# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 23:46:59 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N-{4-[4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-2-yl}-N'-(2,4-difluorophenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1cc(C(=O)c2ccnc(NC(=O)Nc3ccc(F)cc3F)c2)c4c(N)ncnc14
#
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
 6K0  6K0  N-{4-[4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-2-yl}-N'-(2,4-difluorophenyl)urea  ligand  52  33  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6K0
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
 6K0  C5   C  CR15  0   0.023  -4.9041   1.7084  -0.1759
 6K0  C6   C  CR5   0  -0.129  -3.6932   1.0528  -0.1784
 6K0  C7   C  C     0   0.324  -2.4385   1.7929  -0.1998
 6K0  C10  C  CR16  0  -0.347  -1.4085   0.5704   1.7443
 6K0  N12  N  N     0  -0.413   0.9614   0.2760   1.8866
 6K0  C13  C  CR6   0   0.536   1.0954   0.8731   0.7141
 6K0  C15  C  C     0   0.716   3.4709   0.2625   0.4124
 6K0  C20  C  CR16  0  -0.427   7.6595  -1.0237   0.8989
 6K0  C21  C  CR6   0   0.540   8.2216  -1.2961  -0.3331
 6K0  C24  C  CR6   0   0.527   6.4125  -0.2551  -1.4339
 6K0  C26  C  CR16  0  -0.419   0.0086   1.3845  -0.0019
 6K0  C28  C  CR6   0   0.402  -3.3469  -1.5984  -0.1749
 6K0  C2   C  CH1   0  -0.126  -7.3442   1.1487   0.0651
 6K0  C3   C  CH3   0  -0.675  -7.7422   2.2659  -0.8858
 6K0  N4   N  NR5   0  -0.506  -5.9226   0.8258  -0.0705
 6K0  O8   O  O     0  -0.392  -2.3381   2.8811  -0.7360
 6K0  C9   C  CR6   0  -0.010  -1.2609   1.2218   0.5225
 6K0  C11  C  CR16  0  -0.051  -0.2620   0.1314   2.3806
 6K0  O16  O  O     0  -0.474   3.4702  -0.7472   1.0825
 6K0  N17  N  NH1   0  -0.773   4.5894   0.7506  -0.2068
 6K0  C18  C  CR6   0   0.158   5.8046   0.0525  -0.2225
 6K0  C19  C  CR16  0  -0.253   6.4551  -0.3393   0.9430
 6K0  C23  C  CR16  0  -0.565   7.6220  -0.9144  -1.5173
 6K0  F25  F  F     0  -0.299   5.8030   0.1119  -2.5665
 6K0  C27  C  CR56  0  -0.107  -4.0058  -0.3492  -0.0854
 6K0  N29  N  NH2   0  -0.816  -2.0298  -1.7421  -0.3711
 6K0  N30  N  N     0  -0.469  -4.0634  -2.7208  -0.0584
 6K0  C31  C  CR16  0   0.045  -5.3812  -2.6380   0.0756
 6K0  N32  N  N     0  -0.460  -6.1228  -1.5491   0.0828
 6K0  C33  C  CR56  0   0.513  -5.4000  -0.4358  -0.0115
 6K0  H1   H  HCR5  0   0.313  -5.0809   2.7718  -0.1999
 6K0  H2   H  HCR6  0   0.281  -2.3775   0.4238   2.2006
 6K0  H3   H  HCR6  0   0.289   8.1564  -1.3243   1.8110
 6K0  H4   H  HCR6  0   0.289   0.1591   1.8775  -0.9542
 6K0  H5   H  HCH3  0   0.242  -8.7411   1.6737   1.6181
 6K0  H6   H  HCH3  0   0.243  -7.4181   0.6502   2.1766
 6K0  H7   H  HCH3  0   0.231  -7.1338   2.3653   1.8470
 6K0  H8   H  HCH1  0   0.270  -7.8736   0.2402  -0.2225
 6K0  H9   H  HCH3  0   0.232  -7.3090   3.2244  -0.5969
 6K0  H10  H  HCH3  0   0.250  -7.4458   2.0442  -1.9108
