# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 20:10:08 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: ~{N}-[(1~{R})-1-(3-aminophenyl)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)c3cccc(N)c3)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
 S3T  S3T  ~{N}-[(1~{R})-1-(3-aminophenyl)ethyl]-6,7-dimethoxy-2-methyl-quinazolin-4-amine  ligand  47  25  .  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_S3T
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
 S3T  N1   N  N     0  -0.479   -9.8057  -3.3607  -42.0737
 S3T  N3   N  N     0  -0.490  -10.9386  -2.8598  -44.0875
 S3T  C4   C  CR6   0   0.526  -10.4356  -1.6388  -44.1200
 S3T  C5   C  CR66  0  -0.006   -9.5364  -1.1887  -43.1014
 S3T  C6   C  CR16  0  -0.472   -8.9313   0.0876  -43.0688
 S3T  C7   C  CR6   0   0.338   -8.0962   0.4385  -42.0429
 S3T  C8   C  CR6   0   0.333   -7.8327  -0.4981  -40.9935
 S3T  C10  C  CR66  0   0.233   -9.2689  -2.1143  -42.0821
 S3T  C17  C  CR6   0   0.159  -13.1885  -1.2371  -45.5466
 S3T  C21  C  CR16  0  -0.339  -15.8031  -1.2379  -44.5805
 S3T  C22  C  CR16  0  -0.234  -15.3869  -2.2007  -45.4846
 S3T  C24  C  CH1   0  -0.150  -11.7868  -1.2070  -46.1239
 S3T  C12  C  CH3   0  -0.439   -6.7350  -0.9048  -38.9422
 S3T  C14  C  CH3   0  -0.441   -7.6818   2.5951  -42.9146
 S3T  C18  C  CR16  0  -0.379  -13.6019  -0.2695  -44.6413
 S3T  C19  C  CR6   0   0.320  -14.9091  -0.2528  -44.1427
 S3T  C2   C  CR6   0   0.326  -10.5968  -3.6659  -43.0704
 S3T  C23  C  CR16  0  -0.349  -14.0860  -2.2114  -45.9704
 S3T  C25  C  CH3   0  -0.668  -11.7044  -0.2299  -47.2913
 S3T  C9   C  CR16  0  -0.472   -8.4078  -1.7420  -41.0261
 S3T  N15  N  NH1   0  -0.674  -10.7806  -0.8438  -45.1471
 S3T  N20  N  NH2   0  -0.861  -15.3236   0.7431  -43.2815
 S3T  O11  O  O2    0  -0.451   -7.0101  -0.0539  -40.0388
 S3T  O13  O  O2    0  -0.458   -7.4739   1.6203  -41.9133
 S3T  H26  H  HCR6  0   0.280   -9.1194   0.7990  -43.8611
 S3T  H42  H  HCR6  0   0.245  -16.0876  -2.9615  -45.8060
 S3T  H44  H  HCH1  0   0.257  -11.5518  -2.2077  -46.4929
 S3T  H28  H  HCH3  0   0.264   -6.0773  -0.3492  -38.2791
 S3T  H29  H  HCH3  0   0.233   -7.6453  -1.1714  -38.3994
 S3T  H30  H  HCH3  0   0.233   -6.2303  -1.8214  -39.2572
 S3T  H31  H  HCH3  0   0.263   -7.1015   3.4665  -42.6221
 S3T  H32  H  HCH3  0   0.230   -7.3367   2.2527  -43.8940
 S3T  H33  H  HCH3  0   0.230   -8.7345   2.8816  -42.9921
 S3T  H38  H  HCR6  0   0.241  -12.9031   0.4880  -44.3004
 S3T  H43  H  HCR6  0   0.236  -13.7683  -2.9777  -46.6673
 S3T  H47  H  HCH3  0   0.243  -10.7115  -0.2450  -47.7421
 S3T  H45  H  HCH3  0   0.247  -12.4306  -0.4969  -48.0572
 S3T  H46  H  HCH3  0   0.232  -11.9215   0.7894  -46.9658
 S3T  H27  H  HCR6  0   0.280   -8.2227  -2.4735  -40.2512
 S3T  H34  H  HNH1  0   0.410  -10.5135   0.1259  -45.1148
 S3T  H39  H  HNH2  0   0.376  -16.1156   0.5155  -42.7021
 S3T  H40  H  HNH2  0   0.375  -14.5944   1.1957  -42.7536
 S3T  C16  C  CH3   0  -0.730  -11.2100  -5.0338  -43.0757
