# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 00:47:44 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: (8R)-8-[4-(difluoromethoxy)phenyl]-3,3-difluoro-8-[3-(3-methoxyprop-1-yn-1-yl)phenyl]-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCC#Cc1cccc(c1)[C@]2(N=C(N)N3CC(F)(F)CN=C23)c4ccc(OC(F)F)cc4
#
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
 S8Z  S8Z  (8R)-8-[4-(difluoromethoxy)phenyl]-3,3-difluoro-8-[3-(3-methoxyprop-1-yn-1-yl)phenyl]-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine  ligand  53  33  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S8Z
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
 S8Z  C1    C  CH3   0  -0.402   8.2321   2.5430  -0.7465
 S8Z  O2    O  O2    0  -0.481   7.1089   1.7164  -0.5510
 S8Z  C3    C  CH2   0  -0.327   6.4775   1.9772   0.6768
 S8Z  C4    C  CSP   0  -0.022   5.3227   1.1017   0.8228
 S8Z  C5    C  CSP   0   0.204   4.3626   0.3873   0.9578
 S8Z  C6    C  CR6   0  -0.098   3.2280  -0.4630   1.1178
 S8Z  C7    C  CR16  0  -0.298   3.2507  -1.5033   2.0522
 S8Z  C8    C  CR16  0  -0.235   2.1425  -2.3170   2.1926
 S8Z  C9    C  CR16  0  -0.311   1.0068  -2.1076   1.4176
 S8Z  C10   C  CR6   0   0.210   0.9679  -1.0742   0.4890
 S8Z  C11   C  CR16  0  -0.322   2.0865  -0.2606   0.3437
 S8Z  C12   C  CR5   0  -0.178  -0.2142  -0.8451  -0.4483
 S8Z  C13   C  CR5   0   0.496  -1.4361  -1.6655  -0.0388
 S8Z  N14   N  N     0  -0.423  -2.1429  -1.5317   0.9991
 S8Z  C15   C  CH2   0  -0.419  -3.2440  -2.4601   1.1657
 S8Z  C16   C  CT    0   0.685  -3.0199  -3.7730   0.4419
 S8Z  C17   C  CH2   0  -0.388  -2.6389  -3.5813  -1.0143
 S8Z  N18   N  NR5   0  -0.565  -1.5878  -2.5939  -1.0338
 S8Z  C19   C  CR5   0   0.675  -0.6367  -2.3483  -2.0111
 S8Z  N20   N  N     0  -0.466   0.1480  -1.3655  -1.7577
 S8Z  N21   N  NH2   0  -0.851  -0.5717  -3.1580  -3.0836
 S8Z  F22   F  F     0  -0.331  -4.1254  -4.5587   0.5185
 S8Z  F23   F  F     0  -0.343  -2.0135  -4.4594   1.0675
 S8Z  C24   C  CR6   0   0.133  -0.6008   0.6237  -0.4999
 S8Z  C25   C  CR16  0  -0.307  -0.7876   1.2760  -1.7102
 S8Z  C26   C  CR16  0  -0.293  -1.1707   2.6112  -1.7467
 S8Z  C27   C  CR6   0   0.325  -1.3623   3.2954  -0.5602
 S8Z  C28   C  CR16  0  -0.300  -1.1775   2.6627   0.6606
 S8Z  C29   C  CR16  0  -0.268  -0.7945   1.3324   0.6840
 S8Z  O30   O  O2    0  -0.511  -1.6762   4.6445  -0.5888
 S8Z  C31   C  CH1   0   0.666  -2.9847   4.9891  -0.5981
 S8Z  F32   F  F     0  -0.334  -3.6250   4.4635  -1.6703
 S8Z  F33   F  F     0  -0.333  -3.6320   4.4957   0.4848
 S8Z  H11C  H  HCH3  0   0.210   7.9617   3.6052  -0.7586
 S8Z  H12C  H  HCH3  0   0.210   8.9899   2.3952   0.0313
 S8Z  H13C  H  HCH3  0   0.242   8.6698   2.2861  -1.7096
