# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 03:51:20 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: N-(4-{[(2-amino-4-hydroxyquinazolin-6-yl)methyl](formyl)amino}benzoyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(O)c2cc(CN(C=O)c3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)ccc2n1
#
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
 6DD  6DD  'N-(4-{[(2-amino-4-hydroxyquinazolin-6-yl)methyl](formyl)amino}benzoyl)-L-glutamic acid'  ligand  55  34  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6DD
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
 6DD  C5   C  CR16  0  -0.339  -3.8938  -0.7630  -0.9737
 6DD  C4A  C  CR66  0  -0.073  -4.3411   0.5621  -0.8280
 6DD  C4   C  CR6   0   0.498  -4.4897   1.4864  -1.9030
 6DD  O4   O  OH1   0  -0.585  -4.1820   1.0711  -3.1181
 6DD  N3   N  N     0  -0.504  -4.9080   2.7030  -1.7347
 6DD  C2   C  CR6   0   0.535  -5.2073   3.0910  -0.4676
 6DD  NA2  N  NH2   0  -0.820  -5.6711   4.3477  -0.3485
 6DD  N1   N  N     0  -0.513  -5.1062   2.3488   0.6131
 6DD  C8A  C  CR66  0   0.267  -4.6754   1.0809   0.4399
 6DD  C8   C  CR16  0  -0.313  -4.5487   0.2232   1.5563
 6DD  C7   C  CR16  0  -0.268  -4.1160  -1.0647   1.3937
 6DD  C6   C  CR6   0   0.117  -3.7824  -1.5804   0.1223
 6DD  C9   C  CH2   0  -0.424  -3.2935  -2.9952  -0.0009
 6DD  N10  N  NT    0  -0.527  -2.0152  -3.1764   0.6819
 6DD  CA1  C  C1    0   0.238  -1.9130  -3.9849   1.7673
 6DD  OA1  O  O     0  -0.462  -2.8351  -4.5868   2.2779
 6DD  C14  C  CR6   0   0.362  -0.8983  -2.4390   0.2403
 6DD  C15  C  CR16  0  -0.278  -0.6089  -2.3457  -1.1191
 6DD  C16  C  CR16  0  -0.264   0.4800  -1.6116  -1.5495
 6DD  C13  C  CR16  0  -0.288  -0.0878  -1.7739   1.1559
 6DD  C12  C  CR16  0  -0.281   1.0228  -1.0695   0.7217
 6DD  C11  C  CR6   0  -0.048   1.3206  -0.9818  -0.6348
 6DD  C    C  C     0   0.550   2.4802  -0.2030  -1.1525
 6DD  O    O  O     0  -0.477   2.4707   0.2991  -2.2660
 6DD  N    N  NH1   0  -0.653   3.5292  -0.0742  -0.3131
 6DD  CA   C  CH1   0  -0.194   4.7215   0.6196  -0.7176
 6DD  CT   C  C     0   0.550   5.4867  -0.1929  -1.7540
 6DD  O2   O  O     0  -0.429   5.3227  -1.3672  -1.9535
 6DD  O1   O  OH1   0  -0.590   6.3788   0.5534  -2.3881
 6DD  CB   C  CH2   0  -0.467   5.6116   0.9012   0.4967
 6DD  CG   C  CH2   0  -0.578   4.9044   1.7945   1.5036
 6DD  CD   C  C     0   0.556   5.7578   2.1193   2.6981
 6DD  OE2  O  O     0  -0.442   6.8937   1.7499   2.8599
 6DD  OE1  O  OH1   0  -0.595   5.1061   2.8774   3.5728
 6DD  H1   H  HCR6  0   0.262  -3.6375  -1.1412  -1.9557
 6DD  H3   H  HNH2  0   0.398  -5.5872   4.9790  -1.1257
 6DD  H4   H  HNH2  0   0.397  -5.7666   4.7484   0.5681
 6DD  H5   H  HCR6  0   0.259  -4.8040   0.6039   2.5366
 6DD  H6   H  HCR6  0   0.258  -4.0350  -1.7082   2.2623
