# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 19:26:41 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 2-{(2E,4aR,7aR)-7a-[4-(3-cyanophenyl)thiophen-2-yl]-2-imino-3-methyl-4-oxooctahydro-6H-pyrrolo[3,4-d]pyrimidin-6-yl}pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N)N[C@]2(CN(C[C@H]2C1=O)c3ncccc3C#N)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
 10Q  10Q  2-{(2E,4aR,7aR)-7a-[4-(3-cyanophenyl)thiophen-2-yl]-2-imino-3-methyl-4-oxooctahydro-6H-pyrrolo[3,4-d]pyrimidin-6-yl}pyridine-3-carbonitrile  ligand  52  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_10Q
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
 10Q  C1   C  CR6   0  -0.034  -0.8244   0.0047   0.0543
 10Q  C2   C  CR16  0  -0.418  -1.5683   0.7115  -1.0744
 10Q  N1   N  NR6   0  -0.541  -0.6245   2.7787  -0.1646
 10Q  C3   C  CR6   0   0.622  -0.5791   2.2074   1.1180
 10Q  C4   C  CR6   0   0.599  -1.1510   2.1439  -1.2608
 10Q  N2   N  NR16  0  -0.653  -0.9076   0.8826   1.1893
 10Q  C5   C  CR5   0  -0.091   0.5974  -0.3620  -0.2782
 10Q  N3   N  NT    0  -0.507  -3.0546  -0.6941   0.0551
 10Q  C6   C  CH2   0  -0.214  -1.7192  -1.2084   0.3043
 10Q  C7   C  CH2   0  -0.264  -3.0402   0.5620  -0.6764
 10Q  C8   C  CR15  0  -0.286   1.7256  -0.0218   0.4005
 10Q  C9   C  CR5   0   0.210   2.9224  -0.5138  -0.2057
 10Q  S1   S  S2    0   0.254   0.9842  -1.3011  -1.6742
 10Q  C10  C  CR15  0  -0.567   2.6569  -1.2253  -1.3407
 10Q  C11  C  CR6   0   0.567  -4.1371  -1.4646   0.2825
 10Q  N4   N  NS    0  -0.248   8.6770   0.0476  -1.5821
 10Q  N5   N  N     0  -0.683  -0.2835   2.8332   2.1839
 10Q  C12  C  CR6   0   0.120   4.2694  -0.2827   0.3316
 10Q  C13  C  CR6   0  -0.129  -5.4813  -1.0258   0.1366
 10Q  C14  C  CSP   0   0.053   7.7684   0.0156  -0.8744
 10Q  O1   O  O     0  -0.439  -1.2841   2.6991  -2.3309
 10Q  C15  C  CR16  0  -0.125  -6.5079  -1.9476   0.3435
 10Q  C16  C  CR16  0  -0.316   5.3733  -0.2326  -0.5148
 10Q  C17  C  CH3   0  -0.576  -0.1830   4.1587  -0.2950
 10Q  C18  C  CR6   0   0.032   6.6472  -0.0309   0.0089
 10Q  N6   N  N     0  -0.471  -3.8805  -2.7144   0.6801
 10Q  C19  C  CR16  0  -0.301   4.4738  -0.1142   1.7028
 10Q  C20  C  CR16  0  -0.028  -4.8733  -3.5581   0.8904
 10Q  C21  C  CR16  0  -0.226   5.7442   0.0938   2.2189
 10Q  C22  C  CR16  0  -0.363  -6.2135  -3.2426   0.7151
 10Q  C23  C  CR16  0  -0.254   6.8437   0.1360   1.3793
 10Q  C24  C  CSP   0   0.033  -5.8660   0.3153  -0.1301
 10Q  N7   N  NS    0  -0.256  -6.2457   1.3891  -0.3162
 10Q  H1   H  HCR6  0   0.316  -1.3987   0.1991  -2.0229
 10Q  H2   H  HCH2  0   0.255  -1.4658  -2.0234  -0.3796
 10Q  H3   H  HCH2  0   0.278  -1.6064  -1.5882   1.3206
 10Q  H4   H  HCH2  0   0.268  -3.3756   1.3975  -0.0580
