# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 23:44:01 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 3-{5-[(2E,4aR,7aR)-6-(5-fluoropyrimidin-2-yl)-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophen-3-yl}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N)N[C@]2(CN(C[C@H]2C1=O)c3ncc(F)cn3)c4scc(c4)c5cccc(c5)C#N
#
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
 60Y  60Y  3-{5-[(2E,4aR,7aR)-6-(5-fluoropyrimidin-2-yl)-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophen-3-yl}benzonitrile  ligand  50  32  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_60Y
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
 60Y  C20  C  CR16  0  -0.295  -4.5558   0.7630  -0.9504
 60Y  C13  C  CR6   0   0.347   6.5674  -2.1172  -0.7113
 60Y  C11  C  CR6   0   0.642   4.2818  -0.9244  -0.1191
 60Y  C17  C  CR6   0   0.029  -6.4783  -1.0971  -0.2886
 60Y  C10  C  CH2   0  -0.214   1.8297  -0.9491   0.0323
 60Y  C12  C  CR16  0  -0.138   5.3672  -2.7902  -0.8151
 60Y  C18  C  CR16  0  -0.253  -6.8109  -0.0471  -1.1439
 60Y  C15  C  CR6   0   0.119  -4.2147  -0.2868  -0.0948
 60Y  C14  C  CR16  0  -0.138   6.5407  -0.8047  -0.2848
 60Y  C16  C  CR16  0  -0.313  -5.1923  -1.2229   0.2297
 60Y  C19  C  CR16  0  -0.226  -5.8364   0.8805  -1.4692
 60Y  N6   N  NS    0  -0.250  -8.2683  -2.8512   0.3255
 60Y  C21  C  CSP   0   0.056  -7.4677  -2.0691   0.0521
 60Y  C1   C  CR5   0   0.209  -2.8562  -0.3952   0.4524
 60Y  C    C  CR15  0  -0.566  -2.5521  -0.9343   1.6699
 60Y  C2   C  CR15  0  -0.285  -1.6870   0.0637  -0.2272
 60Y  C3   C  CR5   0  -0.092  -0.5393  -0.1353   0.4751
 60Y  S    S  S2    0   0.254  -0.8750  -0.8881   1.9910
 60Y  C4   C  CR5   0  -0.033   0.8606   0.2348   0.0650
 60Y  N3   N  NR5   0  -0.509   3.1193  -0.3153   0.1804
 60Y  N5   N  N     0  -0.451   5.4015  -0.2034   0.0087
 60Y  N4   N  N     0  -0.452   4.2235  -2.2007  -0.5163
 60Y  C9   C  CH2   0  -0.223   3.0446   1.0511   0.6568
 60Y  C8   C  CR15  0  -0.426   1.5635   1.1898   1.0291
 60Y  C7   C  C     0   0.599   1.0607   2.6036   0.9418
 60Y  O    O  O     0  -0.442   1.1716   3.3658   1.8789
 60Y  N2   N  NT    0  -0.541   0.4785   2.9793  -0.2429
 60Y  C6   C  CH3   0  -0.577  -0.0779   4.3181  -0.3653
 60Y  C5   C  C     0   0.618   0.4619   2.1714  -1.3912
 60Y  N1   N  N     0  -0.681   0.1036   2.5574  -2.5483
 60Y  N    N  NH1   0  -0.650   0.8892   0.8847  -1.2179
 60Y  H1   H  HCR6  0   0.264  -3.8162   1.5108  -1.2053
 60Y  H2   H  HCH2  0   0.251   1.6246  -1.6473   0.8504
 60Y  H3   H  HCH2  0   0.275   1.7495  -1.5117  -0.8994
 60Y  H4   H  HCR6  0   0.292   5.3303  -3.8245  -1.1419
