# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 18:11:52 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: 7-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-5,8-dimethylnaphthalene-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Oc2ccc(F)cc2OCCN3C=CC(=O)NC3=O)c(C)c4cc(ccc14)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
 UNS  UNS  7-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-5,8-dimethylnaphthalene-2-carbonitrile  ligand  53  33  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UNS
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
 UNS  CAH  C  CR6   0   0.069  517.3511  -31.5974  143.8126
 UNS  CAI  C  CR66  0   0.077  516.5634  -32.5266  144.5470
 UNS  CAJ  C  CR66  0   0.104  517.1564  -33.7395  144.9961
 UNS  CAK  C  CR6   0  -0.062  518.5124  -34.0516  144.6964
 UNS  CAL  C  CR6   0   0.374  519.2243  -33.1333  143.9628
 UNS  CAM  C  CR16  0  -0.390  518.6545  -31.9129  143.5444
 UNS  CAY  C  CR16  0  -0.321  515.2044  -32.2696  144.8418
 UNS  CAZ  C  CR16  0  -0.247  514.4451  -33.1575  145.5477
 UNS  CBA  C  CR6   0   0.017  515.0365  -34.3590  145.9943
 UNS  CBB  C  CR16  0  -0.329  516.3556  -34.6432  145.7282
 UNS  CBC  C  CSP   0   0.052  514.2546  -35.2959  146.7345
 UNS  NBD  N  NS    0  -0.250  513.6187  -36.0486  147.3323
 UNS  C0P  C  CR16  0   0.127  517.0664  -35.0949  141.7107
 UNS  C00  C  CR16  0  -0.546  521.6928  -32.1024  140.4803
 UNS  C0D  C  CH2   0  -0.197  519.2220  -33.2901  139.7856
 UNS  C0E  C  CH2   0  -0.344  517.7648  -33.6934  139.8309
 UNS  C0K  C  CR6   0   0.738  517.8236  -36.1261  139.6969
 UNS  C0N  C  CR6   0   0.569  517.1109  -37.4991  141.6319
 UNS  C0O  C  CR16  0  -0.512  516.8353  -36.2667  142.3260
 UNS  N0H  N  NR6   0  -0.523  517.5399  -34.9984  140.4366
 UNS  N0M  N  NR16  0  -0.732  517.5940  -37.3104  140.3449
 UNS  O0A  O  O2    0  -0.504  520.5207  -33.4386  143.6823
 UNS  O0S  O  O     0  -0.465  516.9554  -38.6221  142.0748
 UNS  C01  C  CR6   0   0.550  522.8430  -31.4743  140.9267
 UNS  C02  C  CR16  0  -0.441  523.2165  -31.4479  142.2512
 UNS  C03  C  CR16  0  -0.307  522.3922  -32.0886  143.1690
 UNS  C04  C  CR6   0   0.235  521.2421  -32.7331  142.7602
 UNS  C05  C  CR6   0   0.385  520.8761  -32.7426  141.4051
 UNS  C31  C  CH3   0  -0.757  519.1138  -35.3466  145.1557
 UNS  C32  C  CH3   0  -0.753  516.7749  -30.2980  143.3367
 UNS  H1   H  HCR6  0   0.279  519.2591  -31.1979  142.9995
 UNS  H2   H  HCR6  0   0.270  514.7499  -31.3499  144.4997
 UNS  H3   H  HCR6  0   0.278  513.4068  -32.9502  145.7652
 UNS  H4   H  HCR6  0   0.286  516.7756  -35.5719  146.0882
 UNS  H5   H  HCR6  0   0.306  516.8665  -34.1521  142.1996
 UNS  H6   H  HCR6  0   0.310  521.4630  -32.0937  139.4233
 UNS  H7   H  HCH2  0   0.254  519.7980  -33.9294  139.1123
