# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:01:18 2021
#   Inital geometry file: a 140 line input string
#   Ligand name: 6,6-dimethyl-2-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]-5-(2-morpholin-4-ylethyl)thieno[2,3-c]pyrrol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nccc1Nc2nccc(n2)c3sc4c(c3)C(=O)N(CCN5CCOCC5)C4(C)C
#
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
 KE8  KE8  6,6-dimethyl-2-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]-5-(2-morpholin-4-ylethyl)thieno[2,3-c]pyrrol-4-one  ligand  59  32  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KE8
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
 KE8  C1   C  CH3   0  -0.561  13.6696   9.1154  40.1740
 KE8  C5   C  CR15  0  -0.525  10.2694   9.7922  41.1677
 KE8  C6   C  CR5   0   0.664  11.4333   9.0568  41.2972
 KE8  C8   C  CR6   0   0.606  11.0543   7.3350  43.0134
 KE8  C10  C  CR16  0  -0.014  10.9819   5.6758  44.5349
 KE8  C11  C  CR16  0  -0.402   9.6592   5.9658  44.8248
 KE8  C12  C  CR6   0   0.398   9.0969   7.0195  44.1135
 KE8  C14  C  CR5   0  -0.241   7.7208   7.4455  44.3029
 KE8  C15  C  CR15  0  -0.291   6.7622   6.9497  45.1448
 KE8  C16  C  CR55  0   0.074   5.5555   7.6675  45.0055
 KE8  C21  C  CH2   0  -0.270   2.0283   9.7529  46.6031
 KE8  C23  C  CH2   0  -0.311   0.1877  11.2335  46.1061
 KE8  C24  C  CH2   0  -0.185  -1.2769  11.5024  46.3965
 KE8  C26  C  CH2   0  -0.188  -1.0538  10.6220  48.5329
 KE8  C27  C  CH2   0  -0.304   0.4168  10.3414  48.2918
 KE8  C28  C  CR5   0   0.044   4.3102   9.3892  43.9586
 KE8  C31  C  CR55  0  -0.176   5.6140   8.6660  44.0881
 KE8  N2   N  NR5   0  -0.342  12.3199   9.5652  40.4132
 KE8  N3   N  N     0  -0.295  11.8055  10.5866  39.7155
 KE8  C4   C  CR15  0  -0.064  10.5767  10.7252  40.1655
 KE8  N9   N  N     0  -0.460  11.6905   6.3421  43.6403
 KE8  N13  N  N     0  -0.513   9.7977   7.7023  43.2084
 KE8  C17  C  CR5   0   0.526   4.2023   7.6491  45.5826
 KE8  O18  O  O     0  -0.481   3.7544   6.8958  46.4304
 KE8  N19  N  NR5   0  -0.504   3.5289   8.6579  44.9692
 KE8  C20  C  CH2   0  -0.319   2.1593   8.9803  45.2910
 KE8  N22  N  NT    0  -0.430   0.6490  10.0933  46.8798
 KE8  O25  O  O2    0  -0.485  -1.5028  11.7218  47.7712
 KE8  C29  C  CH3   0  -0.626   3.7213   9.1989  42.5605
 KE8  C30  C  CH3   0  -0.635   4.4502  10.8696  44.3068
 KE8  S32  S  S2    0   0.283   7.1345   8.7818  43.3488
 KE8  H33  H  HCH3  0   0.282  14.1026   9.7522  39.4097
 KE8  H34  H  HCH3  0   0.262  14.2781   9.1910  41.0754
 KE8  H35  H  HCH3  0   0.262  13.6856   8.0848  39.8187
 KE8  H37  H  HCR5  0   0.276   9.3507   9.6749  41.7085
 KE8  H39  H  HCR6  0   0.283  11.4894   4.8684  45.0500
 KE8  H40  H  HCR6  0   0.275   9.1123   5.3984  45.5622
 KE8  H41  H  HCR5  0   0.276   6.9135   6.1215  45.8222
 KE8  H44  H  HCH2  0   0.245   2.3936   9.1155  47.4107
 KE8  H45  H  HCH2  0   0.207   2.6787  10.6423  46.5862
