# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 22:40:40 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2cc3nc(NCCc4ccc(cc4)C(O)=O)[nH]c3cc2C(=O)N1
#
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
 2YY  2YY  '4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzoic acid'  ligand  43  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2YY
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
 2YY  C1   C  CR66  0  -0.157  -4.4477  -0.8228  -0.1694
 2YY  C2   C  CR16  0  -0.352  -3.0704  -1.0670  -0.2832
 2YY  C3   C  CR56  0   0.355  -2.2348   0.0073  -0.1524
 2YY  C4   C  CR56  0   0.198  -2.7107   1.3222   0.0866
 2YY  C5   C  CR16  0  -0.453  -4.0706   1.5555   0.1965
 2YY  C6   C  CR66  0   0.276  -4.9548   0.4775   0.0698
 2YY  C7   C  CR6   0   0.543  -5.3828  -1.9219  -0.2993
 2YY  N8   N  N     0  -0.526  -6.2998   0.7277   0.1888
 2YY  C9   C  CR6   0   0.637  -7.1164  -0.2653   0.0639
 2YY  N10  N  NH2   0  -0.833  -8.4536  -0.0722   0.1134
 2YY  N11  N  NR16  0  -0.719  -6.7032  -1.5491  -0.1715
 2YY  N12  N  NR15  0  -0.748  -0.8624   0.1418  -0.2010
 2YY  N13  N  N     0  -0.541  -1.6646   2.1963   0.1752
 2YY  C14  C  CR5   0   0.691  -0.5856   1.4584  -0.0017
 2YY  N15  N  NH1   0  -0.689   0.6644   1.9429  -0.0130
 2YY  C16  C  CH2   0  -0.269   1.8455   1.1078   0.0276
 2YY  C17  C  CH2   0  -0.551   3.0952   1.9695  -0.1200
 2YY  O18  O  O     0  -0.473  -5.0874  -3.0894  -0.5070
 2YY  C19  C  CR6   0  -0.097   6.6084  -0.5104   0.0124
 2YY  C20  C  C     0   0.531   7.8138  -1.3730   0.0056
 2YY  O21  O  O     0  -0.440   8.2898  -1.8560  -0.9945
 2YY  C22  C  CR16  0  -0.239   5.9956  -0.2172  -1.2044
 2YY  C23  C  CR16  0  -0.290   4.8719   0.5892  -1.2450
 2YY  C24  C  CR6   0   0.125   4.3341   1.1231  -0.0760
 2YY  C25  C  CR16  0  -0.288   4.9486   0.8232   1.1372
 2YY  C26  C  CR16  0  -0.243   6.0740   0.0173   1.1869
 2YY  O27  O  OH1   0  -0.594   8.3227  -1.5648   1.2150
 2YY  H1   H  HCR6  0   0.268  -2.7011  -2.0673  -0.4673
 2YY  H2   H  HCR6  0   0.246  -4.4581   2.5493   0.3806
 2YY  H4   H  HNH2  0   0.402  -8.7547   0.8191   0.4714
 2YY  H5   H  HNH2  0   0.405  -9.0551  -0.8444   0.3494
 2YY  H6   H  HNR5  0   0.427  -0.1984  -0.6023  -0.3431
 2YY  H8   H  HNH1  0   0.404   0.7526   2.8939   0.3097
 2YY  H9   H  HCH2  0   0.249   1.8987   0.5350   0.9607
 2YY  H10  H  HCH2  0   0.251   1.8120   0.3877  -0.7941
 2YY  H11  H  HCH2  0   0.268   3.0451   2.5179  -1.0632
 2YY  H12  H  HCH2  0   0.267   3.1217   2.7083   0.6850
 2YY  H13  H  HCR6  0   0.266   6.3999  -0.6168  -2.1247
 2YY  H14  H  HCR6  0   0.259   4.4106   0.8121  -2.1993
 2YY  H15  H  HCR6  0   0.260   4.5466   1.2299   2.0573
 2YY  H16  H  HCR6  0   0.267   6.5273  -0.1901   2.1463
 2YY  H17  H  HOH1  0   0.487   9.1058  -2.1322   1.1583
 2YY  H3   H  HNR6  0   0.420  -7.3931  -2.2819  -0.2751

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
