# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 00:11:49 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (8S)-3,3-difluoro-8-(2'-fluoro-3'-methoxybiphenyl-3-yl)-8-(pyridin-4-yl)-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1F)c2cccc(c2)[C@]3(N=C(N)N4CC(F)(F)CN=C34)c5ccncc5
#
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
 QN7  QN7  (8S)-3,3-difluoro-8-(2'-fluoro-3'-methoxybiphenyl-3-yl)-8-(pyridin-4-yl)-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine  ligand  53  33  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QN7
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
 QN7  C1    C  CH3   0  -0.437   8.0531  -0.0700  -0.2543
 QN7  O2    O  O2    0  -0.466   6.7927   0.0710   0.3740
 QN7  C3    C  CR6   0   0.255   5.7301  -0.5083  -0.2052
 QN7  C4    C  CR16  0  -0.386   5.7511  -1.2538  -1.3776
 QN7  C5    C  CR16  0  -0.245   4.5683  -1.7900  -1.8769
 QN7  C6    C  CR16  0  -0.306   3.3683  -1.5958  -1.2210
 QN7  C7    C  CR6   0  -0.143   3.3191  -0.8556  -0.0349
 QN7  C8    C  CR6   0   0.443   4.5039  -0.3253   0.4391
 QN7  F9    F  F     0  -0.303   4.5011   0.4219   1.5542
 QN7  C10   C  CR6   0   0.122   2.0346  -0.6321   0.6625
 QN7  C11   C  CR16  0  -0.306   1.8815  -0.8973   2.0220
 QN7  C12   C  CR16  0  -0.226   0.6501  -0.7025   2.6272
 QN7  C13   C  CR16  0  -0.320  -0.4347  -0.2379   1.8962
 QN7  C14   C  CR6   0   0.181  -0.2980   0.0254   0.5376
 QN7  C15   C  CR16  0  -0.351   0.9382  -0.1760  -0.0657
 QN7  C16   C  CR5   0  -0.192  -1.4428   0.5967  -0.3068
 QN7  C17   C  CR5   0   0.552  -2.7905  -0.0426   0.0381
 QN7  N18   N  N     0  -0.450  -3.4252   0.0030   1.1294
 QN7  C19   C  CH2   0  -0.414  -4.6931  -0.6956   1.1933
 QN7  C20   C  CT    0   0.685  -4.7901  -1.8357   0.1999
 QN7  C21   C  CH2   0  -0.390  -4.4153  -1.4174  -1.2090
 QN7  N22   N  NR5   0  -0.572  -3.1756  -0.6885  -1.1088
 QN7  C23   C  CR5   0   0.688  -2.2330  -0.4405  -2.0895
 QN7  N24   N  N     0  -0.478  -1.2463   0.2822  -1.7071
 QN7  N25   N  NH2   0  -0.850  -2.3816  -0.9939  -3.3067
 QN7  F26   F  F     0  -0.344  -3.9524  -2.8417   0.5934
 QN7  F27   F  F     0  -0.333  -6.0449  -2.3585   0.1934
 QN7  C28   C  CR6   0   0.258  -1.4715   2.1082  -0.0945
 QN7  C29   C  CR16  0  -0.374  -1.0236   2.9674  -1.0892
 QN7  C30   C  CR16  0  -0.059  -1.0199   4.3340  -0.8494
 QN7  N31   N  N     0  -0.409  -1.4274   4.8855   0.2864
 QN7  C32   C  CR16  0  -0.062  -1.8577   4.0598   1.2345
 QN7  C33   C  CR16  0  -0.365  -1.8960   2.6815   1.0998
 QN7  H11C  H  HCH3  0   0.263   8.7648   0.4740   0.3612
 QN7  H12C  H  HCH3  0   0.232   8.3641  -1.1160  -0.3127
 QN7  H13C  H  HCH3  0   0.232   8.0568   0.3583  -1.2597
 QN7  H4    H  HCR6  0   0.291   6.6771  -1.4233  -1.9096
 QN7  H5    H  HCR6  0   0.264   4.5973  -2.3722  -2.7882
 QN7  H6    H  HCR6  0   0.261   2.4564  -2.0282  -1.6113
 QN7  H11   H  HCR6  0   0.253   2.7096  -1.2808   2.6036
