# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 01:32:58 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 3-{5-[(2E,4aR,7aR)-2-imino-6-(3-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: COc1cccnc1N2C[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
 10V  10V  3-{5-[(2E,4aR,7aR)-2-imino-6-(3-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 PERFECT
;

data_comp_10V
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
 10V  C1   C  CR16  0  -0.226  -5.8576  -0.1283   2.1712
 10V  C2   C  CR16  0  -0.254  -6.9478  -0.1214   1.3185
 10V  C3   C  CR6   0   0.032  -6.7350   0.1141  -0.0393
 10V  C4   C  CR16  0  -0.316  -5.4544   0.3354  -0.5380
 10V  C5   C  CR6   0   0.120  -4.3594   0.3365   0.3219
 10V  C6   C  CR16  0  -0.301  -4.5807   0.0993   1.6803
 10V  C7   C  CR5   0   0.210  -3.0053   0.5877  -0.1876
 10V  C8   C  CR15  0  -0.287  -1.8185   0.0532   0.4018
 10V  C9   C  CR5   0  -0.089  -0.6793   0.4263  -0.2407
 10V  S1   S  S2    0   0.251  -1.0448   1.4481  -1.5834
 10V  C10  C  CR15  0  -0.568  -2.7222   1.3634  -1.2753
 10V  C11  C  CT    0  -0.028   0.7360   0.0294   0.0858
 10V  C12  C  CH1   0  -0.424   1.4733  -0.6618  -1.0559
 10V  C13  C  C     0   0.596   1.0347  -2.0812  -1.2764
 10V  N1   N  NT    0  -0.542   0.5094  -2.7378  -0.1914
 10V  C14  C  C     0   0.619   0.4732  -2.1948   1.1042
 10V  N2   N  NH1   0  -0.651   0.7969  -0.8729   1.2021
 10V  N3   N  N     0  -0.687   0.1845  -2.8460   2.1580
 10V  C15  C  CH2   0  -0.211   1.6543   1.2201   0.3496
 10V  C16  C  CH3   0  -0.576   0.0549  -4.1104  -0.3508
 10V  O1   O  O     0  -0.443   1.1493  -2.6133  -2.3610
 10V  C17  C  CSP   0   0.053  -7.8460   0.1187  -0.9367
 10V  N4   N  NS    0  -0.249  -8.7453   0.1235  -1.6568
 10V  C18  C  CH2   0  -0.228   2.9497  -0.5429  -0.6517
 10V  N5   N  NT    0  -0.504   2.9800   0.6666   0.1666
 10V  C19  C  CR16  0  -0.292   6.4190   1.9541   0.3314
 10V  C20  C  CR6   0   0.274   5.3971   1.0314   0.2492
 10V  C21  C  CR6   0   0.432   4.0580   1.5105   0.2656
 10V  C23  C  CR16  0  -0.090   4.7934   3.6724   0.5533
 10V  C24  C  CR16  0  -0.340   6.1168   3.3097   0.4845
 10V  C25  C  CH3   0  -0.436   6.8870  -0.8083   0.1630
 10V  N6   N  N     0  -0.461   3.7959   2.7951   0.4368
 10V  H1   H  HCR6  0   0.278  -6.0029  -0.3042   3.2281
 10V  H2   H  HCR6  0   0.285  -7.9465  -0.2972   1.6933
 10V  H3   H  HCR6  0   0.279  -5.3158   0.4903  -1.6001
 10V  H4   H  HCR6  0   0.270  -3.7491   0.1086   2.3729
 10V  H5   H  HCR5  0   0.266  -1.8276  -0.6038   1.2604
 10V  H6   H  HCR5  0   0.301  -3.4104   1.9145  -1.8985
 10V  H7   H  HCH1  0   0.307   1.3079  -0.1238  -1.9908
 10V  H8   H  H     0   0.356   0.0460  -3.8338   1.9984
 10V  H10  H  HCH2  0   0.237   1.4344   2.0264  -0.3585
