# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 15:24:24 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 2-fluoro-5-{5-[(2E,4aR,7aR)-2-imino-3-methyl-4-oxo-6-phenyloctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophen-2-yl}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N)N[C@]2(CN(C[C@H]2C1=O)c3ccccc3)c4sc(cc4)c5ccc(F)c(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
 10W  10W  2-fluoro-5-{5-[(2E,4aR,7aR)-2-imino-3-methyl-4-oxo-6-phenyloctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophen-2-yl}benzonitrile  ligand  52  32  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_10W
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
 10W  C1   C  C     0   0.598  -2.0280   2.0430  -1.5005
 10W  N1   N  NT    0  -0.541  -2.1005   2.9750  -0.4973
 10W  C2   C  C     0   0.620  -2.3036   2.6482   0.8529
 10W  N2   N  NH1   0  -0.653  -2.2115   1.3213   1.1650
 10W  N3   N  N     0  -0.686  -2.5785   3.4844   1.7708
 10W  C3   C  CH3   0  -0.575  -2.0833   4.3879  -0.8445
 10W  O1   O  O     0  -0.443  -1.9725   2.3559  -2.6715
 10W  C4   C  CH1   0  -0.424  -2.0323   0.5992  -1.0839
 10W  C5   C  CT    0  -0.022  -1.5199   0.3706   0.3377
 10W  C6   C  CH2   0  -0.226  -2.0673  -1.0270   0.6417
 10W  N4   N  NT    0  -0.535  -3.3228  -1.0542  -0.0645
 10W  C7   C  CH2   0  -0.240  -3.4376  -0.0118  -1.0585
 10W  C8   C  CR5   0  -0.094  -0.0266   0.4832   0.4818
 10W  C9   C  CR15  0  -0.221   0.6748   1.3337   1.2831
 10W  C10  C  CR15  0  -0.213   2.0790   1.1872   1.1578
 10W  C11  C  CR5   0  -0.216   2.4414   0.2248   0.2594
 10W  S1   S  S2    0   0.235   1.0421  -0.5142  -0.4331
 10W  C12  C  CR6   0   0.152   3.7865  -0.1981  -0.1228
 10W  C13  C  CR16  0  -0.302   4.8456  -0.0239   0.7627
 10W  C14  C  CR6   0  -0.156   6.1359  -0.4039   0.4037
 10W  C15  C  CR6   0   0.567   6.3588  -0.9750  -0.8433
 10W  C16  C  CR16  0  -0.387   5.3262  -1.1672  -1.7343
 10W  C17  C  CR16  0  -0.283   4.0500  -0.7723  -1.3706
 10W  C18  C  CSP   0   0.071   7.2247  -0.2273   1.3042
 10W  N5   N  NS    0  -0.234   8.1009  -0.0819   2.0370
 10W  F1   F  F     0  -0.281   7.5982  -1.3374  -1.1640
 10W  C19  C  CR6   0   0.406  -4.3164  -1.9560   0.1872
 10W  C20  C  CR16  0  -0.364  -4.1310  -3.0111   1.0974
 10W  C21  C  CR16  0  -0.239  -5.1520  -3.9137   1.3476
 10W  C22  C  CR16  0  -0.300  -6.3797  -3.8083   0.7062
 10W  C23  C  CR16  0  -0.239  -6.5661  -2.7729  -0.2007
 10W  C24  C  CR16  0  -0.367  -5.5593  -1.8578  -0.4618
 10W  H1   H  H     0   0.357  -2.7121   4.4272   1.4334
 10W  H3   H  HCH3  0   0.263  -3.0789   4.8258  -0.7723
 10W  H4   H  HCH3  0   0.263  -1.4059   4.9240  -0.1832
 10W  H5   H  HCH3  0   0.281  -1.7305   4.5033  -1.8621