 6K0  H11  H  HCH3  0   0.255  -8.8251   2.3816  -0.8650
 6K0  H12  H  HCR6  0   0.272  -0.3313  -0.3598   3.3443
 6K0  H13  H  HNH1  0   0.420   2.4225   1.7232  -0.5660
 6K0  H14  H  HNH1  0   0.413   4.5136   1.5616  -0.8019
 6K0  H15  H  HCR6  0   0.287   6.0188  -0.0988   1.9017
 6K0  H16  H  HCR6  0   0.308   8.0722  -1.1322  -2.4769
 6K0  H17  H  HNH2  0   0.408  -1.4456  -0.9715  -0.6398
 6K0  H18  H  HNH2  0   0.400  -1.6738  -2.6660  -0.5493
 6K0  H19  H  HCR6  0   0.252  -5.9055  -3.5828   0.1754
 6K0  N14  N  NH1   0  -0.773   2.3643   1.0507   0.1831
 6K0  C1   C  CH3   0  -0.644  -7.6740   1.4774   1.5146
 6K0  F22  F  F     0  -0.308   9.3901  -1.9468  -0.3901

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
 6K0  N29  C28  single    1.339  0.020  1.339
 6K0  N30  C28  aromatic  1.337  0.020  1.337
 6K0  N30  C31  aromatic  1.327  0.020  1.327
 6K0  C28  C27  aromatic  1.415  0.020  1.415
 6K0  O8   C7   double    1.217  0.020  1.217
 6K0  C31  N32  aromatic  1.318  0.020  1.318
 6K0  C7   C9   single    1.495  0.020  1.495
 6K0  C7   C6   single    1.457  0.020  1.457
 6K0  C27  C6   aromatic  1.439  0.020  1.439
 6K0  C27  C33  aromatic  1.399  0.020  1.399
 6K0  C19  C20  aromatic  1.386  0.020  1.386
 6K0  C19  C18  aromatic  1.391  0.020  1.391
 6K0  C26  C9   aromatic  1.383  0.020  1.383
 6K0  C26  C13  aromatic  1.398  0.020  1.398
 6K0  C20  C21  aromatic  1.381  0.020  1.381
 6K0  C9   C10  aromatic  1.392  0.020  1.392
 6K0  C6   C5   aromatic  1.377  0.020  1.377
 6K0  C15  N17  single    1.368  0.020  1.368
 6K0  C15  N14  single    1.378  0.020  1.378
 6K0  C15  O16  double    1.212  0.020  1.212
 6K0  N17  C18  single    1.402  0.020  1.402
 6K0  C18  C24  aromatic  1.390  0.020  1.390
 6K0  C13  N14  single    1.387  0.020  1.387
 6K0  C13  N12  aromatic  1.323  0.020  1.323
 6K0  N32  C33  aromatic  1.331  0.020  1.331
 6K0  C33  N4   aromatic  1.367  0.020  1.367
 6K0  C10  C11  aromatic  1.383  0.020  1.383
 6K0  C21  F22  single    1.339  0.020  1.339
 6K0  C21  C23  aromatic  1.381  0.020  1.381
 6K0  N12  C11  aromatic  1.327  0.020  1.327
 6K0  C24  C23  aromatic  1.380  0.020  1.380
 6K0  C24  F25  single    1.338  0.020  1.338
 6K0  C5   N4   aromatic  1.352  0.020  1.352
 6K0  N4   C2   single    1.464  0.020  1.464
 6K0  C2   C3   single    1.520  0.020  1.520
 6K0  C2   C1   single    1.522  0.020  1.522
 6K0  C5   H1   single    0.930  0.020  1.080
 6K0  C10  H2   single    0.930  0.020  1.080
 6K0  C20  H3   single    0.930  0.020  1.080
 6K0  C26  H4   single    0.930  0.020  1.080
 6K0  C1   H5   single    0.970  0.020  1.090
 6K0  C1   H6   single    0.970  0.020  1.090
 6K0  C1   H7   single    0.970  0.020  1.090
 6K0  C2   H8   single    0.970  0.020  1.090
 6K0  C3   H9   single    0.970  0.020  1.090
 6K0  C3   H10  single    0.970  0.020  1.090
