# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:40:15 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 5-[6-[(4-methylsulfonylpiperazin-1-yl)methyl]-4-morpholin-4-yl-thieno[3,2-d]pyrimidin-2-yl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)N1CCN(CC1)Cc2sc3c(c2)nc(nc3N4CCOCC4)c5ccc(N)nc5
#
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
 JZX  JZX  5-[6-[(4-methylsulfonylpiperazin-1-yl)methyl]-4-morpholin-4-yl-thieno[3,2-d]pyrimidin-2-yl]pyridin-2-amine  ligand  60  33  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JZX
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
 JZX  C1    C  CR6   0   0.366   2.9135  -0.4732   0.2263
 JZX  N1    N  N     0  -0.492   1.6904  -0.9397   0.0666
 JZX  O1    O  O2    0  -0.480   3.9956   5.5694  -0.8729
 JZX  S1    S  S2    0   0.200  -0.3020   2.1392  -1.1888
 JZX  C2    C  CR6   0   0.578   2.4272   1.7132  -0.3573
 JZX  N2    N  N     0  -0.515   3.2953   0.7913   0.0385
 JZX  O2    O  OS    0  -0.668  -6.9041  -1.6977   2.6795
 JZX  S2    S  S     0   1.349  -6.7131  -2.3360   1.3856
 JZX  C3    C  CR56  0   0.341   0.7869  -0.0443  -0.3506
 JZX  N3    N  NT    0  -0.425  -3.4756  -0.2476  -0.8474
 JZX  O3    O  OS    0  -0.668  -7.8666  -2.5204   0.5176
 JZX  C4    C  CR56  0  -0.343   1.0906   1.3032  -0.5828
 JZX  N4    N  NT    0  -0.512   2.9044   2.9713  -0.5513
 JZX  C5    C  CR5   0  -0.168  -1.2688   0.7069  -1.1057
 JZX  N5    N  N     0  -0.584  -5.6144  -1.4254   0.5520
 JZX  C6    C  CR15  0  -0.236  -0.5763  -0.3586  -0.6416
 JZX  N6    N  N     0  -0.458   6.2489  -1.8412   1.2244
 JZX  C7    C  CH2   0  -0.312  -2.6993   0.7442  -1.5519
 JZX  N7    N  NH2   0  -0.827   6.9835  -3.9323   1.8213
 JZX  C8    C  CR6   0  -0.129   3.9514  -1.4208   0.6575
 JZX  C9    C  CH2   0  -0.281  -4.6878  -0.6307  -1.5416
 JZX  C10   C  CH2   0  -0.312  -5.3407  -1.8032  -0.8346
 JZX  C11   C  CH2   0  -0.309  -4.4108  -1.0025   1.2686
 JZX  C12   C  CH2   0  -0.284  -3.7711   0.1459   0.5155
 JZX  C13   C  CH2   0  -0.321   4.3192   3.2283  -0.3115
 JZX  C14   C  CH2   0  -0.192   4.7726   4.4221  -1.1294
 JZX  C15   C  CH2   0  -0.180   2.6429   5.3195  -1.1667
 JZX  C16   C  CH2   0  -0.335   2.0932   4.1636  -0.3518
 JZX  C17   C  CR16  0  -0.080   5.2733  -1.0318   0.8371
 JZX  C18   C  CR6   0   0.461   5.9597  -3.1216   1.4631
 JZX  C19   C  CR16  0  -0.168   3.6594  -2.7680   0.9131
 JZX  C20   C  CR16  0  -0.373   4.6519  -3.6248   1.3143
 JZX  C21   C  CH3   0  -0.804  -5.9675  -3.9291   1.6567
 JZX  H6    H  HCR5  0   0.265  -1.0063  -1.3401  -0.5042
 JZX  H7    H  HCH2  0   0.281  -2.7309   0.5192  -2.6220
 JZX  H7A   H  HCH2  0   0.233  -3.1041   1.7633  -1.4445
 JZX  HN7   H  HNH2  0   0.388   7.8390  -3.4971   2.1234
 JZX  HN7A  H  HNH2  0   0.397   6.7762  -4.8209   2.2440
 JZX  H9    H  HCH2  0   0.212  -5.4124   0.1962  -1.6117
 JZX  H9A   H  HCH2  0   0.257  -4.4384  -0.9381  -2.5587
 JZX  H10   H  HCH2  0   0.238  -4.6736  -2.6730  -0.8811
 JZX  H10A  H  HCH2  0   0.276  -6.2706  -2.0543  -1.3401
