# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:16:36 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (2~{S})-2-[[4-[[3-(aminomethyl)phenyl]amino]quinazolin-2-yl]amino]-3-methyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](Nc1nc(Nc2cccc(CN)c2)c3ccccc3n1)C(O)=O
#
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
 E88  E88  '(2~{S})-2-[[4-[[3-(aminomethyl)phenyl]amino]quinazolin-2-yl]amino]-3-methyl-butanoic acid'  ligand  49  27  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E88
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
 E88  N1   N  NH1    0  -0.659  -2.1135  -1.0474  -0.6605
 E88  C5   C  CH1    0  -0.271  -4.1061  -2.4281  -0.8308
 E88  C7   C  CH3    0  -0.648  -5.6221  -2.4017  -0.9914
 E88  C15  C  C      0   0.409  -3.9181  -0.6488   1.0069
 E88  C21  C  CR6    0   0.256  -1.1785   2.3193  -0.3612
 E88  C22  C  CR6    0  -0.068   0.2289   2.2302  -0.2756
 E88  C28  C  CR16   0  -0.428   4.2474  -0.2607  -0.0640
 E88  O17  O  OC    -1  -0.612  -5.0572  -0.1624   1.1597
 E88  O16  O  O      0  -0.604  -3.0748  -0.8729   1.8934
 E88  C3   C  CH1    0  -0.138  -3.5426  -1.0468  -0.4425
 E88  C11  C  CH3    0  -0.659  -3.6955  -3.5431   0.1289
 E88  C19  C  C      0   0.589  -1.3731   0.0671  -0.5049
 E88  N24  N  N      0  -0.529  -0.0356  -0.1483  -0.4308
 E88  C23  C  C      0   0.541   0.7549   0.8838  -0.3156
 E88  C43  C  CR16   0  -0.313   0.9973   3.4027  -0.1694
 E88  C45  C  CR16   0  -0.269   0.3951   4.6367  -0.1403
 E88  C47  C  CR16   0  -0.247  -1.0038   4.7294  -0.2189
 E88  C49  C  CR16   0  -0.324  -1.7737   3.5999  -0.3268
 E88  N20  N  N      0  -0.526  -1.9751   1.2340  -0.4751
 E88  N25  N  NH1    0  -0.786   2.0943   0.7047  -0.2283
 E88  C27  C  CR6    0   0.400   2.8755  -0.4523  -0.2685
 E88  C35  C  CR16   0  -0.329   2.3963  -1.7412  -0.5031
 E88  C33  C  CR16   0  -0.234   3.2964  -2.8000  -0.5256
 E88  C31  C  CR16   0  -0.323   4.6508  -2.6056  -0.3177
 E88  C30  C  CR6    0   0.092   5.1395  -1.3196  -0.0885
 E88  C37  C  CH2    0  -0.327   6.6206  -1.1003   0.1012
 E88  N40  N  NH2    0  -0.797   6.9205   0.1334   0.8024
 E88  H1   H  HNH1   0   0.376  -1.6144  -1.9044  -0.4835
 E88  H2   H  HCH1   0   0.224  -3.6789  -2.6607  -1.8136
 E88  H3   H  HCH3   0   0.219  -5.9322  -1.6385  -1.7070
 E88  H4   H  HCH3   0   0.217  -5.9804  -3.3656  -1.3561
 E88  H5   H  HCH3   0   0.223  -6.1217  -2.1920  -0.0466
 E88  H6   H  HCR6   0   0.260   4.6266   0.7372   0.1259
 E88  H8   H  HCH1   0   0.222  -3.9844  -0.3132  -1.1227
 E88  H9   H  HCH3   0   0.222  -4.1008  -3.3819   1.1285
 E88  H10  H  HCH3   0   0.224  -4.0736  -4.5017  -0.2294
 E88  H11  H  HCH3   0   0.220  -2.6136  -3.6472   0.2278
 E88  H12  H  HCR6   0   0.252   2.0781   3.3670  -0.1127
 E88  H13  H  HCR6   0   0.260   0.9972   5.5312  -0.0581
 E88  H14  H  HCR6   0   0.260  -1.4776   5.7026  -0.1951
 E88  H15  H  HCR6   0   0.253  -2.8525   3.6648  -0.3885
 E88  H16  H  HNH1   0   0.426   2.6382   1.5397  -0.0883
 E88  H17  H  HCR6   0   0.287   1.3456  -1.9185  -0.6571
 E88  H18  H  HCR6   0   0.252   2.9192  -3.7990  -0.7040
