# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 10:03:42 2021
#   Inital geometry file: a 145 line input string
#   Ligand name: N-({4-[(1R)-2-(2-amino-4-hydroxyquinazolin-6-yl)-1-carboxyethyl]phenyl}carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(O)c2cc(C[C@@H](C(O)=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
 NHR  NHR  'N-({4-[(1R)-2-(2-amino-4-hydroxyquinazolin-6-yl)-1-carboxyethyl]phenyl}carbonyl)-L-glutamic acid'  ligand  57  35  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NHR
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
 NHR  N1    N  N     0  -0.513  37.2425  22.6058   6.5470
 NHR  C2    C  CR6   0   0.526  36.0489  22.1134   6.7892
 NHR  NA2   N  NH2   0  -0.819  35.5031  22.3091   8.0059
 NHR  N3    N  N     0  -0.476  35.2953  21.3809   5.9319
 NHR  C4    C  CR6   0   0.494  35.7876  21.1335   4.7585
 NHR  O4    O  OH1   0  -0.580  35.0065  20.4147   3.9650
 NHR  C4A   C  CR66  0  -0.091  37.0771  21.5988   4.3497
 NHR  C8A   C  CR66  0   0.256  37.7651  22.3503   5.3282
 NHR  C8    C  CR16  0  -0.309  39.0432  22.8481   4.9979
 NHR  C7    C  CR16  0  -0.270  39.5889  22.6002   3.7669
 NHR  C9    C  CH2   0  -0.505  39.5559  21.5579   1.4618
 NHR  C10   C  CH1   0  -0.461  40.1369  20.1373   1.4356
 NHR  CA1   C  C     0   0.569  40.7867  19.8203   0.1041
 NHR  OA1   O  O     0  -0.429  40.8850  20.5890  -0.8181
 NHR  C6    C  CR6   0   0.127  38.9072  21.8514   2.7859
 NHR  C5    C  CR16  0  -0.369  37.6603  21.3627   3.0917
 NHR  C16   C  CR16  0  -0.275  43.1797  20.4493   3.6822
 NHR  C11   C  CR6   0  -0.034  42.8535  19.5918   4.7314
 NHR  C17   C  C     0   0.535  43.7428  19.4240   5.9136
 NHR  O17   O  O     0  -0.477  43.3036  19.1816   7.0290
 NHR  C12   C  CR16  0  -0.252  41.6411  18.9105   4.6987
 NHR  C13   C  CR16  0  -0.291  40.7835  19.0617   3.6220
 NHR  C14   C  CR6   0   0.153  41.1062  19.9121   2.5709
 NHR  C15   C  CR16  0  -0.272  42.3099  20.6099   2.6171
 NHR  N     N  NH1   0  -0.653  45.0615  19.5586   5.6844
 NHR  CA    C  CH1   0  -0.235  46.0176  19.5847   6.7624
 NHR  C     C  C     0   0.568  45.9360  18.3383   7.6333
 NHR  O     O  O     0  -0.433  46.1227  18.3382   8.8227
 NHR  CB    C  CH2   0  -0.448  45.9500  20.8640   7.6029
 NHR  CG    C  CH2   0  -0.558  45.8263  22.1281   6.7509
 NHR  CD    C  C     0   0.527  46.8686  22.2508   5.6732
 NHR  OE1   O  O     0  -0.441  46.6341  22.3848   4.4966
 NHR  OE2   O  OH1   0  -0.588  48.1031  22.1929   6.1618
 NHR  OT    O  OH1   0  -0.588  45.7219  17.2448   6.9197
 NHR  OA2   O  OH1   0  -0.586  41.2368  18.5736   0.0707
 NHR  HNA1  H  HNH2  0   0.396  34.5241  22.1212   8.1330
 NHR  HNA2  H  HNH2  0   0.394  35.9216  22.9869   8.6189
 NHR  H4O   H  HOH1  0   0.495  35.4112  20.2417   3.1073
 NHR  H8    H  HCR6  0   0.256  39.5814  23.4287   5.7358
 NHR  H7    H  HCR6  0   0.254  40.5717  22.9932   3.5358
 NHR  H91   H  HCH2  0   0.260  40.3459  22.2869   1.2696
