# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:40:26 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-{[(3S)-3-amino-1-(5-ethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)pyrrolidin-3-yl]methyl}-2,4-difluorobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c[nH]c2ncnc(N3CC[C@](N)(CNC(=O)c4ccc(F)cc4F)C3)c12
#
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
 WFE  WFE  N-{[(3S)-3-amino-1-(5-ethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)pyrrolidin-3-yl]methyl}-2,4-difluorobenzamide  ligand  51  29  .  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_WFE
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
 WFE  C1    C  CH3   0  -0.669   2.6268   2.7729  -1.0441
 WFE  C2    C  CH2   0  -0.558   3.3983   1.8858  -2.0201
 WFE  C3    C  CR5   0  -0.013   4.5407   1.1706  -1.3706
 WFE  C4    C  CR15  0  -0.069   5.8422   1.4553  -1.6654
 WFE  N5    N  NR15  0  -0.659   6.6844   0.7755  -0.8268
 WFE  C6    C  CR56  0   0.468   5.9501   0.0590   0.0480
 WFE  N7    N  N     0  -0.452   6.4575  -0.6407   1.0652
 WFE  C8    C  CR16  0   0.035   5.5248  -1.1694   1.8260
 WFE  N9    N  N     0  -0.491   4.2121  -1.1361   1.6377
 WFE  C10   C  CR6   0   0.459   3.7073  -0.5000   0.5730
 WFE  N11   N  NT    0  -0.489   2.3730  -0.6277   0.4022
 WFE  C12   C  CH2   0  -0.316   1.6879  -0.5562  -0.8876
 WFE  C13   C  CH2   0  -0.465   0.5028  -1.4928  -0.7126
 WFE  C14   C  CT    0   0.031   0.1772  -1.3887   0.7842
 WFE  N15   N  NH2   0  -0.800  -0.5896  -2.4791   1.3496
 WFE  C16   C  CH2   0  -0.273  -0.5247  -0.0647   1.1201
 WFE  N17   N  NH1   0  -0.644  -1.8342   0.0627   0.5219
 WFE  C18   C  C     0   0.527  -2.9882  -0.0254   1.2119
 WFE  O19   O  O     0  -0.468  -3.0549  -0.2451   2.4093
 WFE  C20   C  CR6   0  -0.266  -4.2156   0.1453   0.3752
 WFE  C21   C  CR16  0  -0.238  -4.3503  -0.4929  -0.8562
 WFE  C22   C  CR16  0  -0.412  -5.5075  -0.3865  -1.6098
 WFE  C23   C  CR6   0   0.552  -6.5394   0.3856  -1.1126
 WFE  F24   F  F     0  -0.302  -7.6625   0.5086  -1.8247
 WFE  C25   C  CR16  0  -0.557  -6.4557   1.0449   0.0990
 WFE  C26   C  CR6   0   0.567  -5.2903   0.9020   0.8246
 WFE  F27   F  F     0  -0.291  -5.1965   1.5540   1.9844
 WFE  C28   C  CH2   0  -0.247   1.5839  -1.3599   1.3838
 WFE  C29   C  CR56  0  -0.088   4.5851   0.2342  -0.2690
 WFE  H1    H  HCH3  0   0.231   1.7748   3.2450  -1.5346
 WFE  H1A   H  HCH3  0   0.220   2.2502   2.2078  -0.1897
 WFE  H1B   H  HCH3  0   0.230   3.2687   3.5622  -0.6514
 WFE  H2    H  HCH2  0   0.238   2.7194   1.1943  -2.5197
 WFE  H2A   H  HCH2  0   0.249   3.8072   2.5116  -2.8167
 WFE  H4    H  HCR5  0   0.285   6.2345   2.1255  -2.4137
