# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 18:08:39 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (8R)-3,3-difluoro-8-[4-fluoro-3-(pyridin-3-yl)phenyl]-8-(4-methoxy-3-methylphenyl)-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1C)[C@@]2(N=C(N)N3CC(F)(F)CN=C23)c4ccc(F)c(c4)c5cccnc5
#
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
 2QH  2QH  (8R)-3,3-difluoro-8-[4-fluoro-3-(pyridin-3-yl)phenyl]-8-(4-methoxy-3-methylphenyl)-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine  ligand  56  34  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2QH
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
 2QH  C1   C  CH3   0  -0.713  -0.2795   5.0553  -0.5819
 2QH  C2   C  CR6   0   0.017  -1.0612   3.8303  -0.2108
 2QH  C3   C  CR16  0  -0.310  -0.5205   2.5656  -0.3478
 2QH  C4   C  CR6   0   0.184  -1.2214   1.4053  -0.0086
 2QH  C5   C  CR16  0  -0.323  -2.5091   1.5410   0.4755
 2QH  C6   C  CR16  0  -0.372  -3.0859   2.8013   0.6244
 2QH  C7   C  CR6   0   0.337  -2.3725   3.9417   0.2851
 2QH  O8   O  O2    0  -0.464  -2.8526   5.1960   0.3959
 2QH  C9   C  CH3   0  -0.436  -4.1684   5.3753   0.8776
 2QH  C10  C  CR5   0  -0.184  -0.5386   0.0664  -0.2620
 2QH  C11  C  CR5   0   0.500  -1.4151  -1.1149   0.1489
 2QH  N12  N  N     0  -0.429  -1.7550  -1.4579   1.3163
 2QH  C13  C  CH2   0  -0.418  -2.6072  -2.6241   1.4370
 2QH  C14  C  CT    0   0.685  -3.4317  -2.8834   0.1919
 2QH  C15  C  CH2   0  -0.389  -2.5924  -2.9032  -1.0720
 2QH  N16  N  NR5   0  -0.565  -1.7627  -1.7247  -1.0285
 2QH  C17  C  CR5   0   0.673  -1.0925  -1.0910  -2.0622
 2QH  N18  N  N     0  -0.466  -0.3664  -0.0991  -1.6985
 2QH  N19  N  NH2   0  -0.852  -1.2894  -1.5081  -3.3275
 2QH  F20  F  F     0  -0.333  -4.1078  -4.0574   0.3010
 2QH  F21  F  F     0  -0.344  -4.3788  -1.9027   0.0719
 2QH  C22  C  CR6   0   0.161   0.7853  -0.0154   0.4805
 2QH  C23  C  CR16  0  -0.267   0.8459   0.3157   1.8320
 2QH  C24  C  CR16  0  -0.399   2.0372   0.2123   2.5290
 2QH  C25  C  CR6   0   0.510   3.1684  -0.2167   1.8616
 2QH  C26  C  CR6   0  -0.124   3.1589  -0.5443   0.5146
 2QH  C27  C  CR16  0  -0.352   1.9395  -0.4388  -0.1585
 2QH  C28  C  CR6   0   0.002   4.3683  -1.0057  -0.1912
 2QH  C29  C  CR16  0  -0.182   5.5841  -0.3289  -0.1273
 2QH  C30  C  CR16  0  -0.318   6.6629  -0.8121  -0.8483
 2QH  C31  C  CR16  0  -0.068   6.4944  -1.9570  -1.6125
 2QH  N32  N  N     0  -0.399   5.3441  -2.6164  -1.6830
 2QH  C33  C  CR16  0  -0.089   4.3168  -2.1490  -0.9883
 2QH  F34  F  F     0  -0.306   4.3130  -0.3331   2.5543
 2QH  H1   H  HCH3  0   0.242  -0.1404   5.7222   0.2708
 2QH  H2   H  HCH3  0   0.242   0.7070   4.7824  -0.9539
 2QH  H3   H  HCH3  0   0.242  -0.7789   5.6354  -1.3599
 2QH  H4   H  HCR6  0   0.243   0.4896   2.4784  -0.7326
 2QH  H5   H  HCR6  0   0.244  -3.0964   0.6759   0.7521
 2QH  H6   H  HCR6  0   0.276  -4.0954   2.8649   1.0076
 2QH  H7   H  HCH3  0   0.227  -4.2888   4.9898   1.8935