 10V  H11  H  HCH2  0   0.267   1.5128   1.6263   1.3535
 10V  H12  H  HCH3  0   0.262   0.7541  -4.8144   0.1007
 10V  H13  H  HCH3  0   0.263  -0.9256  -4.2357   0.1050
 10V  H14  H  HCH3  0   0.281  -0.0286  -4.3389  -1.4063
 10V  H15  H  HCH2  0   0.247   3.2795  -1.4197  -0.0919
 10V  H16  H  HCH2  0   0.263   3.5742  -0.4613  -1.5411
 10V  H17  H  HCR6  0   0.289   7.4541   1.6404   0.3087
 10V  H18  H  HCR6  0   0.252   4.5053   4.7069   0.7013
 10V  H19  H  HCR6  0   0.262   6.9039   4.0459   0.5627
 10V  H20  H  HCH3  0   0.230   7.4385  -0.4620  -0.7151
 10V  H21  H  HCH3  0   0.229   7.4442  -0.5310   1.0617
 10V  H22  H  HCH3  0   0.261   6.8021  -1.8910   0.1212
 10V  H23  H  HNH1  0   0.398   0.6626  -0.4883   2.1253
 10V  O2   O  O2    0  -0.468   5.5679  -0.3020   0.1874

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
 10V  C6   C1   aromatic  1.387  0.020  1.387
 10V  C6   C5   aromatic  1.397  0.020  1.397
 10V  C1   C2   aromatic  1.384  0.020  1.384
 10V  C10  S1   aromatic  1.708  0.020  1.708
 10V  C10  C7   aromatic  1.366  0.020  1.366
 10V  S1   C9   aromatic  1.726  0.020  1.726
 10V  C23  N6   aromatic  1.333  0.020  1.333
 10V  C23  C24  aromatic  1.374  0.020  1.374
 10V  C5   C7   single    1.468  0.020  1.468
 10V  C5   C4   aromatic  1.392  0.020  1.392
 10V  C2   C3   aromatic  1.394  0.020  1.394
 10V  C7   C8   aromatic  1.429  0.020  1.429
 10V  N6   C21  aromatic  1.322  0.020  1.322
 10V  C24  C19  aromatic  1.397  0.020  1.397
 10V  C9   C8   aromatic  1.360  0.020  1.360
 10V  C9   C11  single    1.506  0.020  1.506
 10V  C4   C3   aromatic  1.392  0.020  1.392
 10V  C3   C17  single    1.428  0.020  1.428
 10V  C15  C11  single    1.527  0.020  1.527
 10V  C15  N5   single    1.448  0.020  1.448
 10V  C21  N5   single    1.373  0.020  1.373
 10V  C21  C20  aromatic  1.422  0.020  1.422
 10V  C11  C12  single    1.525  0.020  1.525
 10V  C11  N2   single    1.437  0.020  1.437
 10V  N5   C18  single    1.461  0.020  1.461
 10V  C19  C20  aromatic  1.379  0.020  1.379
 10V  C17  N4   triple    1.152  0.020  1.152
 10V  C12  C18  single    1.535  0.020  1.535
 10V  C12  C13  single    1.502  0.020  1.502
 10V  C20  O2   single    1.346  0.020  1.346
 10V  N2   C14  single    1.364  0.020  1.364
 10V  C13  O1   double    1.213  0.020  1.213
 10V  C13  N1   single    1.373  0.020  1.373
 10V  O2   C25  single    1.413  0.020  1.413
 10V  C14  N1   single    1.405  0.020  1.405
 10V  C14  N3   double    1.272  0.020  1.272
 10V  N1   C16  single    1.455  0.020  1.455
 10V  C1   H1   single    0.930  0.020  1.080
 10V  C2   H2   single    0.930  0.020  1.080
 10V  C4   H3   single    0.930  0.020  1.080
 10V  C6   H4   single    0.930  0.020  1.080
 10V  C8   H5   single    0.930  0.020  1.080
 10V  C10  H6   single    0.930  0.020  1.080
