# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 17:04:07 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]prop-2-en-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C=CC(=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
 G5K  G5K  1-[(3S)-3-{[4-(morpholin-4-ylmethyl)-6-([1,3]thiazolo[5,4-b]pyridin-2-ylamino)pyrimidin-2-yl]amino}pyrrolidin-1-yl]prop-2-en-1-one  ligand  59  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_G5K
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
 G5K  C1   C  C2    0  -0.472   5.2920   4.1424   2.0164
 G5K  C2   C  C1    0  -0.330   4.4364   3.8605   1.0397
 G5K  C3   C  C     0   0.542   3.2093   3.0600   1.2993
 G5K  O4   O  O     0  -0.508   2.9970   2.5389   2.3903
 G5K  N5   N  NR5   0  -0.490   2.3478   2.9294   0.2761
 G5K  C6   C  CH2   0  -0.285   2.4518   3.5613  -1.0413
 G5K  C7   C  CH2   0  -0.488   1.0954   3.2873  -1.6757
 G5K  C8   C  CR15  0  -0.101   0.6888   1.9591  -1.0504
 G5K  C9   C  CH2   0  -0.247   1.1522   2.1143   0.4015
 G5K  N10  N  NH1   0  -0.670  -0.7113   1.6792  -1.2051
 G5K  C11  C  CR6   0   0.605  -1.2703   0.4727  -0.9891
 G5K  N12  N  N     0  -0.487  -2.6022   0.4167  -1.0228
 G5K  C13  C  CR6   0   0.281  -3.1557  -0.7701  -0.8013
 G5K  C14  C  CH2   0  -0.330  -4.6571  -0.8581  -0.8614
 G5K  N15  N  NT    0  -0.417  -5.3156   0.2259  -0.1732
 G5K  C16  C  CH2   0  -0.306  -5.0729   0.1931   1.2585
 G5K  C17  C  CH2   0  -0.188  -5.7788   1.3544   1.9306
 G5K  O18  O  O2    0  -0.484  -7.1641   1.3471   1.6657
 G5K  C19  C  CH2   0  -0.191  -7.4058   1.3854   0.2766
 G5K  C20  C  CH2   0  -0.304  -6.7437   0.2222  -0.4356
 G5K  C21  C  CR16  0  -0.489  -2.4062  -1.9058  -0.5557
 G5K  C22  C  CR6   0   0.618  -1.0211  -1.7336  -0.5690
 G5K  N23  N  NH1   0  -0.738  -0.2007  -2.8083  -0.3526
 G5K  C24  C  CR5   0   0.304   1.1584  -2.8407  -0.3380
 G5K  N25  N  N     0  -0.458   1.7797  -3.9564  -0.1313
 G5K  C26  C  CR56  0   0.281   3.1336  -3.7657  -0.1586
 G5K  C27  C  CR16  0  -0.217   4.1245  -4.7252   0.0187
 G5K  C28  C  CR16  0  -0.322   5.4415  -4.3037  -0.0513
 G5K  C29  C  CR16  0  -0.095   5.7292  -2.9609  -0.2925
 G5K  N30  N  N     0  -0.405   4.7955  -2.0315  -0.4655
 G5K  C31  C  CR56  0  -0.040   3.5489  -2.4479  -0.3956
 G5K  S32  S  S2    0   0.204   2.1498  -1.4184  -0.5913
 G5K  N33  N  N     0  -0.539  -0.4514  -0.5623  -0.7749
 G5K  H1   H  H     0   0.256   5.1296   3.8121   3.0343
 G5K  H2   H  H     0   0.261   6.1868   4.7179   1.8235
 G5K  H3   H  H     0   0.275   4.6389   4.2105   0.0355
 G5K  H4   H  HCH2  0   0.263   2.6540   4.6288  -0.9618
 G5K  H5   H  HCH2  0   0.252   3.2531   3.1055  -1.6288
 G5K  H6   H  HCH2  0   0.251   0.3806   4.0670  -1.3984
 G5K  H7   H  HCH2  0   0.270   1.1499   3.2486  -2.7624
 G5K  H8   H  HCR5  0   0.268   1.2601   1.1563  -1.5213
 G5K  H9   H  HCH2  0   0.254   1.3692   1.1576   0.8757
 G5K  H10  H  HCH2  0   0.239   0.3833   2.6215   0.9941
