# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 00:13:47 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 3-{5-[(2E,4aR,7aR)-6-(5-fluoro-4-methoxypyrimidin-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: COc1nc(ncc1F)N2C[C@H]3C(=O)N(C)C(=N)N[C@]3(C2)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
 60W  60W  3-{5-[(2E,4aR,7aR)-6-(5-fluoro-4-methoxypyrimidin-2-yl)-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophen-3-yl}benzonitrile  ligand  54  34  .  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_60W
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
 60W  C1   C  CR5   0   0.209  -3.3046   0.6635  -0.2430
 60W  C2   C  CR15  0  -0.285  -2.1522   0.0848   0.3721
 60W  C3   C  CR5   0  -0.090  -0.9922   0.3671  -0.2795
 60W  C4   C  CT    0  -0.032   0.3953  -0.1058   0.0625
 60W  C5   C  C     0   0.618  -0.0435  -2.2491   1.1830
 60W  C8   C  CH1   0  -0.427   1.0746  -0.9057  -1.0487
 60W  C11  C  CR6   0   0.639   3.8451   0.9268   0.4146
 60W  C12  C  CR6   0   0.447   6.0999   0.6871   0.4993
 60W  C13  C  CH3   0  -0.418   7.1215  -1.2334  -0.3972
 60W  C14  C  CR6   0   0.300   6.1870   1.9268   1.1460
 60W  C15  C  CR16  0  -0.159   5.0186   2.5960   1.3842
 60W  C16  C  CR6   0   0.119  -4.6724   0.5044   0.2671
 60W  C17  C  CR16  0  -0.316  -5.7622   0.5219  -0.5989
 60W  C20  C  CR16  0  -0.226  -6.1987   0.1902   2.1252
 60W  C21  C  CR16  0  -0.300  -4.9103   0.3347   1.6328
 60W  C22  C  CSP   0   0.053  -8.1596   0.4015  -1.0026
 60W  N6   N  NS    0  -0.248  -9.0529   0.4172  -1.7299
 60W  C18  C  CR6   0   0.032  -7.0541   0.3832  -0.0986
 60W  C19  C  CR16  0  -0.253  -7.2838   0.2146   1.2662
 60W  C    C  CR15  0  -0.567  -2.9746   1.3811  -1.3571
 60W  S    S  S2    0   0.253  -1.2945   1.3584  -1.6606
 60W  C10  C  CH2   0  -0.213   1.3944   1.0327   0.2869
 60W  N3   N  NT    0  -0.507   2.6669   0.3984   0.0355
 60W  C9   C  CH2   0  -0.218   2.5602  -0.8613  -0.6724
 60W  C7   C  C     0   0.598   0.5460  -2.3050  -1.1910
 60W  O    O  O     0  -0.442   0.6405  -2.9036  -2.2421
 60W  N2   N  NT    0  -0.541  -0.0333  -2.8627  -0.0795
 60W  N1   N  N     0  -0.684  -0.4120  -2.8110   2.2625
 60W  N    N  NH1   0  -0.650   0.4049  -0.9580   1.2211
 60W  N5   N  N     0  -0.479   3.8323   2.1115   1.0205
 60W  F    F  F     0  -0.303   7.3791   2.4231   1.5106
 60W  N4   N  N     0  -0.506   4.9382   0.2000   0.1430
 60W  O1   O  O2    0  -0.454   7.2169   0.0262   0.2656
 60W  H1   H  HCR5  0   0.269  -2.2028  -0.5398   1.2533
 60W  H2   H  HCH3  0   0.263  -1.6021  -4.2119   0.2437
 60W  H3   H  HCH3  0   0.282  -0.6545  -4.4922  -1.2142
 60W  H4   H  HCH3  0   0.262   0.0200  -4.9289   0.3551
 60W  H5   H  HCH1  0   0.312   0.9330  -0.4103  -2.0109
 60W  H6   H  HCH3  0   0.254   8.1400  -1.6031  -0.4725
