# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 18:25:11 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 1-isoquinolin-6-yl-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCC(=O)N1CCCC1)Nc2ccc3cnccc3c2
#
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
 3ZG  3ZG  1-isoquinolin-6-yl-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea  ligand  40  22  .  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_3ZG
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
 3ZG  C4   C  CR16  0  -0.352  -2.9574  -1.8628   0.0385
 3ZG  C5   C  CR16  0  -0.286  -4.3169  -1.8031   0.0579
 3ZG  C6   C  CR66  0  -0.025  -4.9755  -0.5535   0.0375
 3ZG  C7   C  CR16  0  -0.092  -6.3800  -0.4272   0.0569
 3ZG  C8   C  CR16  0  -0.083  -6.2651   1.8433  -0.0068
 3ZG  N2   N  N     0  -0.416  -7.0124   0.7169   0.0366
 3ZG  C9   C  CR16  0  -0.389  -4.8985   1.8516  -0.0276
 3ZG  C10  C  CR66  0   0.244  -4.1962   0.6246  -0.0044
 3ZG  C11  C  CR16  0  -0.407  -2.7879   0.5512  -0.0228
 3ZG  C12  C  CH2   0  -0.260   6.2879  -0.7038  -0.1127
 3ZG  N3   N  NT    0  -0.473   5.0294   0.0372  -0.1079
 3ZG  C13  C  CH2   0  -0.485   7.3212   0.3580   0.2446
 3ZG  C14  C  CH2   0  -0.475   6.7203   1.6391  -0.3249
 3ZG  C15  C  CH2   0  -0.278   5.2318   1.4825  -0.0360
 3ZG  O1   O  O     0  -0.517   0.0201   1.2550  -0.0438
 3ZG  C2   C  C     0   0.760   0.2143   0.0485  -0.0403
 3ZG  N    N  NH1   0  -0.700   1.4473  -0.4954  -0.0561
 3ZG  C1   C  CH2   0  -0.362   2.6263   0.3193  -0.0968
 3ZG  C    C  C     0   0.529   3.8490  -0.5833  -0.1409
 3ZG  O    O  O     0  -0.506   3.7378  -1.8036  -0.2024
 3ZG  C3   C  CR6   0   0.402  -2.1648  -0.6791  -0.0011
 3ZG  H1   H  HCR6  0   0.277  -2.4622  -2.8268   0.0541
 3ZG  H2   H  HCR6  0   0.265  -4.8995  -2.7156   0.0907
 3ZG  H3   H  HNH1  0   0.414  -0.5165  -1.8572  -0.0066
 3ZG  H4   H  HCR6  0   0.264  -6.9869  -1.3281   0.0914
 3ZG  H5   H  HCR6  0   0.261  -6.8164   2.7763  -0.0257
 3ZG  H6   H  HCR6  0   0.264  -4.3589   2.7896  -0.0644
 3ZG  H7   H  HCR6  0   0.280  -2.2178   1.4656  -0.0542
 3ZG  H9   H  HCH2  0   0.241   6.4760  -1.1274  -1.1033
 3ZG  H10  H  HCH2  0   0.241   7.4195   0.4369   1.3295
 3ZG  H11  H  HCH2  0   0.255   8.3042   0.1253  -0.1618
 3ZG  H12  H  HCH2  0   0.256   7.1285   2.5446   0.1210
 3ZG  H13  H  HCH2  0   0.243   6.8871   1.6911  -1.4028
 3ZG  H14  H  HCH2  0   0.259   4.6131   2.0111  -0.7622
 3ZG  H15  H  HCH2  0   0.248   4.9803   1.8600   0.9596
 3ZG  H16  H  HNH1  0   0.401   1.5905  -1.4943  -0.0818
 3ZG  H17  H  HCH2  0   0.276   2.6312   0.9712  -0.9771
 3ZG  H18  H  HCH2  0   0.274   2.6892   0.9768   0.7768
