# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 22:00:31 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 2-[(1S)-1-({6-amino-5-[(1H-pyrazol-4-yl)ethynyl]pyrimidin-4-yl}amino)ethyl]-5-chloro-3-phenylquinazolin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1ncnc(N)c1C#Cc2c[nH]nc2)C3=Nc4cccc(Cl)c4C(=O)N3c5ccccc5
#
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
 68R  68R  2-[(1S)-1-({6-amino-5-[(1H-pyrazol-4-yl)ethynyl]pyrimidin-4-yl}amino)ethyl]-5-chloro-3-phenylquinazolin-4(3H)-one  ligand  54  35  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_68R
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
 68R  C10  C   CR6   0   0.565   2.6150  -0.5912   0.6697
 68R  C13  C   CR6   0   0.274   0.5909  -1.8614   0.8378
 68R  C15  C   CR16  0  -0.255  -0.1564  -3.9880   1.6439
 68R  C17  C   CR16  0  -0.256  -1.2015  -1.9669   2.4211
 68R  C20  C   CH3   0  -0.639  -0.0535  -1.3580  -3.4301
 68R  C22  C   CR6   0   0.541  -2.2354  -1.3208  -0.7744
 68R  C24  C   CR6   0   0.468  -4.2923  -1.2708   0.4483
 68R  C26  C   CR16  0   0.072  -3.3261  -3.2077  -0.1958
 68R  C01  C   CR16  0  -0.221   5.4830   1.5398  -0.5738
 68R  C02  C   CR16  0  -0.248   5.1182   1.6885  -1.9111
 68R  C03  C   CR16  0  -0.306   3.9654   1.1121  -2.3891
 68R  C04  C   CR66  0   0.249   3.1496   0.3695  -1.5289
 68R  C05  C   CR66  0  -0.010   3.5011   0.2051  -0.1770
 68R  C06  C   CR6   0  -0.092   4.6853   0.8088   0.2816
 68R  N07  N   N     0  -0.465   2.0093  -0.1770  -2.0585
 68R  C08  C   CR6   0   0.508   1.2278  -0.8599  -1.3106
 68R  N09  N   NR6   0  -0.661   1.4784  -1.0836   0.0224
 68R  O11  O   O     0  -0.427   2.7947  -0.8443   1.8407
 68R  C14  C   CR16  0  -0.244   0.7003  -3.2421   0.8462
 68R  C16  C   CR16  0  -0.238  -1.1074  -3.3527   2.4291
 68R  C18  C   CR16  0  -0.248  -0.3484  -1.2170   1.6273
 68R  C19  C   CH1   0  -0.222  -0.0476  -1.4240  -1.9110
 68R  N21  N   NH1   0  -0.668  -1.1715  -0.7192  -1.3379
 68R  C23  C   CR6   0  -0.347  -3.2414  -0.5532  -0.1560
 68R  N25  N   N     0  -0.475  -4.3241  -2.6119   0.4249
 68R  N27  N   N     0  -0.476  -2.2969  -2.6541  -0.8064
 68R  N28  N   NH2   0  -0.827  -5.2875  -0.6456   1.0869
 68R  C29  C   CSP   0   0.094  -3.1725   0.8559  -0.1054
 68R  C30  C   CSP   0   0.134  -3.0945   2.0637  -0.0652
 68R  C31  C   CR5   0  -0.308  -3.0193   3.4727  -0.0231
 68R  C32  C   CR15  0  -0.009  -2.0150   4.2523   0.5259
 68R  N33  N   NR15  0  -0.418  -2.3739   5.5219   0.3185
 68R  N34  N   N     0  -0.255  -3.5343   5.6478  -0.3188
 68R  C35  C   CR15  0  -0.117  -3.9402   4.4162  -0.5369
 68R  H1   H   HCR6  0   0.261  -0.0783  -5.0671   1.6492
 68R  H2   H   HCR6  0   0.261  -1.9444  -1.4660   3.0275
 68R  H3   H   HCH3  0   0.232  -0.0088  -0.3311  -3.7885
 68R  H4   H   HCH3  0   0.237   0.7883  -1.9048  -3.8518
 68R  H5   H   HCH3  0   0.242  -0.9740  -1.8136  -3.7938
 68R  H6   H   HCR6  0   0.250  -3.3589  -4.2928  -0.2140