 NHR  H92   H  HCH2  0   0.271  38.8269  21.6592   0.6555
 NHR  H101  H  HCH1  0   0.310  39.3113  19.4257   1.5487
 NHR  H5    H  HCR6  0   0.248  37.1384  20.7857   2.3345
 NHR  H161  H  HCR6  0   0.254  44.0952  21.0291   3.7023
 NHR  H121  H  HCR6  0   0.262  41.3692  18.2516   5.5129
 NHR  H131  H  HCR6  0   0.259  39.8473  18.5176   3.6047
 NHR  H151  H  HCR6  0   0.265  42.5723  21.3000   1.8234
 NHR  HN    H  HNH1  0   0.415  45.4062  19.6156   4.7405
 NHR  HA    H  HCH1  0   0.318  47.0035  19.5331   6.2877
 NHR  HB1   H  HCH2  0   0.265  45.0939  20.8314   8.2756
 NHR  HB2   H  HCH2  0   0.263  46.8403  20.9161   8.2291
 NHR  HG1   H  HCH2  0   0.267  44.8464  22.1860   6.2800
 NHR  HG2   H  HCH2  0   0.294  45.9126  22.9957   7.4105
 NHR  HOE1  H  HOH1  0   0.482  48.7498  22.2702   5.4442
 NHR  HOT   H  HOH1  0   0.484  45.7192  16.4678   7.4986
 NHR  HOA1  H  HOH1  0   0.483  41.6475  18.3894  -0.7877

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
 NHR  N1   C2    aromatic  1.314  0.020  1.314
 NHR  N1   C8A   aromatic  1.351  0.020  1.351
 NHR  C2   NA2   single    1.348  0.020  1.348
 NHR  C2   N3    aromatic  1.356  0.020  1.356
 NHR  NA2  HNA1  single    0.890  0.020  1.040
 NHR  NA2  HNA2  single    0.890  0.020  1.040
 NHR  N3   C4    aromatic  1.296  0.020  1.296
 NHR  C4   O4    single    1.325  0.020  1.325
 NHR  C4   C4A   aromatic  1.431  0.020  1.431
 NHR  O4   H4O   single    0.850  0.020  0.980
 NHR  C4A  C8A   aromatic  1.413  0.020  1.413
 NHR  C4A  C5    aromatic  1.407  0.020  1.407
 NHR  C8A  C8    aromatic  1.411  0.020  1.411
 NHR  C8   C7    aromatic  1.369  0.020  1.369
 NHR  C8   H8    single    0.930  0.020  1.080
 NHR  C7   C6    aromatic  1.410  0.020  1.410
 NHR  C7   H7    single    0.930  0.020  1.080
 NHR  C9   C10   single    1.535  0.020  1.535
 NHR  C9   C6    single    1.503  0.020  1.503
 NHR  C9   H91   single    0.970  0.020  1.090
 NHR  C9   H92   single    0.970  0.020  1.090
 NHR  C10  CA1   single    1.515  0.020  1.515
 NHR  C10  C14   single    1.510  0.020  1.510
 NHR  C10  H101  single    0.970  0.020  1.090
 NHR  CA1  OA1   double    1.205  0.020  1.205
 NHR  CA1  OA2   single    1.326  0.020  1.326
 NHR  C6   C5    aromatic  1.374  0.020  1.374
 NHR  C5   H5    single    0.930  0.020  1.080
 NHR  C16  C11   aromatic  1.394  0.020  1.394
 NHR  C16  C15   aromatic  1.385  0.020  1.385
 NHR  C16  H161  single    0.930  0.020  1.080
 NHR  C11  C17   single    1.489  0.020  1.489
 NHR  C11  C12   aromatic  1.391  0.020  1.391
 NHR  C17  O17   double    1.223  0.020  1.223
 NHR  C17  N     single    1.345  0.020  1.345
 NHR  C12  C13   aromatic  1.385  0.020  1.385
 NHR  C12  H121  single    0.930  0.020  1.080
 NHR  C13  C14   aromatic  1.390  0.020  1.390
 NHR  C13  H131  single    0.930  0.020  1.080
 NHR  C14  C15   aromatic  1.392  0.020  1.392
 NHR  C15  H151  single    0.930  0.020  1.080
 NHR  N    CA    single    1.441  0.020  1.441