 2QH  H8   H  HCH3  0   0.259  -4.3521   6.4469   0.8863
 2QH  H9   H  HCH3  0   0.227  -4.9083   4.8964   0.2308
 2QH  H10  H  HCH2  0   0.268  -1.9984  -3.5091   1.6449
 2QH  H11  H  HCH2  0   0.273  -3.2772  -2.4957   2.2902
 2QH  H12  H  HCH2  0   0.291  -1.9907  -3.8151  -1.0969
 2QH  H13  H  HCH2  0   0.300  -3.2375  -2.8873  -1.9526
 2QH  H14  H  HNH2  0   0.414  -1.5557  -2.4644  -3.4950
 2QH  H15  H  HNH2  0   0.406  -0.6595  -1.1312  -4.0171
 2QH  H16  H  HCR6  0   0.262  -0.0391   0.6628   2.3480
 2QH  H17  H  HCR6  0   0.280   2.0902   0.4574   3.5817
 2QH  H18  H  HCR6  0   0.264   1.9015  -0.6728  -1.2142
 2QH  H19  H  HCR6  0   0.270   5.6845   0.5761   0.4571
 2QH  H20  H  HCR6  0   0.275   7.6187  -0.3073  -0.8244
 2QH  H21  H  HCR6  0   0.268   7.3200  -2.3557  -2.1911
 2QH  H22  H  HCR6  0   0.263   3.3932  -2.7160  -1.0530

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
 2QH  F34  C25  single    1.343  0.020  1.343
 2QH  C24  C25  aromatic  1.382  0.020  1.382
 2QH  C24  C23  aromatic  1.384  0.020  1.384
 2QH  C25  C26  aromatic  1.386  0.020  1.386
 2QH  C29  C30  aromatic  1.385  0.020  1.385
 2QH  C29  C28  aromatic  1.393  0.020  1.393
 2QH  C23  C22  aromatic  1.393  0.020  1.393
 2QH  C30  C31  aromatic  1.387  0.020  1.387
 2QH  C26  C28  single    1.474  0.020  1.474
 2QH  C26  C27  aromatic  1.397  0.020  1.397
 2QH  F20  C14  single    1.359  0.020  1.359
 2QH  C28  C33  aromatic  1.395  0.020  1.395
 2QH  C31  N32  aromatic  1.328  0.020  1.328
 2QH  C13  N12  single    1.449  0.020  1.449
 2QH  C13  C14  single    1.516  0.020  1.516
 2QH  C33  N32  aromatic  1.325  0.020  1.325
 2QH  N12  C11  double    1.263  0.020  1.263
 2QH  C22  C27  aromatic  1.386  0.020  1.386
 2QH  C22  C10  single    1.520  0.020  1.520
 2QH  C14  F21  single    1.369  0.020  1.369
 2QH  C14  C15  single    1.517  0.020  1.517
 2QH  C11  C10  single    1.527  0.020  1.527
 2QH  C11  N16  single    1.371  0.020  1.371
 2QH  C10  C4   single    1.524  0.020  1.524
 2QH  C10  N18  single    1.456  0.020  1.456
 2QH  C3   C4   aromatic  1.397  0.020  1.397
 2QH  C3   C2   aromatic  1.382  0.020  1.382
 2QH  C15  N16  single    1.442  0.020  1.442
 2QH  C1   C2   single    1.500  0.020  1.500
 2QH  N16  C17  single    1.385  0.020  1.385
 2QH  C4   C5   aromatic  1.382  0.020  1.382
 2QH  N18  C17  double    1.282  0.020  1.282
 2QH  C17  N19  single    1.347  0.020  1.347
 2QH  C2   C7   aromatic  1.406  0.020  1.406
 2QH  C5   C6   aromatic  1.394  0.020  1.394
 2QH  C7   C6   aromatic  1.387  0.020  1.387
 2QH  C7   O8   single    1.348  0.020  1.348
 2QH  O8   C9   single    1.413  0.020  1.413
 2QH  C1   H1   single    0.970  0.020  1.090
 2QH  C1   H2   single    0.970  0.020  1.090
 2QH  C1   H3   single    0.970  0.020  1.090
 2QH  C3   H4   single    0.930  0.020  1.080
 2QH  C5   H5   single    0.930  0.020  1.080
 2QH  C6   H6   single    0.930  0.020  1.080
 2QH  C9   H7   single    0.970  0.020  1.090