 68R  H7   H   HCR6  0   0.290   6.3904   1.9977  -0.2060
 68R  H8   H   HCR6  0   0.281   5.7526   2.2656  -2.5699
 68R  H9   H   HCR6  0   0.274   3.6684   1.2200  -3.4233
 68R  H10  H   HCR6  0   0.269   1.4473  -3.7311   0.2335
 68R  H11  H   HCR6  0   0.260  -1.7765  -3.9376   3.0463
 68R  H12  H   HCR6  0   0.267  -0.4234  -0.1372   1.6091
 68R  H13  H   HCH1  0   0.306  -0.1484  -2.4676  -1.6110
 68R  H14  H   HNH1  0   0.402  -1.1712   0.2886  -1.3894
 68R  H15  H   HNH2  0   0.400  -6.0579  -1.1817   1.4461
 68R  H16  H   HNH2  0   0.406  -5.3786   0.3551   1.0668
 68R  H17  H   HCR5  0   0.296  -1.1011   3.9834   1.0292
 68R  H18  H   HNR5  0   0.430  -1.8588   6.3451   0.5888
 68R  H19  H   HCR5  0   0.264  -4.8698   4.2187  -1.0486
 68R  CL1  CL  CL    0  -0.098   5.2181   0.6912   1.9202

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
 68R  CL1  C06  single    1.727  0.020  1.727
 68R  C01  C02  aromatic  1.394  0.020  1.394
 68R  C01  C06  aromatic  1.379  0.020  1.379
 68R  C02  C03  aromatic  1.375  0.020  1.375
 68R  C06  C05  aromatic  1.406  0.020  1.406
 68R  C03  C04  aromatic  1.399  0.020  1.399
 68R  C05  C04  aromatic  1.407  0.020  1.407
 68R  C05  C10  single    1.462  0.020  1.462
 68R  C04  N07  single    1.371  0.020  1.371
 68R  O11  C10  double    1.211  0.020  1.211
 68R  C10  N09  single    1.398  0.020  1.398
 68R  N07  C08  double    1.279  0.020  1.279
 68R  N09  C08  single    1.375  0.020  1.375
 68R  N09  C13  single    1.434  0.020  1.434
 68R  C08  C19  single    1.518  0.020  1.518
 68R  C32  N33  aromatic  1.335  0.020  1.335
 68R  C32  C31  aromatic  1.385  0.020  1.385
 68R  N33  N34  aromatic  1.330  0.020  1.330
 68R  C13  C18  aromatic  1.386  0.020  1.386
 68R  C13  C14  aromatic  1.385  0.020  1.385
 68R  C18  C17  aromatic  1.386  0.020  1.386
 68R  C20  C19  single    1.521  0.020  1.521
 68R  C14  C15  aromatic  1.388  0.020  1.388
 68R  C19  N21  single    1.445  0.020  1.445
 68R  N34  C35  aromatic  1.315  0.020  1.315
 68R  C31  C30  single    1.412  0.020  1.412
 68R  C31  C35  aromatic  1.415  0.020  1.415
 68R  C17  C16  aromatic  1.389  0.020  1.389
 68R  N21  C22  single    1.346  0.020  1.346
 68R  C30  C29  triple    1.211  0.020  1.211
 68R  C15  C16  aromatic  1.387  0.020  1.387
 68R  C29  C23  single    1.412  0.020  1.412
 68R  C22  C23  aromatic  1.408  0.020  1.408
 68R  C22  N27  aromatic  1.335  0.020  1.335
 68R  C23  C24  aromatic  1.409  0.020  1.409
 68R  N27  C26  aromatic  1.319  0.020  1.319
 68R  C24  N28  single    1.338  0.020  1.338
 68R  C24  N25  aromatic  1.342  0.020  1.342
 68R  C26  N25  aromatic  1.318  0.020  1.318
 68R  C15  H1   single    0.930  0.020  1.080
 68R  C17  H2   single    0.930  0.020  1.080
 68R  C20  H3   single    0.970  0.020  1.090
 68R  C20  H4   single    0.970  0.020  1.090
 68R  C20  H5   single    0.970  0.020  1.090
 68R  C26  H6   single    0.930  0.020  1.080
