# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 06:17:54 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: ~{N}-[(1~{R})-1-[3-azanyl-5-(trifluoromethyl)phenyl]ethyl]-6,7-dimethoxy-2-methyl-quinazolin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2nc(C)nc(N[C@H](C)c3cc(N)cc(c3)C(F)(F)F)c2cc1OC
#
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
 S3Z  S3Z  ~{N}-[(1~{R})-1-[3-azanyl-5-(trifluoromethyl)phenyl]ethyl]-6,7-dimethoxy-2-methyl-quinazolin-4-amine  ligand  50  29  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S3Z
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
 S3Z  N1   N  N     0  -0.484   -9.8726  -3.4760  -42.0580
 S3Z  N3   N  N     0  -0.493  -11.0876  -2.7996  -43.9687
 S3Z  C4   C  CR6   0   0.532  -10.5917  -1.5777  -43.9181
 S3Z  C5   C  CR66  0  -0.005   -9.6597  -1.2115  -42.8907
 S3Z  C6   C  CR16  0  -0.469   -9.0675   0.0638  -42.7532
 S3Z  C7   C  CR6   0   0.339   -8.1921   0.3221  -41.7322
 S3Z  C8   C  CR6   0   0.333   -7.8702  -0.7110  -40.7972
 S3Z  C10  C  CR66  0   0.237   -9.3429  -2.2266  -41.9762
 S3Z  C17  C  CR6   0   0.189  -13.3818  -0.7001  -45.2612
 S3Z  C21  C  CR16  0  -0.370  -15.8718  -0.2136  -44.1063
 S3Z  C22  C  CR6   0  -0.168  -15.3993  -1.5091  -44.2442
 S3Z  C24  C  CH1   0  -0.191  -12.0064  -0.9714  -45.8467
 S3Z  C26  C  CT    0   1.048  -16.2592  -2.6459  -43.7845
 S3Z  C12  C  CH3   0  -0.439   -6.6399  -1.3190  -38.8741
 S3Z  C14  C  CH3   0  -0.441   -7.8588   2.5723  -42.3762
 S3Z  C18  C  CR16  0  -0.385  -13.8451   0.5989  -45.1118
 S3Z  C19  C  CR6   0   0.357  -15.0968   0.8647  -44.5457
 S3Z  C2   C  CR6   0   0.327  -10.7033  -3.6932  -43.0427
 S3Z  C23  C  CR16  0  -0.384  -14.1647  -1.7657  -44.8280
 S3Z  C25  C  CH3   0  -0.662  -11.7206  -0.1824  -47.1161
 S3Z  C9   C  CR16  0  -0.473   -8.4394  -1.9513  -40.9274
 S3Z  F27  F  F     0  -0.308  -15.5423  -3.7332  -43.4738
 S3Z  F28  F  F     0  -0.310  -16.9814  -2.3326  -42.7005
 S3Z  F29  F  F     0  -0.316  -17.1394  -3.0242  -44.7256
 S3Z  N15  N  NH1   0  -0.661  -10.9685  -0.7002  -44.8650
 S3Z  N20  N  NH2   0  -0.862  -15.5769   2.1498  -44.4650
 S3Z  O11  O  O2    0  -0.451   -7.0059  -0.3547  -39.8426
 S3Z  O13  O  O2    0  -0.458   -7.5763   1.4935  -41.5090
 S3Z  H30  H  HCR6  0   0.280   -9.3006   0.8502  -43.4579
 S3Z  H45  H  HCR6  0   0.269  -16.8368  -0.0153  -43.6553
 S3Z  H47  H  HCH1  0   0.270  -11.9484  -2.0324  -46.0864
 S3Z  H32  H  HCH3  0   0.264   -5.9479  -0.8264  -38.1962
 S3Z  H33  H  HCH3  0   0.233   -7.5042  -1.6702  -38.3048
 S3Z  H34  H  HCH3  0   0.233   -6.1410  -2.1795  -39.3268
