# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 22:55:13 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 5-chloro-7-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-8-methylnaphthalene-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(Oc2ccccc2OCCN3C=CC(=O)NC3=O)cc(Cl)c4ccc(cc14)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
 7AY  7AY  5-chloro-7-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-8-methylnaphthalene-2-carbonitrile  ligand  50  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_7AY
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
 7AY  CAH  C   CR6   0  -0.144   2.1868   1.0156  -0.8620
 7AY  CAI  C   CR66  0   0.197   2.6453  -0.2981  -0.6140
 7AY  CAJ  C   CR66  0   0.118   2.1245  -0.9709   0.5318
 7AY  CAK  C   CR6   0  -0.070   1.1523  -0.3571   1.3684
 7AY  CAL  C   CR6   0   0.358   0.7617   0.9280   1.0607
 7AY  CAM  C   CR16  0  -0.280   1.2799   1.6239  -0.0452
 7AY  CAY  C   CR16  0  -0.290   3.5890  -0.9469  -1.4441
 7AY  CAZ  C   CR16  0  -0.250   4.0264  -2.2073  -1.1685
 7AY  CBA  C   CR6   0   0.021   3.5267  -2.8721  -0.0269
 7AY  CBB  C   CR16  0  -0.350   2.6065  -2.2741   0.7976
 7AY  CBC  C   CSP   0   0.057   3.9884  -4.1881   0.2776
 7AY  NBD  N   NS    0  -0.246   4.3644  -5.2515   0.5124
 7AY  C0P  C   CR16  0   0.129  -1.1639  -1.5194  -0.8598
 7AY  C00  C   CR16  0  -0.385  -2.4580   3.8040   0.2717
 7AY  C0D  C   CH2   0  -0.191  -2.6656   1.4633  -1.3180
 7AY  C0E  C   CH2   0  -0.352  -2.3118   0.2311  -2.1207
 7AY  C0K  C   CR6   0   0.735  -3.5409  -1.5826  -1.0472
 7AY  C0N  C   CR6   0   0.568  -2.3251  -3.3169   0.2391
 7AY  C0O  C   CR16  0  -0.505  -1.1063  -2.6326  -0.1100
 7AY  N0H  N   NR6   0  -0.522  -2.3281  -0.9936  -1.3330
 7AY  N0M  N   NR16  0  -0.731  -3.4624  -2.7135  -0.2787
 7AY  O0A  O   O2    0  -0.495  -0.1292   1.5038   1.9042
 7AY  O0B  O   O2    0  -0.464  -1.7884   1.5203  -0.2089
 7AY  O0S  O   O     0  -0.465  -2.4143  -4.3269   0.9126
 7AY  C01  C   CR16  0  -0.245  -2.2816   4.9282   1.0715
 7AY  C02  C   CR16  0  -0.279  -1.3668   4.9210   2.1105
 7AY  C03  C   CR16  0  -0.315  -0.6225   3.7732   2.3568
 7AY  C04  C   CR6   0   0.231  -0.7987   2.6516   1.5704
 7AY  C05  C   CR6   0   0.370  -1.7148   2.6533   0.5093
 7AY  C31  C   CH3   0  -0.724   0.5465  -1.0411   2.5580
 7AY  CL1  CL  CL    0  -0.111   2.7865   1.9007  -2.2221
 7AY  H1   H   HCR6  0   0.308   0.9701   2.6407  -0.2481
 7AY  H2   H   HCR6  0   0.269   3.9741  -0.4351  -2.3143
 7AY  H3   H   HCR6  0   0.284   4.7481  -2.6943  -1.8089
 7AY  H4   H   HCR6  0   0.293   2.2609  -2.8148   1.6661
 7AY  H5   H   HCR6  0   0.302  -0.2678  -0.9875  -1.1462