 68R  C01  H7   single    0.930  0.020  1.080
 68R  C02  H8   single    0.930  0.020  1.080
 68R  C03  H9   single    0.930  0.020  1.080
 68R  C14  H10  single    0.930  0.020  1.080
 68R  C16  H11  single    0.930  0.020  1.080
 68R  C18  H12  single    0.930  0.020  1.080
 68R  C19  H13  single    0.970  0.020  1.090
 68R  N21  H14  single    0.860  0.020  1.020
 68R  N28  H15  single    0.860  0.020  1.020
 68R  N28  H16  single    0.860  0.020  1.020
 68R  C32  H17  single    0.930  0.020  1.080
 68R  N33  H18  single    0.860  0.020  1.020
 68R  C35  H19  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
 68R  O11  C10  N09  119.66  3.000
 68R  N09  C10  C05  114.62  3.000
 68R  O11  C10  C05  125.72  3.000
 68R  C18  C13  C14  120.90  3.000
 68R  C14  C13  N09  119.68  3.000
 68R  C18  C13  N09  119.41  3.000
 68R  H1   C15  C16  120.23  3.000
 68R  H1   C15  C14  119.62  3.000
 68R  C16  C15  C14  120.15  3.000
 68R  H2   C17  C18  119.56  3.000
 68R  H2   C17  C16  120.35  3.000
 68R  C18  C17  C16  120.09  3.000
 68R  H5   C20  H4   108.29  3.000
 68R  H5   C20  H3   108.62  3.000
 68R  H4   C20  H3   108.33  3.000
 68R  H5   C20  C19  108.58  3.000
 68R  H4   C20  C19  111.23  3.000
 68R  H3   C20  C19  111.70  3.000
 68R  N27  C22  C23  121.46  3.000
 68R  N27  C22  N21  118.21  3.000
 68R  C23  C22  N21  120.32  3.000
 68R  N28  C24  N25  117.25  3.000
 68R  N25  C24  C23  121.29  3.000
 68R  N28  C24  C23  121.45  3.000
 68R  H6   C26  N27  115.81  3.000
 68R  H6   C26  N25  115.90  3.000
 68R  N27  C26  N25  128.28  3.000
 68R  H7   C01  C06  119.93  3.000
 68R  H7   C01  C02  120.06  3.000
 68R  C06  C01  C02  120.00  3.000
 68R  H8   C02  C03  120.25  3.000
 68R  H8   C02  C01  119.19  3.000
 68R  C03  C02  C01  120.55  3.000
 68R  H9   C03  C04  118.74  3.000
 68R  H9   C03  C02  121.41  3.000
 68R  C04  C03  C02  119.86  3.000
 68R  N07  C04  C05  122.18  3.000
 68R  N07  C04  C03  117.33  3.000
 68R  C05  C04  C03  120.49  3.000
 68R  C06  C05  C04  118.28  3.000
 68R  C04  C05  C10  117.97  3.000
 68R  C06  C05  C10  123.75  3.000
 68R  C05  C06  C01  120.82  3.000
 68R  C05  C06  CL1  122.68  3.000
 68R  C01  C06  CL1  116.49  3.000
 68R  C08  N07  C04  119.68  3.000
 68R  C19  C08  N09  118.43  3.000
 68R  C19  C08  N07  118.71  3.000
 68R  N09  C08  N07  122.85  3.000
 68R  C08  N09  C13  121.78  3.000
 68R  C13  N09  C10  115.52  3.000
 68R  C08  N09  C10  122.69  3.000
 68R  H10  C14  C15  120.55  3.000
 68R  H10  C14  C13  120.08  3.000
 68R  C15  C14  C13  119.37  3.000
 68R  H11  C16  C17  120.04  3.000
 68R  H11  C16  C15  119.95  3.000
 68R  C17  C16  C15  120.01  3.000
 68R  H12  C18  C17  120.44  3.000
 68R  H12  C18  C13  120.08  3.000
 68R  C17  C18  C13  119.47  3.000
 68R  H13  C19  N21  106.60  3.000
 68R  H13  C19  C08  108.93  3.000
 68R  N21  C19  C08  108.37  3.000
 68R  H13  C19  C20  108.42  3.000
 68R  N21  C19  C20  111.84  3.000
 68R  C08  C19  C20  112.47  3.000