 2YY  O21  C20  double    1.208  0.020  1.208
 2YY  O27  C20  single    1.326  0.020  1.326
 2YY  C20  C19  single    1.482  0.020  1.482
 2YY  C19  C22  aromatic  1.394  0.020  1.394
 2YY  C19  C26  aromatic  1.394  0.020  1.394
 2YY  C22  C23  aromatic  1.384  0.020  1.384
 2YY  C26  C25  aromatic  1.385  0.020  1.385
 2YY  C23  C24  aromatic  1.393  0.020  1.393
 2YY  C25  C24  aromatic  1.393  0.020  1.393
 2YY  C24  C17  single    1.501  0.020  1.501
 2YY  C17  C16  single    1.525  0.020  1.525
 2YY  C16  N15  single    1.447  0.020  1.447
 2YY  N15  C14  single    1.341  0.020  1.341
 2YY  C14  N13  aromatic  1.319  0.020  1.319
 2YY  C14  N12  aromatic  1.360  0.020  1.360
 2YY  N13  C4   aromatic  1.366  0.020  1.366
 2YY  N12  C3   aromatic  1.380  0.020  1.380
 2YY  C4   C3   aromatic  1.419  0.020  1.419
 2YY  C4   C5   aromatic  1.384  0.020  1.384
 2YY  C3   C2   aromatic  1.367  0.020  1.367
 2YY  C5   C6   aromatic  1.400  0.020  1.400
 2YY  C2   C1   aromatic  1.403  0.020  1.403
 2YY  C6   C1   aromatic  1.416  0.020  1.416
 2YY  C6   N8   single    1.373  0.020  1.373
 2YY  C1   C7   single    1.449  0.020  1.449
 2YY  N8   C9   double    1.292  0.020  1.292
 2YY  C7   O18  double    1.222  0.020  1.222
 2YY  C7   N11  single    1.378  0.020  1.378
 2YY  C9   N11  single    1.369  0.020  1.369
 2YY  C9   N10  single    1.352  0.020  1.352
 2YY  C2   H1   single    0.930  0.020  1.080
 2YY  C5   H2   single    0.930  0.020  1.080
 2YY  N10  H4   single    0.890  0.020  1.040
 2YY  N10  H5   single    0.890  0.020  1.040
 2YY  N12  H6   single    0.860  0.020  1.020
 2YY  N15  H8   single    0.890  0.020  1.040
 2YY  C16  H9   single    0.970  0.020  1.090
 2YY  C16  H10  single    0.970  0.020  1.090
 2YY  C17  H11  single    0.970  0.020  1.090
 2YY  C17  H12  single    0.970  0.020  1.090
 2YY  C22  H13  single    0.930  0.020  1.080
 2YY  C23  H14  single    0.930  0.020  1.080
 2YY  C25  H15  single    0.930  0.020  1.080
 2YY  C26  H16  single    0.930  0.020  1.080
 2YY  O27  H17  single    0.850  0.020  0.980
 2YY  N11  H3   single    0.860  0.020  1.020

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
 2YY  C7   C1   C6   118.73  3.000
 2YY  C7   C1   C2   119.61  3.000
 2YY  C6   C1   C2   121.66  3.000
 2YY  H1   C2   C3   122.28  3.000
 2YY  H1   C2   C1   120.63  3.000
 2YY  C3   C2   C1   117.08  3.000
 2YY  N12  C3   C4   104.43  3.000
 2YY  C4   C3   C2   122.65  3.000
 2YY  N12  C3   C2   132.92  3.000
 2YY  N13  C4   C5   129.74  3.000
 2YY  C5   C4   C3   119.94  3.000
 2YY  N13  C4   C3   110.32  3.000
 2YY  H2   C5   C6   119.75  3.000
 2YY  H2   C5   C4   121.33  3.000
 2YY  C6   C5   C4   118.92  3.000
 2YY  N8   C6   C5   118.06  3.000
 2YY  N8   C6   C1   122.19  3.000
 2YY  C5   C6   C1   119.75  3.000
 2YY  O18  C7   N11  120.38  3.000
 2YY  N11  C7   C1   113.88  3.000