 KE8  H46  H  HCH2  0   0.200   0.7822  12.1361  46.3308
 KE8  H48  H  HCH2  0   0.237  -1.6063  12.3954  45.8633
 KE8  H49  H  HCH2  0   0.201  -1.8780  10.6534  46.0405
 KE8  H50  H  HCH2  0   0.237  -1.2249  10.8595  49.5839
 KE8  H51  H  HCH2  0   0.200  -1.6380   9.7239  48.2878
 KE8  H53  H  HCH2  0   0.244   0.7088   9.4608  48.8687
 KE8  H52  H  HCH2  0   0.198   1.0186  11.1883  48.6640
 KE8  H36  H  HCR5  0   0.257   9.9335  11.4926  39.7615
 KE8  H42  H  HCH2  0   0.251   1.7437   9.5496  44.4593
 KE8  H43  H  HCH2  0   0.260   1.5737   8.0615  45.3554
 KE8  H56  H  HCH3  0   0.249   2.7269   9.6402  42.4884
 KE8  H54  H  HCH3  0   0.246   4.3511   9.6885  41.8177
 KE8  H55  H  HCH3  0   0.249   3.6494   8.1408  42.3098
 KE8  H58  H  HCH3  0   0.249   4.8598  11.0004  45.3078
 KE8  H59  H  HCH3  0   0.251   5.1180  11.3572  43.5965
 KE8  H57  H  HCH3  0   0.245   3.4889  11.3829  44.2547
 KE8  N7   N  NH1   0  -0.782  11.8099   8.0022  42.0974
 KE8  H47  H  HCH2  0   0.242   0.2960  11.0367  45.0373
 KE8  H38  H  HNH1  0   0.427  12.7534   7.6546  42.0103

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
 KE8  C4   N3   aromatic  1.316  0.020  1.316
 KE8  C4   C5   aromatic  1.403  0.020  1.403
 KE8  N3   N2   aromatic  1.340  0.020  1.340
 KE8  C5   C6   aromatic  1.383  0.020  1.383
 KE8  N2   C6   aromatic  1.351  0.020  1.351
 KE8  N2   C1   single    1.443  0.020  1.443
 KE8  C6   N7   single    1.376  0.020  1.376
 KE8  C29  C28  single    1.529  0.020  1.529
 KE8  N7   C8   single    1.362  0.020  1.362
 KE8  C8   N13  aromatic  1.324  0.020  1.324
 KE8  C8   N9   aromatic  1.335  0.020  1.335
 KE8  S32  C31  aromatic  1.695  0.020  1.695
 KE8  S32  C14  aromatic  1.743  0.020  1.743
 KE8  N13  C12  aromatic  1.333  0.020  1.333
 KE8  C28  C31  single    1.497  0.020  1.497
 KE8  C28  C30  single    1.527  0.020  1.527
 KE8  C28  N19  single    1.472  0.020  1.472
 KE8  N9   C10  aromatic  1.322  0.020  1.322
 KE8  C31  C16  aromatic  1.357  0.020  1.357
 KE8  C12  C14  single    1.453  0.020  1.453
 KE8  C12  C11  aromatic  1.390  0.020  1.390
 KE8  C14  C15  aromatic  1.369  0.020  1.369
 KE8  C10  C11  aromatic  1.385  0.020  1.385
 KE8  N19  C20  single    1.443  0.020  1.443
 KE8  N19  C17  single    1.359  0.020  1.359
 KE8  C16  C15  aromatic  1.411  0.020  1.411
 KE8  C16  C17  single    1.471  0.020  1.471
 KE8  C20  C21  single    1.528  0.020  1.528
 KE8  C17  O18  double    1.219  0.020  1.219
 KE8  C23  C24  single    1.517  0.020  1.517
 KE8  C23  N22  single    1.453  0.020  1.453
 KE8  C21  N22  single    1.447  0.020  1.447
 KE8  C24  O25  single    1.410  0.020  1.410
 KE8  N22  C27  single    1.452  0.020  1.452
 KE8  O25  C26  single    1.411  0.020  1.411
 KE8  C27  C26  single    1.516  0.020  1.516
 KE8  C1   H33  single    0.970  0.020  1.090
 KE8  C1   H34  single    0.970  0.020  1.090
 KE8  C1   H35  single    0.970  0.020  1.090
