# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:41:18 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 4-[4-[(dimethylamino)methyl]-2,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(c(OC)cc1CN(C)C)C2=CN(C)C(=O)c3cnccc23
#
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
 5U6  5U6  4-[4-[(dimethylamino)methyl]-2,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one  ligand  49  26  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5U6
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
 5U6  N3   N  N     0  -0.414  -3.6853   1.9819   2.3274
 5U6  C4   C  CR16  0  -0.055  -4.2413   1.2002   1.4275
 5U6  C5   C  CR66  0   0.366  -2.1135   0.4927   0.5368
 5U6  C6   C  CR66  0  -0.274  -3.5148   0.4367   0.5067
 5U6  C7   C  CR6   0   0.565  -4.2296  -0.3812  -0.4685
 5U6  C10  C  CR6   0  -0.066  -1.3666  -0.2860  -0.4080
 5U6  C13  C  CR16  0  -0.404   2.2375  -0.7807   0.5644
 5U6  C17  C  CR6   0   0.358   0.8487  -0.8201   0.6112
 5U6  C20  C  CR6   0   0.340   2.1747   0.2850  -1.5845
 5U6  C21  C  CR6   0  -0.028   2.9146  -0.2251  -0.5141
 5U6  C24  C  CH3   0  -0.516   6.3981  -0.6653   0.7362
 5U6  C26  C  CH3   0  -0.436   0.8358  -1.8498   2.7503
 5U6  C18  C  CR6   0  -0.095   0.1102  -0.2755  -0.4413
 5U6  C1   C  CR16  0  -0.405  -1.5313   1.3381   1.4927
 5U6  N8   N  NR6   0  -0.532  -3.4289  -1.0752  -1.3474
 5U6  C2   C  CR16  0  -0.060  -2.3456   2.0446   2.3441
 5U6  C16  C  CH3   0  -0.522   4.8676   1.0124   1.4698
 5U6  C9   C  CR16  0   0.008  -2.0652  -1.0202  -1.3027
 5U6  C12  C  CH3   0  -0.520  -4.0887  -1.8985  -2.3510
 5U6  C19  C  CR16  0  -0.408   0.7845   0.2661  -1.5310
 5U6  C14  C  CH2   0  -0.298   4.4249  -0.2164  -0.5400
 5U6  O22  O  O2    0  -0.475   2.8782   0.7801  -2.6290
 5U6  N15  N  NT    0  -0.410   5.0113  -0.2551   0.7845
 5U6  O11  O  O     0  -0.478  -5.4476  -0.4630  -0.5332
 5U6  C23  C  CH3   0  -0.436   2.1737   1.3505  -3.7108
 5U6  H1   H  HCR6  0   0.272  -5.3248   1.1609   1.4147
 5U6  H2   H  HCR6  0   0.274   2.8352  -1.1828   1.3718
 5U6  H3   H  HCH3  0   0.233   6.8000  -0.7287   1.7485
 5U6  H4   H  HCH3  0   0.234   6.4822  -1.6532   0.2808
 5U6  H5   H  HCH3  0   0.192   7.0397   0.0239   0.1655
 5U6  H6   H  HCH3  0   0.226   1.4992  -2.6815   2.4973
 5U6  H7   H  HCH3  0   0.224   1.4255  -1.0676   3.2363
 5U6  H8   H  HCH3  0   0.258   0.0825  -2.2053   3.4491
 5U6  H9   H  HCR6  0   0.264  -0.4582   1.4519   1.5586
 5U6  H10  H  HCR6  0   0.272  -1.9077   2.7018   3.0868
 5U6  H11  H  HCH3  0   0.237   3.8160   1.2881   1.5505
 5U6  H12  H  HCH3  0   0.234   5.2669   0.9351   2.4819
 5U6  H13  H  HCH3  0   0.197   5.3922   1.8357   0.9603
 5U6  H14  H  HCR6  0   0.308  -1.5563  -1.6213  -2.0435
 5U6  H15  H  HCH3  0   0.262  -4.7258  -2.6429  -1.8783
 5U6  H16  H  HCH3  0   0.262  -4.6956  -1.2848  -3.0136
 5U6  H17  H  HCH3  0   0.259  -3.3340  -2.4090  -2.9409