 E88  H19  H  HCR6   0   0.244   5.3303  -3.4495  -0.3294
 E88  H20  H  HCH2   0   0.216   7.0427  -1.9963   0.5760
 E88  H21  H  HCH2   0   0.244   7.0868  -1.0437  -0.8870
 E88  H22  H  HNH2   0   0.345   6.6727   0.0406   1.7794
 E88  H23  H  HNH2   0   0.357   7.9185   0.2954   0.7798

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
 E88  C7   C5   single    1.525  0.020  1.525
 E88  C37  N40  single    1.450  0.020  1.450
 E88  C37  C30  single    1.509  0.020  1.509
 E88  C5   C3   single    1.542  0.020  1.542
 E88  C5   C11  single    1.527  0.020  1.527
 E88  C30  C28  aromatic  1.385  0.020  1.385
 E88  C30  C31  aromatic  1.395  0.020  1.395
 E88  C28  C27  aromatic  1.400  0.020  1.400
 E88  N1   C3   single    1.446  0.020  1.446
 E88  N1   C19  single    1.347  0.020  1.347
 E88  C3   C15  single    1.549  0.020  1.549
 E88  C31  C33  aromatic  1.384  0.020  1.384
 E88  C19  N24  aromatic  1.357  0.020  1.357
 E88  C19  N20  aromatic  1.313  0.020  1.313
 E88  N24  C23  aromatic  1.305  0.020  1.305
 E88  C27  N25  single    1.397  0.020  1.397
 E88  C27  C35  aromatic  1.395  0.020  1.395
 E88  N25  C23  single    1.354  0.020  1.354
 E88  N20  C21  aromatic  1.351  0.020  1.351
 E88  C23  C22  aromatic  1.446  0.020  1.446
 E88  C33  C35  aromatic  1.390  0.020  1.390
 E88  C21  C22  aromatic  1.413  0.020  1.413
 E88  C21  C49  aromatic  1.413  0.020  1.413
 E88  C22  C43  aromatic  1.406  0.020  1.406
 E88  C49  C47  aromatic  1.371  0.020  1.371
 E88  C43  C45  aromatic  1.373  0.020  1.373
 E88  C47  C45  aromatic  1.404  0.020  1.404
 E88  C15  O16  deloc     1.244  0.020  1.244
 E88  C15  O17  deloc     1.248  0.020  1.248
 E88  N1   H1   single    0.890  0.020  1.040
 E88  C5   H2   single    0.970  0.020  1.090
 E88  C7   H3   single    0.970  0.020  1.090
 E88  C7   H4   single    0.970  0.020  1.090
 E88  C7   H5   single    0.970  0.020  1.090
 E88  C28  H6   single    0.930  0.020  1.080
 E88  C3   H8   single    0.970  0.020  1.090
 E88  C11  H9   single    0.970  0.020  1.090
 E88  C11  H10  single    0.970  0.020  1.090
 E88  C11  H11  single    0.970  0.020  1.090
 E88  C43  H12  single    0.930  0.020  1.080
 E88  C45  H13  single    0.930  0.020  1.080
 E88  C47  H14  single    0.930  0.020  1.080
 E88  C49  H15  single    0.930  0.020  1.080
 E88  N25  H16  single    0.860  0.020  1.020
 E88  C35  H17  single    0.930  0.020  1.080
 E88  C33  H18  single    0.930  0.020  1.080
 E88  C31  H19  single    0.930  0.020  1.080
 E88  C37  H20  single    0.970  0.020  1.090
 E88  C37  H21  single    0.970  0.020  1.090
 E88  N40  H22  single    0.890  0.020  1.040
 E88  N40  H23  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
 E88  H1   N1   C19  114.29  3.000
 E88  H1   N1   C3   117.62  3.000
 E88  C19  N1   C3   121.71  3.000
 E88  H2   C5   C11  107.67  3.000
 E88  H2   C5   C3   105.87  3.000
 E88  C11  C5   C3   113.43  3.000
 E88  H2   C5   C7   107.26  3.000
 E88  C11  C5   C7   110.25  3.000
 E88  C3   C5   C7   111.99  3.000
 E88  H5   C7   H4   108.02  3.000
 E88  H5   C7   H3   107.69  3.000
 E88  H4   C7   H3   107.78  3.000
