# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 01:24:32 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 5-[(2E,4aR,7aR)-6-(5-fluoro-4-methoxy-6-methylpyrimidin-2-yl)-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophene-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1nc(nc(C)c1F)N2C[C@H]3C(=O)N(C)C(=N)N[C@]3(C2)c4sc(cc4)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
 60V  60V  5-[(2E,4aR,7aR)-6-(5-fluoro-4-methoxy-6-methylpyrimidin-2-yl)-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophene-2-carbonitrile  ligand  47  29  .  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_60V
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
 60V  N1   N  NH1   0  -0.651  -1.2653  -1.0280   1.2997
 60V  C2   C  CR15  0  -0.118  -4.4058   1.8055   0.6442
 60V  C3   C  CR5   0  -0.260  -4.0505   2.5038  -0.4776
 60V  C6   C  C     0   0.619  -2.0930  -2.1165   1.2906
 60V  C8   C  C     0   0.600  -1.9617  -2.1081  -1.1523
 60V  C9   C  CH1   0  -0.430  -0.9863  -0.9692  -1.0496
 60V  C10  C  CH2   0  -0.221   0.4720  -1.4339  -0.9371
 60V  C11  C  CH2   0  -0.207   0.1550   0.6361   0.2773
 60V  C12  C  CR6   0   0.631   2.4284  -0.2245  -0.0705
 60V  C13  C  CR6   0   0.125   4.5105  -1.0763  -0.4094
 60V  C16  C  CR6   0   0.446   4.1614   0.9877   0.7252
 60V  C17  C  CH3   0  -0.418   3.7778   3.0210   1.8466
 60V  C15  C  CR6   0   0.311   5.0384   0.0168   0.2354
 60V  C14  C  CH3   0  -0.730   5.3838  -2.1470  -0.9783
 60V  N5   N  N     0  -0.498   3.1888  -1.1991  -0.5585
 60V  O1   O  O2    0  -0.458   4.6759   2.0315   1.3494
 60V  N6   N  N     0  -0.509   2.8655   0.8686   0.5664
 60V  N4   N  NT    0  -0.511   1.0945  -0.3375  -0.2258
 60V  O    O  O     0  -0.439  -2.2464  -2.5913  -2.2274
 60V  N3   N  NT    0  -0.542  -2.4972  -2.5680   0.0243
 60V  C7   C  CH3   0  -0.576  -3.4721  -3.6482  -0.0154
 60V  N2   N  N     0  -0.681  -2.4244  -2.6508   2.3951
 60V  C5   C  CT    0  -0.030  -1.1807  -0.1095   0.1994
 60V  C    C  CR5   0  -0.083  -2.3758   0.8065   0.1391
 60V  C1   C  CR15  0  -0.231  -3.4431   0.8338   0.9925
 60V  S    S  S2    0   0.318  -2.5367   1.9760  -1.1088
 60V  C4   C  CSP   0   0.063  -4.7756   3.5409  -1.0982
 60V  N    N  NS    0  -0.241  -5.3684   4.3878  -1.6098
 60V  H1   H  HCR5  0   0.297  -5.3197   1.9843   1.1909
 60V  H2   H  HCH1  0   0.314  -1.0990  -0.3623  -1.9500
 60V  H3   H  HCH2  0   0.253   0.5634  -2.3736  -0.3851
 60V  H4   H  HCH2  0   0.270   0.9121  -1.5852  -1.9225
 60V  H5   H  HCH2  0   0.279   0.3866   0.9495   1.2965
 60V  H6   H  HCH2  0   0.250   0.1333   1.5382  -0.3438
 60V  H7   H  HCH3  0   0.238   3.2196   3.4946   1.0394
 60V  H8   H  HCH3  0   0.238   3.0735   2.5978   2.5622
 60V  H9   H  HCH3  0   0.253   4.4004   3.7607   2.3414
 60V  H10  H  HCH3  0   0.266   5.7987  -1.8286  -1.9366
 60V  H11  H  HCH3  0   0.257   6.2221  -2.3865  -0.3260
 60V  H12  H  HCH3  0   0.259   4.8033  -3.0506  -1.1486
 60V  H13  H  HCH3  0   0.264  -4.3337  -3.3938   0.5989
