# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 08:45:25 2022
#   Inital geometry file: a 153 line input string
#   Ligand name: N-[(4-{[(2-amino-4-oxo-1,4-dihydroquinazolin-6-yl)methyl](prop-2-yn-1-yl)amino}phenyl)carbonyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2cc(CN(CC#C)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
 CB3  CB3  'N-[(4-{[(2-amino-4-oxo-1,4-dihydroquinazolin-6-yl)methyl](prop-2-yn-1-yl)amino}phenyl)carbonyl]-L-glutamic acid'  ligand  56  35  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CB3
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
 CB3  N1    N  NC1    0  -0.749  48.2271  34.3132  23.0675
 CB3  C2    C  C      0   0.668  48.3939  34.5040  24.3967
 CB3  NA2   N  NH2    0  -0.824  49.1735  33.6356  25.0466
 CB3  N3    N  N      0  -0.530  47.8219  35.4737  25.0693
 CB3  C4    C  C      0   0.441  47.0059  36.3636  24.4451
 CB3  O4    O  OC     0  -0.475  46.4703  37.2765  25.0638
 CB3  C4A   C  C      0  -0.136  46.7829  36.1964  22.9943
 CB3  C5    C  C1     0  -0.328  45.9565  37.0611  22.2770
 CB3  C6    C  C      0   0.077  45.7515  36.8939  20.9227
 CB3  C7    C  C1     0  -0.283  46.4020  35.8349  20.2777
 CB3  C8    C  C1     0  -0.313  47.2231  34.9646  20.9630
 CB3  C8A   C  C      0   0.413  47.4151  35.1484  22.3331
 CB3  C9    C  CH2    0  -0.376  44.8491  37.7983  20.1100
 CB3  N10   N  NT     0  -0.512  44.3848  38.9865  20.7855
 CB3  C11   C  C      0  -0.063  47.0712  42.0891  21.7493
 CB3  C12   C  C1     0  -0.283  45.7632  42.0904  22.2281
 CB3  C13   C  C1     0  -0.333  44.8758  41.0734  21.9250
 CB3  C14   C  C      0   0.386  45.2587  39.9979  21.1062
 CB3  C15   C  C1     0  -0.321  46.5827  39.9938  20.6317
 CB3  C16   C  C1     0  -0.262  47.4570  41.0112  20.9546
 CB3  O     O  O      0  -0.507  49.2844  42.8959  21.9788
 CB3  N     N  NH1    0  -0.638  47.5976  44.3246  22.4591
 CB3  CA    C  CH1    0  -0.220  48.3740  45.4115  23.0147
 CB3  CB    C  CH2    0  -0.394  48.6265  46.5277  21.9919
 CB3  CG    C  CH2    0  -0.578  49.3669  46.0806  20.7429
 CB3  CD    C  C      0   0.409  49.6707  47.1872  19.7130
 CB3  OE1   O  O      0  -0.605  49.3230  48.3530  19.9872
 CB3  OE2   O  OC    -1  -0.627  50.2518  46.8125  18.6717
 CB3  CT    C  C      0   0.422  47.6308  46.0015  24.2413
 CB3  O1    O  O      0  -0.600  48.3096  46.7407  24.9763
 CB3  O2    O  OC    -1  -0.598  46.4211  45.7184  24.3611
 CB3  CP1   C  CH2    0  -0.479  43.0264  39.0100  21.2784
 CB3  CP2   C  CSP    0   0.257  42.8899  38.6503  22.6936
 CB3  CP3   C  CSP1   0  -0.502  42.7898  38.3543  23.8540
 CB3  HN1   H  HNC1   0   0.428  48.6930  33.5479  22.6002
 CB3  HN21  H  HNH2   0   0.412  49.3783  33.8109  26.0150
 CB3  HN22  H  HNH2   0   0.415  49.7195  32.9371  24.5724
 CB3  H5    H  H      0   0.259  45.4769  37.8682  22.8136
 CB3  H7    H  H      0   0.261  46.2602  35.6905  19.2125
 CB3  H8    H  H      0   0.276  47.7164  34.1506  20.4464