 E88  H5   C7   C5   111.60  3.000
 E88  H4   C7   C5   110.27  3.000
 E88  H3   C7   C5   111.33  3.000
 E88  C3   C15  O16  117.14  3.000
 E88  O16  C15  O17  127.00  3.000
 E88  C3   C15  O17  115.84  3.000
 E88  N20  C21  C49  118.81  3.000
 E88  C49  C21  C22  118.39  3.000
 E88  N20  C21  C22  122.81  3.000
 E88  C43  C22  C23  125.44  3.000
 E88  C43  C22  C21  119.77  3.000
 E88  C23  C22  C21  114.79  3.000
 E88  H6   C28  C30  118.79  3.000
 E88  H6   C28  C27  119.61  3.000
 E88  C30  C28  C27  121.60  3.000
 E88  H8   C3   C15  108.16  3.000
 E88  H8   C3   C5   107.27  3.000
 E88  C15  C3   C5   112.16  3.000
 E88  H8   C3   N1   107.81  3.000
 E88  C15  C3   N1   112.38  3.000
 E88  C5   C3   N1   108.85  3.000
 E88  H11  C11  H10  106.83  3.000
 E88  H11  C11  H9   107.43  3.000
 E88  H10  C11  H9   107.59  3.000
 E88  H11  C11  C5   113.14  3.000
 E88  H10  C11  C5   109.99  3.000
 E88  H9   C11  C5   111.60  3.000
 E88  N20  C19  N24  126.27  3.000
 E88  N20  C19  N1   119.07  3.000
 E88  N24  C19  N1   114.63  3.000
 E88  C23  N24  C19  118.45  3.000
 E88  N25  C23  N24  120.01  3.000
 E88  N25  C23  C22  118.76  3.000
 E88  N24  C23  C22  121.23  3.000
 E88  H12  C43  C45  117.78  3.000
 E88  H12  C43  C22  121.47  3.000
 E88  C45  C43  C22  120.75  3.000
 E88  H13  C45  C47  120.29  3.000
 E88  H13  C45  C43  120.05  3.000
 E88  C47  C45  C43  119.66  3.000
 E88  H14  C47  C49  119.77  3.000
 E88  H14  C47  C45  119.61  3.000
 E88  C49  C47  C45  120.63  3.000
 E88  H15  C49  C47  120.98  3.000
 E88  H15  C49  C21  118.22  3.000
 E88  C47  C49  C21  120.80  3.000
 E88  C19  N20  C21  116.45  3.000
 E88  H16  N25  C27  112.89  3.000
 E88  H16  N25  C23  115.71  3.000
 E88  C27  N25  C23  131.37  3.000
 E88  C35  C27  N25  125.32  3.000
 E88  C35  C27  C28  119.18  3.000
 E88  N25  C27  C28  115.49  3.000
 E88  H17  C35  C33  120.28  3.000
 E88  H17  C35  C27  120.76  3.000
 E88  C33  C35  C27  118.95  3.000
 E88  H18  C33  C31  119.69  3.000
 E88  H18  C33  C35  118.68  3.000
 E88  C31  C33  C35  121.63  3.000
 E88  H19  C31  C30  120.01  3.000
 E88  H19  C31  C33  120.18  3.000
 E88  C30  C31  C33  119.81  3.000
 E88  C37  C30  C31  119.90  3.000
 E88  C31  C30  C28  118.83  3.000
 E88  C37  C30  C28  121.25  3.000
 E88  H21  C37  H20  105.59  3.000
 E88  H21  C37  N40  107.73  3.000
 E88  H20  C37  N40  113.92  3.000
 E88  H21  C37  C30  108.19  3.000
 E88  H20  C37  C30  108.24  3.000
 E88  N40  C37  C30  112.79  3.000
 E88  H23  N40  H22  106.13  3.000
 E88  H23  N40  C37  109.24  3.000
 E88  H22  N40  C37  109.76  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
 E88  CONST_01  N24  C19  N20  C21     0.00   0.0  0
 E88  CONST_02  N24  C23  C22  C21     0.00   0.0  0
 E88  CONST_03  C45  C43  C22  C21     0.00   0.0  0
 E88  CONST_04  C45  C47  C49  C21     0.00   0.0  0
 E88  CONST_05  C19  N24  C23  C22     0.00   0.0  0
 E88  CONST_06  C19  N20  C21  C22     0.00   0.0  0
 E88  CONST_07  C47  C49  C21  C22     0.00   0.0  0
 E88  CONST_08  C47  C45  C43  C22     0.00   0.0  0
 E88  CONST_09  C33  C31  C30  C28     0.00   0.0  0