 2QH  C9   H8   single    0.970  0.020  1.090
 2QH  C9   H9   single    0.970  0.020  1.090
 2QH  C13  H10  single    0.970  0.020  1.090
 2QH  C13  H11  single    0.970  0.020  1.090
 2QH  C15  H12  single    0.970  0.020  1.090
 2QH  C15  H13  single    0.970  0.020  1.090
 2QH  N19  H14  single    0.890  0.020  1.040
 2QH  N19  H15  single    0.890  0.020  1.040
 2QH  C23  H16  single    0.930  0.020  1.080
 2QH  C24  H17  single    0.930  0.020  1.080
 2QH  C27  H18  single    0.930  0.020  1.080
 2QH  C29  H19  single    0.930  0.020  1.080
 2QH  C30  H20  single    0.930  0.020  1.080
 2QH  C31  H21  single    0.930  0.020  1.080
 2QH  C33  H22  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
 2QH  H3   C1   H2   107.71  3.000
 2QH  H3   C1   H1   106.88  3.000
 2QH  H2   C1   H1   107.73  3.000
 2QH  H3   C1   C2   111.84  3.000
 2QH  H2   C1   C2   110.61  3.000
 2QH  H1   C1   C2   111.85  3.000
 2QH  C7   C2   C3   118.18  3.000
 2QH  C7   C2   C1   120.57  3.000
 2QH  C3   C2   C1   121.26  3.000
 2QH  H4   C3   C4   119.11  3.000
 2QH  H4   C3   C2   118.24  3.000
 2QH  C4   C3   C2   122.64  3.000
 2QH  C10  C4   C5   124.18  3.000
 2QH  C5   C4   C3   118.09  3.000
 2QH  C10  C4   C3   117.67  3.000
 2QH  H5   C5   C6   118.11  3.000
 2QH  H5   C5   C4   121.12  3.000
 2QH  C6   C5   C4   120.77  3.000
 2QH  H6   C6   C7   121.21  3.000
 2QH  H6   C6   C5   118.50  3.000
 2QH  C7   C6   C5   120.29  3.000
 2QH  O8   C7   C6   124.18  3.000
 2QH  O8   C7   C2   115.78  3.000
 2QH  C6   C7   C2   120.04  3.000
 2QH  C9   O8   C7   118.55  3.000
 2QH  H9   C9   H8   108.79  3.000
 2QH  H9   C9   H7   108.71  3.000
 2QH  H8   C9   H7   108.76  3.000
 2QH  H9   C9   O8   111.90  3.000
 2QH  H8   C9   O8   106.57  3.000
 2QH  H7   C9   O8   112.01  3.000
 2QH  C22  C10  N18  111.89  3.000
 2QH  N18  C10  C11  104.20  3.000
 2QH  C22  C10  C11  109.07  3.000
 2QH  N18  C10  C4   108.47  3.000
 2QH  C11  C10  C4   112.19  3.000
 2QH  C22  C10  C4   110.87  3.000
 2QH  N16  C11  N12  127.21  3.000
 2QH  N16  C11  C10  104.98  3.000
 2QH  N12  C11  C10  127.81  3.000
 2QH  C13  N12  C11  116.97  3.000
 2QH  H11  C13  H10  106.73  3.000
 2QH  H11  C13  C14  109.16  3.000
 2QH  H10  C13  C14  108.68  3.000
 2QH  H11  C13  N12  109.34  3.000
 2QH  H10  C13  N12  109.85  3.000
 2QH  C14  C13  N12  112.90  3.000
 2QH  F21  C14  F20  106.36  3.000
 2QH  F21  C14  C15  108.61  3.000
 2QH  F20  C14  C15  109.32  3.000
 2QH  C15  C14  C13  112.68  3.000
 2QH  F21  C14  C13  109.01  3.000
 2QH  F20  C14  C13  110.64  3.000
 2QH  H13  C15  H12  108.61  3.000
 2QH  H13  C15  N16  110.64  3.000
 2QH  H12  C15  N16  111.46  3.000
 2QH  H13  C15  C14  110.17  3.000
 2QH  H12  C15  C14  109.54  3.000
 2QH  N16  C15  C14  106.41  3.000
 2QH  C17  N16  C15  129.03  3.000
 2QH  C17  N16  C11  108.35  3.000
 2QH  C15  N16  C11  122.37  3.000
 2QH  N19  C17  N18  126.08  3.000
 2QH  N19  C17  N16  119.26  3.000
 2QH  N18  C17  N16  114.60  3.000