 6K0  C3   H11  single    0.970  0.020  1.090
 6K0  C11  H12  single    0.930  0.020  1.080
 6K0  N14  H13  single    0.860  0.020  1.020
 6K0  N17  H14  single    0.860  0.020  1.020
 6K0  C19  H15  single    0.930  0.020  1.080
 6K0  C23  H16  single    0.930  0.020  1.080
 6K0  N29  H17  single    0.890  0.020  1.040
 6K0  N29  H18  single    0.890  0.020  1.040
 6K0  C31  H19  single    0.930  0.020  1.080

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
 6K0  H1   C5   N4   121.47  3.000
 6K0  H1   C5   C6   127.86  3.000
 6K0  N4   C5   C6   110.60  3.000
 6K0  C27  C6   C7   133.06  3.000
 6K0  C27  C6   C5   105.82  3.000
 6K0  C7   C6   C5   121.03  3.000
 6K0  C9   C7   O8   119.31  3.000
 6K0  C9   C7   C6   118.50  3.000
 6K0  O8   C7   C6   122.12  3.000
 6K0  H2   C10  C11  120.39  3.000
 6K0  H2   C10  C9   121.93  3.000
 6K0  C11  C10  C9   117.67  3.000
 6K0  C11  N12  C13  118.20  3.000
 6K0  N14  C13  C26  117.92  3.000
 6K0  N14  C13  N12  119.33  3.000
 6K0  C26  C13  N12  122.70  3.000
 6K0  N17  C15  O16  123.22  3.000
 6K0  O16  C15  N14  124.62  3.000
 6K0  N17  C15  N14  112.16  3.000
 6K0  H3   C20  C19  120.65  3.000
 6K0  H3   C20  C21  120.70  3.000
 6K0  C19  C20  C21  118.65  3.000
 6K0  C23  C21  F22  118.47  3.000
 6K0  C23  C21  C20  122.25  3.000
 6K0  F22  C21  C20  119.28  3.000
 6K0  F25  C24  C23  118.64  3.000
 6K0  F25  C24  C18  118.56  3.000
 6K0  C23  C24  C18  122.80  3.000
 6K0  H4   C26  C9   120.96  3.000
 6K0  H4   C26  C13  120.58  3.000
 6K0  C9   C26  C13  118.44  3.000
 6K0  N30  C28  N29  116.73  3.000
 6K0  N30  C28  C27  119.09  3.000
 6K0  N29  C28  C27  124.18  3.000
 6K0  H8   C2   N4   105.26  3.000
 6K0  H8   C2   C3   108.68  3.000
 6K0  N4   C2   C3   111.00  3.000
 6K0  H8   C2   C1   109.02  3.000
 6K0  C3   C2   C1   112.35  3.000
 6K0  N4   C2   C1   110.25  3.000
 6K0  H11  C3   H10  108.06  3.000
 6K0  H11  C3   H9   107.24  3.000
 6K0  H10  C3   H9   108.65  3.000
 6K0  H11  C3   C2   109.05  3.000
 6K0  H10  C3   C2   111.57  3.000
 6K0  H9   C3   C2   112.09  3.000
 6K0  C33  N4   C2   124.80  3.000
 6K0  C2   N4   C5   126.50  3.000
 6K0  C33  N4   C5   108.54  3.000
 6K0  C26  C9   C10  119.01  3.000
 6K0  C10  C9   C7   121.28  3.000
 6K0  C26  C9   C7   119.66  3.000
 6K0  H12  C11  N12  116.06  3.000
 6K0  H12  C11  C10  120.00  3.000
 6K0  N12  C11  C10  123.94  3.000
 6K0  H14  N17  C18  117.32  3.000
 6K0  H14  N17  C15  119.49  3.000
 6K0  C18  N17  C15  122.42  3.000
 6K0  C19  C18  N17  122.44  3.000
 6K0  N17  C18  C24  119.95  3.000
 6K0  C19  C18  C24  117.61  3.000
 6K0  H15  C19  C18  119.46  3.000
 6K0  H15  C19  C20  119.28  3.000
 6K0  C18  C19  C20  121.25  3.000
 6K0  H16  C23  C24  120.95  3.000
 6K0  H16  C23  C21  121.61  3.000
 6K0  C24  C23  C21  117.43  3.000
 6K0  C33  C27  C28  114.37  3.000
