# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 17:08:39 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 3-{5-[(2E,4aR,7aR)-2-imino-6-(6-methoxypyridin-2-yl)-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: COc1cccc(n1)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
 10O  10O  3-{5-[(2E,4aR,7aR)-2-imino-6-(6-methoxypyridin-2-yl)-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophen-3-yl}benzonitrile  ligand  55  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 OK
;

data_comp_10O
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
 10O  C1   C  CT    0  -0.030  -0.8268   0.4903  -0.1899
 10O  C2   C  CH1   0  -0.425  -1.5435   1.4730  -1.1142
 10O  N1   N  NT    0  -0.541  -0.4895   3.2197   0.2403
 10O  C3   C  C     0   0.621  -0.4706   2.3643   1.3541
 10O  C4   C  C     0   0.600  -1.0677   2.8908  -0.9601
 10O  N2   N  NH1   0  -0.653  -0.8773   1.0817   1.1203
 10O  C5   C  CR5   0  -0.093   0.5837   0.1663  -0.6025
 10O  N3   N  NT    0  -0.507  -3.0730  -0.1056  -0.3496
 10O  C6   C  CH2   0  -0.209  -1.7692  -0.7142  -0.2165
 10O  C7   C  CH2   0  -0.238  -3.0212   1.2815  -0.7544
 10O  C8   C  CR15  0  -0.283   1.7091   0.2608   0.1551
 10O  C9   C  CR5   0   0.209   2.8946  -0.1358  -0.5361
 10O  S1   S  S2    0   0.254   0.9605  -0.4059  -2.1861
 10O  C10  C  CR15  0  -0.566   2.6248  -0.5216  -1.8181
 10O  C11  C  CR6   0   0.542  -4.2240  -0.7571  -0.0577
 10O  N4   N  NS    0  -0.248   8.2471  -2.7179  -0.5276
 10O  N5   N  N     0  -0.683  -0.1296   2.7065   2.5299
 10O  C12  C  CR6   0   0.118   4.2335  -0.1257   0.0672
 10O  C13  C  CSP   0   0.053   7.4510  -1.9614  -0.1795
 10O  O1   O  O     0  -0.442  -1.1903   3.6935  -1.8613
 10O  N6   N  N     0  -0.523  -4.0985  -2.0407   0.2966
 10O  C14  C  CR16  0  -0.315   5.2043  -1.0379  -0.3366
 10O  C15  C  CH3   0  -0.576   0.0505   4.5583   0.4230
 10O  C16  C  CR6   0   0.032   6.4688  -1.0155   0.2454
 10O  C17  C  CR16  0  -0.295   4.5609   0.7970   1.0631
 10O  C18  C  CR16  0  -0.442  -5.4746  -0.1255  -0.1248
 10O  C19  C  CR16  0  -0.226   5.8192   0.8099   1.6457
 10O  C20  C  CR6   0   0.523  -5.1758  -2.7318   0.5978
 10O  C21  C  CR16  0  -0.254   6.7857  -0.0958   1.2442
 10O  C22  C  CR16  0  -0.143  -6.5903  -0.8836   0.1899
 10O  C23  C  CR16  0  -0.438  -6.4708  -2.2114   0.5615
 10O  O2   O  O2    0  -0.476  -5.0394  -4.0120   0.9591
 10O  C24  C  CH3   0  -0.411  -3.7313  -4.5607   1.0093
 10O  H1   H  HCH1  0   0.312  -1.3937   1.1917  -2.1593
 10O  H2   H  HCH2  0   0.244  -1.5367  -1.3738  -1.0593
 10O  H3   H  HCH2  0   0.270  -1.6837  -1.3140   0.6911
 10O  H4   H  HCH2  0   0.251  -3.3386   1.9484   0.0547
 10O  H5   H  HCH2  0   0.268  -3.6578   1.4829  -1.6180
 10O  H6   H  HCR5  0   0.268   1.7021   0.5802   1.1879
 10O  H7   H  HCR5  0   0.301   3.3205  -0.8468  -2.5774
