# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 03:56:03 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 5-{(2E,4aR,7aR)-6-[5-fluoro-4-methyl-6-(methylsulfanyl)pyrimidin-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: CSc1nc(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
 954  954  5-{(2E,4aR,7aR)-6-[5-fluoro-4-methyl-6-(methylsulfanyl)pyrimidin-2-yl]-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl}thiophene-2-carbonitrile  ligand  47  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_954
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
 954  F    F  F     0  -0.302  -6.1598  -0.4864  -0.5566
 954  C15  C  CR6   0   0.423  -4.8354  -0.5151  -0.3298
 954  C13  C  CR6   0   0.142  -4.2430  -1.5746   0.3258
 954  C14  C  CH3   0  -0.737  -5.0438  -2.7400   0.8066
 954  N5   N  N     0  -0.487  -2.9289  -1.5724   0.5335
 954  C16  C  CR6   0  -0.034  -4.0445   0.5406  -0.7582
 954  S1   S  S2    0   0.065  -4.8088   1.8746  -1.5895
 954  C17  C  CH3   0  -0.763  -3.3928   2.9381  -1.9300
 954  N6   N  N     0  -0.465  -2.7450   0.5410  -0.5414
 954  C12  C  CR6   0   0.633  -2.2379  -0.5205   0.0933
 954  N4   N  NR5   0  -0.513  -0.9079  -0.5207   0.3085
 954  C10  C  CH2   0  -0.221  -0.2179  -1.5989   0.9863
 954  C9   C  CR15  0  -0.434   1.2141  -1.0572   1.0969
 954  N3   N  NT    0  -0.543   2.7962  -2.5384  -0.0408
 954  N1   N  NH1   0  -0.654   1.4588  -1.0398  -1.2561
 954  C11  C  CH2   0  -0.211  -0.0284   0.5198  -0.1694
 954  C5   C  CR5   0  -0.026   1.3449  -0.1563  -0.1307
 954  C    C  CR5   0  -0.085   2.4890   0.8223  -0.0669
 954  C1   C  CR15  0  -0.229   3.4895   0.9879  -0.9836
 954  C2   C  CR15  0  -0.118   4.4076   1.9977  -0.6235
 954  C3   C  CR5   0  -0.259   4.0861   2.5850   0.5699
 954  S    S  S2    0   0.318   2.6601   1.9044   1.2561
 954  C4   C  CSP   0   0.063   4.7844   3.6208   1.2226
 954  N    N  NS    0  -0.241   5.3536   4.4683   1.7594
 954  C8   C  C     0   0.601   2.2527  -2.1420   1.1547
 954  C7   C  CH3   0  -0.577   3.8254  -3.5676  -0.0425
 954  C6   C  C     0   0.623   2.3428  -2.0824  -1.2894
 954  H1   H  HCH3  0   0.265  -5.4913  -3.2775  -0.0306
 954  H2   H  HCH3  0   0.261  -4.4074  -3.4280   1.3571
 954  H3   H  HCH3  0   0.262  -5.8587  -2.4204   1.4565
 954  H4   H  HCH3  0   0.279  -2.9189   3.2691  -1.0100
 954  H5   H  HCH3  0   0.279  -2.6639   2.4334  -2.5584
 954  H6   H  HCH3  0   0.284  -3.7929   3.7990  -2.4613
 954  H7   H  HCH2  0   0.271  -0.6382  -1.8004   1.9713
 954  H8   H  HCH2  0   0.254  -0.2617  -2.5266   0.4089
 954  H9   H  HCR5  0   0.315   1.3038  -0.4704   2.0133
 954  H10  H  H     0   0.357   3.2619  -3.3942  -2.3403
 954  H12  H  HCH2  0   0.280  -0.2898   0.8549  -1.1743
 954  H13  H  HCH2  0   0.251  -0.0443   1.3989   0.4837
 954  H14  H  HCR5  0   0.283   3.5731   0.4079  -1.8908
 954  H15  H  HCR5  0   0.297   5.2659   2.2837  -1.2133
 954  H16  H  HCH3  0   0.263   3.4336  -4.5209  -0.3974