 KE8  C5   H37  single    0.930  0.020  1.080
 KE8  C10  H39  single    0.930  0.020  1.080
 KE8  C11  H40  single    0.930  0.020  1.080
 KE8  C15  H41  single    0.930  0.020  1.080
 KE8  C21  H44  single    0.970  0.020  1.090
 KE8  C21  H45  single    0.970  0.020  1.090
 KE8  C23  H47  single    0.970  0.020  1.090
 KE8  C23  H46  single    0.970  0.020  1.090
 KE8  C24  H48  single    0.970  0.020  1.090
 KE8  C24  H49  single    0.970  0.020  1.090
 KE8  C26  H50  single    0.970  0.020  1.090
 KE8  C26  H51  single    0.970  0.020  1.090
 KE8  C27  H53  single    0.970  0.020  1.090
 KE8  C27  H52  single    0.970  0.020  1.090
 KE8  C4   H36  single    0.930  0.020  1.080
 KE8  N7   H38  single    0.860  0.020  1.020
 KE8  C20  H42  single    0.970  0.020  1.090
 KE8  C20  H43  single    0.970  0.020  1.090
 KE8  C29  H56  single    0.970  0.020  1.090
 KE8  C29  H54  single    0.970  0.020  1.090
 KE8  C29  H55  single    0.970  0.020  1.090
 KE8  C30  H58  single    0.970  0.020  1.090
 KE8  C30  H59  single    0.970  0.020  1.090
 KE8  C30  H57  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
 KE8  H35  C1   H34  109.07  3.000
 KE8  H35  C1   H33  108.63  3.000
 KE8  H34  C1   H33  108.60  3.000
 KE8  H35  C1   N2   111.25  3.000
 KE8  H34  C1   N2   111.31  3.000
 KE8  H33  C1   N2   107.89  3.000
 KE8  H37  C5   C4   128.35  3.000
 KE8  H37  C5   C6   127.99  3.000
 KE8  C4   C5   C6   103.66  3.000
 KE8  N7   C6   N2   119.28  3.000
 KE8  N7   C6   C5   133.81  3.000
 KE8  N2   C6   C5   106.91  3.000
 KE8  N13  C8   N9   126.12  3.000
 KE8  N9   C8   N7   114.56  3.000
 KE8  N13  C8   N7   119.33  3.000
 KE8  H39  C10  N9   116.50  3.000
 KE8  H39  C10  C11  120.25  3.000
 KE8  N9   C10  C11  123.25  3.000
 KE8  H40  C11  C12  122.90  3.000
 KE8  H40  C11  C10  121.12  3.000
 KE8  C12  C11  C10  115.98  3.000
 KE8  N13  C12  C14  115.86  3.000
 KE8  C14  C12  C11  122.59  3.000
 KE8  N13  C12  C11  121.54  3.000
 KE8  S32  C14  C15  112.25  3.000
 KE8  C15  C14  C12  129.59  3.000
 KE8  S32  C14  C12  118.16  3.000
 KE8  H41  C15  C16  124.86  3.000
 KE8  H41  C15  C14  124.41  3.000
 KE8  C16  C15  C14  110.74  3.000
 KE8  C17  C16  C31  108.30  3.000
 KE8  C17  C16  C15  137.86  3.000
 KE8  C31  C16  C15  113.84  3.000
 KE8  H45  C21  H44  106.57  3.000
 KE8  H45  C21  N22  112.06  3.000
 KE8  H44  C21  N22  108.34  3.000
 KE8  H45  C21  C20  110.13  3.000
 KE8  H44  C21  C20  108.14  3.000
 KE8  N22  C21  C20  111.39  3.000
 KE8  H46  C23  H47  107.04  3.000
 KE8  H46  C23  N22  111.24  3.000
 KE8  H47  C23  N22  110.38  3.000
 KE8  H46  C23  C24  109.63  3.000
 KE8  H47  C23  C24  108.36  3.000
 KE8  N22  C23  C24  110.10  3.000
 KE8  H49  C24  H48  107.98  3.000
 KE8  H49  C24  O25  110.38  3.000
 KE8  H48  C24  O25  107.51  3.000
 KE8  H49  C24  C23  109.20  3.000
 KE8  H48  C24  C23  110.06  3.000
 KE8  O25  C24  C23  111.64  3.000
 KE8  H51  C26  H50  108.02  3.000