 60Y  H5   H  HCR6  0   0.284  -7.8114   0.0349  -1.5453
 60Y  H6   H  HCR6  0   0.293   7.4549  -0.2294  -0.1799
 60Y  H7   H  HCR6  0   0.280  -4.9574  -2.0609   0.8726
 60Y  H8   H  HCR6  0   0.278  -6.0762   1.7051  -2.1263
 60Y  H9   H  HCR5  0   0.301  -3.2287  -1.3379   2.4084
 60Y  H10  H  HCR5  0   0.270  -1.7081   0.5025  -1.2150
 60Y  H11  H  HCH2  0   0.269   3.6852   1.2168   1.5223
 60Y  H12  H  HCH2  0   0.253   3.3453   1.7595  -0.1202
 60Y  H13  H  HCR5  0   0.312   1.4203   0.8591   2.0603
 60Y  H14  H  HCH3  0   0.262   0.5479   4.9535  -0.9916
 60Y  H15  H  HCH3  0   0.263  -1.0782   4.2662  -0.7912
 60Y  H16  H  HCH3  0   0.283  -0.1501   4.7692   0.6170
 60Y  H17  H  H     0   0.355  -0.1065   3.5440  -2.6009
 60Y  H18  H  HNH1  0   0.399   0.7547   0.3044  -2.0332
 60Y  F    F  F     0  -0.302   7.7257  -2.7226  -1.0103

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
 60Y  C    S    aromatic  1.708  0.020  1.708
 60Y  C    C1   aromatic  1.366  0.020  1.366
 60Y  C20  C19  aromatic  1.387  0.020  1.387
 60Y  C20  C15  aromatic  1.397  0.020  1.397
 60Y  S    C3   aromatic  1.725  0.020  1.725
 60Y  C19  C18  aromatic  1.384  0.020  1.384
 60Y  C1   C15  single    1.469  0.020  1.469
 60Y  C1   C2   aromatic  1.428  0.020  1.428
 60Y  C15  C16  aromatic  1.392  0.020  1.392
 60Y  C18  C17  aromatic  1.394  0.020  1.394
 60Y  C3   C2   aromatic  1.360  0.020  1.360
 60Y  C3   C4   single    1.505  0.020  1.505
 60Y  C12  N4   aromatic  1.321  0.020  1.321
 60Y  C12  C13  aromatic  1.380  0.020  1.380
 60Y  N4   C11  aromatic  1.338  0.020  1.338
 60Y  C10  C4   single    1.530  0.020  1.530
 60Y  C10  N3   single    1.445  0.020  1.445
 60Y  C16  C17  aromatic  1.392  0.020  1.392
 60Y  C17  C21  single    1.428  0.020  1.428
 60Y  C4   C8   single    1.528  0.020  1.528
 60Y  C4   N    single    1.438  0.020  1.438
 60Y  C13  F    single    1.341  0.020  1.341
 60Y  C13  C14  aromatic  1.380  0.020  1.380
 60Y  C11  N3   single    1.346  0.020  1.346
 60Y  C11  N5   aromatic  1.338  0.020  1.338
 60Y  N3   C9   single    1.449  0.020  1.449
 60Y  C8   C9   single    1.533  0.020  1.533
 60Y  C8   C7   single    1.503  0.020  1.503
 60Y  C14  N5   aromatic  1.321  0.020  1.321
 60Y  C21  N6   triple    1.152  0.020  1.152
 60Y  N    C5   single    1.367  0.020  1.367
 60Y  C7   O    double    1.213  0.020  1.213
 60Y  C7   N2   single    1.372  0.020  1.372
 60Y  C5   N2   single    1.404  0.020  1.404
 60Y  C5   N1   double    1.271  0.020  1.271
 60Y  N2   C6   single    1.455  0.020  1.455
 60Y  C20  H1   single    0.930  0.020  1.080
 60Y  C10  H2   single    0.970  0.020  1.090