 JZX  H11   H  HCH2  0   0.276  -4.6736  -0.6716   2.2708
 JZX  H11A  H  HCH2  0   0.238  -3.6882  -1.8240   1.3509
 JZX  H12   H  HCH2  0   0.259  -2.8449   0.4127   1.0272
 JZX  H12A  H  HCH2  0   0.218  -4.4353   1.0247   0.5492
 JZX  H13   H  HCH2  0   0.236   4.4996   3.4057   0.7559
 JZX  H13A  H  HCH2  0   0.275   4.9061   2.3606  -0.6009
 JZX  H14   H  HCH2  0   0.209   4.7366   4.1647  -2.1972
 JZX  H14A  H  HCH2  0   0.247   5.8064   4.6594  -0.8756
 JZX  H15   H  HCH2  0   0.249   2.0792   6.2232  -0.9321
 JZX  H15A  H  HCH2  0   0.211   2.5109   5.1034  -2.2361
 JZX  H16   H  HCH2  0   0.262   1.0610   4.0137  -0.6554
 JZX  H16A  H  HCH2  0   0.250   2.0783   4.4269   0.7129
 JZX  H17   H  HCR6  0   0.263   5.5581  -0.0013   0.6567
 JZX  H19   H  HCR6  0   0.260   2.6475  -3.1323   0.7945
 JZX  H20   H  HCR6  0   0.269   4.4419  -4.6669   1.5170
 JZX  H21   H  HCH3  0   0.310  -6.6867  -4.5474   2.1914
 JZX  H21A  H  HCH3  0   0.291  -5.7289  -4.3896   0.7001
 JZX  H21B  H  HCH3  0   0.291  -5.0659  -3.8157   2.2550

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
 JZX  C1   N1    aromatic  1.319  0.020  1.319
 JZX  C1   N2    aromatic  1.334  0.020  1.334
 JZX  C1   C8    single    1.470  0.020  1.470
 JZX  N1   C3    aromatic  1.339  0.020  1.339
 JZX  O1   C14   single    1.409  0.020  1.409
 JZX  O1   C15   single    1.407  0.020  1.407
 JZX  S1   C4    aromatic  1.734  0.020  1.734
 JZX  S1   C5    aromatic  1.730  0.020  1.730
 JZX  C2   N2    aromatic  1.327  0.020  1.327
 JZX  C2   C4    aromatic  1.416  0.020  1.416
 JZX  C2   N4    single    1.359  0.020  1.359
 JZX  O2   S2    double    1.455  0.020  1.455
 JZX  S2   O3    double    1.455  0.020  1.455
 JZX  S2   N5    single    1.653  0.020  1.653
 JZX  S2   C21   single    1.780  0.020  1.780
 JZX  C3   C4    aromatic  1.401  0.020  1.401
 JZX  C3   C6    aromatic  1.429  0.020  1.429
 JZX  N3   C7    single    1.443  0.020  1.443
 JZX  N3   C9    single    1.448  0.020  1.448
 JZX  N3   C12   single    1.449  0.020  1.449
 JZX  N4   C13   single    1.458  0.020  1.458
 JZX  N4   C16   single    1.456  0.020  1.456
 JZX  C5   C6    aromatic  1.353  0.020  1.353
 JZX  C5   C7    single    1.499  0.020  1.499
 JZX  N5   C10   single    1.463  0.020  1.463
 JZX  N5   C11   single    1.463  0.020  1.463
 JZX  N6   C17   aromatic  1.325  0.020  1.325
 JZX  N6   C18   aromatic  1.334  0.020  1.334
 JZX  N7   C18   single    1.354  0.020  1.354
 JZX  C8   C17   aromatic  1.390  0.020  1.390
 JZX  C8   C19   aromatic  1.402  0.020  1.402
 JZX  C9   C10   single    1.517  0.020  1.517
 JZX  C11  C12   single    1.515  0.020  1.515
 JZX  C13  C14   single    1.516  0.020  1.516
 JZX  C15  C16   single    1.517  0.020  1.517
 JZX  C18  C20   aromatic  1.409  0.020  1.409
 JZX  C19  C20   aromatic  1.371  0.020  1.371
 JZX  C6   H6    single    0.930  0.020  1.080
 JZX  C7   H7    single    0.970  0.020  1.090
 JZX  C7   H7A   single    0.970  0.020  1.090
 JZX  N7   HN7   single    0.890  0.020  1.040
 JZX  N7   HN7A  single    0.890  0.020  1.040
 JZX  C9   H9    single    0.970  0.020  1.090
