# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 14:58:08 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5-(1,3-benzothiazol-2-yl)-2-(morpholin-4-yl)-6-[(3R)-piperidin-3-ylamino]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=NC(=C1c2sc3ccccc3n2)N[C@@H]4CCCNC4)N5CCOCC5
#
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
 4S3  4S3  5-(1,3-benzothiazol-2-yl)-2-(morpholin-4-yl)-6-[(3R)-piperidin-3-ylamino]pyrimidin-4(3H)-one  ligand  53  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4S3
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
 4S3  C01  C  CR6   0   0.562  -0.3395  -0.1514  -0.1187
 4S3  N02  N  N     0  -0.547  -1.6759  -0.0469  -0.1623
 4S3  C03  C  CR6   0   0.811  -2.2337   1.1305  -0.3041
 4S3  N04  N  NR16  0  -0.755  -1.4863   2.2542  -0.4331
 4S3  C05  C  CR6   0   0.530  -0.0973   2.2558  -0.3862
 4S3  C06  C  CR6   0  -0.318   0.5139   0.9850  -0.2086
 4S3  N07  N  NH1   0  -0.683   0.1546  -1.3760   0.0322
 4S3  N08  N  NT    0  -0.509  -3.5683   1.2251  -0.3290
 4S3  O09  O  O     0  -0.489   0.4951   3.3258  -0.5014
 4S3  C10  C  CR5   0   0.115   1.9400   0.9021  -0.1254
 4S3  C11  C  CH1   0  -0.062  -0.6425  -2.5774   0.1699
 4S3  C12  C  CH2   0  -0.311  -1.0900  -3.1248  -1.1924
 4S3  N13  N  NH1   0  -0.578  -1.8322  -4.3675  -1.0973
 4S3  C14  C  CH2   0  -0.314  -1.1070  -5.3868  -0.3548
 4S3  C15  C  CH2   0  -0.447  -0.6461  -4.9298   1.0265
 4S3  C16  C  CH2   0  -0.462   0.1547  -3.6358   0.9245
 4S3  C17  C  CH2   0  -0.347  -4.3380   2.4587  -0.3531
 4S3  C18  C  CH2   0  -0.176  -5.3401   2.4486   0.7923
 4S3  O19  O  O2    0  -0.479  -6.1666   1.3102   0.7554
 4S3  C20  C  CH2   0  -0.185  -5.4038   0.1253   0.8250
 4S3  C21  C  CH2   0  -0.334  -4.4134   0.0388  -0.3208
 4S3  S22  S  S2    0   0.220   2.9568   2.3409  -0.2216
 4S3  C23  C  CR56  0  -0.273   4.3533   1.3307  -0.0202
 4S3  C24  C  CR56  0   0.409   3.9548  -0.0084   0.0974
 4S3  N25  N  N     0  -0.540   2.6023  -0.2102   0.0322
 4S3  C26  C  CR16  0  -0.288   5.6928   1.6969   0.0298
 4S3  C27  C  CR16  0  -0.274   6.6386   0.6989   0.2006
 4S3  C28  C  CR16  0  -0.261   6.2518  -0.6398   0.3187
 4S3  C29  C  CR16  0  -0.324   4.9183  -1.0036   0.2683
 4S3  H1   H  HNR6  0   0.427  -1.9118   3.1512  -0.6144
 4S3  H2   H  HNH1  0   0.418   1.1704  -1.4420   0.0559
 4S3  H3   H  HCH1  0   0.241  -1.5377  -2.3305   0.7485
 4S3  H4   H  HCH2  0   0.243  -1.7037  -2.3820  -1.7062
 4S3  H5   H  HCH2  0   0.216  -0.2034  -3.2919  -1.8147
 4S3  H6   H  HNH1  0   0.340  -2.7198  -4.1914  -0.6404
 4S3  H8   H  HCH2  0   0.237  -1.7382  -6.2740  -0.2737
 4S3  H9   H  HCH2  0   0.216  -0.2321  -5.6781  -0.9468