 10W  H6   H  HCH1  0   0.311  -1.4162   0.0530  -1.8011
 10W  H7   H  HCH2  0   0.243  -1.3724  -1.7990   0.2897
 10W  H8   H  HCH2  0   0.267  -2.1902  -1.1692   1.7189
 10W  H9   H  HCH2  0   0.245  -4.2012   0.7282  -0.7910
 10W  H10  H  HCH2  0   0.264  -3.7010  -0.4074  -2.0424
 10W  H11  H  HCR5  0   0.269   0.2120   2.0531   1.9438
 10W  H12  H  HCR5  0   0.272   2.7896   1.7924   1.7029
 10W  H13  H  HCR6  0   0.294   4.6798   0.3966   1.7454
 10W  H14  H  HCR6  0   0.305   5.5161  -1.6099  -2.7025
 10W  H15  H  HCR6  0   0.282   3.2502  -0.9068  -2.0880
 10W  H16  H  HCR6  0   0.264  -3.1846  -3.1364   1.6071
 10W  H17  H  HCR6  0   0.251  -4.9781  -4.7158   2.0542
 10W  H18  H  HCR6  0   0.245  -7.1716  -4.5172   0.9075
 10W  H19  H  HCR6  0   0.250  -7.5128  -2.6686  -0.7163
 10W  H20  H  HCR6  0   0.267  -5.7457  -1.0616  -1.1704
 10W  H21  H  HNH1  0   0.399  -2.2463   1.1396   2.1574

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
 10W  C16  C17  aromatic  1.385  0.020  1.385
 10W  C16  C15  aromatic  1.377  0.020  1.377
 10W  C17  C12  aromatic  1.399  0.020  1.399
 10W  C10  C9   aromatic  1.417  0.020  1.417
 10W  C10  C11  aromatic  1.366  0.020  1.366
 10W  C9   C8   aromatic  1.363  0.020  1.363
 10W  F1   C15  single    1.331  0.020  1.331
 10W  C15  C14  aromatic  1.390  0.020  1.390
 10W  C21  C20  aromatic  1.386  0.020  1.386
 10W  C21  C22  aromatic  1.389  0.020  1.389
 10W  C12  C11  single    1.461  0.020  1.461
 10W  C12  C13  aromatic  1.392  0.020  1.392
 10W  C11  S1   aromatic  1.727  0.020  1.727
 10W  C20  C19  aromatic  1.406  0.020  1.406
 10W  C22  C23  aromatic  1.389  0.020  1.389
 10W  C8   S1   aromatic  1.725  0.020  1.725
 10W  C8   C5   single    1.504  0.020  1.504
 10W  C6   N4   single    1.441  0.020  1.441
 10W  C6   C5   single    1.531  0.020  1.531
 10W  C13  C14  aromatic  1.392  0.020  1.392
 10W  C14  C18  single    1.424  0.020  1.424
 10W  C19  N4   single    1.365  0.020  1.365
 10W  C19  C24  aromatic  1.406  0.020  1.406
 10W  N4   C7   single    1.445  0.020  1.445
 10W  C5   C4   single    1.528  0.020  1.528
 10W  C5   N2   single    1.438  0.020  1.438
 10W  C23  C24  aromatic  1.385  0.020  1.385
 10W  C4   C7   single    1.533  0.020  1.533
 10W  C4   C1   single    1.503  0.020  1.503
 10W  C18  N5   triple    1.151  0.020  1.151
 10W  N2   C2   single    1.366  0.020  1.366
 10W  C1   O1   double    1.213  0.020  1.213
 10W  C1   N1   single    1.371  0.020  1.371
 10W  C2   N1   single    1.404  0.020  1.404
 10W  C2   N3   double    1.272  0.020  1.272
 10W  N1   C3   single    1.455  0.020  1.455
 10W  N3   H1   single    0.890  0.020  1.040
 10W  C3   H3   single    0.970  0.020  1.090
 10W  C3   H4   single    0.970  0.020  1.090