 S8Z  H31C  H  HCH2  0   0.242   7.1631   1.8161   1.5209
 S8Z  H32C  H  HCH2  0   0.242   6.1478   3.0241   0.7406
 S8Z  H7    H  HCR6  0   0.261   4.1322  -1.6654   2.6582
 S8Z  H11   H  HCR6  0   0.258   2.0798   0.5472  -0.3773
 S8Z  H8    H  HCR6  0   0.265   2.1551  -3.1239   2.9130
 S8Z  H9    H  HCR6  0   0.249   0.1579  -2.7629   1.5564
 S8Z  H151  H  HCH2  0   0.274  -3.3918  -2.6570   2.2299
 S8Z  H152  H  HCH2  0   0.269  -4.1712  -2.0098   0.7979
 S8Z  H171  H  HCH2  0   0.301  -2.2903  -4.5248  -1.4379
 S8Z  H172  H  HCH2  0   0.293  -3.5113  -3.2454  -1.5799
 S8Z  H211  H  HNH2  0   0.415  -1.3978  -3.6486  -3.3845
 S8Z  H212  H  HNH2  0   0.408   0.0242  -2.8503  -3.8349
 S8Z  H25   H  HCR6  0   0.261  -0.6286   0.7440  -2.6376
 S8Z  H29   H  HCR6  0   0.257  -0.6414   0.8477   1.6389
 S8Z  H26   H  HCR6  0   0.271  -1.2972   3.1136  -2.6966
 S8Z  H28   H  HCR6  0   0.272  -1.3102   3.2074   1.5860
 S8Z  H31   H  HCH1  0   0.214  -3.0639   6.0733  -0.6148

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
 S8Z  C1   O2    single    1.408  0.020  1.408
 S8Z  O2   C3    single    1.405  0.020  1.405
 S8Z  C3   C4    single    1.457  0.020  1.457
 S8Z  C4   C5    triple    1.204  0.020  1.204
 S8Z  C5   C6    single    1.427  0.020  1.427
 S8Z  C6   C7    aromatic  1.399  0.020  1.399
 S8Z  C6   C11   aromatic  1.394  0.020  1.394
 S8Z  C7   C8    aromatic  1.382  0.020  1.382
 S8Z  C8   C9    aromatic  1.391  0.020  1.391
 S8Z  C9   C10   aromatic  1.390  0.020  1.390
 S8Z  C10  C11   aromatic  1.391  0.020  1.391
 S8Z  C10  C12   single    1.526  0.020  1.526
 S8Z  C12  C13   single    1.528  0.020  1.528
 S8Z  C12  N20   single    1.455  0.020  1.455
 S8Z  C12  C24   single    1.520  0.020  1.520
 S8Z  C13  N14   double    1.263  0.020  1.263
 S8Z  C13  N18   single    1.369  0.020  1.369
 S8Z  N14  C15   single    1.450  0.020  1.450
 S8Z  C15  C16   single    1.516  0.020  1.516
 S8Z  C16  C17   single    1.517  0.020  1.517
 S8Z  C16  F22   single    1.358  0.020  1.358
 S8Z  C16  F23   single    1.369  0.020  1.369
 S8Z  C17  N18   single    1.442  0.020  1.442
 S8Z  N18  C19   single    1.386  0.020  1.386
 S8Z  C19  N20   double    1.283  0.020  1.283
 S8Z  C19  N21   single    1.345  0.020  1.345
 S8Z  C24  C25   aromatic  1.387  0.020  1.387
 S8Z  C24  C29   aromatic  1.393  0.020  1.393
 S8Z  C25  C26   aromatic  1.390  0.020  1.390
 S8Z  C26  C27   aromatic  1.383  0.020  1.383
 S8Z  C27  C28   aromatic  1.387  0.020  1.387
 S8Z  C27  O30   single    1.385  0.020  1.385
 S8Z  C28  C29   aromatic  1.385  0.020  1.385
 S8Z  O30  C31   single    1.353  0.020  1.353
 S8Z  C31  F32   single    1.355  0.020  1.355
 S8Z  C31  F33   single    1.355  0.020  1.355
