# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:48:28 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-{2-methoxy-4-[(1-methylpiperidin-4-yl)oxy]phenyl}-4-(1H-pyrrolo[2,3-c]pyridin-3-yl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC2CCN(C)CC2)ccc1Nc3nccc(n3)c4c[nH]c5cnccc45
#
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
 DYK  DYK  N-{2-methoxy-4-[(1-methylpiperidin-4-yl)oxy]phenyl}-4-(1H-pyrrolo[2,3-c]pyridin-3-yl)pyrimidin-2-amine  ligand  58  32  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DYK
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
 DYK  C     C  CH3   0  -0.516   8.4671   2.0336  -0.7730
 DYK  N     N  NT    0  -0.413   7.7818   0.7767  -0.5828
 DYK  O     O  O2    0  -0.489   4.8130  -0.1938   1.0764
 DYK  C1    C  CH2   0  -0.277   7.6860   0.4352   0.8247
 DYK  N1    N  NH1   0  -0.746  -0.7091  -0.2938   0.5525
 DYK  O1    O  O2    0  -0.465   0.7647  -2.1658  -0.6675
 DYK  C2    C  CH2   0  -0.450   7.0555  -0.9368   1.0108
 DYK  N2    N  N     0  -0.457  -0.9436   1.8434  -0.3022
 DYK  C3    C  CH1   0  -0.025   5.6966  -1.0368   0.3380
 DYK  N3    N  N     0  -0.507  -2.8113   0.4216   0.0703
 DYK  C4    C  CH2   0  -0.474   5.8091  -0.5819  -1.1120
 DYK  N4    N  NR15  0  -0.678  -7.2658   1.2542  -0.6586
 DYK  C5    C  CH2   0  -0.271   6.4773   0.7805  -1.2194
 DYK  N5    N  N     0  -0.416  -7.5624  -2.1501   0.6765
 DYK  C6    C  CR6   0   0.424   3.4821  -0.2544   0.8852
 DYK  C7    C  CR16  0  -0.393   2.7267   0.7431   1.4985
 DYK  C8    C  CR16  0  -0.253   1.3479   0.7239   1.3901
 DYK  C9    C  CR6   0   0.206   0.6903  -0.2532   0.6559
 DYK  C10   C  CR6   0   0.383   1.4544  -1.2460   0.0291
 DYK  C11   C  CR16  0  -0.536   2.8422  -1.2531   0.1519
 DYK  C12   C  CH3   0  -0.439   1.4654  -3.2242  -1.2913
 DYK  C13   C  CR6   0   0.567  -1.5047   0.7014   0.0873
 DYK  C14   C  CR16  0  -0.024  -1.7854   2.7746  -0.7356
 DYK  C15   C  CR16  0  -0.406  -3.1512   2.6039  -0.7928
 DYK  C16   C  CR6   0   0.255  -3.6406   1.3622  -0.3662
 DYK  C17   C  CR5   0  -0.057  -5.0556   1.0417  -0.3748
 DYK  C18   C  CR15  0  -0.037  -6.0755   1.8698  -0.7974
 DYK  C19   C  CR56  0   0.256  -7.0714   0.0028  -0.1406
 DYK  C20   C  CR56  0   0.158  -5.6878  -0.1727   0.0539
 DYK  C21   C  CR16  0  -0.431  -5.2717  -1.3995   0.5816
 DYK  C22   C  CR16  0  -0.093  -6.2463  -2.3335   0.8685
 DYK  C23   C  CR16  0  -0.098  -7.9777  -1.0010   0.1792
 DYK  H     H  HCH3  0   0.231   9.4739   1.9787  -0.3553
 DYK  HA    H  HCH3  0   0.231   8.5581   2.2528  -1.8382
 DYK  HB    H  HCH3  0   0.189   7.9555   2.8868  -0.3000
 DYK  H1    H  HCH2  0   0.235   8.6920   0.4275   1.2515
 DYK  H1A   H  HCH2  0   0.191   7.1127   1.1918   1.3872
 DYK  HN1   H  HNH1  0   0.395  -1.1763  -1.1695   0.7295
 DYK  H2    H  HCH2  0   0.235   7.7027  -1.6956   0.5645
 DYK  H2A   H  HCH2  0   0.245   6.9723  -1.1741   2.0735
 DYK  H3    H  HCH1  0   0.250   5.3501  -2.0750   0.3898
 DYK  H4    H  HCH2  0   0.239   6.4069  -1.3226  -1.6496
 DYK  H4A   H  HCH2  0   0.248   4.8322  -0.5518  -1.5993
