# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 16:36:33 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 1-[(3S)-3-{[4-(morpholin-4-ylmethyl)-6-([1,3]thiazolo[5,4-b]pyridin-2-ylamino)pyrimidin-2-yl]amino}pyrrolidin-1-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CC[C@@H](C1)Nc2nc(CN3CCOCC3)cc(Nc4sc5ncccc5n4)n2
#
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
 G6K  G6K  1-[(3S)-3-{[4-(morpholin-4-ylmethyl)-6-([1,3]thiazolo[5,4-b]pyridin-2-ylamino)pyrimidin-2-yl]amino}pyrrolidin-1-yl]propan-1-one  ligand  61  33  .  2021-08-10  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_G6K
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
 G6K  C1   C  CH3   0  -0.654   6.3095   4.6541   0.7937
 G6K  C2   C  CH2   0  -0.582   5.3281   3.7645   0.0514
 G6K  C3   C  C     0   0.563   3.8946   3.9511   0.5021
 G6K  O4   O  O     0  -0.510   3.5656   4.8226   1.2987
 G6K  N5   N  NT    0  -0.479   2.9918   3.1028  -0.0211
 G6K  C6   C  CH2   0  -0.277   3.2696   2.0474  -0.9926
 G6K  C7   C  CH2   0  -0.476   1.8817   1.6153  -1.4377
 G6K  C8   C  CH1   0  -0.104   1.0518   1.8227  -0.1712
 G6K  C9   C  CH2   0  -0.247   1.5961   3.1391   0.3792
 G6K  N10  N  NH1   0  -0.674  -0.3734   1.8676  -0.3472
 G6K  C11  C  CR6   0   0.610  -1.1400   0.7758  -0.5308
 G6K  N12  N  N     0  -0.487  -2.4274   0.9839  -0.8067
 G6K  C13  C  CR6   0   0.283  -3.1838  -0.0957  -0.9789
 G6K  C14  C  CH2   0  -0.339  -4.6338   0.1393  -1.3052
 G6K  N15  N  NT    0  -0.417  -5.3194   0.8473  -0.2465
 G6K  C16  C  CH2   0  -0.305  -6.6291   1.3000  -0.6806
 G6K  C17  C  CH2   0  -0.190  -7.3178   2.0535   0.4402
 G6K  O18  O  O2    0  -0.484  -7.4365   1.2606   1.6008
 G6K  C19  C  CH2   0  -0.188  -6.1677   0.8247   2.0359
 G6K  C20  C  CH2   0  -0.306  -5.4430   0.0435   0.9571
 G6K  C21  C  CR16  0  -0.484  -2.6816  -1.3794  -0.8827
 G6K  C22  C  CR6   0   0.615  -1.3187  -1.4776  -0.5926
 G6K  N23  N  NH1   0  -0.738  -0.7330  -2.7113  -0.4909
 G6K  C24  C  CR5   0   0.303   0.5753  -3.0047  -0.2639
 G6K  N25  N  N     0  -0.457   0.9733  -4.2355  -0.2468
 G6K  C26  C  CR56  0   0.281   2.3179  -4.3035  -0.0057
 G6K  C27  C  CR16  0  -0.217   3.1040  -5.4477   0.0774
 G6K  C28  C  CR16  0  -0.322   4.4553  -5.2773   0.3268
 G6K  C29  C  CR16  0  -0.096   4.9766  -3.9934   0.4823
 G6K  N30  N  N     0  -0.404   4.2406  -2.8899   0.4056
 G6K  C31  C  CR56  0  -0.040   2.9583  -3.0689   0.1694
 G6K  S32  S  S2    0   0.205   1.7925  -1.7763   0.0182
 G6K  N33  N  N     0  -0.539  -0.5521  -0.4207  -0.4154
 G6K  H1   H  HCH3  0   0.227   6.2845   4.4724   1.8677
 G6K  H2   H  HCH3  0   0.232   7.3235   4.4563   0.4479
 G6K  H3   H  HCH3  0   0.227   6.1036   5.7105   0.6275
 G6K  H4   H  HCH2  0   0.267   5.3863   3.9595  -1.0244
 G6K  H5   H  HCH2  0   0.261   5.6086   2.7137   0.1697
 G6K  H6   H  HCH2  0   0.260   3.8746   2.4126  -1.8227
 G6K  H7   H  HCH2  0   0.240   3.8103   1.2182  -0.5255
 G6K  H8   H  HCH2  0   0.247   1.5103   2.2691  -2.2312
 G6K  H9   H  HCH2  0   0.260   1.8573   0.5898  -1.8024
