# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 17:41:01 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: methyl 4-[(3-{(1R)-2-cyano-1-[(5-methyl-3H-imidazo[4,5-b]pyridin-2-yl)amino]ethyl}phenyl)methyl]piperidine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)N1CCC(CC1)Cc2cccc(c2)[C@@H](CC#N)Nc3[nH]c4nc(C)ccc4n3
#
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
 F0Y  F0Y  'methyl 4-[(3-{(1R)-2-cyano-1-[(5-methyl-3H-imidazo[4,5-b]pyridin-2-yl)amino]ethyl}phenyl)methyl]piperidine-1-carboxylate'  ligand  60  32  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_F0Y
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
 F0Y  C1   C  C     0   0.756  -6.6555  -1.8060   0.4432
 F0Y  C2   C  CH2   0  -0.316  -5.3132  -0.1152  -0.7892
 F0Y  C3   C  CH2   0  -0.413  -3.9287   0.1944  -0.2322
 F0Y  O1   O  O     0  -0.533  -7.3145  -2.1884   1.3929
 F0Y  C11  C  CR16  0  -0.392  -0.5490   1.2070   0.1546
 F0Y  C12  C  CH1   0  -0.240   1.5300   0.7562  -1.1762
 F0Y  C13  C  CH2   0  -0.514   1.3928   0.3675  -2.6624
 F0Y  C14  C  CSP   0   0.116   2.4663  -0.5166  -3.0849
 F0Y  C15  C  CR5   0   0.699   3.8930   0.7559  -0.3866
 F0Y  C16  C  CR56  0   0.111   5.8733   0.3948   0.3014
 F0Y  C17  C  CR16  0  -0.242   7.2053   0.3967   0.6728
 F0Y  C18  C  CR16  0  -0.351   7.6960  -0.7642   1.2679
 F0Y  C19  C  CR6   0   0.209   6.8767  -1.8751   1.4730
 F0Y  C20  C  CH3   0  -0.720   7.4074  -3.1266   2.1049
 F0Y  C21  C  CR56  0   0.429   5.1480  -0.7821   0.5603
 F0Y  C22  C  CH2   0  -0.421  -5.0078   0.7613   1.9514
 F0Y  C23  C  CH2   0  -0.316  -6.3610   0.4340   1.3330
 F0Y  N1   N  NS    0  -0.260   3.3230  -1.2166  -3.4000
 F0Y  N2   N  NH1   0  -0.676   2.8059   1.3689  -0.8959
 F0Y  N5   N  NR15  0  -0.731   3.8767  -0.5177   0.1077
 F0Y  N4   N  N     0  -0.443   5.5849  -1.8846   1.1146
 F0Y  N3   N  N     0  -0.532   5.0669   1.3348  -0.2906
 F0Y  C10  C  CR6   0   0.212   0.3877   1.6580  -0.7683
 F0Y  C9   C  CR16  0  -0.335   0.2526   2.9334  -1.3066
 F0Y  C8   C  CR16  0  -0.221  -0.8012   3.7429  -0.9067
 F0Y  C7   C  CR16  0  -0.318  -1.7258   3.2834   0.0199
 F0Y  C6   C  CR6   0   0.166  -1.6152   2.0042   0.5596
 F0Y  C5   C  CH2   0  -0.500  -2.6374   1.4920   1.5351
 F0Y  C4   C  CH1   0  -0.243  -4.0033   1.2205   0.8961
 F0Y  N    N  NT    0  -0.477  -6.2140  -0.5438   0.2690
 F0Y  O    O  O2    0  -0.481  -6.3090  -2.6118  -0.5656
 F0Y  C    C  CH3   0  -0.410  -6.7736  -3.9551  -0.5069
 F0Y  H1   H  HCH2  0   0.237  -5.7342   0.7883  -1.2432
 F0Y  H2   H  HCH2  0   0.270  -5.2556  -0.8637  -1.5731
 F0Y  H3   H  HCH2  0   0.221  -3.4696  -0.7309   0.1338
 F0Y  H4   H  HCH2  0   0.241  -3.2992   0.5624  -1.0460
 F0Y  H5   H  HCR6  0   0.251  -0.4461   0.2100   0.5697
 F0Y  H6   H  HCH1  0   0.291   1.4493  -0.1547  -0.5837
 F0Y  H7   H  HCH2  0   0.327   0.4387  -0.1348  -2.8307
 F0Y  H8   H  HCH2  0   0.319   1.4103   1.2557  -3.2965