 S8Z  C1   H11C  single    0.970  0.020  1.090
 S8Z  C1   H12C  single    0.970  0.020  1.090
 S8Z  C1   H13C  single    0.970  0.020  1.090
 S8Z  C3   H31C  single    0.970  0.020  1.090
 S8Z  C3   H32C  single    0.970  0.020  1.090
 S8Z  C7   H7    single    0.930  0.020  1.080
 S8Z  C11  H11   single    0.930  0.020  1.080
 S8Z  C8   H8    single    0.930  0.020  1.080
 S8Z  C9   H9    single    0.930  0.020  1.080
 S8Z  C15  H151  single    0.970  0.020  1.090
 S8Z  C15  H152  single    0.970  0.020  1.090
 S8Z  C17  H171  single    0.970  0.020  1.090
 S8Z  C17  H172  single    0.970  0.020  1.090
 S8Z  N21  H211  single    0.890  0.020  1.040
 S8Z  N21  H212  single    0.890  0.020  1.040
 S8Z  C25  H25   single    0.930  0.020  1.080
 S8Z  C29  H29   single    0.930  0.020  1.080
 S8Z  C26  H26   single    0.930  0.020  1.080
 S8Z  C28  H28   single    0.930  0.020  1.080
 S8Z  C31  H31   single    0.970  0.020  1.090

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
 S8Z  H13C  C1   H12C  108.54  3.000
 S8Z  H13C  C1   H11C  108.55  3.000
 S8Z  H12C  C1   H11C  108.00  3.000
 S8Z  H13C  C1   O2    107.76  3.000
 S8Z  H12C  C1   O2    111.95  3.000
 S8Z  H11C  C1   O2    111.94  3.000
 S8Z  C3    O2   C1    111.76  3.000
 S8Z  H32C  C3   H31C  106.38  3.000
 S8Z  H32C  C3   C4    109.20  3.000
 S8Z  H31C  C3   C4    109.24  3.000
 S8Z  H32C  C3   O2    111.23  3.000
 S8Z  H31C  C3   O2    111.32  3.000
 S8Z  C4    C3   O2    109.41  3.000
 S8Z  C5    C4   C3    180.00  3.000
 S8Z  C6    C5   C4    180.00  3.000
 S8Z  C11   C6   C7    119.50  3.000
 S8Z  C11   C6   C5    120.16  3.000
 S8Z  C7    C6   C5    120.35  3.000
 S8Z  H7    C7   C8    120.54  3.000
 S8Z  H7    C7   C6    119.93  3.000
 S8Z  C8    C7   C6    119.52  3.000
 S8Z  H8    C8   C9    119.53  3.000
 S8Z  H8    C8   C7    119.83  3.000
 S8Z  C9    C8   C7    120.63  3.000
 S8Z  H9    C9   C10   120.96  3.000
 S8Z  H9    C9   C8    118.57  3.000
 S8Z  C10   C9   C8    120.47  3.000
 S8Z  C12   C10  C11   118.10  3.000
 S8Z  C12   C10  C9    122.94  3.000
 S8Z  C11   C10  C9    118.83  3.000
 S8Z  H11   C11  C10   120.07  3.000
 S8Z  H11   C11  C6    118.89  3.000
 S8Z  C10   C11  C6    121.04  3.000
 S8Z  C24   C12  N20   112.24  3.000
 S8Z  C24   C12  C13   108.94  3.000
 S8Z  N20   C12  C13   104.38  3.000
 S8Z  C24   C12  C10   111.29  3.000
 S8Z  N20   C12  C10   107.83  3.000
 S8Z  C13   C12  C10   111.98  3.000
 S8Z  N18   C13  N14   127.38  3.000
 S8Z  N18   C13  C12   104.95  3.000
 S8Z  N14   C13  C12   127.67  3.000
 S8Z  C15   N14  C13   116.85  3.000
 S8Z  H152  C15  H151  106.68  3.000
 S8Z  H152  C15  C16   108.73  3.000
 S8Z  H151  C15  C16   109.21  3.000
 S8Z  H152  C15  N14   109.96  3.000