 G6K  H10  H  HCH1  0   0.266   1.2841   1.0281   0.5411
 G6K  H11  H  HCH2  0   0.259   1.4898   3.2120   1.4614
 G6K  H12  H  HCH2  0   0.238   1.0796   3.9966  -0.0672
 G6K  H13  H  HNH1  0   0.393  -0.8049   2.7511  -0.5708
 G6K  H14  H  HCH2  0   0.263  -4.6772   0.7498  -2.2119
 G6K  H15  H  HCH2  0   0.220  -5.1163  -0.8225  -1.5428
 G6K  H17  H  HCH2  0   0.244  -6.5144   1.9674  -1.5384
 G6K  H18  H  HCH2  0   0.199  -7.2668   0.4594  -1.0051
 G6K  H19  H  HCH2  0   0.201  -6.7560   2.9722   0.6603
 G6K  H20  H  HCH2  0   0.238  -8.3246   2.3411   0.1341
 G6K  H21  H  HCH2  0   0.202  -5.5511   1.6828   2.3396
 G6K  H22  H  HCH2  0   0.238  -6.3194   0.1948   2.9137
 G6K  H23  H  HCH2  0   0.199  -5.9768  -0.9025   0.7590
 G6K  H24  H  HCH2  0   0.246  -4.4515  -0.2238   1.3309
 G6K  H25  H  HCR6  0   0.281  -3.3028  -2.2523  -1.0240
 G6K  H26  H  HNH1  0   0.430  -1.3211  -3.5201  -0.6378
 G6K  H27  H  HCR6  0   0.278   2.6707  -6.4309  -0.0514
 G6K  H28  H  HCR6  0   0.276   5.1140  -6.1311   0.4020
 G6K  H29  H  HCR6  0   0.268   6.0338  -3.8555   0.6746

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
 G6K  C19  O18  single    1.410  0.020  1.410
 G6K  C19  C20  single    1.516  0.020  1.516
 G6K  O18  C17  single    1.411  0.020  1.411
 G6K  C17  C16  single    1.516  0.020  1.516
 G6K  C20  N15  single    1.453  0.020  1.453
 G6K  N15  C16  single    1.452  0.020  1.452
 G6K  N15  C14  single    1.447  0.020  1.447
 G6K  C14  C13  single    1.505  0.020  1.505
 G6K  C21  C13  aromatic  1.382  0.020  1.382
 G6K  C21  C22  aromatic  1.397  0.020  1.397
 G6K  C13  N12  aromatic  1.329  0.020  1.329
 G6K  N23  C22  single    1.369  0.020  1.369
 G6K  N23  C24  single    1.360  0.020  1.360
 G6K  C22  N33  aromatic  1.318  0.020  1.318
 G6K  N12  C11  aromatic  1.333  0.020  1.333
 G6K  N25  C24  aromatic  1.294  0.020  1.294
 G6K  N25  C26  aromatic  1.368  0.020  1.368
 G6K  C24  S32  aromatic  1.752  0.020  1.752
 G6K  N33  C11  aromatic  1.338  0.020  1.338
 G6K  C11  N10  single    1.347  0.020  1.347
 G6K  C26  C27  aromatic  1.391  0.020  1.391
 G6K  C26  C31  aromatic  1.402  0.020  1.402
 G6K  C27  C28  aromatic  1.385  0.020  1.385
 G6K  N10  C8   single    1.437  0.020  1.437
 G6K  S32  C31  aromatic  1.747  0.020  1.747
 G6K  C31  N30  aromatic  1.316  0.020  1.316
 G6K  C28  C29  aromatic  1.394  0.020  1.394
 G6K  C7   C8   single    1.528  0.020  1.528
 G6K  C7   C6   single    1.520  0.020  1.520
 G6K  C8   C9   single    1.527  0.020  1.527
 G6K  N30  C29  aromatic  1.329  0.020  1.329
 G6K  C9   N5   single    1.452  0.020  1.452
 G6K  C6   N5   single    1.461  0.020  1.461
 G6K  N5   C3   single    1.345  0.020  1.345
 G6K  C3   C2   single    1.514  0.020  1.514
 G6K  C3   O4   double    1.226  0.020  1.226
 G6K  C2   C1   single    1.518  0.020  1.518
 G6K  C1   H1   single    0.970  0.020  1.090
 G6K  C1   H2   single    0.970  0.020  1.090
 G6K  C1   H3   single    0.970  0.020  1.090
 G6K  C2   H4   single    0.970  0.020  1.090