 2QH  C17  N18  C10  107.51  3.000
 2QH  H15  N19  H14  114.02  3.000
 2QH  H15  N19  C17  115.85  3.000
 2QH  H14  N19  C17  119.29  3.000
 2QH  C27  C22  C23  118.95  3.000
 2QH  C27  C22  C10  121.11  3.000
 2QH  C23  C22  C10  119.94  3.000
 2QH  H16  C23  C24  119.21  3.000
 2QH  H16  C23  C22  120.24  3.000
 2QH  C24  C23  C22  120.55  3.000
 2QH  H17  C24  C25  120.02  3.000
 2QH  H17  C24  C23  121.00  3.000
 2QH  C25  C24  C23  118.99  3.000
 2QH  F34  C25  C26  119.11  3.000
 2QH  C26  C25  C24  122.49  3.000
 2QH  F34  C25  C24  118.39  3.000
 2QH  C28  C26  C27  120.60  3.000
 2QH  C27  C26  C25  117.15  3.000
 2QH  C28  C26  C25  122.24  3.000
 2QH  H18  C27  C26  118.98  3.000
 2QH  H18  C27  C22  119.13  3.000
 2QH  C26  C27  C22  121.87  3.000
 2QH  C33  C28  C29  117.18  3.000
 2QH  C33  C28  C26  119.99  3.000
 2QH  C29  C28  C26  122.81  3.000
 2QH  H19  C29  C30  120.06  3.000
 2QH  H19  C29  C28  120.81  3.000
 2QH  C30  C29  C28  119.12  3.000
 2QH  H20  C30  C31  120.34  3.000
 2QH  H20  C30  C29  120.95  3.000
 2QH  C31  C30  C29  118.71  3.000
 2QH  H21  C31  N32  116.67  3.000
 2QH  H21  C31  C30  120.34  3.000
 2QH  N32  C31  C30  123.00  3.000
 2QH  C33  N32  C31  117.94  3.000
 2QH  H22  C33  N32  116.36  3.000
 2QH  H22  C33  C28  119.57  3.000
 2QH  N32  C33  C28  124.06  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
 2QH  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 2QH  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 2QH  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 2QH  CONST_04  C6   C7   C2   C3      0.00   0.0  0
 2QH  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 2QH  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 2QH  CONST_07  C25  C24  C23  C22     0.00   0.0  0
 2QH  CONST_08  C25  C26  C27  C22     0.00   0.0  0
 2QH  CONST_09  C28  C26  C27  C22   180.00   0.0  0
 2QH  CONST_10  C26  C25  C24  C23     0.00   0.0  0
 2QH  CONST_11  C26  C27  C22  C23     0.00   0.0  0
 2QH  CONST_12  C28  C26  C25  C24   180.00   0.0  0
 2QH  CONST_13  C27  C26  C25  C24     0.00   0.0  0
 2QH  CONST_14  C27  C22  C23  C24     0.00   0.0  0
 2QH  CONST_17  C30  C29  C28  C26   180.00   0.0  0
 2QH  CONST_18  N32  C33  C28  C26   180.00   0.0  0
 2QH  CONST_21  C31  C30  C29  C28     0.00   0.0  0
 2QH  CONST_22  C31  N32  C33  C28     0.00   0.0  0
 2QH  CONST_23  N32  C31  C30  C29     0.00   0.0  0
 2QH  CONST_24  N32  C33  C28  C29     0.00   0.0  0
 2QH  CONST_25  C33  C28  C29  C30     0.00   0.0  0
 2QH  CONST_26  C33  N32  C31  C30     0.00   0.0  0
 2QH  CONST_27  C10  C4   C3   C2    180.00   0.0  0
 2QH  CONST_28  C10  C4   C5   C6    180.00   0.0  0
 2QH  CONST_29  C24  C23  C22  C10   180.00   0.0  0
 2QH  CONST_30  C26  C27  C22  C10   180.00   0.0  0
 2QH  CONST_31  C13  N12  C11  C10   180.00   0.0  0
 2QH  CONST_32  C15  N16  C11  C10   180.00   0.0  0
 2QH  CONST_33  C17  N16  C11  C10     0.00   0.0  0
 2QH  CONST_34  N16  C17  N18  C10     0.00   0.0  0