 4S3  H10  H  HCH2  0   0.219  -1.5177  -4.7758   1.6711
 4S3  H11  H  HCH2  0   0.233  -0.0428  -5.7088   1.4989
 4S3  H12  H  HCH2  0   0.221   1.0938  -3.8343   0.3936
 4S3  H13  H  HCH2  0   0.247   0.4237  -3.2656   1.9167
 4S3  H14  H  HCH2  0   0.269  -3.7125   3.3415  -0.2431
 4S3  H15  H  HCH2  0   0.267  -4.8543   2.5394  -1.3139
 4S3  H16  H  HCH2  0   0.215  -4.7945   2.5019   1.7443
 4S3  H17  H  HCH2  0   0.253  -5.9819   3.3269   0.7187
 4S3  H18  H  HCH2  0   0.213  -4.8630   0.0695   1.7797
 4S3  H19  H  HCH2  0   0.250  -6.0956  -0.7159   0.7761
 4S3  H20  H  HCH2  0   0.257  -4.9460  -0.0123  -1.2756
 4S3  H21  H  HCH2  0   0.291  -3.7989  -0.8514  -0.2251
 4S3  H22  H  HCR6  0   0.267   5.9923   2.7330  -0.0622
 4S3  H23  H  HCR6  0   0.257   7.6881   0.9588   0.2428
 4S3  H24  H  HCR6  0   0.257   7.0080  -1.4021   0.4515
 4S3  H25  H  HCR6  0   0.256   4.6169  -2.0393   0.3609

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
 4S3  C27  C28  aromatic  1.398  0.020  1.398
 4S3  C27  C26  aromatic  1.386  0.020  1.386
 4S3  C28  C29  aromatic  1.383  0.020  1.383
 4S3  C26  C23  aromatic  1.390  0.020  1.390
 4S3  C29  C24  aromatic  1.396  0.020  1.396
 4S3  C23  C24  aromatic  1.402  0.020  1.402
 4S3  C23  S22  aromatic  1.735  0.020  1.735
 4S3  C24  N25  aromatic  1.369  0.020  1.369
 4S3  S22  C10  aromatic  1.764  0.020  1.764
 4S3  N25  C10  aromatic  1.304  0.020  1.304
 4S3  C10  C06  single    1.431  0.020  1.431
 4S3  O09  C05  double    1.228  0.020  1.228
 4S3  C06  C05  single    1.421  0.020  1.421
 4S3  C06  C01  double    1.424  0.020  1.424
 4S3  C05  N04  single    1.390  0.020  1.390
 4S3  N07  C01  single    1.329  0.020  1.329
 4S3  N07  C11  single    1.448  0.020  1.448
 4S3  C16  C11  single    1.525  0.020  1.525
 4S3  C16  C15  single    1.525  0.020  1.525
 4S3  C01  N02  single    1.341  0.020  1.341
 4S3  N04  C03  single    1.356  0.020  1.356
 4S3  C11  C12  single    1.535  0.020  1.535
 4S3  C15  C14  single    1.526  0.020  1.526
 4S3  N02  C03  double    1.311  0.020  1.311
 4S3  C03  N08  single    1.338  0.020  1.338
 4S3  C12  N13  single    1.451  0.020  1.451
 4S3  C14  N13  single    1.455  0.020  1.455
 4S3  N08  C21  single    1.457  0.020  1.457
 4S3  N08  C17  single    1.454  0.020  1.454
 4S3  C21  C20  single    1.517  0.020  1.517
 4S3  C17  C18  single    1.522  0.020  1.522
 4S3  C20  O19  single    1.411  0.020  1.411
 4S3  C18  O19  single    1.407  0.020  1.407
 4S3  N04  H1   single    0.860  0.020  1.020
 4S3  N07  H2   single    0.860  0.020  1.020
 4S3  C11  H3   single    0.970  0.020  1.090
 4S3  C12  H4   single    0.970  0.020  1.090