 7AY  H6   H   HCR6  0   0.290  -3.1879   3.8378  -0.5253
 7AY  H7   H   HCH2  0   0.255  -2.5432   2.3318  -1.9720
 7AY  H8   H   HCH2  0   0.250  -3.7051   1.4365  -0.9810
 7AY  H9   H   HCH2  0   0.295  -3.0052   0.1430  -2.9550
 7AY  H10  H   HCH2  0   0.278  -1.3137   0.3333  -2.5439
 7AY  H11  H   HCR6  0   0.284  -0.1586  -3.0211   0.2286
 7AY  H12  H   HNR6  0   0.427  -4.3492  -3.1568  -0.0716
 7AY  H13  H   HCR6  0   0.265  -2.8732   5.8117   0.8717
 7AY  H14  H   HCR6  0   0.262  -1.2283   5.7969   2.7292
 7AY  H15  H   HCR6  0   0.275   0.0916   3.7398   3.1698
 7AY  H16  H   HCH3  0   0.265   0.9809  -0.6737   3.4898
 7AY  H17  H   HCH3  0   0.259  -0.5266  -0.8634   2.6048
 7AY  H18  H   HCH3  0   0.247   0.6832  -2.1182   2.5394
 7AY  O0Q  O   O     0  -0.478  -4.5960  -1.1361  -1.4474

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
 7AY  O0Q  C0K  double    1.214  0.020  1.214
 7AY  C0E  C0D  single    1.512  0.020  1.512
 7AY  C0E  N0H  single    1.456  0.020  1.456
 7AY  C0K  N0H  single    1.378  0.020  1.378
 7AY  C0K  N0M  single    1.370  0.020  1.370
 7AY  C0D  O0B  single    1.415  0.020  1.415
 7AY  N0H  C0P  single    1.362  0.020  1.362
 7AY  N0M  C0N  single    1.388  0.020  1.388
 7AY  C0P  C0O  double    1.343  0.020  1.343
 7AY  O0B  C05  single    1.343  0.020  1.343
 7AY  C0N  C0O  single    1.441  0.020  1.441
 7AY  C0N  O0S  double    1.217  0.020  1.217
 7AY  C00  C05  aromatic  1.390  0.020  1.390
 7AY  C00  C01  aromatic  1.391  0.020  1.391
 7AY  C05  C04  aromatic  1.402  0.020  1.402
 7AY  C01  C02  aromatic  1.384  0.020  1.384
 7AY  C04  O0A  single    1.370  0.020  1.370
 7AY  C04  C03  aromatic  1.381  0.020  1.381
 7AY  C02  C03  aromatic  1.390  0.020  1.390
 7AY  O0A  CAL  single    1.355  0.020  1.355
 7AY  CAM  CAL  aromatic  1.406  0.020  1.406
 7AY  CAM  CAH  aromatic  1.364  0.020  1.364
 7AY  CAL  CAK  aromatic  1.378  0.020  1.378
 7AY  CL1  CAH  single    1.730  0.020  1.730
 7AY  CAH  CAI  aromatic  1.413  0.020  1.413
 7AY  CAK  C31  single    1.500  0.020  1.500
 7AY  CAK  CAJ  aromatic  1.422  0.020  1.422
 7AY  CAI  CAJ  aromatic  1.427  0.020  1.427
 7AY  CAI  CAY  aromatic  1.414  0.020  1.414
 7AY  CAJ  CBB  aromatic  1.415  0.020  1.415
 7AY  CAY  CAZ  aromatic  1.362  0.020  1.362
 7AY  CBB  CBA  aromatic  1.373  0.020  1.373
 7AY  CAZ  CBA  aromatic  1.412  0.020  1.412
 7AY  CBA  CBC  single    1.428  0.020  1.428
 7AY  CBC  NBD  triple    1.152  0.020  1.152
 7AY  CAM  H1   single    0.930  0.020  1.080
 7AY  CAY  H2   single    0.930  0.020  1.080
 7AY  CAZ  H3   single    0.930  0.020  1.080
 7AY  CBB  H4   single    0.930  0.020  1.080