 60W  H7   H  HCH3  0   0.239   6.5157  -1.9387   0.1709
 60W  H8   H  HCH3  0   0.239   6.6966  -1.1258  -1.3951
 60W  H9   H  HCR6  0   0.290   5.0322   3.5591   1.8838
 60W  H10  H  HCR6  0   0.279  -5.6127   0.6265  -1.6655
 60W  H11  H  HCR6  0   0.278  -6.3569   0.0648   3.1875
 60W  H12  H  HCR6  0   0.271  -4.0809   0.3307   2.3279
 60W  H13  H  HCR6  0   0.285  -8.2914   0.1026   1.6418
 60W  H14  H  HCR5  0   0.301  -3.6300   1.9455  -2.0033
 60W  H15  H  HCH2  0   0.250   1.2060   1.8577  -0.4074
 60W  H16  H  HCH2  0   0.274   1.3250   1.4344   1.2988
 60W  H17  H  HCH2  0   0.252   2.8549  -1.7020  -0.0380
 60W  H18  H  HCH2  0   0.269   3.1919  -0.8828  -1.5601
 60W  H19  H  H     0   0.356  -0.6446  -3.7881   2.1530
 60W  H20  H  HNH1  0   0.399   0.2708  -0.5173   2.1195
 60W  C6   C  CH3   0  -0.576  -0.5965  -4.2011  -0.1725

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
 60W  C13  O1   single    1.427  0.020  1.427
 60W  O1   C12  single    1.319  0.020  1.319
 60W  C    S    aromatic  1.708  0.020  1.708
 60W  C    C1   aromatic  1.366  0.020  1.366
 60W  S    C3   aromatic  1.727  0.020  1.727
 60W  C12  N4   aromatic  1.309  0.020  1.309
 60W  C12  C14  aromatic  1.401  0.020  1.401
 60W  C21  C20  aromatic  1.387  0.020  1.387
 60W  C21  C16  aromatic  1.397  0.020  1.397
 60W  F    C14  single    1.342  0.020  1.342
 60W  C20  C19  aromatic  1.384  0.020  1.384
 60W  N4   C11  aromatic  1.341  0.020  1.341
 60W  C14  C15  aromatic  1.367  0.020  1.367
 60W  C1   C16  single    1.468  0.020  1.468
 60W  C1   C2   aromatic  1.429  0.020  1.429
 60W  C16  C17  aromatic  1.392  0.020  1.392
 60W  C10  N3   single    1.444  0.020  1.444
 60W  C10  C4   single    1.531  0.020  1.531
 60W  C3   C2   aromatic  1.360  0.020  1.360
 60W  C3   C4   single    1.505  0.020  1.505
 60W  C19  C18  aromatic  1.394  0.020  1.394
 60W  C11  N3   single    1.346  0.020  1.346
 60W  C11  N5   aromatic  1.331  0.020  1.331
 60W  C15  N5   aromatic  1.332  0.020  1.332
 60W  C17  C18  aromatic  1.392  0.020  1.392
 60W  N3   C9   single    1.449  0.020  1.449
 60W  C4   C8   single    1.528  0.020  1.528
 60W  C4   N    single    1.438  0.020  1.438
 60W  C18  C22  single    1.428  0.020  1.428
 60W  C8   C9   single    1.533  0.020  1.533
 60W  C8   C7   single    1.503  0.020  1.503
 60W  N    C5   single    1.367  0.020  1.367
 60W  C22  N6   triple    1.152  0.020  1.152
 60W  C7   O    double    1.213  0.020  1.213
 60W  C7   N2   single    1.372  0.020  1.372
 60W  C5   N2   single    1.404  0.020  1.404
 60W  C5   N1   double    1.272  0.020  1.272
 60W  N2   C6   single    1.455  0.020  1.455
 60W  C2   H1   single    0.930  0.020  1.080
 60W  C6   H2   single    0.970  0.020  1.090
 60W  C6   H3   single    0.970  0.020  1.090