 S3T  H41  H  HCR6  0   0.249  -16.8205  -1.2443  -44.2067
 S3T  H35  H  HCH3  0   0.242  -11.6025  -5.2849  -44.0584
 S3T  H36  H  HCH3  0   0.245  -10.4841  -5.7882  -42.7761
 S3T  H37  H  HCH3  0   0.252  -12.0369  -5.0807  -42.3637

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
 S3T  C25  C24  single    1.525  0.020  1.525
 S3T  C24  C17  single    1.516  0.020  1.516
 S3T  C24  N15  single    1.449  0.020  1.449
 S3T  C17  C23  aromatic  1.391  0.020  1.391
 S3T  C17  C18  aromatic  1.388  0.020  1.388
 S3T  C23  C22  aromatic  1.389  0.020  1.389
 S3T  C18  C19  aromatic  1.399  0.020  1.399
 S3T  N15  C4   single    1.344  0.020  1.344
 S3T  C22  C21  aromatic  1.385  0.020  1.385
 S3T  C19  C21  aromatic  1.401  0.020  1.401
 S3T  C19  N20  single    1.380  0.020  1.380
 S3T  N3   C4   aromatic  1.321  0.020  1.321
 S3T  N3   C2   aromatic  1.342  0.020  1.342
 S3T  C4   C5   aromatic  1.431  0.020  1.431
 S3T  C16  C2   single    1.499  0.020  1.499
 S3T  C2   N1   aromatic  1.309  0.020  1.309
 S3T  C5   C6   aromatic  1.413  0.020  1.413
 S3T  C5   C10  aromatic  1.403  0.020  1.403
 S3T  C6   C7   aromatic  1.369  0.020  1.369
 S3T  C14  O13  single    1.413  0.020  1.413
 S3T  N1   C10  aromatic  1.357  0.020  1.357
 S3T  C10  C9   aromatic  1.413  0.020  1.413
 S3T  C7   O13  single    1.342  0.020  1.342
 S3T  C7   C8   aromatic  1.431  0.020  1.431
 S3T  C9   C8   aromatic  1.371  0.020  1.371
 S3T  C8   O11  single    1.336  0.020  1.336
 S3T  O11  C12  single    1.415  0.020  1.415
 S3T  C6   H26  single    0.930  0.020  1.080
 S3T  C21  H41  single    0.930  0.020  1.080
 S3T  C22  H42  single    0.930  0.020  1.080
 S3T  C24  H44  single    0.970  0.020  1.090
 S3T  C12  H28  single    0.970  0.020  1.090
 S3T  C12  H29  single    0.970  0.020  1.090
 S3T  C12  H30  single    0.970  0.020  1.090
 S3T  C14  H31  single    0.970  0.020  1.090
 S3T  C14  H32  single    0.970  0.020  1.090
 S3T  C14  H33  single    0.970  0.020  1.090
 S3T  C16  H35  single    0.970  0.020  1.090
 S3T  C16  H36  single    0.970  0.020  1.090
 S3T  C16  H37  single    0.970  0.020  1.090
 S3T  C18  H38  single    0.930  0.020  1.080
 S3T  C23  H43  single    0.930  0.020  1.080
 S3T  C25  H47  single    0.970  0.020  1.090
 S3T  C25  H45  single    0.970  0.020  1.090
 S3T  C25  H46  single    0.970  0.020  1.090
 S3T  C9   H27  single    0.930  0.020  1.080
 S3T  N15  H34  single    0.860  0.020  1.020
 S3T  N20  H39  single    0.890  0.020  1.040
 S3T  N20  H40  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
 S3T  C2   N1   C10  116.65  3.000
 S3T  C2   N3   C4   118.48  3.000
 S3T  N15  C4   C5   121.28  3.000
 S3T  C5   C4   N3   120.82  3.000
 S3T  N15  C4   N3   117.90  3.000
 S3T  C10  C5   C6   119.85  3.000
 S3T  C10  C5   C4   115.43  3.000
 S3T  C6   C5   C4   124.71  3.000
 S3T  H26  C6   C7   119.12  3.000
 S3T  H26  C6   C5   120.20  3.000
 S3T  C7   C6   C5   120.68  3.000
 S3T  O13  C7   C8   114.84  3.000
 S3T  C8   C7   C6   119.62  3.000
 S3T  O13  C7   C6   125.54  3.000