 QN7  H15   H  HCR6  0   0.256   1.0477   0.0337  -1.1212
 QN7  H12   H  HCR6  0   0.258   0.5292  -0.9192   3.6806
 QN7  H13   H  HCR6  0   0.268  -1.3878  -0.0965   2.3873
 QN7  H191  H  HCH2  0   0.275  -4.8385  -1.0843   2.2035
 QN7  H192  H  HCH2  0   0.269  -5.5106   0.0067   1.0059
 QN7  H211  H  HCH2  0   0.301  -4.2936  -2.2998  -1.8396
 QN7  H212  H  HCH2  0   0.292  -5.2086  -0.7964  -1.6317
 QN7  H251  H  HNH2  0   0.415  -3.3058  -1.2131  -3.6418
 QN7  H252  H  HNH2  0   0.407  -1.7529  -0.6605  -4.0194
 QN7  H29   H  HCR6  0   0.268  -0.6819   2.5848  -2.0394
 QN7  H33   H  HCR6  0   0.271  -2.2707   2.0810   1.9160
 QN7  H30   H  HCR6  0   0.261  -0.6710   5.0127  -1.6205
 QN7  H32   H  HCR6  0   0.262  -2.1957   4.5157   2.1589

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
 QN7  C1   O2    single    1.415  0.020  1.415
 QN7  O2   C3    single    1.342  0.020  1.342
 QN7  C3   C4    aromatic  1.390  0.020  1.390
 QN7  C3   C8    aromatic  1.397  0.020  1.397
 QN7  C4   C5    aromatic  1.391  0.020  1.391
 QN7  C5   C6    aromatic  1.381  0.020  1.381
 QN7  C6   C7    aromatic  1.399  0.020  1.399
 QN7  C7   C8    aromatic  1.382  0.020  1.382
 QN7  C7   C10   single    1.479  0.020  1.479
 QN7  C8   F9    single    1.342  0.020  1.342
 QN7  C10  C11   aromatic  1.394  0.020  1.394
 QN7  C10  C15   aromatic  1.393  0.020  1.393
 QN7  C11  C12   aromatic  1.386  0.020  1.386
 QN7  C12  C13   aromatic  1.388  0.020  1.388
 QN7  C13  C14   aromatic  1.391  0.020  1.391
 QN7  C14  C15   aromatic  1.390  0.020  1.390
 QN7  C14  C16   single    1.533  0.020  1.533
 QN7  C16  C17   single    1.531  0.020  1.531
 QN7  C16  N24   single    1.448  0.020  1.448
 QN7  C16  C28   single    1.527  0.020  1.527
 QN7  C17  N18   double    1.263  0.020  1.263
 QN7  C17  N22   single    1.371  0.020  1.371
 QN7  N18  C19   single    1.449  0.020  1.449
 QN7  C19  C20   single    1.515  0.020  1.515
 QN7  C20  C21   single    1.517  0.020  1.517
 QN7  C20  F26   single    1.367  0.020  1.367
 QN7  C20  F27   single    1.359  0.020  1.359
 QN7  C21  N22   single    1.442  0.020  1.442
 QN7  N22  C23   single    1.383  0.020  1.383
 QN7  C23  N24   double    1.281  0.020  1.281
 QN7  C23  N25   single    1.345  0.020  1.345
 QN7  C28  C29   aromatic  1.389  0.020  1.389
 QN7  C28  C33   aromatic  1.391  0.020  1.391
 QN7  C29  C30   aromatic  1.387  0.020  1.387
 QN7  C30  N31   aromatic  1.327  0.020  1.327
 QN7  N31  C32   aromatic  1.329  0.020  1.329
 QN7  C32  C33   aromatic  1.385  0.020  1.385
 QN7  C1   H11C  single    0.970  0.020  1.090
 QN7  C1   H12C  single    0.970  0.020  1.090
 QN7  C1   H13C  single    0.970  0.020  1.090
 QN7  C4   H4    single    0.930  0.020  1.080
 QN7  C5   H5    single    0.930  0.020  1.080
 QN7  C6   H6    single    0.930  0.020  1.080
 QN7  C11  H11   single    0.930  0.020  1.080
 QN7  C15  H15   single    0.930  0.020  1.080