 G6K  C2   H5   single    0.970  0.020  1.090
 G6K  C6   H6   single    0.970  0.020  1.090
 G6K  C6   H7   single    0.970  0.020  1.090
 G6K  C7   H8   single    0.970  0.020  1.090
 G6K  C7   H9   single    0.970  0.020  1.090
 G6K  C8   H10  single    0.970  0.020  1.090
 G6K  C9   H11  single    0.970  0.020  1.090
 G6K  C9   H12  single    0.970  0.020  1.090
 G6K  N10  H13  single    0.860  0.020  1.020
 G6K  C14  H14  single    0.970  0.020  1.090
 G6K  C14  H15  single    0.970  0.020  1.090
 G6K  C16  H17  single    0.970  0.020  1.090
 G6K  C16  H18  single    0.970  0.020  1.090
 G6K  C17  H19  single    0.970  0.020  1.090
 G6K  C17  H20  single    0.970  0.020  1.090
 G6K  C19  H21  single    0.970  0.020  1.090
 G6K  C19  H22  single    0.970  0.020  1.090
 G6K  C20  H23  single    0.970  0.020  1.090
 G6K  C20  H24  single    0.970  0.020  1.090
 G6K  C21  H25  single    0.930  0.020  1.080
 G6K  N23  H26  single    0.860  0.020  1.020
 G6K  C27  H27  single    0.930  0.020  1.080
 G6K  C28  H28  single    0.930  0.020  1.080
 G6K  C29  H29  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
 G6K  H3   C1   H2   107.67  3.000
 G6K  H3   C1   H1   107.93  3.000
 G6K  H2   C1   H1   107.70  3.000
 G6K  H3   C1   C2   111.81  3.000
 G6K  H2   C1   C2   109.88  3.000
 G6K  H1   C1   C2   111.68  3.000
 G6K  H5   C2   H4   105.29  3.000
 G6K  H5   C2   C3   109.20  3.000
 G6K  H4   C2   C3   108.72  3.000
 G6K  H5   C2   C1   110.13  3.000
 G6K  H4   C2   C1   109.98  3.000
 G6K  C3   C2   C1   113.21  3.000
 G6K  N5   C3   O4   121.41  3.000
 G6K  O4   C3   C2   122.36  3.000
 G6K  N5   C3   C2   116.23  3.000
 G6K  C9   N5   C6   112.58  3.000
 G6K  C6   N5   C3   125.92  3.000
 G6K  C9   N5   C3   121.48  3.000
 G6K  H7   C6   H6   107.73  3.000
 G6K  H7   C6   C7   111.13  3.000
 G6K  H6   C6   C7   112.27  3.000
 G6K  H7   C6   N5   110.94  3.000
 G6K  H6   C6   N5   111.71  3.000
 G6K  C7   C6   N5   103.08  3.000
 G6K  H9   C7   H8   108.22  3.000
 G6K  H9   C7   C8   113.16  3.000
 G6K  H8   C7   C8   109.63  3.000
 G6K  H9   C7   C6   112.72  3.000
 G6K  H8   C7   C6   110.65  3.000
 G6K  C8   C7   C6   102.39  3.000
 G6K  H10  C8   N10  108.28  3.000
 G6K  H10  C8   C9   108.44  3.000
 G6K  N10  C8   C9   111.76  3.000
 G6K  H10  C8   C7   109.04  3.000
 G6K  C9   C8   C7   102.83  3.000
 G6K  N10  C8   C7   116.19  3.000
 G6K  H12  C9   H11  107.82  3.000
 G6K  H12  C9   C8   111.08  3.000
 G6K  H11  C9   C8   112.38  3.000
 G6K  H12  C9   N5   111.11  3.000
 G6K  H11  C9   N5   111.66  3.000
 G6K  C8   C9   N5   102.81  3.000
 G6K  H13  N10  C11  115.88  3.000
 G6K  H13  N10  C8   118.63  3.000
 G6K  C11  N10  C8   123.78  3.000
 G6K  N33  C11  N12  125.57  3.000
 G6K  N33  C11  N10  117.59  3.000
 G6K  N12  C11  N10  116.84  3.000
 G6K  C13  N12  C11  116.72  3.000
 G6K  C21  C13  C14  120.69  3.000
 G6K  C21  C13  N12  122.59  3.000
 G6K  C14  C13  N12  116.71  3.000
 G6K  H15  C14  H14  106.92  3.000
 G6K  H15  C14  N15  112.17  3.000
 G6K  H14  C14  N15  108.34  3.000