 10V  C12  H7   single    0.970  0.020  1.090
 10V  N3   H8   single    0.890  0.020  1.040
 10V  C15  H10  single    0.970  0.020  1.090
 10V  C15  H11  single    0.970  0.020  1.090
 10V  C16  H12  single    0.970  0.020  1.090
 10V  C16  H13  single    0.970  0.020  1.090
 10V  C16  H14  single    0.970  0.020  1.090
 10V  C18  H15  single    0.970  0.020  1.090
 10V  C18  H16  single    0.970  0.020  1.090
 10V  C19  H17  single    0.930  0.020  1.080
 10V  C23  H18  single    0.930  0.020  1.080
 10V  C24  H19  single    0.930  0.020  1.080
 10V  C25  H20  single    0.970  0.020  1.090
 10V  C25  H21  single    0.970  0.020  1.090
 10V  C25  H22  single    0.970  0.020  1.090
 10V  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
 10V  H1   C1   C6   119.76  3.000
 10V  H1   C1   C2   119.81  3.000
 10V  C6   C1   C2   120.42  3.000
 10V  H2   C2   C3   120.40  3.000
 10V  H2   C2   C1   120.88  3.000
 10V  C3   C2   C1   118.72  3.000
 10V  C17  C3   C4   119.34  3.000
 10V  C17  C3   C2   119.58  3.000
 10V  C4   C3   C2   121.07  3.000
 10V  H3   C4   C5   120.35  3.000
 10V  H3   C4   C3   119.48  3.000
 10V  C5   C4   C3   120.16  3.000
 10V  C7   C5   C6   120.84  3.000
 10V  C7   C5   C4   120.74  3.000
 10V  C6   C5   C4   118.42  3.000
 10V  H4   C6   C5   119.95  3.000
 10V  H4   C6   C1   118.84  3.000
 10V  C5   C6   C1   121.20  3.000
 10V  C10  C7   C8   111.64  3.000
 10V  C8   C7   C5   123.98  3.000
 10V  C10  C7   C5   124.38  3.000
 10V  H5   C8   C9   123.30  3.000
 10V  H5   C8   C7   123.22  3.000
 10V  C9   C8   C7   113.47  3.000
 10V  C11  C9   S1   121.57  3.000
 10V  C11  C9   C8   127.78  3.000
 10V  S1   C9   C8   110.64  3.000
 10V  C10  S1   C9    92.19  3.000
 10V  H6   C10  S1   119.78  3.000
 10V  H6   C10  C7   128.13  3.000
 10V  S1   C10  C7   112.06  3.000
 10V  C15  C11  N2   109.27  3.000
 10V  N2   C11  C12  106.06  3.000
 10V  C15  C11  C12  101.08  3.000
 10V  N2   C11  C9   111.95  3.000
 10V  C12  C11  C9   114.31  3.000
 10V  C15  C11  C9   113.41  3.000
 10V  H7   C12  C18  109.46  3.000
 10V  H7   C12  C13  107.21  3.000
 10V  C18  C12  C13  113.12  3.000
 10V  H7   C12  C11  110.16  3.000
 10V  C13  C12  C11  113.40  3.000
 10V  C18  C12  C11  103.47  3.000
 10V  O1   C13  N1   122.20  3.000
 10V  N1   C13  C12  116.60  3.000
 10V  O1   C13  C12  121.20  3.000
 10V  C16  N1   C14  117.23  3.000
 10V  C16  N1   C13  118.96  3.000
 10V  C14  N1   C13  123.63  3.000
 10V  N3   C14  N2   119.36  3.000
 10V  N3   C14  N1   124.88  3.000
 10V  N2   C14  N1   115.75  3.000
 10V  H23  N2   C14  113.79  3.000
 10V  H23  N2   C11  117.76  3.000
 10V  C14  N2   C11  122.86  3.000
 10V  H8   N3   C14  113.62  3.000
 10V  H11  C15  H10  107.13  3.000
 10V  H11  C15  N5   112.14  3.000
 10V  H10  C15  N5   112.54  3.000