 5U6  H18  H  HCR6  0   0.276   0.1932   0.6875  -2.3333
 5U6  H19  H  HCH2  0   0.255   4.7662  -1.1006  -1.0884
 5U6  H20  H  HCH2  0   0.216   4.7880   0.6505  -1.1129
 5U6  H22  H  HCH3  0   0.259   2.9222   1.6853  -4.4251
 5U6  H23  H  HCH3  0   0.226   1.5191   0.6255  -4.2029
 5U6  H24  H  HCH3  0   0.225   1.5734   2.2115  -3.4030
 5U6  O25  O  O2    0  -0.467   0.1390  -1.3644   1.6227

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
 5U6  C26  O25  single    1.412  0.020  1.412
 5U6  O25  C17  single    1.350  0.020  1.350
 5U6  C13  C17  aromatic  1.390  0.020  1.390
 5U6  C13  C21  aromatic  1.389  0.020  1.389
 5U6  C17  C18  aromatic  1.396  0.020  1.396
 5U6  C14  C21  single    1.511  0.020  1.511
 5U6  C14  N15  single    1.449  0.020  1.449
 5U6  C21  C20  aromatic  1.398  0.020  1.398
 5U6  C16  N15  single    1.448  0.020  1.448
 5U6  C18  C10  single    1.477  0.020  1.477
 5U6  C18  C19  aromatic  1.391  0.020  1.391
 5U6  N15  C24  single    1.447  0.020  1.447
 5U6  C1   C5   aromatic  1.403  0.020  1.403
 5U6  C1   C2   aromatic  1.374  0.020  1.374
 5U6  C10  C5   single    1.434  0.020  1.434
 5U6  C10  C9   double    1.352  0.020  1.352
 5U6  C20  C19  aromatic  1.391  0.020  1.391
 5U6  C20  O22  single    1.353  0.020  1.353
 5U6  C5   C6   aromatic  1.403  0.020  1.403
 5U6  C2   N3   aromatic  1.341  0.020  1.341
 5U6  C9   N8   single    1.365  0.020  1.365
 5U6  C6   C4   aromatic  1.400  0.020  1.400
 5U6  C6   C7   single    1.460  0.020  1.460
 5U6  N3   C4   aromatic  1.315  0.020  1.315
 5U6  N8   C7   single    1.377  0.020  1.377
 5U6  N8   C12  single    1.456  0.020  1.456
 5U6  C7   O11  double    1.222  0.020  1.222
 5U6  O22  C23  single    1.411  0.020  1.411
 5U6  C4   H1   single    0.930  0.020  1.080
 5U6  C13  H2   single    0.930  0.020  1.080
 5U6  C24  H3   single    0.970  0.020  1.090
 5U6  C24  H4   single    0.970  0.020  1.090
 5U6  C24  H5   single    0.970  0.020  1.090
 5U6  C26  H6   single    0.970  0.020  1.090
 5U6  C26  H7   single    0.970  0.020  1.090
 5U6  C26  H8   single    0.970  0.020  1.090
 5U6  C1   H9   single    0.930  0.020  1.080
 5U6  C2   H10  single    0.930  0.020  1.080
 5U6  C16  H11  single    0.970  0.020  1.090
 5U6  C16  H12  single    0.970  0.020  1.090
 5U6  C16  H13  single    0.970  0.020  1.090
 5U6  C9   H14  single    0.930  0.020  1.080
 5U6  C12  H15  single    0.970  0.020  1.090
 5U6  C12  H16  single    0.970  0.020  1.090
 5U6  C12  H17  single    0.970  0.020  1.090
 5U6  C19  H18  single    0.930  0.020  1.080
 5U6  C14  H19  single    0.970  0.020  1.090
 5U6  C14  H20  single    0.970  0.020  1.090
 5U6  C23  H22  single    0.970  0.020  1.090
 5U6  C23  H23  single    0.970  0.020  1.090
 5U6  C23  H24  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
 5U6  C2   N3   C4   117.29  3.000
 5U6  H1   C4   C6   119.42  3.000
 5U6  H1   C4   N3   116.87  3.000