 S8Z  H151  C15  N14   109.28  3.000
 S8Z  C16   C15  N14   112.80  3.000
 S8Z  F23   C16  F22   106.40  3.000
 S8Z  F23   C16  C17   108.49  3.000
 S8Z  F22   C16  C17   109.36  3.000
 S8Z  F23   C16  C15   108.94  3.000
 S8Z  F22   C16  C15   110.72  3.000
 S8Z  C17   C16  C15   112.70  3.000
 S8Z  H172  C17  H171  108.65  3.000
 S8Z  H172  C17  N18   111.37  3.000
 S8Z  H171  C17  N18   110.72  3.000
 S8Z  H172  C17  C16   109.58  3.000
 S8Z  H171  C17  C16   110.09  3.000
 S8Z  N18   C17  C16   106.41  3.000
 S8Z  C19   N18  C17   129.14  3.000
 S8Z  C19   N18  C13   108.44  3.000
 S8Z  C17   N18  C13   122.35  3.000
 S8Z  N21   C19  N20   126.08  3.000
 S8Z  N21   C19  N18   119.26  3.000
 S8Z  N20   C19  N18   114.61  3.000
 S8Z  C19   N20  C12   107.43  3.000
 S8Z  H212  N21  H211  114.30  3.000
 S8Z  H212  N21  C19   116.07  3.000
 S8Z  H211  N21  C19   119.46  3.000
 S8Z  C29   C24  C25   118.90  3.000
 S8Z  C29   C24  C12   119.88  3.000
 S8Z  C25   C24  C12   121.21  3.000
 S8Z  H25   C25  C26   119.40  3.000
 S8Z  H25   C25  C24   119.82  3.000
 S8Z  C26   C25  C24   120.78  3.000
 S8Z  H26   C26  C27   120.48  3.000
 S8Z  H26   C26  C25   120.10  3.000
 S8Z  C27   C26  C25   119.41  3.000
 S8Z  O30   C27  C28   119.50  3.000
 S8Z  O30   C27  C26   119.70  3.000
 S8Z  C28   C27  C26   120.72  3.000
 S8Z  H28   C28  C29   120.21  3.000
 S8Z  H28   C28  C27   120.45  3.000
 S8Z  C29   C28  C27   119.34  3.000
 S8Z  H29   C29  C28   118.99  3.000
 S8Z  H29   C29  C24   120.16  3.000
 S8Z  C28   C29  C24   120.85  3.000
 S8Z  C31   O30  C27   117.86  3.000
 S8Z  H31   C31  F33   109.92  3.000
 S8Z  H31   C31  F32   109.89  3.000
 S8Z  F33   C31  F32   105.39  3.000
 S8Z  H31   C31  O30   108.94  3.000
 S8Z  F33   C31  O30   111.34  3.000
 S8Z  F32   C31  O30   111.32  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
 S8Z  CONST_01  C9    C8   C7   C6     0.00   0.0  0
 S8Z  CONST_02  C9    C10  C11  C6     0.00   0.0  0
 S8Z  CONST_03  C10   C11  C6   C7     0.00   0.0  0
 S8Z  CONST_04  C10   C9   C8   C7     0.00   0.0  0
 S8Z  CONST_05  C11   C6   C7   C8     0.00   0.0  0
 S8Z  CONST_06  C11   C10  C9   C8     0.00   0.0  0
 S8Z  CONST_07  C27   C26  C25  C24    0.00   0.0  0
 S8Z  CONST_08  C27   C28  C29  C24    0.00   0.0  0
 S8Z  CONST_09  C28   C29  C24  C25    0.00   0.0  0
 S8Z  CONST_10  C28   C27  C26  C25    0.00   0.0  0
 S8Z  CONST_11  C29   C24  C25  C26    0.00   0.0  0
 S8Z  CONST_12  C29   C28  C27  C26    0.00   0.0  0
 S8Z  CONST_13  C12   C10  C11  C6   180.00   0.0  0
 S8Z  CONST_14  C12   C10  C9   C8   180.00   0.0  0
 S8Z  CONST_15  C26   C25  C24  C12  180.00   0.0  0
 S8Z  CONST_16  C28   C29  C24  C12  180.00   0.0  0
 S8Z  CONST_17  C15   N14  C13  C12  180.00   0.0  0
