# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:40:15 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 7-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}naphthalene-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=O)N(CCOc2ccccc2Oc3ccc4ccc(cc4c3)C#N)C=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
 7AX  7AX  7-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}naphthalene-2-carbonitrile  ligand  47  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7AX
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
 7AX  CAH  C  CR16  0  -0.295   1.2851   0.1104  -1.6274
 7AX  CAI  C  CR66  0   0.114   2.2364   0.9053  -0.9540
 7AX  CAJ  C  CR66  0   0.145   2.6519   0.5046   0.3420
 7AX  CAK  C  CR16  0  -0.414   2.1175  -0.6645   0.9194
 7AX  CAL  C  CR6   0   0.398   1.2042  -1.4175   0.2285
 7AX  CAM  C  CR16  0  -0.319   0.7779  -1.0249  -1.0595
 7AX  CAY  C  CR16  0  -0.270   2.7712   2.0820  -1.5253
 7AX  CAZ  C  CR16  0  -0.259   3.6824   2.8386  -0.8491
 7AX  CBA  C  CR6   0   0.002   4.0913   2.4372   0.4469
 7AX  CBB  C  CR16  0  -0.315   3.5920   1.2982   1.0324
 7AX  CBC  C  CSP   0   0.053   5.0406   3.2326   1.1561
 7AX  NBD  N  NS    0  -0.252   5.8088   3.8800   1.7209
 7AX  C0P  C  CR16  0   0.107  -1.0323   1.4070   1.2095
 7AX  C00  C  CR16  0  -0.387  -2.4717  -3.8108  -0.2732
 7AX  C0D  C  CH2   0  -0.191  -3.0994  -1.2989   0.8593
 7AX  C0E  C  CH2   0  -0.352  -3.0855   0.0876   1.4596
 7AX  C0K  C  CR6   0   0.733  -2.7265   1.5343  -0.4656
 7AX  C0N  C  CR6   0   0.573  -0.6628   2.8926  -0.6468
 7AX  C0O  C  CR16  0  -0.495  -0.2423   2.3065   0.6005
 7AX  N0H  N  NR6   0  -0.520  -2.2489   1.0261   0.7216
 7AX  N0M  N  NR16  0  -0.730  -1.8921   2.4224  -1.0888
 7AX  O0A  O  O2    0  -0.502   0.7713  -2.5535   0.8349
 7AX  O0B  O  O2    0  -0.460  -1.7750  -1.7956   0.8898
 7AX  O0S  O  O     0  -0.461  -0.0517   3.7205  -1.2965
 7AX  C01  C  CR16  0  -0.244  -2.0799  -5.0002  -0.8786
 7AX  C02  C  CR16  0  -0.281  -0.7446  -5.3620  -0.9345
 7AX  C03  C  CR16  0  -0.303   0.2140  -4.5227  -0.3779
 7AX  C04  C  CR6   0   0.217  -0.1702  -3.3432   0.2281
 7AX  C05  C  CR6   0   0.361  -1.5175  -2.9677   0.2864
 7AX  H1   H  HCR6  0   0.270   0.9548   0.4044  -2.6158
 7AX  H2   H  HCR6  0   0.270   2.4380  -0.9698   1.9082
 7AX  H3   H  HCR6  0   0.285   0.0635  -1.6204  -1.6119
 7AX  H4   H  HCR6  0   0.263   2.4471   2.3804  -2.5135
 7AX  H5   H  HCR6  0   0.275   4.0901   3.7391  -1.2866
 7AX  H6   H  HCR6  0   0.279   3.9132   1.0064   2.0241
 7AX  H7   H  HCR6  0   0.317  -0.7462   0.9460   2.1434
 7AX  H8   H  HCR6  0   0.290  -3.5233  -3.5609  -0.2382
 7AX  H9   H  HCH2  0   0.253  -3.7703  -1.9285   1.4530
 7AX  H10  H  HCH2  0   0.246  -3.4810  -1.2728  -0.1645
 7AX  H11  H  HCH2  0   0.291  -4.1069   0.4629   1.5020
 7AX  H12  H  HCH2  0   0.283  -2.7166   0.0522   2.4835
 7AX  H13  H  HCR6  0   0.287   0.7041   2.5915   1.0319
 7AX  H14  H  HNR6  0   0.424  -2.2385   2.8012  -1.9619
 7AX  H15  H  HCR6  0   0.264  -2.8369  -5.6457  -1.3041
 7AX  H16  H  HCR6  0   0.262  -0.4436  -6.2877  -1.4053
 7AX  H17  H  HCR6  0   0.274   1.2643  -4.7843  -0.4069