 S3T  O11  C8   C9   125.23  3.000
 S3T  O11  C8   C7   114.82  3.000
 S3T  C9   C8   C7   119.95  3.000
 S3T  C9   C10  C5   119.05  3.000
 S3T  C9   C10  N1   118.59  3.000
 S3T  C5   C10  N1   122.36  3.000
 S3T  C23  C17  C18  119.66  3.000
 S3T  C18  C17  C24  120.65  3.000
 S3T  C23  C17  C24  119.64  3.000
 S3T  H41  C21  C19  119.70  3.000
 S3T  H41  C21  C22  120.21  3.000
 S3T  C19  C21  C22  120.09  3.000
 S3T  H42  C22  C23  119.80  3.000
 S3T  H42  C22  C21  119.19  3.000
 S3T  C23  C22  C21  121.02  3.000
 S3T  H44  C24  N15  107.95  3.000
 S3T  H44  C24  C25  108.47  3.000
 S3T  N15  C24  C25  108.55  3.000
 S3T  H44  C24  C17  108.02  3.000
 S3T  N15  C24  C17  112.98  3.000
 S3T  C25  C24  C17  110.75  3.000
 S3T  H30  C12  H29  108.86  3.000
 S3T  H30  C12  H28  108.97  3.000
 S3T  H29  C12  H28  109.01  3.000
 S3T  H30  C12  O11  111.77  3.000
 S3T  H29  C12  O11  111.70  3.000
 S3T  H28  C12  O11  106.45  3.000
 S3T  H33  C14  H32  108.80  3.000
 S3T  H33  C14  H31  108.84  3.000
 S3T  H32  C14  H31  108.88  3.000
 S3T  H33  C14  O13  111.88  3.000
 S3T  H32  C14  O13  111.85  3.000
 S3T  H31  C14  O13  106.49  3.000
 S3T  H38  C18  C19  118.76  3.000
 S3T  H38  C18  C17  119.97  3.000
 S3T  C19  C18  C17  121.27  3.000
 S3T  N20  C19  C18  120.77  3.000
 S3T  N20  C19  C21  120.72  3.000
 S3T  C18  C19  C21  118.46  3.000
 S3T  C16  C2   N3   116.18  3.000
 S3T  C16  C2   N1   117.57  3.000
 S3T  N3   C2   N1   126.24  3.000
 S3T  H43  C23  C22  120.34  3.000
 S3T  H43  C23  C17  120.15  3.000
 S3T  C22  C23  C17  119.51  3.000
 S3T  H46  C25  H45  107.82  3.000
 S3T  H46  C25  H47  108.50  3.000
 S3T  H45  C25  H47  108.24  3.000
 S3T  H46  C25  C24  111.06  3.000
 S3T  H45  C25  C24  110.21  3.000
 S3T  H47  C25  C24  110.91  3.000
 S3T  H27  C9   C10  117.49  3.000
 S3T  H27  C9   C8   121.67  3.000
 S3T  C10  C9   C8   120.84  3.000
 S3T  H34  N15  C24  116.59  3.000
 S3T  H34  N15  C4   118.51  3.000
 S3T  C24  N15  C4   123.05  3.000
 S3T  H40  N20  H39  111.66  3.000
 S3T  H40  N20  C19  115.70  3.000
 S3T  H39  N20  C19  115.59  3.000
 S3T  C12  O11  C8   118.26  3.000
 S3T  C14  O13  C7   118.10  3.000
 S3T  H37  C16  H36  107.20  3.000
 S3T  H37  C16  H35  107.81  3.000
 S3T  H36  C16  H35  109.23  3.000
 S3T  H37  C16  C2   110.27  3.000
 S3T  H36  C16  C2   111.01  3.000
 S3T  H35  C16  C2   111.19  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
 S3T  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 S3T  CONST_02  C4   C5   C10  N1      0.00   0.0  0
 S3T  CONST_03  C6   C5   C10  N1    180.00   0.0  0
 S3T  CONST_04  C8   C9   C10  N1    180.00   0.0  0
 S3T  CONST_05  C6   C5   C4   N3    180.00   0.0  0
 S3T  CONST_06  C10  C5   C4   N3      0.00   0.0  0
 S3T  CONST_07  C10  N1   C2   N3      0.00   0.0  0
 S3T  CONST_08  C7   C6   C5   C4    180.00   0.0  0
 S3T  CONST_09  C9   C10  C5   C4    180.00   0.0  0
 S3T  CONST_10  C2   N3   C4   C5      0.00   0.0  0
 S3T  CONST_11  C8   C7   C6   C5      0.00   0.0  0
 S3T  CONST_12  C2   N1   C10  C5      0.00   0.0  0