 UNS  H8   H  HCH2  0   0.259  519.2665  -32.2656  139.4049
 UNS  H9   H  HCH2  0   0.276  517.1968  -32.9646  140.4072
 UNS  H10  H  HCH2  0   0.295  517.3658  -33.6827  138.8179
 UNS  H11  H  HCR6  0   0.286  516.4383  -36.2945  143.3287
 UNS  H12  H  HNR6  0   0.427  517.8001  -38.1439  139.8076
 UNS  H13  H  HCR6  0   0.285  524.1205  -30.9473  142.5684
 UNS  H14  H  HCR6  0   0.285  522.6535  -32.0939  144.2191
 UNS  H15  H  HCH3  0   0.253  519.0559  -35.4494  146.2405
 UNS  H16  H  HCH3  0   0.248  518.5884  -36.1997  144.7215
 UNS  H17  H  HCH3  0   0.270  520.1594  -35.4371  144.8774
 UNS  H18  H  HCH3  0   0.253  515.9447  -30.4567  142.6461
 UNS  H19  H  HCH3  0   0.253  516.3947  -29.6980  144.1649
 UNS  H20  H  HCH3  0   0.262  517.5287  -29.7097  142.8173
 UNS  F33  F  F     0  -0.315  523.6207  -30.8694  140.0160
 UNS  O0B  O  O2    0  -0.459  519.7338  -33.3732  141.1043
 UNS  O0Q  O  O     0  -0.479  518.2424  -36.0736  138.5590

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
 UNS  O0Q  C0K  double    1.214  0.020  1.214
 UNS  C0E  C0D  single    1.513  0.020  1.513
 UNS  C0E  N0H  single    1.456  0.020  1.456
 UNS  C0D  O0B  single    1.417  0.020  1.417
 UNS  C0K  N0H  single    1.378  0.020  1.378
 UNS  C0K  N0M  single    1.369  0.020  1.369
 UNS  N0H  C0P  single    1.363  0.020  1.363
 UNS  N0M  C0N  single    1.388  0.020  1.388
 UNS  O0B  C05  single    1.339  0.020  1.339
 UNS  C0P  C0O  double    1.344  0.020  1.344
 UNS  C00  C05  aromatic  1.390  0.020  1.390
 UNS  C00  C01  aromatic  1.384  0.020  1.384
 UNS  F33  C01  single    1.342  0.020  1.342
 UNS  C0N  C0O  single    1.441  0.020  1.441
 UNS  C0N  O0S  double    1.217  0.020  1.217
 UNS  C05  C04  aromatic  1.404  0.020  1.404
 UNS  C01  C02  aromatic  1.376  0.020  1.376
 UNS  C04  O0A  single    1.367  0.020  1.367
 UNS  C04  C03  aromatic  1.380  0.020  1.380
 UNS  C02  C03  aromatic  1.390  0.020  1.390
 UNS  O0A  CAL  single    1.361  0.020  1.361
 UNS  CAM  CAL  aromatic  1.410  0.020  1.410
 UNS  CAM  CAH  aromatic  1.368  0.020  1.368
 UNS  CAL  CAK  aromatic  1.374  0.020  1.374
 UNS  C32  CAH  single    1.499  0.020  1.499
 UNS  CAH  CAI  aromatic  1.422  0.020  1.422
 UNS  CAK  C31  single    1.500  0.020  1.500
 UNS  CAK  CAJ  aromatic  1.423  0.020  1.423
 UNS  CAI  CAJ  aromatic  1.423  0.020  1.423
 UNS  CAI  CAY  aromatic  1.414  0.020  1.414
 UNS  CAJ  CBB  aromatic  1.412  0.020  1.412
 UNS  CAY  CAZ  aromatic  1.365  0.020  1.365
 UNS  CBB  CBA  aromatic  1.375  0.020  1.375
 UNS  CAZ  CBA  aromatic  1.412  0.020  1.412
 UNS  CBA  CBC  single    1.427  0.020  1.427
 UNS  CBC  NBD  triple    1.152  0.020  1.152
 UNS  CAM  H1   single    0.930  0.020  1.080
 UNS  CAY  H2   single    0.930  0.020  1.080
 UNS  CAZ  H3   single    0.930  0.020  1.080