 6DD  H7   H  HCH2  0   0.294  -4.0010  -3.6899   0.4487
 6DD  H8   H  HCH2  0   0.280  -3.1984  -3.2785  -1.0498
 6DD  H9   H  H     0   0.225  -0.8830  -4.0580   2.1434
 6DD  H10  H  HCR6  0   0.278  -1.2211  -2.8581  -1.8483
 6DD  H11  H  HCR6  0   0.267   0.6907  -1.5472  -2.6085
 6DD  H12  H  HCR6  0   0.286  -0.3352  -1.7795   2.2092
 6DD  H13  H  HCR6  0   0.265   1.6219  -0.5483   1.4574
 6DD  H14  H  HNH1  0   0.411   3.6051  -0.7084   0.4676
 6DD  H15  H  HCH1  0   0.296   4.4406   1.5728  -1.1735
 6DD  H16  H  HOH1  0   0.486   6.8882   0.0130  -3.0114
 6DD  H17  H  HCH2  0   0.261   5.9049  -0.0442   0.9607
 6DD  H18  H  HCH2  0   0.275   6.5275   1.3842   0.1565
 6DD  H19  H  HCH2  0   0.290   4.6027   2.7346   1.0313
 6DD  H20  H  HCH2  0   0.285   3.9778   1.3354   1.8581
 6DD  H21  H  HOH1  0   0.480   5.6784   3.0795   4.3281
 6DD  H2   H  HOH1  0   0.484  -4.3321   1.7876  -3.7519

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
 6DD  CG   CB   single    1.521  0.020  1.521
 6DD  CG   CD   single    1.504  0.020  1.504
 6DD  CB   CA   single    1.532  0.020  1.532
 6DD  O    C    double    1.222  0.020  1.222
 6DD  CD   OE2  double    1.205  0.020  1.205
 6DD  CD   OE1  single    1.328  0.020  1.328
 6DD  C    C11  single    1.490  0.020  1.490
 6DD  C    N    single    1.350  0.020  1.350
 6DD  C16  C15  aromatic  1.382  0.020  1.382
 6DD  C16  C11  aromatic  1.393  0.020  1.393
 6DD  O4   C4   single    1.320  0.020  1.320
 6DD  N3   C4   aromatic  1.297  0.020  1.297
 6DD  N3   C2   aromatic  1.359  0.020  1.359
 6DD  CA   N    single    1.438  0.020  1.438
 6DD  CA   CT   single    1.523  0.020  1.523
 6DD  NA2  C2   single    1.345  0.020  1.345
 6DD  C15  C14  aromatic  1.393  0.020  1.393
 6DD  C11  C12  aromatic  1.392  0.020  1.392
 6DD  O2   CT   double    1.202  0.020  1.202
 6DD  C4   C4A  aromatic  1.426  0.020  1.426
 6DD  C2   N1   aromatic  1.315  0.020  1.315
 6DD  OA1  CA1  double    1.214  0.020  1.214
 6DD  CT   O1   single    1.325  0.020  1.325
 6DD  C4A  C5   aromatic  1.406  0.020  1.406
 6DD  C4A  C8A  aromatic  1.410  0.020  1.410
 6DD  N1   C8A  aromatic  1.350  0.020  1.350
 6DD  C14  N10  single    1.409  0.020  1.409
 6DD  C14  C13  aromatic  1.392  0.020  1.392
 6DD  C12  C13  aromatic  1.385  0.020  1.385
 6DD  CA1  N10  single    1.357  0.020  1.357
 6DD  C5   C6   aromatic  1.372  0.020  1.372
 6DD  C8A  C8   aromatic  1.414  0.020  1.414
 6DD  N10  C9   single    1.461  0.020  1.461
 6DD  C6   C7   aromatic  1.412  0.020  1.412
 6DD  C6   C9   single    1.502  0.020  1.502
 6DD  C8   C7   aromatic  1.368  0.020  1.368
 6DD  C5   H1   single    0.930  0.020  1.080
 6DD  NA2  H3   single    0.890  0.020  1.040
 6DD  NA2  H4   single    0.890  0.020  1.040
 6DD  C8   H5   single    0.930  0.020  1.080
 6DD  C7   H6   single    0.930  0.020  1.080