 F0Y  H9   H  HCR6  0   0.260   7.8437   1.2565   0.5147
 F0Y  H10  H  HCR6  0   0.256   8.7319  -0.8104   1.5765
 F0Y  H11  H  HCH3  0   0.245   6.8018  -3.4197   2.9634
 F0Y  H12  H  HCH3  0   0.246   7.3897  -3.9595   1.3995
 F0Y  H13  H  HCH3  0   0.241   8.4338  -2.9991   2.4448
 F0Y  H14  H  HCH2  0   0.239  -5.1376   1.5349   2.7129
 F0Y  H15  H  HCH2  0   0.223  -4.6231  -0.1285   2.4613
 F0Y  H16  H  HCH2  0   0.264  -7.0514   0.0600   2.0842
 F0Y  H17  H  HCH2  0   0.238  -6.8036   1.3413   0.9090
 F0Y  H18  H  HNH1  0   0.407   2.9796   2.2944  -1.2572
 F0Y  H19  H  HNR5  0   0.423   3.1033  -1.1623   0.1432
 F0Y  H21  H  HCR6  0   0.256   0.9588   3.3111  -2.0374
 F0Y  H22  H  HCR6  0   0.259  -0.9010   4.7385  -1.3196
 F0Y  H23  H  HCR6  0   0.251  -2.5407   3.9287   0.3278
 F0Y  H24  H  HCH2  0   0.239  -2.2718   0.5730   2.0021
 F0Y  H25  H  HCH2  0   0.250  -2.7689   2.2213   2.3399
 F0Y  H26  H  HCH1  0   0.226  -4.3698   2.1636   0.4684
 F0Y  H27  H  HCH3  0   0.232  -6.4057  -4.4745   0.3780
 F0Y  H28  H  HCH3  0   0.232  -7.8625  -4.0084  -0.5258
 F0Y  H29  H  HCH3  0   0.246  -6.3798  -4.4431  -1.3942

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
 F0Y  C    O    single    1.423  0.020  1.423
 F0Y  C23  N    single    1.452  0.020  1.452
 F0Y  C23  C22  single    1.523  0.020  1.523
 F0Y  O    C1   single    1.337  0.020  1.337
 F0Y  N    C1   single    1.349  0.020  1.349
 F0Y  N    C2   single    1.454  0.020  1.454
 F0Y  C1   O1   double    1.218  0.020  1.218
 F0Y  C22  C4   single    1.528  0.020  1.528
 F0Y  C2   C3   single    1.524  0.020  1.524
 F0Y  C4   C3   single    1.527  0.020  1.527
 F0Y  C4   C5   single    1.532  0.020  1.532
 F0Y  C18  C17  aromatic  1.394  0.020  1.394
 F0Y  C18  C19  aromatic  1.396  0.020  1.396
 F0Y  C20  C19  single    1.499  0.020  1.499
 F0Y  C17  C16  aromatic  1.383  0.020  1.383
 F0Y  C5   C6   single    1.503  0.020  1.503
 F0Y  C19  N4   aromatic  1.341  0.020  1.341
 F0Y  C7   C6   aromatic  1.393  0.020  1.393
 F0Y  C7   C8   aromatic  1.387  0.020  1.387
 F0Y  C6   C11  aromatic  1.392  0.020  1.392
 F0Y  C8   C9   aromatic  1.388  0.020  1.388
 F0Y  C16  C21  aromatic  1.407  0.020  1.407
 F0Y  C16  N3   aromatic  1.373  0.020  1.373
 F0Y  N4   C21  aromatic  1.309  0.020  1.309
 F0Y  C21  N5   aromatic  1.375  0.020  1.375
 F0Y  N3   C15  aromatic  1.312  0.020  1.312
 F0Y  C11  C10  aromatic  1.390  0.020  1.390
 F0Y  C9   C10  aromatic  1.391  0.020  1.391
 F0Y  C10  C12  single    1.511  0.020  1.511
 F0Y  N5   C15  aromatic  1.366  0.020  1.366
 F0Y  C15  N2   single    1.348  0.020  1.348
 F0Y  C12  N2   single    1.443  0.020  1.443
 F0Y  C12  C13  single    1.542  0.020  1.542
 F0Y  C13  C14  single    1.453  0.020  1.453
 F0Y  C14  N1   triple    1.150  0.020  1.150
 F0Y  C2   H1   single    0.970  0.020  1.090
 F0Y  C2   H2   single    0.970  0.020  1.090
 F0Y  C3   H3   single    0.970  0.020  1.090