 NHR  N    HN    single    0.860  0.020  1.020
 NHR  CA   C     single    1.523  0.020  1.523
 NHR  CA   CB    single    1.532  0.020  1.532
 NHR  CA   HA    single    0.970  0.020  1.090
 NHR  C    O     double    1.204  0.020  1.204
 NHR  C    OT    single    1.323  0.020  1.323
 NHR  CB   CG    single    1.529  0.020  1.529
 NHR  CB   HB1   single    0.970  0.020  1.090
 NHR  CB   HB2   single    0.970  0.020  1.090
 NHR  CG   CD    single    1.504  0.020  1.504
 NHR  CG   HG1   single    0.970  0.020  1.090
 NHR  CG   HG2   single    0.970  0.020  1.090
 NHR  CD   OE1   double    1.207  0.020  1.207
 NHR  CD   OE2   single    1.329  0.020  1.329
 NHR  OE2  HOE1  single    0.850  0.020  0.980
 NHR  OT   HOT   single    0.850  0.020  0.980
 NHR  OA2  HOA1  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
 NHR  C8A   N1   C2    116.56  3.000
 NHR  N3    C2   NA2   115.09  3.000
 NHR  N3    C2   N1    126.21  3.000
 NHR  NA2   C2   N1    118.68  3.000
 NHR  HNA2  NA2  HNA1  117.04  3.000
 NHR  HNA2  NA2  C2    118.67  3.000
 NHR  HNA1  NA2  C2    118.78  3.000
 NHR  C4    N3   C2    117.66  3.000
 NHR  C4A   C4   O4    122.45  3.000
 NHR  C4A   C4   N3    122.61  3.000
 NHR  O4    C4   N3    114.94  3.000
 NHR  H4O   O4   C4    112.49  3.000
 NHR  C5    C4A  C8A   120.45  3.000
 NHR  C5    C4A  C4    125.08  3.000
 NHR  C8A   C4A  C4    114.46  3.000
 NHR  C8    C8A  C4A   117.83  3.000
 NHR  C8    C8A  N1    119.68  3.000
 NHR  C4A   C8A  N1    122.50  3.000
 NHR  H8    C8   C7    120.79  3.000
 NHR  H8    C8   C8A   118.70  3.000
 NHR  C7    C8   C8A   120.51  3.000
 NHR  H7    C7   C6    118.87  3.000
 NHR  H7    C7   C8    119.19  3.000
 NHR  C6    C7   C8    121.94  3.000
 NHR  H92   C9   H91   106.92  3.000
 NHR  H92   C9   C6    110.14  3.000
 NHR  H91   C9   C6    109.68  3.000
 NHR  H92   C9   C10   109.03  3.000
 NHR  H91   C9   C10   109.94  3.000
 NHR  C6    C9   C10   111.04  3.000
 NHR  H101  C10  C14   108.01  3.000
 NHR  H101  C10  CA1   106.13  3.000
 NHR  C14   C10  CA1   110.75  3.000
 NHR  H101  C10  C9    108.31  3.000
 NHR  C14   C10  C9    111.61  3.000
 NHR  CA1   C10  C9    111.77  3.000
 NHR  OA2   CA1  OA1   123.57  3.000
 NHR  OA2   CA1  C10   111.38  3.000
 NHR  OA1   CA1  C10   125.05  3.000
 NHR  C5    C6   C9    121.21  3.000
 NHR  C5    C6   C7    118.23  3.000
 NHR  C9    C6   C7    120.53  3.000
 NHR  H5    C5   C6    118.04  3.000
 NHR  H5    C5   C4A   120.91  3.000
 NHR  C6    C5   C4A   121.05  3.000
 NHR  H161  C16  C15   118.87  3.000
 NHR  H161  C16  C11   120.86  3.000
 NHR  C15   C16  C11   120.23  3.000
 NHR  C12   C11  C17   118.95  3.000
 NHR  C12   C11  C16   119.19  3.000
 NHR  C17   C11  C16   121.82  3.000
 NHR  N     C17  O17   121.82  3.000
 NHR  N     C17  C11   116.04  3.000
 NHR  O17   C17  C11   122.14  3.000
 NHR  H121  C12  C13   119.73  3.000
 NHR  H121  C12  C11   119.97  3.000
 NHR  C13   C12  C11   120.30  3.000
