# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 07:54:28 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: methyl 4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1ccc(CCNc2[nH]c3cc4C(=O)NC(=Nc4cc3n2)N)cc1
#
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
 2YW  2YW  'methyl 4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzoate'  ligand  46  28  .  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_2YW
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
 2YW  C1   C  CR66  0  -0.156  -4.7880  -0.8418  -0.1989
 2YW  C2   C  CR16  0  -0.352  -3.4078  -1.0417  -0.3565
 2YW  C3   C  CR56  0   0.355  -2.5965   0.0425  -0.1689
 2YW  C4   C  CR56  0   0.198  -3.0991   1.3257   0.1675
 2YW  C5   C  CR16  0  -0.453  -4.4617   1.5157   0.3188
 2YW  C6   C  CR66  0   0.275  -5.3217   0.4260   0.1376
 2YW  C7   C  CR6   0   0.543  -5.6980  -1.9541  -0.3829
 2YW  N8   N  N     0  -0.526  -6.6693   0.6319   0.3028
 2YW  C9   C  CR6   0   0.637  -7.4633  -0.3723   0.1309
 2YW  N10  N  NH2   0  -0.833  -8.8033  -0.2203   0.2265
 2YW  N11  N  NR16  0  -0.719  -7.0238  -1.6259  -0.2008
 2YW  N12  N  NR15  0  -0.748  -1.2290   0.2146  -0.2335
 2YW  N13  N  N     0  -0.541  -2.0728   2.2180   0.2962
 2YW  C14  C  CR5   0   0.692  -0.9800   1.5210   0.0507
 2YW  N15  N  NH1   0  -0.689   0.2577   2.0363   0.0522
 2YW  C16  C  CH2   0  -0.269   1.4591   1.2307   0.0049
 2YW  C17  C  CH2   0  -0.553   2.6854   2.1351  -0.0690
 2YW  O18  O  O     0  -0.473  -5.3784  -3.0969  -0.6749
 2YW  C19  C  CR6   0  -0.097   6.2571  -0.2623  -0.1760
 2YW  C20  C  C     0   0.594   7.4789  -1.0990  -0.2675
 2YW  O21  O  O2    0  -0.456   8.0313  -1.3283   0.9126
 2YW  C22  C  CH3   0  -0.424   9.2125  -2.1287   0.9473
 2YW  C23  C  CR16  0  -0.240   5.5991   0.0791  -1.3560
 2YW  C24  C  CR16  0  -0.289   4.4576   0.8605  -1.3203
 2YW  C25  C  CR6   0   0.125   3.9452   1.3200  -0.1090
 2YW  C26  C  CR16  0  -0.289   4.6051   0.9725   1.0669
 2YW  C27  C  CR16  0  -0.249   5.7494   0.1925   1.0400
 2YW  O28  O  O     0  -0.449   7.9245  -1.5264  -1.3060
 2YW  H1   H  HCR6  0   0.269  -3.0185  -2.0176  -0.6150
 2YW  H2   H  HCR6  0   0.246  -4.8696   2.4844   0.5775
 2YW  H3   H  HNH2  0   0.402  -9.1178   0.6381   0.6478
 2YW  H4   H  HNH2  0   0.405  -9.3768  -1.0225   0.4295
 2YW  H5   H  HNR6  0   0.420  -7.6977  -2.3682  -0.3374
 2YW  H6   H  HNR5  0   0.427  -0.5505  -0.5032  -0.4305
 2YW  H8   H  HNH1  0   0.404   0.3292   2.9616   0.4459
 2YW  H9   H  HCH2  0   0.249   1.5370   0.5745   0.8795
 2YW  H10  H  HCH2  0   0.251   1.4367   0.5906  -0.8813
 2YW  H11  H  HCH2  0   0.269   2.6134   2.7666  -0.9571
 2YW  H12  H  HCH2  0   0.266   2.6988   2.7967   0.8008
 2YW  H13  H  HCH3  0   0.241   9.0236  -3.1329   0.5685
 2YW  H14  H  HCH3  0   0.241  10.0190  -1.6735   0.3732
 2YW  H15  H  HCH3  0   0.254   9.5016  -2.1860   1.9923
 2YW  H16  H  HCR6  0   0.263   5.9826  -0.2625  -2.3080
 2YW  H17  H  HCR6  0   0.258   3.9615   1.1204  -2.2476
 2YW  H18  H  HCR6  0   0.259   4.2226   1.3198   2.0190
