# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 08:07:48 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-7-fluoronaphthalene-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(Oc2ccccc2OCCN3C=CC(=O)NC3=O)c4ccc(cc4c1)C#N
#
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
 M9A  M9A  5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-7-fluoronaphthalene-2-carbonitrile  ligand  47  31  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M9A
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
 M9A  C1   C  CR6   0   0.009  -2.4121  -2.7743  -0.7592
 M9A  N1   N  NR6   0  -0.525   2.1449  -0.9364   1.3699
 M9A  O1   O  O2    0  -0.459   1.7347   1.6478   0.3941
 M9A  C2   C  CR16  0  -0.238  -1.5028  -2.2953  -1.7289
 M9A  N2   N  NR16  0  -0.732   0.4161  -2.4581   1.1441
 M9A  C3   C  CR16  0  -0.271  -1.0506  -1.0107  -1.6486
 M9A  C4   C  CR66  0   0.002  -1.4852  -0.1536  -0.6118
 M9A  C5   C  CR6   0   0.389  -1.0246   1.1856  -0.4962
 M9A  C6   C  CR6   0   0.230   0.5720   2.7247  -1.3132
 M9A  C7   C  CR16  0  -0.313   0.3342   3.8062  -2.1380
 M9A  C8   C  CR16  0  -0.279   1.1629   4.9204  -2.0753
 M9A  C9   C  CR16  0  -0.244   2.2196   4.9322  -1.1804
 M9A  C10  C  CR16  0  -0.377   2.4549   3.8484  -0.3416
 M9A  C11  C  CR6   0   0.368   1.6255   2.7338  -0.3906
 M9A  C12  C  CH2   0  -0.194   2.9636   1.3884   1.0409
 M9A  C13  C  CH2   0  -0.357   2.7612   0.2284   1.9916
 M9A  C14  C  CR16  0   0.104   2.8396  -1.6506   0.4403
 M9A  C15  C  CR16  0  -0.504   2.3646  -2.7575  -0.1555
 M9A  C16  C  CR6   0   0.578   1.0601  -3.2517   0.2100
 M9A  C17  C  CR6   0   0.740   0.8727  -1.3151   1.7505
 M9A  C18  C  CR16  0  -0.507  -1.4548   1.9954   0.5190
 M9A  C19  C  CR6   0   0.563  -2.3581   1.4733   1.4549
 M9A  C20  C  CR16  0  -0.503  -2.8439   0.2057   1.4045
 M9A  C21  C  CR66  0   0.153  -2.4051  -0.6316   0.3553
 M9A  C22  C  CR16  0  -0.324  -2.8591  -1.9634   0.2562
 M9A  N    N  NS    0  -0.250  -3.2111  -5.2234  -0.8842
 M9A  C    C  CSP   0   0.059  -2.8543  -4.1296  -0.8253
 M9A  O    O  O2    0  -0.499  -0.1782   1.5878  -1.4683
 M9A  F    F  F     0  -0.313  -2.7537   2.2948   2.4367
 M9A  H1   H  HCR6  0   0.280  -1.1601  -2.9496  -2.5176
 M9A  H2   H  HNR6  0   0.423  -0.5063  -2.7558   1.4363
 M9A  H3   H  HCR6  0   0.271  -0.3478  -0.6546  -2.3880
 M9A  H4   H  HCR6  0   0.276  -0.4876   3.7639  -2.8413
 M9A  H5   H  HCR6  0   0.262   0.9809   5.7653  -2.7250
 M9A  H6   H  HCR6  0   0.265   2.8767   5.7898  -1.1255
 M9A  H7   H  HCR6  0   0.285   3.2892   3.8893   0.3450
 M9A  H8   H  HCH2  0   0.241   3.7397   1.1806   0.2962
 M9A  H9   H  HCH2  0   0.258   3.3048   2.2358   1.6423
 M9A  H10  H  HCH2  0   0.291   2.1338   0.5338   2.8238
 M9A  H11  H  HCH2  0   0.290   3.7310  -0.0557   2.4019
 M9A  H12  H  HCR6  0   0.321   3.8274  -1.2747   0.2105
 M9A  H13  H  HCR6  0   0.291   2.9589  -3.2907  -0.8810
 M9A  H14  H  HCR6  0   0.301  -1.1225   3.0214   0.6158
 M9A  H15  H  HCR6  0   0.279  -3.5388  -0.1605   2.1485
 M9A  H16  H  HCR6  0   0.286  -3.5540  -2.3429   0.9943
 M9A  O2   O  O     0  -0.464   0.5299  -4.2613  -0.2169