 60W  C6   H4   single    0.970  0.020  1.090
 60W  C8   H5   single    0.970  0.020  1.090
 60W  C13  H6   single    0.970  0.020  1.090
 60W  C13  H7   single    0.970  0.020  1.090
 60W  C13  H8   single    0.970  0.020  1.090
 60W  C15  H9   single    0.930  0.020  1.080
 60W  C17  H10  single    0.930  0.020  1.080
 60W  C20  H11  single    0.930  0.020  1.080
 60W  C21  H12  single    0.930  0.020  1.080
 60W  C19  H13  single    0.930  0.020  1.080
 60W  C    H14  single    0.930  0.020  1.080
 60W  C10  H15  single    0.970  0.020  1.090
 60W  C10  H16  single    0.970  0.020  1.090
 60W  C9   H17  single    0.970  0.020  1.090
 60W  C9   H18  single    0.970  0.020  1.090
 60W  N1   H19  single    0.890  0.020  1.040
 60W  N    H20  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
 60W  C    C1   C16  124.43  3.000
 60W  C16  C1   C2   123.91  3.000
 60W  C    C1   C2   111.66  3.000
 60W  H1   C2   C3   123.38  3.000
 60W  H1   C2   C1   123.17  3.000
 60W  C3   C2   C1   113.43  3.000
 60W  S    C3   C4   121.56  3.000
 60W  C4   C3   C2   127.74  3.000
 60W  S    C3   C2   110.68  3.000
 60W  N    C4   C10  108.55  3.000
 60W  N    C4   C8   105.83  3.000
 60W  C10  C4   C8   101.87  3.000
 60W  N    C4   C3   112.04  3.000
 60W  C8   C4   C3   114.14  3.000
 60W  C10  C4   C3   113.65  3.000
 60W  N    C5   N1   119.25  3.000
 60W  N1   C5   N2   124.93  3.000
 60W  N    C5   N2   115.81  3.000
 60W  H5   C8   C7   107.07  3.000
 60W  H5   C8   C9   109.21  3.000
 60W  C7   C8   C9   113.03  3.000
 60W  H5   C8   C4   110.23  3.000
 60W  C7   C8   C4   113.57  3.000
 60W  C9   C8   C4   103.71  3.000
 60W  N4   C11  N5   125.65  3.000
 60W  N5   C11  N3   118.00  3.000
 60W  N4   C11  N3   116.36  3.000
 60W  O1   C12  N4   121.12  3.000
 60W  N4   C12  C14  120.67  3.000
 60W  O1   C12  C14  118.21  3.000
 60W  H8   C13  H7   108.94  3.000
 60W  H8   C13  H6   109.62  3.000
 60W  H7   C13  H6   109.70  3.000
 60W  H8   C13  O1   111.36  3.000
 60W  H7   C13  O1   111.50  3.000
 60W  H6   C13  O1   105.67  3.000
 60W  F    C14  C15  122.06  3.000
 60W  C15  C14  C12  117.42  3.000
 60W  F    C14  C12  120.53  3.000
 60W  H9   C15  N5   117.37  3.000
 60W  H9   C15  C14  120.27  3.000
 60W  N5   C15  C14  122.37  3.000
 60W  C21  C16  C17  118.46  3.000
 60W  C17  C16  C1   120.78  3.000
 60W  C21  C16  C1   120.77  3.000
 60W  H10  C17  C18  119.47  3.000
 60W  H10  C17  C16  120.41  3.000
 60W  C18  C17  C16  120.11  3.000
 60W  H11  C20  C19  119.81  3.000
 60W  H11  C20  C21  119.79  3.000
 60W  C19  C20  C21  120.40  3.000
 60W  H12  C21  C20  118.92  3.000
 60W  H12  C21  C16  119.87  3.000
 60W  C20  C21  C16  121.21  3.000
 60W  C18  C22  N6   180.00  3.000
 60W  C19  C18  C22  119.58  3.000
 60W  C22  C18  C17  119.31  3.000