 60V  H14  H  HCH3  0   0.283  -3.8101  -3.7882  -1.0347
 60V  H15  H  HCH3  0   0.264  -3.0413  -4.5850   0.3380
 60V  H16  H  H     0   0.358  -2.9622  -3.4993   2.2900
 60V  H18  H  HCR5  0   0.285  -3.5443   0.1815   1.8474
 60V  H19  H  HNH1  0   0.402  -1.0892  -0.6656   2.2253
 60V  F    F  F     0  -0.305   6.3648   0.1665   0.3953

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
 60V  C17  O1   single    1.426  0.020  1.426
 60V  O1   C16  single    1.321  0.020  1.321
 60V  C2   C1   aromatic  1.411  0.020  1.411
 60V  C2   C3   aromatic  1.368  0.020  1.368
 60V  C16  N6   aromatic  1.311  0.020  1.311
 60V  C16  C15  aromatic  1.397  0.020  1.397
 60V  C1   C    aromatic  1.367  0.020  1.367
 60V  F    C15  single    1.344  0.020  1.344
 60V  N6   C12  aromatic  1.338  0.020  1.338
 60V  C4   C3   single    1.409  0.020  1.409
 60V  C4   N    triple    1.153  0.020  1.153
 60V  C3   S    aromatic  1.723  0.020  1.723
 60V  C15  C13  aromatic  1.374  0.020  1.374
 60V  C11  N4   single    1.443  0.020  1.443
 60V  C11  C5   single    1.532  0.020  1.532
 60V  C    S    aromatic  1.718  0.020  1.718
 60V  C    C5   single    1.507  0.020  1.507
 60V  C12  N4   single    1.348  0.020  1.348
 60V  C12  N5   aromatic  1.329  0.020  1.329
 60V  C13  N5   aromatic  1.336  0.020  1.336
 60V  C13  C14  single    1.494  0.020  1.494
 60V  N4   C10  single    1.448  0.020  1.448
 60V  C5   C9   single    1.529  0.020  1.529
 60V  C5   N1   single    1.436  0.020  1.436
 60V  C9   C10  single    1.535  0.020  1.535
 60V  C9   C8   single    1.503  0.020  1.503
 60V  N1   C6   single    1.368  0.020  1.368
 60V  C8   O    double    1.213  0.020  1.213
 60V  C8   N3   single    1.372  0.020  1.372
 60V  C6   N3   single    1.404  0.020  1.404
 60V  C6   N2   double    1.271  0.020  1.271
 60V  N3   C7   single    1.456  0.020  1.456
 60V  C2   H1   single    0.930  0.020  1.080
 60V  C9   H2   single    0.970  0.020  1.090
 60V  C10  H3   single    0.970  0.020  1.090
 60V  C10  H4   single    0.970  0.020  1.090
 60V  C11  H5   single    0.970  0.020  1.090
 60V  C11  H6   single    0.970  0.020  1.090
 60V  C17  H7   single    0.970  0.020  1.090
 60V  C17  H8   single    0.970  0.020  1.090
 60V  C17  H9   single    0.970  0.020  1.090
 60V  C14  H10  single    0.970  0.020  1.090
 60V  C14  H11  single    0.970  0.020  1.090
 60V  C14  H12  single    0.970  0.020  1.090
 60V  C7   H13  single    0.970  0.020  1.090
 60V  C7   H14  single    0.970  0.020  1.090
 60V  C7   H15  single    0.970  0.020  1.090
 60V  N2   H16  single    0.890  0.020  1.040
 60V  C1   H18  single    0.930  0.020  1.080
 60V  N1   H19  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
 60V  H19  N1   C5   117.56  3.000
 60V  H19  N1   C6   113.42  3.000
 60V  C5   N1   C6   122.67  3.000
 60V  H1   C2   C1   124.49  3.000
 60V  H1   C2   C3   123.38  3.000
 60V  C1   C2   C3   112.12  3.000
 60V  C4   C3   S    121.07  3.000
