# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 12:05:47 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 3-{5-[(2E,4aR,7aR)-6-benzoyl-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)C(=O)c3ccccc3)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
 10J  10J  3-{5-[(2E,4aR,7aR)-6-benzoyl-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophen-3-yl}benzonitrile  ligand  54  33  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_10J
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
 10J  C1   C  CR6   0  -0.024  -0.6750  -0.4127  -0.1554
 10J  C2   C  CR16  0  -0.425  -1.3966   0.6097  -1.0286
 10J  N3   N  NR6   0  -0.541  -0.6506   2.2817   0.5951
 10J  C4   C  CR6   0   0.619  -0.6304   1.3063   1.6052
 10J  C5   C  CR6   0   0.596  -1.0523   2.0345  -0.6929
 10J  N6   N  NR16  0  -0.652  -0.8640   0.0220   1.2003
 10J  N7   N  NT    0  -0.467  -2.8784  -1.1266  -0.4546
 10J  C8   C  CR5   0  -0.083   0.7780  -0.5997  -0.4958
 10J  C9   C  CH2   0  -0.240  -1.5304  -1.6586  -0.3915
 10J  C10  C  C     0   0.515  -3.9138  -1.7794   0.1111
 10J  C11  C  CH2   0  -0.233  -2.8842   0.2904  -0.8160
 10J  C12  C  CR15  0  -0.287   1.8537  -0.3607   0.3012
 10J  C13  C  CR5   0   0.214   3.1048  -0.6037  -0.3449
 10J  S14  S  S2    0   0.254   1.2815  -1.1365  -2.0568
 10J  C15  C  CR15  0  -0.570   2.9317  -1.0311  -1.6307
 10J  C16  C  CR6   0   0.033   6.7717   0.0708   0.1669
 10J  C17  C  CR6   0  -0.058  -5.2438  -1.1005   0.0634
 10J  C18  C  CR6   0   0.123   4.4109  -0.4117   0.2992
 10J  N19  N  NS    0  -0.248   8.8396   0.6510  -1.2630
 10J  C20  C  CSP   0   0.054   7.9157   0.3917  -0.6254
 10J  N21  N  N     0  -0.684  -0.4304   1.5408   2.8385
 10J  C22  C  CR16  0  -0.318   5.5389  -0.1022  -0.4560
 10J  O23  O  O     0  -0.439  -1.1375   2.9114  -1.5265
 10J  C24  C  CR16  0  -0.254   6.9028  -0.0499   1.5499
 10J  O25  O  O     0  -0.478  -3.7961  -2.8769   0.6367
 10J  C26  C  CR16  0  -0.277  -5.9599  -0.9448   1.2473
 10J  C27  C  CR16  0  -0.302   4.5507  -0.5326   1.6834
 10J  C28  C  CR16  0  -0.226   5.7797  -0.3519   2.3002
 10J  C29  C  CH3   0  -0.578  -0.2893   3.6389   0.9772
 10J  C30  C  CR16  0  -0.244  -7.2183  -0.3617   1.2271
 10J  C31  C  CR16  0  -0.266  -5.8119  -0.7012  -1.1429
 10J  C32  C  CR16  0  -0.245  -7.0813  -0.1405  -1.1631
 10J  C33  C  CR16  0  -0.252  -7.7819   0.0391   0.0222
 10J  H1   H  HCR6  0   0.314  -1.1388   0.4560  -2.0780
 10J  H2   H  HCH2  0   0.263  -1.2527  -2.1391  -1.3340
 10J  H3   H  HCH2  0   0.288  -1.4195  -2.3938   0.4041
 10J  H4   H  HCH2  0   0.268  -3.3224   0.8912  -0.0166
 10J  H5   H  HCH2  0   0.279  -3.4416   0.4888  -1.7289
 10J  H6   H  HCR5  0   0.269   1.7677  -0.0037   1.3182
 10J  H7   H  HCR5  0   0.302   3.6880  -1.3138  -2.3476
 10J  H8   H  H     0   0.357  -0.3491   2.5241   3.0554