 4S3  C12  H5   single    0.970  0.020  1.090
 4S3  N13  H6   single    0.890  0.020  1.040
 4S3  C14  H8   single    0.970  0.020  1.090
 4S3  C14  H9   single    0.970  0.020  1.090
 4S3  C15  H10  single    0.970  0.020  1.090
 4S3  C15  H11  single    0.970  0.020  1.090
 4S3  C16  H12  single    0.970  0.020  1.090
 4S3  C16  H13  single    0.970  0.020  1.090
 4S3  C17  H14  single    0.970  0.020  1.090
 4S3  C17  H15  single    0.970  0.020  1.090
 4S3  C18  H16  single    0.970  0.020  1.090
 4S3  C18  H17  single    0.970  0.020  1.090
 4S3  C20  H18  single    0.970  0.020  1.090
 4S3  C20  H19  single    0.970  0.020  1.090
 4S3  C21  H20  single    0.970  0.020  1.090
 4S3  C21  H21  single    0.970  0.020  1.090
 4S3  C26  H22  single    0.930  0.020  1.080
 4S3  C27  H23  single    0.930  0.020  1.080
 4S3  C28  H24  single    0.930  0.020  1.080
 4S3  C29  H25  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
 4S3  N07  C01  C06  121.30  3.000
 4S3  N07  C01  N02  116.48  3.000
 4S3  C06  C01  N02  122.20  3.000
 4S3  C03  N02  C01  119.84  3.000
 4S3  N08  C03  N04  119.31  3.000
 4S3  N08  C03  N02  119.34  3.000
 4S3  N04  C03  N02  121.35  3.000
 4S3  H1   N04  C05  115.24  3.000
 4S3  H1   N04  C03  121.42  3.000
 4S3  C05  N04  C03  123.28  3.000
 4S3  O09  C05  C06  125.67  3.000
 4S3  C06  C05  N04  115.66  3.000
 4S3  O09  C05  N04  118.67  3.000
 4S3  C10  C06  C05  119.18  3.000
 4S3  C05  C06  C01  117.62  3.000
 4S3  C10  C06  C01  123.19  3.000
 4S3  H2   N07  C11  119.54  3.000
 4S3  H2   N07  C01  115.68  3.000
 4S3  C11  N07  C01  124.78  3.000
 4S3  C21  N08  C17  112.57  3.000
 4S3  C17  N08  C03  126.03  3.000
 4S3  C21  N08  C03  121.40  3.000
 4S3  N25  C10  S22  114.17  3.000
 4S3  N25  C10  C06  124.23  3.000
 4S3  S22  C10  C06  121.59  3.000
 4S3  H3   C11  C16  108.82  3.000
 4S3  H3   C11  C12  108.14  3.000
 4S3  C16  C11  C12  110.13  3.000
 4S3  H3   C11  N07  108.26  3.000
 4S3  C12  C11  N07  111.83  3.000
 4S3  C16  C11  N07  109.58  3.000
 4S3  H5   C12  H4   106.92  3.000
 4S3  H5   C12  N13  108.69  3.000
 4S3  H4   C12  N13  109.03  3.000
 4S3  H5   C12  C11  108.81  3.000
 4S3  H4   C12  C11  109.81  3.000
 4S3  N13  C12  C11  113.36  3.000
 4S3  H6   N13  C14  109.16  3.000
 4S3  H6   N13  C12  109.19  3.000
 4S3  C14  N13  C12  112.25  3.000
 4S3  H9   C14  H8   106.60  3.000
 4S3  H9   C14  C15  109.11  3.000
 4S3  H8   C14  C15  110.53  3.000
 4S3  H9   C14  N13  107.97  3.000
 4S3  H8   C14  N13  108.60  3.000
 4S3  C15  C14  N13  113.75  3.000
 4S3  H11  C15  H10  106.58  3.000
 4S3  H11  C15  C16  110.12  3.000
 4S3  H10  C15  C16  109.75  3.000
 4S3  H11  C15  C14  110.15  3.000