 10O  H8   H  H     0   0.356   0.0569   3.6945   2.6281
 10O  H10  H  HCR6  0   0.280   4.9776  -1.7813  -1.0896
 10O  H11  H  HCH3  0   0.262   1.0471   4.4991   0.8566
 10O  H12  H  HCH3  0   0.282   0.1257   5.0506  -0.5391
 10O  H13  H  HCH3  0   0.262  -0.5877   5.1600   1.0701
 10O  H14  H  HCR6  0   0.263   3.8278   1.5253   1.3852
 10O  H15  H  HCR6  0   0.268  -5.5753   0.9132  -0.4049
 10O  H16  H  HCR6  0   0.278   6.0460   1.5342   2.4160
 10O  H17  H  HCR6  0   0.284   7.7649  -0.1026   1.7019
 10O  H18  H  HCR6  0   0.265  -7.5710  -0.4270   0.1452
 10O  H19  H  HCR6  0   0.258  -7.3291  -2.8190   0.8111
 10O  H20  H  HCH3  0   0.226  -3.2399  -4.5347   0.0358
 10O  H21  H  HCH3  0   0.226  -3.0981  -4.0417   1.7304
 10O  H22  H  HCH3  0   0.242  -3.8551  -5.5950   1.3211
 10O  H23  H  HNH1  0   0.399  -0.7648   0.4685   1.9145

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
 10O  C24  O2   single    1.419  0.020  1.419
 10O  O2   C20  single    1.337  0.020  1.337
 10O  C10  S1   aromatic  1.708  0.020  1.708
 10O  C10  C9   aromatic  1.366  0.020  1.366
 10O  S1   C5   aromatic  1.725  0.020  1.725
 10O  C17  C19  aromatic  1.387  0.020  1.387
 10O  C17  C12  aromatic  1.397  0.020  1.397
 10O  C20  N6   aromatic  1.315  0.020  1.315
 10O  C20  C23  aromatic  1.396  0.020  1.396
 10O  C19  C21  aromatic  1.384  0.020  1.384
 10O  N6   C11  aromatic  1.337  0.020  1.337
 10O  C9   C12  single    1.469  0.020  1.469
 10O  C9   C8   aromatic  1.428  0.020  1.428
 10O  C23  C22  aromatic  1.384  0.020  1.384
 10O  C12  C14  aromatic  1.392  0.020  1.392
 10O  C6   N3   single    1.445  0.020  1.445
 10O  C6   C1   single    1.530  0.020  1.530
 10O  C5   C8   aromatic  1.360  0.020  1.360
 10O  C5   C1   single    1.505  0.020  1.505
 10O  C21  C16  aromatic  1.394  0.020  1.394
 10O  C11  N3   single    1.354  0.020  1.354
 10O  C11  C18  aromatic  1.403  0.020  1.403
 10O  C22  C18  aromatic  1.385  0.020  1.385
 10O  N3   C7   single    1.446  0.020  1.446
 10O  C1   C2   single    1.528  0.020  1.528
 10O  C1   N2   single    1.438  0.020  1.438
 10O  C14  C16  aromatic  1.392  0.020  1.392
 10O  C16  C13  single    1.428  0.020  1.428
 10O  C2   C7   single    1.533  0.020  1.533
 10O  C2   C4   single    1.503  0.020  1.503
 10O  N2   C3   single    1.366  0.020  1.366
 10O  C13  N4   triple    1.152  0.020  1.152
 10O  C4   O1   double    1.213  0.020  1.213
 10O  C4   N1   single    1.372  0.020  1.372
 10O  C3   N1   single    1.405  0.020  1.405
 10O  C3   N5   double    1.271  0.020  1.271
 10O  N1   C15  single    1.455  0.020  1.455
 10O  C2   H1   single    0.970  0.020  1.090
 10O  C6   H2   single    0.970  0.020  1.090
 10O  C6   H3   single    0.970  0.020  1.090
 10O  C7   H4   single    0.970  0.020  1.090