 7AX  O0Q  O  O     0  -0.484  -3.8070   1.2225  -0.9252

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
 7AX  C01  C00  aromatic  1.391  0.020  1.391
 7AX  C01  C02  aromatic  1.385  0.020  1.385
 7AX  C00  C05  aromatic  1.391  0.020  1.391
 7AX  C02  C03  aromatic  1.390  0.020  1.390
 7AX  C05  O0B  single    1.343  0.020  1.343
 7AX  C05  C04  aromatic  1.400  0.020  1.400
 7AX  C0D  O0B  single    1.415  0.020  1.415
 7AX  C0D  C0E  single    1.511  0.020  1.511
 7AX  C03  C04  aromatic  1.381  0.020  1.381
 7AX  O0Q  C0K  double    1.215  0.020  1.215
 7AX  C04  O0A  single    1.371  0.020  1.371
 7AX  C0E  N0H  single    1.458  0.020  1.458
 7AX  C0K  N0H  single    1.377  0.020  1.377
 7AX  C0K  N0M  single    1.369  0.020  1.369
 7AX  N0H  C0P  single    1.365  0.020  1.365
 7AX  O0A  CAL  single    1.359  0.020  1.359
 7AX  N0M  C0N  single    1.388  0.020  1.388
 7AX  C0P  C0O  double    1.343  0.020  1.343
 7AX  CAK  CAL  aromatic  1.371  0.020  1.371
 7AX  CAK  CAJ  aromatic  1.409  0.020  1.409
 7AX  CAL  CAM  aromatic  1.412  0.020  1.412
 7AX  C0N  C0O  single    1.441  0.020  1.441
 7AX  C0N  O0S  double    1.217  0.020  1.217
 7AX  CBB  CAJ  aromatic  1.411  0.020  1.411
 7AX  CBB  CBA  aromatic  1.375  0.020  1.375
 7AX  CAJ  CAI  aromatic  1.419  0.020  1.419
 7AX  CAM  CAH  aromatic  1.367  0.020  1.367
 7AX  NBD  CBC  triple    1.153  0.020  1.153
 7AX  CBC  CBA  single    1.427  0.020  1.427
 7AX  CBA  CAZ  aromatic  1.417  0.020  1.417
 7AX  CAI  CAH  aromatic  1.411  0.020  1.411
 7AX  CAI  CAY  aromatic  1.413  0.020  1.413
 7AX  CAZ  CAY  aromatic  1.364  0.020  1.364
 7AX  CAH  H1   single    0.930  0.020  1.080
 7AX  CAK  H2   single    0.930  0.020  1.080
 7AX  CAM  H3   single    0.930  0.020  1.080
 7AX  CAY  H4   single    0.930  0.020  1.080
 7AX  CAZ  H5   single    0.930  0.020  1.080
 7AX  CBB  H6   single    0.930  0.020  1.080
 7AX  C0P  H7   single    0.930  0.020  1.080
 7AX  C00  H8   single    0.930  0.020  1.080
 7AX  C0D  H9   single    0.970  0.020  1.090
 7AX  C0D  H10  single    0.970  0.020  1.090
 7AX  C0E  H11  single    0.970  0.020  1.090
 7AX  C0E  H12  single    0.970  0.020  1.090
 7AX  C0O  H13  single    0.930  0.020  1.080
 7AX  N0M  H14  single    0.860  0.020  1.020
 7AX  C01  H15  single    0.930  0.020  1.080
 7AX  C02  H16  single    0.930  0.020  1.080
 7AX  C03  H17  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
 7AX  H1   CAH  CAM  119.45  3.000
 7AX  H1   CAH  CAI  119.23  3.000
 7AX  CAM  CAH  CAI  121.32  3.000
 7AX  CAY  CAI  CAJ  119.58  3.000
 7AX  CAY  CAI  CAH  122.10  3.000
 7AX  CAJ  CAI  CAH  118.32  3.000
 7AX  CBB  CAJ  CAK  121.26  3.000
 7AX  CBB  CAJ  CAI  118.91  3.000
 7AX  CAK  CAJ  CAI  119.84  3.000
 7AX  H2   CAK  CAL  120.16  3.000
 7AX  H2   CAK  CAJ  119.71  3.000
 7AX  CAL  CAK  CAJ  120.13  3.000
 7AX  O0A  CAL  CAM  122.91  3.000
 7AX  CAM  CAL  CAK  120.54  3.000
 7AX  O0A  CAL  CAK  116.53  3.000
 7AX  H3   CAM  CAL  120.80  3.000
 7AX  H3   CAM  CAH  119.34  3.000
 7AX  CAL  CAM  CAH  119.85  3.000
 7AX  H4   CAY  CAZ  120.00  3.000
 7AX  H4   CAY  CAI  119.05  3.000