 2YW  H19  H  HCR6  0   0.264   6.2380  -0.0534   1.9725

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
 2YW  O28  C20  double    1.208  0.020  1.208
 2YW  C27  C26  aromatic  1.385  0.020  1.385
 2YW  C27  C19  aromatic  1.394  0.020  1.394
 2YW  C26  C25  aromatic  1.392  0.020  1.392
 2YW  C20  C19  single    1.484  0.020  1.484
 2YW  C20  O21  single    1.323  0.020  1.323
 2YW  C19  C23  aromatic  1.394  0.020  1.394
 2YW  C25  C17  single    1.501  0.020  1.501
 2YW  C25  C24  aromatic  1.393  0.020  1.393
 2YW  C17  C16  single    1.526  0.020  1.526
 2YW  C23  C24  aromatic  1.384  0.020  1.384
 2YW  C22  O21  single    1.427  0.020  1.427
 2YW  C16  N15  single    1.447  0.020  1.447
 2YW  N15  C14  single    1.341  0.020  1.341
 2YW  C14  N13  aromatic  1.319  0.020  1.319
 2YW  C14  N12  aromatic  1.360  0.020  1.360
 2YW  N13  C4   aromatic  1.366  0.020  1.366
 2YW  N12  C3   aromatic  1.380  0.020  1.380
 2YW  C4   C3   aromatic  1.419  0.020  1.419
 2YW  C4   C5   aromatic  1.384  0.020  1.384
 2YW  C3   C2   aromatic  1.367  0.020  1.367
 2YW  C5   C6   aromatic  1.400  0.020  1.400
 2YW  C2   C1   aromatic  1.403  0.020  1.403
 2YW  C6   C1   aromatic  1.416  0.020  1.416
 2YW  C6   N8   single    1.373  0.020  1.373
 2YW  C1   C7   single    1.449  0.020  1.449
 2YW  N8   C9   double    1.292  0.020  1.292
 2YW  C7   O18  double    1.222  0.020  1.222
 2YW  C7   N11  single    1.378  0.020  1.378
 2YW  C9   N11  single    1.369  0.020  1.369
 2YW  C9   N10  single    1.352  0.020  1.352
 2YW  C2   H1   single    0.930  0.020  1.080
 2YW  C5   H2   single    0.930  0.020  1.080
 2YW  N10  H3   single    0.890  0.020  1.040
 2YW  N10  H4   single    0.890  0.020  1.040
 2YW  N11  H5   single    0.860  0.020  1.020
 2YW  N12  H6   single    0.860  0.020  1.020
 2YW  N15  H8   single    0.890  0.020  1.040
 2YW  C16  H9   single    0.970  0.020  1.090
 2YW  C16  H10  single    0.970  0.020  1.090
 2YW  C17  H11  single    0.970  0.020  1.090
 2YW  C17  H12  single    0.970  0.020  1.090
 2YW  C22  H13  single    0.970  0.020  1.090
 2YW  C22  H14  single    0.970  0.020  1.090
 2YW  C22  H15  single    0.970  0.020  1.090
 2YW  C23  H16  single    0.930  0.020  1.080
 2YW  C24  H17  single    0.930  0.020  1.080
 2YW  C26  H18  single    0.930  0.020  1.080
 2YW  C27  H19  single    0.930  0.020  1.080

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
 2YW  C7   C1   C6   118.74  3.000
 2YW  C7   C1   C2   119.61  3.000
 2YW  C6   C1   C2   121.65  3.000
 2YW  H1   C2   C3   122.31  3.000
 2YW  H1   C2   C1   120.61  3.000
 2YW  C3   C2   C1   117.08  3.000
 2YW  N12  C3   C4   104.44  3.000
 2YW  C4   C3   C2   122.66  3.000
 2YW  N12  C3   C2   132.90  3.000
 2YW  N13  C4   C5   129.77  3.000
 2YW  C5   C4   C3   119.93  3.000
 2YW  N13  C4   C3   110.31  3.000
 2YW  H2   C5   C6   119.74  3.000
 2YW  H2   C5   C4   121.33  3.000
 2YW  C6   C5   C4   118.93  3.000
 2YW  N8   C6   C5   118.07  3.000
 2YW  N8   C6   C1   122.18  3.000
 2YW  C5   C6   C1   119.75  3.000