 68R  H14  N21  C19  117.82  3.000
 68R  H14  N21  C22  117.90  3.000
 68R  C19  N21  C22  124.25  3.000
 68R  C29  C23  C24  121.97  3.000
 68R  C24  C23  C22  116.33  3.000
 68R  C29  C23  C22  121.66  3.000
 68R  C26  N25  C24  116.24  3.000
 68R  C26  N27  C22  116.37  3.000
 68R  H16  N28  H15  117.96  3.000
 68R  H16  N28  C24  121.55  3.000
 68R  H15  N28  C24  119.46  3.000
 68R  C30  C29  C23  180.00  3.000
 68R  C31  C30  C29  180.00  3.000
 68R  C35  C31  C32  103.92  3.000
 68R  C35  C31  C30  128.32  3.000
 68R  C32  C31  C30  127.76  3.000
 68R  H17  C32  N33  122.54  3.000
 68R  H17  C32  C31  131.28  3.000
 68R  N33  C32  C31  106.18  3.000
 68R  H18  N33  N34  119.80  3.000
 68R  H18  N33  C32  126.68  3.000
 68R  N34  N33  C32  113.51  3.000
 68R  C35  N34  N33  105.08  3.000
 68R  H19  C35  N34  121.06  3.000
 68R  H19  C35  C31  127.63  3.000
 68R  N34  C35  C31  111.31  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
 68R  CONST_01  C16  C17  C18  C13    0.00   0.0  0
 68R  CONST_02  C16  C15  C14  C13    0.00   0.0  0
 68R  CONST_03  C18  C13  C14  C15    0.00   0.0  0
 68R  CONST_04  C18  C17  C16  C15    0.00   0.0  0
 68R  CONST_05  C14  C13  C18  C17    0.00   0.0  0
 68R  CONST_06  C14  C15  C16  C17    0.00   0.0  0
 68R  CONST_07  N25  C24  C23  C22    0.00   0.0  0
 68R  CONST_08  N25  C26  N27  C22    0.00   0.0  0
 68R  CONST_09  N27  C22  C23  C24    0.00   0.0  0
 68R  CONST_10  N27  C26  N25  C24    0.00   0.0  0
 68R  CONST_11  C23  C22  N27  C26    0.00   0.0  0
 68R  CONST_12  C23  C24  N25  C26    0.00   0.0  0
 68R  CONST_13  C04  C03  C02  C01    0.00   0.0  0
 68R  CONST_14  C04  C05  C06  C01    0.00   0.0  0
 68R  CONST_15  C05  C06  C01  C02    0.00   0.0  0
 68R  CONST_16  C05  C04  C03  C02    0.00   0.0  0
 68R  CONST_17  C06  C01  C02  C03    0.00   0.0  0
 68R  CONST_18  C06  C05  C04  C03    0.00   0.0  0
 68R  CONST_19  N34  N33  C32  C31    0.00   0.0  0
 68R  CONST_20  N33  N34  C35  C31    0.00   0.0  0
 68R  CONST_21  C35  N34  N33  C32    0.00   0.0  0
 68R  CONST_22  N34  C35  C31  C32    0.00   0.0  0
 68R  CONST_23  C35  C31  C32  N33    0.00   0.0  0
 68R  CONST_24  N09  C13  C14  C15  180.00   0.0  0
 68R  CONST_25  N09  C13  C18  C17  180.00   0.0  0
 68R  CONST_26  N07  C08  N09  C10    0.00   0.0  0
 68R  CONST_27  C05  C10  N09  C13  180.00   0.0  0
 68R  CONST_28  N07  C08  N09  C13  180.00   0.0  0
 68R  CONST_29  N09  C08  N07  C04    0.00   0.0  0
 68R  CONST_30  C08  N09  C10  C05    0.00   0.0  0
 68R  CONST_31  CL1  C06  C05  C10    0.00   0.0  0
 68R  CONST_32  N28  C24  C23  C22  180.00   0.0  0
 68R  CONST_33  N21  C22  C23  C24  180.00   0.0  0
 68R  CONST_34  N21  C22  N27  C26  180.00   0.0  0
 68R  CONST_35  N28  C24  N25  C26  180.00   0.0  0
 68R  CONST_36  C02  C01  C06  CL1  180.00   0.0  0
 68R  CONST_37  C04  C05  C06  CL1  180.00   0.0  0
 68R  CONST_38  C29  C23  C24  N25  180.00   0.0  0