 10Q  H5   H  HCH2  0   0.284  -3.6712   0.5205  -1.5648
 10Q  H6   H  HCR5  0   0.270   1.7205   0.5817   1.2978
 10Q  H7   H  HCR5  0   0.302   3.3556  -1.7334  -1.9884
 10Q  H8   H  H     0   0.358  -0.1451   3.8247   2.0475
 10Q  H10  H  HCR6  0   0.294  -7.5343  -1.6268   0.2250
 10Q  H11  H  HCR6  0   0.279   5.2468  -0.3346  -1.5846
 10Q  H12  H  HCH3  0   0.264   0.7972   4.2822   0.1617
 10Q  H13  H  HCH3  0   0.282  -0.1035   4.4116  -1.3451
 10Q  H14  H  HCH3  0   0.263  -0.8880   4.8456   0.1735
 10Q  H15  H  HCR6  0   0.271   3.6339  -0.1608   2.3835
 10Q  H16  H  HCR6  0   0.277  -4.5866  -4.5517   1.2162
 10Q  H17  H  HCR6  0   0.278   5.8768   0.2160   3.2851
 10Q  H18  H  HCR6  0   0.277  -6.9883  -3.9749   0.8849
 10Q  H19  H  HCR6  0   0.285   7.8374   0.2964   1.7739
 10Q  H20  H  HNR6  0   0.400  -0.7561   0.4795   2.1023

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
 10Q  N7   C24  triple    1.154  0.020  1.154
 10Q  C10  S1   aromatic  1.707  0.020  1.707
 10Q  C10  C9   aromatic  1.366  0.020  1.366
 10Q  S1   C5   aromatic  1.726  0.020  1.726
 10Q  C24  C13  single    1.420  0.020  1.420
 10Q  C19  C21  aromatic  1.387  0.020  1.387
 10Q  C19  C12  aromatic  1.396  0.020  1.396
 10Q  C21  C23  aromatic  1.384  0.020  1.384
 10Q  C9   C12  single    1.468  0.020  1.468
 10Q  C9   C8   aromatic  1.429  0.020  1.429
 10Q  C12  C16  aromatic  1.392  0.020  1.392
 10Q  C13  C15  aromatic  1.395  0.020  1.395
 10Q  C13  C11  aromatic  1.421  0.020  1.421
 10Q  C15  C22  aromatic  1.379  0.020  1.379
 10Q  C5   C8   aromatic  1.360  0.020  1.360
 10Q  C5   C1   single    1.505  0.020  1.505
 10Q  C6   N3   single    1.453  0.020  1.453
 10Q  C6   C1   single    1.528  0.020  1.528
 10Q  C23  C18  aromatic  1.394  0.020  1.394
 10Q  C11  N3   single    1.348  0.020  1.348
 10Q  C11  N6   aromatic  1.336  0.020  1.336
 10Q  N3   C7   single    1.454  0.020  1.454
 10Q  C16  C18  aromatic  1.392  0.020  1.392
 10Q  C1   C2   single    1.526  0.020  1.526
 10Q  C1   N2   single    1.437  0.020  1.437
 10Q  C22  C20  aromatic  1.388  0.020  1.388
 10Q  C18  C14  single    1.428  0.020  1.428
 10Q  C2   C7   single    1.532  0.020  1.532
 10Q  C2   C4   single    1.503  0.020  1.503
 10Q  N6   C20  aromatic  1.320  0.020  1.320
 10Q  N2   C3   single    1.367  0.020  1.367
 10Q  C14  N4   triple    1.152  0.020  1.152
 10Q  C4   O1   double    1.213  0.020  1.213
 10Q  C4   N1   single    1.372  0.020  1.372
 10Q  C3   N1   single    1.405  0.020  1.405
 10Q  C3   N5   double    1.271  0.020  1.271
 10Q  N1   C17  single    1.455  0.020  1.455
 10Q  C2   H1   single    0.970  0.020  1.090
 10Q  C6   H2   single    0.970  0.020  1.090
 10Q  C6   H3   single    0.970  0.020  1.090