 G5K  H11  H  HNH1  0   0.393  -1.3511   2.4572  -1.2421
 G5K  H12  H  HCH2  0   0.267  -4.9480  -0.8230  -1.9170
 G5K  H13  H  HCH2  0   0.220  -4.9729  -1.8449  -0.4851
 G5K  H15  H  HCH2  0   0.200  -5.4104  -0.7586   1.7057
 G5K  H16  H  HCH2  0   0.247  -4.0023   0.2806   1.4559
 G5K  H17  H  HCH2  0   0.237  -5.6510   1.2939   3.0124
 G5K  H18  H  HCH2  0   0.201  -5.3283   2.2973   1.5883
 G5K  H19  H  HCH2  0   0.238  -8.4863   1.3474   0.1300
 G5K  H20  H  HCH2  0   0.201  -7.0390   2.3295  -0.1513
 G5K  H21  H  HCH2  0   0.244  -6.9147   0.3215  -1.5106
 G5K  H22  H  HCH2  0   0.199  -7.2170  -0.7228  -0.1161
 G5K  H23  H  HCR6  0   0.280  -2.8654  -2.8638  -0.3570
 G5K  H24  H  HNH1  0   0.430  -0.6394  -3.7028  -0.1833
 G5K  H25  H  HCR6  0   0.278   3.8688  -5.7606   0.2028
 G5K  H26  H  HCR6  0   0.276   6.2524  -5.0065   0.0791
 G5K  H27  H  HCR6  0   0.267   6.7582  -2.6272  -0.3487

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
 G5K  C28  C27  aromatic  1.385  0.020  1.385
 G5K  C28  C29  aromatic  1.394  0.020  1.394
 G5K  C27  C26  aromatic  1.391  0.020  1.391
 G5K  C29  N30  aromatic  1.329  0.020  1.329
 G5K  C26  C31  aromatic  1.402  0.020  1.402
 G5K  C26  N25  aromatic  1.368  0.020  1.368
 G5K  N30  C31  aromatic  1.316  0.020  1.316
 G5K  C31  S32  aromatic  1.748  0.020  1.748
 G5K  N25  C24  aromatic  1.294  0.020  1.294
 G5K  C24  S32  aromatic  1.752  0.020  1.752
 G5K  C24  N23  single    1.360  0.020  1.360
 G5K  N23  C22  single    1.369  0.020  1.369
 G5K  C22  C21  aromatic  1.396  0.020  1.396
 G5K  C22  N33  aromatic  1.319  0.020  1.319
 G5K  C7   C6   single    1.522  0.020  1.522
 G5K  C7   C8   single    1.523  0.020  1.523
 G5K  C21  C13  aromatic  1.383  0.020  1.383
 G5K  N33  C11  aromatic  1.337  0.020  1.337
 G5K  C6   N5   single    1.465  0.020  1.465
 G5K  C11  N10  single    1.347  0.020  1.347
 G5K  C11  N12  aromatic  1.333  0.020  1.333
 G5K  C13  C14  single    1.505  0.020  1.505
 G5K  C13  N12  aromatic  1.328  0.020  1.328
 G5K  C8   N10  single    1.436  0.020  1.436
 G5K  C8   C9   single    1.532  0.020  1.532
 G5K  C14  N15  single    1.443  0.020  1.443
 G5K  N5   C9   single    1.452  0.020  1.452
 G5K  N5   C3   single    1.344  0.020  1.344
 G5K  O4   C3   double    1.228  0.020  1.228
 G5K  C3   C2   single    1.488  0.020  1.488
 G5K  N15  C20  single    1.452  0.020  1.452
 G5K  N15  C16  single    1.452  0.020  1.452
 G5K  C20  C19  single    1.516  0.020  1.516
 G5K  C16  C17  single    1.516  0.020  1.516
 G5K  C2   C1   double    1.329  0.020  1.329
 G5K  C19  O18  single    1.410  0.020  1.410
 G5K  C17  O18  single    1.410  0.020  1.410
 G5K  C1   H1   single    0.930  0.020  1.080
 G5K  C1   H2   single    0.930  0.020  1.080
 G5K  C2   H3   single    0.930  0.020  1.080
 G5K  C6   H4   single    0.970  0.020  1.090
 G5K  C6   H5   single    0.970  0.020  1.090
 G5K  C7   H6   single    0.970  0.020  1.090