 QN7  C12  H12   single    0.930  0.020  1.080
 QN7  C13  H13   single    0.930  0.020  1.080
 QN7  C19  H191  single    0.970  0.020  1.090
 QN7  C19  H192  single    0.970  0.020  1.090
 QN7  C21  H211  single    0.970  0.020  1.090
 QN7  C21  H212  single    0.970  0.020  1.090
 QN7  N25  H251  single    0.890  0.020  1.040
 QN7  N25  H252  single    0.890  0.020  1.040
 QN7  C29  H29   single    0.930  0.020  1.080
 QN7  C33  H33   single    0.930  0.020  1.080
 QN7  C30  H30   single    0.930  0.020  1.080
 QN7  C32  H32   single    0.930  0.020  1.080

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
 QN7  H13C  C1   H12C  108.96  3.000
 QN7  H13C  C1   H11C  108.82  3.000
 QN7  H12C  C1   H11C  108.84  3.000
 QN7  H13C  C1   O2    111.86  3.000
 QN7  H12C  C1   O2    111.87  3.000
 QN7  H11C  C1   O2    106.37  3.000
 QN7  C3    O2   C1    118.08  3.000
 QN7  C8    C3   C4    118.20  3.000
 QN7  C8    C3   O2    116.07  3.000
 QN7  C4    C3   O2    125.72  3.000
 QN7  H4    C4   C5    119.41  3.000
 QN7  H4    C4   C3    120.81  3.000
 QN7  C5    C4   C3    119.78  3.000
 QN7  H5    C5   C6    119.93  3.000
 QN7  H5    C5   C4    119.14  3.000
 QN7  C6    C5   C4    120.93  3.000
 QN7  H6    C6   C7    119.18  3.000
 QN7  H6    C6   C5    120.31  3.000
 QN7  C7    C6   C5    120.50  3.000
 QN7  C10   C7   C8    121.67  3.000
 QN7  C10   C7   C6    120.69  3.000
 QN7  C8    C7   C6    117.62  3.000
 QN7  F9    C8   C7    119.79  3.000
 QN7  F9    C8   C3    117.24  3.000
 QN7  C7    C8   C3    122.96  3.000
 QN7  C15   C10  C11   119.07  3.000
 QN7  C15   C10  C7    119.12  3.000
 QN7  C11   C10  C7    121.79  3.000
 QN7  H11   C11  C12   119.67  3.000
 QN7  H11   C11  C10   120.51  3.000
 QN7  C12   C11  C10   119.79  3.000
 QN7  H12   C12  C13   119.49  3.000
 QN7  H12   C12  C11   119.75  3.000
 QN7  C13   C12  C11   120.76  3.000
 QN7  H13   C13  C14   120.37  3.000
 QN7  H13   C13  C12   119.55  3.000
 QN7  C14   C13  C12   120.07  3.000
 QN7  C16   C14  C15   118.62  3.000
 QN7  C16   C14  C13   122.37  3.000
 QN7  C15   C14  C13   118.94  3.000
 QN7  H15   C15  C14   119.04  3.000
 QN7  H15   C15  C10   119.60  3.000
 QN7  C14   C15  C10   121.36  3.000
 QN7  C28   C16  N24   110.61  3.000
 QN7  C28   C16  C17   111.44  3.000
 QN7  N24   C16  C17   104.27  3.000
 QN7  C28   C16  C14   107.84  3.000
 QN7  N24   C16  C14   110.51  3.000
 QN7  C17   C16  C14   112.19  3.000
 QN7  N22   C17  N18   126.75  3.000
 QN7  N22   C17  C16   104.80  3.000
 QN7  N18   C17  C16   128.45  3.000
 QN7  C19   N18  C17   117.41  3.000
 QN7  H192  C19  H191  106.70  3.000
 QN7  H192  C19  C20   108.84  3.000
 QN7  H191  C19  C20   109.27  3.000
 QN7  H192  C19  N18   109.69  3.000
 QN7  H191  C19  N18   109.20  3.000
 QN7  C20   C19  N18   112.94  3.000
 QN7  F27   C20  F26   106.50  3.000
 QN7  F27   C20  C21   109.25  3.000
 QN7  F26   C20  C21   108.60  3.000
 QN7  F27   C20  C19   110.58  3.000