 CB3  H91   H  HCH2   0   0.268  45.3563  38.0690  19.1785
 CB3  H92   H  HCH2   0   0.286  43.9693  37.2324  19.7994
 CB3  H12   H  H      0   0.245  45.4108  42.8728  22.8898
 CB3  H13   H  H      0   0.265  43.8867  41.1244  22.3566
 CB3  H15   H  H      0   0.267  46.9472  39.1886  20.0103
 CB3  H16   H  H      0   0.250  48.4687  40.9630  20.5738
 CB3  HN    H  HNH1   0   0.385  46.6031  44.4451  22.5759
 CB3  HA    H  HCH1   0   0.223  49.3370  45.0112  23.3407
 CB3  HB1   H  HCH2   0   0.198  47.6655  46.9723  21.7128
 CB3  HB2   H  HCH2   0   0.208  49.1928  47.3141  22.4933
 CB3  HG1   H  HCH2   0   0.209  50.3146  45.6081  21.0252
 CB3  HG2   H  HCH2   0   0.215  48.8014  45.2948  20.2325
 CB3  HP11  H  HCH2   0   0.292  42.5810  39.9944  21.1116
 CB3  HP12  H  HCH2   0   0.305  42.4328  38.3182  20.6796
 CB3  HP3   H  H      0   0.281  42.7009  38.0876  24.8826
 CB3  C     C  C      0   0.519  48.0827  43.1371  22.0767

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
 CB3  N1   C2    aromatic  1.353  0.020  1.353
 CB3  N1   C8A   aromatic  1.377  0.020  1.377
 CB3  N1   HN1   single    0.868  0.020  1.014
 CB3  C2   NA2   single    1.336  0.020  1.336
 CB3  C2   N3    aromatic  1.311  0.020  1.311
 CB3  NA2  HN21  single    0.868  0.020  1.013
 CB3  NA2  HN22  single    0.868  0.020  1.013
 CB3  N3   C4    aromatic  1.359  0.020  1.359
 CB3  C4   O4    double    1.226  0.020  1.226
 CB3  C4   C4A   aromatic  1.477  0.020  1.477
 CB3  C4A  C5    aromatic  1.395  0.020  1.395
 CB3  C4A  C8A   aromatic  1.391  0.020  1.391
 CB3  C5   C6    aromatic  1.380  0.020  1.380
 CB3  C5   H5    single    0.929  0.020  1.085
 CB3  C6   C7    aromatic  1.400  0.020  1.400
 CB3  C6   C9    single    1.514  0.020  1.514
 CB3  C7   C8    aromatic  1.379  0.020  1.379
 CB3  C7   H7    single    0.929  0.020  1.085
 CB3  C8   C8A   aromatic  1.396  0.020  1.396
 CB3  C8   H8    single    0.929  0.020  1.085
 CB3  C9   N10   single    1.443  0.020  1.443
 CB3  C9   H91   single    0.939  0.020  1.096
 CB3  C9   H92   single    0.939  0.020  1.096
 CB3  N10  C14   single    1.375  0.020  1.375
 CB3  N10  CP1   single    1.445  0.020  1.445
 CB3  C11  C12   aromatic  1.393  0.020  1.393
 CB3  C11  C16   aromatic  1.394  0.020  1.394
 CB3  C11  C     single    1.493  0.020  1.493
 CB3  C12  C13   aromatic  1.383  0.020  1.383
 CB3  C12  H12   single    0.929  0.020  1.085
 CB3  C13  C14   aromatic  1.405  0.020  1.405
 CB3  C13  H13   single    0.929  0.020  1.085
 CB3  C14  C15   aromatic  1.406  0.020  1.406
 CB3  C15  C16   aromatic  1.380  0.020  1.380
 CB3  C15  H15   single    0.929  0.020  1.085
 CB3  C16  H16   single    0.929  0.020  1.085
 CB3  C    O     double    1.230  0.020  1.230
 CB3  C    N     single    1.339  0.020  1.339
 CB3  N    CA    single    1.447  0.020  1.447
 CB3  N    HN    single    0.868  0.020  1.013
 CB3  CA   CB    single    1.535  0.020  1.535
 CB3  CA   CT    single    1.551  0.020  1.551
 CB3  CA   HA    single    0.939  0.020  1.096