 S3T  CONST_13  C8   C9   C10  C5      0.00   0.0  0
 S3T  CONST_14  C9   C10  C5   C6      0.00   0.0  0
 S3T  CONST_15  C9   C8   C7   C6      0.00   0.0  0
 S3T  CONST_16  C10  C5   C6   C7      0.00   0.0  0
 S3T  CONST_17  C10  C9   C8   C7      0.00   0.0  0
 S3T  CONST_18  C21  C22  C23  C17     0.00   0.0  0
 S3T  CONST_19  C21  C19  C18  C17     0.00   0.0  0
 S3T  CONST_20  C18  C17  C23  C22     0.00   0.0  0
 S3T  CONST_21  C18  C19  C21  C22     0.00   0.0  0
 S3T  CONST_22  C23  C17  C18  C19     0.00   0.0  0
 S3T  CONST_23  C23  C22  C21  C19     0.00   0.0  0
 S3T  CONST_24  C9   C10  N1   C2    180.00   0.0  0
 S3T  CONST_25  C16  C2   N3   C4    180.00   0.0  0
 S3T  CONST_26  O13  C7   C6   C5    180.00   0.0  0
 S3T  CONST_27  N15  C4   C5   C6      0.00   0.0  0
 S3T  CONST_28  O11  C8   C7   C6    180.00   0.0  0
 S3T  CONST_29  N15  C4   C5   C10   180.00   0.0  0
 S3T  CONST_30  C16  C2   N1   C10   180.00   0.0  0
 S3T  CONST_31  O11  C8   C9   C10   180.00   0.0  0
 S3T  CONST_32  N20  C19  C18  C17   180.00   0.0  0
 S3T  CONST_33  C24  C17  C23  C22   180.00   0.0  0
 S3T  CONST_34  N20  C19  C21  C22   180.00   0.0  0
 S3T  CONST_35  C19  C18  C17  C24   180.00   0.0  0
 S3T  CONST_36  N15  C4   N3   C2    180.00   0.0  0
 S3T  CONST_37  O13  C7   C8   C9    180.00   0.0  0
 S3T  CONST_38  H27  C9   C10  N1      0.00   0.0  0
 S3T  CONST_39  H26  C6   C5   C4      0.00   0.0  0
 S3T  CONST_40  H42  C22  C23  C17   180.00   0.0  0
 S3T  CONST_41  H43  C23  C22  C21   180.00   0.0  0
 S3T  CONST_42  H38  C18  C19  C21   180.00   0.0  0
 S3T  CONST_43  H41  C21  C19  C18   180.00   0.0  0
 S3T  CONST_44  C24  N15  C4   N3      0.00   0.0  0
 S3T  CONST_45  C24  N15  C4   C5    180.00   0.0  0
 S3T  CONST_46  H34  N15  C4   N3    180.00   0.0  0
 S3T  Var_01    C9   C8   O11  C12    -2.30  30.0  1
 S3T  Var_02    H35  C16  C2   N1   -163.61  30.0  2
 S3T  Var_03    H31  C14  O13  C7    179.71  30.0  3
 S3T  Var_04    H28  C12  O11  C8   -178.49  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
 S3T  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
 S3T  plan-1  C17  0.020
 S3T  plan-1  C21  0.020
 S3T  plan-1  C22  0.020
 S3T  plan-1  C24  0.020
 S3T  plan-1  C18  0.020
 S3T  plan-1  C19  0.020
 S3T  plan-1  C23  0.020
 S3T  plan-1  N20  0.020
 S3T  plan-1  H42  0.020
 S3T  plan-1  H38  0.020
 S3T  plan-1  H43  0.020
 S3T  plan-1  H41  0.020
 S3T  plan-2  N1   0.020
 S3T  plan-2  N3   0.020
 S3T  plan-2  C4   0.020
 S3T  plan-2  C5   0.020
 S3T  plan-2  C6   0.020
 S3T  plan-2  C7   0.020
 S3T  plan-2  C8   0.020
 S3T  plan-2  C10  0.020
 S3T  plan-2  C2   0.020
 S3T  plan-2  C9   0.020
 S3T  plan-2  N15  0.020
 S3T  plan-2  O11  0.020
 S3T  plan-2  O13  0.020
 S3T  plan-2  H26  0.020
 S3T  plan-2  H27  0.020
 S3T  plan-2  C16  0.020
 S3T  plan-3  C4   0.020
 S3T  plan-3  C24  0.020
 S3T  plan-3  N15  0.020
 S3T  plan-3  H34  0.020
 S3T  plan-4  C19  0.020
 S3T  plan-4  N20  0.020
 S3T  plan-4  H39  0.020
 S3T  plan-4  H40  0.020