 10Q  C7   H4   single    0.970  0.020  1.090
 10Q  C7   H5   single    0.970  0.020  1.090
 10Q  C8   H6   single    0.930  0.020  1.080
 10Q  C10  H7   single    0.930  0.020  1.080
 10Q  N5   H8   single    0.890  0.020  1.040
 10Q  C15  H10  single    0.930  0.020  1.080
 10Q  C16  H11  single    0.930  0.020  1.080
 10Q  C17  H12  single    0.970  0.020  1.090
 10Q  C17  H13  single    0.970  0.020  1.090
 10Q  C17  H14  single    0.970  0.020  1.090
 10Q  C19  H15  single    0.930  0.020  1.080
 10Q  C20  H16  single    0.930  0.020  1.080
 10Q  C21  H17  single    0.930  0.020  1.080
 10Q  C22  H18  single    0.930  0.020  1.080
 10Q  C23  H19  single    0.930  0.020  1.080
 10Q  N2   H20  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
 10Q  C6   C1   C5   113.32  3.000
 10Q  C6   C1   N2   108.77  3.000
 10Q  C5   C1   N2   112.20  3.000
 10Q  N2   C1   C2   105.84  3.000
 10Q  C6   C1   C2   101.73  3.000
 10Q  C5   C1   C2   114.20  3.000
 10Q  H1   C2   C7   109.22  3.000
 10Q  H1   C2   C4   107.24  3.000
 10Q  C7   C2   C4   113.07  3.000
 10Q  H1   C2   C1   110.47  3.000
 10Q  C4   C2   C1   113.44  3.000
 10Q  C7   C2   C1   103.36  3.000
 10Q  C17  N1   C4   118.94  3.000
 10Q  C17  N1   C3   117.24  3.000
 10Q  C4   N1   C3   123.63  3.000
 10Q  N5   C3   N2   119.31  3.000
 10Q  N5   C3   N1   124.96  3.000
 10Q  N2   C3   N1   115.72  3.000
 10Q  O1   C4   N1   122.36  3.000
 10Q  N1   C4   C2   116.64  3.000
 10Q  O1   C4   C2   121.00  3.000
 10Q  H20  N2   C3   113.46  3.000
 10Q  H20  N2   C1   117.49  3.000
 10Q  C3   N2   C1   122.47  3.000
 10Q  S1   C5   C8   110.72  3.000
 10Q  C8   C5   C1   127.76  3.000
 10Q  S1   C5   C1   121.51  3.000
 10Q  C11  N3   C7   125.93  3.000
 10Q  C7   N3   C6   112.53  3.000
 10Q  C11  N3   C6   120.46  3.000
 10Q  H3   C6   H2   107.42  3.000
 10Q  H3   C6   N3   112.22  3.000
 10Q  H2   C6   N3   111.68  3.000
 10Q  H3   C6   C1   111.61  3.000
 10Q  H2   C6   C1   110.71  3.000
 10Q  N3   C6   C1   103.25  3.000
 10Q  H5   C7   H4   108.22  3.000
 10Q  H5   C7   N3   111.80  3.000
 10Q  H4   C7   N3   111.90  3.000
 10Q  H5   C7   C2   110.37  3.000
 10Q  H4   C7   C2   111.56  3.000
 10Q  N3   C7   C2   102.98  3.000
 10Q  H6   C8   C9   123.23  3.000
 10Q  H6   C8   C5   123.36  3.000
 10Q  C9   C8   C5   113.39  3.000
 10Q  C12  C9   C10  124.36  3.000
 10Q  C12  C9   C8   123.98  3.000
 10Q  C10  C9   C8   111.66  3.000
 10Q  C10  S1   C5    92.14  3.000
 10Q  H7   C10  S1   119.73  3.000
 10Q  H7   C10  C9   128.16  3.000
 10Q  S1   C10  C9   112.09  3.000
 10Q  N6   C11  C13  120.05  3.000
 10Q  N6   C11  N3   115.50  3.000
 10Q  C13  C11  N3   124.45  3.000
 10Q  H8   N5   C3   113.69  3.000