 UNS  CBB  H4   single    0.930  0.020  1.080
 UNS  C0P  H5   single    0.930  0.020  1.080
 UNS  C00  H6   single    0.930  0.020  1.080
 UNS  C0D  H7   single    0.970  0.020  1.090
 UNS  C0D  H8   single    0.970  0.020  1.090
 UNS  C0E  H9   single    0.970  0.020  1.090
 UNS  C0E  H10  single    0.970  0.020  1.090
 UNS  C0O  H11  single    0.930  0.020  1.080
 UNS  N0M  H12  single    0.860  0.020  1.020
 UNS  C02  H13  single    0.930  0.020  1.080
 UNS  C03  H14  single    0.930  0.020  1.080
 UNS  C31  H15  single    0.970  0.020  1.090
 UNS  C31  H16  single    0.970  0.020  1.090
 UNS  C31  H17  single    0.970  0.020  1.090
 UNS  C32  H18  single    0.970  0.020  1.090
 UNS  C32  H19  single    0.970  0.020  1.090
 UNS  C32  H20  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
 UNS  C32  CAH  CAM  120.27  3.000
 UNS  C32  CAH  CAI  121.15  3.000
 UNS  CAM  CAH  CAI  118.58  3.000
 UNS  CAY  CAI  CAJ  119.32  3.000
 UNS  CAY  CAI  CAH  121.40  3.000
 UNS  CAJ  CAI  CAH  119.28  3.000
 UNS  CBB  CAJ  CAK  120.61  3.000
 UNS  CBB  CAJ  CAI  118.22  3.000
 UNS  CAK  CAJ  CAI  121.16  3.000
 UNS  C31  CAK  CAL  122.19  3.000
 UNS  C31  CAK  CAJ  120.45  3.000
 UNS  CAL  CAK  CAJ  117.35  3.000
 UNS  O0A  CAL  CAM  121.18  3.000
 UNS  CAM  CAL  CAK  121.83  3.000
 UNS  O0A  CAL  CAK  116.97  3.000
 UNS  H1   CAM  CAL  119.66  3.000
 UNS  H1   CAM  CAH  118.58  3.000
 UNS  CAL  CAM  CAH  121.77  3.000
 UNS  H2   CAY  CAZ  118.89  3.000
 UNS  H2   CAY  CAI  119.50  3.000
 UNS  CAZ  CAY  CAI  121.61  3.000
 UNS  H3   CAZ  CBA  120.13  3.000
 UNS  H3   CAZ  CAY  120.90  3.000
 UNS  CBA  CAZ  CAY  118.97  3.000
 UNS  CBC  CBA  CBB  119.35  3.000
 UNS  CBC  CBA  CAZ  119.56  3.000
 UNS  CBB  CBA  CAZ  121.09  3.000
 UNS  H4   CBB  CBA  119.06  3.000
 UNS  H4   CBB  CAJ  120.14  3.000
 UNS  CBA  CBB  CAJ  120.80  3.000
 UNS  NBD  CBC  CBA  180.00  3.000
 UNS  H5   C0P  N0H  115.19  3.000
 UNS  H5   C0P  C0O  121.46  3.000
 UNS  N0H  C0P  C0O  123.34  3.000
 UNS  H6   C00  C05  121.94  3.000
 UNS  H6   C00  C01  119.20  3.000
 UNS  C05  C00  C01  118.86  3.000
 UNS  H8   C0D  H7   108.18  3.000
 UNS  H8   C0D  O0B  111.35  3.000
 UNS  H7   C0D  O0B  110.41  3.000
 UNS  H8   C0D  C0E  107.41  3.000
 UNS  H7   C0D  C0E  111.74  3.000
 UNS  O0B  C0D  C0E  107.73  3.000
 UNS  H10  C0E  H9   107.14  3.000
 UNS  H10  C0E  N0H  109.82  3.000
 UNS  H9   C0E  N0H  107.40  3.000
 UNS  H10  C0E  C0D  108.82  3.000
 UNS  H9   C0E  C0D  109.87  3.000
 UNS  N0H  C0E  C0D  113.59  3.000
 UNS  O0Q  C0K  N0M  122.61  3.000
 UNS  N0M  C0K  N0H  114.78  3.000
 UNS  O0Q  C0K  N0H  122.61  3.000
 UNS  O0S  C0N  N0M  120.50  3.000
 UNS  O0S  C0N  C0O  126.11  3.000
 UNS  N0M  C0N  C0O  113.39  3.000
 UNS  H11  C0O  C0N  119.74  3.000
 UNS  H11  C0O  C0P  120.76  3.000
 UNS  C0N  C0O  C0P  119.50  3.000