 10V  H11  C15  C11  111.78  3.000
 10V  H10  C15  C11  109.97  3.000
 10V  N5   C15  C11  103.34  3.000
 10V  H14  C16  H13  108.32  3.000
 10V  H14  C16  H12  108.47  3.000
 10V  H13  C16  H12  109.27  3.000
 10V  H14  C16  N1   109.26  3.000
 10V  H13  C16  N1   110.13  3.000
 10V  H12  C16  N1   111.32  3.000
 10V  N4   C17  C3   180.00  3.000
 10V  H16  C18  H15  107.80  3.000
 10V  H16  C18  N5   112.53  3.000
 10V  H15  C18  N5   111.82  3.000
 10V  H16  C18  C12  110.00  3.000
 10V  H15  C18  C12  111.31  3.000
 10V  N5   C18  C12  103.38  3.000
 10V  C21  N5   C18  124.46  3.000
 10V  C18  N5   C15  111.61  3.000
 10V  C21  N5   C15  118.35  3.000
 10V  H17  C19  C24  119.38  3.000
 10V  H17  C19  C20  120.91  3.000
 10V  C24  C19  C20  119.69  3.000
 10V  O2   C20  C21  116.99  3.000
 10V  O2   C20  C19  124.86  3.000
 10V  C21  C20  C19  118.14  3.000
 10V  N6   C21  C20  121.02  3.000
 10V  C20  C21  N5   122.11  3.000
 10V  N6   C21  N5   116.81  3.000
 10V  H18  C23  N6   116.16  3.000
 10V  H18  C23  C24  120.99  3.000
 10V  N6   C23  C24  122.85  3.000
 10V  H19  C24  C23  121.21  3.000
 10V  H19  C24  C19  120.75  3.000
 10V  C23  C24  C19  118.03  3.000
 10V  H22  C25  H21  108.91  3.000
 10V  H22  C25  H20  108.91  3.000
 10V  H21  C25  H20  108.84  3.000
 10V  H22  C25  O2   106.54  3.000
 10V  H21  C25  O2   111.76  3.000
 10V  H20  C25  O2   111.80  3.000
 10V  C23  N6   C21  120.15  3.000
 10V  C25  O2   C20  118.31  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
 10V  CONST_01  C7   C5   C6   C1   180.00   0.0  0
 10V  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 10V  CONST_03  C4   C3   C2   C1     0.00   0.0  0
 10V  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 10V  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 10V  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 10V  CONST_07  C6   C5   C4   C3     0.00   0.0  0
 10V  CONST_08  C7   C5   C4   C3   180.00   0.0  0
 10V  CONST_11  S1   C10  C7   C5   180.00   0.0  0
 10V  CONST_12  C9   C8   C7   C5   180.00   0.0  0
 10V  CONST_15  C9   S1   C10  C7     0.00   0.0  0
 10V  CONST_16  S1   C9   C8   C7     0.00   0.0  0
 10V  CONST_17  S1   C10  C7   C8     0.00   0.0  0
 10V  CONST_18  C10  S1   C9   C8     0.00   0.0  0
 10V  CONST_19  C10  C7   C8   C9     0.00   0.0  0
 10V  CONST_20  N6   C23  C24  C19    0.00   0.0  0
 10V  CONST_21  N6   C21  C20  C19    0.00   0.0  0
 10V  CONST_22  C23  N6   C21  C20    0.00   0.0  0
 10V  CONST_23  C23  C24  C19  C20    0.00   0.0  0
 10V  CONST_24  C24  C23  N6   C21    0.00   0.0  0
 10V  CONST_25  C24  C19  C20  C21    0.00   0.0  0
 10V  CONST_26  C11  C9   C8   C7   180.00   0.0  0
 10V  CONST_27  C11  C9   S1   C10  180.00   0.0  0
 10V  CONST_28  C23  N6   C21  N5   180.00   0.0  0