 DYK  H5    H  HCH2  0   0.192   5.8179   1.5571  -0.7940
 DYK  H5A   H  HCH2  0   0.236   6.6074   1.0328  -2.2748
 DYK  H7    H  HCR6  0   0.257   3.2214   1.5192   2.0677
 DYK  H8    H  HCR6  0   0.261   0.7663   1.4898   1.8847
 DYK  H11   H  HCR6  0   0.299   3.4156  -2.0312  -0.3300
 DYK  H12   H  HCH3  0   0.229   2.1655  -2.8616  -2.0483
 DYK  H12A  H  HCH3  0   0.231   2.0103  -3.8351  -0.5675
 DYK  H12B  H  HCH3  0   0.264   0.7160  -3.8428  -1.7782
 DYK  H14   H  HCR6  0   0.266  -1.3405   3.7101  -1.0576
 DYK  H15   H  HCR6  0   0.258  -3.7927   3.3958  -1.1491
 DYK  H18   H  HCR5  0   0.303  -6.0284   2.8711  -1.1960
 DYK  H21   H  HCR6  0   0.264  -4.2297  -1.6167   0.7597
 DYK  H22   H  HCR6  0   0.255  -5.9596  -3.2946   1.2800
 DYK  H23   H  HCR6  0   0.271  -9.0441  -0.8683   0.0281
 DYK  HN4   H  HNR5  0   0.425  -8.1547   1.6631  -0.8976

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
 DYK  C    N     single    1.444  0.020  1.444
 DYK  N    C1    single    1.452  0.020  1.452
 DYK  N    C5    single    1.452  0.020  1.452
 DYK  O    C3    single    1.427  0.020  1.427
 DYK  O    C6    single    1.346  0.020  1.346
 DYK  C1   C2    single    1.521  0.020  1.521
 DYK  N1   C9    single    1.404  0.020  1.404
 DYK  N1   C13   single    1.356  0.020  1.356
 DYK  O1   C10   single    1.344  0.020  1.344
 DYK  O1   C12   single    1.414  0.020  1.414
 DYK  C2   C3    single    1.520  0.020  1.520
 DYK  N2   C13   aromatic  1.331  0.020  1.331
 DYK  N2   C14   aromatic  1.328  0.020  1.328
 DYK  C3   C4    single    1.524  0.020  1.524
 DYK  N3   C13   aromatic  1.336  0.020  1.336
 DYK  N3   C16   aromatic  1.328  0.020  1.328
 DYK  C4   C5    single    1.521  0.020  1.521
 DYK  N4   C18   aromatic  1.347  0.020  1.347
 DYK  N4   C19   aromatic  1.368  0.020  1.368
 DYK  N5   C22   aromatic  1.343  0.020  1.343
 DYK  N5   C23   aromatic  1.319  0.020  1.319
 DYK  C6   C7    aromatic  1.393  0.020  1.393
 DYK  C6   C11   aromatic  1.394  0.020  1.394
 DYK  C7   C8    aromatic  1.383  0.020  1.383
 DYK  C8   C9    aromatic  1.388  0.020  1.388
 DYK  C9   C10   aromatic  1.401  0.020  1.401
 DYK  C10  C11   aromatic  1.393  0.020  1.393
 DYK  C14  C15   aromatic  1.378  0.020  1.378
 DYK  C15  C16   aromatic  1.401  0.020  1.401
 DYK  C16  C17   single    1.451  0.020  1.451
 DYK  C17  C18   aromatic  1.380  0.020  1.380
 DYK  C17  C20   aromatic  1.435  0.020  1.435
 DYK  C19  C20   aromatic  1.408  0.020  1.408
 DYK  C19  C23   aromatic  1.390  0.020  1.390
 DYK  C20  C21   aromatic  1.399  0.020  1.399
 DYK  C21  C22   aromatic  1.380  0.020  1.380
 DYK  C    H     single    0.970  0.020  1.090
 DYK  C    HA    single    0.970  0.020  1.090
 DYK  C    HB    single    0.970  0.020  1.090
 DYK  C1   H1    single    0.970  0.020  1.090
 DYK  C1   H1A   single    0.970  0.020  1.090
 DYK  N1   HN1   single    0.860  0.020  1.020
 DYK  C2   H2    single    0.970  0.020  1.090
 DYK  C2   H2A   single    0.970  0.020  1.090
 DYK  C3   H3    single    0.970  0.020  1.090
 DYK  C4   H4    single    0.970  0.020  1.090