 KE8  H51  C26  O25  110.32  3.000
 KE8  H50  C26  O25  107.49  3.000
 KE8  H51  C26  C27  109.20  3.000
 KE8  H50  C26  C27  110.22  3.000
 KE8  O25  C26  C27  111.53  3.000
 KE8  H52  C27  H53  107.14  3.000
 KE8  H52  C27  N22  111.83  3.000
 KE8  H53  C27  N22  109.45  3.000
 KE8  H52  C27  C26  109.46  3.000
 KE8  H53  C27  C26  108.93  3.000
 KE8  N22  C27  C26  109.95  3.000
 KE8  C30  C28  C29  111.38  3.000
 KE8  C30  C28  N19  111.94  3.000
 KE8  C29  C28  N19  111.20  3.000
 KE8  N19  C28  C31   99.38  3.000
 KE8  C30  C28  C31  111.64  3.000
 KE8  C29  C28  C31  110.76  3.000
 KE8  S32  C31  C28  135.31  3.000
 KE8  C28  C31  C16  112.11  3.000
 KE8  S32  C31  C16  112.57  3.000
 KE8  N3   N2   C6   112.07  3.000
 KE8  C6   N2   C1   127.23  3.000
 KE8  N3   N2   C1   120.70  3.000
 KE8  C4   N3   N2   105.11  3.000
 KE8  H36  C4   N3   120.21  3.000
 KE8  H36  C4   C5   127.54  3.000
 KE8  N3   C4   C5   112.25  3.000
 KE8  C10  N9   C8   115.92  3.000
 KE8  C12  N13  C8   117.19  3.000
 KE8  N19  C17  O18  126.18  3.000
 KE8  O18  C17  C16  128.19  3.000
 KE8  N19  C17  C16  105.63  3.000
 KE8  C20  N19  C17  122.36  3.000
 KE8  C17  N19  C28  114.56  3.000
 KE8  C20  N19  C28  123.08  3.000
 KE8  H43  C20  H42  106.26  3.000
 KE8  H43  C20  N19  109.53  3.000
 KE8  H42  C20  N19  107.96  3.000
 KE8  H43  C20  C21  109.20  3.000
 KE8  H42  C20  C21  110.99  3.000
 KE8  N19  C20  C21  112.68  3.000
 KE8  C27  N22  C23  109.45  3.000
 KE8  C27  N22  C21  112.23  3.000
 KE8  C23  N22  C21  112.66  3.000
 KE8  C26  O25  C24  110.73  3.000
 KE8  H55  C29  H54  108.51  3.000
 KE8  H55  C29  H56  108.52  3.000
 KE8  H54  C29  H56  107.46  3.000
 KE8  H55  C29  C28  110.89  3.000
 KE8  H54  C29  C28  110.16  3.000
 KE8  H56  C29  C28  111.18  3.000
 KE8  H57  C30  H59  107.35  3.000
 KE8  H57  C30  H58  108.58  3.000
 KE8  H59  C30  H58  108.34  3.000
 KE8  H57  C30  C28  111.37  3.000
 KE8  H59  C30  C28  109.95  3.000
 KE8  H58  C30  C28  111.13  3.000
 KE8  C31  S32  C14   90.61  3.000
 KE8  H38  N7   C8   114.08  3.000
 KE8  H38  N7   C6   118.00  3.000
 KE8  C8   N7   C6   127.92  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
 KE8  CONST_01  N2   N3   C4   C5      0.00   0.0  0
 KE8  CONST_02  N3   N2   C6   C5      0.00   0.0  0
 KE8  CONST_03  N3   C4   C5   C6      0.00   0.0  0
 KE8  CONST_04  C4   N3   N2   C6      0.00   0.0  0
 KE8  CONST_05  C14  C12  N13  C8    180.00   0.0  0
 KE8  CONST_06  C11  C12  N13  C8      0.00   0.0  0
 KE8  CONST_07  C11  C10  N9   C8      0.00   0.0  0
 KE8  CONST_08  N13  C8   N9   C10     0.00   0.0  0
 KE8  CONST_09  N13  C12  C11  C10     0.00   0.0  0
 KE8  CONST_10  C14  C12  C11  C10   180.00   0.0  0
 KE8  CONST_11  S32  C14  C12  C11   180.00   0.0  0
 KE8  CONST_12  C15  C14  C12  C11     0.00   0.0  0
 KE8  CONST_13  N9   C8   N13  C12     0.00   0.0  0
 KE8  CONST_14  C31  S32  C14  C12   180.00   0.0  0