 10W  C3   H5   single    0.970  0.020  1.090
 10W  C4   H6   single    0.970  0.020  1.090
 10W  C6   H7   single    0.970  0.020  1.090
 10W  C6   H8   single    0.970  0.020  1.090
 10W  C7   H9   single    0.970  0.020  1.090
 10W  C7   H10  single    0.970  0.020  1.090
 10W  C9   H11  single    0.930  0.020  1.080
 10W  C10  H12  single    0.930  0.020  1.080
 10W  C13  H13  single    0.930  0.020  1.080
 10W  C16  H14  single    0.930  0.020  1.080
 10W  C17  H15  single    0.930  0.020  1.080
 10W  C20  H16  single    0.930  0.020  1.080
 10W  C21  H17  single    0.930  0.020  1.080
 10W  C22  H18  single    0.930  0.020  1.080
 10W  C23  H19  single    0.930  0.020  1.080
 10W  C24  H20  single    0.930  0.020  1.080
 10W  N2   H21  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
 10W  C4   C1   O1   121.03  3.000
 10W  O1   C1   N1   122.22  3.000
 10W  C4   C1   N1   116.75  3.000
 10W  C3   N1   C2   117.21  3.000
 10W  C3   N1   C1   119.00  3.000
 10W  C2   N1   C1   123.58  3.000
 10W  N3   C2   N2   119.23  3.000
 10W  N3   C2   N1   124.92  3.000
 10W  N2   C2   N1   115.84  3.000
 10W  H21  N2   C5   117.60  3.000
 10W  H21  N2   C2   113.39  3.000
 10W  C5   N2   C2   122.91  3.000
 10W  H1   N3   C2   113.65  3.000
 10W  H5   C3   H4   108.41  3.000
 10W  H5   C3   H3   108.48  3.000
 10W  H4   C3   H3   109.29  3.000
 10W  H5   C3   N1   109.36  3.000
 10W  H4   C3   N1   109.93  3.000
 10W  H3   C3   N1   111.31  3.000
 10W  H6   C4   C7   109.20  3.000
 10W  H6   C4   C5   110.31  3.000
 10W  C7   C4   C5   103.44  3.000
 10W  H6   C4   C1   107.27  3.000
 10W  C7   C4   C1   112.97  3.000
 10W  C5   C4   C1   113.62  3.000
 10W  C8   C5   C6   113.84  3.000
 10W  C6   C5   C4   101.61  3.000
 10W  C8   C5   C4   114.25  3.000
 10W  C4   C5   N2   105.97  3.000
 10W  C6   C5   N2   108.50  3.000
 10W  C8   C5   N2   111.89  3.000
 10W  H8   C6   H7   107.20  3.000
 10W  H8   C6   N4   112.49  3.000
 10W  H7   C6   N4   112.43  3.000
 10W  H8   C6   C5   110.75  3.000
 10W  H7   C6   C5   110.62  3.000
 10W  N4   C6   C5   103.38  3.000
 10W  C19  N4   C7   123.06  3.000
 10W  C7   N4   C6   113.13  3.000
 10W  C19  N4   C6   123.80  3.000
 10W  H10  C7   H9   107.22  3.000
 10W  H10  C7   N4   112.17  3.000
 10W  H9   C7   N4   111.99  3.000
 10W  H10  C7   C4   110.51  3.000
 10W  H9   C7   C4   111.94  3.000
 10W  N4   C7   C4   103.07  3.000
 10W  S1   C8   C9   110.73  3.000
 10W  S1   C8   C5   121.40  3.000
 10W  C9   C8   C5   127.87  3.000
 10W  H11  C9   C10  123.16  3.000
 10W  H11  C9   C8   123.67  3.000
 10W  C10  C9   C8   113.17  3.000
 10W  H12  C10  C11  123.50  3.000
 10W  H12  C10  C9   123.29  3.000
 10W  C11  C10  C9   113.20  3.000
