# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 15:38:03 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-7-fluoronaphthalene-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(Oc2cc(F)cc3cc(ccc23)C#N)c(OCCN4C=CC(=O)NC4=O)c1
#
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
 7N1  7N1  5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-7-fluoronaphthalene-2-carbonitrile  ligand  47  32  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7N1
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
 7N1  CAH  C  CR6   0   0.381  -1.3834  -1.1837   0.3357
 7N1  CAI  C  CR66  0   0.005  -2.2228  -0.0362   0.3699
 7N1  CAJ  C  CR66  0   0.152  -3.2431   0.0770  -0.6095
 7N1  CAK  C  CR16  0  -0.512  -3.4139  -0.9258  -1.5910
 7N1  CAL  C  CR6   0   0.561  -2.5766  -1.9956  -1.5623
 7N1  CAM  C  CR16  0  -0.506  -1.5566  -2.1548  -0.6138
 7N1  CAY  C  CR16  0  -0.272  -2.0675   0.9824   1.3382
 7N1  CAZ  C  CR16  0  -0.248  -2.8893   2.0724   1.3428
 7N1  CBA  C  CR6   0   0.016  -3.9067   2.1825   0.3670
 7N1  CBB  C  CR16  0  -0.314  -4.0816   1.2104  -0.5874
 7N1  CBC  C  CSP   0   0.056  -4.7644   3.3237   0.3766
 7N1  NBD  N  NS    0  -0.245  -5.4484   4.2506   0.3895
 7N1  C0P  C  CR16  0   0.120   0.8674   2.1196  -0.5460
 7N1  C00  C  CR16  0  -0.547   2.6231  -2.9157   0.2277
 7N1  C0D  C  CH2   0  -0.190   2.5022  -0.6121  -1.4277
 7N1  C0E  C  CH2   0  -0.363   2.1302   0.6980  -2.0847
 7N1  C0K  C  CR6   0   0.735   3.2207   2.4460  -0.7776
 7N1  C0N  C  CR6   0   0.568   1.8979   3.8340   0.7915
 7N1  C0O  C  CR16  0  -0.510   0.7364   3.0892   0.3750
 7N1  N0H  N  NR6   0  -0.520   2.0567   1.7959  -1.1292
 7N1  N0M  N  NR16  0  -0.731   3.0649   3.4374   0.1548
 7N1  O0A  O  O2    0  -0.495  -0.4408  -1.2422   1.3019
 7N1  O0S  O  O     0  -0.465   1.9165   4.7324   1.6130
 7N1  C01  C  CR6   0   0.555   2.5851  -4.0052   1.0824
 7N1  C02  C  CR16  0  -0.444   1.5726  -4.2141   1.9923
 7N1  C03  C  CR16  0  -0.288   0.5417  -3.2823   2.0420
 7N1  C04  C  CR6   0   0.213   0.5526  -2.1842   1.2098
 7N1  C05  C  CR6   0   0.397   1.5931  -1.9855   0.2918
 7N1  F01  F  F     0  -0.308  -2.7090  -2.9649  -2.4756
 7N1  H1   H  HCR6  0   0.285  -4.1909  -0.8386  -2.3385
 7N1  H2   H  HCR6  0   0.307  -0.9333  -3.0385  -0.6522
 7N1  H3   H  HCR6  0   0.279  -1.2884   0.9061   2.0830
 7N1  H4   H  HCR6  0   0.287  -2.7682   2.8480   2.0861
 7N1  H5   H  HCR6  0   0.287  -4.8642   1.3051  -1.3288
 7N1  H6   H  HCR6  0   0.305   0.0151   1.5506  -0.8894