 DYK  C4   H4A   single    0.970  0.020  1.090
 DYK  N4   HN4   single    0.860  0.020  1.020
 DYK  C5   H5    single    0.970  0.020  1.090
 DYK  C5   H5A   single    0.970  0.020  1.090
 DYK  C7   H7    single    0.930  0.020  1.080
 DYK  C8   H8    single    0.930  0.020  1.080
 DYK  C11  H11   single    0.930  0.020  1.080
 DYK  C12  H12   single    0.970  0.020  1.090
 DYK  C12  H12A  single    0.970  0.020  1.090
 DYK  C12  H12B  single    0.970  0.020  1.090
 DYK  C14  H14   single    0.930  0.020  1.080
 DYK  C15  H15   single    0.930  0.020  1.080
 DYK  C18  H18   single    0.930  0.020  1.080
 DYK  C21  H21   single    0.930  0.020  1.080
 DYK  C22  H22   single    0.930  0.020  1.080
 DYK  C23  H23   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
 DYK  HB    C    HA    107.59  3.000
 DYK  HB    C    H     107.65  3.000
 DYK  HA    C    H     107.87  3.000
 DYK  HB    C    N     113.40  3.000
 DYK  HA    C    N     110.05  3.000
 DYK  H     C    N     110.09  3.000
 DYK  C5    N    C1    111.51  3.000
 DYK  C5    N    C     111.50  3.000
 DYK  C1    N    C     111.33  3.000
 DYK  C6    O    C3    120.81  3.000
 DYK  H1A   C1   H1    106.50  3.000
 DYK  H1A   C1   C2    109.92  3.000
 DYK  H1    C1   C2    109.11  3.000
 DYK  H1A   C1   N     111.55  3.000
 DYK  H1    C1   N     108.64  3.000
 DYK  C2    C1   N     110.98  3.000
 DYK  HN1   N1   C13   115.19  3.000
 DYK  HN1   N1   C9    118.30  3.000
 DYK  C13   N1   C9    126.07  3.000
 DYK  C12   O1   C10   119.11  3.000
 DYK  H2A   C2   H2    106.96  3.000
 DYK  H2A   C2   C3    110.40  3.000
 DYK  H2    C2   C3    107.65  3.000
 DYK  H2A   C2   C1    110.27  3.000
 DYK  H2    C2   C1    109.32  3.000
 DYK  C3    C2   C1    112.07  3.000
 DYK  C14   N2   C13   115.47  3.000
 DYK  H3    C3   C4    110.56  3.000
 DYK  H3    C3   C2    108.91  3.000
 DYK  C4    C3   C2    109.61  3.000
 DYK  H3    C3   O     109.84  3.000
 DYK  C4    C3   O     111.20  3.000
 DYK  C2    C3   O     106.60  3.000
 DYK  C16   N3   C13   117.81  3.000
 DYK  H4A   C4   H4    106.76  3.000
 DYK  H4A   C4   C5    109.68  3.000
 DYK  H4    C4   C5    109.39  3.000
 DYK  H4A   C4   C3    111.52  3.000
 DYK  H4    C4   C3    107.82  3.000
 DYK  C5    C4   C3    111.53  3.000
 DYK  HN4   N4   C19   125.91  3.000
 DYK  HN4   N4   C18   124.73  3.000
 DYK  C19   N4   C18   109.35  3.000
 DYK  H5A   C5   H5    106.31  3.000
 DYK  H5A   C5   C4    109.10  3.000
 DYK  H5    C5   C4    109.90  3.000
 DYK  H5A   C5   N     108.49  3.000
 DYK  H5    C5   N     111.69  3.000
 DYK  C4    C5   N     111.19  3.000
 DYK  C23   N5   C22   118.79  3.000
 DYK  C11   C6   C7    119.69  3.000
 DYK  C11   C6   O     124.10  3.000
 DYK  C7    C6   O     116.19  3.000
 DYK  H7    C7   C8    120.46  3.000
 DYK  H7    C7   C6    119.80  3.000
 DYK  C8    C7   C6    119.73  3.000
 DYK  H8    C8   C9    119.07  3.000
 DYK  H8    C8   C7    119.36  3.000
 DYK  C9    C8   C7    121.57  3.000
 DYK  C10   C9   C8    118.51  3.000
 DYK  C10   C9   N1    119.36  3.000
 DYK  C8    C9   N1    122.11  3.000
 DYK  C11   C10  C9    120.50  3.000