 UNS  C0K  N0H  C0E  118.57  3.000
 UNS  C0K  N0H  C0P  121.03  3.000
 UNS  C0E  N0H  C0P  120.40  3.000
 UNS  H12  N0M  C0N  116.80  3.000
 UNS  H12  N0M  C0K  115.25  3.000
 UNS  C0N  N0M  C0K  127.94  3.000
 UNS  C04  O0A  CAL  121.73  3.000
 UNS  F33  C01  C02  119.16  3.000
 UNS  C02  C01  C00  122.98  3.000
 UNS  F33  C01  C00  117.86  3.000
 UNS  H13  C02  C03  121.04  3.000
 UNS  H13  C02  C01  121.21  3.000
 UNS  C03  C02  C01  117.75  3.000
 UNS  H14  C03  C04  119.10  3.000
 UNS  H14  C03  C02  119.99  3.000
 UNS  C04  C03  C02  120.91  3.000
 UNS  C05  C04  C03  120.42  3.000
 UNS  C03  C04  O0A  118.75  3.000
 UNS  C05  C04  O0A  120.67  3.000
 UNS  C04  C05  O0B  116.26  3.000
 UNS  C04  C05  C00  119.07  3.000
 UNS  O0B  C05  C00  124.66  3.000
 UNS  H17  C31  H16  107.24  3.000
 UNS  H17  C31  H15  107.34  3.000
 UNS  H16  C31  H15  107.23  3.000
 UNS  H17  C31  CAK  112.31  3.000
 UNS  H16  C31  CAK  111.09  3.000
 UNS  H15  C31  CAK  111.38  3.000
 UNS  H20  C32  H19  107.84  3.000
 UNS  H20  C32  H18  107.67  3.000
 UNS  H19  C32  H18  107.17  3.000
 UNS  H20  C32  CAH  110.73  3.000
 UNS  H19  C32  CAH  111.69  3.000
 UNS  H18  C32  CAH  111.55  3.000
 UNS  C05  O0B  C0D  119.32  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
 UNS  CONST_01  CAK  CAL  CAM  CAH    0.00   0.0  0
 UNS  CONST_02  CAK  CAJ  CAI  CAH    0.00   0.0  0
 UNS  CONST_03  CBB  CAJ  CAI  CAH  180.00   0.0  0
 UNS  CONST_04  CAZ  CAY  CAI  CAH  180.00   0.0  0
 UNS  CONST_05  CAL  CAM  CAH  CAI    0.00   0.0  0
 UNS  CONST_06  CAL  CAK  CAJ  CAI    0.00   0.0  0
 UNS  CONST_07  CBA  CBB  CAJ  CAI    0.00   0.0  0
 UNS  CONST_08  CBA  CAZ  CAY  CAI    0.00   0.0  0
 UNS  CONST_09  CAM  CAL  CAK  CAJ    0.00   0.0  0
 UNS  CONST_10  CAM  CAH  CAI  CAJ    0.00   0.0  0
 UNS  CONST_11  CAZ  CAY  CAI  CAJ    0.00   0.0  0
 UNS  CONST_12  CAZ  CBA  CBB  CAJ    0.00   0.0  0
 UNS  CONST_13  CAY  CAI  CAJ  CAK  180.00   0.0  0
 UNS  CONST_14  CBA  CBB  CAJ  CAK  180.00   0.0  0
 UNS  CONST_15  CBB  CAJ  CAK  CAL  180.00   0.0  0
 UNS  CONST_16  CAY  CAI  CAH  CAM  180.00   0.0  0
 UNS  CONST_17  CBB  CAJ  CAI  CAY    0.00   0.0  0
 UNS  CONST_18  CBB  CBA  CAZ  CAY    0.00   0.0  0
 UNS  CONST_19  C03  C04  C05  C00    0.00   0.0  0
 UNS  CONST_20  C03  C02  C01  C00    0.00   0.0  0
 UNS  CONST_21  C04  C05  C00  C01    0.00   0.0  0
 UNS  CONST_22  C04  C03  C02  C01    0.00   0.0  0
 UNS  CONST_23  C05  C00  C01  C02    0.00   0.0  0
 UNS  CONST_24  C05  C04  C03  C02    0.00   0.0  0
 UNS  CONST_25  N0M  C0K  N0H  C0P    0.00   0.0  0
 UNS  CONST_26  C0O  C0N  N0M  C0K    0.00   0.0  0
 UNS  CONST_27  N0H  C0K  N0M  C0N    0.00   0.0  0
 UNS  CONST_28  O0A  CAL  CAM  CAH  180.00   0.0  0
 UNS  CONST_29  C31  CAK  CAJ  CAI  180.00   0.0  0