 6DD  C9   H7   single    0.970  0.020  1.090
 6DD  C9   H8   single    0.970  0.020  1.090
 6DD  CA1  H9   single    0.930  0.020  1.080
 6DD  C15  H10  single    0.930  0.020  1.080
 6DD  C16  H11  single    0.930  0.020  1.080
 6DD  C13  H12  single    0.930  0.020  1.080
 6DD  C12  H13  single    0.930  0.020  1.080
 6DD  N    H14  single    0.890  0.020  1.040
 6DD  CA   H15  single    0.970  0.020  1.090
 6DD  O1   H16  single    0.850  0.020  0.980
 6DD  CB   H17  single    0.970  0.020  1.090
 6DD  CB   H18  single    0.970  0.020  1.090
 6DD  CG   H19  single    0.970  0.020  1.090
 6DD  CG   H20  single    0.970  0.020  1.090
 6DD  OE1  H21  single    0.850  0.020  0.980
 6DD  O4   H2   single    0.850  0.020  0.980

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
 6DD  H1   C5   C6   119.81  3.000
 6DD  H1   C5   C4A  119.89  3.000
 6DD  C6   C5   C4A  120.30  3.000
 6DD  C8A  C4A  C4   114.51  3.000
 6DD  C8A  C4A  C5   121.02  3.000
 6DD  C4   C4A  C5   124.48  3.000
 6DD  N3   C4   O4   119.30  3.000
 6DD  N3   C4   C4A  122.94  3.000
 6DD  O4   C4   C4A  117.76  3.000
 6DD  H2   O4   C4   109.48  3.000
 6DD  C2   N3   C4   117.37  3.000
 6DD  N1   C2   NA2  118.76  3.000
 6DD  N1   C2   N3   126.05  3.000
 6DD  NA2  C2   N3   115.18  3.000
 6DD  H4   NA2  H3   117.58  3.000
 6DD  H4   NA2  C2   119.08  3.000
 6DD  H3   NA2  C2   119.33  3.000
 6DD  C8A  N1   C2   116.68  3.000
 6DD  C8   C8A  N1   119.80  3.000
 6DD  C8   C8A  C4A  117.75  3.000
 6DD  N1   C8A  C4A  122.44  3.000
 6DD  H5   C8   C7   120.89  3.000
 6DD  H5   C8   C8A  118.74  3.000
 6DD  C7   C8   C8A  120.37  3.000
 6DD  H6   C7   C6   119.15  3.000
 6DD  H6   C7   C8   119.15  3.000
 6DD  C6   C7   C8   121.70  3.000
 6DD  C9   C6   C7   119.66  3.000
 6DD  C9   C6   C5   121.48  3.000
 6DD  C7   C6   C5   118.86  3.000
 6DD  H8   C9   H7   106.74  3.000
 6DD  H8   C9   N10  109.94  3.000
 6DD  H7   C9   N10  107.25  3.000
 6DD  H8   C9   C6   110.61  3.000
 6DD  H7   C9   C6   110.83  3.000
 6DD  N10  C9   C6   111.31  3.000
 6DD  C14  N10  CA1  120.17  3.000
 6DD  CA1  N10  C9   120.91  3.000
 6DD  C14  N10  C9   118.83  3.000
 6DD  H9   CA1  OA1  122.35  3.000
 6DD  H9   CA1  N10  112.57  3.000
 6DD  OA1  CA1  N10  125.08  3.000
 6DD  C13  C14  C15  119.27  3.000
 6DD  C13  C14  N10  120.36  3.000
 6DD  C15  C14  N10  120.36  3.000
 6DD  H10  C15  C16  119.20  3.000
 6DD  H10  C15  C14  120.58  3.000
 6DD  C16  C15  C14  120.21  3.000
 6DD  H11  C16  C11  119.90  3.000
 6DD  H11  C16  C15  119.34  3.000
 6DD  C11  C16  C15  120.74  3.000
 6DD  H12  C13  C12  119.43  3.000
 6DD  H12  C13  C14  120.31  3.000
 6DD  C12  C13  C14  120.24  3.000
 6DD  H13  C12  C11  120.91  3.000
 6DD  H13  C12  C13  118.40  3.000
 6DD  C11  C12  C13  120.62  3.000
 6DD  C    C11  C12  122.57  3.000
 6DD  C12  C11  C16  118.85  3.000