 F0Y  C3   H4   single    0.970  0.020  1.090
 F0Y  C11  H5   single    0.930  0.020  1.080
 F0Y  C12  H6   single    0.970  0.020  1.090
 F0Y  C13  H7   single    0.970  0.020  1.090
 F0Y  C13  H8   single    0.970  0.020  1.090
 F0Y  C17  H9   single    0.930  0.020  1.080
 F0Y  C18  H10  single    0.930  0.020  1.080
 F0Y  C20  H11  single    0.970  0.020  1.090
 F0Y  C20  H12  single    0.970  0.020  1.090
 F0Y  C20  H13  single    0.970  0.020  1.090
 F0Y  C22  H14  single    0.970  0.020  1.090
 F0Y  C22  H15  single    0.970  0.020  1.090
 F0Y  C23  H16  single    0.970  0.020  1.090
 F0Y  C23  H17  single    0.970  0.020  1.090
 F0Y  N2   H18  single    0.860  0.020  1.020
 F0Y  N5   H19  single    0.860  0.020  1.020
 F0Y  C9   H21  single    0.930  0.020  1.080
 F0Y  C8   H22  single    0.930  0.020  1.080
 F0Y  C7   H23  single    0.930  0.020  1.080
 F0Y  C5   H24  single    0.970  0.020  1.090
 F0Y  C5   H25  single    0.970  0.020  1.090
 F0Y  C4   H26  single    0.970  0.020  1.090
 F0Y  C    H27  single    0.970  0.020  1.090
 F0Y  C    H28  single    0.970  0.020  1.090
 F0Y  C    H29  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
 F0Y  O    C1   N    112.45  3.000
 F0Y  N    C1   O1   124.88  3.000
 F0Y  O    C1   O1   122.66  3.000
 F0Y  H2   C2   H1   106.86  3.000
 F0Y  H2   C2   N    110.81  3.000
 F0Y  H1   C2   N    107.86  3.000
 F0Y  H2   C2   C3   110.84  3.000
 F0Y  H1   C2   C3   109.45  3.000
 F0Y  N    C2   C3   110.89  3.000
 F0Y  H4   C3   H3   106.96  3.000
 F0Y  H4   C3   C4   110.62  3.000
 F0Y  H3   C3   C4   109.95  3.000
 F0Y  H4   C3   C2   108.64  3.000
 F0Y  H3   C3   C2   109.33  3.000
 F0Y  C4   C3   C2   111.23  3.000
 F0Y  H5   C11  C6   119.19  3.000
 F0Y  H5   C11  C10  119.23  3.000
 F0Y  C6   C11  C10  121.58  3.000
 F0Y  H6   C12  C10  107.22  3.000
 F0Y  H6   C12  N2   108.35  3.000
 F0Y  C10  C12  N2   111.26  3.000
 F0Y  H6   C12  C13  107.86  3.000
 F0Y  N2   C12  C13  111.89  3.000
 F0Y  C10  C12  C13  110.07  3.000
 F0Y  H8   C13  H7   107.40  3.000
 F0Y  H8   C13  C14  108.32  3.000
 F0Y  H7   C13  C14  108.72  3.000
 F0Y  H8   C13  C12  110.69  3.000
 F0Y  H7   C13  C12  110.02  3.000
 F0Y  C14  C13  C12  111.58  3.000
 F0Y  N1   C14  C13  180.00  3.000
 F0Y  N3   C15  N5   113.29  3.000
 F0Y  N5   C15  N2   123.43  3.000
 F0Y  N3   C15  N2   123.26  3.000
 F0Y  N3   C16  C21  110.45  3.000
 F0Y  N3   C16  C17  132.90  3.000
 F0Y  C21  C16  C17  116.64  3.000
 F0Y  H9   C17  C18  121.08  3.000
 F0Y  H9   C17  C16  122.00  3.000
 F0Y  C18  C17  C16  116.91  3.000
 F0Y  H10  C18  C19  119.09  3.000
 F0Y  H10  C18  C17  119.64  3.000
 F0Y  C19  C18  C17  121.28  3.000
 F0Y  N4   C19  C20  116.61  3.000
 F0Y  N4   C19  C18  122.14  3.000
 F0Y  C20  C19  C18  121.25  3.000
 F0Y  H13  C20  H12  107.84  3.000
 F0Y  H13  C20  H11  108.01  3.000
 F0Y  H12  C20  H11  107.13  3.000
 F0Y  H13  C20  C19  111.57  3.000
 F0Y  H12  C20  C19  111.04  3.000