 68R  CONST_39  C29  C23  C22  N27  180.00   0.0  0
 68R  CONST_40  N33  C32  C31  C30  180.00   0.0  0
 68R  CONST_41  N34  C35  C31  C30  180.00   0.0  0
 68R  CONST_42  C19  C08  N09  C10  180.00   0.0  0
 68R  CONST_43  O11  C10  N09  C13    0.00   0.0  0
 68R  CONST_44  C19  C08  N09  C13    0.00   0.0  0
 68R  CONST_45  C19  C08  N07  C04  180.00   0.0  0
 68R  CONST_46  O11  C10  N09  C08  180.00   0.0  0
 68R  CONST_47  H2   C17  C18  C13  180.00   0.0  0
 68R  CONST_48  H1   C15  C14  C13  180.00   0.0  0
 68R  CONST_49  H6   C26  N27  C22  180.00   0.0  0
 68R  CONST_50  H9   C03  C02  C01  180.00   0.0  0
 68R  CONST_51  H7   C01  C02  C03  180.00   0.0  0
 68R  CONST_52  H8   C02  C03  C04  180.00   0.0  0
 68R  CONST_53  H12  C18  C13  N09    0.00   0.0  0
 68R  CONST_54  H10  C14  C13  N09    0.00   0.0  0
 68R  CONST_55  H11  C16  C15  C14  180.00   0.0  0
 68R  CONST_56  H18  N33  C32  C31  180.00   0.0  0
 68R  CONST_57  H19  C35  C31  C32  180.00   0.0  0
 68R  CONST_58  H17  C32  N33  N34  180.00   0.0  0
 68R  CONST_59  C23  C22  N21  C19  180.00   0.0  0
 68R  CONST_60  N27  C22  N21  C19    0.00   0.0  0
 68R  CONST_61  H14  N21  C22  C23    0.00   0.0  0
 68R  CONST_62  H15  N28  C24  C23  180.00   0.0  0
 68R  CONST_63  H16  N28  C24  C23    0.00   0.0  0
 68R  Var_01    C18  C13  N09  C10   83.57  30.0  2

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
 68R  chir_01  C19  C08  C20  N21  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
 68R  plan-1  C29  0.020
 68R  plan-1  C30  0.020
 68R  plan-1  C31  0.020
 68R  plan-1  C32  0.020
 68R  plan-1  N33  0.020
 68R  plan-1  N34  0.020
 68R  plan-1  C35  0.020
 68R  plan-1  H17  0.020
 68R  plan-1  H18  0.020
 68R  plan-1  H19  0.020
 68R  plan-2  C13  0.020
 68R  plan-2  C15  0.020
 68R  plan-2  C17  0.020
 68R  plan-2  N09  0.020
 68R  plan-2  C14  0.020
 68R  plan-2  C16  0.020
 68R  plan-2  C18  0.020
 68R  plan-2  H1   0.020
 68R  plan-2  H2   0.020
 68R  plan-2  H10  0.020
 68R  plan-2  H11  0.020
 68R  plan-2  H12  0.020
 68R  plan-3  C22  0.020
 68R  plan-3  C24  0.020
 68R  plan-3  C26  0.020
 68R  plan-3  N21  0.020
 68R  plan-3  C23  0.020
 68R  plan-3  N25  0.020
 68R  plan-3  N27  0.020
 68R  plan-3  N28  0.020
 68R  plan-3  C29  0.020
 68R  plan-3  C30  0.020
 68R  plan-3  H6   0.020
 68R  plan-4  C10  0.020
 68R  plan-4  C13  0.020
 68R  plan-4  C01  0.020
 68R  plan-4  C02  0.020
 68R  plan-4  C03  0.020
 68R  plan-4  C04  0.020
 68R  plan-4  C05  0.020
 68R  plan-4  C06  0.020
 68R  plan-4  N07  0.020
 68R  plan-4  C08  0.020
 68R  plan-4  N09  0.020
 68R  plan-4  O11  0.020
 68R  plan-4  C19  0.020
 68R  plan-4  H7   0.020
 68R  plan-4  H8   0.020
 68R  plan-4  H9   0.020
 68R  plan-4  CL1  0.020
 68R  plan-5  C22  0.020
 68R  plan-5  C19  0.020
 68R  plan-5  N21  0.020
 68R  plan-5  H14  0.020
 68R  plan-6  C24  0.020
 68R  plan-6  N28  0.020
 68R  plan-6  H15  0.020
 68R  plan-6  H16  0.020