 NHR  H131  C13  C14   119.73  3.000
 NHR  H131  C13  C12   119.53  3.000
 NHR  C14   C13  C12   120.73  3.000
 NHR  C15   C14  C13   118.84  3.000
 NHR  C15   C14  C10   120.35  3.000
 NHR  C13   C14  C10   120.72  3.000
 NHR  H151  C15  C14   120.28  3.000
 NHR  H151  C15  C16   119.01  3.000
 NHR  C14   C15  C16   120.70  3.000
 NHR  HN    N    CA    118.25  3.000
 NHR  HN    N    C17   120.08  3.000
 NHR  CA    N    C17   121.64  3.000
 NHR  HA    CA   CB    108.46  3.000
 NHR  HA    CA   C     104.93  3.000
 NHR  CB    CA   C     111.55  3.000
 NHR  HA    CA   N     105.79  3.000
 NHR  CB    CA   N     113.34  3.000
 NHR  C     CA   N     112.18  3.000
 NHR  OT    C    O     123.90  3.000
 NHR  OT    C    CA    112.12  3.000
 NHR  O     C    CA    123.84  3.000
 NHR  HB2   CB   HB1   106.78  3.000
 NHR  HB2   CB   CG    110.28  3.000
 NHR  HB1   CB   CG    107.77  3.000
 NHR  HB2   CB   CA    108.61  3.000
 NHR  HB1   CB   CA    110.39  3.000
 NHR  CG    CB   CA    112.84  3.000
 NHR  HG2   CG   HG1   106.84  3.000
 NHR  HG2   CG   CD    108.23  3.000
 NHR  HG1   CG   CD    108.03  3.000
 NHR  HG2   CG   CB    108.26  3.000
 NHR  HG1   CG   CB    110.96  3.000
 NHR  CD    CG   CB    114.24  3.000
 NHR  OE2   CD   OE1   122.93  3.000
 NHR  OE2   CD   CG    112.13  3.000
 NHR  OE1   CD   CG    124.94  3.000
 NHR  HOE1  OE2  CD    110.13  3.000
 NHR  HOT   OT   C     109.93  3.000
 NHR  HOA1  OA2  CA1   110.18  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
 NHR  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 NHR  CONST_02  C4    C4A  C8A  N1     0.00   0.0  0
 NHR  CONST_03  C5    C4A  C8A  N1   180.00   0.0  0
 NHR  CONST_04  C7    C8   C8A  N1   180.00   0.0  0
 NHR  CONST_05  C4A   C8A  N1   C2     0.00   0.0  0
 NHR  CONST_06  C8    C8A  N1   C2   180.00   0.0  0
 NHR  CONST_07  C4A   C4   N3   C2     0.00   0.0  0
 NHR  CONST_08  C8A   N1   C2   N3     0.00   0.0  0
 NHR  CONST_09  C8A   C4A  C4   N3     0.00   0.0  0
 NHR  CONST_10  C5    C4A  C4   N3   180.00   0.0  0
 NHR  CONST_11  C8    C8A  C4A  C4   180.00   0.0  0
 NHR  CONST_12  C6    C5   C4A  C4   180.00   0.0  0
 NHR  CONST_13  C7    C8   C8A  C4A    0.00   0.0  0
 NHR  CONST_14  C7    C6   C5   C4A    0.00   0.0  0
 NHR  CONST_15  C6    C5   C4A  C8A    0.00   0.0  0
 NHR  CONST_16  C6    C7   C8   C8A    0.00   0.0  0
 NHR  CONST_17  C5    C4A  C8A  C8     0.00   0.0  0
 NHR  CONST_18  C5    C6   C7   C8     0.00   0.0  0
 NHR  CONST_19  C13   C12  C11  C16    0.00   0.0  0
 NHR  CONST_20  C13   C14  C15  C16    0.00   0.0  0
 NHR  CONST_21  C14   C15  C16  C11    0.00   0.0  0
 NHR  CONST_22  C14   C13  C12  C11    0.00   0.0  0
 NHR  CONST_23  C15   C16  C11  C12    0.00   0.0  0
 NHR  CONST_24  C15   C14  C13  C12    0.00   0.0  0
 NHR  CONST_25  O4    C4   N3   C2   180.00   0.0  0
 NHR  CONST_26  C8A   N1   C2   NA2  180.00   0.0  0
 NHR  CONST_27  C4    N3   C2   NA2  180.00   0.0  0
 NHR  CONST_28  C8A   C4A  C4   O4   180.00   0.0  0