 7AY  C0P  H5   single    0.930  0.020  1.080
 7AY  C00  H6   single    0.930  0.020  1.080
 7AY  C0D  H7   single    0.970  0.020  1.090
 7AY  C0D  H8   single    0.970  0.020  1.090
 7AY  C0E  H9   single    0.970  0.020  1.090
 7AY  C0E  H10  single    0.970  0.020  1.090
 7AY  C0O  H11  single    0.930  0.020  1.080
 7AY  N0M  H12  single    0.860  0.020  1.020
 7AY  C01  H13  single    0.930  0.020  1.080
 7AY  C02  H14  single    0.930  0.020  1.080
 7AY  C03  H15  single    0.930  0.020  1.080
 7AY  C31  H16  single    0.970  0.020  1.090
 7AY  C31  H17  single    0.970  0.020  1.090
 7AY  C31  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
 7AY  CL1  CAH  CAM  118.24  3.000
 7AY  CL1  CAH  CAI  120.07  3.000
 7AY  CAM  CAH  CAI  121.69  3.000
 7AY  CAY  CAI  CAJ  119.89  3.000
 7AY  CAY  CAI  CAH  122.67  3.000
 7AY  CAJ  CAI  CAH  117.43  3.000
 7AY  CBB  CAJ  CAK  121.34  3.000
 7AY  CBB  CAJ  CAI  117.44  3.000
 7AY  CAK  CAJ  CAI  121.22  3.000
 7AY  C31  CAK  CAL  119.21  3.000
 7AY  C31  CAK  CAJ  123.08  3.000
 7AY  CAL  CAK  CAJ  117.71  3.000
 7AY  O0A  CAL  CAM  121.45  3.000
 7AY  CAM  CAL  CAK  122.20  3.000
 7AY  O0A  CAL  CAK  116.33  3.000
 7AY  H1   CAM  CAL  120.47  3.000
 7AY  H1   CAM  CAH  119.82  3.000
 7AY  CAL  CAM  CAH  119.71  3.000
 7AY  H2   CAY  CAZ  119.12  3.000
 7AY  H2   CAY  CAI  119.55  3.000
 7AY  CAZ  CAY  CAI  121.32  3.000
 7AY  H3   CAZ  CBA  120.20  3.000
 7AY  H3   CAZ  CAY  120.76  3.000
 7AY  CBA  CAZ  CAY  119.04  3.000
 7AY  CBC  CBA  CBB  119.36  3.000
 7AY  CBC  CBA  CAZ  119.47  3.000
 7AY  CBB  CBA  CAZ  121.17  3.000
 7AY  H4   CBB  CBA  118.66  3.000
 7AY  H4   CBB  CAJ  120.22  3.000
 7AY  CBA  CBB  CAJ  121.12  3.000
 7AY  NBD  CBC  CBA  180.00  3.000
 7AY  H5   C0P  N0H  115.25  3.000
 7AY  H5   C0P  C0O  121.35  3.000
 7AY  N0H  C0P  C0O  123.39  3.000
 7AY  H6   C00  C05  120.84  3.000
 7AY  H6   C00  C01  118.96  3.000
 7AY  C05  C00  C01  120.19  3.000
 7AY  H8   C0D  H7   108.07  3.000
 7AY  H8   C0D  O0B  110.41  3.000
 7AY  H7   C0D  O0B  111.54  3.000
 7AY  H8   C0D  C0E  111.47  3.000
 7AY  H7   C0D  C0E  107.66  3.000
 7AY  O0B  C0D  C0E  107.68  3.000
 7AY  H10  C0E  H9   107.08  3.000
 7AY  H10  C0E  N0H  107.42  3.000
 7AY  H9   C0E  N0H  109.84  3.000
 7AY  H10  C0E  C0D  110.13  3.000
 7AY  H9   C0E  C0D  108.89  3.000
 7AY  N0H  C0E  C0D  113.30  3.000
 7AY  O0Q  C0K  N0M  122.59  3.000
 7AY  N0M  C0K  N0H  114.76  3.000
 7AY  O0Q  C0K  N0H  122.65  3.000
 7AY  O0S  C0N  N0M  120.47  3.000
 7AY  O0S  C0N  C0O  126.17  3.000
 7AY  N0M  C0N  C0O  113.35  3.000
 7AY  H11  C0O  C0N  119.74  3.000
 7AY  H11  C0O  C0P  120.75  3.000
 7AY  C0N  C0O  C0P  119.51  3.000