 S3Z  H35  H  HCH3  0   0.263   -7.2798   3.4183  -42.0147
 S3Z  H36  H  HCH3  0   0.230   -7.5623   2.3560  -43.4061
 S3Z  H37  H  HCH3  0   0.230   -8.9193   2.8388  -42.3632
 S3Z  H39  H  HCH3  0   0.247  -11.0559  -5.4920  -44.1449
 S3Z  H40  H  HCH3  0   0.241  -10.9606  -5.7213  -42.3915
 S3Z  H41  H  HCH3  0   0.246  -12.3974  -4.9952  -43.1318
 S3Z  H42  H  HCR6  0   0.259  -13.2369   1.4354  -45.4389
 S3Z  H46  H  HCR6  0   0.255  -13.7925  -2.7747  -44.9370
 S3Z  H50  H  HCH3  0   0.247  -10.7609  -0.4818  -47.5367
 S3Z  H48  H  HCH3  0   0.245  -12.4925  -0.3724  -47.8608
 S3Z  H49  H  HCH3  0   0.233  -11.6858   0.8934  -46.9375
 S3Z  H31  H  HCR6  0   0.281   -8.2161  -2.7535  -40.2371
 S3Z  H38  H  HNH1  0   0.408  -10.6890   0.2630  -44.7733
 S3Z  H43  H  HNH2  0   0.382  -16.3015   2.3135  -43.7849
 S3Z  H44  H  HNH2  0   0.382  -14.8879   2.8846  -44.4727
 S3Z  C16  C  CH3   0  -0.729  -11.3088  -5.0557  -43.1774

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
 S3Z  C25  C24  single    1.522  0.020  1.522
 S3Z  C24  C17  single    1.519  0.020  1.519
 S3Z  C24  N15  single    1.454  0.020  1.454
 S3Z  F29  C26  single    1.343  0.020  1.343
 S3Z  C17  C18  aromatic  1.387  0.020  1.387
 S3Z  C17  C23  aromatic  1.391  0.020  1.391
 S3Z  C18  C19  aromatic  1.399  0.020  1.399
 S3Z  C23  C22  aromatic  1.390  0.020  1.390
 S3Z  N15  C4   single    1.345  0.020  1.345
 S3Z  C19  N20  single    1.374  0.020  1.374
 S3Z  C19  C21  aromatic  1.399  0.020  1.399
 S3Z  C22  C21  aromatic  1.386  0.020  1.386
 S3Z  C22  C26  single    1.498  0.020  1.498
 S3Z  C26  F28  single    1.340  0.020  1.340
 S3Z  C26  F27  single    1.339  0.020  1.339
 S3Z  N3   C4   aromatic  1.320  0.020  1.320
 S3Z  N3   C2   aromatic  1.343  0.020  1.343
 S3Z  C4   C5   aromatic  1.435  0.020  1.435
 S3Z  C16  C2   single    1.497  0.020  1.497
 S3Z  C2   N1   aromatic  1.306  0.020  1.306
 S3Z  C5   C6   aromatic  1.413  0.020  1.413
 S3Z  C5   C10  aromatic  1.403  0.020  1.403
 S3Z  C6   C7   aromatic  1.369  0.020  1.369
 S3Z  C14  O13  single    1.413  0.020  1.413
 S3Z  N1   C10  aromatic  1.359  0.020  1.359
 S3Z  C10  C9   aromatic  1.411  0.020  1.411
 S3Z  C7   O13  single    1.342  0.020  1.342
 S3Z  C7   C8   aromatic  1.430  0.020  1.430
 S3Z  C9   C8   aromatic  1.371  0.020  1.371
 S3Z  C8   O11  single    1.336  0.020  1.336
 S3Z  O11  C12  single    1.415  0.020  1.415
 S3Z  C6   H30  single    0.930  0.020  1.080
 S3Z  C21  H45  single    0.930  0.020  1.080
 S3Z  C24  H47  single    0.970  0.020  1.090