 3ZG  N1   N  NH1   0  -0.797  -0.7965  -0.8880  -0.0158
 3ZG  H8   H  HCH2  0   0.251   6.2599  -1.5256   0.6027

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
 3ZG  N2   C8   aromatic  1.352  0.020  1.352
 3ZG  N2   C7   aromatic  1.307  0.020  1.307
 3ZG  C8   C9   aromatic  1.367  0.020  1.367
 3ZG  C7   C6   aromatic  1.410  0.020  1.410
 3ZG  C9   C10  aromatic  1.414  0.020  1.414
 3ZG  C6   C10  aromatic  1.413  0.020  1.413
 3ZG  C6   C5   aromatic  1.413  0.020  1.413
 3ZG  C10  C11  aromatic  1.410  0.020  1.410
 3ZG  C5   C4   aromatic  1.361  0.020  1.361
 3ZG  C11  C3   aromatic  1.379  0.020  1.379
 3ZG  C4   C3   aromatic  1.425  0.020  1.425
 3ZG  C3   N1   single    1.384  0.020  1.384
 3ZG  O1   C2   double    1.222  0.020  1.222
 3ZG  N1   C2   single    1.378  0.020  1.378
 3ZG  C2   N    single    1.348  0.020  1.348
 3ZG  N    C1   single    1.434  0.020  1.434
 3ZG  C1   C    single    1.520  0.020  1.520
 3ZG  O    C    double    1.227  0.020  1.227
 3ZG  C    N3   single    1.334  0.020  1.334
 3ZG  N3   C12  single    1.460  0.020  1.460
 3ZG  N3   C15  single    1.461  0.020  1.461
 3ZG  C12  C13  single    1.524  0.020  1.524
 3ZG  C13  C14  single    1.525  0.020  1.525
 3ZG  C15  C14  single    1.524  0.020  1.524
 3ZG  C4   H1   single    0.930  0.020  1.080
 3ZG  C5   H2   single    0.930  0.020  1.080
 3ZG  N1   H3   single    0.860  0.020  1.020
 3ZG  C7   H4   single    0.930  0.020  1.080
 3ZG  C8   H5   single    0.930  0.020  1.080
 3ZG  C9   H6   single    0.930  0.020  1.080
 3ZG  C11  H7   single    0.930  0.020  1.080
 3ZG  C12  H8   single    0.970  0.020  1.090
 3ZG  C12  H9   single    0.970  0.020  1.090
 3ZG  C13  H10  single    0.970  0.020  1.090
 3ZG  C13  H11  single    0.970  0.020  1.090
 3ZG  C14  H12  single    0.970  0.020  1.090
 3ZG  C14  H13  single    0.970  0.020  1.090
 3ZG  C15  H14  single    0.970  0.020  1.090
 3ZG  C15  H15  single    0.970  0.020  1.090
 3ZG  N    H16  single    0.860  0.020  1.020
 3ZG  C1   H17  single    0.970  0.020  1.090
 3ZG  C1   H18  single    0.970  0.020  1.090

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
 3ZG  H1   C4   C3   119.01  3.000
 3ZG  H1   C4   C5   119.68  3.000
 3ZG  C3   C4   C5   121.30  3.000
 3ZG  H2   C5   C6   119.66  3.000
 3ZG  H2   C5   C4   120.05  3.000
 3ZG  C6   C5   C4   120.29  3.000
 3ZG  C10  C6   C7   118.36  3.000
 3ZG  C10  C6   C5   118.73  3.000
 3ZG  C7   C6   C5   122.91  3.000
 3ZG  H4   C7   N2   117.11  3.000
 3ZG  H4   C7   C6   118.84  3.000
 3ZG  N2   C7   C6   124.05  3.000
 3ZG  H5   C8   C9   120.20  3.000
 3ZG  H5   C8   N2   115.88  3.000