 6DD  C    C11  C16  118.55  3.000
 6DD  N    C    O    122.26  3.000
 6DD  N    C    C11  116.02  3.000
 6DD  O    C    C11  121.71  3.000
 6DD  H14  N    CA   117.31  3.000
 6DD  H14  N    C    118.68  3.000
 6DD  CA   N    C    121.04  3.000
 6DD  H15  CA   CB   108.64  3.000
 6DD  H15  CA   CT   108.09  3.000
 6DD  CB   CA   CT   110.22  3.000
 6DD  H15  CA   N    108.96  3.000
 6DD  CT   CA   N    110.53  3.000
 6DD  CB   CA   N    110.34  3.000
 6DD  O1   CT   O2   124.24  3.000
 6DD  O1   CT   CA   111.32  3.000
 6DD  O2   CT   CA   124.43  3.000
 6DD  H16  O1   CT   110.34  3.000
 6DD  H18  CB   H17  106.87  3.000
 6DD  H18  CB   CG   109.70  3.000
 6DD  H17  CB   CG   110.60  3.000
 6DD  H18  CB   CA   108.80  3.000
 6DD  H17  CB   CA   109.48  3.000
 6DD  CG   CB   CA   111.27  3.000
 6DD  H20  CG   H19  105.49  3.000
 6DD  H20  CG   CD   108.31  3.000
 6DD  H19  CG   CD   108.29  3.000
 6DD  H20  CG   CB   111.23  3.000
 6DD  H19  CG   CB   110.31  3.000
 6DD  CD   CG   CB   112.89  3.000
 6DD  OE1  CD   OE2  123.29  3.000
 6DD  OE1  CD   CG   111.59  3.000
 6DD  OE2  CD   CG   125.13  3.000
 6DD  H21  OE1  CD   110.03  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
 6DD  CONST_01  N3   C4   C4A  C5    180.00   0.0  0
 6DD  CONST_02  N1   C8A  C4A  C5    180.00   0.0  0
 6DD  CONST_03  C8   C8A  C4A  C5      0.00   0.0  0
 6DD  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 6DD  CONST_05  C2   N3   C4   C4A     0.00   0.0  0
 6DD  CONST_06  C7   C6   C5   C4A     0.00   0.0  0
 6DD  CONST_07  C2   N1   C8A  C4A     0.00   0.0  0
 6DD  CONST_08  C7   C8   C8A  C4A     0.00   0.0  0
 6DD  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 6DD  CONST_10  C6   C5   C4A  C4    180.00   0.0  0
 6DD  CONST_11  N1   C8A  C4A  C4      0.00   0.0  0
 6DD  CONST_12  C8   C8A  C4A  C4    180.00   0.0  0
 6DD  CONST_13  C8A  C4A  C4   N3      0.00   0.0  0
 6DD  CONST_14  C8A  N1   C2   N3      0.00   0.0  0
 6DD  CONST_15  C8   C8A  N1   C2    180.00   0.0  0
 6DD  CONST_16  C7   C8   C8A  N1    180.00   0.0  0
 6DD  CONST_17  C6   C5   C4A  C8A     0.00   0.0  0
 6DD  CONST_18  C6   C7   C8   C8A     0.00   0.0  0
 6DD  CONST_19  C11  C16  C15  C14     0.00   0.0  0
 6DD  CONST_20  C11  C12  C13  C14     0.00   0.0  0
 6DD  CONST_21  C12  C11  C16  C15     0.00   0.0  0
 6DD  CONST_22  C12  C13  C14  C15     0.00   0.0  0
 6DD  CONST_23  C13  C14  C15  C16     0.00   0.0  0
 6DD  CONST_24  C13  C12  C11  C16     0.00   0.0  0
 6DD  CONST_25  O4   C4   C4A  C5      0.00   0.0  0
 6DD  CONST_26  C9   C6   C5   C4A   180.00   0.0  0
 6DD  CONST_27  NA2  C2   N3   C4    180.00   0.0  0
 6DD  CONST_28  C2   N3   C4   O4    180.00   0.0  0
 6DD  CONST_29  C8A  C4A  C4   O4    180.00   0.0  0
 6DD  CONST_30  C8A  N1   C2   NA2   180.00   0.0  0