 954  H17  H  HCH3  0   0.264   4.6565  -3.2618  -0.6750
 954  H18  H  HCH3  0   0.283   4.1979  -3.7032   0.9654
 954  H11  H  HNH1  0   0.402   1.2347  -0.6702  -2.1682
 954  O    O  O     0  -0.439   2.5798  -2.6374   2.2124
 954  N2   N  N     0  -0.680   2.6775  -2.5737  -2.4121

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
 954  C2   C1   aromatic  1.411  0.020  1.411
 954  C2   C3   aromatic  1.368  0.020  1.368
 954  C1   C    aromatic  1.367  0.020  1.367
 954  C14  C13  single    1.493  0.020  1.493
 954  N    C4   triple    1.153  0.020  1.153
 954  C4   C3   single    1.409  0.020  1.409
 954  C3   S    aromatic  1.723  0.020  1.723
 954  C    S    aromatic  1.718  0.020  1.718
 954  C    C5   single    1.507  0.020  1.507
 954  N5   C13  aromatic  1.330  0.020  1.330
 954  N5   C12  aromatic  1.333  0.020  1.333
 954  C13  C15  aromatic  1.380  0.020  1.380
 954  C11  C5   single    1.531  0.020  1.531
 954  C11  N4   single    1.444  0.020  1.444
 954  C5   C9   single    1.528  0.020  1.528
 954  C5   N1   single    1.435  0.020  1.435
 954  C12  N4   single    1.347  0.020  1.347
 954  C12  N6   aromatic  1.337  0.020  1.337
 954  N4   C10  single    1.448  0.020  1.448
 954  C15  F    single    1.344  0.020  1.344
 954  C15  C16  aromatic  1.387  0.020  1.387
 954  C9   C10  single    1.535  0.020  1.535
 954  C9   C8   single    1.503  0.020  1.503
 954  N6   C16  aromatic  1.317  0.020  1.317
 954  C16  S1   single    1.748  0.020  1.748
 954  N1   C6   single    1.367  0.020  1.367
 954  C8   O    double    1.213  0.020  1.213
 954  C8   N3   single    1.372  0.020  1.372
 954  S1   C17  single    1.803  0.020  1.803
 954  C6   N3   single    1.404  0.020  1.404
 954  C6   N2   double    1.270  0.020  1.270
 954  N3   C7   single    1.456  0.020  1.456
 954  C14  H1   single    0.970  0.020  1.090
 954  C14  H2   single    0.970  0.020  1.090
 954  C14  H3   single    0.970  0.020  1.090
 954  C17  H4   single    0.970  0.020  1.090
 954  C17  H5   single    0.970  0.020  1.090
 954  C17  H6   single    0.970  0.020  1.090
 954  C10  H7   single    0.970  0.020  1.090
 954  C10  H8   single    0.970  0.020  1.090
 954  C9   H9   single    0.970  0.020  1.090
 954  N2   H10  single    0.890  0.020  1.040
 954  C11  H12  single    0.970  0.020  1.090
 954  C11  H13  single    0.970  0.020  1.090
 954  C1   H14  single    0.930  0.020  1.080
 954  C2   H15  single    0.930  0.020  1.080
 954  C7   H16  single    0.970  0.020  1.090
 954  C7   H17  single    0.970  0.020  1.090
 954  C7   H18  single    0.970  0.020  1.090
 954  N1   H11  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
 954  C16  C15  C13  119.11  3.000
 954  C16  C15  F    119.58  3.000
 954  C13  C15  F    121.31  3.000
 954  N5   C13  C14  118.73  3.000
 954  N5   C13  C15  119.80  3.000
 954  C14  C13  C15  121.47  3.000
 954  H3   C14  H2   108.74  3.000
 954  H3   C14  H1   107.17  3.000
 954  H2   C14  H1   108.47  3.000