 7N1  H7   H  HCR6  0   0.311   3.4467  -2.8125  -0.4660
 7N1  H8   H  HCH2  0   0.259   2.5481  -1.3937  -2.1924
 7N1  H9   H  HCH2  0   0.250   3.4837  -0.5440  -0.9501
 7N1  H10  H  HCH2  0   0.298   2.8605   0.9322  -2.8557
 7N1  H11  H  HCH2  0   0.288   1.1598   0.6174  -2.5731
 7N1  H12  H  HCR6  0   0.289  -0.2279   3.3189   0.8003
 7N1  H13  H  HNR6  0   0.426   3.9132   3.9299   0.4076
 7N1  H14  H  HCR6  0   0.287   1.5761  -5.0773   2.6426
 7N1  H15  H  HCR6  0   0.290  -0.2735  -3.4114   2.7420
 7N1  F02  F  F     0  -0.312   3.5873  -4.8925   1.0089
 7N1  O0B  O  O2    0  -0.458   1.4957  -0.8932  -0.4720
 7N1  O0Q  O  O     0  -0.478   4.2996   2.1650  -1.2567

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
 7N1  F02  C01  single    1.341  0.020  1.341
 7N1  C01  C00  aromatic  1.385  0.020  1.385
 7N1  C01  C02  aromatic  1.377  0.020  1.377
 7N1  C00  C05  aromatic  1.389  0.020  1.389
 7N1  C02  C03  aromatic  1.391  0.020  1.391
 7N1  C05  O0B  single    1.336  0.020  1.336
 7N1  C05  C04  aromatic  1.402  0.020  1.402
 7N1  C03  C04  aromatic  1.378  0.020  1.378
 7N1  C0D  O0B  single    1.416  0.020  1.416
 7N1  C0D  C0E  single    1.512  0.020  1.512
 7N1  O0Q  C0K  double    1.214  0.020  1.214
 7N1  C04  O0A  single    1.372  0.020  1.372
 7N1  C0E  N0H  single    1.457  0.020  1.457
 7N1  C0K  N0H  single    1.379  0.020  1.379
 7N1  C0K  N0M  single    1.370  0.020  1.370
 7N1  N0H  C0P  single    1.364  0.020  1.364
 7N1  N0M  C0N  single    1.387  0.020  1.387
 7N1  O0A  CAH  single    1.351  0.020  1.351
 7N1  CAM  CAH  aromatic  1.369  0.020  1.369
 7N1  CAM  CAL  aromatic  1.402  0.020  1.402
 7N1  CAH  CAI  aromatic  1.422  0.020  1.422
 7N1  C0P  C0O  double    1.344  0.020  1.344
 7N1  C0N  O0S  double    1.217  0.020  1.217
 7N1  C0N  C0O  single    1.441  0.020  1.441
 7N1  F01  CAL  single    1.338  0.020  1.338
 7N1  CAL  CAK  aromatic  1.359  0.020  1.359
 7N1  CAI  CAY  aromatic  1.414  0.020  1.414
 7N1  CAI  CAJ  aromatic  1.419  0.020  1.419
 7N1  CAY  CAZ  aromatic  1.365  0.020  1.365
 7N1  CAK  CAJ  aromatic  1.413  0.020  1.413
 7N1  CAJ  CBB  aromatic  1.410  0.020  1.410
 7N1  CAZ  CBA  aromatic  1.414  0.020  1.414
 7N1  CBB  CBA  aromatic  1.374  0.020  1.374
 7N1  CBA  CBC  single    1.428  0.020  1.428
 7N1  CBC  NBD  triple    1.152  0.020  1.152
 7N1  CAK  H1   single    0.930  0.020  1.080
 7N1  CAM  H2   single    0.930  0.020  1.080
 7N1  CAY  H3   single    0.930  0.020  1.080
 7N1  CAZ  H4   single    0.930  0.020  1.080