 G5K  C7   H7   single    0.970  0.020  1.090
 G5K  C8   H8   single    0.970  0.020  1.090
 G5K  C9   H9   single    0.970  0.020  1.090
 G5K  C9   H10  single    0.970  0.020  1.090
 G5K  N10  H11  single    0.860  0.020  1.020
 G5K  C14  H12  single    0.970  0.020  1.090
 G5K  C14  H13  single    0.970  0.020  1.090
 G5K  C16  H15  single    0.970  0.020  1.090
 G5K  C16  H16  single    0.970  0.020  1.090
 G5K  C17  H17  single    0.970  0.020  1.090
 G5K  C17  H18  single    0.970  0.020  1.090
 G5K  C19  H19  single    0.970  0.020  1.090
 G5K  C19  H20  single    0.970  0.020  1.090
 G5K  C20  H21  single    0.970  0.020  1.090
 G5K  C20  H22  single    0.970  0.020  1.090
 G5K  C21  H23  single    0.930  0.020  1.080
 G5K  N23  H24  single    0.860  0.020  1.020
 G5K  C27  H25  single    0.930  0.020  1.080
 G5K  C28  H26  single    0.930  0.020  1.080
 G5K  C29  H27  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
 G5K  H2   C1   H1   117.02  3.000
 G5K  H2   C1   C2   120.98  3.000
 G5K  H1   C1   C2   122.00  3.000
 G5K  H3   C2   C3   119.34  3.000
 G5K  H3   C2   C1   119.52  3.000
 G5K  C3   C2   C1   121.13  3.000
 G5K  N5   C3   O4   121.64  3.000
 G5K  O4   C3   C2   121.73  3.000
 G5K  N5   C3   C2   116.62  3.000
 G5K  C9   N5   C6   112.22  3.000
 G5K  C9   N5   C3   121.09  3.000
 G5K  C6   N5   C3   126.68  3.000
 G5K  H5   C6   H4   108.17  3.000
 G5K  H5   C6   C7   110.74  3.000
 G5K  H4   C6   C7   111.85  3.000
 G5K  H5   C6   N5   110.83  3.000
 G5K  H4   C6   N5   111.73  3.000
 G5K  C7   C6   N5   103.53  3.000
 G5K  H7   C7   H6   108.13  3.000
 G5K  H7   C7   C8   113.09  3.000
 G5K  H6   C7   C8   110.07  3.000
 G5K  H7   C7   C6   112.19  3.000
 G5K  H6   C7   C6   110.39  3.000
 G5K  C8   C7   C6   102.93  3.000
 G5K  H8   C8   N10  108.68  3.000
 G5K  H8   C8   C9   108.96  3.000
 G5K  N10  C8   C9   114.63  3.000
 G5K  H8   C8   C7   108.93  3.000
 G5K  C9   C8   C7   102.71  3.000
 G5K  N10  C8   C7   112.70  3.000
 G5K  H10  C9   H9   108.11  3.000
 G5K  H10  C9   C8   110.33  3.000
 G5K  H9   C9   C8   112.57  3.000
 G5K  H10  C9   N5   111.39  3.000
 G5K  H9   C9   N5   111.49  3.000
 G5K  C8   C9   N5   102.94  3.000
 G5K  H11  N10  C11  115.71  3.000
 G5K  H11  N10  C8   118.19  3.000
 G5K  C11  N10  C8   124.18  3.000
 G5K  N33  C11  N12  125.68  3.000
 G5K  N12  C11  N10  116.62  3.000
 G5K  N33  C11  N10  117.70  3.000
 G5K  C13  N12  C11  116.72  3.000
 G5K  C21  C13  C14  119.98  3.000
 G5K  C14  C13  N12  117.47  3.000
 G5K  C21  C13  N12  122.53  3.000
 G5K  H13  C14  H12  106.35  3.000
 G5K  H13  C14  N15  112.27  3.000
 G5K  H12  C14  N15  108.32  3.000
 G5K  H13  C14  C13  108.94  3.000
 G5K  H12  C14  C13  107.54  3.000
 G5K  N15  C14  C13  113.09  3.000
 G5K  C20  N15  C16  110.03  3.000
 G5K  C16  N15  C14  112.14  3.000
 G5K  C20  N15  C14  111.14  3.000
 G5K  H16  C16  H15  107.19  3.000
 G5K  H16  C16  C17  108.35  3.000
 G5K  H15  C16  C17  109.77  3.000