 S3Z  C12  H32  single    0.970  0.020  1.090
 S3Z  C12  H33  single    0.970  0.020  1.090
 S3Z  C12  H34  single    0.970  0.020  1.090
 S3Z  C14  H35  single    0.970  0.020  1.090
 S3Z  C14  H36  single    0.970  0.020  1.090
 S3Z  C14  H37  single    0.970  0.020  1.090
 S3Z  C16  H39  single    0.970  0.020  1.090
 S3Z  C16  H40  single    0.970  0.020  1.090
 S3Z  C16  H41  single    0.970  0.020  1.090
 S3Z  C18  H42  single    0.930  0.020  1.080
 S3Z  C23  H46  single    0.930  0.020  1.080
 S3Z  C25  H50  single    0.970  0.020  1.090
 S3Z  C25  H48  single    0.970  0.020  1.090
 S3Z  C25  H49  single    0.970  0.020  1.090
 S3Z  C9   H31  single    0.930  0.020  1.080
 S3Z  N15  H38  single    0.860  0.020  1.020
 S3Z  N20  H43  single    0.890  0.020  1.040
 S3Z  N20  H44  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
 S3Z  C2   N1   C10  116.48  3.000
 S3Z  C2   N3   C4   118.82  3.000
 S3Z  N15  C4   C5   121.32  3.000
 S3Z  C5   C4   N3   120.53  3.000
 S3Z  N15  C4   N3   118.15  3.000
 S3Z  C10  C5   C6   119.68  3.000
 S3Z  C10  C5   C4   115.40  3.000
 S3Z  C6   C5   C4   124.92  3.000
 S3Z  H30  C6   C7   119.11  3.000
 S3Z  H30  C6   C5   120.17  3.000
 S3Z  C7   C6   C5   120.72  3.000
 S3Z  O13  C7   C8   114.74  3.000
 S3Z  C8   C7   C6   119.67  3.000
 S3Z  O13  C7   C6   125.59  3.000
 S3Z  O11  C8   C9   125.29  3.000
 S3Z  O11  C8   C7   114.84  3.000
 S3Z  C9   C8   C7   119.87  3.000
 S3Z  C9   C10  C5   119.20  3.000
 S3Z  C9   C10  N1   118.26  3.000
 S3Z  C5   C10  N1   122.54  3.000
 S3Z  C23  C17  C18  119.71  3.000
 S3Z  C23  C17  C24  119.51  3.000
 S3Z  C18  C17  C24  120.74  3.000
 S3Z  H45  C21  C19  118.90  3.000
 S3Z  H45  C21  C22  121.07  3.000
 S3Z  C19  C21  C22  120.03  3.000
 S3Z  C23  C22  C26  119.93  3.000
 S3Z  C26  C22  C21  118.90  3.000
 S3Z  C23  C22  C21  121.15  3.000
 S3Z  H47  C24  N15  106.99  3.000
 S3Z  H47  C24  C25  108.15  3.000
 S3Z  N15  C24  C25  109.41  3.000
 S3Z  H47  C24  C17  107.88  3.000
 S3Z  N15  C24  C17  110.65  3.000
 S3Z  C25  C24  C17  113.51  3.000
 S3Z  F29  C26  F28  106.24  3.000
 S3Z  F28  C26  F27  106.90  3.000
 S3Z  F29  C26  F27  106.55  3.000
 S3Z  F27  C26  C22  112.35  3.000
 S3Z  F28  C26  C22  112.35  3.000
 S3Z  F29  C26  C22  112.03  3.000
 S3Z  H34  C12  H33  108.89  3.000
 S3Z  H34  C12  H32  108.94  3.000
 S3Z  H33  C12  H32  108.93  3.000
 S3Z  H34  C12  O11  111.78  3.000
 S3Z  H33  C12  O11  111.78  3.000
 S3Z  H32  C12  O11  106.42  3.000
 S3Z  H37  C14  H36  108.80  3.000
 S3Z  H37  C14  H35  108.83  3.000
 S3Z  H36  C14  H35  108.83  3.000