 CB3  CB   CG    single    1.519  0.020  1.519
 CB3  CB   HB1   single    0.939  0.020  1.096
 CB3  CB   HB2   single    0.939  0.020  1.096
 CB3  CG   CD    single    1.542  0.020  1.542
 CB3  CG   HG1   single    0.939  0.020  1.096
 CB3  CG   HG2   single    0.939  0.020  1.096
 CB3  CD   OE1   deloc     1.247  0.020  1.247
 CB3  CD   OE2   deloc     1.250  0.020  1.250
 CB3  CT   O1    deloc     1.244  0.020  1.244
 CB3  CT   O2    deloc     1.248  0.020  1.248
 CB3  CP1  CP2   single    1.467  0.020  1.467
 CB3  CP1  HP11  single    0.939  0.020  1.096
 CB3  CP1  HP12  single    0.939  0.020  1.096
 CB3  CP2  CP3   triple    1.202  0.020  1.202
 CB3  CP3  HP3   single    0.913  0.020  1.066

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
 CB3  HN1   N1   C8A   118.98  3.000
 CB3  HN1   N1   C2    120.28  3.000
 CB3  C8A   N1   C2    120.73  3.000
 CB3  N3    C2   NA2   119.07  3.000
 CB3  N3    C2   N1    123.66  3.000
 CB3  NA2   C2   N1    117.27  3.000
 CB3  HN22  NA2  HN21  117.70  3.000
 CB3  HN22  NA2  C2    122.63  3.000
 CB3  HN21  NA2  C2    118.31  3.000
 CB3  C4    N3   C2    120.70  3.000
 CB3  C4A   C4   O4    120.93  3.000
 CB3  C4A   C4   N3    117.87  3.000
 CB3  O4    C4   N3    121.20  3.000
 CB3  C8A   C4A  C5    119.47  3.000
 CB3  C8A   C4A  C4    118.91  3.000
 CB3  C5    C4A  C4    121.62  3.000
 CB3  H5    C5   C6    120.77  3.000
 CB3  H5    C5   C4A   118.06  3.000
 CB3  C6    C5   C4A   121.17  3.000
 CB3  C9    C6   C7    118.78  3.000
 CB3  C9    C6   C5    122.88  3.000
 CB3  C7    C6   C5    118.34  3.000
 CB3  H7    C7   C8    118.83  3.000
 CB3  H7    C7   C6    119.50  3.000
 CB3  C8    C7   C6    121.67  3.000
 CB3  H8    C8   C8A   120.30  3.000
 CB3  H8    C8   C7    120.57  3.000
 CB3  C8A   C8   C7    119.13  3.000
 CB3  C8    C8A  C4A   120.22  3.000
 CB3  C8    C8A  N1    121.66  3.000
 CB3  C4A   C8A  N1    118.13  3.000
 CB3  H92   C9   H91   105.05  3.000
 CB3  H92   C9   N10   107.50  3.000
 CB3  H91   C9   N10   110.10  3.000
 CB3  H92   C9   C6    108.88  3.000
 CB3  H91   C9   C6    109.16  3.000
 CB3  N10   C9   C6    115.61  3.000
 CB3  CP1   N10  C14   120.39  3.000
 CB3  CP1   N10  C9    118.38  3.000
 CB3  C14   N10  C9    120.69  3.000
 CB3  C     C11  C16   118.72  3.000
 CB3  C     C11  C12   124.08  3.000
 CB3  C16   C11  C12   117.17  3.000
 CB3  H12   C12  C13   117.13  3.000
 CB3  H12   C12  C11   121.06  3.000
 CB3  C13   C12  C11   121.77  3.000
 CB3  H13   C13  C14   121.23  3.000
 CB3  H13   C13  C12   117.71  3.000
 CB3  C14   C13  C12   121.04  3.000
 CB3  C15   C14  C13   117.09  3.000
 CB3  C15   C14  N10   121.17  3.000
 CB3  C13   C14  N10   121.74  3.000
 CB3  H15   C15  C16   118.05  3.000
 CB3  H15   C15  C14   120.92  3.000
 CB3  C16   C15  C14   121.03  3.000
 CB3  H16   C16  C15   118.51  3.000
 CB3  H16   C16  C11   119.60  3.000
 CB3  C15   C16  C11   121.89  3.000
 CB3  HN    N    CA    113.26  3.000
 CB3  HN    N    C     119.77  3.000
