# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 23:14:35 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 6-amino-4-(2-hydroxyethyl)-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1[nH]c2c(CCO)c3N=C(N)NC(=O)c3cc2n1
#
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
 PK3  PK3  6-amino-4-(2-hydroxyethyl)-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one  ligand  34  20  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PK3
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
 PK3  N6    N  NR15  0  -0.755  -2.5215   0.1942  -0.2975
 PK3  C11   C  CR5   0   0.669  -3.1807  -0.9872  -0.0829
 PK3  N5    N  NH1   0  -0.676  -4.5210  -1.0590  -0.1103
 PK3  C12   C  CH3   0  -0.548  -5.3732   0.1066  -0.0928
 PK3  N4    N  N     0  -0.535  -2.3715  -1.9973   0.1212
 PK3  C6    C  CR56  0   0.169  -1.1070  -1.4610   0.0321
 PK3  C7    C  CR56  0   0.351  -1.1761  -0.0721  -0.2342
 PK3  C8    C  CR6   0  -0.037  -0.0823   0.7563  -0.3777
 PK3  C9    C  CH2   0  -0.537  -0.2306   2.2269  -0.6317
 PK3  C3    C  CR66  0   0.212   1.1787   0.1425  -0.2318
 PK3  N2    N  N     0  -0.515   2.2933   0.9335  -0.3446
 PK3  C4    C  CR6   0   0.641   3.4538   0.3796  -0.2300
 PK3  N3    N  NH2   0  -0.836   4.5853   1.1008  -0.3941
 PK3  N1    N  NR16  0  -0.718   3.6207  -0.9569   0.0119
 PK3  C1    C  CR6   0   0.547   2.5803  -1.8461   0.1594
 PK3  O1    O  O     0  -0.472   2.8044  -3.0266   0.3796
 PK3  C2    C  CR66  0  -0.137   1.2636  -1.2465   0.0267
 PK3  C5    C  CR16  0  -0.417   0.1277  -2.0544   0.1599
 PK3  C10   C  CH2   0  -0.134  -0.3878   2.9990   0.6707
 PK3  O2    O  OH1   0  -0.672  -0.5493   4.3664   0.3647
 PK3  HN6   H  HNR5  0   0.422  -2.9471   1.0827  -0.5062
 PK3  HN5   H  HNH1  0   0.403  -4.9094  -1.9279   0.2164
 PK3  H12   H  HCH3  0   0.270  -6.4063  -0.2265  -0.1254
 PK3  H12A  H  HCH3  0   0.240  -5.2413   0.7196   0.8028
 PK3  H12B  H  HCH3  0   0.244  -5.2060   0.7339  -0.9697
 PK3  H9    H  HCH2  0   0.255   0.6423   2.5987  -1.1689
 PK3  H9A   H  HCH2  0   0.238  -1.0995   2.4141  -1.2697
 PK3  HN3   H  HNH2  0   0.402   4.4760   2.1013  -0.3755
 PK3  HN3A  H  HNH2  0   0.405   5.4503   0.7633  -0.0052
 PK3  HN1   H  HNR6  0   0.420   4.5559  -1.3362   0.0852
 PK3  H5    H  HCR6  0   0.252   0.2267  -3.1133   0.3591
 PK3  H10   H  HCH2  0   0.194  -1.2511   2.6066   1.2240
 PK3  H10A  H  HCH2  0   0.198   0.4963   2.8260   1.2975
 PK3  HO2   H  HOH1  0   0.454  -0.6928   4.8434   1.1868

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
 PK3  N6   C11   aromatic  1.370  0.020  1.370
 PK3  N6   C7    aromatic  1.373  0.020  1.373
 PK3  C11  N5    single    1.343  0.020  1.343
 PK3  C11  N4    aromatic  1.310  0.020  1.310
 PK3  N5   C12   single    1.444  0.020  1.444
 PK3  N4   C6    aromatic  1.376  0.020  1.376
 PK3  C6   C7    aromatic  1.416  0.020  1.416
 PK3  C6   C5    aromatic  1.376  0.020  1.376
 PK3  C7   C8    aromatic  1.380  0.020  1.380
 PK3  C8   C9    single    1.500  0.020  1.500
 PK3  C8   C3    aromatic  1.410  0.020  1.410
 PK3  C9   C10   single    1.522  0.020  1.522