 5U6  C6   C4   N3   123.71  3.000
 5U6  C1   C5   C10  124.06  3.000
 5U6  C10  C5   C6   118.97  3.000
 5U6  C1   C5   C6   116.96  3.000
 5U6  C7   C6   C5   121.73  3.000
 5U6  C7   C6   C4   119.41  3.000
 5U6  C5   C6   C4   118.86  3.000
 5U6  O11  C7   N8   120.80  3.000
 5U6  O11  C7   C6   124.10  3.000
 5U6  N8   C7   C6   115.10  3.000
 5U6  C9   C10  C18  120.37  3.000
 5U6  C9   C10  C5   117.50  3.000
 5U6  C18  C10  C5   122.11  3.000
 5U6  H2   C13  C21  117.30  3.000
 5U6  H2   C13  C17  121.07  3.000
 5U6  C21  C13  C17  121.62  3.000
 5U6  O25  C17  C18  116.35  3.000
 5U6  C18  C17  C13  119.47  3.000
 5U6  O25  C17  C13  124.18  3.000
 5U6  O22  C20  C19  123.65  3.000
 5U6  O22  C20  C21  116.71  3.000
 5U6  C19  C20  C21  119.64  3.000
 5U6  C14  C21  C20  120.94  3.000
 5U6  C20  C21  C13  118.85  3.000
 5U6  C14  C21  C13  120.19  3.000
 5U6  H5   C24  H4   107.79  3.000
 5U6  H5   C24  H3   107.62  3.000
 5U6  H4   C24  H3   107.84  3.000
 5U6  H5   C24  N15  113.47  3.000
 5U6  H4   C24  N15  110.15  3.000
 5U6  H3   C24  N15  109.79  3.000
 5U6  H8   C26  H7   108.78  3.000
 5U6  H8   C26  H6   108.68  3.000
 5U6  H7   C26  H6   108.64  3.000
 5U6  H8   C26  O25  106.49  3.000
 5U6  H7   C26  O25  112.04  3.000
 5U6  H6   C26  O25  112.10  3.000
 5U6  C19  C18  C17  119.07  3.000
 5U6  C19  C18  C10  120.33  3.000
 5U6  C17  C18  C10  120.60  3.000
 5U6  H9   C1   C2   119.77  3.000
 5U6  H9   C1   C5   121.13  3.000
 5U6  C2   C1   C5   119.10  3.000
 5U6  C12  N8   C9   119.85  3.000
 5U6  C12  N8   C7   117.48  3.000
 5U6  C9   N8   C7   122.66  3.000
 5U6  H10  C2   C1   119.79  3.000
 5U6  H10  C2   N3   116.13  3.000
 5U6  C1   C2   N3   124.08  3.000
 5U6  H13  C16  H12  107.93  3.000
 5U6  H13  C16  H11  107.73  3.000
 5U6  H12  C16  H11  107.60  3.000
 5U6  H13  C16  N15  112.84  3.000
 5U6  H12  C16  N15  109.93  3.000
 5U6  H11  C16  N15  110.62  3.000
 5U6  H14  C9   N8   115.17  3.000
 5U6  H14  C9   C10  120.80  3.000
 5U6  N8   C9   C10  124.03  3.000
 5U6  H17  C12  H16  108.79  3.000
 5U6  H17  C12  H15  108.76  3.000
 5U6  H16  C12  H15  108.90  3.000
 5U6  H17  C12  N8   108.99  3.000
 5U6  H16  C12  N8   110.70  3.000
 5U6  H15  C12  N8   110.66  3.000
 5U6  H18  C19  C18  117.87  3.000
 5U6  H18  C19  C20  120.81  3.000
 5U6  C18  C19  C20  121.31  3.000
 5U6  H20  C14  H19  105.81  3.000
 5U6  H20  C14  N15  111.30  3.000
 5U6  H19  C14  N15  108.06  3.000
 5U6  H20  C14  C21  110.08  3.000
 5U6  H19  C14  C21  108.40  3.000
 5U6  N15  C14  C21  112.88  3.000
 5U6  C23  O22  C20  118.69  3.000
 5U6  C14  N15  C16  111.66  3.000
 5U6  C16  N15  C24  111.04  3.000
 5U6  C14  N15  C24  111.41  3.000
 5U6  H24  C23  H23  108.65  3.000
 5U6  H24  C23  H22  108.67  3.000
 5U6  H23  C23  H22  108.70  3.000
 5U6  H24  C23  O22  112.11  3.000
 5U6  H23  C23  O22  112.07  3.000
 5U6  H22  C23  O22  106.52  3.000