 QN7  F26   C20  C19   109.02  3.000
 QN7  C21   C20  C19   112.69  3.000
 QN7  H212  C21  H211  108.48  3.000
 QN7  H212  C21  N22   111.34  3.000
 QN7  H211  C21  N22   110.68  3.000
 QN7  H212  C21  C20   109.68  3.000
 QN7  H211  C21  C20   109.96  3.000
 QN7  N22   C21  C20   106.70  3.000
 QN7  C23   N22  C21   128.88  3.000
 QN7  C23   N22  C17   108.49  3.000
 QN7  C21   N22  C17   122.53  3.000
 QN7  N25   C23  N24   125.95  3.000
 QN7  N25   C23  N22   119.51  3.000
 QN7  N24   C23  N22   114.49  3.000
 QN7  C23   N24  C16   107.84  3.000
 QN7  H252  N25  H251  114.17  3.000
 QN7  H252  N25  C23   115.79  3.000
 QN7  H251  N25  C23   119.47  3.000
 QN7  C33   C28  C29   117.28  3.000
 QN7  C33   C28  C16   122.22  3.000
 QN7  C29   C28  C16   120.46  3.000
 QN7  H29   C29  C30   120.02  3.000
 QN7  H29   C29  C28   120.87  3.000
 QN7  C30   C29  C28   119.11  3.000
 QN7  H30   C30  N31   116.57  3.000
 QN7  H30   C30  C29   119.61  3.000
 QN7  N31   C30  C29   123.82  3.000
 QN7  C32   N31  C30   116.87  3.000
 QN7  H32   C32  C33   119.49  3.000
 QN7  H32   C32  N31   116.60  3.000
 QN7  C33   C32  N31   123.91  3.000
 QN7  H33   C33  C32   119.28  3.000
 QN7  H33   C33  C28   121.70  3.000
 QN7  C32   C33  C28   119.01  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
 QN7  CONST_01  C6    C5   C4   C3     0.00   0.0  0
 QN7  CONST_02  C6    C7   C8   C3     0.00   0.0  0
 QN7  CONST_03  C10   C7   C8   C3   180.00   0.0  0
 QN7  CONST_04  C7    C8   C3   C4     0.00   0.0  0
 QN7  CONST_05  C7    C6   C5   C4     0.00   0.0  0
 QN7  CONST_06  C8    C3   C4   C5     0.00   0.0  0
 QN7  CONST_07  C8    C7   C6   C5     0.00   0.0  0
 QN7  CONST_08  C10   C7   C6   C5   180.00   0.0  0
 QN7  CONST_11  C12   C11  C10  C7   180.00   0.0  0
 QN7  CONST_12  C14   C15  C10  C7   180.00   0.0  0
 QN7  CONST_15  C13   C12  C11  C10    0.00   0.0  0
 QN7  CONST_16  C13   C14  C15  C10    0.00   0.0  0
 QN7  CONST_17  C14   C15  C10  C11    0.00   0.0  0
 QN7  CONST_18  C14   C13  C12  C11    0.00   0.0  0
 QN7  CONST_19  C15   C10  C11  C12    0.00   0.0  0
 QN7  CONST_20  C15   C14  C13  C12    0.00   0.0  0
 QN7  CONST_21  N31   C30  C29  C28    0.00   0.0  0
 QN7  CONST_22  N31   C32  C33  C28    0.00   0.0  0
 QN7  CONST_23  C32   C33  C28  C29    0.00   0.0  0
 QN7  CONST_24  C32   N31  C30  C29    0.00   0.0  0
 QN7  CONST_25  C33   C28  C29  C30    0.00   0.0  0
 QN7  CONST_26  C33   C32  N31  C30    0.00   0.0  0
 QN7  CONST_27  C16   C14  C15  C10  180.00   0.0  0
 QN7  CONST_28  C16   C14  C13  C12  180.00   0.0  0
 QN7  CONST_29  C30   C29  C28  C16  180.00   0.0  0
 QN7  CONST_30  C32   C33  C28  C16  180.00   0.0  0
 QN7  CONST_31  C19   N18  C17  C16  180.00   0.0  0
 QN7  CONST_32  C21   N22  C17  C16  180.00   0.0  0
 QN7  CONST_33  C23   N22  C17  C16    0.00   0.0  0
 QN7  CONST_34  N22   C23  N24  C16    0.00   0.0  0
 QN7  CONST_35  N24   C23  N22  C17    0.00   0.0  0