 M9A  O3   O  O     0  -0.466   0.2106  -0.7149   2.5684

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
 M9A  C9   C8   aromatic  1.385  0.020  1.385
 M9A  C9   C10  aromatic  1.391  0.020  1.391
 M9A  C8   C7   aromatic  1.390  0.020  1.390
 M9A  C10  C11  aromatic  1.390  0.020  1.390
 M9A  C7   C6   aromatic  1.381  0.020  1.381
 M9A  C11  C6   aromatic  1.400  0.020  1.400
 M9A  C11  O1   single    1.344  0.020  1.344
 M9A  O3   C17  double    1.211  0.020  1.211
 M9A  C12  O1   single    1.413  0.020  1.413
 M9A  C12  C13  single    1.513  0.020  1.513
 M9A  C6   O    single    1.371  0.020  1.371
 M9A  C17  N2   single    1.372  0.020  1.372
 M9A  C17  N1   single    1.381  0.020  1.381
 M9A  C13  N1   single    1.457  0.020  1.457
 M9A  N2   C16  single    1.385  0.020  1.385
 M9A  O    C5   single    1.350  0.020  1.350
 M9A  N1   C14  single    1.363  0.020  1.363
 M9A  C18  C5   aromatic  1.368  0.020  1.368
 M9A  C18  C19  aromatic  1.402  0.020  1.402
 M9A  C5   C4   aromatic  1.421  0.020  1.421
 M9A  C16  O2   double    1.218  0.020  1.218
 M9A  C16  C15  single    1.442  0.020  1.442
 M9A  C14  C15  double    1.344  0.020  1.344
 M9A  F    C19  single    1.340  0.020  1.340
 M9A  C19  C20  aromatic  1.358  0.020  1.358
 M9A  C4   C3   aromatic  1.414  0.020  1.414
 M9A  C4   C21  aromatic  1.418  0.020  1.418
 M9A  C3   C2   aromatic  1.364  0.020  1.364
 M9A  C20  C21  aromatic  1.412  0.020  1.412
 M9A  C21  C22  aromatic  1.411  0.020  1.411
 M9A  C2   C1   aromatic  1.413  0.020  1.413
 M9A  C22  C1   aromatic  1.374  0.020  1.374
 M9A  C1   C    single    1.427  0.020  1.427
 M9A  C    N    triple    1.152  0.020  1.152
 M9A  C2   H1   single    0.930  0.020  1.080
 M9A  N2   H2   single    0.860  0.020  1.020
 M9A  C3   H3   single    0.930  0.020  1.080
 M9A  C7   H4   single    0.930  0.020  1.080
 M9A  C8   H5   single    0.930  0.020  1.080
 M9A  C9   H6   single    0.930  0.020  1.080
 M9A  C10  H7   single    0.930  0.020  1.080
 M9A  C12  H8   single    0.970  0.020  1.090
 M9A  C12  H9   single    0.970  0.020  1.090
 M9A  C13  H10  single    0.970  0.020  1.090
 M9A  C13  H11  single    0.970  0.020  1.090
 M9A  C14  H12  single    0.930  0.020  1.080
 M9A  C15  H13  single    0.930  0.020  1.080
 M9A  C18  H14  single    0.930  0.020  1.080
 M9A  C20  H15  single    0.930  0.020  1.080
 M9A  C22  H16  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
 M9A  C    C1   C22  119.59  3.000
 M9A  C    C1   C2   119.31  3.000
 M9A  C22  C1   C2   121.09  3.000
 M9A  C17  N1   C14  120.93  3.000
 M9A  C14  N1   C13  119.63  3.000
 M9A  C17  N1   C13  119.43  3.000
 M9A  C12  O1   C11  119.09  3.000
 M9A  H1   C2   C3   120.54  3.000
 M9A  H1   C2   C1   119.98  3.000
 M9A  C3   C2   C1   119.48  3.000
 M9A  H2   N2   C17  114.87  3.000
 M9A  H2   N2   C16  116.74  3.000
 M9A  C17  N2   C16  128.38  3.000
 M9A  H3   C3   C4   120.13  3.000
 M9A  H3   C3   C2   119.05  3.000
 M9A  C4   C3   C2   120.81  3.000
 M9A  C21  C4   C5   118.20  3.000
 M9A  C21  C4   C3   119.69  3.000
 M9A  C5   C4   C3   122.10  3.000
 M9A  O    C5   C18  123.71  3.000
 M9A  C18  C5   C4   121.09  3.000
 M9A  O    C5   C4   115.18  3.000