 DYK  C11   C10  O1    123.59  3.000
 DYK  C9    C10  O1    115.91  3.000
 DYK  H11   C11  C10   119.55  3.000
 DYK  H11   C11  C6    120.46  3.000
 DYK  C10   C11  C6    119.99  3.000
 DYK  H12B  C12  H12A  108.80  3.000
 DYK  H12B  C12  H12   108.68  3.000
 DYK  H12A  C12  H12   108.95  3.000
 DYK  H12B  C12  O1    106.38  3.000
 DYK  H12A  C12  O1    111.92  3.000
 DYK  H12   C12  O1    112.00  3.000
 DYK  N3    C13  N2    126.03  3.000
 DYK  N3    C13  N1    115.10  3.000
 DYK  N2    C13  N1    118.86  3.000
 DYK  H14   C14  C15   120.07  3.000
 DYK  H14   C14  N2    116.21  3.000
 DYK  C15   C14  N2    123.72  3.000
 DYK  H15   C15  C16   122.89  3.000
 DYK  H15   C15  C14   120.79  3.000
 DYK  C16   C15  C14   116.32  3.000
 DYK  C17   C16  C15   122.31  3.000
 DYK  C17   C16  N3    117.04  3.000
 DYK  C15   C16  N3    120.65  3.000
 DYK  C20   C17  C18   105.89  3.000
 DYK  C20   C17  C16   127.95  3.000
 DYK  C18   C17  C16   126.16  3.000
 DYK  H18   C18  C17   129.63  3.000
 DYK  H18   C18  N4    120.05  3.000
 DYK  C17   C18  N4    110.32  3.000
 DYK  C23   C19  C20   121.26  3.000
 DYK  C23   C19  N4    130.93  3.000
 DYK  C20   C19  N4    107.81  3.000
 DYK  C21   C20  C19   116.98  3.000
 DYK  C21   C20  C17   136.39  3.000
 DYK  C19   C20  C17   106.63  3.000
 DYK  H21   C21  C22   120.76  3.000
 DYK  H21   C21  C20   121.73  3.000
 DYK  C22   C21  C20   117.51  3.000
 DYK  H22   C22  C21   119.48  3.000
 DYK  H22   C22  N5    115.76  3.000
 DYK  C21   C22  N5    124.76  3.000
 DYK  H23   C23  C19   121.37  3.000
 DYK  H23   C23  N5    117.93  3.000
 DYK  C19   C23  N5    120.70  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
 DYK  CONST_01  C16  N3   C13  N2      0.00   0.0  0
 DYK  CONST_02  C16  C15  C14  N2      0.00   0.0  0
 DYK  CONST_03  C14  N2   C13  N3      0.00   0.0  0
 DYK  CONST_04  C14  C15  C16  N3      0.00   0.0  0
 DYK  CONST_05  C18  C17  C16  N3    180.00   0.0  0
 DYK  CONST_06  C20  C17  C16  N3      0.00   0.0  0
 DYK  CONST_07  C16  C17  C18  N4    180.00   0.0  0
 DYK  CONST_08  C20  C17  C18  N4      0.00   0.0  0
 DYK  CONST_09  C17  C20  C19  N4      0.00   0.0  0
 DYK  CONST_10  C21  C20  C19  N4    180.00   0.0  0
 DYK  CONST_11  N5   C23  C19  N4    180.00   0.0  0
 DYK  CONST_12  C20  C21  C22  N5      0.00   0.0  0
 DYK  CONST_13  C20  C19  C23  N5      0.00   0.0  0
 DYK  CONST_14  C9   C8   C7   C6      0.00   0.0  0
 DYK  CONST_15  C9   C10  C11  C6      0.00   0.0  0
 DYK  CONST_16  C10  C11  C6   C7      0.00   0.0  0
 DYK  CONST_17  C10  C9   C8   C7      0.00   0.0  0
 DYK  CONST_18  C11  C6   C7   C8      0.00   0.0  0
 DYK  CONST_19  C11  C10  C9   C8      0.00   0.0  0
 DYK  CONST_20  C15  C14  N2   C13     0.00   0.0  0
 DYK  CONST_21  C15  C16  N3   C13     0.00   0.0  0
 DYK  CONST_22  C17  C16  N3   C13   180.00   0.0  0
 DYK  CONST_23  C17  C16  C15  C14   180.00   0.0  0
 DYK  CONST_24  C18  C17  C16  C15     0.00   0.0  0
 DYK  CONST_25  C20  C17  C16  C15   180.00   0.0  0
 DYK  CONST_26  C19  C20  C17  C16   180.00   0.0  0
 DYK  CONST_27  C21  C20  C17  C16     0.00   0.0  0