 60Y  C10  H3   single    0.970  0.020  1.090
 60Y  C12  H4   single    0.930  0.020  1.080
 60Y  C18  H5   single    0.930  0.020  1.080
 60Y  C14  H6   single    0.930  0.020  1.080
 60Y  C16  H7   single    0.930  0.020  1.080
 60Y  C19  H8   single    0.930  0.020  1.080
 60Y  C    H9   single    0.930  0.020  1.080
 60Y  C2   H10  single    0.930  0.020  1.080
 60Y  C9   H11  single    0.970  0.020  1.090
 60Y  C9   H12  single    0.970  0.020  1.090
 60Y  C8   H13  single    0.970  0.020  1.090
 60Y  C6   H14  single    0.970  0.020  1.090
 60Y  C6   H15  single    0.970  0.020  1.090
 60Y  C6   H16  single    0.970  0.020  1.090
 60Y  N1   H17  single    0.890  0.020  1.040
 60Y  N    H18  single    0.890  0.020  1.040

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
 60Y  H1   C20  C19  118.98  3.000
 60Y  H1   C20  C15  119.78  3.000
 60Y  C19  C20  C15  121.23  3.000
 60Y  F    C13  C14  120.99  3.000
 60Y  C14  C13  C12  118.05  3.000
 60Y  F    C13  C12  120.96  3.000
 60Y  N4   C11  N5   125.38  3.000
 60Y  N5   C11  N3   117.23  3.000
 60Y  N4   C11  N3   117.39  3.000
 60Y  C21  C17  C16  119.31  3.000
 60Y  C21  C17  C18  119.58  3.000
 60Y  C16  C17  C18  121.11  3.000
 60Y  H3   C10  H2   107.18  3.000
 60Y  H3   C10  N3   112.29  3.000
 60Y  H2   C10  N3   111.74  3.000
 60Y  H3   C10  C4   111.75  3.000
 60Y  H2   C10  C4   111.02  3.000
 60Y  N3   C10  C4   102.92  3.000
 60Y  H4   C12  N4   117.64  3.000
 60Y  H4   C12  C13  121.13  3.000
 60Y  N4   C12  C13  121.23  3.000
 60Y  H5   C18  C19  120.89  3.000
 60Y  H5   C18  C17  120.36  3.000
 60Y  C19  C18  C17  118.74  3.000
 60Y  C1   C15  C16  120.88  3.000
 60Y  C16  C15  C20  118.48  3.000
 60Y  C1   C15  C20  120.65  3.000
 60Y  H6   C14  N5   117.62  3.000
 60Y  H6   C14  C13  121.18  3.000
 60Y  N5   C14  C13  121.20  3.000
 60Y  H7   C16  C15  120.46  3.000
 60Y  H7   C16  C17  119.46  3.000
 60Y  C15  C16  C17  120.08  3.000
 60Y  H8   C19  C18  119.85  3.000
 60Y  H8   C19  C20  119.79  3.000
 60Y  C18  C19  C20  120.36  3.000
 60Y  N6   C21  C17  180.00  3.000
 60Y  C2   C1   C    111.64  3.000
 60Y  C2   C1   C15  123.80  3.000
 60Y  C    C1   C15  124.56  3.000
 60Y  H9   C    S    119.78  3.000
 60Y  H9   C    C1   128.15  3.000
 60Y  S    C    C1   112.06  3.000
 60Y  H10  C2   C3   123.21  3.000
 60Y  H10  C2   C1   123.31  3.000
 60Y  C3   C2   C1   113.46  3.000
 60Y  C4   C3   S    121.84  3.000
 60Y  C4   C3   C2   127.46  3.000
 60Y  S    C3   C2   110.69  3.000
 60Y  C3   S    C     92.16  3.000
 60Y  N    C4   C8   105.73  3.000
 60Y  N    C4   C3   111.87  3.000
 60Y  C8   C4   C3   114.18  3.000
 60Y  N    C4   C10  108.54  3.000