 10J  H10  H  HCR6  0   0.279   5.4640   0.0211  -1.5284
 10J  H11  H  HCR6  0   0.285   7.8643   0.0930   2.0234
 10J  H12  H  HCR6  0   0.264  -5.5297  -1.2650   2.1876
 10J  H13  H  HCR6  0   0.269   3.6917  -0.7843   2.2917
 10J  H14  H  HCR6  0   0.278   5.8617  -0.4514   3.3737
 10J  H15  H  HCH3  0   0.264   0.6819   3.6423   1.4690
 10J  H16  H  HCH3  0   0.283  -0.2268   4.2544   0.0886
 10J  H17  H  HCH3  0   0.263  -1.0335   4.0727   1.6448
 10J  H18  H  HCR6  0   0.263  -7.7624  -0.2258   2.1525
 10J  H19  H  HCR6  0   0.271  -5.2766  -0.8440  -2.0735
 10J  H20  H  HCR6  0   0.263  -7.5220   0.1545  -2.1060
 10J  H21  H  HCR6  0   0.263  -8.7669   0.4874   0.0072
 10J  H22  H  HNR6  0   0.400  -0.7291  -0.6595   1.9329

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
 10J  C28  C27  aromatic  1.387  0.020  1.387
 10J  C28  C24  aromatic  1.384  0.020  1.384
 10J  C27  C18  aromatic  1.396  0.020  1.396
 10J  C15  S14  aromatic  1.708  0.020  1.708
 10J  C15  C13  aromatic  1.366  0.020  1.366
 10J  S14  C8   aromatic  1.726  0.020  1.726
 10J  C24  C16  aromatic  1.394  0.020  1.394
 10J  C18  C13  single    1.469  0.020  1.469
 10J  C18  C22  aromatic  1.392  0.020  1.392
 10J  C13  C12  aromatic  1.429  0.020  1.429
 10J  O25  C10  double    1.223  0.020  1.223
 10J  C8   C12  aromatic  1.360  0.020  1.360
 10J  C8   C1   single    1.504  0.020  1.504
 10J  C9   C1   single    1.530  0.020  1.530
 10J  C9   N7   single    1.451  0.020  1.451
 10J  C16  C22  aromatic  1.392  0.020  1.392
 10J  C16  C20  single    1.428  0.020  1.428
 10J  C10  N7   single    1.348  0.020  1.348
 10J  C10  C17  single    1.494  0.020  1.494
 10J  C1   C2   single    1.526  0.020  1.526
 10J  C1   N6   single    1.436  0.020  1.436
 10J  N7   C11  single    1.462  0.020  1.462
 10J  C31  C17  aromatic  1.392  0.020  1.392
 10J  C31  C32  aromatic  1.388  0.020  1.388
 10J  C20  N19  triple    1.152  0.020  1.152
 10J  C2   C11  single    1.536  0.020  1.536
 10J  C2   C5   single    1.504  0.020  1.504
 10J  C17  C26  aromatic  1.392  0.020  1.392
 10J  N6   C4   single    1.367  0.020  1.367
 10J  C32  C33  aromatic  1.389  0.020  1.389
 10J  C5   O23  double    1.213  0.020  1.213
 10J  C5   N3   single    1.372  0.020  1.372
 10J  C4   N3   single    1.404  0.020  1.404
 10J  C4   N21  double    1.271  0.020  1.271
 10J  C26  C30  aromatic  1.387  0.020  1.387
 10J  N3   C29  single    1.455  0.020  1.455
 10J  C33  C30  aromatic  1.389  0.020  1.389
 10J  C2   H1   single    0.970  0.020  1.090
 10J  C9   H2   single    0.970  0.020  1.090
 10J  C9   H3   single    0.970  0.020  1.090
 10J  C11  H4   single    0.970  0.020  1.090
 10J  C11  H5   single    0.970  0.020  1.090
 10J  C12  H6   single    0.930  0.020  1.080
 10J  C15  H7   single    0.930  0.020  1.080