 10W  C12  C11  S1   121.14  3.000
 10W  S1   C11  C10  110.51  3.000
 10W  C12  C11  C10  128.35  3.000
 10W  C11  S1   C8    92.40  3.000
 10W  C17  C12  C13  118.41  3.000
 10W  C13  C12  C11  119.87  3.000
 10W  C17  C12  C11  121.72  3.000
 10W  H13  C13  C14  118.85  3.000
 10W  H13  C13  C12  120.68  3.000
 10W  C14  C13  C12  120.47  3.000
 10W  C18  C14  C15  119.73  3.000
 10W  C18  C14  C13  120.78  3.000
 10W  C15  C14  C13  119.49  3.000
 10W  F1   C15  C16  120.30  3.000
 10W  F1   C15  C14  118.53  3.000
 10W  C16  C15  C14  121.17  3.000
 10W  H14  C16  C17  120.92  3.000
 10W  H14  C16  C15  120.30  3.000
 10W  C17  C16  C15  118.77  3.000
 10W  H15  C17  C16  118.12  3.000
 10W  H15  C17  C12  120.19  3.000
 10W  C16  C17  C12  121.68  3.000
 10W  N5   C18  C14  180.00  3.000
 10W  C24  C19  C20  117.91  3.000
 10W  C24  C19  N4   120.81  3.000
 10W  C20  C19  N4   121.28  3.000
 10W  H16  C20  C21  118.95  3.000
 10W  H16  C20  C19  120.47  3.000
 10W  C21  C20  C19  120.58  3.000
 10W  H17  C21  C22  119.95  3.000
 10W  H17  C21  C20  118.82  3.000
 10W  C22  C21  C20  121.23  3.000
 10W  H18  C22  C23  120.78  3.000
 10W  H18  C22  C21  120.76  3.000
 10W  C23  C22  C21  118.46  3.000
 10W  H19  C23  C24  118.81  3.000
 10W  H19  C23  C22  120.00  3.000
 10W  C24  C23  C22  121.19  3.000
 10W  H20  C24  C23  118.96  3.000
 10W  H20  C24  C19  120.41  3.000
 10W  C23  C24  C19  120.63  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
 10W  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 10W  CONST_02  C10  C11  S1   C8     0.00   0.0  0
 10W  CONST_03  C12  C11  S1   C8   180.00   0.0  0
 10W  CONST_04  C12  C11  C10  C9   180.00   0.0  0
 10W  CONST_05  S1   C11  C10  C9     0.00   0.0  0
 10W  CONST_06  C11  S1   C8   C9     0.00   0.0  0
 10W  CONST_07  S1   C8   C9   C10    0.00   0.0  0
 10W  CONST_10  C16  C17  C12  C11  180.00   0.0  0
 10W  CONST_11  C14  C13  C12  C11  180.00   0.0  0
 10W  CONST_14  C15  C16  C17  C12    0.00   0.0  0
 10W  CONST_15  C15  C14  C13  C12    0.00   0.0  0
 10W  CONST_16  C16  C17  C12  C13    0.00   0.0  0
 10W  CONST_17  C16  C15  C14  C13    0.00   0.0  0
 10W  CONST_18  C17  C16  C15  C14    0.00   0.0  0
 10W  CONST_19  C17  C12  C13  C14    0.00   0.0  0
 10W  CONST_20  C22  C21  C20  C19    0.00   0.0  0
 10W  CONST_21  C22  C23  C24  C19    0.00   0.0  0
 10W  CONST_22  C23  C22  C21  C20    0.00   0.0  0
 10W  CONST_23  C23  C24  C19  C20    0.00   0.0  0
 10W  CONST_24  C24  C19  C20  C21    0.00   0.0  0
 10W  CONST_25  C24  C23  C22  C21    0.00   0.0  0
 10W  CONST_26  C10  C9   C8   C5   180.00   0.0  0
 10W  CONST_27  C11  S1   C8   C5   180.00   0.0  0
 10W  CONST_28  C21  C20  C19  N4   180.00   0.0  0