 F0Y  H11  C20  C19  111.07  3.000
 F0Y  N4   C21  N5   127.58  3.000
 F0Y  N5   C21  C16  104.79  3.000
 F0Y  N4   C21  C16  127.63  3.000
 F0Y  H15  C22  H14  106.99  3.000
 F0Y  H15  C22  C4   109.56  3.000
 F0Y  H14  C22  C4   110.28  3.000
 F0Y  H15  C22  C23  109.05  3.000
 F0Y  H14  C22  C23  109.23  3.000
 F0Y  C4   C22  C23  111.61  3.000
 F0Y  H17  C23  H16  107.22  3.000
 F0Y  H17  C23  N    108.37  3.000
 F0Y  H16  C23  N    109.81  3.000
 F0Y  H17  C23  C22  109.77  3.000
 F0Y  H16  C23  C22  110.96  3.000
 F0Y  N    C23  C22  110.62  3.000
 F0Y  H18  N2   C15  114.44  3.000
 F0Y  H18  N2   C12  118.19  3.000
 F0Y  C15  N2   C12  126.40  3.000
 F0Y  H19  N5   C21  125.10  3.000
 F0Y  H19  N5   C15  128.20  3.000
 F0Y  C21  N5   C15  106.69  3.000
 F0Y  C21  N4   C19  115.39  3.000
 F0Y  C16  N3   C15  104.77  3.000
 F0Y  C9   C10  C12  121.07  3.000
 F0Y  C12  C10  C11  119.66  3.000
 F0Y  C9   C10  C11  119.27  3.000
 F0Y  H21  C9   C8   119.06  3.000
 F0Y  H21  C9   C10  121.13  3.000
 F0Y  C8   C9   C10  119.81  3.000
 F0Y  H22  C8   C7   119.86  3.000
 F0Y  H22  C8   C9   119.78  3.000
 F0Y  C7   C8   C9   120.36  3.000
 F0Y  H23  C7   C6   119.75  3.000
 F0Y  H23  C7   C8   119.58  3.000
 F0Y  C6   C7   C8   120.67  3.000
 F0Y  C5   C6   C7   120.70  3.000
 F0Y  C7   C6   C11  118.31  3.000
 F0Y  C5   C6   C11  120.98  3.000
 F0Y  H25  C5   H24  106.63  3.000
 F0Y  H25  C5   C4   108.53  3.000
 F0Y  H24  C5   C4   109.10  3.000
 F0Y  H25  C5   C6   109.39  3.000
 F0Y  H24  C5   C6   109.64  3.000
 F0Y  C4   C5   C6   113.33  3.000
 F0Y  H26  C4   C5   107.92  3.000
 F0Y  H26  C4   C22  107.92  3.000
 F0Y  C5   C4   C22  110.57  3.000
 F0Y  H26  C4   C3   107.79  3.000
 F0Y  C5   C4   C3   112.56  3.000
 F0Y  C22  C4   C3   109.91  3.000
 F0Y  C23  N    C2   113.41  3.000
 F0Y  C2   N    C1   124.93  3.000
 F0Y  C23  N    C1   120.16  3.000
 F0Y  C    O    C1   116.96  3.000
 F0Y  H29  C    H28  109.01  3.000
 F0Y  H29  C    H27  109.07  3.000
 F0Y  H28  C    H27  109.14  3.000
 F0Y  H29  C    O    105.78  3.000
 F0Y  H28  C    O    111.81  3.000
 F0Y  H27  C    O    111.92  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
 F0Y  CONST_01  C8   C7   C6   C11     0.00   0.0  0
 F0Y  CONST_02  C8   C9   C10  C11     0.00   0.0  0
 F0Y  CONST_03  C17  C16  N3   C15   180.00   0.0  0
 F0Y  CONST_04  C21  C16  N3   C15     0.00   0.0  0
 F0Y  CONST_05  C16  C21  N5   C15     0.00   0.0  0
 F0Y  CONST_06  N4   C21  N5   C15   180.00   0.0  0
 F0Y  CONST_07  C19  C18  C17  C16     0.00   0.0  0
 F0Y  CONST_08  C19  N4   C21  C16     0.00   0.0  0
 F0Y  CONST_09  N5   C15  N3   C16     0.00   0.0  0
 F0Y  CONST_10  N4   C19  C18  C17     0.00   0.0  0
 F0Y  CONST_11  N4   C21  C16  C17     0.00   0.0  0
 F0Y  CONST_12  N5   C21  C16  C17   180.00   0.0  0
 F0Y  CONST_13  C21  C16  C17  C18     0.00   0.0  0
 F0Y  CONST_14  N3   C16  C17  C18   180.00   0.0  0
