3.000
 X2E  C5'   C4'  C3'   103.62  3.000
 X2E  H4'   C4'  C08   108.00  3.000
 X2E  C5'   C4'  C08   113.63  3.000
 X2E  C3'   C4'  C08   115.25  3.000
 X2E  H5'A  C5'  H5'   107.26  3.000
 X2E  H5'A  C5'  C4'   109.88  3.000
 X2E  H5'   C5'  C4'   113.26  3.000
 X2E  H5'A  C5'  N1'   108.78  3.000
 X2E  H5'   C5'  N1'   111.07  3.000
 X2E  C4'   C5'  N1'   106.54  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
 X2E  CONST_01  C04  C05  C06  N01     0.00   0.0  0
 X2E  CONST_02  C04  C03  C02  N01     0.00   0.0  0
 X2E  CONST_03  C05  C06  N01  C02     0.00   0.0  0
 X2E  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 X2E  CONST_05  C06  N01  C02  C03     0.00   0.0  0
 X2E  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 X2E  CONST_07  C24  C25  C26  C21     0.00   0.0  0
 X2E  CONST_08  C24  C23  C22  C21     0.00   0.0  0
 X2E  CONST_09  C25  C26  C21  C22     0.00   0.0  0
 X2E  CONST_10  C25  C24  C23  C22     0.00   0.0  0
 X2E  CONST_11  C26  C21  C22  C23     0.00   0.0  0
 X2E  CONST_12  C26  C25  C24  C23     0.00   0.0  0
 X2E  CONST_13  C08  C06  N01  C02   180.00   0.0  0
 X2E  CONST_14  C07  C04  C03  C02   180.00   0.0  0
 X2E  CONST_15  C06  N01  C02  N02   180.00   0.0  0
 X2E  CONST_16  C04  C03  C02  N02   180.00   0.0  0
 X2E  CONST_17  C08  C06  C05  C04   180.00   0.0  0
 X2E  CONST_18  C07  C04  C05  C06   180.00   0.0  0
 X2E  CONST_19  C25  C26  C21  C14   180.00   0.0  0
 X2E  CONST_20  C23  C22  C21  C14   180.00   0.0  0
 X2E  CONST_21  F25  C25  C26  C21   180.00   0.0  0
 X2E  CONST_22  F25  C25  C24  C23   180.00   0.0  0
 X2E  CONST_23  H05  C05  C06  N01   180.00   0.0  0
 X2E  CONST_24  H03  C03  C02  N01   180.00   0.0  0
 X2E  CONST_25  H23  C23  C22  C21   180.00   0.0  0
 X2E  CONST_26  H26  C26  C21  C22   180.00   0.0  0
 X2E  CONST_27  H24  C24  C23  C22   180.00   0.0  0
 X2E  CONST_28  H22  C22  C23  C24   180.00   0.0  0
 X2E  Var_01    C4'  C5'  N1'  C2'    39.21  30.0  1
 X2E  Var_02    C5'  N1'  C2'  C3'   -35.16  30.0  1
 X2E  Var_03    C4'  C08  C06  N01   -77.18  30.0  3
 X2E  Var_04    C26  C21  C14  C13   -70.05  30.0  3
 X2E  Var_05    H07  C07  C04  C03   101.58  30.0  2
 X2E  Var_06    H10  C10  O09  C3'   -67.54  30.0  1
 X2E  Var_07    N11  C11  C10  O09    60.04  30.0  2
 X2E  Var_08    C13  N11  C11  C10  -170.74  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
 X2E  chir_01  C13  N11  C15  C14  positiv
 X2E  chir_02  C3'  O09  C2'  C4'  negativ
 X2E  chir_03  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
 X2E  plan-1  N01   0.020
 X2E  plan-1  C02   0.020
 X2E  plan-1  N02   0.020
 X2E  plan-1  C03   0.020
 X2E  plan-1  C04   0.020
 X2E  plan-1  C05   0.020
 X2E  plan-1  C06   0.020
 X2E  plan-1  C07   0.020
 X2E  plan-1  C08   0.020
 X2E  plan-1  H03   0.020
 X2E  plan-1  H05   0.020
 X2E  plan-2  C14   0.020
 X2E  plan-2  C21   0.020
 X2E  plan-2  C22   0.020
 X2E  plan-2  C23   0.020
 X2E  plan-2  C24   0.020
 X2E  plan-2  C25   0.020
 X2E  plan-2  F25   0.020
 X2E  plan-2  C26   0.020
 X2E  plan-2  H22   0.020
 X2E  plan-2  H23   0.020
 X2E  plan-2  H24   0.020
 X2E  plan-2  H26   0.020
 X2E  plan-3  C02   0.020
 X2E  plan-3  N02   0.020
 X2E  plan-3  HN02  0.020
 X2E  plan-3  HN0A  0.020