 JZX  C9   H9A   single    0.970  0.020  1.090
 JZX  C10  H10   single    0.970  0.020  1.090
 JZX  C10  H10A  single    0.970  0.020  1.090
 JZX  C11  H11   single    0.970  0.020  1.090
 JZX  C11  H11A  single    0.970  0.020  1.090
 JZX  C12  H12   single    0.970  0.020  1.090
 JZX  C12  H12A  single    0.970  0.020  1.090
 JZX  C13  H13   single    0.970  0.020  1.090
 JZX  C13  H13A  single    0.970  0.020  1.090
 JZX  C14  H14   single    0.970  0.020  1.090
 JZX  C14  H14A  single    0.970  0.020  1.090
 JZX  C15  H15   single    0.970  0.020  1.090
 JZX  C15  H15A  single    0.970  0.020  1.090
 JZX  C16  H16   single    0.970  0.020  1.090
 JZX  C16  H16A  single    0.970  0.020  1.090
 JZX  C17  H17   single    0.930  0.020  1.080
 JZX  C19  H19   single    0.930  0.020  1.080
 JZX  C20  H20   single    0.930  0.020  1.080
 JZX  C21  H21   single    0.970  0.020  1.090
 JZX  C21  H21A  single    0.970  0.020  1.090
 JZX  C21  H21B  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
 JZX  C8    C1   N2    116.76  3.000
 JZX  C8    C1   N1    117.54  3.000
 JZX  N2    C1   N1    125.71  3.000
 JZX  C3    N1   C1    115.28  3.000
 JZX  C15   O1   C14   110.34  3.000
 JZX  C5    S1   C4     91.88  3.000
 JZX  N4    C2   C4    125.20  3.000
 JZX  N4    C2   N2    117.13  3.000
 JZX  C4    C2   N2    117.64  3.000
 JZX  C2    N2   C1    120.89  3.000
 JZX  C21   S2   N5    106.95  3.000
 JZX  C21   S2   O3    108.03  3.000
 JZX  N5    S2   O3    107.21  3.000
 JZX  C21   S2   O2    108.19  3.000
 JZX  N5    S2   O2    107.10  3.000
 JZX  O3    S2   O2    118.81  3.000
 JZX  C6    C3   C4    112.62  3.000
 JZX  C6    C3   N1    124.07  3.000
 JZX  C4    C3   N1    123.29  3.000
 JZX  C12   N3   C9    110.60  3.000
 JZX  C12   N3   C7    112.47  3.000
 JZX  C9    N3   C7    113.46  3.000
 JZX  C3    C4   C2    117.18  3.000
 JZX  C3    C4   S1    110.35  3.000
 JZX  C2    C4   S1    132.39  3.000
 JZX  C16   N4   C13   111.95  3.000
 JZX  C16   N4   C2    122.88  3.000
 JZX  C13   N4   C2    118.70  3.000
 JZX  C7    C5   C6    127.61  3.000
 JZX  C7    C5   S1    119.90  3.000
 JZX  C6    C5   S1    112.49  3.000
 JZX  C11   N5   C10   112.64  3.000
 JZX  C11   N5   S2    117.33  3.000
 JZX  C10   N5   S2    117.39  3.000
 JZX  H6    C6   C5    123.74  3.000
 JZX  H6    C6   C3    123.61  3.000
 JZX  C5    C6   C3    112.64  3.000
 JZX  C18   N6   C17   118.61  3.000
 JZX  H7A   C7   H7    105.96  3.000
 JZX  H7A   C7   C5    110.16  3.000
 JZX  H7    C7   C5    108.28  3.000
 JZX  H7A   C7   N3    112.98  3.000
 JZX  H7    C7   N3    108.70  3.000
 JZX  C5    C7   N3    110.54  3.000
 JZX  HN7A  N7   HN7   115.54  3.000
 JZX  HN7A  N7   C18   118.97  3.000
 JZX  HN7   N7   C18   117.60  3.000
 JZX  C19   C8   C17   116.34  3.000
 JZX  C19   C8   C1    121.72  3.000
 JZX  C17   C8   C1    121.94  3.000
 JZX  H9A   C9   H9    107.60  3.000
 JZX  H9A   C9   C10   108.36  3.000
 JZX  H9    C9   C10   109.08  3.000
 JZX  H9A   C9   N3    109.26  3.000
 JZX  H9    C9   N3    112.48  3.000