 10V  CONST_29  C19  C20  C21  N5   180.00   0.0  0
 10V  CONST_31  C14  N1   C13  C12    0.00   0.0  0
 10V  CONST_32  N2   C14  N1   C13    0.00   0.0  0
 10V  CONST_33  C17  C3   C2   C1   180.00   0.0  0
 10V  CONST_34  C17  C3   C4   C5   180.00   0.0  0
 10V  CONST_35  O2   C20  C21  N5     0.00   0.0  0
 10V  CONST_36  O2   C20  C19  C24  180.00   0.0  0
 10V  CONST_37  N6   C21  C20  O2   180.00   0.0  0
 10V  CONST_39  C16  N1   C13  C12  180.00   0.0  0
 10V  CONST_40  N3   C14  N1   C13  180.00   0.0  0
 10V  CONST_41  O1   C13  N1   C14  180.00   0.0  0
 10V  CONST_42  C16  N1   C14  N2   180.00   0.0  0
 10V  CONST_43  H4   C6   C1   C2   180.00   0.0  0
 10V  CONST_44  H3   C4   C3   C2   180.00   0.0  0
 10V  CONST_45  H1   C1   C2   C3   180.00   0.0  0
 10V  CONST_46  H2   C2   C3   C4   180.00   0.0  0
 10V  CONST_47  H6   C10  C7   C5     0.00   0.0  0
 10V  CONST_48  H5   C8   C7   C5     0.00   0.0  0
 10V  CONST_49  H18  C23  C24  C19  180.00   0.0  0
 10V  CONST_50  H19  C24  C19  C20  180.00   0.0  0
 10V  CONST_51  H17  C19  C20  C21  180.00   0.0  0
 10V  CONST_52  H23  N2   C14  N1   180.00   0.0  0
 10V  CONST_53  C16  N1   C14  N3     0.00   0.0  0
 10V  CONST_54  O1   C13  N1   C16    0.00   0.0  0
 10V  CONST_55  H8   N3   C14  N1     0.00   0.0  0
 10V  Var_01    C21  N5   C15  C11  176.63  30.0  1
 10V  Var_02    C15  N5   C18  C12    3.58  30.0  1
 10V  Var_03    N6   C21  N5   C15   -4.30  30.0  1
 10V  Var_04    H12  C16  N1   C13  105.28  30.0  3
 10V  Var_05    H20  C25  O2   C20  -61.58  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
 10V  chir_01  C11  C15  C12  N2   negativ
 10V  chir_02  C12  C11  C18  C13  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
 10V  plan-1  C5   0.020
 10V  plan-1  C7   0.020
 10V  plan-1  C8   0.020
 10V  plan-1  C9   0.020
 10V  plan-1  S1   0.020
 10V  plan-1  C10  0.020
 10V  plan-1  C11  0.020
 10V  plan-1  H5   0.020
 10V  plan-1  H6   0.020
 10V  plan-2  C1   0.020
 10V  plan-2  C2   0.020
 10V  plan-2  C3   0.020
 10V  plan-2  C4   0.020
 10V  plan-2  C5   0.020
 10V  plan-2  C6   0.020
 10V  plan-2  C7   0.020
 10V  plan-2  C17  0.020
 10V  plan-2  N4   0.020
 10V  plan-2  H1   0.020
 10V  plan-2  H2   0.020
 10V  plan-2  H3   0.020
 10V  plan-2  H4   0.020
 10V  plan-3  N5   0.020
 10V  plan-3  C19  0.020
 10V  plan-3  C20  0.020
 10V  plan-3  C21  0.020
 10V  plan-3  C23  0.020
 10V  plan-3  C24  0.020
 10V  plan-3  N6   0.020
 10V  plan-3  H17  0.020
 10V  plan-3  H18  0.020
 10V  plan-3  H19  0.020
 10V  plan-3  O2   0.020
 10V  plan-4  C11  0.020
 10V  plan-4  C12  0.020
 10V  plan-4  C13  0.020
 10V  plan-4  N1   0.020
 10V  plan-4  C14  0.020
 10V  plan-4  N2   0.020
 10V  plan-4  N3   0.020
 10V  plan-4  C16  0.020
 10V  plan-4  O1   0.020
 10V  plan-4  H8   0.020
 10V  plan-4  H23  0.020