 10J  N21  H8   single    0.890  0.020  1.040
 10J  C22  H10  single    0.930  0.020  1.080
 10J  C24  H11  single    0.930  0.020  1.080
 10J  C26  H12  single    0.930  0.020  1.080
 10J  C27  H13  single    0.930  0.020  1.080
 10J  C28  H14  single    0.930  0.020  1.080
 10J  C29  H15  single    0.970  0.020  1.090
 10J  C29  H16  single    0.970  0.020  1.090
 10J  C29  H17  single    0.970  0.020  1.090
 10J  C30  H18  single    0.930  0.020  1.080
 10J  C31  H19  single    0.930  0.020  1.080
 10J  C32  H20  single    0.930  0.020  1.080
 10J  C33  H21  single    0.930  0.020  1.080
 10J  N6   H22  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
 10J  C9   C1   C8   113.83  3.000
 10J  C9   C1   N6   108.58  3.000
 10J  C8   C1   N6   112.23  3.000
 10J  N6   C1   C2   105.97  3.000
 10J  C9   C1   C2   101.12  3.000
 10J  C8   C1   C2   114.24  3.000
 10J  H1   C2   C11  109.42  3.000
 10J  H1   C2   C5   107.10  3.000
 10J  C11  C2   C5   112.81  3.000
 10J  H1   C2   C1   110.12  3.000
 10J  C5   C2   C1   113.50  3.000
 10J  C11  C2   C1   103.85  3.000
 10J  C29  N3   C5   119.16  3.000
 10J  C29  N3   C4   117.08  3.000
 10J  C5   N3   C4   123.67  3.000
 10J  N21  C4   N6   119.19  3.000
 10J  N21  C4   N3   124.89  3.000
 10J  N6   C4   N3   115.92  3.000
 10J  O23  C5   N3   122.39  3.000
 10J  N3   C5   C2   116.58  3.000
 10J  O23  C5   C2   121.03  3.000
 10J  H22  N6   C4   113.35  3.000
 10J  H22  N6   C1   117.59  3.000
 10J  C4   N6   C1   122.79  3.000
 10J  C11  N7   C10  124.73  3.000
 10J  C11  N7   C9   111.70  3.000
 10J  C10  N7   C9   121.19  3.000
 10J  S14  C8   C12  110.73  3.000
 10J  C12  C8   C1   127.57  3.000
 10J  S14  C8   C1   121.69  3.000
 10J  H3   C9   H2   107.89  3.000
 10J  H3   C9   N7   111.96  3.000
 10J  H2   C9   N7   111.07  3.000
 10J  H3   C9   C1   112.35  3.000
 10J  H2   C9   C1   110.42  3.000
 10J  N7   C9   C1   103.16  3.000
 10J  O25  C10  C17  120.49  3.000
 10J  C17  C10  N7   116.76  3.000
 10J  O25  C10  N7   122.75  3.000
 10J  H5   C11  H4   107.96  3.000
 10J  H5   C11  N7   112.72  3.000
 10J  H4   C11  N7   110.73  3.000
 10J  H5   C11  C2   110.00  3.000
 10J  H4   C11  C2   112.06  3.000
 10J  N7   C11  C2   103.40  3.000
 10J  H6   C12  C13  123.45  3.000
 10J  H6   C12  C8   123.11  3.000
 10J  C13  C12  C8   113.43  3.000
 10J  C18  C13  C15  124.49  3.000
 10J  C18  C13  C12  123.92  3.000
 10J  C15  C13  C12  111.59  3.000
 10J  C15  S14  C8    92.12  3.000
 10J  H7   C15  S14  119.67  3.000
 10J  H7   C15  C13  128.18  3.000
 10J  S14  C15  C13  112.13  3.000
 10J  C24  C16  C22  121.09  3.000
 10J  C22  C16  C20  119.29  3.000
 10J  C24  C16  C20  119.62  3.000
 10J  C31  C17  C26  119.66  3.000
 10J  C26  C17  C10  118.79  3.000
 10J  C31  C17  C10  121.42  3.000
 10J  C27  C18  C22  118.41  3.000