 10O  C7   H5   single    0.970  0.020  1.090
 10O  C8   H6   single    0.930  0.020  1.080
 10O  C10  H7   single    0.930  0.020  1.080
 10O  N5   H8   single    0.890  0.020  1.040
 10O  C14  H10  single    0.930  0.020  1.080
 10O  C15  H11  single    0.970  0.020  1.090
 10O  C15  H12  single    0.970  0.020  1.090
 10O  C15  H13  single    0.970  0.020  1.090
 10O  C17  H14  single    0.930  0.020  1.080
 10O  C18  H15  single    0.930  0.020  1.080
 10O  C19  H16  single    0.930  0.020  1.080
 10O  C21  H17  single    0.930  0.020  1.080
 10O  C22  H18  single    0.930  0.020  1.080
 10O  C23  H19  single    0.930  0.020  1.080
 10O  C24  H20  single    0.970  0.020  1.090
 10O  C24  H21  single    0.970  0.020  1.090
 10O  C24  H22  single    0.970  0.020  1.090
 10O  N2   H23  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
 10O  C6   C1   C5   113.78  3.000
 10O  C5   C1   N2   111.79  3.000
 10O  C6   C1   N2   108.54  3.000
 10O  N2   C1   C2   105.67  3.000
 10O  C5   C1   C2   114.35  3.000
 10O  C6   C1   C2   101.95  3.000
 10O  H1   C2   C7   108.94  3.000
 10O  H1   C2   C4   107.30  3.000
 10O  C7   C2   C4   113.51  3.000
 10O  H1   C2   C1   110.41  3.000
 10O  C4   C2   C1   113.34  3.000
 10O  C7   C2   C1   103.29  3.000
 10O  C15  N1   C4   119.12  3.000
 10O  C15  N1   C3   117.11  3.000
 10O  C4   N1   C3   123.60  3.000
 10O  N5   C3   N2   119.41  3.000
 10O  N5   C3   N1   124.97  3.000
 10O  N2   C3   N1   115.61  3.000
 10O  O1   C4   N1   122.26  3.000
 10O  N1   C4   C2   116.68  3.000
 10O  O1   C4   C2   121.06  3.000
 10O  H23  N2   C3   113.74  3.000
 10O  H23  N2   C1   117.58  3.000
 10O  C3   N2   C1   122.11  3.000
 10O  S1   C5   C8   110.71  3.000
 10O  C8   C5   C1   127.44  3.000
 10O  S1   C5   C1   121.85  3.000
 10O  C11  N3   C7   123.52  3.000
 10O  C7   N3   C6   113.42  3.000
 10O  C11  N3   C6   122.98  3.000
 10O  H3   C6   H2   107.00  3.000
 10O  H3   C6   N3   112.26  3.000
 10O  H2   C6   N3   111.98  3.000
 10O  H3   C6   C1   111.73  3.000
 10O  H2   C6   C1   110.90  3.000
 10O  N3   C6   C1   103.05  3.000
 10O  H5   C7   H4   107.64  3.000
 10O  H5   C7   N3   112.18  3.000
 10O  H4   C7   N3   111.52  3.000
 10O  H5   C7   C2   110.70  3.000
 10O  H4   C7   C2   112.12  3.000
 10O  N3   C7   C2   102.72  3.000
 10O  H6   C8   C9   123.35  3.000
 10O  H6   C8   C5   123.19  3.000
 10O  C9   C8   C5   113.45  3.000
 10O  C12  C9   C10  124.59  3.000
 10O  C12  C9   C8   123.78  3.000
 10O  C10  C9   C8   111.64  3.000
 10O  C10  S1   C5    92.15  3.000
 10O  H7   C10  S1   119.77  3.000
 10O  H7   C10  C9   128.16  3.000
 10O  S1   C10  C9   112.05  3.000
 10O  C18  C11  N6   121.91  3.000
 10O  C18  C11  N3   122.06  3.000
 10O  N6   C11  N3   116.04  3.000
 10O  H8   N5   C3   113.75  3.000
 10O  C17  C12  C14  118.45  3.000