 7N1  CBB  H5   single    0.930  0.020  1.080
 7N1  C0P  H6   single    0.930  0.020  1.080
 7N1  C00  H7   single    0.930  0.020  1.080
 7N1  C0D  H8   single    0.970  0.020  1.090
 7N1  C0D  H9   single    0.970  0.020  1.090
 7N1  C0E  H10  single    0.970  0.020  1.090
 7N1  C0E  H11  single    0.970  0.020  1.090
 7N1  C0O  H12  single    0.930  0.020  1.080
 7N1  N0M  H13  single    0.860  0.020  1.020
 7N1  C02  H14  single    0.930  0.020  1.080
 7N1  C03  H15  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
 7N1  O0A  CAH  CAM  123.61  3.000
 7N1  CAM  CAH  CAI  120.95  3.000
 7N1  O0A  CAH  CAI  115.43  3.000
 7N1  CAY  CAI  CAJ  119.62  3.000
 7N1  CAJ  CAI  CAH  118.17  3.000
 7N1  CAY  CAI  CAH  122.20  3.000
 7N1  CBB  CAJ  CAK  120.62  3.000
 7N1  CBB  CAJ  CAI  118.74  3.000
 7N1  CAK  CAJ  CAI  120.64  3.000
 7N1  H1   CAK  CAL  121.38  3.000
 7N1  H1   CAK  CAJ  120.63  3.000
 7N1  CAL  CAK  CAJ  118.00  3.000
 7N1  F01  CAL  CAM  116.83  3.000
 7N1  F01  CAL  CAK  119.66  3.000
 7N1  CAM  CAL  CAK  123.51  3.000
 7N1  H2   CAM  CAL  119.20  3.000
 7N1  H2   CAM  CAH  122.07  3.000
 7N1  CAL  CAM  CAH  118.73  3.000
 7N1  H3   CAY  CAZ  119.22  3.000
 7N1  H3   CAY  CAI  120.03  3.000
 7N1  CAZ  CAY  CAI  120.76  3.000
 7N1  H4   CAZ  CBA  119.95  3.000
 7N1  H4   CAZ  CAY  120.51  3.000
 7N1  CBA  CAZ  CAY  119.54  3.000
 7N1  CBC  CBA  CBB  119.60  3.000
 7N1  CBC  CBA  CAZ  119.33  3.000
 7N1  CBB  CBA  CAZ  121.07  3.000
 7N1  H5   CBB  CBA  120.41  3.000
 7N1  H5   CBB  CAJ  119.32  3.000
 7N1  CBA  CBB  CAJ  120.27  3.000
 7N1  NBD  CBC  CBA  180.00  3.000
 7N1  H6   C0P  N0H  115.27  3.000
 7N1  H6   C0P  C0O  121.39  3.000
 7N1  N0H  C0P  C0O  123.33  3.000
 7N1  H7   C00  C05  122.01  3.000
 7N1  H7   C00  C01  119.45  3.000
 7N1  C05  C00  C01  118.54  3.000
 7N1  H9   C0D  H8   108.18  3.000
 7N1  H9   C0D  O0B  110.82  3.000
 7N1  H8   C0D  O0B  111.07  3.000
 7N1  H9   C0D  C0E  110.89  3.000
 7N1  H8   C0D  C0E  109.00  3.000
 7N1  O0B  C0D  C0E  106.88  3.000
 7N1  H11  C0E  H10  107.23  3.000
 7N1  H11  C0E  N0H  107.74  3.000
 7N1  H10  C0E  N0H  109.66  3.000
 7N1  H11  C0E  C0D  110.48  3.000
 7N1  H10  C0E  C0D  109.23  3.000
 7N1  N0H  C0E  C0D  112.36  3.000
 7N1  O0Q  C0K  N0M  122.51  3.000
 7N1  N0M  C0K  N0H  114.76  3.000
 7N1  O0Q  C0K  N0H  122.73  3.000
 7N1  O0S  C0N  N0M  120.52  3.000
 7N1  O0S  C0N  C0O  126.06  3.000
 7N1  N0M  C0N  C0O  113.42  3.000
 7N1  H12  C0O  C0N  119.76  3.000
 7N1  H12  C0O  C0P  120.74  3.000