 10W  CONST_29  C23  C24  C19  N4   180.00   0.0  0
 10W  CONST_30  N2   C2   N1   C1     0.00   0.0  0
 10W  CONST_32  C4   C1   N1   C2     0.00   0.0  0
 10W  CONST_33  C18  C14  C13  C12  180.00   0.0  0
 10W  CONST_34  F1   C15  C14  C13  180.00   0.0  0
 10W  CONST_35  C18  C14  C15  C16  180.00   0.0  0
 10W  CONST_36  F1   C15  C16  C17  180.00   0.0  0
 10W  CONST_37  N3   C2   N1   C1   180.00   0.0  0
 10W  CONST_38  O1   C1   N1   C2   180.00   0.0  0
 10W  CONST_39  C3   N1   C2   N2   180.00   0.0  0
 10W  CONST_41  C4   C1   N1   C3   180.00   0.0  0
 10W  CONST_42  H11  C9   C8   C5     0.00   0.0  0
 10W  CONST_43  H16  C20  C19  N4     0.00   0.0  0
 10W  CONST_44  H20  C24  C19  N4     0.00   0.0  0
 10W  CONST_45  H12  C10  C9   C8   180.00   0.0  0
 10W  CONST_46  H15  C17  C12  C11    0.00   0.0  0
 10W  CONST_47  H13  C13  C12  C11    0.00   0.0  0
 10W  CONST_48  H14  C16  C17  C12  180.00   0.0  0
 10W  CONST_49  H17  C21  C20  C19  180.00   0.0  0
 10W  CONST_50  H19  C23  C24  C19  180.00   0.0  0
 10W  CONST_51  H18  C22  C21  C20  180.00   0.0  0
 10W  CONST_52  H21  N2   C2   N1   180.00   0.0  0
 10W  CONST_53  C3   N1   C2   N3     0.00   0.0  0
 10W  CONST_54  O1   C1   N1   C3     0.00   0.0  0
 10W  CONST_55  H1   N3   C2   N1     0.00   0.0  0
 10W  Var_01    C6   N4   C7   C4     7.90  30.0  1
 10W  Var_02    C20  C19  N4   C6    -5.47  30.0  3
 10W  Var_03    H3   C3   N1   C1   103.74  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
 10W  chir_01  C4  C5  C7  C1  negativ
 10W  chir_02  C5  C4  C6  C8  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
 10W  plan-1  C5   0.020
 10W  plan-1  C8   0.020
 10W  plan-1  C9   0.020
 10W  plan-1  C10  0.020
 10W  plan-1  C11  0.020
 10W  plan-1  S1   0.020
 10W  plan-1  C12  0.020
 10W  plan-1  H11  0.020
 10W  plan-1  H12  0.020
 10W  plan-2  C11  0.020
 10W  plan-2  C12  0.020
 10W  plan-2  C13  0.020
 10W  plan-2  C14  0.020
 10W  plan-2  C15  0.020
 10W  plan-2  C16  0.020
 10W  plan-2  C17  0.020
 10W  plan-2  C18  0.020
 10W  plan-2  N5   0.020
 10W  plan-2  F1   0.020
 10W  plan-2  H13  0.020
 10W  plan-2  H14  0.020
 10W  plan-2  H15  0.020
 10W  plan-3  N4   0.020
 10W  plan-3  C19  0.020
 10W  plan-3  C20  0.020
 10W  plan-3  C21  0.020
 10W  plan-3  C22  0.020
 10W  plan-3  C23  0.020
 10W  plan-3  C24  0.020
 10W  plan-3  H16  0.020
 10W  plan-3  H17  0.020
 10W  plan-3  H18  0.020
 10W  plan-3  H19  0.020
 10W  plan-3  H20  0.020
 10W  plan-4  C1   0.020
 10W  plan-4  N1   0.020
 10W  plan-4  C2   0.020
 10W  plan-4  N2   0.020
 10W  plan-4  N3   0.020
 10W  plan-4  C3   0.020
 10W  plan-4  O1   0.020
 10W  plan-4  C4   0.020
 10W  plan-4  C5   0.020
 10W  plan-4  H1   0.020
 10W  plan-4  H21  0.020