 10Q  C19  C12  C16  118.46  3.000
 10Q  C16  C12  C9   120.70  3.000
 10Q  C19  C12  C9   120.83  3.000
 10Q  C24  C13  C15  116.89  3.000
 10Q  C15  C13  C11  118.47  3.000
 10Q  C24  C13  C11  124.53  3.000
 10Q  C18  C14  N4   180.00  3.000
 10Q  H10  C15  C22  120.69  3.000
 10Q  H10  C15  C13  119.08  3.000
 10Q  C22  C15  C13  120.22  3.000
 10Q  H11  C16  C18  119.52  3.000
 10Q  H11  C16  C12  120.33  3.000
 10Q  C18  C16  C12  120.15  3.000
 10Q  H14  C17  H13  108.48  3.000
 10Q  H14  C17  H12  109.31  3.000
 10Q  H13  C17  H12  108.31  3.000
 10Q  H14  C17  N1   111.28  3.000
 10Q  H13  C17  N1   109.31  3.000
 10Q  H12  C17  N1   110.09  3.000
 10Q  C23  C18  C16  121.07  3.000
 10Q  C16  C18  C14  119.38  3.000
 10Q  C23  C18  C14  119.55  3.000
 10Q  C20  N6   C11  120.05  3.000
 10Q  H15  C19  C21  118.90  3.000
 10Q  H15  C19  C12  119.92  3.000
 10Q  C21  C19  C12  121.17  3.000
 10Q  H16  C20  C22  120.11  3.000
 10Q  H16  C20  N6   115.77  3.000
 10Q  C22  C20  N6   124.12  3.000
 10Q  H17  C21  C23  119.82  3.000
 10Q  H17  C21  C19  119.75  3.000
 10Q  C23  C21  C19  120.42  3.000
 10Q  H18  C22  C20  121.27  3.000
 10Q  H18  C22  C15  121.75  3.000
 10Q  C20  C22  C15  116.97  3.000
 10Q  H19  C23  C21  120.88  3.000
 10Q  H19  C23  C18  120.40  3.000
 10Q  C21  C23  C18  118.72  3.000
 10Q  N7   C24  C13  180.00  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
 10Q  CONST_01  C9   C10  S1   C5      0.00   0.0  0
 10Q  CONST_02  C10  C9   C8   C5      0.00   0.0  0
 10Q  CONST_03  C12  C9   C8   C5    180.00   0.0  0
 10Q  CONST_04  S1   C10  C9   C8      0.00   0.0  0
 10Q  CONST_07  C10  S1   C5   C8      0.00   0.0  0
 10Q  CONST_08  C21  C19  C12  C9    180.00   0.0  0
 10Q  CONST_09  C18  C16  C12  C9    180.00   0.0  0
 10Q  CONST_10  S1   C5   C8   C9      0.00   0.0  0
 10Q  CONST_11  C12  C9   C10  S1    180.00   0.0  0
 10Q  CONST_14  C22  C15  C13  C11     0.00   0.0  0
 10Q  CONST_15  C22  C20  N6   C11     0.00   0.0  0
 10Q  CONST_16  C23  C21  C19  C12     0.00   0.0  0
 10Q  CONST_17  C23  C18  C16  C12     0.00   0.0  0
 10Q  CONST_18  C20  C22  C15  C13     0.00   0.0  0
 10Q  CONST_19  C20  N6   C11  C13     0.00   0.0  0
 10Q  CONST_20  N6   C11  C13  C15     0.00   0.0  0
 10Q  CONST_21  N6   C20  C22  C15     0.00   0.0  0
 10Q  CONST_22  C21  C19  C12  C16     0.00   0.0  0
 10Q  CONST_23  C21  C23  C18  C16     0.00   0.0  0
 10Q  CONST_24  C19  C21  C23  C18     0.00   0.0  0
 10Q  CONST_25  C19  C12  C16  C18     0.00   0.0  0
 10Q  CONST_26  C10  S1   C5   C1    180.00   0.0  0
 10Q  CONST_27  C9   C8   C5   C1    180.00   0.0  0
 10Q  CONST_28  C15  C13  C11  N3    180.00   0.0  0
 10Q  CONST_29  C20  N6   C11  N3    180.00   0.0  0