 PK3  C3   N2    single    1.371  0.020  1.371
 PK3  C3   C2    aromatic  1.415  0.020  1.415
 PK3  N2   C4    double    1.291  0.020  1.291
 PK3  C4   N3    single    1.352  0.020  1.352
 PK3  C4   N1    single    1.368  0.020  1.368
 PK3  N1   C1    single    1.377  0.020  1.377
 PK3  C1   O1    double    1.222  0.020  1.222
 PK3  C1   C2    single    1.453  0.020  1.453
 PK3  C2   C5    aromatic  1.400  0.020  1.400
 PK3  C10  O2    single    1.410  0.020  1.410
 PK3  N6   HN6   single    0.860  0.020  1.020
 PK3  N5   HN5   single    0.890  0.020  1.040
 PK3  C12  H12   single    0.970  0.020  1.090
 PK3  C12  H12A  single    0.970  0.020  1.090
 PK3  C12  H12B  single    0.970  0.020  1.090
 PK3  C9   H9    single    0.970  0.020  1.090
 PK3  C9   H9A   single    0.970  0.020  1.090
 PK3  N3   HN3   single    0.890  0.020  1.040
 PK3  N3   HN3A  single    0.890  0.020  1.040
 PK3  N1   HN1   single    0.860  0.020  1.020
 PK3  C5   H5    single    0.930  0.020  1.080
 PK3  C10  H10   single    0.970  0.020  1.090
 PK3  C10  H10A  single    0.970  0.020  1.090
 PK3  O2   HO2   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
 PK3  HN6   N6   C7    126.50  3.000
 PK3  HN6   N6   C11   126.16  3.000
 PK3  C7    N6   C11   107.28  3.000
 PK3  N4    C11  N5    125.35  3.000
 PK3  N4    C11  N6    113.09  3.000
 PK3  N5    C11  N6    121.56  3.000
 PK3  HN5   N5   C12   117.73  3.000
 PK3  HN5   N5   C11   115.15  3.000
 PK3  C12   N5   C11   123.08  3.000
 PK3  H12B  C12  H12A  108.52  3.000
 PK3  H12B  C12  H12   107.34  3.000
 PK3  H12A  C12  H12   108.14  3.000
 PK3  H12B  C12  N5    111.34  3.000
 PK3  H12A  C12  N5    113.03  3.000
 PK3  H12   C12  N5    108.27  3.000
 PK3  C6    N4   C11   104.89  3.000
 PK3  C5    C6   C7    118.97  3.000
 PK3  C5    C6   N4    130.57  3.000
 PK3  C7    C6   N4    110.46  3.000
 PK3  C8    C7   C6    124.74  3.000
 PK3  C8    C7   N6    130.97  3.000
 PK3  C6    C7   N6    104.29  3.000
 PK3  C3    C8   C9    122.19  3.000
 PK3  C3    C8   C7    115.91  3.000
 PK3  C9    C8   C7    121.88  3.000
 PK3  H9A   C9   H9    106.87  3.000
 PK3  H9A   C9   C10   109.27  3.000
 PK3  H9    C9   C10   109.35  3.000
 PK3  H9A   C9   C8    110.18  3.000
 PK3  H9    C9   C8    109.80  3.000
 PK3  C10   C9   C8    111.27  3.000
 PK3  C2    C3   N2    122.16  3.000
 PK3  C2    C3   C8    119.98  3.000
 PK3  N2    C3   C8    117.86  3.000
 PK3  C4    N2   C3    118.42  3.000
 PK3  N1    C4   N3    116.13  3.000
 PK3  N1    C4   N2    122.98  3.000
 PK3  N3    C4   N2    120.85  3.000
 PK3  HN3A  N3   HN3   114.80  3.000
 PK3  HN3A  N3   C4    119.56  3.000
 PK3  HN3   N3   C4    115.91  3.000
 PK3  HN1   N1   C1    116.66  3.000
 PK3  HN1   N1   C4    119.45  3.000
 PK3  C1    N1   C4    123.89  3.000
 PK3  C2    C1   O1    125.56  3.000
 PK3  C2    C1   N1    114.12  3.000
 PK3  O1    C1   N1    120.32  3.000
 PK3  C5    C2   C1    119.23  3.000
 PK3  C5    C2   C3    122.34  3.000
 PK3  C1    C2   C3    118.43  3.000
 PK3  H5    C5   C2    120.52  3.000
 PK3  H5    C5   C6    121.42  3.000
 PK3  C2    C5   C6    118.05  3.000