 60W  C19  C18  C17  121.10  3.000
 60W  H13  C19  C18  120.40  3.000
 60W  H13  C19  C20  120.88  3.000
 60W  C18  C19  C20  118.72  3.000
 60W  H14  C    S    119.86  3.000
 60W  H14  C    C1   128.05  3.000
 60W  S    C    C1   112.07  3.000
 60W  C    S    C3    92.16  3.000
 60W  H16  C10  H15  107.45  3.000
 60W  H16  C10  N3   112.29  3.000
 60W  H15  C10  N3   111.86  3.000
 60W  H16  C10  C4   111.61  3.000
 60W  H15  C10  C4   110.80  3.000
 60W  N3   C10  C4   102.87  3.000
 60W  C9   N3   C10  113.71  3.000
 60W  C9   N3   C11  122.92  3.000
 60W  C10  N3   C11  123.37  3.000
 60W  H18  C9   H17  107.53  3.000
 60W  H18  C9   N3   111.87  3.000
 60W  H17  C9   N3   111.41  3.000
 60W  H18  C9   C8   111.17  3.000
 60W  H17  C9   C8   112.41  3.000
 60W  N3   C9   C8   102.50  3.000
 60W  N2   C7   O    122.29  3.000
 60W  N2   C7   C8   116.77  3.000
 60W  O    C7   C8   120.94  3.000
 60W  C7   N2   C6   119.05  3.000
 60W  C6   N2   C5   117.17  3.000
 60W  C7   N2   C5   123.65  3.000
 60W  H19  N1   C5   113.71  3.000
 60W  H20  N    C5   113.17  3.000
 60W  H20  N    C4   117.22  3.000
 60W  C5   N    C4   122.33  3.000
 60W  C15  N5   C11  116.08  3.000
 60W  C12  N4   C11  117.82  3.000
 60W  C13  O1   C12  117.92  3.000
 60W  H4   C6   H3   108.45  3.000
 60W  H4   C6   H2   109.32  3.000
 60W  H3   C6   H2   108.40  3.000
 60W  H4   C6   N2   111.37  3.000
 60W  H3   C6   N2   109.23  3.000
 60W  H2   C6   N2   110.02  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
 60W  CONST_01  C3   S    C    C1      0.00   0.0  0
 60W  CONST_02  C20  C21  C16  C1    180.00   0.0  0
 60W  CONST_03  C18  C17  C16  C1    180.00   0.0  0
 60W  CONST_04  S    C3   C2   C1      0.00   0.0  0
 60W  CONST_05  S    C    C1   C2      0.00   0.0  0
 60W  CONST_08  C    S    C3   C2      0.00   0.0  0
 60W  CONST_09  C    C1   C2   C3      0.00   0.0  0
 60W  CONST_10  C16  C1   C2   C3    180.00   0.0  0
 60W  CONST_11  C14  C12  N4   C11     0.00   0.0  0
 60W  CONST_12  C14  C15  N5   C11     0.00   0.0  0
 60W  CONST_13  N5   C11  N4   C12     0.00   0.0  0
 60W  CONST_14  N5   C15  C14  C12     0.00   0.0  0
 60W  CONST_15  N4   C12  C14  C15     0.00   0.0  0
 60W  CONST_16  N4   C11  N5   C15     0.00   0.0  0
 60W  CONST_17  C19  C20  C21  C16     0.00   0.0  0
 60W  CONST_18  S    C    C1   C16   180.00   0.0  0
 60W  CONST_19  C19  C18  C17  C16     0.00   0.0  0
 60W  CONST_20  C20  C21  C16  C17     0.00   0.0  0
 60W  CONST_22  C20  C19  C18  C17     0.00   0.0  0
 60W  CONST_23  C18  C19  C20  C21     0.00   0.0  0
 60W  CONST_25  C18  C17  C16  C21     0.00   0.0  0
 60W  CONST_26  C4   C3   C2   C1    180.00   0.0  0
 60W  CONST_27  C    S    C3   C4    180.00   0.0  0
 60W  CONST_28  N3   C11  N4   C12   180.00   0.0  0