 10Q  CONST_31  C3   N1   C4   C2      0.00   0.0  0
 10Q  CONST_32  N2   C3   N1   C4      0.00   0.0  0
 10Q  CONST_33  C24  C13  C11  N3      0.00   0.0  0
 10Q  CONST_34  C14  C18  C16  C12   180.00   0.0  0
 10Q  CONST_35  C21  C23  C18  C14   180.00   0.0  0
 10Q  CONST_36  C24  C13  C11  N6    180.00   0.0  0
 10Q  CONST_37  C24  C13  C15  C22   180.00   0.0  0
 10Q  CONST_39  C17  N1   C4   C2    180.00   0.0  0
 10Q  CONST_40  O1   C4   N1   C3    180.00   0.0  0
 10Q  CONST_41  N5   C3   N1   C4    180.00   0.0  0
 10Q  CONST_42  C17  N1   C3   N2    180.00   0.0  0
 10Q  CONST_43  H6   C8   C5   C1      0.00   0.0  0
 10Q  CONST_44  H7   C10  S1   C5    180.00   0.0  0
 10Q  CONST_45  H15  C19  C12  C9      0.00   0.0  0
 10Q  CONST_46  H11  C16  C12  C9      0.00   0.0  0
 10Q  CONST_47  H10  C15  C13  C11   180.00   0.0  0
 10Q  CONST_48  H16  C20  N6   C11   180.00   0.0  0
 10Q  CONST_49  H17  C21  C19  C12   180.00   0.0  0
 10Q  CONST_50  H18  C22  C15  C13   180.00   0.0  0
 10Q  CONST_51  H19  C23  C18  C16   180.00   0.0  0
 10Q  CONST_52  H20  N2   C3   N1    180.00   0.0  0
 10Q  CONST_53  C17  N1   C3   N5      0.00   0.0  0
 10Q  CONST_54  C17  N1   C4   O1      0.00   0.0  0
 10Q  CONST_55  H8   N5   C3   N1      0.00   0.0  0
 10Q  Var_01    C11  N3   C6   C1   -174.69  30.0  1
 10Q  Var_02    C6   N3   C7   C2      8.51  30.0  1
 10Q  Var_03    C13  C11  N3   C6    176.48  30.0  1
 10Q  Var_04    H12  C17  N1   C3     51.20  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
 10Q  chir_01  C1  C6  C2  N2  negativ
 10Q  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
 10Q  plan-1  C1   0.020
 10Q  plan-1  C5   0.020
 10Q  plan-1  C8   0.020
 10Q  plan-1  C9   0.020
 10Q  plan-1  S1   0.020
 10Q  plan-1  C10  0.020
 10Q  plan-1  C12  0.020
 10Q  plan-1  H6   0.020
 10Q  plan-1  H7   0.020
 10Q  plan-2  N3   0.020
 10Q  plan-2  C11  0.020
 10Q  plan-2  C13  0.020
 10Q  plan-2  C15  0.020
 10Q  plan-2  N6   0.020
 10Q  plan-2  C20  0.020
 10Q  plan-2  C22  0.020
 10Q  plan-2  C24  0.020
 10Q  plan-2  N7   0.020
 10Q  plan-2  H10  0.020
 10Q  plan-2  H16  0.020
 10Q  plan-2  H18  0.020
 10Q  plan-3  C9   0.020
 10Q  plan-3  N4   0.020
 10Q  plan-3  C12  0.020
 10Q  plan-3  C14  0.020
 10Q  plan-3  C16  0.020
 10Q  plan-3  C18  0.020
 10Q  plan-3  C19  0.020
 10Q  plan-3  C21  0.020
 10Q  plan-3  C23  0.020
 10Q  plan-3  H11  0.020
 10Q  plan-3  H15  0.020
 10Q  plan-3  H17  0.020
 10Q  plan-3  H19  0.020
 10Q  plan-4  C1   0.020
 10Q  plan-4  C2   0.020
 10Q  plan-4  N1   0.020
 10Q  plan-4  C3   0.020
 10Q  plan-4  C4   0.020
 10Q  plan-4  N2   0.020
 10Q  plan-4  N5   0.020
 10Q  plan-4  O1   0.020
 10Q  plan-4  C17  0.020
 10Q  plan-4  H8   0.020
 10Q  plan-4  H20  0.020