 6K0  C33  C27  C6   106.27  3.000
 6K0  C28  C27  C6   138.99  3.000
 6K0  H18  N29  H17  116.85  3.000
 6K0  H18  N29  C28  118.20  3.000
 6K0  H17  N29  C28  121.96  3.000
 6K0  C31  N30  C28  119.25  3.000
 6K0  H19  C31  N32  116.56  3.000
 6K0  H19  C31  N30  115.77  3.000
 6K0  N32  C31  N30  127.66  3.000
 6K0  C33  N32  C31  112.67  3.000
 6K0  N32  C33  C27  126.65  3.000
 6K0  N32  C33  N4   124.59  3.000
 6K0  C27  C33  N4   108.76  3.000
 6K0  H13  N14  C15  117.30  3.000
 6K0  H13  N14  C13  115.00  3.000
 6K0  C15  N14  C13  126.72  3.000
 6K0  H7   C1   H6   108.44  3.000
 6K0  H7   C1   H5   108.01  3.000
 6K0  H6   C1   H5   107.99  3.000
 6K0  H7   C1   C2   111.00  3.000
 6K0  H6   C1   C2   111.32  3.000
 6K0  H5   C1   C2   109.96  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
 6K0  CONST_01  C28  C27  C6   C5    180.00   0.0  0
 6K0  CONST_02  C33  C27  C6   C5      0.00   0.0  0
 6K0  CONST_03  C27  C33  N4   C5      0.00   0.0  0
 6K0  CONST_04  N32  C33  N4   C5    180.00   0.0  0
 6K0  CONST_05  N30  C28  C27  C6    180.00   0.0  0
 6K0  CONST_06  N32  C33  C27  C6    180.00   0.0  0
 6K0  CONST_07  N4   C33  C27  C6      0.00   0.0  0
 6K0  CONST_08  C33  N4   C5   C6      0.00   0.0  0
 6K0  CONST_09  C13  C26  C9   C10     0.00   0.0  0
 6K0  CONST_10  C13  N12  C11  C10     0.00   0.0  0
 6K0  CONST_11  C9   C26  C13  N12     0.00   0.0  0
 6K0  CONST_12  C9   C10  C11  N12     0.00   0.0  0
 6K0  CONST_13  C24  C18  C19  C20     0.00   0.0  0
 6K0  CONST_14  C24  C23  C21  C20     0.00   0.0  0
 6K0  CONST_15  C18  C19  C20  C21     0.00   0.0  0
 6K0  CONST_16  C18  C24  C23  C21     0.00   0.0  0
 6K0  CONST_17  C11  C10  C9   C26     0.00   0.0  0
 6K0  CONST_18  C11  N12  C13  C26     0.00   0.0  0
 6K0  CONST_19  N32  C31  N30  C28     0.00   0.0  0
 6K0  CONST_20  N32  C33  C27  C28     0.00   0.0  0
 6K0  CONST_21  N4   C33  C27  C28   180.00   0.0  0
 6K0  CONST_22  C31  N32  C33  N4    180.00   0.0  0
 6K0  CONST_23  C27  C6   C5   N4      0.00   0.0  0
 6K0  CONST_24  C23  C21  C20  C19     0.00   0.0  0
 6K0  CONST_25  C23  C24  C18  C19     0.00   0.0  0
 6K0  CONST_26  C31  N30  C28  C27     0.00   0.0  0
 6K0  CONST_27  C31  N32  C33  C27     0.00   0.0  0
 6K0  CONST_28  C33  C27  C28  N30     0.00   0.0  0
 6K0  CONST_29  C33  N32  C31  N30     0.00   0.0  0
 6K0  CONST_30  N29  C28  C27  C6      0.00   0.0  0
 6K0  CONST_31  C2   N4   C5   C6    180.00   0.0  0
 6K0  CONST_32  C13  C26  C9   C7    180.00   0.0  0
 6K0  CONST_33  C11  C10  C9   C7    180.00   0.0  0
 6K0  CONST_34  C28  C27  C6   C7      0.00   0.0  0
 6K0  CONST_35  C33  C27  C6   C7    180.00   0.0  0
 6K0  CONST_36  N4   C5   C6   C7    180.00   0.0  0
 6K0  CONST_37  N17  C18  C19  C20   180.00   0.0  0
 6K0  CONST_38  F25  C24  C23  C21   180.00   0.0  0
 6K0  CONST_39  F22  C21  C23  C24   180.00   0.0  0