 4S3  H10  C15  C14  109.54  3.000
 4S3  C16  C15  C14  110.62  3.000
 4S3  H13  C16  H12  106.86  3.000
 4S3  H13  C16  C15  110.86  3.000
 4S3  H12  C16  C15  109.17  3.000
 4S3  H13  C16  C11  110.05  3.000
 4S3  H12  C16  C11  109.49  3.000
 4S3  C15  C16  C11  110.34  3.000
 4S3  H15  C17  H14  107.48  3.000
 4S3  H15  C17  C18  110.54  3.000
 4S3  H14  C17  C18  107.94  3.000
 4S3  H15  C17  N08  109.09  3.000
 4S3  H14  C17  N08  112.48  3.000
 4S3  C18  C17  N08  109.30  3.000
 4S3  H17  C18  H16  108.16  3.000
 4S3  H17  C18  O19  107.71  3.000
 4S3  H16  C18  O19  110.71  3.000
 4S3  H17  C18  C17  109.36  3.000
 4S3  H16  C18  C17  108.95  3.000
 4S3  O19  C18  C17  111.86  3.000
 4S3  C20  O19  C18  111.13  3.000
 4S3  H19  C20  H18  108.18  3.000
 4S3  H19  C20  C21  109.66  3.000
 4S3  H18  C20  C21  109.40  3.000
 4S3  H19  C20  O19  107.62  3.000
 4S3  H18  C20  O19  110.59  3.000
 4S3  C21  C20  O19  111.32  3.000
 4S3  H21  C21  H20  108.30  3.000
 4S3  H21  C21  C20  110.46  3.000
 4S3  H20  C21  C20  110.12  3.000
 4S3  H21  C21  N08  109.86  3.000
 4S3  H20  C21  N08  108.39  3.000
 4S3  C20  C21  N08  109.67  3.000
 4S3  C23  S22  C10   89.01  3.000
 4S3  C26  C23  C24  121.51  3.000
 4S3  C24  C23  S22  109.69  3.000
 4S3  C26  C23  S22  128.79  3.000
 4S3  C29  C24  N25  125.64  3.000
 4S3  N25  C24  C23  114.68  3.000
 4S3  C29  C24  C23  119.67  3.000
 4S3  C24  N25  C10  112.44  3.000
 4S3  H22  C26  C27  120.73  3.000
 4S3  H22  C26  C23  121.06  3.000
 4S3  C27  C26  C23  118.21  3.000
 4S3  H23  C27  C28  119.66  3.000
 4S3  H23  C27  C26  119.60  3.000
 4S3  C28  C27  C26  120.74  3.000
 4S3  H24  C28  C29  119.54  3.000
 4S3  H24  C28  C27  119.44  3.000
 4S3  C29  C28  C27  121.03  3.000
 4S3  H25  C29  C28  121.13  3.000
 4S3  H25  C29  C24  120.03  3.000
 4S3  C28  C29  C24  118.85  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
 4S3  CONST_01  C26  C23  S22  C10   180.00   0.0  0
 4S3  CONST_02  C24  C23  S22  C10     0.00   0.0  0
 4S3  CONST_03  C29  C24  N25  C10   180.00   0.0  0
 4S3  CONST_04  C23  C24  N25  C10     0.00   0.0  0
 4S3  CONST_05  C27  C26  C23  S22   180.00   0.0  0
 4S3  CONST_06  C29  C24  C23  S22   180.00   0.0  0
 4S3  CONST_07  N25  C24  C23  S22     0.00   0.0  0
 4S3  CONST_08  C24  N25  C10  S22     0.00   0.0  0
 4S3  CONST_09  C28  C27  C26  C23     0.00   0.0  0
 4S3  CONST_10  C28  C29  C24  C23     0.00   0.0  0
 4S3  CONST_11  N25  C10  S22  C23     0.00   0.0  0
 4S3  CONST_12  C27  C28  C29  C24     0.00   0.0  0
 4S3  CONST_13  C27  C26  C23  C24     0.00   0.0  0
 4S3  CONST_14  C28  C29  C24  N25   180.00   0.0  0
 4S3  CONST_15  C26  C23  C24  N25   180.00   0.0  0