 G5K  H16  C16  N15  109.89  3.000
 G5K  H15  C16  N15  111.57  3.000
 G5K  C17  C16  N15  109.99  3.000
 G5K  H18  C17  H17  107.95  3.000
 G5K  H18  C17  O18  110.38  3.000
 G5K  H17  C17  O18  107.52  3.000
 G5K  H18  C17  C16  109.15  3.000
 G5K  H17  C17  C16  110.03  3.000
 G5K  O18  C17  C16  111.72  3.000
 G5K  C19  O18  C17  110.68  3.000
 G5K  H20  C19  H19  107.94  3.000
 G5K  H20  C19  C20  109.28  3.000
 G5K  H19  C19  C20  110.04  3.000
 G5K  H20  C19  O18  110.45  3.000
 G5K  H19  C19  O18  107.52  3.000
 G5K  C20  C19  O18  111.53  3.000
 G5K  H22  C20  H21  107.18  3.000
 G5K  H22  C20  C19  109.48  3.000
 G5K  H21  C20  C19  108.91  3.000
 G5K  H22  C20  N15  111.80  3.000
 G5K  H21  C20  N15  109.35  3.000
 G5K  C19  C20  N15  110.04  3.000
 G5K  H23  C21  C22  122.19  3.000
 G5K  H23  C21  C13  122.03  3.000
 G5K  C22  C21  C13  115.78  3.000
 G5K  N33  C22  N23  117.58  3.000
 G5K  N33  C22  C21  122.67  3.000
 G5K  N23  C22  C21  119.75  3.000
 G5K  H24  N23  C24  114.27  3.000
 G5K  H24  N23  C22  117.46  3.000
 G5K  C24  N23  C22  128.27  3.000
 G5K  S32  C24  N25  116.84  3.000
 G5K  S32  C24  N23  123.00  3.000
 G5K  N25  C24  N23  120.16  3.000
 G5K  C26  N25  C24  110.61  3.000
 G5K  C31  C26  C27  117.33  3.000
 G5K  C31  C26  N25  115.33  3.000
 G5K  C27  C26  N25  127.34  3.000
 G5K  H25  C27  C28  121.64  3.000
 G5K  H25  C27  C26  120.90  3.000
 G5K  C28  C27  C26  117.47  3.000
 G5K  H26  C28  C29  119.48  3.000
 G5K  H26  C28  C27  120.63  3.000
 G5K  C29  C28  C27  119.88  3.000
 G5K  H27  C29  N30  116.44  3.000
 G5K  H27  C29  C28  120.11  3.000
 G5K  N30  C29  C28  123.45  3.000
 G5K  C31  N30  C29  115.93  3.000
 G5K  S32  C31  N30  124.46  3.000
 G5K  S32  C31  C26  109.60  3.000
 G5K  N30  C31  C26  125.94  3.000
 G5K  C31  S32  C24   87.63  3.000
 G5K  C22  N33  C11  116.61  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
 G5K  CONST_01  C21  C22  N33  C11     0.00   0.0  0
 G5K  CONST_02  C21  C13  N12  C11     0.00   0.0  0
 G5K  CONST_03  C22  N33  C11  N12     0.00   0.0  0
 G5K  CONST_04  C22  C21  C13  N12     0.00   0.0  0
 G5K  CONST_05  N33  C22  C21  C13     0.00   0.0  0
 G5K  CONST_06  N33  C11  N12  C13     0.00   0.0  0
 G5K  CONST_07  C27  C26  N25  C24   180.00   0.0  0
 G5K  CONST_08  C31  C26  N25  C24     0.00   0.0  0
 G5K  CONST_09  C26  C31  S32  C24     0.00   0.0  0
 G5K  CONST_10  N30  C31  S32  C24   180.00   0.0  0
 G5K  CONST_11  C28  C27  C26  N25   180.00   0.0  0
 G5K  CONST_12  N30  C31  C26  N25   180.00   0.0  0
 G5K  CONST_13  S32  C31  C26  N25     0.00   0.0  0
 G5K  CONST_14  C31  S32  C24  N25     0.00   0.0  0
 G5K  CONST_15  C29  C28  C27  C26     0.00   0.0  0
 G5K  CONST_16  C29  N30  C31  C26     0.00   0.0  0
 G5K  CONST_17  S32  C24  N25  C26     0.00   0.0  0
 G5K  CONST_18  N30  C29  C28  C27     0.00   0.0  0
 G5K  CONST_19  N30  C31  C26  C27     0.00   0.0  0
 G5K  CONST_20  S32  C31  C26  C27   180.00   0.0  0