 60Y  C8   C4   C10  101.87  3.000
 60Y  C3   C4   C10  113.87  3.000
 60Y  C9   N3   C10  113.67  3.000
 60Y  C9   N3   C11  122.98  3.000
 60Y  C10  N3   C11  123.34  3.000
 60Y  C14  N5   C11  117.08  3.000
 60Y  C12  N4   C11  117.07  3.000
 60Y  H12  C9   H11  107.71  3.000
 60Y  H12  C9   C8   112.30  3.000
 60Y  H11  C9   C8   111.18  3.000
 60Y  H12  C9   N3   111.30  3.000
 60Y  H11  C9   N3   111.98  3.000
 60Y  C8   C9   N3   102.41  3.000
 60Y  H13  C8   C7   107.20  3.000
 60Y  H13  C8   C9   109.18  3.000
 60Y  C7   C8   C9   113.21  3.000
 60Y  H13  C8   C4   110.24  3.000
 60Y  C7   C8   C4   113.41  3.000
 60Y  C9   C8   C4   103.56  3.000
 60Y  N2   C7   O    122.26  3.000
 60Y  N2   C7   C8   116.71  3.000
 60Y  O    C7   C8   121.03  3.000
 60Y  C5   N2   C6   117.14  3.000
 60Y  C6   N2   C7   119.12  3.000
 60Y  C5   N2   C7   123.61  3.000
 60Y  H16  C6   H15  108.27  3.000
 60Y  H16  C6   H14  108.45  3.000
 60Y  H15  C6   H14  109.31  3.000
 60Y  H16  C6   N2   109.42  3.000
 60Y  H15  C6   N2   109.91  3.000
 60Y  H14  C6   N2   111.42  3.000
 60Y  N    C5   N1   119.29  3.000
 60Y  N1   C5   N2   124.96  3.000
 60Y  N    C5   N2   115.74  3.000
 60Y  H17  N1   C5   113.74  3.000
 60Y  H18  N    C5   113.39  3.000
 60Y  H18  N    C4   117.25  3.000
 60Y  C5   N    C4   122.15  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
 60Y  CONST_01  C17  C18  C19  C20     0.00   0.0  0
 60Y  CONST_04  C17  C16  C15  C20     0.00   0.0  0
 60Y  CONST_05  C11  N4   C12  C13     0.00   0.0  0
 60Y  CONST_06  C11  N5   C14  C13     0.00   0.0  0
 60Y  CONST_07  C1   C15  C16  C17   180.00   0.0  0
 60Y  CONST_08  N5   C11  N4   C12     0.00   0.0  0
 60Y  CONST_09  N5   C14  C13  C12     0.00   0.0  0
 60Y  CONST_10  C15  C20  C19  C18     0.00   0.0  0
 60Y  CONST_11  C15  C16  C17  C18     0.00   0.0  0
 60Y  CONST_12  S    C    C1   C15   180.00   0.0  0
 60Y  CONST_13  C3   C2   C1   C15   180.00   0.0  0
 60Y  CONST_14  N4   C12  C13  C14     0.00   0.0  0
 60Y  CONST_15  N4   C11  N5   C14     0.00   0.0  0
 60Y  CONST_16  C19  C20  C15  C16     0.00   0.0  0
 60Y  CONST_19  C19  C18  C17  C16     0.00   0.0  0
 60Y  CONST_20  C1   C15  C20  C19   180.00   0.0  0
 60Y  CONST_21  C3   S    C    C1      0.00   0.0  0
 60Y  CONST_22  S    C3   C2   C1      0.00   0.0  0
 60Y  CONST_23  C2   C3   S    C       0.00   0.0  0
 60Y  CONST_24  C3   C2   C1   C       0.00   0.0  0
 60Y  CONST_25  S    C    C1   C2      0.00   0.0  0
 60Y  CONST_26  N3   C11  N4   C12   180.00   0.0  0
 60Y  CONST_27  N3   C11  N5   C14   180.00   0.0  0
 60Y  CONST_28  C4   C3   C2   C1    180.00   0.0  0