 NHR  CONST_29  C5    C4A  C4   O4     0.00   0.0  0
 NHR  CONST_30  C9    C6   C5   C4A  180.00   0.0  0
 NHR  CONST_31  C9    C6   C7   C8   180.00   0.0  0
 NHR  CONST_32  C12   C13  C14  C10  180.00   0.0  0
 NHR  CONST_33  C16   C15  C14  C10  180.00   0.0  0
 NHR  CONST_34  C15   C16  C11  C17  180.00   0.0  0
 NHR  CONST_35  C13   C12  C11  C17  180.00   0.0  0
 NHR  CONST_36  H8    C8   C8A  N1     0.00   0.0  0
 NHR  CONST_37  H5    C5   C4A  C4     0.00   0.0  0
 NHR  CONST_38  H7    C7   C8   C8A  180.00   0.0  0
 NHR  CONST_39  H121  C12  C11  C16  180.00   0.0  0
 NHR  CONST_40  H151  C15  C16  C11  180.00   0.0  0
 NHR  CONST_41  H131  C13  C12  C11  180.00   0.0  0
 NHR  CONST_42  H161  C16  C11  C12  180.00   0.0  0
 NHR  CONST_43  HNA1  NA2  C2   N1   180.00   0.0  0
 NHR  CONST_44  HNA2  NA2  C2   N1     0.00   0.0  0
 NHR  CONST_45  CA    N    C17  C11  180.00   0.0  0
 NHR  CONST_46  HN    N    C17  C11    0.00   0.0  0
 NHR  CONST_47  CA    N    C17  O17    0.00   0.0  0
 NHR  CONST_48  HOA1  OA2  CA1  C10  180.00   0.0  0
 NHR  CONST_49  HOT   OT   C    CA   180.00   0.0  0
 NHR  CONST_50  HOE1  OE2  CD   CG   180.00   0.0  0
 NHR  Var_01    C10   C9   C6   C7    99.88  30.0  2
 NHR  Var_02    O17   C17  C11  C16  148.28  30.0  2
 NHR  Var_03    CD    CG   CB   CA   -52.23  30.0  3
 NHR  Var_04    OE1   CD   CG   CB   123.75  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
 NHR  chir_01  C10  C9  CA1  C14  negativ
 NHR  chir_02  CA   N   C    CB   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
 NHR  plan-1  C10   0.020
 NHR  plan-1  C16   0.020
 NHR  plan-1  C11   0.020
 NHR  plan-1  C17   0.020
 NHR  plan-1  C12   0.020
 NHR  plan-1  C13   0.020
 NHR  plan-1  C14   0.020
 NHR  plan-1  C15   0.020
 NHR  plan-1  H161  0.020
 NHR  plan-1  H121  0.020
 NHR  plan-1  H131  0.020
 NHR  plan-1  H151  0.020
 NHR  plan-2  CG    0.020
 NHR  plan-2  CD    0.020
 NHR  plan-2  OE1   0.020
 NHR  plan-2  OE2   0.020
 NHR  plan-2  HOE1  0.020
 NHR  plan-3  N1    0.020
 NHR  plan-3  C2    0.020
 NHR  plan-3  NA2   0.020
 NHR  plan-3  N3    0.020
 NHR  plan-3  C4    0.020
 NHR  plan-3  O4    0.020
 NHR  plan-3  C4A   0.020
 NHR  plan-3  C8A   0.020
 NHR  plan-3  C8    0.020
 NHR  plan-3  C7    0.020
 NHR  plan-3  C9    0.020
 NHR  plan-3  C6    0.020
 NHR  plan-3  C5    0.020
 NHR  plan-3  H8    0.020
 NHR  plan-3  H7    0.020
 NHR  plan-3  H5    0.020
 NHR  plan-4  C11   0.020
 NHR  plan-4  C17   0.020
 NHR  plan-4  O17   0.020
 NHR  plan-4  N     0.020
 NHR  plan-4  CA    0.020
 NHR  plan-4  HN    0.020
 NHR  plan-5  C2    0.020
 NHR  plan-5  NA2   0.020
 NHR  plan-5  HNA1  0.020
 NHR  plan-5  HNA2  0.020
 NHR  plan-6  C10   0.020
 NHR  plan-6  CA1   0.020
 NHR  plan-6  OA1   0.020
 NHR  plan-6  OA2   0.020
 NHR  plan-6  HOA1  0.020
 NHR  plan-7  CA    0.020
 NHR  plan-7  C     0.020
 NHR  plan-7  O     0.020
 NHR  plan-7  OT    0.020
 NHR  plan-7  HOT   0.020