 5U6  C26  O25  C17  118.53  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
 5U6  CONST_01  C5   C1   C2   N3      0.00   0.0  0
 5U6  CONST_02  C5   C6   C4   N3      0.00   0.0  0
 5U6  CONST_03  C1   C5   C6   C4      0.00   0.0  0
 5U6  CONST_04  C1   C2   N3   C4      0.00   0.0  0
 5U6  CONST_05  C2   C1   C5   C6      0.00   0.0  0
 5U6  CONST_06  C2   N3   C4   C6      0.00   0.0  0
 5U6  CONST_07  C19  C18  C17  C13     0.00   0.0  0
 5U6  CONST_08  C19  C20  C21  C13     0.00   0.0  0
 5U6  CONST_09  C20  C21  C13  C17     0.00   0.0  0
 5U6  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 5U6  CONST_11  C18  C17  C13  C21     0.00   0.0  0
 5U6  CONST_12  C18  C19  C20  C21     0.00   0.0  0
 5U6  CONST_13  C13  C17  C18  C10   180.00   0.0  0
 5U6  CONST_14  C20  C19  C18  C10   180.00   0.0  0
 5U6  CONST_15  C9   N8   C7   C6      0.00   0.0  0
 5U6  CONST_16  O25  C17  C18  C10     0.00   0.0  0
 5U6  CONST_17  O22  C20  C21  C13   180.00   0.0  0
 5U6  CONST_18  C14  C21  C13  C17   180.00   0.0  0
 5U6  CONST_19  O25  C17  C13  C21   180.00   0.0  0
 5U6  CONST_20  O22  C20  C19  C18   180.00   0.0  0
 5U6  CONST_21  C19  C18  C17  O25   180.00   0.0  0
 5U6  CONST_22  C14  C21  C20  C19   180.00   0.0  0
 5U6  CONST_23  C12  N8   C7   C6    180.00   0.0  0
 5U6  CONST_24  O11  C7   N8   C9    180.00   0.0  0
 5U6  CONST_25  H9   C1   C2   N3    180.00   0.0  0
 5U6  CONST_26  H10  C2   N3   C4    180.00   0.0  0
 5U6  CONST_27  H1   C4   C6   C5    180.00   0.0  0
 5U6  CONST_28  H18  C19  C18  C10     0.00   0.0  0
 5U6  CONST_29  H2   C13  C21  C20   180.00   0.0  0
 5U6  CONST_30  O11  C7   N8   C12     0.00   0.0  0
 5U6  Var_01    C17  C18  C10  C5     67.42  30.0  2
 5U6  Var_02    N15  C14  C21  C13   -25.54  30.0  2
 5U6  Var_03    C18  C17  O25  C26  -175.93  30.0  2
 5U6  Var_04    H15  C12  N8   C7    -58.32  30.0  3
 5U6  Var_05    C16  N15  C14  C21   -73.32  30.0  3
 5U6  Var_06    H6   C26  O25  C17   -63.34  30.0  3
 5U6  Var_07    H22  C23  O22  C20   179.65  30.0  3
 5U6  Var_08    H11  C16  N15  C24  -176.89  30.0  3
 5U6  Var_09    H3   C24  N15  C16    57.39  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
 5U6  plan-1  C10  0.020
 5U6  plan-1  C13  0.020
 5U6  plan-1  C17  0.020
 5U6  plan-1  C20  0.020
 5U6  plan-1  C21  0.020
 5U6  plan-1  C18  0.020
 5U6  plan-1  C19  0.020
 5U6  plan-1  C14  0.020
 5U6  plan-1  O22  0.020
 5U6  plan-1  H2   0.020
 5U6  plan-1  H18  0.020
 5U6  plan-1  O25  0.020
 5U6  plan-2  N3   0.020
 5U6  plan-2  C4   0.020
 5U6  plan-2  C5   0.020
 5U6  plan-2  C6   0.020
 5U6  plan-2  C7   0.020
 5U6  plan-2  C10  0.020
 5U6  plan-2  C18  0.020
 5U6  plan-2  C1   0.020
 5U6  plan-2  N8   0.020
 5U6  plan-2  C2   0.020
 5U6  plan-2  C9   0.020
 5U6  plan-2  C12  0.020
 5U6  plan-2  O11  0.020
 5U6  plan-2  H1   0.020
 5U6  plan-2  H9   0.020
 5U6  plan-2  H10  0.020
 5U6  plan-2  H14  0.020