 2QH  CONST_35  N18  C17  N16  C11     0.00   0.0  0
 2QH  CONST_36  C15  N16  C11  N12     0.00   0.0  0
 2QH  CONST_37  C17  N16  C11  N12   180.00   0.0  0
 2QH  CONST_38  N16  C11  N12  C13     0.00   0.0  0
 2QH  CONST_39  N18  C17  N16  C15   180.00   0.0  0
 2QH  CONST_40  C4   C3   C2   C1    180.00   0.0  0
 2QH  CONST_41  C6   C7   C2   C1    180.00   0.0  0
 2QH  CONST_42  O8   C7   C2   C3    180.00   0.0  0
 2QH  CONST_43  O8   C7   C6   C5    180.00   0.0  0
 2QH  CONST_44  F34  C25  C24  C23   180.00   0.0  0
 2QH  CONST_45  F34  C25  C26  C27   180.00   0.0  0
 2QH  CONST_46  F34  C25  C26  C28     0.00   0.0  0
 2QH  CONST_47  N19  C17  N18  C10   180.00   0.0  0
 2QH  CONST_48  N19  C17  N16  C11   180.00   0.0  0
 2QH  CONST_49  N19  C17  N16  C15     0.00   0.0  0
 2QH  CONST_50  H6   C6   C7   C2    180.00   0.0  0
 2QH  CONST_51  H5   C5   C4   C3    180.00   0.0  0
 2QH  CONST_52  H4   C3   C4   C5    180.00   0.0  0
 2QH  CONST_53  H16  C23  C22  C10     0.00   0.0  0
 2QH  CONST_54  H18  C27  C22  C10     0.00   0.0  0
 2QH  CONST_55  H17  C24  C23  C22   180.00   0.0  0
 2QH  CONST_56  H19  C29  C28  C26     0.00   0.0  0
 2QH  CONST_57  H22  C33  C28  C26     0.00   0.0  0
 2QH  CONST_58  H20  C30  C29  C28   180.00   0.0  0
 2QH  CONST_59  H21  C31  C30  C29   180.00   0.0  0
 2QH  CONST_61  H15  N19  C17  N16   180.00   0.0  0
 2QH  Var_01    C14  C13  N12  C11   -25.21  30.0  1
 2QH  Var_02    C14  C15  N16  C11    25.33  30.0  1
 2QH  Var_03    C15  C14  C13  N12    51.06  30.0  1
 2QH  Var_04    N16  C15  C14  C13   -48.49  30.0  1
 2QH  Var_05    H1   C1   C2   C3   -119.74  30.0  2
 2QH  Var_06    H7   C9   O8   C7     61.24  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
 2QH  chir_01  C10  C11  C4  N18  positiv

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
 2QH  plan-1  C1   0.020
 2QH  plan-1  C2   0.020
 2QH  plan-1  C3   0.020
 2QH  plan-1  C4   0.020
 2QH  plan-1  C5   0.020
 2QH  plan-1  C6   0.020
 2QH  plan-1  C7   0.020
 2QH  plan-1  O8   0.020
 2QH  plan-1  C10  0.020
 2QH  plan-1  H4   0.020
 2QH  plan-1  H5   0.020
 2QH  plan-1  H6   0.020
 2QH  plan-2  C10  0.020
 2QH  plan-2  C22  0.020
 2QH  plan-2  C23  0.020
 2QH  plan-2  C24  0.020
 2QH  plan-2  C25  0.020
 2QH  plan-2  C26  0.020
 2QH  plan-2  C27  0.020
 2QH  plan-2  C28  0.020
 2QH  plan-2  F34  0.020
 2QH  plan-2  H16  0.020
 2QH  plan-2  H17  0.020
 2QH  plan-2  H18  0.020
 2QH  plan-3  C26  0.020
 2QH  plan-3  C28  0.020
 2QH  plan-3  C29  0.020
 2QH  plan-3  C30  0.020
 2QH  plan-3  C31  0.020
 2QH  plan-3  N32  0.020
 2QH  plan-3  C33  0.020
 2QH  plan-3  H19  0.020
 2QH  plan-3  H20  0.020
 2QH  plan-3  H21  0.020
 2QH  plan-3  H22  0.020
 2QH  plan-4  C10  0.020
 2QH  plan-4  C11  0.020
 2QH  plan-4  N12  0.020
 2QH  plan-4  C13  0.020
 2QH  plan-4  C15  0.020
 2QH  plan-4  N16  0.020
 2QH  plan-4  C17  0.020
 2QH  plan-4  N18  0.020
 2QH  plan-4  N19  0.020
 2QH  plan-4  H14  0.020
 2QH  plan-4  H15  0.020