 DYK  CONST_28  C19  N4   C18  C17     0.00   0.0  0
 DYK  CONST_29  C23  C19  C20  C17   180.00   0.0  0
 DYK  CONST_30  C22  C21  C20  C17   180.00   0.0  0
 DYK  CONST_31  C20  C19  N4   C18     0.00   0.0  0
 DYK  CONST_32  C23  C19  N4   C18   180.00   0.0  0
 DYK  CONST_33  C19  C20  C17  C18     0.00   0.0  0
 DYK  CONST_34  C21  C20  C17  C18   180.00   0.0  0
 DYK  CONST_35  C22  C21  C20  C19     0.00   0.0  0
 DYK  CONST_36  C22  N5   C23  C19     0.00   0.0  0
 DYK  CONST_37  C23  C19  C20  C21     0.00   0.0  0
 DYK  CONST_38  C23  N5   C22  C21     0.00   0.0  0
 DYK  CONST_39  C8   C7   C6   O     180.00   0.0  0
 DYK  CONST_40  C10  C11  C6   O     180.00   0.0  0
 DYK  CONST_41  C7   C8   C9   N1    180.00   0.0  0
 DYK  CONST_42  C11  C10  C9   N1    180.00   0.0  0
 DYK  CONST_43  C14  N2   C13  N1    180.00   0.0  0
 DYK  CONST_44  C16  N3   C13  N1    180.00   0.0  0
 DYK  CONST_45  C8   C9   C10  O1    180.00   0.0  0
 DYK  CONST_46  C6   C11  C10  O1    180.00   0.0  0
 DYK  CONST_47  H15  C15  C14  N2    180.00   0.0  0
 DYK  CONST_48  H23  C23  C19  N4      0.00   0.0  0
 DYK  CONST_49  H21  C21  C22  N5    180.00   0.0  0
 DYK  CONST_50  H8   C8   C7   C6    180.00   0.0  0
 DYK  CONST_51  H11  C11  C6   C7    180.00   0.0  0
 DYK  CONST_52  H7   C7   C8   C9    180.00   0.0  0
 DYK  CONST_53  H14  C14  N2   C13   180.00   0.0  0
 DYK  CONST_54  H18  C18  C17  C16     0.00   0.0  0
 DYK  CONST_55  HN4  N4   C18  C17   180.00   0.0  0
 DYK  CONST_56  H22  C22  C21  C20   180.00   0.0  0
 DYK  Var_01    C3   C2   C1   N     -55.55  30.0  1
 DYK  Var_02    C3   C4   C5   N      56.05  30.0  1
 DYK  Var_03    C4   C5   N    C1    -59.47  30.0  1
 DYK  Var_04    C5   N    C1   C2     58.97  30.0  1
 DYK  Var_05    C9   N1   C13  N2     -0.84  30.0  1
 DYK  Var_06    C7   C6   O    C3   -170.52  30.0  2
 DYK  Var_07    C13  N1   C9   C8     57.26  30.0  3
 DYK  Var_08    H    C    N    C1     59.27  30.0  3
 DYK  Var_09    H12  C12  O1   C10   -62.10  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
 DYK  chir_01  C3  O  C2  C4  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
 DYK  plan-1  N1   0.020
 DYK  plan-1  N2   0.020
 DYK  plan-1  N3   0.020
 DYK  plan-1  C13  0.020
 DYK  plan-1  C14  0.020
 DYK  plan-1  C15  0.020
 DYK  plan-1  C16  0.020
 DYK  plan-1  C17  0.020
 DYK  plan-1  H14  0.020
 DYK  plan-1  H15  0.020
 DYK  plan-2  O    0.020
 DYK  plan-2  N1   0.020
 DYK  plan-2  O1   0.020
 DYK  plan-2  C6   0.020
 DYK  plan-2  C7   0.020
 DYK  plan-2  C8   0.020
 DYK  plan-2  C9   0.020
 DYK  plan-2  C10  0.020
 DYK  plan-2  C11  0.020
 DYK  plan-2  H7   0.020
 DYK  plan-2  H8   0.020
 DYK  plan-2  H11  0.020
 DYK  plan-3  N4   0.020
 DYK  plan-3  N5   0.020
 DYK  plan-3  C16  0.020
 DYK  plan-3  C17  0.020
 DYK  plan-3  C18  0.020
 DYK  plan-3  C19  0.020
 DYK  plan-3  C20  0.020
 DYK  plan-3  C21  0.020
 DYK  plan-3  C22  0.020
 DYK  plan-3  C23  0.020
 DYK  plan-3  H18  0.020
 DYK  plan-3  H21  0.020
 DYK  plan-3  H22  0.020
 DYK  plan-3  H23  0.020
 DYK  plan-3  HN4  0.020