 2YW  O18  C7   N11  120.39  3.000
 2YW  N11  C7   C1   113.87  3.000
 2YW  O18  C7   C1   125.73  3.000
 2YW  C9   N8   C6   118.08  3.000
 2YW  N11  C9   N10  115.99  3.000
 2YW  N10  C9   N8   120.82  3.000
 2YW  N11  C9   N8   123.15  3.000
 2YW  H4   N10  H3   114.65  3.000
 2YW  H4   N10  C9   119.29  3.000
 2YW  H3   N10  C9   115.80  3.000
 2YW  H5   N11  C9   119.38  3.000
 2YW  H5   N11  C7   116.63  3.000
 2YW  C9   N11  C7   123.98  3.000
 2YW  H6   N12  C14  127.02  3.000
 2YW  H6   N12  C3   126.01  3.000
 2YW  C14  N12  C3   106.95  3.000
 2YW  C14  N13  C4   105.05  3.000
 2YW  N15  C14  N13  124.16  3.000
 2YW  N13  C14  N12  113.25  3.000
 2YW  N15  C14  N12  122.58  3.000
 2YW  H8   N15  C16  117.70  3.000
 2YW  H8   N15  C14  114.75  3.000
 2YW  C16  N15  C14  123.53  3.000
 2YW  H10  C16  H9   107.32  3.000
 2YW  H10  C16  C17  108.92  3.000
 2YW  H9   C16  C17  109.66  3.000
 2YW  H10  C16  N15  109.60  3.000
 2YW  H9   C16  N15  111.48  3.000
 2YW  C17  C16  N15  109.81  3.000
 2YW  H12  C17  H11  107.34  3.000
 2YW  H12  C17  C25  109.85  3.000
 2YW  H11  C17  C25  110.34  3.000
 2YW  H12  C17  C16  109.28  3.000
 2YW  H11  C17  C16  109.22  3.000
 2YW  C25  C17  C16  110.73  3.000
 2YW  C27  C19  C23  119.13  3.000
 2YW  C23  C19  C20  118.34  3.000
 2YW  C27  C19  C20  122.53  3.000
 2YW  O28  C20  O21  123.46  3.000
 2YW  O21  C20  C19  112.74  3.000
 2YW  O28  C20  C19  123.80  3.000
 2YW  C22  O21  C20  117.67  3.000
 2YW  H15  C22  H14  109.39  3.000
 2YW  H15  C22  H13  109.39  3.000
 2YW  H14  C22  H13  109.28  3.000
 2YW  H15  C22  O21  105.86  3.000
 2YW  H14  C22  O21  111.44  3.000
 2YW  H13  C22  O21  111.40  3.000
 2YW  H16  C23  C24  119.57  3.000
 2YW  H16  C23  C19  120.03  3.000
 2YW  C24  C23  C19  120.39  3.000
 2YW  H17  C24  C25  119.78  3.000
 2YW  H17  C24  C23  119.42  3.000
 2YW  C25  C24  C23  120.80  3.000
 2YW  C26  C25  C24  118.53  3.000
 2YW  C24  C25  C17  120.73  3.000
 2YW  C26  C25  C17  120.71  3.000
 2YW  H18  C26  C27  119.30  3.000
 2YW  H18  C26  C25  119.66  3.000
 2YW  C27  C26  C25  121.04  3.000
 2YW  H19  C27  C26  118.99  3.000
 2YW  H19  C27  C19  120.91  3.000
 2YW  C26  C27  C19  120.10  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
 2YW  CONST_01  N12  C3   C2   C1   180.00   0.0  0
 2YW  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 2YW  CONST_03  C4   C5   C6   C1     0.00   0.0  0
 2YW  CONST_04  C14  N12  C3   C2   180.00   0.0  0
 2YW  CONST_05  N13  C4   C3   C2   180.00   0.0  0
 2YW  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 2YW  CONST_07  C5   C6   C1   C2     0.00   0.0  0
 2YW  CONST_08  N13  C14  N12  C3     0.00   0.0  0
 2YW  CONST_09  C14  N13  C4   C3     0.00   0.0  0
 2YW  CONST_10  C6   C5   C4   C3     0.00   0.0  0
 2YW  CONST_11  C6   C1   C2   C3     0.00   0.0  0
 2YW  CONST_12  N12  C14  N13  C4     0.00   0.0  0
 2YW  CONST_13  C14  N12  C3   C4     0.00   0.0  0
 2YW  CONST_14  C14  N13  C4   C5   180.00   0.0  0
 2YW  CONST_15  N12  C3   C4   C5   180.00   0.0  0