 G6K  H15  C14  C13  109.41  3.000
 G6K  H14  C14  C13  107.77  3.000
 G6K  N15  C14  C13  111.99  3.000
 G6K  C20  N15  C16  110.09  3.000
 G6K  C16  N15  C14  111.18  3.000
 G6K  C20  N15  C14  112.08  3.000
 G6K  H18  C16  H17  107.16  3.000
 G6K  H18  C16  C17  109.47  3.000
 G6K  H17  C16  C17  108.93  3.000
 G6K  H18  C16  N15  111.81  3.000
 G6K  H17  C16  N15  109.29  3.000
 G6K  C17  C16  N15  110.10  3.000
 G6K  H20  C17  H19  107.91  3.000
 G6K  H20  C17  O18  107.54  3.000
 G6K  H19  C17  O18  110.37  3.000
 G6K  H20  C17  C16  110.05  3.000
 G6K  H19  C17  C16  109.35  3.000
 G6K  O18  C17  C16  111.54  3.000
 G6K  C19  O18  C17  110.60  3.000
 G6K  H22  C19  H21  107.84  3.000
 G6K  H22  C19  C20  109.96  3.000
 G6K  H21  C19  C20  109.31  3.000
 G6K  H22  C19  O18  107.55  3.000
 G6K  H21  C19  O18  110.40  3.000
 G6K  C20  C19  O18  111.69  3.000
 G6K  H24  C20  H23  106.88  3.000
 G6K  H24  C20  C19  108.44  3.000
 G6K  H23  C20  C19  109.76  3.000
 G6K  H24  C20  N15  109.97  3.000
 G6K  H23  C20  N15  111.51  3.000
 G6K  C19  C20  N15  110.19  3.000
 G6K  H25  C21  C22  122.09  3.000
 G6K  H25  C21  C13  122.17  3.000
 G6K  C22  C21  C13  115.75  3.000
 G6K  N33  C22  N23  117.63  3.000
 G6K  N33  C22  C21  122.63  3.000
 G6K  N23  C22  C21  119.74  3.000
 G6K  H26  N23  C24  114.29  3.000
 G6K  H26  N23  C22  117.46  3.000
 G6K  C24  N23  C22  128.19  3.000
 G6K  S32  C24  N25  116.81  3.000
 G6K  S32  C24  N23  122.96  3.000
 G6K  N25  C24  N23  120.23  3.000
 G6K  C26  N25  C24  110.61  3.000
 G6K  C31  C26  C27  117.32  3.000
 G6K  C31  C26  N25  115.30  3.000
 G6K  C27  C26  N25  127.38  3.000
 G6K  H27  C27  C28  121.60  3.000
 G6K  H27  C27  C26  120.94  3.000
 G6K  C28  C27  C26  117.46  3.000
 G6K  H28  C28  C29  119.45  3.000
 G6K  H28  C28  C27  120.66  3.000
 G6K  C29  C28  C27  119.88  3.000
 G6K  H29  C29  N30  116.43  3.000
 G6K  H29  C29  C28  120.12  3.000
 G6K  N30  C29  C28  123.45  3.000
 G6K  C31  N30  C29  115.92  3.000
 G6K  S32  C31  N30  124.41  3.000
 G6K  N30  C31  C26  125.97  3.000
 G6K  S32  C31  C26  109.63  3.000
 G6K  C31  S32  C24   87.64  3.000
 G6K  C22  N33  C11  116.75  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
 G6K  CONST_01  C21  C13  N12  C11     0.00   0.0  0
 G6K  CONST_02  C21  C22  N33  C11     0.00   0.0  0
 G6K  CONST_03  C22  C21  C13  N12     0.00   0.0  0
 G6K  CONST_04  C22  N33  C11  N12     0.00   0.0  0
 G6K  CONST_05  N33  C22  C21  C13     0.00   0.0  0
 G6K  CONST_06  N33  C11  N12  C13     0.00   0.0  0
 G6K  CONST_07  C27  C26  N25  C24   180.00   0.0  0
 G6K  CONST_08  C31  C26  N25  C24     0.00   0.0  0
 G6K  CONST_09  C26  C31  S32  C24     0.00   0.0  0
 G6K  CONST_10  N30  C31  S32  C24   180.00   0.0  0
 G6K  CONST_11  C31  S32  C24  N25     0.00   0.0  0
 G6K  CONST_12  C28  C27  C26  N25   180.00   0.0  0
 G6K  CONST_13  S32  C31  C26  N25     0.00   0.0  0
 G6K  CONST_14  N30  C31  C26  N25   180.00   0.0  0
 G6K  CONST_15  S32  C24  N25  C26     0.00   0.0  0
 G6K  CONST_16  C29  C28  C27  C26     0.00   0.0  0