 G5K  CONST_21  C31  C26  C27  C28     0.00   0.0  0
 G5K  CONST_22  C31  N30  C29  C28     0.00   0.0  0
 G5K  CONST_23  S32  C31  N30  C29   180.00   0.0  0
 G5K  CONST_24  C22  N33  C11  N10   180.00   0.0  0
 G5K  CONST_25  C13  N12  C11  N10   180.00   0.0  0
 G5K  CONST_26  N23  C22  N33  C11   180.00   0.0  0
 G5K  CONST_27  C14  C13  N12  C11   180.00   0.0  0
 G5K  CONST_28  N23  C22  C21  C13   180.00   0.0  0
 G5K  CONST_29  C22  C21  C13  C14   180.00   0.0  0
 G5K  CONST_30  C26  N25  C24  N23   180.00   0.0  0
 G5K  CONST_31  C31  S32  C24  N23   180.00   0.0  0
 G5K  CONST_32  N33  C11  N10  C8      0.00   0.0  0
 G5K  CONST_33  N12  C11  N10  C8    180.00   0.0  0
 G5K  CONST_34  H23  C21  C13  N12   180.00   0.0  0
 G5K  CONST_35  H25  C27  C26  N25     0.00   0.0  0
 G5K  CONST_36  H26  C28  C27  C26   180.00   0.0  0
 G5K  CONST_37  H27  C29  C28  C27   180.00   0.0  0
 G5K  CONST_38  C6   N5   C3   C2      0.00   0.0  0
 G5K  CONST_39  C9   N5   C3   C2    180.00   0.0  0
 G5K  CONST_40  C6   N5   C3   O4    180.00   0.0  0
 G5K  CONST_41  C9   N5   C3   O4      0.00   0.0  0
 G5K  CONST_42  H11  N10  C11  N12     0.00   0.0  0
 G5K  Var_01    C8   C7   C6   N5    -30.49  30.0  1
 G5K  Var_02    C8   C9   N5   C6     14.88  30.0  1
 G5K  Var_03    C9   N5   C6   C7      9.79  30.0  1
 G5K  Var_04    O18  C19  C20  N15   -57.29  30.0  1
 G5K  Var_05    O18  C17  C16  N15    56.98  30.0  1
 G5K  Var_06    C19  C20  N15  C16    56.28  30.0  1
 G5K  Var_07    C20  N15  C16  C17   -56.06  30.0  1
 G5K  Var_08    C20  C19  O18  C17    57.60  30.0  1
 G5K  Var_09    N15  C14  C13  N12   -44.46  30.0  2
 G5K  Var_10    C24  N23  C22  C21   179.43  30.0  2
 G5K  Var_11    N25  C24  N23  C22  -179.17  30.0  1
 G5K  Var_12    N5   C3   C2   C1    174.24  30.0  1
 G5K  Var_13    H1   C1   C2   C3     -0.55   0.0  2

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
 G5K  chir_01  C8  C7  N10  C9  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
 G5K  plan-1  N10  0.020
 G5K  plan-1  C11  0.020
 G5K  plan-1  N12  0.020
 G5K  plan-1  C13  0.020
 G5K  plan-1  C14  0.020
 G5K  plan-1  C21  0.020
 G5K  plan-1  C22  0.020
 G5K  plan-1  N23  0.020
 G5K  plan-1  N33  0.020
 G5K  plan-1  H23  0.020
 G5K  plan-2  N23  0.020
 G5K  plan-2  C24  0.020
 G5K  plan-2  N25  0.020
 G5K  plan-2  C26  0.020
 G5K  plan-2  C27  0.020
 G5K  plan-2  C28  0.020
 G5K  plan-2  C29  0.020
 G5K  plan-2  N30  0.020
 G5K  plan-2  C31  0.020
 G5K  plan-2  S32  0.020
 G5K  plan-2  H25  0.020
 G5K  plan-2  H26  0.020
 G5K  plan-2  H27  0.020
 G5K  plan-3  C8   0.020
 G5K  plan-3  N10  0.020
 G5K  plan-3  C11  0.020
 G5K  plan-3  H11  0.020
 G5K  plan-4  C2   0.020
 G5K  plan-4  C3   0.020
 G5K  plan-4  O4   0.020
 G5K  plan-4  N5   0.020
 G5K  plan-4  C6   0.020
 G5K  plan-4  C9   0.020
 G5K  plan-5  C1   0.020
 G5K  plan-5  C2   0.020
 G5K  plan-5  C3   0.020
 G5K  plan-5  H1   0.020
 G5K  plan-5  H2   0.020
 G5K  plan-5  H3   0.020