 CB3  CA    N    C     125.57  3.000
 CB3  HA    CA   CT    109.02  3.000
 CB3  HA    CA   CB    108.68  3.000
 CB3  CT    CA   CB    109.22  3.000
 CB3  HA    CA   N     108.19  3.000
 CB3  CT    CA   N     109.42  3.000
 CB3  CB    CA   N     112.25  3.000
 CB3  HB2   CB   HB1   106.26  3.000
 CB3  HB2   CB   CG    109.69  3.000
 CB3  HB1   CB   CG    109.73  3.000
 CB3  HB2   CB   CA    107.66  3.000
 CB3  HB1   CB   CA    108.71  3.000
 CB3  CG    CB   CA    114.45  3.000
 CB3  HG2   CG   HG1   104.92  3.000
 CB3  HG2   CG   CD    107.79  3.000
 CB3  HG1   CG   CD    108.12  3.000
 CB3  HG2   CG   CB    110.06  3.000
 CB3  HG1   CG   CB    109.67  3.000
 CB3  CD    CG   CB    115.72  3.000
 CB3  OE2   CD   OE1   126.37  3.000
 CB3  OE2   CD   CG    115.65  3.000
 CB3  OE1   CD   CG    117.98  3.000
 CB3  O2    CT   O1    127.37  3.000
 CB3  O2    CT   CA    117.01  3.000
 CB3  O1    CT   CA    115.59  3.000
 CB3  HP12  CP1  HP11  105.40  3.000
 CB3  HP12  CP1  CP2   108.87  3.000
 CB3  HP11  CP1  CP2   109.28  3.000
 CB3  HP12  CP1  N10   108.30  3.000
 CB3  HP11  CP1  N10   110.22  3.000
 CB3  CP2   CP1  N10   114.37  3.000
 CB3  CP3   CP2  CP1   180.00  3.000
 CB3  HP3   CP3  CP2   180.00  3.000
 CB3  N     C    O     123.43  3.000
 CB3  N     C    C11   116.10  3.000
 CB3  O     C    C11   120.47  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
 CB3  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 CB3  CONST_02  C4    C4A  C8A  N1      0.00   0.0  0
 CB3  CONST_03  C5    C4A  C8A  N1    180.00   0.0  0
 CB3  CONST_04  C7    C8   C8A  N1    180.00   0.0  0
 CB3  CONST_05  C4A   C8A  N1   C2      0.00   0.0  0
 CB3  CONST_06  C8    C8A  N1   C2    180.00   0.0  0
 CB3  CONST_07  C4A   C4   N3   C2      0.00   0.0  0
 CB3  CONST_08  C8A   N1   C2   N3      0.00   0.0  0
 CB3  CONST_09  C5    C4A  C4   N3    180.00   0.0  0
 CB3  CONST_10  C8A   C4A  C4   N3      0.00   0.0  0
 CB3  CONST_11  C6    C5   C4A  C4    180.00   0.0  0
 CB3  CONST_12  C8    C8A  C4A  C4    180.00   0.0  0
 CB3  CONST_13  C7    C6   C5   C4A     0.00   0.0  0
 CB3  CONST_14  C7    C8   C8A  C4A     0.00   0.0  0
 CB3  CONST_15  C8    C8A  C4A  C5      0.00   0.0  0
 CB3  CONST_16  C8    C7   C6   C5      0.00   0.0  0
 CB3  CONST_17  C8A   C4A  C5   C6      0.00   0.0  0
 CB3  CONST_18  C8A   C8   C7   C6      0.00   0.0  0
 CB3  CONST_19  C14   C13  C12  C11     0.00   0.0  0
 CB3  CONST_20  C14   C15  C16  C11     0.00   0.0  0
 CB3  CONST_21  C15   C16  C11  C12     0.00   0.0  0
 CB3  CONST_22  C15   C14  C13  C12     0.00   0.0  0
 CB3  CONST_23  C16   C11  C12  C13     0.00   0.0  0
 CB3  CONST_24  C16   C15  C14  C13     0.00   0.0  0
 CB3  CONST_25  O4    C4   N3   C2    180.00   0.0  0
 CB3  CONST_26  C8A   N1   C2   NA2   180.00   0.0  0
 CB3  CONST_27  C4    N3   C2   NA2   180.00   0.0  0
 CB3  CONST_28  C5    C4A  C4   O4      0.00   0.0  0
 CB3  CONST_29  C8A   C4A  C4   O4    180.00   0.0  0
 CB3  CONST_30  C9    C6   C5   C4A   180.00   0.0  0