 60Y  CONST_29  C4   C3   S    C     180.00   0.0  0
 60Y  CONST_31  C5   N2   C7   C8      0.00   0.0  0
 60Y  CONST_32  N    C5   N2   C7      0.00   0.0  0
 60Y  CONST_33  C21  C17  C16  C15   180.00   0.0  0
 60Y  CONST_34  C21  C17  C18  C19   180.00   0.0  0
 60Y  CONST_35  F    C13  C14  N5    180.00   0.0  0
 60Y  CONST_36  N4   C12  C13  F     180.00   0.0  0
 60Y  CONST_38  C6   N2   C7   C8    180.00   0.0  0
 60Y  CONST_39  N1   C5   N2   C7    180.00   0.0  0
 60Y  CONST_40  C5   N2   C7   O     180.00   0.0  0
 60Y  CONST_41  N    C5   N2   C6    180.00   0.0  0
 60Y  CONST_42  H5   C18  C19  C20   180.00   0.0  0
 60Y  CONST_43  H7   C16  C15  C20   180.00   0.0  0
 60Y  CONST_44  H4   C12  N4   C11   180.00   0.0  0
 60Y  CONST_45  H6   C14  N5   C11   180.00   0.0  0
 60Y  CONST_46  H8   C19  C18  C17   180.00   0.0  0
 60Y  CONST_47  H1   C20  C19  C18   180.00   0.0  0
 60Y  CONST_48  H9   C    C1   C15     0.00   0.0  0
 60Y  CONST_49  H10  C2   C1   C15     0.00   0.0  0
 60Y  CONST_50  H18  N    C5   N2    180.00   0.0  0
 60Y  CONST_51  C6   N2   C7   O       0.00   0.0  0
 60Y  CONST_52  N1   C5   N2   C6      0.00   0.0  0
 60Y  CONST_53  H17  N1   C5   N2      0.00   0.0  0
 60Y  Var_01    C4   C10  N3   C11  -163.02  30.0  1
 60Y  Var_02    C8   C9   N3   C11  -172.39  30.0  1
 60Y  Var_03    N4   C11  N3   C10    -3.03  30.0  1
 60Y  Var_04    H14  C6   N2   C7    106.75  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
 60Y  chir_01  C4  C10  C8  N   negativ
 60Y  chir_02  C8  C4   C9  C7  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
 60Y  plan-1  C15  0.020
 60Y  plan-1  C1   0.020
 60Y  plan-1  C    0.020
 60Y  plan-1  C2   0.020
 60Y  plan-1  C3   0.020
 60Y  plan-1  S    0.020
 60Y  plan-1  C4   0.020
 60Y  plan-1  H9   0.020
 60Y  plan-1  H10  0.020
 60Y  plan-2  C20  0.020
 60Y  plan-2  C17  0.020
 60Y  plan-2  C18  0.020
 60Y  plan-2  C15  0.020
 60Y  plan-2  C16  0.020
 60Y  plan-2  C19  0.020
 60Y  plan-2  N6   0.020
 60Y  plan-2  C21  0.020
 60Y  plan-2  C1   0.020
 60Y  plan-2  H1   0.020
 60Y  plan-2  H5   0.020
 60Y  plan-2  H7   0.020
 60Y  plan-2  H8   0.020
 60Y  plan-3  C13  0.020
 60Y  plan-3  C11  0.020
 60Y  plan-3  C12  0.020
 60Y  plan-3  C14  0.020
 60Y  plan-3  N3   0.020
 60Y  plan-3  N5   0.020
 60Y  plan-3  N4   0.020
 60Y  plan-3  H4   0.020
 60Y  plan-3  H6   0.020
 60Y  plan-3  F    0.020
 60Y  plan-4  C4   0.020
 60Y  plan-4  C8   0.020
 60Y  plan-4  C7   0.020
 60Y  plan-4  O    0.020
 60Y  plan-4  N2   0.020
 60Y  plan-4  C6   0.020
 60Y  plan-4  C5   0.020
 60Y  plan-4  N1   0.020
 60Y  plan-4  N    0.020
 60Y  plan-4  H17  0.020
 60Y  plan-4  H18  0.020