 3ZG  C9   C8   N2   123.92  3.000
 3ZG  C8   N2   C7   117.52  3.000
 3ZG  H6   C9   C10  120.32  3.000
 3ZG  H6   C9   C8   120.27  3.000
 3ZG  C10  C9   C8   119.41  3.000
 3ZG  C11  C10  C9   122.74  3.000
 3ZG  C11  C10  C6   120.51  3.000
 3ZG  C9   C10  C6   116.75  3.000
 3ZG  H7   C11  C3   121.21  3.000
 3ZG  H7   C11  C10  118.97  3.000
 3ZG  C3   C11  C10  119.82  3.000
 3ZG  H9   C12  H8   107.87  3.000
 3ZG  H9   C12  C13  111.44  3.000
 3ZG  H8   C12  C13  112.88  3.000
 3ZG  H9   C12  N3   110.35  3.000
 3ZG  H8   C12  N3   111.00  3.000
 3ZG  C13  C12  N3   103.29  3.000
 3ZG  C    N3   C15  125.73  3.000
 3ZG  C15  N3   C12  112.50  3.000
 3ZG  C    N3   C12  121.76  3.000
 3ZG  H11  C13  H10  107.76  3.000
 3ZG  H11  C13  C14  113.32  3.000
 3ZG  H10  C13  C14  110.23  3.000
 3ZG  H11  C13  C12  112.06  3.000
 3ZG  H10  C13  C12  110.13  3.000
 3ZG  C14  C13  C12  103.33  3.000
 3ZG  H13  C14  H12  107.90  3.000
 3ZG  H13  C14  C15  109.95  3.000
 3ZG  H12  C14  C15  111.95  3.000
 3ZG  H13  C14  C13  110.39  3.000
 3ZG  H12  C14  C13  113.45  3.000
 3ZG  C15  C14  C13  103.16  3.000
 3ZG  H15  C15  H14  107.96  3.000
 3ZG  H15  C15  C14  111.20  3.000
 3ZG  H14  C15  C14  112.21  3.000
 3ZG  H15  C15  N3   110.75  3.000
 3ZG  H14  C15  N3   111.59  3.000
 3ZG  C14  C15  N3   103.15  3.000
 3ZG  N    C2   O1   122.94  3.000
 3ZG  N    C2   N1   113.39  3.000
 3ZG  O1   C2   N1   123.67  3.000
 3ZG  H16  N    C1   116.42  3.000
 3ZG  H16  N    C2   121.96  3.000
 3ZG  C1   N    C2   121.56  3.000
 3ZG  H18  C1   H17  106.47  3.000
 3ZG  H18  C1   C    109.47  3.000
 3ZG  H17  C1   C    109.05  3.000
 3ZG  H18  C1   N    111.46  3.000
 3ZG  H17  C1   N    111.39  3.000
 3ZG  C    C1   N    108.95  3.000
 3ZG  O    C    C1   121.27  3.000
 3ZG  O    C    N3   122.96  3.000
 3ZG  C1   C    N3   115.77  3.000
 3ZG  C11  C3   N1   125.52  3.000
 3ZG  N1   C3   C4   115.13  3.000
 3ZG  C11  C3   C4   119.34  3.000
 3ZG  H3   N1   C3   114.79  3.000
 3ZG  H3   N1   C2   116.70  3.000
 3ZG  C3   N1   C2   128.50  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
 3ZG  CONST_01  C7   C6   C5   C4    180.00   0.0  0
 3ZG  CONST_02  C10  C6   C5   C4      0.00   0.0  0
 3ZG  CONST_03  C10  C11  C3   C4      0.00   0.0  0
 3ZG  CONST_04  N2   C7   C6   C5    180.00   0.0  0
 3ZG  CONST_05  C9   C10  C6   C5    180.00   0.0  0
 3ZG  CONST_06  C11  C10  C6   C5      0.00   0.0  0
 3ZG  CONST_07  C11  C3   C4   C5      0.00   0.0  0
 3ZG  CONST_08  C8   N2   C7   C6      0.00   0.0  0
 3ZG  CONST_09  C8   C9   C10  C6      0.00   0.0  0
 3ZG  CONST_10  C3   C11  C10  C6      0.00   0.0  0