 4S3  CONST_16  C29  C28  C27  C26     0.00   0.0  0
 4S3  CONST_17  C29  C24  C23  C26     0.00   0.0  0
 4S3  CONST_18  C23  S22  C10  C06   180.00   0.0  0
 4S3  CONST_19  C24  N25  C10  C06   180.00   0.0  0
 4S3  CONST_20  N04  C03  N02  C01     0.00   0.0  0
 4S3  CONST_21  N08  C03  N02  C01   180.00   0.0  0
 4S3  CONST_22  C05  N04  C03  N02     0.00   0.0  0
 4S3  CONST_23  C21  N08  C03  N02     0.00   0.0  0
 4S3  CONST_24  C17  N08  C03  N02   180.00   0.0  0
 4S3  CONST_25  C06  C05  N04  C03     0.00   0.0  0
 4S3  CONST_26  C06  C01  N02  C03     0.00   0.0  0
 4S3  CONST_27  C21  N08  C03  N04   180.00   0.0  0
 4S3  CONST_28  C17  N08  C03  N04     0.00   0.0  0
 4S3  CONST_29  N08  C03  N04  C05   180.00   0.0  0
 4S3  CONST_30  C11  N07  C01  N02     0.00   0.0  0
 4S3  CONST_31  O09  C05  N04  C03   180.00   0.0  0
 4S3  CONST_32  N07  C01  N02  C03   180.00   0.0  0
 4S3  CONST_33  C11  N07  C01  C06   180.00   0.0  0
 4S3  CONST_34  H22  C26  C23  S22     0.00   0.0  0
 4S3  CONST_35  H23  C27  C26  C23   180.00   0.0  0
 4S3  CONST_36  H25  C29  C24  C23   180.00   0.0  0
 4S3  CONST_37  H24  C28  C29  C24   180.00   0.0  0
 4S3  CONST_38  H1   N04  C03  N02   180.00   0.0  0
 4S3  CONST_39  H2   N07  C01  N02   180.00   0.0  0
 4S3  Var_01    S22  C10  C06  C01  -179.21  30.0  2
 4S3  Var_02    C20  C21  N08  C03   125.41  30.0  1
 4S3  Var_03    C18  C17  N08  C03  -125.93  30.0  1
 4S3  Var_04    O19  C20  C21  N08    55.81  30.0  1
 4S3  Var_05    O19  C18  C17  N08   -55.36  30.0  1
 4S3  Var_06    C14  C15  C16  C11    53.64  30.0  1
 4S3  Var_07    C14  N13  C12  C11   -54.07  30.0  1
 4S3  Var_08    C15  C14  N13  C12    53.48  30.0  1
 4S3  Var_09    C16  C15  C14  N13   -53.58  30.0  1
 4S3  Var_10    C21  C20  O19  C18   -58.92  30.0  1

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
 4S3  chir_01  C11  N07  C16  C12  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
 4S3  plan-1  C06  0.020
 4S3  plan-1  C10  0.020
 4S3  plan-1  S22  0.020
 4S3  plan-1  C23  0.020
 4S3  plan-1  C24  0.020
 4S3  plan-1  N25  0.020
 4S3  plan-1  C26  0.020
 4S3  plan-1  C27  0.020
 4S3  plan-1  C28  0.020
 4S3  plan-1  C29  0.020
 4S3  plan-1  H22  0.020
 4S3  plan-1  H23  0.020
 4S3  plan-1  H24  0.020
 4S3  plan-1  H25  0.020
 4S3  plan-2  C01  0.020
 4S3  plan-2  N02  0.020
 4S3  plan-2  C03  0.020
 4S3  plan-2  N04  0.020
 4S3  plan-2  C05  0.020
 4S3  plan-2  C06  0.020
 4S3  plan-2  N07  0.020
 4S3  plan-2  N08  0.020
 4S3  plan-2  O09  0.020
 4S3  plan-2  C10  0.020
 4S3  plan-2  C11  0.020
 4S3  plan-2  C17  0.020
 4S3  plan-2  C21  0.020
 4S3  plan-2  H1   0.020
 4S3  plan-2  H2   0.020