 954  H3   C14  C13  111.35  3.000
 954  H2   C14  C13  110.06  3.000
 954  H1   C14  C13  110.94  3.000
 954  C12  N5   C13  117.49  3.000
 954  N6   C16  S1   120.62  3.000
 954  S1   C16  C15  118.59  3.000
 954  N6   C16  C15  120.79  3.000
 954  C17  S1   C16  101.33  3.000
 954  H6   C17  H5   109.37  3.000
 954  H6   C17  H4   109.44  3.000
 954  H5   C17  H4   109.79  3.000
 954  H6   C17  S1   105.67  3.000
 954  H5   C17  S1   111.23  3.000
 954  H4   C17  S1   111.24  3.000
 954  C12  N6   C16  116.88  3.000
 954  N4   C12  N6   116.77  3.000
 954  N6   C12  N5   125.92  3.000
 954  N4   C12  N5   117.30  3.000
 954  C11  N4   C10  113.65  3.000
 954  C10  N4   C12  123.03  3.000
 954  C11  N4   C12  123.25  3.000
 954  H8   C10  H7   107.75  3.000
 954  H8   C10  C9   112.01  3.000
 954  H7   C10  C9   111.10  3.000
 954  H8   C10  N4   111.43  3.000
 954  H7   C10  N4   112.14  3.000
 954  C9   C10  N4   102.44  3.000
 954  H9   C9   C8   107.39  3.000
 954  H9   C9   C5   110.50  3.000
 954  C8   C9   C5   113.40  3.000
 954  H9   C9   C10  109.07  3.000
 954  C8   C9   C10  113.12  3.000
 954  C5   C9   C10  103.30  3.000
 954  C6   N3   C7   117.18  3.000
 954  C7   N3   C8   119.05  3.000
 954  C6   N3   C8   123.58  3.000
 954  H11  N1   C6   113.63  3.000
 954  H11  N1   C5   117.74  3.000
 954  C6   N1   C5   122.67  3.000
 954  H13  C11  H12  107.41  3.000
 954  H13  C11  C5   110.63  3.000
 954  H12  C11  C5   111.95  3.000
 954  H13  C11  N4   111.85  3.000
 954  H12  C11  N4   112.36  3.000
 954  C5   C11  N4   102.70  3.000
 954  C    C5   C11  113.28  3.000
 954  C11  C5   N1   108.85  3.000
 954  C    C5   N1   111.88  3.000
 954  N1   C5   C9   105.89  3.000
 954  C11  C5   C9   101.76  3.000
 954  C    C5   C9   114.44  3.000
 954  S    C    C1   111.55  3.000
 954  S    C    C5   121.16  3.000
 954  C1   C    C5   127.30  3.000
 954  H14  C1   C2   123.24  3.000
 954  H14  C1   C    123.70  3.000
 954  C2   C1   C    113.06  3.000
 954  H15  C2   C3   123.33  3.000
 954  H15  C2   C1   124.55  3.000
 954  C3   C2   C1   112.13  3.000
 954  C4   C3   S    121.07  3.000
 954  S    C3   C2   111.86  3.000
 954  C4   C3   C2   127.07  3.000
 954  C3   S    C     91.41  3.000
 954  N    C4   C3   180.00  3.000
 954  N3   C8   O    122.35  3.000
 954  N3   C8   C9   116.67  3.000
 954  O    C8   C9   120.97  3.000
 954  H18  C7   H17  108.26  3.000
 954  H18  C7   H16  108.49  3.000
 954  H17  C7   H16  109.33  3.000
 954  H18  C7   N3   109.30  3.000
 954  H17  C7   N3   110.00  3.000
 954  H16  C7   N3   111.38  3.000
 954  N1   C6   N2   119.12  3.000
 954  N2   C6   N3   125.11  3.000
 954  N1   C6   N3   115.76  3.000
 954  H10  N2   C6   113.82  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
 954  CONST_01  C12  N5   C13  C15     0.00   0.0  0
 954  CONST_02  C12  N6   C16  C15     0.00   0.0  0
 954  CONST_03  N6   C12  N5   C13     0.00   0.0  0
 954  CONST_04  N6   C16  C15  C13     0.00   0.0  0