 2YY  O18  C7   C1   125.73  3.000
 2YY  C9   N8   C6   118.08  3.000
 2YY  N11  C9   N10  116.02  3.000
 2YY  N10  C9   N8   120.79  3.000
 2YY  N11  C9   N8   123.14  3.000
 2YY  H5   N10  H4   114.65  3.000
 2YY  H5   N10  C9   119.33  3.000
 2YY  H4   N10  C9   115.81  3.000
 2YY  H3   N11  C9   119.40  3.000
 2YY  H3   N11  C7   116.62  3.000
 2YY  C9   N11  C7   123.98  3.000
 2YY  H6   N12  C14  126.99  3.000
 2YY  H6   N12  C3   126.06  3.000
 2YY  C14  N12  C3   106.95  3.000
 2YY  C14  N13  C4   105.05  3.000
 2YY  N15  C14  N13  124.16  3.000
 2YY  N13  C14  N12  113.25  3.000
 2YY  N15  C14  N12  122.57  3.000
 2YY  H8   N15  C16  117.65  3.000
 2YY  H8   N15  C14  114.82  3.000
 2YY  C16  N15  C14  123.52  3.000
 2YY  H10  C16  H9   107.29  3.000
 2YY  H10  C16  C17  108.94  3.000
 2YY  H9   C16  C17  109.75  3.000
 2YY  H10  C16  N15  109.51  3.000
 2YY  H9   C16  N15  111.41  3.000
 2YY  C17  C16  N15  109.88  3.000
 2YY  H12  C17  H11  107.33  3.000
 2YY  H12  C17  C24  109.85  3.000
 2YY  H11  C17  C24  110.26  3.000
 2YY  H12  C17  C16  109.30  3.000
 2YY  H11  C17  C16  109.25  3.000
 2YY  C24  C17  C16  110.78  3.000
 2YY  C26  C19  C22  119.17  3.000
 2YY  C26  C19  C20  122.40  3.000
 2YY  C22  C19  C20  118.43  3.000
 2YY  O27  C20  O21  123.09  3.000
 2YY  O27  C20  C19  113.08  3.000
 2YY  O21  C20  C19  123.83  3.000
 2YY  H13  C22  C23  119.60  3.000
 2YY  H13  C22  C19  120.05  3.000
 2YY  C23  C22  C19  120.35  3.000
 2YY  H14  C23  C24  119.74  3.000
 2YY  H14  C23  C22  119.45  3.000
 2YY  C24  C23  C22  120.81  3.000
 2YY  C25  C24  C23  118.56  3.000
 2YY  C25  C24  C17  120.74  3.000
 2YY  C23  C24  C17  120.67  3.000
 2YY  H15  C25  C26  119.30  3.000
 2YY  H15  C25  C24  119.69  3.000
 2YY  C26  C25  C24  121.00  3.000
 2YY  H16  C26  C25  118.95  3.000
 2YY  H16  C26  C19  120.95  3.000
 2YY  C25  C26  C19  120.10  3.000
 2YY  H17  O27  C20  109.97  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
 2YY  CONST_01  N12  C3   C2   C1   180.00   0.0  0
 2YY  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 2YY  CONST_03  C4   C5   C6   C1     0.00   0.0  0
 2YY  CONST_04  C14  N12  C3   C2   180.00   0.0  0
 2YY  CONST_05  N13  C4   C3   C2   180.00   0.0  0
 2YY  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 2YY  CONST_07  C5   C6   C1   C2     0.00   0.0  0
 2YY  CONST_08  N13  C14  N12  C3     0.00   0.0  0
 2YY  CONST_09  C14  N13  C4   C3     0.00   0.0  0
 2YY  CONST_10  C6   C5   C4   C3     0.00   0.0  0
 2YY  CONST_11  C6   C1   C2   C3     0.00   0.0  0
 2YY  CONST_12  N12  C14  N13  C4     0.00   0.0  0
 2YY  CONST_13  C14  N12  C3   C4     0.00   0.0  0
 2YY  CONST_14  C14  N13  C4   C5   180.00   0.0  0
 2YY  CONST_15  N12  C3   C4   C5   180.00   0.0  0
 2YY  CONST_16  N13  C4   C5   C6   180.00   0.0  0
 2YY  CONST_17  N13  C4   C3   N12    0.00   0.0  0
 2YY  CONST_18  C24  C23  C22  C19    0.00   0.0  0