 KE8  CONST_15  C16  C15  C14  C12   180.00   0.0  0
 KE8  CONST_16  N9   C10  C11  C12     0.00   0.0  0
 KE8  CONST_17  C16  C31  S32  C14     0.00   0.0  0
 KE8  CONST_18  C31  C16  C15  C14     0.00   0.0  0
 KE8  CONST_19  C31  S32  C14  C15     0.00   0.0  0
 KE8  CONST_20  N13  C12  C14  C15   180.00   0.0  0
 KE8  CONST_21  S32  C31  C16  C15     0.00   0.0  0
 KE8  CONST_22  S32  C14  C15  C16     0.00   0.0  0
 KE8  CONST_23  C4   C5   C6   N2      0.00   0.0  0
 KE8  CONST_24  S32  C14  C12  N13     0.00   0.0  0
 KE8  CONST_25  C28  N19  C17  C16     0.00   0.0  0
 KE8  CONST_26  C4   N3   N2   C1    180.00   0.0  0
 KE8  CONST_27  C5   C6   N2   C1    180.00   0.0  0
 KE8  CONST_28  N7   C8   N9   C10   180.00   0.0  0
 KE8  CONST_29  N7   C8   N13  C12   180.00   0.0  0
 KE8  CONST_30  N7   C6   N2   N3    180.00   0.0  0
 KE8  CONST_31  N7   C6   C5   C4    180.00   0.0  0
 KE8  CONST_32  C20  N19  C17  C16   180.00   0.0  0
 KE8  CONST_33  O18  C17  N19  C28   180.00   0.0  0
 KE8  CONST_34  H36  C4   C5   C6    180.00   0.0  0
 KE8  CONST_35  H39  C10  N9   C8    180.00   0.0  0
 KE8  CONST_36  H41  C15  C14  C12     0.00   0.0  0
 KE8  CONST_37  H40  C11  C12  C14     0.00   0.0  0
 KE8  CONST_38  H37  C5   C6   N2    180.00   0.0  0
 KE8  CONST_39  C20  N19  C17  O18     0.00   0.0  0
 KE8  Var_01    C26  C27  N22  C23    57.05  30.0  1
 KE8  Var_02    C27  N22  C23  C24   -56.78  30.0  1
 KE8  Var_03    C27  C26  O25  C24    57.38  30.0  1
 KE8  Var_04    O25  C24  C23  N22    57.20  30.0  1
 KE8  Var_05    O25  C26  C27  N22   -57.79  30.0  1
 KE8  Var_06    C8   N7   C6   C5      2.32  30.0  2
 KE8  Var_07    N13  C8   N7   C6     -0.34  30.0  2
 KE8  Var_08    C29  C28  C31  C16  -115.76  30.0  1
 KE8  Var_09    H48  C24  O25  C26  -177.87  30.0  1
 KE8  Var_10    C28  N19  C20  C21  -102.96  30.0  2
 KE8  Var_11    C20  C21  N22  C23   -78.33  30.0  3
 KE8  Var_12    N22  C21  C20  N19   178.42  30.0  3
 KE8  Var_13    H33  C1   N2   C6   -179.28  30.0  2
 KE8  Var_14    H56  C29  C28  C31   174.45  30.0  3
 KE8  Var_15    H58  C30  C28  C31   -56.23  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
 KE8  plan-1  C1   0.020
 KE8  plan-1  C5   0.020
 KE8  plan-1  C6   0.020
 KE8  plan-1  N2   0.020
 KE8  plan-1  N3   0.020
 KE8  plan-1  C4   0.020
 KE8  plan-1  H37  0.020
 KE8  plan-1  H36  0.020
 KE8  plan-1  N7   0.020
 KE8  plan-2  C8   0.020
 KE8  plan-2  C10  0.020
 KE8  plan-2  C11  0.020
 KE8  plan-2  C12  0.020
 KE8  plan-2  C14  0.020
 KE8  plan-2  N9   0.020
 KE8  plan-2  N13  0.020
 KE8  plan-2  H39  0.020
 KE8  plan-2  H40  0.020
 KE8  plan-2  N7   0.020
 KE8  plan-3  C12  0.020
 KE8  plan-3  C14  0.020
 KE8  plan-3  C15  0.020
 KE8  plan-3  C16  0.020
 KE8  plan-3  C28  0.020
 KE8  plan-3  C31  0.020
 KE8  plan-3  C17  0.020
 KE8  plan-3  O18  0.020
 KE8  plan-3  N19  0.020
 KE8  plan-3  C20  0.020
 KE8  plan-3  S32  0.020
 KE8  plan-3  H41  0.020