 JZX  C10   C9   N3    109.96  3.000
 JZX  H10A  C10  H10   108.49  3.000
 JZX  H10A  C10  C9    109.25  3.000
 JZX  H10   C10  C9    109.35  3.000
 JZX  H10A  C10  N5    109.88  3.000
 JZX  H10   C10  N5    111.02  3.000
 JZX  C9    C10  N5    108.82  3.000
 JZX  H11A  C11  H11   108.53  3.000
 JZX  H11A  C11  C12   109.07  3.000
 JZX  H11   C11  C12   109.24  3.000
 JZX  H11A  C11  N5    111.23  3.000
 JZX  H11   C11  N5    109.91  3.000
 JZX  C12   C11  N5    108.84  3.000
 JZX  H12A  C12  H12   107.59  3.000
 JZX  H12A  C12  C11   109.55  3.000
 JZX  H12   C12  C11   108.10  3.000
 JZX  H12A  C12  N3    111.61  3.000
 JZX  H12   C12  N3    109.54  3.000
 JZX  C11   C12  N3    110.36  3.000
 JZX  H13A  C13  H13   107.42  3.000
 JZX  H13A  C13  C14   108.87  3.000
 JZX  H13   C13  C14   110.38  3.000
 JZX  H13A  C13  N4    109.85  3.000
 JZX  H13   C13  N4    110.38  3.000
 JZX  C14   C13  N4    109.89  3.000
 JZX  H14A  C14  H14   107.95  3.000
 JZX  H14A  C14  C13   109.22  3.000
 JZX  H14   C14  C13   109.26  3.000
 JZX  H14A  C14  O1    107.64  3.000
 JZX  H14   C14  O1    110.45  3.000
 JZX  C13   C14  O1    112.20  3.000
 JZX  H15A  C15  H15   108.08  3.000
 JZX  H15A  C15  C16   109.22  3.000
 JZX  H15   C15  C16   109.17  3.000
 JZX  H15A  C15  O1    110.72  3.000
 JZX  H15   C15  O1    107.75  3.000
 JZX  C16   C15  O1    111.81  3.000
 JZX  H16A  C16  H16   106.94  3.000
 JZX  H16A  C16  C15   110.08  3.000
 JZX  H16   C16  C15   107.42  3.000
 JZX  H16A  C16  N4    109.70  3.000
 JZX  H16   C16  N4    112.22  3.000
 JZX  C15   C16  N4    110.39  3.000
 JZX  H17   C17  C8    119.63  3.000
 JZX  H17   C17  N6    115.83  3.000
 JZX  C8    C17  N6    124.54  3.000
 JZX  C20   C18  N7    121.05  3.000
 JZX  C20   C18  N6    121.67  3.000
 JZX  N7    C18  N6    117.26  3.000
 JZX  H19   C19  C20   119.91  3.000
 JZX  H19   C19  C8    119.89  3.000
 JZX  C20   C19  C8    120.20  3.000
 JZX  H20   C20  C19   121.07  3.000
 JZX  H20   C20  C18   120.27  3.000
 JZX  C19   C20  C18   118.65  3.000
 JZX  H21B  C21  H21A  110.23  3.000
 JZX  H21B  C21  H21   109.67  3.000
 JZX  H21A  C21  H21   109.64  3.000
 JZX  H21B  C21  S2    109.73  3.000
 JZX  H21A  C21  S2    109.68  3.000
 JZX  H21   C21  S2    107.85  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
 JZX  CONST_01  C4   C3   N1   C1      0.00   0.0  0
 JZX  CONST_02  C6   C3   N1   C1    180.00   0.0  0
 JZX  CONST_03  C4   C2   N2   C1      0.00   0.0  0
 JZX  CONST_04  N6   C17  C8   C1    180.00   0.0  0
 JZX  CONST_05  C20  C19  C8   C1    180.00   0.0  0
 JZX  CONST_06  C2   N2   C1   N1      0.00   0.0  0
 JZX  CONST_07  C17  C8   C1   N1    180.00   0.0  0
 JZX  CONST_08  C19  C8   C1   N1      0.00   0.0  0
 JZX  CONST_09  S1   C4   C3   N1    180.00   0.0  0
 JZX  CONST_10  C2   C4   C3   N1      0.00   0.0  0
 JZX  CONST_11  C5   C6   C3   N1    180.00   0.0  0
 JZX  CONST_12  N2   C2   C4   S1    180.00   0.0  0
 JZX  CONST_13  C6   C3   C4   S1      0.00   0.0  0
 JZX  CONST_14  C3   C6   C5   S1      0.00   0.0  0
 JZX  CONST_15  C8   C1   N2   C2    180.00   0.0  0