 10J  C22  C18  C13  120.77  3.000
 10J  C27  C18  C13  120.82  3.000
 10J  N19  C20  C16  180.00  3.000
 10J  H8   N21  C4   113.61  3.000
 10J  H10  C22  C18  120.45  3.000
 10J  H10  C22  C16  119.38  3.000
 10J  C18  C22  C16  120.16  3.000
 10J  H11  C24  C28  120.86  3.000
 10J  H11  C24  C16  120.44  3.000
 10J  C28  C24  C16  118.70  3.000
 10J  H12  C26  C30  119.84  3.000
 10J  H12  C26  C17  120.07  3.000
 10J  C30  C26  C17  120.08  3.000
 10J  H13  C27  C28  118.92  3.000
 10J  H13  C27  C18  119.86  3.000
 10J  C28  C27  C18  121.21  3.000
 10J  H14  C28  C27  119.79  3.000
 10J  H14  C28  C24  119.78  3.000
 10J  C27  C28  C24  120.43  3.000
 10J  H17  C29  H16  108.41  3.000
 10J  H17  C29  H15  109.34  3.000
 10J  H16  C29  H15  108.51  3.000
 10J  H17  C29  N3   111.25  3.000
 10J  H16  C29  N3   109.21  3.000
 10J  H15  C29  N3   110.06  3.000
 10J  H18  C30  C33  120.10  3.000
 10J  H18  C30  C26  119.77  3.000
 10J  C33  C30  C26  120.13  3.000
 10J  H19  C31  C32  119.53  3.000
 10J  H19  C31  C17  120.34  3.000
 10J  C32  C31  C17  120.12  3.000
 10J  H20  C32  C33  120.21  3.000
 10J  H20  C32  C31  119.70  3.000
 10J  C33  C32  C31  120.09  3.000
 10J  H21  C33  C32  120.06  3.000
 10J  H21  C33  C30  120.05  3.000
 10J  C32  C33  C30  119.88  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
 10J  CONST_01  C13  C15  S14  C8     0.00   0.0  0
 10J  CONST_02  C15  C13  C12  C8     0.00   0.0  0
 10J  CONST_03  C18  C13  C12  C8   180.00   0.0  0
 10J  CONST_04  S14  C15  C13  C12    0.00   0.0  0
 10J  CONST_07  C15  S14  C8   C12    0.00   0.0  0
 10J  CONST_08  C28  C27  C18  C13  180.00   0.0  0
 10J  CONST_09  C16  C22  C18  C13  180.00   0.0  0
 10J  CONST_10  S14  C8   C12  C13    0.00   0.0  0
 10J  CONST_11  C18  C13  C15  S14  180.00   0.0  0
 10J  CONST_14  C27  C28  C24  C16    0.00   0.0  0
 10J  CONST_15  C27  C18  C22  C16    0.00   0.0  0
 10J  CONST_16  C33  C32  C31  C17    0.00   0.0  0
 10J  CONST_17  C33  C30  C26  C17    0.00   0.0  0
 10J  CONST_18  C24  C28  C27  C18    0.00   0.0  0
 10J  CONST_19  C24  C16  C22  C18    0.00   0.0  0
 10J  CONST_20  C28  C27  C18  C22    0.00   0.0  0
 10J  CONST_21  C28  C24  C16  C22    0.00   0.0  0
 10J  CONST_22  C32  C31  C17  C26    0.00   0.0  0
 10J  CONST_23  C32  C33  C30  C26    0.00   0.0  0
 10J  CONST_24  C31  C17  C26  C30    0.00   0.0  0
 10J  CONST_25  C31  C32  C33  C30    0.00   0.0  0
 10J  CONST_26  C15  S14  C8   C1   180.00   0.0  0
 10J  CONST_27  C13  C12  C8   C1   180.00   0.0  0
 10J  CONST_29  C4   N3   C5   C2     0.00   0.0  0
 10J  CONST_30  N6   C4   N3   C5     0.00   0.0  0
 10J  CONST_31  C32  C31  C17  C10  180.00   0.0  0
 10J  CONST_32  C30  C26  C17  C10  180.00   0.0  0
 10J  CONST_33  C20  C16  C22  C18  180.00   0.0  0