 3ZG  CONST_11  C3   C4   C5   C6      0.00   0.0  0
 3ZG  CONST_12  C9   C8   N2   C7      0.00   0.0  0
 3ZG  CONST_13  C9   C10  C6   C7      0.00   0.0  0
 3ZG  CONST_14  C11  C10  C6   C7    180.00   0.0  0
 3ZG  CONST_15  C11  C10  C9   C8    180.00   0.0  0
 3ZG  CONST_16  C10  C9   C8   N2      0.00   0.0  0
 3ZG  CONST_17  C10  C6   C7   N2      0.00   0.0  0
 3ZG  CONST_18  C3   C11  C10  C9    180.00   0.0  0
 3ZG  CONST_19  N1   C3   C4   C5    180.00   0.0  0
 3ZG  CONST_20  C10  C11  C3   N1    180.00   0.0  0
 3ZG  CONST_21  H7   C11  C3   C4    180.00   0.0  0
 3ZG  CONST_22  H4   C7   C6   C5      0.00   0.0  0
 3ZG  CONST_23  H6   C9   C10  C6    180.00   0.0  0
 3ZG  CONST_24  H1   C4   C5   C6    180.00   0.0  0
 3ZG  CONST_25  H5   C8   N2   C7    180.00   0.0  0
 3ZG  CONST_26  H2   C5   C6   C7      0.00   0.0  0
 3ZG  CONST_27  C1   C    N3   C12   180.00   0.0  0
 3ZG  CONST_28  O    C    N3   C12     0.00   0.0  0
 3ZG  CONST_29  C1   C    N3   C15     0.00   0.0  0
 3ZG  CONST_30  O    C    N3   C15   180.00   0.0  0
 3ZG  CONST_31  C2   N1   C3   C4    180.00   0.0  0
 3ZG  CONST_32  C2   N1   C3   C11     0.00   0.0  0
 3ZG  CONST_33  H3   N1   C3   C4      0.00   0.0  0
 3ZG  CONST_34  C3   N1   C2   O1      0.00   0.0  0
 3ZG  CONST_35  C3   N1   C2   N     180.00   0.0  0
 3ZG  CONST_36  C1   N    C2   O1      0.00   0.0  0
 3ZG  CONST_37  C1   N    C2   N1    180.00   0.0  0
 3ZG  CONST_38  H16  N    C2   O1    180.00   0.0  0
 3ZG  Var_01    C14  C15  N3   C12    12.88  30.0  1
 3ZG  Var_02    C15  C14  C13  C12    38.49  30.0  1
 3ZG  Var_03    C14  C13  C12  N3    -30.33  30.0  1
 3ZG  Var_04    C13  C14  C15  N3    -31.37  30.0  1
 3ZG  Var_05    C15  N3   C12  C13    11.01  30.0  1
 3ZG  Var_06    N    C1   C    N3   -176.48  30.0  1
 3ZG  Var_07    C    C1   N    C2   -178.59  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
 3ZG  plan-1  C4   0.020
 3ZG  plan-1  C5   0.020
 3ZG  plan-1  C6   0.020
 3ZG  plan-1  C7   0.020
 3ZG  plan-1  C8   0.020
 3ZG  plan-1  N2   0.020
 3ZG  plan-1  C9   0.020
 3ZG  plan-1  C10  0.020
 3ZG  plan-1  C11  0.020
 3ZG  plan-1  C3   0.020
 3ZG  plan-1  H1   0.020
 3ZG  plan-1  H2   0.020
 3ZG  plan-1  H4   0.020
 3ZG  plan-1  H5   0.020
 3ZG  plan-1  H6   0.020
 3ZG  plan-1  H7   0.020
 3ZG  plan-1  N1   0.020
 3ZG  plan-2  C12  0.020
 3ZG  plan-2  N3   0.020
 3ZG  plan-2  C15  0.020
 3ZG  plan-2  C1   0.020
 3ZG  plan-2  C    0.020
 3ZG  plan-2  O    0.020
 3ZG  plan-3  O1   0.020
 3ZG  plan-3  C2   0.020
 3ZG  plan-3  N    0.020
 3ZG  plan-3  C1   0.020
 3ZG  plan-3  C3   0.020
 3ZG  plan-3  H3   0.020
 3ZG  plan-3  H16  0.020
 3ZG  plan-3  N1   0.020