 CB3  CONST_31  C9    C6   C7   C8    180.00   0.0  0
 CB3  CONST_32  C12   C13  C14  N10   180.00   0.0  0
 CB3  CONST_33  C16   C15  C14  N10   180.00   0.0  0
 CB3  CONST_34  C     C11  C12  C13   180.00   0.0  0
 CB3  CONST_35  C     C11  C16  C15   180.00   0.0  0
 CB3  CONST_36  H8    C8   C8A  N1      0.00   0.0  0
 CB3  CONST_37  HN1   N1   C2   N3    180.00   0.0  0
 CB3  CONST_38  H5    C5   C4A  C4      0.00   0.0  0
 CB3  CONST_39  H7    C7   C6   C5    180.00   0.0  0
 CB3  CONST_40  H13   C13  C12  C11   180.00   0.0  0
 CB3  CONST_41  H15   C15  C16  C11   180.00   0.0  0
 CB3  CONST_42  H16   C16  C11  C12   180.00   0.0  0
 CB3  CONST_43  H12   C12  C13  C14   180.00   0.0  0
 CB3  CONST_44  C13   C14  N10  C9    180.00   0.0  0
 CB3  CONST_45  C15   C14  N10  C9      0.00   0.0  0
 CB3  CONST_46  CP1   N10  C14  C13     0.00   0.0  0
 CB3  CONST_47  CP1   N10  C14  C15   180.00   0.0  0
 CB3  CONST_48  HN21  NA2  C2   N1    180.00   0.0  0
 CB3  CONST_49  HN22  NA2  C2   N1      0.00   0.0  0
 CB3  CONST_50  CA    N    C    C11   180.00   0.0  0
 CB3  CONST_51  HN    N    C    C11     0.00   0.0  0
 CB3  CONST_52  CA    N    C    O       0.00   0.0  0
 CB3  Var_01    N10   C9   C6   C5      9.97  30.0  2
 CB3  Var_02    C14   N10  C9   C6     68.42  30.0  3
 CB3  Var_03    O     C    C11  C12   157.85  30.0  2
 CB3  Var_04    CP2   CP1  N10  C14   -75.69  30.0  3
 CB3  Var_05    CD    CG   CB   CA   -178.36  30.0  3
 CB3  Var_06    OE1   CD   CG   CB      1.67  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
 CB3  chir_01  CA  N  CB  CT  negativ

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
 CB3  plan-1  N10   0.020
 CB3  plan-1  C11   0.020
 CB3  plan-1  C12   0.020
 CB3  plan-1  C13   0.020
 CB3  plan-1  C14   0.020
 CB3  plan-1  C15   0.020
 CB3  plan-1  C16   0.020
 CB3  plan-1  H12   0.020
 CB3  plan-1  H13   0.020
 CB3  plan-1  H15   0.020
 CB3  plan-1  H16   0.020
 CB3  plan-1  C     0.020
 CB3  plan-2  CG    0.020
 CB3  plan-2  CD    0.020
 CB3  plan-2  OE1   0.020
 CB3  plan-2  OE2   0.020
 CB3  plan-3  CA    0.020
 CB3  plan-3  CT    0.020
 CB3  plan-3  O1    0.020
 CB3  plan-3  O2    0.020
 CB3  plan-4  N1    0.020
 CB3  plan-4  C2    0.020
 CB3  plan-4  NA2   0.020
 CB3  plan-4  N3    0.020
 CB3  plan-4  C4    0.020
 CB3  plan-4  O4    0.020
 CB3  plan-4  C4A   0.020
 CB3  plan-4  C5    0.020
 CB3  plan-4  C6    0.020
 CB3  plan-4  C7    0.020
 CB3  plan-4  C8    0.020
 CB3  plan-4  C8A   0.020
 CB3  plan-4  C9    0.020
 CB3  plan-4  HN1   0.020
 CB3  plan-4  H5    0.020
 CB3  plan-4  H7    0.020
 CB3  plan-4  H8    0.020
 CB3  plan-5  C11   0.020
 CB3  plan-5  O     0.020
 CB3  plan-5  N     0.020
 CB3  plan-5  CA    0.020
 CB3  plan-5  HN    0.020
 CB3  plan-5  C     0.020
 CB3  plan-6  C2    0.020
 CB3  plan-6  NA2   0.020
 CB3  plan-6  HN21  0.020
 CB3  plan-6  HN22  0.020
 CB3  plan-7  C9    0.020
 CB3  plan-7  N10   0.020
 CB3  plan-7  C14   0.020
 CB3  plan-7  CP1   0.020