 6K0  CONST_40  C27  C33  N4   C2    180.00   0.0  0
 6K0  CONST_41  N32  C33  N4   C2      0.00   0.0  0
 6K0  CONST_42  N14  C13  C26  C9    180.00   0.0  0
 6K0  CONST_43  N14  C13  N12  C11   180.00   0.0  0
 6K0  CONST_44  C23  C24  C18  N17   180.00   0.0  0
 6K0  CONST_45  F22  C21  C20  C19   180.00   0.0  0
 6K0  CONST_46  F25  C24  C18  C19   180.00   0.0  0
 6K0  CONST_47  C31  N30  C28  N29   180.00   0.0  0
 6K0  CONST_48  C33  C27  C28  N29   180.00   0.0  0
 6K0  CONST_49  H4   C26  C9   C10   180.00   0.0  0
 6K0  CONST_50  H2   C10  C11  N12   180.00   0.0  0
 6K0  CONST_51  H12  C11  N12  C13   180.00   0.0  0
 6K0  CONST_52  H16  C23  C21  C20   180.00   0.0  0
 6K0  CONST_53  H15  C19  C20  C21   180.00   0.0  0
 6K0  CONST_54  H19  C31  N30  C28   180.00   0.0  0
 6K0  CONST_55  H3   C20  C19  C18   180.00   0.0  0
 6K0  CONST_56  H1   C5   C6   C27   180.00   0.0  0
 6K0  CONST_63  H17  N29  C28  C27     0.00   0.0  0
 6K0  CONST_64  H18  N29  C28  C27   180.00   0.0  0
 6K0  CONST_65  O16  C15  N14  C13     0.00   0.0  0
 6K0  CONST_66  C18  N17  C15  O16     0.00   0.0  0
 6K0  CONST_67  N17  C15  N14  C13   180.00   0.0  0
 6K0  CONST_68  C18  N17  C15  N14   180.00   0.0  0
 6K0  Var_01    C9   C7   C6   C5    146.48  30.0  2
 6K0  Var_02    C26  C9   C7   C6    144.24  30.0  2
 6K0  Var_03    C3   C2   N4   C5     43.48  30.0  2
 6K0  Var_04    H9   C3   C2   N4    -69.56  30.0  3
 6K0  Var_05    H5   C1   C2   N4   -177.50  30.0  3

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
 6K0  plan-1  C7   0.020
 6K0  plan-1  C10  0.020
 6K0  plan-1  N12  0.020
 6K0  plan-1  C13  0.020
 6K0  plan-1  C26  0.020
 6K0  plan-1  C9   0.020
 6K0  plan-1  C11  0.020
 6K0  plan-1  H2   0.020
 6K0  plan-1  H4   0.020
 6K0  plan-1  H12  0.020
 6K0  plan-1  N14  0.020
 6K0  plan-2  C6   0.020
 6K0  plan-2  C7   0.020
 6K0  plan-2  O8   0.020
 6K0  plan-2  C9   0.020
 6K0  plan-3  C20  0.020
 6K0  plan-3  C21  0.020
 6K0  plan-3  C24  0.020
 6K0  plan-3  N17  0.020
 6K0  plan-3  C18  0.020
 6K0  plan-3  C19  0.020
 6K0  plan-3  C23  0.020
 6K0  plan-3  F25  0.020
 6K0  plan-3  H3   0.020
 6K0  plan-3  H15  0.020
 6K0  plan-3  H16  0.020
 6K0  plan-3  F22  0.020
 6K0  plan-4  C5   0.020
 6K0  plan-4  C6   0.020
 6K0  plan-4  C7   0.020
 6K0  plan-4  C28  0.020
 6K0  plan-4  C2   0.020
 6K0  plan-4  N4   0.020
 6K0  plan-4  C27  0.020
 6K0  plan-4  N29  0.020
 6K0  plan-4  N30  0.020
 6K0  plan-4  C31  0.020
 6K0  plan-4  N32  0.020
 6K0  plan-4  C33  0.020
 6K0  plan-4  H1   0.020
 6K0  plan-4  H19  0.020
 6K0  plan-5  C13  0.020
 6K0  plan-5  C15  0.020
 6K0  plan-5  O16  0.020
 6K0  plan-5  N17  0.020
 6K0  plan-5  C18  0.020
 6K0  plan-5  H13  0.020
 6K0  plan-5  H14  0.020
 6K0  plan-5  N14  0.020
 6K0  plan-6  C28  0.020
 6K0  plan-6  N29  0.020
 6K0  plan-6  H17  0.020
 6K0  plan-6  H18  0.020