 S3Z  H37  C14  O13  111.89  3.000
 S3Z  H36  C14  O13  111.90  3.000
 S3Z  H35  C14  O13  106.49  3.000
 S3Z  H42  C18  C19  118.50  3.000
 S3Z  H42  C18  C17  120.16  3.000
 S3Z  C19  C18  C17  121.35  3.000
 S3Z  N20  C19  C18  120.93  3.000
 S3Z  N20  C19  C21  120.59  3.000
 S3Z  C18  C19  C21  118.45  3.000
 S3Z  C16  C2   N3   115.33  3.000
 S3Z  C16  C2   N1   118.44  3.000
 S3Z  N3   C2   N1   126.23  3.000
 S3Z  H46  C23  C22  121.38  3.000
 S3Z  H46  C23  C17  119.32  3.000
 S3Z  C22  C23  C17  119.29  3.000
 S3Z  H49  C25  H48  107.86  3.000
 S3Z  H49  C25  H50  107.82  3.000
 S3Z  H48  C25  H50  108.20  3.000
 S3Z  H49  C25  C24  112.37  3.000
 S3Z  H48  C25  C24  110.29  3.000
 S3Z  H50  C25  C24  110.17  3.000
 S3Z  H31  C9   C10  117.50  3.000
 S3Z  H31  C9   C8   121.65  3.000
 S3Z  C10  C9   C8   120.85  3.000
 S3Z  H38  N15  C24  115.98  3.000
 S3Z  H38  N15  C4   118.82  3.000
 S3Z  C24  N15  C4   123.62  3.000
 S3Z  H44  N20  H43  112.25  3.000
 S3Z  H44  N20  C19  116.28  3.000
 S3Z  H43  N20  C19  116.29  3.000
 S3Z  C12  O11  C8   118.34  3.000
 S3Z  C14  O13  C7   118.21  3.000
 S3Z  H41  C16  H40  108.86  3.000
 S3Z  H41  C16  H39  106.88  3.000
 S3Z  H40  C16  H39  108.79  3.000
 S3Z  H41  C16  C2   110.44  3.000
 S3Z  H40  C16  C2   111.26  3.000
 S3Z  H39  C16  C2   110.49  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
 S3Z  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 S3Z  CONST_02  C4   C5   C10  N1      0.00   0.0  0
 S3Z  CONST_03  C6   C5   C10  N1    180.00   0.0  0
 S3Z  CONST_04  C8   C9   C10  N1    180.00   0.0  0
 S3Z  CONST_05  C6   C5   C4   N3    180.00   0.0  0
 S3Z  CONST_06  C10  C5   C4   N3      0.00   0.0  0
 S3Z  CONST_07  C10  N1   C2   N3      0.00   0.0  0
 S3Z  CONST_08  C7   C6   C5   C4    180.00   0.0  0
 S3Z  CONST_09  C9   C10  C5   C4    180.00   0.0  0
 S3Z  CONST_10  C2   N3   C4   C5      0.00   0.0  0
 S3Z  CONST_11  C8   C7   C6   C5      0.00   0.0  0
 S3Z  CONST_12  C2   N1   C10  C5      0.00   0.0  0
 S3Z  CONST_13  C8   C9   C10  C5      0.00   0.0  0
 S3Z  CONST_14  C9   C10  C5   C6      0.00   0.0  0
 S3Z  CONST_15  C9   C8   C7   C6      0.00   0.0  0
 S3Z  CONST_16  C10  C5   C6   C7      0.00   0.0  0
 S3Z  CONST_17  C10  C9   C8   C7      0.00   0.0  0
 S3Z  CONST_18  C21  C19  C18  C17     0.00   0.0  0
 S3Z  CONST_19  C21  C22  C23  C17     0.00   0.0  0
 S3Z  CONST_20  C18  C17  C23  C22     0.00   0.0  0
 S3Z  CONST_21  C18  C19  C21  C22     0.00   0.0  0
 S3Z  CONST_22  C23  C17  C18  C19     0.00   0.0  0
 S3Z  CONST_23  C23  C22  C21  C19     0.00   0.0  0