 10J  CONST_34  C28  C24  C16  C20  180.00   0.0  0
 10J  CONST_35  C17  C10  N7   C9   180.00   0.0  0
 10J  CONST_38  C29  N3   C5   C2   180.00   0.0  0
 10J  CONST_39  O23  C5   N3   C4   180.00   0.0  0
 10J  CONST_40  N21  C4   N3   C5   180.00   0.0  0
 10J  CONST_41  C29  N3   C4   N6   180.00   0.0  0
 10J  CONST_42  H6   C12  C8   C1     0.00   0.0  0
 10J  CONST_43  H7   C15  S14  C8   180.00   0.0  0
 10J  CONST_44  H13  C27  C18  C13    0.00   0.0  0
 10J  CONST_45  H10  C22  C18  C13    0.00   0.0  0
 10J  CONST_46  H14  C28  C24  C16  180.00   0.0  0
 10J  CONST_47  H20  C32  C31  C17  180.00   0.0  0
 10J  CONST_48  H18  C30  C26  C17  180.00   0.0  0
 10J  CONST_49  H11  C24  C16  C22  180.00   0.0  0
 10J  CONST_50  H19  C31  C17  C26  180.00   0.0  0
 10J  CONST_51  H21  C33  C30  C26  180.00   0.0  0
 10J  CONST_52  H12  C26  C17  C31  180.00   0.0  0
 10J  CONST_53  H22  N6   C4   N3   180.00   0.0  0
 10J  CONST_54  O25  C10  N7   C9     0.00   0.0  0
 10J  CONST_55  O25  C10  N7   C11  180.00   0.0  0
 10J  CONST_56  C29  N3   C4   N21    0.00   0.0  0
 10J  CONST_57  C29  N3   C5   O23    0.00   0.0  0
 10J  CONST_58  H8   N21  C4   N3     0.00   0.0  0
 10J  Var_01    C11  N7   C9   C1    22.95  30.0  1
 10J  Var_02    C9   N7   C11  C2     1.89  30.0  1
 10J  Var_03    C31  C17  C10  N7    56.21  30.0  2
 10J  Var_04    H15  C29  N3   C4    53.98  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
 10J  chir_01  C1  C9  C2   N6  negativ
 10J  chir_02  C2  C1  C11  C5  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
 10J  plan-1  C1   0.020
 10J  plan-1  C8   0.020
 10J  plan-1  C12  0.020
 10J  plan-1  C13  0.020
 10J  plan-1  S14  0.020
 10J  plan-1  C15  0.020
 10J  plan-1  C18  0.020
 10J  plan-1  H6   0.020
 10J  plan-1  H7   0.020
 10J  plan-2  C13  0.020
 10J  plan-2  C16  0.020
 10J  plan-2  C18  0.020
 10J  plan-2  N19  0.020
 10J  plan-2  C20  0.020
 10J  plan-2  C22  0.020
 10J  plan-2  C24  0.020
 10J  plan-2  C27  0.020
 10J  plan-2  C28  0.020
 10J  plan-2  H10  0.020
 10J  plan-2  H11  0.020
 10J  plan-2  H13  0.020
 10J  plan-2  H14  0.020
 10J  plan-3  C10  0.020
 10J  plan-3  C17  0.020
 10J  plan-3  C26  0.020
 10J  plan-3  C30  0.020
 10J  plan-3  C31  0.020
 10J  plan-3  C32  0.020
 10J  plan-3  C33  0.020
 10J  plan-3  H12  0.020
 10J  plan-3  H18  0.020
 10J  plan-3  H19  0.020
 10J  plan-3  H20  0.020
 10J  plan-3  H21  0.020
 10J  plan-4  N7   0.020
 10J  plan-4  C9   0.020
 10J  plan-4  C10  0.020
 10J  plan-4  C11  0.020
 10J  plan-4  C17  0.020
 10J  plan-4  O25  0.020
 10J  plan-5  C1   0.020
 10J  plan-5  C2   0.020
 10J  plan-5  N3   0.020
 10J  plan-5  C4   0.020
 10J  plan-5  C5   0.020
 10J  plan-5  N6   0.020
 10J  plan-5  N21  0.020
 10J  plan-5  O23  0.020
 10J  plan-5  C29  0.020
 10J  plan-5  H8   0.020
 10J  plan-5  H22  0.020