 60V  S    C3   C2   111.84  3.000
 60V  C4   C3   C2   127.09  3.000
 60V  N2   C6   N3   125.01  3.000
 60V  N2   C6   N1   119.12  3.000
 60V  N3   C6   N1   115.86  3.000
 60V  N3   C8   O    122.36  3.000
 60V  N3   C8   C9   116.66  3.000
 60V  O    C8   C9   120.99  3.000
 60V  H2   C9   C5   110.37  3.000
 60V  H2   C9   C10  109.08  3.000
 60V  C5   C9   C10  103.37  3.000
 60V  H2   C9   C8   107.33  3.000
 60V  C10  C9   C8   113.09  3.000
 60V  C5   C9   C8   113.54  3.000
 60V  H4   C10  H3   107.66  3.000
 60V  H4   C10  N4   112.07  3.000
 60V  H3   C10  N4   111.52  3.000
 60V  H4   C10  C9   111.07  3.000
 60V  H3   C10  C9   112.12  3.000
 60V  N4   C10  C9   102.44  3.000
 60V  H6   C11  H5   107.29  3.000
 60V  H6   C11  C5   110.78  3.000
 60V  H5   C11  C5   111.86  3.000
 60V  H6   C11  N4   111.76  3.000
 60V  H5   C11  N4   112.40  3.000
 60V  C5   C11  N4   102.80  3.000
 60V  N4   C12  N6   116.52  3.000
 60V  N4   C12  N5   117.55  3.000
 60V  N6   C12  N5   125.93  3.000
 60V  N5   C13  C14  118.03  3.000
 60V  C14  C13  C15  121.60  3.000
 60V  N5   C13  C15  120.36  3.000
 60V  N6   C16  O1   120.95  3.000
 60V  N6   C16  C15  120.99  3.000
 60V  O1   C16  C15  118.06  3.000
 60V  H9   C17  H8   109.63  3.000
 60V  H9   C17  H7   109.58  3.000
 60V  H8   C17  H7   108.92  3.000
 60V  H9   C17  O1   105.68  3.000
 60V  H8   C17  O1   111.51  3.000
 60V  H7   C17  O1   111.47  3.000
 60V  F    C15  C16  120.02  3.000
 60V  F    C15  C13  121.55  3.000
 60V  C16  C15  C13  118.43  3.000
 60V  H12  C14  H11  108.78  3.000
 60V  H12  C14  H10  107.92  3.000
 60V  H11  C14  H10  107.30  3.000
 60V  H12  C14  C13  110.07  3.000
 60V  H11  C14  C13  112.30  3.000
 60V  H10  C14  C13  110.33  3.000
 60V  C13  N5   C12  117.24  3.000
 60V  C17  O1   C16  117.90  3.000
 60V  C16  N6   C12  117.04  3.000
 60V  C12  N4   C11  123.20  3.000
 60V  C12  N4   C10  123.08  3.000
 60V  C11  N4   C10  113.71  3.000
 60V  C7   N3   C8   119.12  3.000
 60V  C7   N3   C6   117.14  3.000
 60V  C8   N3   C6   123.60  3.000
 60V  H15  C7   H14  108.50  3.000
 60V  H15  C7   H13  109.32  3.000
 60V  H14  C7   H13  108.32  3.000
 60V  H15  C7   N3   111.36  3.000
 60V  H14  C7   N3   109.31  3.000
 60V  H13  C7   N3   109.96  3.000
 60V  H16  N2   C6   113.67  3.000
 60V  C    C5   C11  113.43  3.000
 60V  C    C5   C9   114.20  3.000
 60V  C11  C5   C9   101.80  3.000
 60V  C9   C5   N1   105.90  3.000
 60V  C    C5   N1   111.89  3.000
 60V  C11  C5   N1   108.90  3.000
 60V  S    C    C1   111.53  3.000
 60V  S    C    C5   121.14  3.000
 60V  C1   C    C5   127.33  3.000
 60V  H18  C1   C    123.74  3.000
 60V  H18  C1   C2   123.17  3.000
 60V  C    C1   C2   113.09  3.000
 60V  C    S    C3    91.42  3.000
 60V  N    C4   C3   180.00  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
 60V  CONST_01  S    C    C1   C2     0.00   0.0  0
 60V  CONST_02  C    S    C3   C2     0.00   0.0  0
 60V  CONST_03  C    C1   C2   C3     0.00   0.0  0