 UNS  CONST_30  O0A  CAL  CAK  CAJ  180.00   0.0  0
 UNS  CONST_31  C32  CAH  CAI  CAJ  180.00   0.0  0
 UNS  CONST_32  CBC  CBA  CBB  CAJ  180.00   0.0  0
 UNS  CONST_33  C32  CAH  CAM  CAL  180.00   0.0  0
 UNS  CONST_34  C31  CAK  CAL  CAM  180.00   0.0  0
 UNS  CONST_35  C32  CAH  CAI  CAY    0.00   0.0  0
 UNS  CONST_36  CBC  CBA  CAZ  CAY  180.00   0.0  0
 UNS  CONST_37  C31  CAK  CAJ  CBB    0.00   0.0  0
 UNS  CONST_38  O0A  C04  C05  C00  180.00   0.0  0
 UNS  CONST_39  C02  C03  C04  O0A  180.00   0.0  0
 UNS  CONST_40  C01  C00  C05  O0B  180.00   0.0  0
 UNS  CONST_41  C03  C04  C05  O0B  180.00   0.0  0
 UNS  CONST_42  F33  C01  C02  C03  180.00   0.0  0
 UNS  CONST_43  F33  C01  C00  C05  180.00   0.0  0
 UNS  CONST_44  O0Q  C0K  N0H  C0P  180.00   0.0  0
 UNS  CONST_45  N0M  C0K  N0H  C0E  180.00   0.0  0
 UNS  CONST_46  O0S  C0N  N0M  C0K  180.00   0.0  0
 UNS  CONST_47  O0Q  C0K  N0M  C0N  180.00   0.0  0
 UNS  CONST_48  H2   CAY  CAI  CAH    0.00   0.0  0
 UNS  CONST_49  H1   CAM  CAH  CAI  180.00   0.0  0
 UNS  CONST_50  H4   CBB  CAJ  CAI  180.00   0.0  0
 UNS  CONST_51  H3   CAZ  CAY  CAI  180.00   0.0  0
 UNS  CONST_52  H13  C02  C01  C00  180.00   0.0  0
 UNS  CONST_53  H14  C03  C02  C01  180.00   0.0  0
 UNS  CONST_54  H6   C00  C01  C02  180.00   0.0  0
 UNS  CONST_55  H12  N0M  C0N  C0O  180.00   0.0  0
 UNS  CONST_56  O0Q  C0K  N0H  C0E    0.00   0.0  0
 UNS  Var_01    C05  C04  O0A  CAL  -64.39  30.0  1
 UNS  Var_02    C0D  C0E  N0H  C0P  103.09  30.0  2
 UNS  Var_03    C04  C05  O0B  C0D  172.68  30.0  2
 UNS  Var_04    H18  C32  CAH  CAI  -61.52  30.0  2
 UNS  Var_05    H15  C31  CAK  CAJ  -58.12  30.0  2
 UNS  Var_06    O0B  C0D  C0E  N0H  -54.60  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
 UNS  plan-1  C00  0.020
 UNS  plan-1  O0A  0.020
 UNS  plan-1  C01  0.020
 UNS  plan-1  C02  0.020
 UNS  plan-1  C03  0.020
 UNS  plan-1  C04  0.020
 UNS  plan-1  C05  0.020
 UNS  plan-1  H6   0.020
 UNS  plan-1  H13  0.020
 UNS  plan-1  H14  0.020
 UNS  plan-1  F33  0.020
 UNS  plan-1  O0B  0.020
 UNS  plan-2  C0P  0.020
 UNS  plan-2  C0E  0.020
 UNS  plan-2  C0K  0.020
 UNS  plan-2  C0N  0.020
 UNS  plan-2  C0O  0.020
 UNS  plan-2  N0H  0.020
 UNS  plan-2  N0M  0.020
 UNS  plan-2  O0S  0.020
 UNS  plan-2  H5   0.020
 UNS  plan-2  H11  0.020
 UNS  plan-2  H12  0.020
 UNS  plan-2  O0Q  0.020
 UNS  plan-3  CAH  0.020
 UNS  plan-3  CAI  0.020
 UNS  plan-3  CAJ  0.020
 UNS  plan-3  CAK  0.020
 UNS  plan-3  CAL  0.020
 UNS  plan-3  CAM  0.020
 UNS  plan-3  CAY  0.020
 UNS  plan-3  CAZ  0.020
 UNS  plan-3  CBA  0.020
 UNS  plan-3  CBB  0.020
 UNS  plan-3  CBC  0.020
 UNS  plan-3  NBD  0.020
 UNS  plan-3  O0A  0.020
 UNS  plan-3  C31  0.020
 UNS  plan-3  C32  0.020
 UNS  plan-3  H1   0.020
 UNS  plan-3  H2   0.020
 UNS  plan-3  H3   0.020
 UNS  plan-3  H4   0.020