 954  CONST_05  C16  C15  C13  N5      0.00   0.0  0
 954  CONST_06  C16  N6   C12  N5      0.00   0.0  0
 954  CONST_07  C3   C2   C1   C       0.00   0.0  0
 954  CONST_08  C2   C3   S    C       0.00   0.0  0
 954  CONST_09  S    C3   C2   C1      0.00   0.0  0
 954  CONST_10  C3   S    C    C1      0.00   0.0  0
 954  CONST_11  S    C    C1   C2      0.00   0.0  0
 954  CONST_12  N4   C12  N5   C13   180.00   0.0  0
 954  CONST_13  N4   C12  N6   C16   180.00   0.0  0
 954  CONST_14  C2   C1   C    C5    180.00   0.0  0
 954  CONST_15  C3   S    C    C5    180.00   0.0  0
 954  CONST_16  C6   N3   C8   C9      0.00   0.0  0
 954  CONST_18  C8   N3   C6   N1      0.00   0.0  0
 954  CONST_19  N5   C13  C15  F     180.00   0.0  0
 954  CONST_20  N6   C16  C15  F     180.00   0.0  0
 954  CONST_21  S1   C16  C15  C13   180.00   0.0  0
 954  CONST_22  C12  N5   C13  C14   180.00   0.0  0
 954  CONST_23  C16  C15  C13  C14   180.00   0.0  0
 954  CONST_24  C12  N6   C16  S1    180.00   0.0  0
 954  CONST_25  C4   C3   S    C     180.00   0.0  0
 954  CONST_26  C4   C3   C2   C1    180.00   0.0  0
 954  CONST_27  C7   N3   C8   C9    180.00   0.0  0
 954  CONST_28  C6   N3   C8   O     180.00   0.0  0
 954  CONST_30  C8   N3   C6   N2    180.00   0.0  0
 954  CONST_31  C7   N3   C6   N1    180.00   0.0  0
 954  CONST_32  H14  C1   C    C5      0.00   0.0  0
 954  CONST_33  H15  C2   C1   C     180.00   0.0  0
 954  CONST_34  H11  N1   C6   N3    180.00   0.0  0
 954  CONST_35  C7   N3   C8   O       0.00   0.0  0
 954  CONST_36  C7   N3   C6   N2      0.00   0.0  0
 954  CONST_37  H10  N2   C6   N3      0.00   0.0  0
 954  Var_01    C11  N4   C12  N5    176.91  30.0  2
 954  Var_02    C5   C11  N4   C12  -160.49  30.0  1
 954  Var_03    C9   C10  N4   C12  -174.52  30.0  1
 954  Var_04    N6   C16  S1   C17     0.46  30.0  1
 954  Var_05    H1   C14  C13  C15    64.02  30.0  2
 954  Var_06    H16  C7   N3   C8    105.46  30.0  3
 954  Var_07    H4   C17  S1   C16   -61.78  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
 954  chir_01  C9  C5  C10  C8  negativ
 954  chir_02  C5  C9  C11  C   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
 954  plan-1  C5   0.020
 954  plan-1  C    0.020
 954  plan-1  C1   0.020
 954  plan-1  C2   0.020
 954  plan-1  C3   0.020
 954  plan-1  S    0.020
 954  plan-1  C4   0.020
 954  plan-1  N    0.020
 954  plan-1  H14  0.020
 954  plan-1  H15  0.020
 954  plan-2  F    0.020
 954  plan-2  C15  0.020
 954  plan-2  C13  0.020
 954  plan-2  C14  0.020
 954  plan-2  N5   0.020
 954  plan-2  C16  0.020
 954  plan-2  S1   0.020
 954  plan-2  N6   0.020
 954  plan-2  C12  0.020
 954  plan-2  N4   0.020
 954  plan-3  C9   0.020
 954  plan-3  N3   0.020
 954  plan-3  N1   0.020
 954  plan-3  C5   0.020
 954  plan-3  C8   0.020
 954  plan-3  C7   0.020
 954  plan-3  C6   0.020
 954  plan-3  H10  0.020
 954  plan-3  H11  0.020
 954  plan-3  O    0.020
 954  plan-3  N2   0.020