 10O  C14  C12  C9   120.81  3.000
 10O  C17  C12  C9   120.74  3.000
 10O  C16  C13  N4   180.00  3.000
 10O  C20  N6   C11  119.22  3.000
 10O  H10  C14  C16  119.48  3.000
 10O  H10  C14  C12  120.40  3.000
 10O  C16  C14  C12  120.11  3.000
 10O  H13  C15  H12  108.49  3.000
 10O  H13  C15  H11  109.25  3.000
 10O  H12  C15  H11  108.36  3.000
 10O  H13  C15  N1   111.41  3.000
 10O  H12  C15  N1   109.41  3.000
 10O  H11  C15  N1   109.87  3.000
 10O  C21  C16  C14  121.10  3.000
 10O  C14  C16  C13  119.32  3.000
 10O  C21  C16  C13  119.58  3.000
 10O  H14  C17  C19  118.91  3.000
 10O  H14  C17  C12  119.87  3.000
 10O  C19  C17  C12  121.23  3.000
 10O  H15  C18  C22  120.66  3.000
 10O  H15  C18  C11  121.90  3.000
 10O  C22  C18  C11  117.44  3.000
 10O  H16  C19  C21  119.90  3.000
 10O  H16  C19  C17  119.72  3.000
 10O  C21  C19  C17  120.38  3.000
 10O  O2   C20  C23  117.29  3.000
 10O  C23  C20  N6   123.92  3.000
 10O  O2   C20  N6   118.79  3.000
 10O  H17  C21  C19  120.92  3.000
 10O  H17  C21  C16  120.34  3.000
 10O  C19  C21  C16  118.74  3.000
 10O  H18  C22  C23  119.60  3.000
 10O  H18  C22  C18  119.30  3.000
 10O  C23  C22  C18  121.10  3.000
 10O  H19  C23  C22  122.19  3.000
 10O  H19  C23  C20  121.41  3.000
 10O  C22  C23  C20  116.40  3.000
 10O  C24  O2   C20  118.27  3.000
 10O  H22  C24  H21  109.21  3.000
 10O  H22  C24  H20  109.26  3.000
 10O  H21  C24  H20  108.48  3.000
 10O  H22  C24  O2   105.84  3.000
 10O  H21  C24  O2   111.98  3.000
 10O  H20  C24  O2   111.99  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
 10O  CONST_01  C9   C10  S1   C5      0.00   0.0  0
 10O  CONST_02  C10  C9   C8   C5      0.00   0.0  0
 10O  CONST_03  C12  C9   C8   C5    180.00   0.0  0
 10O  CONST_04  S1   C10  C9   C8      0.00   0.0  0
 10O  CONST_07  C10  S1   C5   C8      0.00   0.0  0
 10O  CONST_08  C19  C17  C12  C9    180.00   0.0  0
 10O  CONST_09  C16  C14  C12  C9    180.00   0.0  0
 10O  CONST_10  S1   C5   C8   C9      0.00   0.0  0
 10O  CONST_11  C12  C9   C10  S1    180.00   0.0  0
 10O  CONST_14  C23  C20  N6   C11     0.00   0.0  0
 10O  CONST_15  C23  C22  C18  C11     0.00   0.0  0
 10O  CONST_16  C21  C19  C17  C12     0.00   0.0  0
 10O  CONST_17  C21  C16  C14  C12     0.00   0.0  0
 10O  CONST_18  C22  C23  C20  N6      0.00   0.0  0
 10O  CONST_19  C22  C18  C11  N6      0.00   0.0  0
 10O  CONST_20  C19  C17  C12  C14     0.00   0.0  0
 10O  CONST_21  C19  C21  C16  C14     0.00   0.0  0
 10O  CONST_22  C17  C19  C21  C16     0.00   0.0  0
 10O  CONST_23  C17  C12  C14  C16     0.00   0.0  0
 10O  CONST_24  C20  N6   C11  C18     0.00   0.0  0
 10O  CONST_25  C20  C23  C22  C18     0.00   0.0  0
 10O  CONST_26  C10  S1   C5   C1    180.00   0.0  0
 10O  CONST_27  C9   C8   C5   C1    180.00   0.0  0
 10O  CONST_28  C20  N6   C11  N3    180.00   0.0  0