 WFE  H8    H  HCR6  0   0.242   5.8618  -1.7102   2.7049
 WFE  H12   H  HCH2  0   0.245   1.3407   0.4566  -1.0977
 WFE  H12A  H  HCH2  0   0.262   2.3469  -0.8615  -1.7017
 WFE  H13   H  HCH2  0   0.250  -0.3314  -1.2410  -1.3695
 WFE  H13A  H  HCH2  0   0.253   0.7949  -2.5223  -0.9354
 WFE  HN15  H  HNH2  0   0.348  -1.5119  -2.5027   0.9316
 WFE  HN1A  H  HNH2  0   0.348  -0.1592  -3.3622   1.0989
 WFE  H16   H  HCH2  0   0.267  -0.6275   0.0155   2.2015
 WFE  H16A  H  HCH2  0   0.262   0.0828   0.7808   0.7912
 WFE  HN17  H  HNH1  0   0.411  -1.8790   0.4019  -0.4254
 WFE  H21   H  HCR6  0   0.285  -3.5418  -1.1066  -1.2317
 WFE  H22   H  HCR6  0   0.294  -5.6029  -0.8962  -2.5584
 WFE  H25   H  HCR6  0   0.310  -7.2695   1.6558   0.4670
 WFE  H28   H  HCH2  0   0.243   1.9580  -2.3806   1.5177
 WFE  H28A  H  HCH2  0   0.249   1.6143  -0.8747   2.3612
 WFE  HN5   H  HNR5  0   0.409   7.6891   0.8426  -0.8201

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
 WFE  C2   C1    single    1.528  0.020  1.528
 WFE  C1   H1    single    0.970  0.020  1.090
 WFE  C1   H1A   single    0.970  0.020  1.090
 WFE  C1   H1B   single    0.970  0.020  1.090
 WFE  C2   C3    single    1.496  0.020  1.496
 WFE  C2   H2    single    0.970  0.020  1.090
 WFE  C2   H2A   single    0.970  0.020  1.090
 WFE  C3   C29   aromatic  1.447  0.020  1.447
 WFE  C3   C4    aromatic  1.365  0.020  1.365
 WFE  C4   N5    aromatic  1.369  0.020  1.369
 WFE  C4   H4    single    0.930  0.020  1.080
 WFE  C6   N5    aromatic  1.348  0.020  1.348
 WFE  C29  C6    aromatic  1.412  0.020  1.412
 WFE  C6   N7    aromatic  1.335  0.020  1.335
 WFE  C8   N7    aromatic  1.315  0.020  1.315
 WFE  N9   C8    aromatic  1.327  0.020  1.327
 WFE  C8   H8    single    0.930  0.020  1.080
 WFE  C10  N9    aromatic  1.339  0.020  1.339
 WFE  N11  C10   single    1.351  0.020  1.351
 WFE  C10  C29   aromatic  1.421  0.020  1.421
 WFE  C28  N11   single    1.457  0.020  1.457
 WFE  C12  N11   single    1.462  0.020  1.462
 WFE  C13  C12   single    1.521  0.020  1.521
 WFE  C12  H12   single    0.970  0.020  1.090
 WFE  C12  H12A  single    0.970  0.020  1.090
 WFE  C14  C13   single    1.535  0.020  1.535
 WFE  C13  H13   single    0.970  0.020  1.090
 WFE  C13  H13A  single    0.970  0.020  1.090
 WFE  C16  C14   single    1.536  0.020  1.536
 WFE  N15  C14   single    1.448  0.020  1.448
 WFE  C14  C28   single    1.529  0.020  1.529
 WFE  N15  HN15  single    0.890  0.020  1.040
 WFE  N15  HN1A  single    0.890  0.020  1.040
 WFE  C16  N17   single    1.445  0.020  1.445
 WFE  C16  H16   single    0.970  0.020  1.090
 WFE  C16  H16A  single    0.970  0.020  1.090
 WFE  N17  C18   single    1.347  0.020  1.347