 E88  CONST_10  C33  C35  C27  C28     0.00   0.0  0
 E88  CONST_11  C49  C21  N20  C19   180.00   0.0  0
 E88  CONST_12  C43  C22  C23  N24   180.00   0.0  0
 E88  CONST_13  N20  C19  N24  C23     0.00   0.0  0
 E88  CONST_14  N20  C21  C22  C23     0.00   0.0  0
 E88  CONST_15  C49  C21  C22  C23   180.00   0.0  0
 E88  CONST_16  C45  C43  C22  C23   180.00   0.0  0
 E88  CONST_17  N20  C21  C22  C43   180.00   0.0  0
 E88  CONST_18  C49  C21  C22  C43     0.00   0.0  0
 E88  CONST_19  C49  C47  C45  C43     0.00   0.0  0
 E88  CONST_20  N20  C21  C49  C47   180.00   0.0  0
 E88  CONST_21  C31  C30  C28  C27     0.00   0.0  0
 E88  CONST_22  C31  C33  C35  C27     0.00   0.0  0
 E88  CONST_23  C30  C28  C27  C35     0.00   0.0  0
 E88  CONST_24  C30  C31  C33  C35     0.00   0.0  0
 E88  CONST_25  C23  N24  C19  N1    180.00   0.0  0
 E88  CONST_26  C21  N20  C19  N1    180.00   0.0  0
 E88  CONST_27  N25  C23  C22  C21   180.00   0.0  0
 E88  CONST_28  N25  C23  N24  C19   180.00   0.0  0
 E88  CONST_29  N25  C23  C22  C43     0.00   0.0  0
 E88  CONST_30  C30  C28  C27  N25   180.00   0.0  0
 E88  CONST_31  C33  C35  C27  N25   180.00   0.0  0
 E88  CONST_32  C37  C30  C28  C27   180.00   0.0  0
 E88  CONST_33  C37  C30  C31  C33   180.00   0.0  0
 E88  CONST_34  H12  C43  C22  C21   180.00   0.0  0
 E88  CONST_35  H14  C47  C49  C21   180.00   0.0  0
 E88  CONST_36  H15  C49  C21  C22   180.00   0.0  0
 E88  CONST_37  H13  C45  C43  C22   180.00   0.0  0
 E88  CONST_38  H19  C31  C30  C28   180.00   0.0  0
 E88  CONST_39  H17  C35  C27  C28   180.00   0.0  0
 E88  CONST_40  H18  C33  C35  C27   180.00   0.0  0
 E88  CONST_41  H6   C28  C27  C35   180.00   0.0  0
 E88  CONST_42  N24  C19  N1   C3    180.00   0.0  0
 E88  CONST_44  H1   N1   C19  N24     0.00   0.0  0
 E88  Var_01    C27  N25  C23  C22  -178.37  30.0  2
 E88  Var_02    C23  N25  C27  C28  -176.28  30.0  2
 E88  Var_03    N40  C37  C30  C28    22.77  30.0  3
 E88  Var_04    H22  N40  C37  C30    72.35  30.0  3
 E88  Var_05    H9   C11  C5   C7    -62.49  30.0  3
 E88  Var_06    H3   C7   C5   C3     55.13  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
 E88  chir_01  C3  C5  N1  C15  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
 E88  plan-1  C28  0.020
 E88  plan-1  N25  0.020
 E88  plan-1  C27  0.020
 E88  plan-1  C35  0.020
 E88  plan-1  C33  0.020
 E88  plan-1  C31  0.020
 E88  plan-1  C30  0.020
 E88  plan-1  C37  0.020
 E88  plan-1  H6   0.020
 E88  plan-1  H17  0.020
 E88  plan-1  H18  0.020
 E88  plan-1  H19  0.020
 E88  plan-2  N1   0.020
 E88  plan-2  C21  0.020
 E88  plan-2  C22  0.020
 E88  plan-2  C19  0.020
 E88  plan-2  N24  0.020
 E88  plan-2  C23  0.020
 E88  plan-2  C43  0.020
 E88  plan-2  C45  0.020
 E88  plan-2  C47  0.020
 E88  plan-2  C49  0.020
 E88  plan-2  N20  0.020
 E88  plan-2  N25  0.020
 E88  plan-2  H12  0.020
 E88  plan-2  H13  0.020
 E88  plan-2  H14  0.020
 E88  plan-2  H15  0.020
 E88  plan-3  N1   0.020
 E88  plan-3  C3   0.020
 E88  plan-3  C19  0.020
 E88  plan-3  H1   0.020
 E88  plan-4  C15  0.020
 E88  plan-4  O17  0.020
 E88  plan-4  O16  0.020
 E88  plan-4  C3   0.020