 10O  CONST_29  C22  C18  C11  N3    180.00   0.0  0
 10O  CONST_31  C3   N1   C4   C2      0.00   0.0  0
 10O  CONST_32  N2   C3   N1   C4      0.00   0.0  0
 10O  CONST_33  O2   C20  N6   C11   180.00   0.0  0
 10O  CONST_34  C13  C16  C14  C12   180.00   0.0  0
 10O  CONST_35  C19  C21  C16  C13   180.00   0.0  0
 10O  CONST_36  O2   C20  C23  C22   180.00   0.0  0
 10O  CONST_38  C15  N1   C4   C2    180.00   0.0  0
 10O  CONST_39  O1   C4   N1   C3    180.00   0.0  0
 10O  CONST_40  N5   C3   N1   C4    180.00   0.0  0
 10O  CONST_41  C15  N1   C3   N2    180.00   0.0  0
 10O  CONST_42  H6   C8   C5   C1      0.00   0.0  0
 10O  CONST_43  H7   C10  S1   C5    180.00   0.0  0
 10O  CONST_44  H15  C18  C11  N3      0.00   0.0  0
 10O  CONST_45  H14  C17  C12  C9      0.00   0.0  0
 10O  CONST_46  H10  C14  C12  C9      0.00   0.0  0
 10O  CONST_47  H18  C22  C18  C11   180.00   0.0  0
 10O  CONST_48  H16  C19  C17  C12   180.00   0.0  0
 10O  CONST_49  H19  C23  C20  N6    180.00   0.0  0
 10O  CONST_50  H17  C21  C16  C14   180.00   0.0  0
 10O  CONST_51  H23  N2   C3   N1    180.00   0.0  0
 10O  CONST_52  C15  N1   C3   N5      0.00   0.0  0
 10O  CONST_53  C15  N1   C4   O1      0.00   0.0  0
 10O  CONST_54  H8   N5   C3   N1      0.00   0.0  0
 10O  Var_01    C11  N3   C6   C1   -161.66  30.0  1
 10O  Var_02    C6   N3   C7   C2      9.41  30.0  1
 10O  Var_03    N6   C11  N3   C6     -3.62  30.0  2
 10O  Var_04    H11  C15  N1   C3     51.93  30.0  3
 10O  Var_05    H20  C24  O2   C20   -61.04  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
 10O  chir_01  C1  C5  C2  N2  positiv
 10O  chir_02  C2  C1  C7  C4  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
 10O  plan-1  C1   0.020
 10O  plan-1  C5   0.020
 10O  plan-1  C8   0.020
 10O  plan-1  C9   0.020
 10O  plan-1  S1   0.020
 10O  plan-1  C10  0.020
 10O  plan-1  C12  0.020
 10O  plan-1  H6   0.020
 10O  plan-1  H7   0.020
 10O  plan-2  C9   0.020
 10O  plan-2  N4   0.020
 10O  plan-2  C12  0.020
 10O  plan-2  C13  0.020
 10O  plan-2  C14  0.020
 10O  plan-2  C16  0.020
 10O  plan-2  C17  0.020
 10O  plan-2  C19  0.020
 10O  plan-2  C21  0.020
 10O  plan-2  H10  0.020
 10O  plan-2  H14  0.020
 10O  plan-2  H16  0.020
 10O  plan-2  H17  0.020
 10O  plan-3  N3   0.020
 10O  plan-3  C11  0.020
 10O  plan-3  N6   0.020
 10O  plan-3  C18  0.020
 10O  plan-3  C20  0.020
 10O  plan-3  C22  0.020
 10O  plan-3  C23  0.020
 10O  plan-3  O2   0.020
 10O  plan-3  H15  0.020
 10O  plan-3  H18  0.020
 10O  plan-3  H19  0.020
 10O  plan-4  C1   0.020
 10O  plan-4  C2   0.020
 10O  plan-4  N1   0.020
 10O  plan-4  C3   0.020
 10O  plan-4  C4   0.020
 10O  plan-4  N2   0.020
 10O  plan-4  N5   0.020
 10O  plan-4  O1   0.020
 10O  plan-4  C15  0.020
 10O  plan-4  H8   0.020
 10O  plan-4  H23  0.020