 WFE  N17  HN17  single    0.860  0.020  1.020
 WFE  O19  C18   double    1.219  0.020  1.219
 WFE  C18  C20   single    1.495  0.020  1.495
 WFE  C21  C20   aromatic  1.393  0.020  1.393
 WFE  C20  C26   aromatic  1.389  0.020  1.389
 WFE  C21  C22   aromatic  1.385  0.020  1.385
 WFE  C21  H21   single    0.930  0.020  1.080
 WFE  C22  C23   aromatic  1.381  0.020  1.381
 WFE  C22  H22   single    0.930  0.020  1.080
 WFE  C23  C25   aromatic  1.382  0.020  1.382
 WFE  C23  F24   single    1.336  0.020  1.336
 WFE  C26  C25   aromatic  1.380  0.020  1.380
 WFE  C25  H25   single    0.930  0.020  1.080
 WFE  C26  F27   single    1.334  0.020  1.334
 WFE  C28  H28   single    0.970  0.020  1.090
 WFE  C28  H28A  single    0.970  0.020  1.090
 WFE  N5   HN5   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
 WFE  H1B   C1   H1A   107.22  3.000
 WFE  H1B   C1   H1    107.97  3.000
 WFE  H1A   C1   H1    107.85  3.000
 WFE  H1B   C1   C2    110.67  3.000
 WFE  H1A   C1   C2    111.94  3.000
 WFE  H1    C1   C2    111.01  3.000
 WFE  H2A   C2   H2    105.21  3.000
 WFE  H2A   C2   C3    107.73  3.000
 WFE  H2    C2   C3    111.79  3.000
 WFE  H2A   C2   C1    108.80  3.000
 WFE  H2    C2   C1    110.27  3.000
 WFE  C3    C2   C1    112.69  3.000
 WFE  C29   C3   C4    105.68  3.000
 WFE  C4    C3   C2    122.33  3.000
 WFE  C29   C3   C2    131.57  3.000
 WFE  H4    C4   N5    120.65  3.000
 WFE  H4    C4   C3    128.79  3.000
 WFE  N5    C4   C3    110.54  3.000
 WFE  HN5   N5   C6    125.07  3.000
 WFE  HN5   N5   C4    125.78  3.000
 WFE  C6    N5   C4    109.04  3.000
 WFE  C29   C6   N7    127.12  3.000
 WFE  N7    C6   N5    124.47  3.000
 WFE  C29   C6   N5    108.35  3.000
 WFE  C8    N7   C6    112.46  3.000
 WFE  H8    C8   N9    115.76  3.000
 WFE  H8    C8   N7    116.65  3.000
 WFE  N9    C8   N7    127.58  3.000
 WFE  C10   N9   C8    119.86  3.000
 WFE  C29   C10  N11   125.73  3.000
 WFE  C29   C10  N9    118.93  3.000
 WFE  N11   C10  N9    115.33  3.000
 WFE  C28   N11  C12   111.42  3.000
 WFE  C12   N11  C10   124.72  3.000
 WFE  C28   N11  C10   119.82  3.000
 WFE  H12A  C12  H12   107.96  3.000
 WFE  H12A  C12  C13   112.60  3.000
 WFE  H12   C12  C13   110.24  3.000
 WFE  H12A  C12  N11   111.19  3.000
 WFE  H12   C12  N11   111.36  3.000
 WFE  C13   C12  N11   103.50  3.000
 WFE  H13A  C13  H13   107.39  3.000
 WFE  H13A  C13  C14   108.62  3.000
 WFE  H13   C13  C14   114.15  3.000
 WFE  H13A  C13  C12   110.39  3.000
 WFE  H13   C13  C12   112.60  3.000
 WFE  C14   C13  C12   103.63  3.000
 WFE  C28   C14  C16   108.57  3.000
 WFE  C28   C14  N15   110.37  3.000
 WFE  C16   C14  N15   108.77  3.000
 WFE  C28   C14  C13   100.86  3.000
 WFE  N15   C14  C13   116.22  3.000