 7AY  C0K  N0H  C0E  118.77  3.000
 7AY  C0K  N0H  C0P  121.01  3.000
 7AY  C0E  N0H  C0P  120.19  3.000
 7AY  H12  N0M  C0N  116.80  3.000
 7AY  H12  N0M  C0K  115.21  3.000
 7AY  C0N  N0M  C0K  127.98  3.000
 7AY  C04  O0A  CAL  121.70  3.000
 7AY  C05  O0B  C0D  119.14  3.000
 7AY  H13  C01  C02  120.27  3.000
 7AY  H13  C01  C00  118.98  3.000
 7AY  C02  C01  C00  120.74  3.000
 7AY  H14  C02  C03  119.93  3.000
 7AY  H14  C02  C01  120.66  3.000
 7AY  C03  C02  C01  119.41  3.000
 7AY  H15  C03  C04  119.12  3.000
 7AY  H15  C03  C02  120.79  3.000
 7AY  C04  C03  C02  120.09  3.000
 7AY  C05  C04  C03  120.89  3.000
 7AY  C03  C04  O0A  118.64  3.000
 7AY  C05  C04  O0A  120.32  3.000
 7AY  C04  C05  O0B  116.07  3.000
 7AY  C04  C05  C00  118.66  3.000
 7AY  O0B  C05  C00  125.27  3.000
 7AY  H18  C31  H17  106.66  3.000
 7AY  H18  C31  H16  107.35  3.000
 7AY  H17  C31  H16  107.49  3.000
 7AY  H18  C31  CAK  112.82  3.000
 7AY  H17  C31  CAK  110.97  3.000
 7AY  H16  C31  CAK  111.27  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
 7AY  CONST_01  CAK  CAL  CAM  CAH     0.00   0.0  0
 7AY  CONST_02  CAK  CAJ  CAI  CAH     0.00   0.0  0
 7AY  CONST_03  CBB  CAJ  CAI  CAH   180.00   0.0  0
 7AY  CONST_04  CAZ  CAY  CAI  CAH   180.00   0.0  0
 7AY  CONST_05  CAL  CAM  CAH  CAI     0.00   0.0  0
 7AY  CONST_06  CAL  CAK  CAJ  CAI     0.00   0.0  0
 7AY  CONST_07  CBA  CBB  CAJ  CAI     0.00   0.0  0
 7AY  CONST_08  CBA  CAZ  CAY  CAI     0.00   0.0  0
 7AY  CONST_09  CAM  CAL  CAK  CAJ     0.00   0.0  0
 7AY  CONST_10  CAM  CAH  CAI  CAJ     0.00   0.0  0
 7AY  CONST_11  CAZ  CAY  CAI  CAJ     0.00   0.0  0
 7AY  CONST_12  CAZ  CBA  CBB  CAJ     0.00   0.0  0
 7AY  CONST_13  CAY  CAI  CAJ  CAK   180.00   0.0  0
 7AY  CONST_14  CBA  CBB  CAJ  CAK   180.00   0.0  0
 7AY  CONST_15  CBB  CAJ  CAK  CAL   180.00   0.0  0
 7AY  CONST_16  CAY  CAI  CAH  CAM   180.00   0.0  0
 7AY  CONST_17  CBB  CAJ  CAI  CAY     0.00   0.0  0
 7AY  CONST_18  CBB  CBA  CAZ  CAY     0.00   0.0  0
 7AY  CONST_19  C03  C04  C05  C00     0.00   0.0  0
 7AY  CONST_20  C03  C02  C01  C00     0.00   0.0  0
 7AY  CONST_21  C04  C05  C00  C01     0.00   0.0  0
 7AY  CONST_22  C04  C03  C02  C01     0.00   0.0  0
 7AY  CONST_23  C05  C00  C01  C02     0.00   0.0  0
 7AY  CONST_24  C05  C04  C03  C02     0.00   0.0  0
 7AY  CONST_25  N0M  C0K  N0H  C0P     0.00   0.0  0
 7AY  CONST_26  C0O  C0N  N0M  C0K     0.00   0.0  0
 7AY  CONST_27  N0H  C0K  N0M  C0N     0.00   0.0  0
 7AY  CONST_28  O0A  CAL  CAM  CAH   180.00   0.0  0
 7AY  CONST_29  C31  CAK  CAJ  CAI   180.00   0.0  0
 7AY  CONST_30  O0A  CAL  CAK  CAJ   180.00   0.0  0
 7AY  CONST_31  CL1  CAH  CAI  CAJ   180.00   0.0  0