 60V  CONST_04  C1   C    S    C3     0.00   0.0  0
 60V  CONST_05  C15  C16  N6   C12    0.00   0.0  0
 60V  CONST_06  C15  C13  N5   C12    0.00   0.0  0
 60V  CONST_07  N6   C16  C15  C13    0.00   0.0  0
 60V  CONST_08  N6   C12  N5   C13    0.00   0.0  0
 60V  CONST_09  N5   C12  N6   C16    0.00   0.0  0
 60V  CONST_10  N5   C13  C15  C16    0.00   0.0  0
 60V  CONST_11  S    C3   C2   C1     0.00   0.0  0
 60V  CONST_12  C5   C    C1   C2   180.00   0.0  0
 60V  CONST_13  C5   C    S    C3   180.00   0.0  0
 60V  CONST_14  N4   C12  N5   C13  180.00   0.0  0
 60V  CONST_15  N4   C12  N6   C16  180.00   0.0  0
 60V  CONST_16  C8   N3   C6   N1     0.00   0.0  0
 60V  CONST_17  C9   C8   N3   C6     0.00   0.0  0
 60V  CONST_19  O1   C16  N6   C12  180.00   0.0  0
 60V  CONST_20  C14  C13  N5   C12  180.00   0.0  0
 60V  CONST_21  O1   C16  C15  C13  180.00   0.0  0
 60V  CONST_22  C14  C13  C15  C16  180.00   0.0  0
 60V  CONST_23  N6   C16  C15  F    180.00   0.0  0
 60V  CONST_24  N5   C13  C15  F    180.00   0.0  0
 60V  CONST_25  C4   C3   S    C    180.00   0.0  0
 60V  CONST_26  C4   C3   C2   C1   180.00   0.0  0
 60V  CONST_27  C7   N3   C6   N1   180.00   0.0  0
 60V  CONST_28  O    C8   N3   C6   180.00   0.0  0
 60V  CONST_29  N2   C6   N3   C8   180.00   0.0  0
 60V  CONST_30  C7   N3   C8   C9   180.00   0.0  0
 60V  CONST_32  H18  C1   C2   C3   180.00   0.0  0
 60V  CONST_33  H1   C2   C1   C    180.00   0.0  0
 60V  CONST_34  H19  N1   C6   N3   180.00   0.0  0
 60V  CONST_35  C7   N3   C8   O      0.00   0.0  0
 60V  CONST_36  N2   C6   N3   C7     0.00   0.0  0
 60V  CONST_37  H16  N2   C6   N1   180.00   0.0  0
 60V  Var_01    C11  N4   C10  C9     8.71  30.0  1
 60V  Var_02    C5   C11  N4   C10   16.11  30.0  1
 60V  Var_03    N6   C12  N4   C10  177.54  30.0  2
 60V  Var_04    N6   C16  O1   C17    0.14  30.0  2
 60V  Var_05    H13  C7   N3   C6    52.26  30.0  3
 60V  Var_06    H10  C14  C13  C15  -79.31  30.0  2
 60V  Var_07    H7   C17  O1   C16  -62.68  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
 60V  chir_01  C9  C5  C10  C8   negativ
 60V  chir_02  C5  C9  C    C11  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
 60V  plan-1  C2   0.020
 60V  plan-1  C3   0.020
 60V  plan-1  C5   0.020
 60V  plan-1  C    0.020
 60V  plan-1  C1   0.020
 60V  plan-1  S    0.020
 60V  plan-1  C4   0.020
 60V  plan-1  N    0.020
 60V  plan-1  H1   0.020
 60V  plan-1  H18  0.020
 60V  plan-2  C12  0.020
 60V  plan-2  C13  0.020
 60V  plan-2  C16  0.020
 60V  plan-2  C15  0.020
 60V  plan-2  C14  0.020
 60V  plan-2  N5   0.020
 60V  plan-2  O1   0.020
 60V  plan-2  N6   0.020
 60V  plan-2  N4   0.020
 60V  plan-2  F    0.020
 60V  plan-3  N1   0.020
 60V  plan-3  C6   0.020
 60V  plan-3  C8   0.020
 60V  plan-3  C9   0.020
 60V  plan-3  O    0.020
 60V  plan-3  N3   0.020
 60V  plan-3  C7   0.020
 60V  plan-3  N2   0.020
 60V  plan-3  C5   0.020
 60V  plan-3  H16  0.020
 60V  plan-3  H19  0.020