 WFE  C16   C14  C13   111.63  3.000
 WFE  HN1A  N15  HN15  105.32  3.000
 WFE  HN1A  N15  C14   109.55  3.000
 WFE  HN15  N15  C14   109.79  3.000
 WFE  H16A  C16  H16   107.13  3.000
 WFE  H16A  C16  N17   108.12  3.000
 WFE  H16   C16  N17   108.60  3.000
 WFE  H16A  C16  C14   110.33  3.000
 WFE  H16   C16  C14   108.89  3.000
 WFE  N17   C16  C14   113.55  3.000
 WFE  HN17  N17  C18   117.75  3.000
 WFE  HN17  N17  C16   117.34  3.000
 WFE  C18   N17  C16   123.93  3.000
 WFE  C20   C18  O19   121.68  3.000
 WFE  C20   C18  N17   114.14  3.000
 WFE  O19   C18  N17   124.16  3.000
 WFE  C26   C20  C21   117.42  3.000
 WFE  C26   C20  C18   121.08  3.000
 WFE  C21   C20  C18   121.44  3.000
 WFE  H21   C21  C22   118.61  3.000
 WFE  H21   C21  C20   119.61  3.000
 WFE  C22   C21  C20   121.77  3.000
 WFE  H22   C22  C23   120.89  3.000
 WFE  H22   C22  C21   121.00  3.000
 WFE  C23   C22  C21   118.11  3.000
 WFE  C25   C23  F24   118.33  3.000
 WFE  F24   C23  C22   119.19  3.000
 WFE  C25   C23  C22   122.48  3.000
 WFE  H25   C25  C26   120.97  3.000
 WFE  H25   C25  C23   121.46  3.000
 WFE  C26   C25  C23   117.56  3.000
 WFE  F27   C26  C25   117.77  3.000
 WFE  F27   C26  C20   119.55  3.000
 WFE  C25   C26  C20   122.65  3.000
 WFE  H28A  C28  H28   107.17  3.000
 WFE  H28A  C28  C14   112.64  3.000
 WFE  H28   C28  C14   110.15  3.000
 WFE  H28A  C28  N11   111.40  3.000
 WFE  H28   C28  N11   111.46  3.000
 WFE  C14   C28  N11   104.10  3.000
 WFE  C10   C29  C6    113.58  3.000
 WFE  C10   C29  C3    140.08  3.000
 WFE  C6    C29  C3    106.32  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
 WFE  CONST_01  N5    C6   C29  C3      0.00   0.0  0
 WFE  CONST_02  N7    C6   C29  C3    180.00   0.0  0
 WFE  CONST_03  N9    C10  C29  C3    180.00   0.0  0
 WFE  CONST_04  C6    N5   C4   C3      0.00   0.0  0
 WFE  CONST_05  C6    C29  C3   C4      0.00   0.0  0
 WFE  CONST_06  C10   C29  C3   C4    180.00   0.0  0
 WFE  CONST_07  C29   C6   N5   C4      0.00   0.0  0
 WFE  CONST_08  N7    C6   N5   C4    180.00   0.0  0
 WFE  CONST_09  C29   C3   C4   N5      0.00   0.0  0
 WFE  CONST_10  C10   C29  C6   N5    180.00   0.0  0
 WFE  CONST_11  C8    N7   C6   N5    180.00   0.0  0
 WFE  CONST_12  N9    C10  C29  C6      0.00   0.0  0
 WFE  CONST_13  N9    C8   N7   C6      0.00   0.0  0
 WFE  CONST_14  C10   C29  C6   N7      0.00   0.0  0
 WFE  CONST_15  C10   N9   C8   N7      0.00   0.0  0
 WFE  CONST_16  C29   C6   N7   C8      0.00   0.0  0
 WFE  CONST_17  C29   C10  N9   C8      0.00   0.0  0
 WFE  CONST_18  C23   C22  C21  C20     0.00   0.0  0
 WFE  CONST_19  C23   C25  C26  C20     0.00   0.0  0
 WFE  CONST_20  C25   C26  C20  C21     0.00   0.0  0