 60W  CONST_29  N3   C11  N5   C15   180.00   0.0  0
 60W  CONST_31  C8   C7   N2   C5      0.00   0.0  0
 60W  CONST_32  N    C5   N2   C7      0.00   0.0  0
 60W  CONST_33  O1   C12  N4   C11   180.00   0.0  0
 60W  CONST_34  O1   C12  C14  C15   180.00   0.0  0
 60W  CONST_35  C22  C18  C17  C16   180.00   0.0  0
 60W  CONST_36  C22  C18  C19  C20   180.00   0.0  0
 60W  CONST_37  F    C14  C15  N5    180.00   0.0  0
 60W  CONST_38  N4   C12  C14  F     180.00   0.0  0
 60W  CONST_40  O    C7   N2   C5    180.00   0.0  0
 60W  CONST_41  C8   C7   N2   C6    180.00   0.0  0
 60W  CONST_42  N    C5   N2   C6    180.00   0.0  0
 60W  CONST_43  N1   C5   N2   C7    180.00   0.0  0
 60W  CONST_44  H12  C21  C16  C1      0.00   0.0  0
 60W  CONST_45  H10  C17  C16  C1      0.00   0.0  0
 60W  CONST_46  H14  C    C1   C2    180.00   0.0  0
 60W  CONST_47  H1   C2   C3   C4      0.00   0.0  0
 60W  CONST_48  H9   C15  N5   C11   180.00   0.0  0
 60W  CONST_49  H11  C20  C21  C16   180.00   0.0  0
 60W  CONST_50  H13  C19  C18  C17   180.00   0.0  0
 60W  CONST_51  H20  N    C5   N2    180.00   0.0  0
 60W  CONST_52  O    C7   N2   C6      0.00   0.0  0
 60W  CONST_53  N1   C5   N2   C6      0.00   0.0  0
 60W  CONST_54  H19  N1   C5   N2      0.00   0.0  0
 60W  Var_01    C11  N3   C10  C4   -163.81  30.0  1
 60W  Var_02    C10  N3   C9   C8      7.84  30.0  1
 60W  Var_03    N4   C11  N3   C10   178.15  30.0  1
 60W  Var_04    N4   C12  O1   C13     0.45  30.0  2
 60W  Var_05    H2   C6   N2   C5     53.04  30.0  3
 60W  Var_06    H6   C13  O1   C12  -179.17  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
 60W  chir_01  C4  C3  C8  N   positiv
 60W  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
 60W  plan-1  C1   0.020
 60W  plan-1  C2   0.020
 60W  plan-1  C3   0.020
 60W  plan-1  C4   0.020
 60W  plan-1  C16  0.020
 60W  plan-1  C    0.020
 60W  plan-1  S    0.020
 60W  plan-1  H1   0.020
 60W  plan-1  H14  0.020
 60W  plan-2  C11  0.020
 60W  plan-2  C12  0.020
 60W  plan-2  C14  0.020
 60W  plan-2  C15  0.020
 60W  plan-2  N3   0.020
 60W  plan-2  N5   0.020
 60W  plan-2  F    0.020
 60W  plan-2  N4   0.020
 60W  plan-2  O1   0.020
 60W  plan-2  H9   0.020
 60W  plan-3  C1   0.020
 60W  plan-3  C16  0.020
 60W  plan-3  C17  0.020
 60W  plan-3  C20  0.020
 60W  plan-3  C21  0.020
 60W  plan-3  C22  0.020
 60W  plan-3  N6   0.020
 60W  plan-3  C18  0.020
 60W  plan-3  C19  0.020
 60W  plan-3  H10  0.020
 60W  plan-3  H11  0.020
 60W  plan-3  H12  0.020
 60W  plan-3  H13  0.020
 60W  plan-4  C4   0.020
 60W  plan-4  C5   0.020
 60W  plan-4  C8   0.020
 60W  plan-4  C7   0.020
 60W  plan-4  O    0.020
 60W  plan-4  N2   0.020
 60W  plan-4  N1   0.020
 60W  plan-4  N    0.020
 60W  plan-4  H19  0.020
 60W  plan-4  H20  0.020
 60W  plan-4  C6   0.020