 7N1  C0N  C0O  C0P  119.50  3.000
 7N1  C0K  N0H  C0E  118.67  3.000
 7N1  C0K  N0H  C0P  121.02  3.000
 7N1  C0E  N0H  C0P  120.22  3.000
 7N1  H13  N0M  C0N  116.80  3.000
 7N1  H13  N0M  C0K  115.25  3.000
 7N1  C0N  N0M  C0K  127.95  3.000
 7N1  C04  O0A  CAH  119.13  3.000
 7N1  F02  C01  C02  119.04  3.000
 7N1  C02  C01  C00  123.17  3.000
 7N1  F02  C01  C00  117.79  3.000
 7N1  H14  C02  C03  121.07  3.000
 7N1  H14  C02  C01  121.09  3.000
 7N1  C03  C02  C01  117.84  3.000
 7N1  H15  C03  C04  119.45  3.000
 7N1  H15  C03  C02  120.11  3.000
 7N1  C04  C03  C02  120.43  3.000
 7N1  C05  C04  C03  120.96  3.000
 7N1  C03  C04  O0A  120.06  3.000
 7N1  C05  C04  O0A  118.95  3.000
 7N1  C04  C05  O0B  115.85  3.000
 7N1  C04  C05  C00  119.05  3.000
 7N1  O0B  C05  C00  125.09  3.000
 7N1  C05  O0B  C0D  119.75  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
 7N1  CONST_01  CAK  CAL  CAM  CAH    0.00   0.0  0
 7N1  CONST_02  CAZ  CAY  CAI  CAH  180.00   0.0  0
 7N1  CONST_03  CAK  CAJ  CAI  CAH    0.00   0.0  0
 7N1  CONST_04  CBB  CAJ  CAI  CAH  180.00   0.0  0
 7N1  CONST_05  CAL  CAM  CAH  CAI    0.00   0.0  0
 7N1  CONST_06  CBA  CAZ  CAY  CAI    0.00   0.0  0
 7N1  CONST_07  CAL  CAK  CAJ  CAI    0.00   0.0  0
 7N1  CONST_08  CBA  CBB  CAJ  CAI    0.00   0.0  0
 7N1  CONST_09  CAM  CAH  CAI  CAJ    0.00   0.0  0
 7N1  CONST_10  CAZ  CAY  CAI  CAJ    0.00   0.0  0
 7N1  CONST_11  CAM  CAL  CAK  CAJ    0.00   0.0  0
 7N1  CONST_12  CAZ  CBA  CBB  CAJ    0.00   0.0  0
 7N1  CONST_13  CAY  CAI  CAJ  CAK  180.00   0.0  0
 7N1  CONST_14  CBA  CBB  CAJ  CAK  180.00   0.0  0
 7N1  CONST_15  CBB  CAJ  CAK  CAL  180.00   0.0  0
 7N1  CONST_16  CAY  CAI  CAH  CAM  180.00   0.0  0
 7N1  CONST_17  CBB  CAJ  CAI  CAY    0.00   0.0  0
 7N1  CONST_18  CBB  CBA  CAZ  CAY    0.00   0.0  0
 7N1  CONST_19  C03  C02  C01  C00    0.00   0.0  0
 7N1  CONST_20  C03  C04  C05  C00    0.00   0.0  0
 7N1  CONST_21  C04  C05  C00  C01    0.00   0.0  0
 7N1  CONST_22  C04  C03  C02  C01    0.00   0.0  0
 7N1  CONST_23  C05  C00  C01  C02    0.00   0.0  0
 7N1  CONST_24  C05  C04  C03  C02    0.00   0.0  0
 7N1  CONST_25  N0M  C0K  N0H  C0P    0.00   0.0  0
 7N1  CONST_26  C0O  C0N  N0M  C0K    0.00   0.0  0
 7N1  CONST_27  N0H  C0K  N0M  C0N    0.00   0.0  0
 7N1  CONST_28  F01  CAL  CAM  CAH  180.00   0.0  0
 7N1  CONST_29  O0A  CAH  CAI  CAJ  180.00   0.0  0
 7N1  CONST_30  F01  CAL  CAK  CAJ  180.00   0.0  0
 7N1  CONST_31  CBC  CBA  CBB  CAJ  180.00   0.0  0