 S3Z  CONST_24  C9   C10  N1   C2    180.00   0.0  0
 S3Z  CONST_25  C16  C2   N3   C4    180.00   0.0  0
 S3Z  CONST_26  O13  C7   C6   C5    180.00   0.0  0
 S3Z  CONST_27  N15  C4   C5   C6      0.00   0.0  0
 S3Z  CONST_28  O11  C8   C7   C6    180.00   0.0  0
 S3Z  CONST_29  N15  C4   C5   C10   180.00   0.0  0
 S3Z  CONST_30  C16  C2   N1   C10   180.00   0.0  0
 S3Z  CONST_31  O11  C8   C9   C10   180.00   0.0  0
 S3Z  CONST_32  N20  C19  C18  C17   180.00   0.0  0
 S3Z  CONST_33  C26  C22  C23  C17   180.00   0.0  0
 S3Z  CONST_34  C24  C17  C23  C22   180.00   0.0  0
 S3Z  CONST_35  N20  C19  C21  C22   180.00   0.0  0
 S3Z  CONST_36  C19  C18  C17  C24   180.00   0.0  0
 S3Z  CONST_37  C19  C21  C22  C26   180.00   0.0  0
 S3Z  CONST_38  N15  C4   N3   C2    180.00   0.0  0
 S3Z  CONST_39  O13  C7   C8   C9    180.00   0.0  0
 S3Z  CONST_40  H31  C9   C10  N1      0.00   0.0  0
 S3Z  CONST_41  H30  C6   C5   C4      0.00   0.0  0
 S3Z  CONST_42  H42  C18  C19  C21   180.00   0.0  0
 S3Z  CONST_43  H46  C23  C22  C21   180.00   0.0  0
 S3Z  CONST_44  H45  C21  C19  C18   180.00   0.0  0
 S3Z  CONST_45  C24  N15  C4   N3      0.00   0.0  0
 S3Z  CONST_46  C24  N15  C4   C5    180.00   0.0  0
 S3Z  CONST_47  H38  N15  C4   N3    180.00   0.0  0
 S3Z  Var_01    F29  C26  C22  C21    84.93  30.0  2
 S3Z  Var_02    C9   C8   O11  C12    -0.31  30.0  1
 S3Z  Var_03    H39  C16  C2   N1   -120.73  30.0  2
 S3Z  Var_04    H35  C14  O13  C7    178.99  30.0  3
 S3Z  Var_05    H32  C12  O11  C8   -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
 S3Z  chir_01  C24  C25  C17  N15  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
 S3Z  plan-1  C17  0.020
 S3Z  plan-1  C21  0.020
 S3Z  plan-1  C22  0.020
 S3Z  plan-1  C24  0.020
 S3Z  plan-1  C26  0.020
 S3Z  plan-1  C18  0.020
 S3Z  plan-1  C19  0.020
 S3Z  plan-1  C23  0.020
 S3Z  plan-1  N20  0.020
 S3Z  plan-1  H45  0.020
 S3Z  plan-1  H42  0.020
 S3Z  plan-1  H46  0.020
 S3Z  plan-2  N1   0.020
 S3Z  plan-2  N3   0.020
 S3Z  plan-2  C4   0.020
 S3Z  plan-2  C5   0.020
 S3Z  plan-2  C6   0.020
 S3Z  plan-2  C7   0.020
 S3Z  plan-2  C8   0.020
 S3Z  plan-2  C10  0.020
 S3Z  plan-2  C2   0.020
 S3Z  plan-2  C9   0.020
 S3Z  plan-2  N15  0.020
 S3Z  plan-2  O11  0.020
 S3Z  plan-2  O13  0.020
 S3Z  plan-2  H30  0.020
 S3Z  plan-2  H31  0.020
 S3Z  plan-2  C16  0.020
 S3Z  plan-3  C4   0.020
 S3Z  plan-3  C24  0.020
 S3Z  plan-3  N15  0.020
 S3Z  plan-3  H38  0.020
 S3Z  plan-4  C19  0.020
 S3Z  plan-4  N20  0.020
 S3Z  plan-4  H43  0.020
 S3Z  plan-4  H44  0.020