 PK3  H10A  C10  H10   106.82  3.000
 PK3  H10A  C10  O2    111.65  3.000
 PK3  H10   C10  O2    111.46  3.000
 PK3  H10A  C10  C9    108.99  3.000
 PK3  H10   C10  C9    109.34  3.000
 PK3  O2    C10  C9    108.54  3.000
 PK3  HO2   O2   C10   108.22  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
 PK3  CONST_01  C6   N4   C11  N6      0.00   0.0  0
 PK3  CONST_02  N4   C6   C7   N6      0.00   0.0  0
 PK3  CONST_03  C5   C6   C7   N6    180.00   0.0  0
 PK3  CONST_04  C3   C8   C7   N6    180.00   0.0  0
 PK3  CONST_05  C6   C7   N6   C11     0.00   0.0  0
 PK3  CONST_06  C8   C7   N6   C11   180.00   0.0  0
 PK3  CONST_07  C7   C6   N4   C11     0.00   0.0  0
 PK3  CONST_08  C5   C6   N4   C11   180.00   0.0  0
 PK3  CONST_09  C7   N6   C11  N4      0.00   0.0  0
 PK3  CONST_10  C8   C7   C6   N4    180.00   0.0  0
 PK3  CONST_11  C2   C5   C6   N4    180.00   0.0  0
 PK3  CONST_12  C3   C8   C7   C6      0.00   0.0  0
 PK3  CONST_13  C3   C2   C5   C6      0.00   0.0  0
 PK3  CONST_14  C2   C5   C6   C7      0.00   0.0  0
 PK3  CONST_15  C2   C3   C8   C7      0.00   0.0  0
 PK3  CONST_16  C5   C6   C7   C8      0.00   0.0  0
 PK3  CONST_17  C5   C2   C3   C8      0.00   0.0  0
 PK3  CONST_18  N1   C4   N2   C3      0.00   0.0  0
 PK3  CONST_19  C1   N1   C4   N2      0.00   0.0  0
 PK3  CONST_20  C2   C1   N1   C4      0.00   0.0  0
 PK3  CONST_21  C9   C8   C7   N6      0.00   0.0  0
 PK3  CONST_22  C7   N6   C11  N5    180.00   0.0  0
 PK3  CONST_23  C6   N4   C11  N5    180.00   0.0  0
 PK3  CONST_24  C9   C8   C7   C6    180.00   0.0  0
 PK3  CONST_25  N2   C3   C8   C9      0.00   0.0  0
 PK3  CONST_26  C2   C3   C8   C9    180.00   0.0  0
 PK3  CONST_27  N3   C4   N2   C3    180.00   0.0  0
 PK3  CONST_28  O1   C1   N1   C4    180.00   0.0  0
 PK3  CONST_29  C1   N1   C4   N3    180.00   0.0  0
 PK3  CONST_30  HN6  N6   C11  N4    180.00   0.0  0
 PK3  CONST_31  H5   C5   C6   N4      0.00   0.0  0
 PK3  CONST_32  HN1  N1   C4   N2    180.00   0.0  0
 PK3  CONST_33  C12  N5   C11  N6      0.00   0.0  0
 PK3  CONST_34  N4   C11  N5   C12   180.00   0.0  0
 PK3  CONST_35  HN5  N5   C11  N6    180.00   0.0  0
 PK3  CONST_36  HN3  N3   C4   N2      0.00   0.0  0
 PK3  Var_01    C10  C9   C8   C7     85.81  30.0  2
 PK3  Var_02    O2   C10  C9   C8   -178.83  30.0  3
 PK3  Var_03    H12  C12  N5   C11   179.81  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
 PK3  plan-1  N6    0.020
 PK3  plan-1  C11   0.020
 PK3  plan-1  N5    0.020
 PK3  plan-1  N4    0.020
 PK3  plan-1  C6    0.020
 PK3  plan-1  C7    0.020
 PK3  plan-1  C8    0.020
 PK3  plan-1  C9    0.020
 PK3  plan-1  C3    0.020
 PK3  plan-1  N2    0.020
 PK3  plan-1  C4    0.020
 PK3  plan-1  N3    0.020
 PK3  plan-1  N1    0.020
 PK3  plan-1  C1    0.020
 PK3  plan-1  O1    0.020
 PK3  plan-1  C2    0.020
 PK3  plan-1  C5    0.020
 PK3  plan-1  HN6   0.020
 PK3  plan-1  HN3   0.020
 PK3  plan-1  HN3A  0.020
 PK3  plan-1  HN1   0.020
 PK3  plan-1  H5    0.020
 PK3  plan-2  C11   0.020
 PK3  plan-2  N5    0.020
 PK3  plan-2  C12   0.020
 PK3  plan-2  HN5   0.020