 7N1  CONST_32  O0A  CAH  CAM  CAL  180.00   0.0  0
 7N1  CONST_33  O0A  CAH  CAI  CAY    0.00   0.0  0
 7N1  CONST_34  CBC  CBA  CAZ  CAY  180.00   0.0  0
 7N1  CONST_35  O0A  C04  C05  C00  180.00   0.0  0
 7N1  CONST_36  C02  C03  C04  O0A  180.00   0.0  0
 7N1  CONST_37  C01  C00  C05  O0B  180.00   0.0  0
 7N1  CONST_38  C03  C04  C05  O0B  180.00   0.0  0
 7N1  CONST_39  F02  C01  C02  C03  180.00   0.0  0
 7N1  CONST_40  F02  C01  C00  C05  180.00   0.0  0
 7N1  CONST_41  O0Q  C0K  N0H  C0P  180.00   0.0  0
 7N1  CONST_42  N0M  C0K  N0H  C0E  180.00   0.0  0
 7N1  CONST_43  O0S  C0N  N0M  C0K  180.00   0.0  0
 7N1  CONST_44  O0Q  C0K  N0M  C0N  180.00   0.0  0
 7N1  CONST_45  H3   CAY  CAI  CAH    0.00   0.0  0
 7N1  CONST_46  H2   CAM  CAH  CAI  180.00   0.0  0
 7N1  CONST_47  H4   CAZ  CAY  CAI  180.00   0.0  0
 7N1  CONST_48  H1   CAK  CAJ  CAI  180.00   0.0  0
 7N1  CONST_49  H5   CBB  CAJ  CAI  180.00   0.0  0
 7N1  CONST_50  H14  C02  C01  C00  180.00   0.0  0
 7N1  CONST_51  H15  C03  C02  C01  180.00   0.0  0
 7N1  CONST_52  H7   C00  C01  C02  180.00   0.0  0
 7N1  CONST_53  H13  N0M  C0N  C0O  180.00   0.0  0
 7N1  CONST_54  O0Q  C0K  N0H  C0E    0.00   0.0  0
 7N1  Var_01    C05  C04  O0A  CAH   75.43  30.0  1
 7N1  Var_02    C0D  C0E  N0H  C0P  -93.08  30.0  2
 7N1  Var_03    C04  C05  O0B  C0D  179.99  30.0  1
 7N1  Var_04    O0B  C0D  C0E  N0H   60.25  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
 7N1  plan-1  C0P  0.020
 7N1  plan-1  C0E  0.020
 7N1  plan-1  C0K  0.020
 7N1  plan-1  C0N  0.020
 7N1  plan-1  C0O  0.020
 7N1  plan-1  N0H  0.020
 7N1  plan-1  N0M  0.020
 7N1  plan-1  O0S  0.020
 7N1  plan-1  H6   0.020
 7N1  plan-1  H12  0.020
 7N1  plan-1  H13  0.020
 7N1  plan-1  O0Q  0.020
 7N1  plan-2  C00  0.020
 7N1  plan-2  O0A  0.020
 7N1  plan-2  C01  0.020
 7N1  plan-2  C02  0.020
 7N1  plan-2  C03  0.020
 7N1  plan-2  C04  0.020
 7N1  plan-2  C05  0.020
 7N1  plan-2  H7   0.020
 7N1  plan-2  H14  0.020
 7N1  plan-2  H15  0.020
 7N1  plan-2  F02  0.020
 7N1  plan-2  O0B  0.020
 7N1  plan-3  CAH  0.020
 7N1  plan-3  CAI  0.020
 7N1  plan-3  CAJ  0.020
 7N1  plan-3  CAK  0.020
 7N1  plan-3  CAL  0.020
 7N1  plan-3  CAM  0.020
 7N1  plan-3  CAY  0.020
 7N1  plan-3  CAZ  0.020
 7N1  plan-3  CBA  0.020
 7N1  plan-3  CBB  0.020
 7N1  plan-3  CBC  0.020
 7N1  plan-3  NBD  0.020
 7N1  plan-3  O0A  0.020
 7N1  plan-3  F01  0.020
 7N1  plan-3  H1   0.020
 7N1  plan-3  H2   0.020
 7N1  plan-3  H3   0.020
 7N1  plan-3  H4   0.020
 7N1  plan-3  H5   0.020