 WFE  CONST_21  C25   C23  C22  C21     0.00   0.0  0
 WFE  CONST_22  C26   C20  C21  C22     0.00   0.0  0
 WFE  CONST_23  C26   C25  C23  C22     0.00   0.0  0
 WFE  CONST_24  N11   C10  C29  C3      0.00   0.0  0
 WFE  CONST_25  N11   C10  C29  C6    180.00   0.0  0
 WFE  CONST_26  N11   C10  N9   C8    180.00   0.0  0
 WFE  CONST_27  C6    C29  C3   C2    180.00   0.0  0
 WFE  CONST_28  C10   C29  C3   C2      0.00   0.0  0
 WFE  CONST_29  N5    C4   C3   C2    180.00   0.0  0
 WFE  CONST_30  C22   C21  C20  C18   180.00   0.0  0
 WFE  CONST_31  C25   C26  C20  C18   180.00   0.0  0
 WFE  CONST_32  F27   C26  C20  C21   180.00   0.0  0
 WFE  CONST_33  F24   C23  C22  C21   180.00   0.0  0
 WFE  CONST_34  F27   C26  C25  C23   180.00   0.0  0
 WFE  CONST_35  C26   C25  C23  F24   180.00   0.0  0
 WFE  CONST_36  HN5   N5   C4   C3    180.00   0.0  0
 WFE  CONST_37  H4    C4   N5   C6    180.00   0.0  0
 WFE  CONST_38  H8    C8   N7   C6    180.00   0.0  0
 WFE  CONST_39  H22   C22  C21  C20   180.00   0.0  0
 WFE  CONST_40  H25   C25  C26  C20   180.00   0.0  0
 WFE  CONST_41  H21   C21  C22  C23   180.00   0.0  0
 WFE  CONST_42  C20   C18  N17  C16   180.00   0.0  0
 WFE  CONST_43  HN17  N17  C18  C20     0.00   0.0  0
 WFE  CONST_44  O19   C18  N17  C16     0.00   0.0  0
 WFE  Var_01    C28   N11  C10  N9      3.12  30.0  2
 WFE  Var_02    C14   C28  N11  C10  -175.14  30.0  1
 WFE  Var_03    C13   C12  N11  C10   148.34  30.0  1
 WFE  Var_04    C14   C13  C12  N11    30.73  30.0  1
 WFE  Var_05    C29   C3   C2   C1     59.42  30.0  2
 WFE  Var_06    C21   C20  C18  N17    44.74  30.0  2
 WFE  Var_07    C18   N17  C16  C14   107.12  30.0  3
 WFE  Var_08    H1    C1   C2   C3   -177.43  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
 WFE  chir_01  C14  C13  N15  C28  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
 WFE  plan-1  C18   0.020
 WFE  plan-1  C20   0.020
 WFE  plan-1  C21   0.020
 WFE  plan-1  C22   0.020
 WFE  plan-1  C23   0.020
 WFE  plan-1  F24   0.020
 WFE  plan-1  C25   0.020
 WFE  plan-1  C26   0.020
 WFE  plan-1  F27   0.020
 WFE  plan-1  H21   0.020
 WFE  plan-1  H22   0.020
 WFE  plan-1  H25   0.020
 WFE  plan-2  C2    0.020
 WFE  plan-2  C3    0.020
 WFE  plan-2  C4    0.020
 WFE  plan-2  N5    0.020
 WFE  plan-2  C6    0.020
 WFE  plan-2  N7    0.020
 WFE  plan-2  C8    0.020
 WFE  plan-2  N9    0.020
 WFE  plan-2  C10   0.020
 WFE  plan-2  N11   0.020
 WFE  plan-2  C29   0.020
 WFE  plan-2  H4    0.020
 WFE  plan-2  H8    0.020
 WFE  plan-2  HN5   0.020
 WFE  plan-3  C16   0.020
 WFE  plan-3  N17   0.020
 WFE  plan-3  C18   0.020
 WFE  plan-3  O19   0.020
 WFE  plan-3  C20   0.020
 WFE  plan-3  HN17  0.020