 2YW  CONST_16  N13  C4   C5   C6   180.00   0.0  0
 2YW  CONST_17  N13  C4   C3   N12    0.00   0.0  0
 2YW  CONST_18  C25  C26  C27  C19    0.00   0.0  0
 2YW  CONST_19  C25  C24  C23  C19    0.00   0.0  0
 2YW  CONST_20  C26  C27  C19  C23    0.00   0.0  0
 2YW  CONST_21  C26  C25  C24  C23    0.00   0.0  0
 2YW  CONST_22  C27  C26  C25  C24    0.00   0.0  0
 2YW  CONST_23  C27  C19  C23  C24    0.00   0.0  0
 2YW  CONST_24  C9   N11  C7   C1     0.00   0.0  0
 2YW  CONST_25  N11  C9   N8   C6     0.00   0.0  0
 2YW  CONST_26  N8   C9   N11  C7     0.00   0.0  0
 2YW  CONST_27  N15  C14  N12  C3   180.00   0.0  0
 2YW  CONST_28  N15  C14  N13  C4   180.00   0.0  0
 2YW  CONST_29  C27  C26  C25  C17  180.00   0.0  0
 2YW  CONST_30  C23  C24  C25  C17  180.00   0.0  0
 2YW  CONST_31  C26  C27  C19  C20  180.00   0.0  0
 2YW  CONST_32  C24  C23  C19  C20  180.00   0.0  0
 2YW  CONST_33  N10  C9   N8   C6   180.00   0.0  0
 2YW  CONST_34  N10  C9   N11  C7   180.00   0.0  0
 2YW  CONST_35  O18  C7   N11  C9   180.00   0.0  0
 2YW  CONST_36  H2   C5   C6   C1   180.00   0.0  0
 2YW  CONST_37  H6   N12  C3   C2     0.00   0.0  0
 2YW  CONST_38  H1   C2   C3   C4   180.00   0.0  0
 2YW  CONST_39  H18  C26  C27  C19  180.00   0.0  0
 2YW  CONST_40  H17  C24  C23  C19  180.00   0.0  0
 2YW  CONST_41  H19  C27  C19  C23  180.00   0.0  0
 2YW  CONST_42  H16  C23  C24  C25  180.00   0.0  0
 2YW  CONST_43  H5   N11  C7   C1   180.00   0.0  0
 2YW  CONST_44  C16  N15  C14  N12    0.00   0.0  0
 2YW  CONST_45  C16  N15  C14  N13  180.00   0.0  0
 2YW  CONST_46  H8   N15  C14  N12  180.00   0.0  0
 2YW  CONST_47  H3   N10  C9   N8     0.00   0.0  0
 2YW  Var_01    C26  C25  C17  C16  -90.80  30.0  2
 2YW  Var_02    C27  C19  C20  O21   -1.47  30.0  2
 2YW  Var_03    C17  C16  N15  C14  176.40  30.0  1
 2YW  Var_04    C25  C17  C16  N15  179.59  30.0  1
 2YW  Var_05    H13  C22  O21  C20  -61.60  30.0  3

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
 2YW  plan-1  C17  0.020
 2YW  plan-1  C19  0.020
 2YW  plan-1  C20  0.020
 2YW  plan-1  C23  0.020
 2YW  plan-1  C24  0.020
 2YW  plan-1  C25  0.020
 2YW  plan-1  C26  0.020
 2YW  plan-1  C27  0.020
 2YW  plan-1  H16  0.020
 2YW  plan-1  H17  0.020
 2YW  plan-1  H18  0.020
 2YW  plan-1  H19  0.020
 2YW  plan-2  C19  0.020
 2YW  plan-2  C20  0.020
 2YW  plan-2  O21  0.020
 2YW  plan-2  O28  0.020
 2YW  plan-3  C1   0.020
 2YW  plan-3  C2   0.020
 2YW  plan-3  C3   0.020
 2YW  plan-3  C4   0.020
 2YW  plan-3  C5   0.020
 2YW  plan-3  C6   0.020
 2YW  plan-3  C7   0.020
 2YW  plan-3  N8   0.020
 2YW  plan-3  C9   0.020
 2YW  plan-3  N10  0.020
 2YW  plan-3  N11  0.020
 2YW  plan-3  N12  0.020
 2YW  plan-3  N13  0.020
 2YW  plan-3  C14  0.020
 2YW  plan-3  N15  0.020
 2YW  plan-3  O18  0.020
 2YW  plan-3  H1   0.020
 2YW  plan-3  H2   0.020
 2YW  plan-3  H3   0.020
 2YW  plan-3  H4   0.020
 2YW  plan-3  H5   0.020
 2YW  plan-3  H6   0.020
 2YW  plan-4  C14  0.020
 2YW  plan-4  N15  0.020
 2YW  plan-4  C16  0.020
 2YW  plan-4  H8   0.020