 M9A  O    C6   C11  119.45  3.000
 M9A  O    C6   C7   119.19  3.000
 M9A  C11  C6   C7   121.20  3.000
 M9A  H4   C7   C8   120.89  3.000
 M9A  H4   C7   C6   119.22  3.000
 M9A  C8   C7   C6   119.88  3.000
 M9A  H5   C8   C9   120.68  3.000
 M9A  H5   C8   C7   119.92  3.000
 M9A  C9   C8   C7   119.41  3.000
 M9A  H6   C9   C10  118.98  3.000
 M9A  H6   C9   C8   120.20  3.000
 M9A  C10  C9   C8   120.82  3.000
 M9A  H7   C10  C11  120.86  3.000
 M9A  H7   C10  C9   118.95  3.000
 M9A  C11  C10  C9   120.18  3.000
 M9A  C10  C11  C6   118.50  3.000
 M9A  C6   C11  O1   116.13  3.000
 M9A  C10  C11  O1   125.36  3.000
 M9A  H9   C12  H8   107.44  3.000
 M9A  H9   C12  C13  106.87  3.000
 M9A  H8   C12  C13  112.11  3.000
 M9A  H9   C12  O1   112.39  3.000
 M9A  H8   C12  O1   109.86  3.000
 M9A  C13  C12  O1   108.18  3.000
 M9A  H11  C13  H10  107.38  3.000
 M9A  H11  C13  C12  108.48  3.000
 M9A  H10  C13  C12  110.06  3.000
 M9A  H11  C13  N1   109.17  3.000
 M9A  H10  C13  N1   107.90  3.000
 M9A  C12  C13  N1   113.66  3.000
 M9A  H12  C14  C15  120.98  3.000
 M9A  H12  C14  N1   115.37  3.000
 M9A  C15  C14  N1   123.64  3.000
 M9A  H13  C15  C16  119.96  3.000
 M9A  H13  C15  C14  120.70  3.000
 M9A  C16  C15  C14  119.32  3.000
 M9A  C15  C16  O2   126.10  3.000
 M9A  C15  C16  N2   113.28  3.000
 M9A  O2   C16  N2   120.61  3.000
 M9A  O3   C17  N2   121.96  3.000
 M9A  N2   C17  N1   114.41  3.000
 M9A  O3   C17  N1   123.62  3.000
 M9A  H14  C18  C19  119.41  3.000
 M9A  H14  C18  C5   122.05  3.000
 M9A  C19  C18  C5   118.53  3.000
 M9A  F    C19  C20  119.59  3.000
 M9A  C20  C19  C18  123.59  3.000
 M9A  F    C19  C18  116.82  3.000
 M9A  H15  C20  C21  120.65  3.000
 M9A  H15  C20  C19  121.33  3.000
 M9A  C21  C20  C19  118.02  3.000
 M9A  C22  C21  C20  120.79  3.000
 M9A  C22  C21  C4   118.64  3.000
 M9A  C20  C21  C4   120.56  3.000
 M9A  H16  C22  C21  119.33  3.000
 M9A  H16  C22  C1   120.38  3.000
 M9A  C21  C22  C1   120.29  3.000
 M9A  N    C    C1   180.00  3.000
 M9A  C6   O    C5   120.58  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
 M9A  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 M9A  CONST_02  C4   C21  C22  C1      0.00   0.0  0
 M9A  CONST_03  C20  C21  C22  C1    180.00   0.0  0
 M9A  CONST_04  C5   C4   C3   C2    180.00   0.0  0
 M9A  CONST_05  C21  C4   C3   C2      0.00   0.0  0
 M9A  CONST_06  C21  C22  C1   C2      0.00   0.0  0
 M9A  CONST_07  C18  C5   C4   C3    180.00   0.0  0
 M9A  CONST_08  C20  C21  C4   C3    180.00   0.0  0
 M9A  CONST_09  C22  C21  C4   C3      0.00   0.0  0
 M9A  CONST_10  C22  C1   C2   C3      0.00   0.0  0
 M9A  CONST_11  C19  C18  C5   C4      0.00   0.0  0
 M9A  CONST_12  C19  C20  C21  C4      0.00   0.0  0
 M9A  CONST_13  C20  C19  C18  C5      0.00   0.0  0
 M9A  CONST_14  C20  C21  C4   C5      0.00   0.0  0
 M9A  CONST_15  C22  C21  C4   C5    180.00   0.0  0
 M9A  CONST_16  C9   C8   C7   C6      0.00   0.0  0
 M9A  CONST_17  C9   C10  C11  C6      0.00   0.0  0
 M9A  CONST_18  C10  C9   C8   C7      0.00   0.0  0
 M9A  CONST_19  C10  C11  C6   C7      0.00   0.0  0