 7AY  CONST_32  CBC  CBA  CBB  CAJ   180.00   0.0  0
 7AY  CONST_33  CL1  CAH  CAM  CAL   180.00   0.0  0
 7AY  CONST_34  C31  CAK  CAL  CAM   180.00   0.0  0
 7AY  CONST_35  CL1  CAH  CAI  CAY     0.00   0.0  0
 7AY  CONST_36  CBC  CBA  CAZ  CAY   180.00   0.0  0
 7AY  CONST_37  C31  CAK  CAJ  CBB     0.00   0.0  0
 7AY  CONST_38  O0A  C04  C05  C00   180.00   0.0  0
 7AY  CONST_39  C02  C03  C04  O0A   180.00   0.0  0
 7AY  CONST_40  C01  C00  C05  O0B   180.00   0.0  0
 7AY  CONST_41  C03  C04  C05  O0B   180.00   0.0  0
 7AY  CONST_42  O0Q  C0K  N0H  C0P   180.00   0.0  0
 7AY  CONST_43  N0M  C0K  N0H  C0E   180.00   0.0  0
 7AY  CONST_44  O0S  C0N  N0M  C0K   180.00   0.0  0
 7AY  CONST_45  O0Q  C0K  N0M  C0N   180.00   0.0  0
 7AY  CONST_46  H2   CAY  CAI  CAH     0.00   0.0  0
 7AY  CONST_47  H1   CAM  CAH  CAI   180.00   0.0  0
 7AY  CONST_48  H4   CBB  CAJ  CAI   180.00   0.0  0
 7AY  CONST_49  H3   CAZ  CAY  CAI   180.00   0.0  0
 7AY  CONST_50  H14  C02  C01  C00   180.00   0.0  0
 7AY  CONST_51  H15  C03  C02  C01   180.00   0.0  0
 7AY  CONST_52  H6   C00  C01  C02   180.00   0.0  0
 7AY  CONST_53  H13  C01  C02  C03   180.00   0.0  0
 7AY  CONST_54  H12  N0M  C0N  C0O   180.00   0.0  0
 7AY  CONST_55  O0Q  C0K  N0H  C0E     0.00   0.0  0
 7AY  Var_01    C05  C04  O0A  CAL    65.35  30.0  1
 7AY  Var_02    C0D  C0E  N0H  C0P   -99.50  30.0  2
 7AY  Var_03    C04  C05  O0B  C0D  -178.28  30.0  2
 7AY  Var_04    H16  C31  CAK  CAJ   103.13  30.0  2
 7AY  Var_05    O0B  C0D  C0E  N0H    54.89  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
 7AY  plan-1  C00  0.020
 7AY  plan-1  O0A  0.020
 7AY  plan-1  O0B  0.020
 7AY  plan-1  C01  0.020
 7AY  plan-1  C02  0.020
 7AY  plan-1  C03  0.020
 7AY  plan-1  C04  0.020
 7AY  plan-1  C05  0.020
 7AY  plan-1  H6   0.020
 7AY  plan-1  H13  0.020
 7AY  plan-1  H14  0.020
 7AY  plan-1  H15  0.020
 7AY  plan-2  C0P  0.020
 7AY  plan-2  C0E  0.020
 7AY  plan-2  C0K  0.020
 7AY  plan-2  C0N  0.020
 7AY  plan-2  C0O  0.020
 7AY  plan-2  N0H  0.020
 7AY  plan-2  N0M  0.020
 7AY  plan-2  O0S  0.020
 7AY  plan-2  H5   0.020
 7AY  plan-2  H11  0.020
 7AY  plan-2  H12  0.020
 7AY  plan-2  O0Q  0.020
 7AY  plan-3  CAH  0.020
 7AY  plan-3  CAI  0.020
 7AY  plan-3  CAJ  0.020
 7AY  plan-3  CAK  0.020
 7AY  plan-3  CAL  0.020
 7AY  plan-3  CAM  0.020
 7AY  plan-3  CAY  0.020
 7AY  plan-3  CAZ  0.020
 7AY  plan-3  CBA  0.020
 7AY  plan-3  CBB  0.020
 7AY  plan-3  CBC  0.020
 7AY  plan-3  NBD  0.020
 7AY  plan-3  O0A  0.020
 7AY  plan-3  C31  0.020
 7AY  plan-3  CL1  0.020
 7AY  plan-3  H1   0.020
 7AY  plan-3  H2   0.020
 7AY  plan-3  H3   0.020
 7AY  plan-3  H4   0.020