 2YY  CONST_19  C24  C25  C26  C19    0.00   0.0  0
 2YY  CONST_20  C25  C26  C19  C22    0.00   0.0  0
 2YY  CONST_21  C25  C24  C23  C22    0.00   0.0  0
 2YY  CONST_22  C26  C19  C22  C23    0.00   0.0  0
 2YY  CONST_23  C26  C25  C24  C23    0.00   0.0  0
 2YY  CONST_24  C9   N11  C7   C1     0.00   0.0  0
 2YY  CONST_25  N11  C9   N8   C6     0.00   0.0  0
 2YY  CONST_26  N8   C9   N11  C7     0.00   0.0  0
 2YY  CONST_27  N15  C14  N12  C3   180.00   0.0  0
 2YY  CONST_28  N15  C14  N13  C4   180.00   0.0  0
 2YY  CONST_29  C22  C23  C24  C17  180.00   0.0  0
 2YY  CONST_30  C26  C25  C24  C17  180.00   0.0  0
 2YY  CONST_31  C23  C22  C19  C20  180.00   0.0  0
 2YY  CONST_32  C25  C26  C19  C20  180.00   0.0  0
 2YY  CONST_33  N10  C9   N8   C6   180.00   0.0  0
 2YY  CONST_34  N10  C9   N11  C7   180.00   0.0  0
 2YY  CONST_35  O18  C7   N11  C9   180.00   0.0  0
 2YY  CONST_36  H2   C5   C6   C1   180.00   0.0  0
 2YY  CONST_37  H6   N12  C3   C2     0.00   0.0  0
 2YY  CONST_38  H1   C2   C3   C4   180.00   0.0  0
 2YY  CONST_39  H14  C23  C22  C19  180.00   0.0  0
 2YY  CONST_40  H15  C25  C26  C19  180.00   0.0  0
 2YY  CONST_41  H16  C26  C19  C22  180.00   0.0  0
 2YY  CONST_42  H13  C22  C23  C24  180.00   0.0  0
 2YY  CONST_43  H3   N11  C7   C1   180.00   0.0  0
 2YY  CONST_44  C16  N15  C14  N12    0.00   0.0  0
 2YY  CONST_45  C16  N15  C14  N13  180.00   0.0  0
 2YY  CONST_46  H8   N15  C14  N12  180.00   0.0  0
 2YY  CONST_47  H4   N10  C9   N8     0.00   0.0  0
 2YY  CONST_49  H17  O27  C20  C19  180.00   0.0  0
 2YY  Var_01    C23  C24  C17  C16   90.00  30.0  2
 2YY  Var_02    C22  C19  C20  O21   -1.09  30.0  2
 2YY  Var_03    C17  C16  N15  C14  175.15  30.0  1
 2YY  Var_04    C24  C17  C16  N15  179.81  30.0  1

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
 2YY  plan-1  C17  0.020
 2YY  plan-1  C19  0.020
 2YY  plan-1  C20  0.020
 2YY  plan-1  C22  0.020
 2YY  plan-1  C23  0.020
 2YY  plan-1  C24  0.020
 2YY  plan-1  C25  0.020
 2YY  plan-1  C26  0.020
 2YY  plan-1  H13  0.020
 2YY  plan-1  H14  0.020
 2YY  plan-1  H15  0.020
 2YY  plan-1  H16  0.020
 2YY  plan-2  C1   0.020
 2YY  plan-2  C2   0.020
 2YY  plan-2  C3   0.020
 2YY  plan-2  C4   0.020
 2YY  plan-2  C5   0.020
 2YY  plan-2  C6   0.020
 2YY  plan-2  C7   0.020
 2YY  plan-2  N8   0.020
 2YY  plan-2  C9   0.020
 2YY  plan-2  N10  0.020
 2YY  plan-2  N11  0.020
 2YY  plan-2  N12  0.020
 2YY  plan-2  N13  0.020
 2YY  plan-2  C14  0.020
 2YY  plan-2  N15  0.020
 2YY  plan-2  O18  0.020
 2YY  plan-2  H1   0.020
 2YY  plan-2  H2   0.020
 2YY  plan-2  H4   0.020
 2YY  plan-2  H5   0.020
 2YY  plan-2  H6   0.020
 2YY  plan-2  H3   0.020
 2YY  plan-3  C14  0.020
 2YY  plan-3  N15  0.020
 2YY  plan-3  C16  0.020
 2YY  plan-3  H8   0.020
 2YY  plan-4  C19  0.020
 2YY  plan-4  C20  0.020
 2YY  plan-4  O21  0.020
 2YY  plan-4  O27  0.020
 2YY  plan-4  H17  0.020