 G6K  CONST_17  C29  N30  C31  C26     0.00   0.0  0
 G6K  CONST_18  S32  C31  C26  C27   180.00   0.0  0
 G6K  CONST_19  N30  C31  C26  C27     0.00   0.0  0
 G6K  CONST_20  N30  C29  C28  C27     0.00   0.0  0
 G6K  CONST_21  C31  C26  C27  C28     0.00   0.0  0
 G6K  CONST_22  C31  N30  C29  C28     0.00   0.0  0
 G6K  CONST_23  S32  C31  N30  C29   180.00   0.0  0
 G6K  CONST_24  C13  N12  C11  N10   180.00   0.0  0
 G6K  CONST_25  C22  N33  C11  N10   180.00   0.0  0
 G6K  CONST_26  C14  C13  N12  C11   180.00   0.0  0
 G6K  CONST_27  N23  C22  N33  C11   180.00   0.0  0
 G6K  CONST_28  N23  C22  C21  C13   180.00   0.0  0
 G6K  CONST_29  C22  C21  C13  C14   180.00   0.0  0
 G6K  CONST_30  C26  N25  C24  N23   180.00   0.0  0
 G6K  CONST_31  C31  S32  C24  N23   180.00   0.0  0
 G6K  CONST_32  N12  C11  N10  C8    180.00   0.0  0
 G6K  CONST_33  N33  C11  N10  C8      0.00   0.0  0
 G6K  CONST_34  H25  C21  C13  N12   180.00   0.0  0
 G6K  CONST_35  H27  C27  C26  N25     0.00   0.0  0
 G6K  CONST_36  H28  C28  C27  C26   180.00   0.0  0
 G6K  CONST_37  H29  C29  C28  C27   180.00   0.0  0
 G6K  CONST_38  C9   N5   C3   C2    180.00   0.0  0
 G6K  CONST_39  C6   N5   C3   C2      0.00   0.0  0
 G6K  CONST_40  C9   N5   C3   O4      0.00   0.0  0
 G6K  CONST_41  C6   N5   C3   O4    180.00   0.0  0
 G6K  CONST_42  H13  N10  C11  N12     0.00   0.0  0
 G6K  Var_01    C8   C7   C6   N5    -32.67  30.0  1
 G6K  Var_02    C8   C9   N5   C6     12.32  30.0  1
 G6K  Var_03    C9   N5   C6   C7     12.96  30.0  1
 G6K  Var_04    O18  C19  C20  N15    56.79  30.0  1
 G6K  Var_05    O18  C17  C16  N15   -57.33  30.0  1
 G6K  Var_06    C19  C20  N15  C16   -55.65  30.0  1
 G6K  Var_07    C20  C19  O18  C17   -57.60  30.0  1
 G6K  Var_08    C20  N15  C16  C17    55.92  30.0  1
 G6K  Var_09    N15  C14  C13  N12   -61.84  30.0  3
 G6K  Var_10    C24  N23  C22  C21   177.50  30.0  3
 G6K  Var_11    N25  C24  N23  C22  -177.37  30.0  2
 G6K  Var_12    N5   C3   C2   C1   -173.74  30.0  2
 G6K  Var_13    H1   C1   C2   C3     58.97  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
 G6K  chir_01  C8  N10  C7  C9  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
 G6K  plan-1  N10  0.020
 G6K  plan-1  C11  0.020
 G6K  plan-1  N12  0.020
 G6K  plan-1  C13  0.020
 G6K  plan-1  C14  0.020
 G6K  plan-1  C21  0.020
 G6K  plan-1  C22  0.020
 G6K  plan-1  N23  0.020
 G6K  plan-1  N33  0.020
 G6K  plan-1  H25  0.020
 G6K  plan-2  N23  0.020
 G6K  plan-2  C24  0.020
 G6K  plan-2  N25  0.020
 G6K  plan-2  C26  0.020
 G6K  plan-2  C27  0.020
 G6K  plan-2  C28  0.020
 G6K  plan-2  C29  0.020
 G6K  plan-2  N30  0.020
 G6K  plan-2  C31  0.020
 G6K  plan-2  S32  0.020
 G6K  plan-2  H27  0.020
 G6K  plan-2  H28  0.020
 G6K  plan-2  H29  0.020
 G6K  plan-3  C8   0.020
 G6K  plan-3  N10  0.020
 G6K  plan-3  C11  0.020
 G6K  plan-3  H13  0.020
 G6K  plan-4  C2   0.020
 G6K  plan-4  C3   0.020
 G6K  plan-4  O4   0.020
 G6K  plan-4  N5   0.020
 G6K  plan-4  C6   0.020
 G6K  plan-4  C9   0.020