 M9A  CONST_20  C11  C10  C9   C8      0.00   0.0  0
 M9A  CONST_21  C11  C6   C7   C8      0.00   0.0  0
 M9A  CONST_22  C21  C4   C5   C18     0.00   0.0  0
 M9A  CONST_23  C21  C20  C19  C18     0.00   0.0  0
 M9A  CONST_24  C22  C21  C20  C19   180.00   0.0  0
 M9A  CONST_25  C16  N2   C17  N1      0.00   0.0  0
 M9A  CONST_26  C14  N1   C17  N2      0.00   0.0  0
 M9A  CONST_27  C17  N2   C16  C15     0.00   0.0  0
 M9A  CONST_28  C9   C10  C11  O1    180.00   0.0  0
 M9A  CONST_29  C7   C6   C11  O1    180.00   0.0  0
 M9A  CONST_30  O    C5   C4   C3      0.00   0.0  0
 M9A  CONST_31  C    C1   C2   C3    180.00   0.0  0
 M9A  CONST_32  F    C19  C18  C5    180.00   0.0  0
 M9A  CONST_33  O    C6   C7   C8    180.00   0.0  0
 M9A  CONST_34  O    C6   C11  C10   180.00   0.0  0
 M9A  CONST_35  O    C5   C18  C19   180.00   0.0  0
 M9A  CONST_36  O    C5   C4   C21   180.00   0.0  0
 M9A  CONST_37  F    C19  C20  C21   180.00   0.0  0
 M9A  CONST_38  C    C1   C22  C21   180.00   0.0  0
 M9A  CONST_39  C13  N1   C17  N2    180.00   0.0  0
 M9A  CONST_40  C17  N2   C16  O2    180.00   0.0  0
 M9A  CONST_41  C16  N2   C17  O3    180.00   0.0  0
 M9A  CONST_42  C14  N1   C17  O3    180.00   0.0  0
 M9A  CONST_43  H3   C3   C2   C1    180.00   0.0  0
 M9A  CONST_44  H16  C22  C1   C2    180.00   0.0  0
 M9A  CONST_45  H14  C18  C5   C4    180.00   0.0  0
 M9A  CONST_46  H1   C2   C3   C4    180.00   0.0  0
 M9A  CONST_47  H15  C20  C21  C4    180.00   0.0  0
 M9A  CONST_48  H5   C8   C7   C6    180.00   0.0  0
 M9A  CONST_49  H7   C10  C11  C6    180.00   0.0  0
 M9A  CONST_50  H6   C9   C8   C7    180.00   0.0  0
 M9A  CONST_51  H4   C7   C8   C9    180.00   0.0  0
 M9A  CONST_52  H2   N2   C17  N1    180.00   0.0  0
 M9A  CONST_53  C13  N1   C17  O3      0.00   0.0  0
 M9A  Var_01    C7   C6   O    C5   -114.13  30.0  2
 M9A  Var_02    C18  C5   O    C6     16.94  30.0  2
 M9A  Var_03    C17  N1   C13  C12  -112.82  30.0  3
 M9A  Var_04    O1   C12  C13  N1     51.50  30.0  1
 M9A  Var_05    C13  C12  O1   C11   172.63  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
 M9A  plan-1  O1   0.020
 M9A  plan-1  C6   0.020
 M9A  plan-1  C7   0.020
 M9A  plan-1  C8   0.020
 M9A  plan-1  C9   0.020
 M9A  plan-1  C10  0.020
 M9A  plan-1  C11  0.020
 M9A  plan-1  O    0.020
 M9A  plan-1  H4   0.020
 M9A  plan-1  H5   0.020
 M9A  plan-1  H6   0.020
 M9A  plan-1  H7   0.020
 M9A  plan-2  N1   0.020
 M9A  plan-2  N2   0.020
 M9A  plan-2  C13  0.020
 M9A  plan-2  C14  0.020
 M9A  plan-2  C15  0.020
 M9A  plan-2  C16  0.020
 M9A  plan-2  C17  0.020
 M9A  plan-2  H2   0.020
 M9A  plan-2  H12  0.020
 M9A  plan-2  H13  0.020
 M9A  plan-2  O2   0.020
 M9A  plan-2  O3   0.020
 M9A  plan-3  C1   0.020
 M9A  plan-3  C2   0.020
 M9A  plan-3  C3   0.020
 M9A  plan-3  C4   0.020
 M9A  plan-3  C5   0.020
 M9A  plan-3  C18  0.020
 M9A  plan-3  C19  0.020
 M9A  plan-3  C20  0.020
 M9A  plan-3  C21  0.020
 M9A  plan-3  C22  0.020
 M9A  plan-3  N    0.020
 M9A  plan-3  C    0.020
 M9A  plan-3  O    0.020
 M9A  plan-3  F    0.020
 M9A  plan-3  H1   0.020
 M9A  plan-3  H3   0.020
 M9A  plan-3  H14  0.020
 M9A  plan-3  H15  0.020
 M9A  plan-3  H16  0.020