 F0Y  CONST_15  C21  N4   C19  C18     0.00   0.0  0
 F0Y  CONST_16  N5   C21  N4   C19   180.00   0.0  0
 F0Y  CONST_17  N3   C15  N5   C21     0.00   0.0  0
 F0Y  CONST_18  N3   C16  C21  N5      0.00   0.0  0
 F0Y  CONST_19  N3   C16  C21  N4    180.00   0.0  0
 F0Y  CONST_20  C7   C6   C11  C10     0.00   0.0  0
 F0Y  CONST_21  C7   C8   C9   C10     0.00   0.0  0
 F0Y  CONST_22  C6   C7   C8   C9      0.00   0.0  0
 F0Y  CONST_23  C6   C11  C10  C9      0.00   0.0  0
 F0Y  CONST_24  C6   C11  C10  C12   180.00   0.0  0
 F0Y  CONST_25  C8   C9   C10  C12   180.00   0.0  0
 F0Y  CONST_26  N2   C15  N3   C16   180.00   0.0  0
 F0Y  CONST_27  C20  C19  C18  C17   180.00   0.0  0
 F0Y  CONST_28  C21  N4   C19  C20   180.00   0.0  0
 F0Y  CONST_29  N2   C15  N5   C21   180.00   0.0  0
 F0Y  CONST_30  C5   C6   C11  C10   180.00   0.0  0
 F0Y  CONST_31  C5   C6   C7   C8    180.00   0.0  0
 F0Y  CONST_32  H23  C7   C6   C11   180.00   0.0  0
 F0Y  CONST_33  H21  C9   C10  C11   180.00   0.0  0
 F0Y  CONST_34  H10  C18  C17  C16   180.00   0.0  0
 F0Y  CONST_35  H19  N5   C21  C16   180.00   0.0  0
 F0Y  CONST_36  H9   C17  C18  C19   180.00   0.0  0
 F0Y  CONST_37  H22  C8   C9   C10   180.00   0.0  0
 F0Y  CONST_38  H5   C11  C10  C9    180.00   0.0  0
 F0Y  CONST_39  N3   C15  N2   C12   180.00   0.0  0
 F0Y  CONST_40  N5   C15  N2   C12     0.00   0.0  0
 F0Y  CONST_41  H18  N2   C15  N5    180.00   0.0  0
 F0Y  Var_01    C22  C23  N    C2    -57.78  30.0  1
 F0Y  Var_02    C23  N    C2   C3     58.01  30.0  1
 F0Y  Var_03    N    C23  C22  C4     54.94  30.0  1
 F0Y  Var_04    N    C2   C3   C4    -55.03  30.0  1
 F0Y  Var_05    C4   C5   C6   C11  -109.00  30.0  2
 F0Y  Var_06    O    C1   N    C2     -7.78  30.0  2
 F0Y  Var_07    H11  C20  C19  C18   126.02  30.0  2
 F0Y  Var_08    H27  C    O    C1    -60.50  30.0  3
 F0Y  Var_09    H7   C13  C14  N1   -118.06  30.0  1

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
 F0Y  chir_01  C12  C10  N2  C13  positiv
 F0Y  chir_02  C4   C22  C3  C5   positiv

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
 F0Y  plan-1  C11  0.020
 F0Y  plan-1  C12  0.020
 F0Y  plan-1  C10  0.020
 F0Y  plan-1  C9   0.020
 F0Y  plan-1  C8   0.020
 F0Y  plan-1  C7   0.020
 F0Y  plan-1  C6   0.020
 F0Y  plan-1  C5   0.020
 F0Y  plan-1  H5   0.020
 F0Y  plan-1  H21  0.020
 F0Y  plan-1  H22  0.020
 F0Y  plan-1  H23  0.020
 F0Y  plan-2  C15  0.020
 F0Y  plan-2  C16  0.020
 F0Y  plan-2  C17  0.020
 F0Y  plan-2  C18  0.020
 F0Y  plan-2  C19  0.020
 F0Y  plan-2  C20  0.020
 F0Y  plan-2  C21  0.020
 F0Y  plan-2  N2   0.020
 F0Y  plan-2  N5   0.020
 F0Y  plan-2  N4   0.020
 F0Y  plan-2  N3   0.020
 F0Y  plan-2  H9   0.020
 F0Y  plan-2  H10  0.020
 F0Y  plan-2  H19  0.020
 F0Y  plan-3  C12  0.020
 F0Y  plan-3  C15  0.020
 F0Y  plan-3  N2   0.020
 F0Y  plan-3  H18  0.020
 F0Y  plan-4  C1   0.020
 F0Y  plan-4  O1   0.020
 F0Y  plan-4  N    0.020
 F0Y  plan-4  O    0.020