 QN7  CONST_36  C21   N22  C17  N18    0.00   0.0  0
 QN7  CONST_37  C23   N22  C17  N18  180.00   0.0  0
 QN7  CONST_38  N22   C17  N18  C19    0.00   0.0  0
 QN7  CONST_39  N24   C23  N22  C21  180.00   0.0  0
 QN7  CONST_40  C5    C4   C3   O2   180.00   0.0  0
 QN7  CONST_41  C7    C8   C3   O2   180.00   0.0  0
 QN7  CONST_42  F9    C8   C3   C4   180.00   0.0  0
 QN7  CONST_43  F9    C8   C7   C6   180.00   0.0  0
 QN7  CONST_44  C10   C7   C8   F9     0.00   0.0  0
 QN7  CONST_45  N25   C23  N24  C16  180.00   0.0  0
 QN7  CONST_46  N25   C23  N22  C17  180.00   0.0  0
 QN7  CONST_47  N25   C23  N22  C21    0.00   0.0  0
 QN7  CONST_48  H5    C5   C4   C3   180.00   0.0  0
 QN7  CONST_49  H6    C6   C5   C4   180.00   0.0  0
 QN7  CONST_50  H4    C4   C5   C6   180.00   0.0  0
 QN7  CONST_51  H11   C11  C10  C7     0.00   0.0  0
 QN7  CONST_52  H15   C15  C10  C7     0.00   0.0  0
 QN7  CONST_53  H12   C12  C11  C10  180.00   0.0  0
 QN7  CONST_54  H13   C13  C12  C11  180.00   0.0  0
 QN7  CONST_55  H29   C29  C28  C16    0.00   0.0  0
 QN7  CONST_56  H33   C33  C28  C16    0.00   0.0  0
 QN7  CONST_57  H30   C30  C29  C28  180.00   0.0  0
 QN7  CONST_58  H32   C32  C33  C28  180.00   0.0  0
 QN7  CONST_60  H252  N25  C23  N22  180.00   0.0  0
 QN7  Var_01    C20   C19  N18  C17   25.02  30.0  1
 QN7  Var_02    C20   C21  N22  C17  -24.96  30.0  1
 QN7  Var_03    C21   C20  C19  N18  -50.50  30.0  1
 QN7  Var_04    N22   C21  C20  C19   47.95  30.0  1
 QN7  Var_05    C4    C3   O2   C1     0.49  30.0  2
 QN7  Var_06    H11C  C1   O2   C3   179.42  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
 QN7  chir_01  C16  C17  N24  C28  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
 QN7  plan-1  O2    0.020
 QN7  plan-1  C3    0.020
 QN7  plan-1  C4    0.020
 QN7  plan-1  C5    0.020
 QN7  plan-1  C6    0.020
 QN7  plan-1  C7    0.020
 QN7  plan-1  C8    0.020
 QN7  plan-1  F9    0.020
 QN7  plan-1  C10   0.020
 QN7  plan-1  H4    0.020
 QN7  plan-1  H5    0.020
 QN7  plan-1  H6    0.020
 QN7  plan-2  C7    0.020
 QN7  plan-2  C10   0.020
 QN7  plan-2  C11   0.020
 QN7  plan-2  C12   0.020
 QN7  plan-2  C13   0.020
 QN7  plan-2  C14   0.020
 QN7  plan-2  C15   0.020
 QN7  plan-2  C16   0.020
 QN7  plan-2  H11   0.020
 QN7  plan-2  H15   0.020
 QN7  plan-2  H12   0.020
 QN7  plan-2  H13   0.020
 QN7  plan-3  C16   0.020
 QN7  plan-3  C28   0.020
 QN7  plan-3  C29   0.020
 QN7  plan-3  C30   0.020
 QN7  plan-3  N31   0.020
 QN7  plan-3  C32   0.020
 QN7  plan-3  C33   0.020
 QN7  plan-3  H29   0.020
 QN7  plan-3  H33   0.020
 QN7  plan-3  H30   0.020
 QN7  plan-3  H32   0.020
 QN7  plan-4  C16   0.020
 QN7  plan-4  C17   0.020
 QN7  plan-4  N18   0.020
 QN7  plan-4  C19   0.020
 QN7  plan-4  C21   0.020
 QN7  plan-4  N22   0.020
 QN7  plan-4  C23   0.020
 QN7  plan-4  N24   0.020
 QN7  plan-4  N25   0.020
 QN7  plan-4  H251  0.020
 QN7  plan-4  H252  0.020