 6DD  CONST_31  C9   C6   C7   C8    180.00   0.0  0
 6DD  CONST_32  C16  C15  C14  N10   180.00   0.0  0
 6DD  CONST_33  C12  C13  C14  N10   180.00   0.0  0
 6DD  CONST_34  C    C11  C16  C15   180.00   0.0  0
 6DD  CONST_35  C    C11  C12  C13   180.00   0.0  0
 6DD  CONST_36  H6   C7   C6   C5    180.00   0.0  0
 6DD  CONST_37  H5   C8   C8A  C4A   180.00   0.0  0
 6DD  CONST_38  H1   C5   C4A  C4      0.00   0.0  0
 6DD  CONST_39  H11  C16  C15  C14   180.00   0.0  0
 6DD  CONST_40  H13  C12  C13  C14   180.00   0.0  0
 6DD  CONST_41  H12  C13  C14  C15   180.00   0.0  0
 6DD  CONST_42  H10  C15  C14  C13   180.00   0.0  0
 6DD  CONST_47  H3   NA2  C2   N3      0.00   0.0  0
 6DD  CONST_48  H4   NA2  C2   N3    180.00   0.0  0
 6DD  CONST_49  C14  N10  CA1  OA1   180.00   0.0  0
 6DD  CONST_50  CA   N    C    C11   180.00   0.0  0
 6DD  CONST_52  H9   CA1  N10  C14     0.00   0.0  0
 6DD  CONST_53  OA1  CA1  N10  C9      0.00   0.0  0
 6DD  CONST_54  CA   N    C    O       0.00   0.0  0
 6DD  CONST_55  H16  O1   CT   CA    180.00   0.0  0
 6DD  CONST_56  H21  OE1  CD   CG    180.00   0.0  0
 6DD  Var_01    N10  C9   C6   C5    114.44  30.0  2
 6DD  Var_02    C14  N10  C9   C6    -61.89  30.0  2
 6DD  Var_03    O    C    C11  C16    26.50  30.0  2
 6DD  Var_04    CD   CG   CB   CA   -178.74  30.0  2
 6DD  Var_05    OE2  CD   CG   CB      1.40  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
 6DD  chir_01  CA  CB  N  CT  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
 6DD  plan-1  N10  0.020
 6DD  plan-1  C14  0.020
 6DD  plan-1  C15  0.020
 6DD  plan-1  C16  0.020
 6DD  plan-1  C13  0.020
 6DD  plan-1  C12  0.020
 6DD  plan-1  C11  0.020
 6DD  plan-1  C    0.020
 6DD  plan-1  H10  0.020
 6DD  plan-1  H11  0.020
 6DD  plan-1  H12  0.020
 6DD  plan-1  H13  0.020
 6DD  plan-2  CA   0.020
 6DD  plan-2  CT   0.020
 6DD  plan-2  O2   0.020
 6DD  plan-2  O1   0.020
 6DD  plan-2  H16  0.020
 6DD  plan-3  CG   0.020
 6DD  plan-3  CD   0.020
 6DD  plan-3  OE2  0.020
 6DD  plan-3  OE1  0.020
 6DD  plan-3  H21  0.020
 6DD  plan-4  C5   0.020
 6DD  plan-4  C4A  0.020
 6DD  plan-4  C4   0.020
 6DD  plan-4  O4   0.020
 6DD  plan-4  N3   0.020
 6DD  plan-4  C2   0.020
 6DD  plan-4  NA2  0.020
 6DD  plan-4  N1   0.020
 6DD  plan-4  C8A  0.020
 6DD  plan-4  C8   0.020
 6DD  plan-4  C7   0.020
 6DD  plan-4  C6   0.020
 6DD  plan-4  C9   0.020
 6DD  plan-4  H1   0.020
 6DD  plan-4  H5   0.020
 6DD  plan-4  H6   0.020
 6DD  plan-5  C9   0.020
 6DD  plan-5  N10  0.020
 6DD  plan-5  CA1  0.020
 6DD  plan-5  OA1  0.020
 6DD  plan-5  C14  0.020
 6DD  plan-5  H9   0.020
 6DD  plan-6  C11  0.020
 6DD  plan-6  C    0.020
 6DD  plan-6  O    0.020
 6DD  plan-6  N    0.020
 6DD  plan-6  CA   0.020
 6DD  plan-6  H14  0.020
 6DD  plan-7  C2   0.020
 6DD  plan-7  NA2  0.020
 6DD  plan-7  H3   0.020
 6DD  plan-7  H4   0.020