 S8Z  CONST_18  C17   N18  C13  C12  180.00   0.0  0
 S8Z  CONST_19  C19   N18  C13  C12    0.00   0.0  0
 S8Z  CONST_20  N18   C19  N20  C12    0.00   0.0  0
 S8Z  CONST_21  N20   C19  N18  C13    0.00   0.0  0
 S8Z  CONST_22  C17   N18  C13  N14    0.00   0.0  0
 S8Z  CONST_23  C19   N18  C13  N14  180.00   0.0  0
 S8Z  CONST_24  N18   C13  N14  C15    0.00   0.0  0
 S8Z  CONST_25  N20   C19  N18  C17  180.00   0.0  0
 S8Z  CONST_26  C8    C7   C6   C5   180.00   0.0  0
 S8Z  CONST_27  C10   C11  C6   C5   180.00   0.0  0
 S8Z  CONST_28  O30   C27  C26  C25  180.00   0.0  0
 S8Z  CONST_29  O30   C27  C28  C29  180.00   0.0  0
 S8Z  CONST_30  N21   C19  N20  C12  180.00   0.0  0
 S8Z  CONST_31  N21   C19  N18  C13  180.00   0.0  0
 S8Z  CONST_32  N21   C19  N18  C17    0.00   0.0  0
 S8Z  CONST_33  H8    C8   C7   C6   180.00   0.0  0
 S8Z  CONST_34  H11   C11  C6   C7   180.00   0.0  0
 S8Z  CONST_35  H9    C9   C8   C7   180.00   0.0  0
 S8Z  CONST_36  H7    C7   C8   C9   180.00   0.0  0
 S8Z  CONST_37  H25   C25  C24  C12    0.00   0.0  0
 S8Z  CONST_38  H29   C29  C24  C12    0.00   0.0  0
 S8Z  CONST_39  H26   C26  C25  C24  180.00   0.0  0
 S8Z  CONST_40  H28   C28  C29  C24  180.00   0.0  0
 S8Z  CONST_42  H212  N21  C19  N18  180.00   0.0  0
 S8Z  Var_01    C16   C15  N14  C13   25.57  30.0  1
 S8Z  Var_02    C16   C17  N18  C13  -24.91  30.0  1
 S8Z  Var_03    C17   C16  C15  N14  -51.33  30.0  1
 S8Z  Var_04    N18   C17  C16  C15   48.38  30.0  1
 S8Z  Var_05    F32   C31  O30  C27  -59.00  30.0  3
 S8Z  Var_06    C4    C3   O2   C1   179.71  30.0  3
 S8Z  Var_07    H11C  C1   O2   C3   -60.85  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
 S8Z  chir_01  C12  C13  N20  C24  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
 S8Z  plan-1  C4    0.020
 S8Z  plan-1  C5    0.020
 S8Z  plan-1  C6    0.020
 S8Z  plan-1  C7    0.020
 S8Z  plan-1  C8    0.020
 S8Z  plan-1  C9    0.020
 S8Z  plan-1  C10   0.020
 S8Z  plan-1  C11   0.020
 S8Z  plan-1  C12   0.020
 S8Z  plan-1  H7    0.020
 S8Z  plan-1  H11   0.020
 S8Z  plan-1  H8    0.020
 S8Z  plan-1  H9    0.020
 S8Z  plan-2  C12   0.020
 S8Z  plan-2  C24   0.020
 S8Z  plan-2  C25   0.020
 S8Z  plan-2  C26   0.020
 S8Z  plan-2  C27   0.020
 S8Z  plan-2  C28   0.020
 S8Z  plan-2  C29   0.020
 S8Z  plan-2  O30   0.020
 S8Z  plan-2  H25   0.020
 S8Z  plan-2  H29   0.020
 S8Z  plan-2  H26   0.020
 S8Z  plan-2  H28   0.020
 S8Z  plan-3  C12   0.020
 S8Z  plan-3  C13   0.020
 S8Z  plan-3  N14   0.020
 S8Z  plan-3  C15   0.020
 S8Z  plan-3  C17   0.020
 S8Z  plan-3  N18   0.020
 S8Z  plan-3  C19   0.020
 S8Z  plan-3  N20   0.020
 S8Z  plan-3  N21   0.020
 S8Z  plan-3  H211  0.020
 S8Z  plan-3  H212  0.020