 JZX  CONST_16  C5   S1   C4   C2    180.00   0.0  0
 JZX  CONST_17  C6   C3   C4   C2    180.00   0.0  0
 JZX  CONST_18  C3   N1   C1   N2      0.00   0.0  0
 JZX  CONST_19  C17  C8   C1   N2      0.00   0.0  0
 JZX  CONST_20  C19  C8   C1   N2    180.00   0.0  0
 JZX  CONST_21  C3   C4   C2   N2      0.00   0.0  0
 JZX  CONST_22  C8   C1   N1   C3    180.00   0.0  0
 JZX  CONST_23  C5   S1   C4   C3      0.00   0.0  0
 JZX  CONST_24  C6   C5   S1   C4      0.00   0.0  0
 JZX  CONST_25  C5   C6   C3   C4      0.00   0.0  0
 JZX  CONST_26  C19  C8   C17  N6      0.00   0.0  0
 JZX  CONST_27  C19  C20  C18  N6      0.00   0.0  0
 JZX  CONST_28  C18  N6   C17  C8      0.00   0.0  0
 JZX  CONST_29  C18  C20  C19  C8      0.00   0.0  0
 JZX  CONST_30  C20  C18  N6   C17     0.00   0.0  0
 JZX  CONST_31  C20  C19  C8   C17     0.00   0.0  0
 JZX  CONST_32  N4   C2   N2   C1    180.00   0.0  0
 JZX  CONST_33  N4   C2   C4   S1      0.00   0.0  0
 JZX  CONST_34  N4   C2   C4   C3    180.00   0.0  0
 JZX  CONST_35  C7   C5   C6   C3    180.00   0.0  0
 JZX  CONST_36  C7   C5   S1   C4    180.00   0.0  0
 JZX  CONST_37  C17  N6   C18  N7    180.00   0.0  0
 JZX  CONST_38  C19  C20  C18  N7    180.00   0.0  0
 JZX  CONST_39  H17  C17  C8   C1      0.00   0.0  0
 JZX  CONST_40  H19  C19  C8   C1      0.00   0.0  0
 JZX  CONST_41  H6   C6   C3   N1      0.00   0.0  0
 JZX  CONST_42  H20  C20  C18  N6    180.00   0.0  0
 JZX  Var_01    N4   C13  C14  O1     55.73  30.0  1
 JZX  Var_02    N4   C16  C15  O1    -55.64  30.0  1
 JZX  Var_03    C14  C13  N4   C2    154.92  30.0  1
 JZX  Var_04    C15  C16  N4   C2   -156.09  30.0  1
 JZX  Var_05    C13  N4   C2   N2     -0.22  30.0  2
 JZX  Var_06    N5   C10  C9   N3     57.65  30.0  1
 JZX  Var_07    N5   C11  C12  N3    -56.96  30.0  1
 JZX  Var_08    C11  C12  N3   C9     60.05  30.0  1
 JZX  Var_09    C11  N5   C10  C9    -57.19  30.0  1
 JZX  Var_10    C12  C11  N5   C10    56.76  30.0  1
 JZX  Var_11    C12  N3   C9   C10   -60.26  30.0  1
 JZX  Var_12    C16  C15  O1   C14    58.73  30.0  1
 JZX  Var_13    N3   C7   C5   S1   -152.20  30.0  2
 JZX  Var_14    C9   N3   C7   C5   -157.75  30.0  1
 JZX  Var_15    C10  N5   S2   O2   -174.84  30.0  3
 JZX  Var_16    H21  C21  S2   N5   -179.07  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
 JZX  plan-1  N7    0.020
 JZX  plan-1  C18   0.020
 JZX  plan-1  HN7   0.020
 JZX  plan-1  HN7A  0.020
 JZX  plan-2  C1    0.020
 JZX  plan-2  N6    0.020
 JZX  plan-2  N7    0.020
 JZX  plan-2  C8    0.020
 JZX  plan-2  C17   0.020
 JZX  plan-2  C18   0.020
 JZX  plan-2  C19   0.020
 JZX  plan-2  C20   0.020
 JZX  plan-2  H17   0.020
 JZX  plan-2  H19   0.020
 JZX  plan-2  H20   0.020
 JZX  plan-3  C1    0.020
 JZX  plan-3  N1    0.020
 JZX  plan-3  S1    0.020
 JZX  plan-3  C2    0.020
 JZX  plan-3  N2    0.020
 JZX  plan-3  C3    0.020
 JZX  plan-3  C4    0.020
 JZX  plan-3  N4    0.020
 JZX  plan-3  C5    0.020
 JZX  plan-3  C6    0.020
 JZX  plan-3  C7    0.020
 JZX  plan-3  C8    0.020
 JZX  plan-3  H6    0.020