 7AX  CAZ  CAY  CAI  120.95  3.000
 7AX  H5   CAZ  CBA  119.82  3.000
 7AX  H5   CAZ  CAY  120.89  3.000
 7AX  CBA  CAZ  CAY  119.29  3.000
 7AX  CBC  CBA  CBB  119.45  3.000
 7AX  CBC  CBA  CAZ  119.25  3.000
 7AX  CBB  CBA  CAZ  121.30  3.000
 7AX  H6   CBB  CBA  120.39  3.000
 7AX  H6   CBB  CAJ  119.63  3.000
 7AX  CBA  CBB  CAJ  119.98  3.000
 7AX  NBD  CBC  CBA  180.00  3.000
 7AX  H7   C0P  N0H  115.21  3.000
 7AX  H7   C0P  C0O  121.47  3.000
 7AX  N0H  C0P  C0O  123.30  3.000
 7AX  H8   C00  C05  120.93  3.000
 7AX  H8   C00  C01  119.05  3.000
 7AX  C05  C00  C01  120.02  3.000
 7AX  H10  C0D  H9   107.92  3.000
 7AX  H10  C0D  O0B  110.82  3.000
 7AX  H9   C0D  O0B  111.10  3.000
 7AX  H10  C0D  C0E  110.70  3.000
 7AX  H9   C0D  C0E  108.53  3.000
 7AX  O0B  C0D  C0E  107.76  3.000
 7AX  H12  C0E  H11  107.01  3.000
 7AX  H12  C0E  N0H  107.61  3.000
 7AX  H11  C0E  N0H  109.64  3.000
 7AX  H12  C0E  C0D  110.29  3.000
 7AX  H11  C0E  C0D  108.85  3.000
 7AX  N0H  C0E  C0D  113.26  3.000
 7AX  O0Q  C0K  N0M  122.45  3.000
 7AX  N0M  C0K  N0H  114.87  3.000
 7AX  O0Q  C0K  N0H  122.68  3.000
 7AX  O0S  C0N  N0M  120.33  3.000
 7AX  O0S  C0N  C0O  126.33  3.000
 7AX  N0M  C0N  C0O  113.34  3.000
 7AX  H13  C0O  C0N  119.67  3.000
 7AX  H13  C0O  C0P  120.78  3.000
 7AX  C0N  C0O  C0P  119.56  3.000
 7AX  C0K  N0H  C0E  118.36  3.000
 7AX  C0K  N0H  C0P  120.95  3.000
 7AX  C0E  N0H  C0P  120.68  3.000
 7AX  H14  N0M  C0N  116.78  3.000
 7AX  H14  N0M  C0K  115.25  3.000
 7AX  C0N  N0M  C0K  127.92  3.000
 7AX  C04  O0A  CAL  120.21  3.000
 7AX  C05  O0B  C0D  118.43  3.000
 7AX  H15  C01  C02  120.20  3.000
 7AX  H15  C01  C00  118.96  3.000
 7AX  C02  C01  C00  120.84  3.000
 7AX  H16  C02  C03  119.94  3.000
 7AX  H16  C02  C01  120.65  3.000
 7AX  C03  C02  C01  119.41  3.000
 7AX  H17  C03  C04  119.22  3.000
 7AX  H17  C03  C02  120.81  3.000
 7AX  C04  C03  C02  119.97  3.000
 7AX  C05  C04  C03  121.02  3.000
 7AX  C03  C04  O0A  119.70  3.000
 7AX  C05  C04  O0A  119.22  3.000
 7AX  C04  C05  O0B  115.93  3.000
 7AX  C04  C05  C00  118.74  3.000
 7AX  O0B  C05  C00  125.33  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
 7AX  CONST_01  CAK  CAL  CAM  CAH     0.00   0.0  0
 7AX  CONST_02  CAK  CAJ  CAI  CAH     0.00   0.0  0
 7AX  CONST_03  CBB  CAJ  CAI  CAH   180.00   0.0  0
 7AX  CONST_04  CAZ  CAY  CAI  CAH   180.00   0.0  0
 7AX  CONST_05  CAL  CAK  CAJ  CAI     0.00   0.0  0
 7AX  CONST_06  CBA  CBB  CAJ  CAI     0.00   0.0  0
 7AX  CONST_07  CAL  CAM  CAH  CAI     0.00   0.0  0
 7AX  CONST_08  CBA  CAZ  CAY  CAI     0.00   0.0  0
 7AX  CONST_09  CAM  CAL  CAK  CAJ     0.00   0.0  0
 7AX  CONST_10  CAZ  CBA  CBB  CAJ     0.00   0.0  0
 7AX  CONST_11  CAM  CAH  CAI  CAJ     0.00   0.0  0
 7AX  CONST_12  CAZ  CAY  CAI  CAJ     0.00   0.0  0
 7AX  CONST_13  CBA  CBB  CAJ  CAK   180.00   0.0  0
 7AX  CONST_14  CAY  CAI  CAJ  CAK   180.00   0.0  0
 7AX  CONST_15  CBB  CAJ  CAK  CAL   180.00   0.0  0
 7AX  CONST_16  CAY  CAI  CAH  CAM   180.00   0.0  0
 7AX  CONST_17  CBB  CAJ  CAI  CAY     0.00   0.0  0
 7AX  CONST_18  CBB  CBA  CAZ  CAY     0.00   0.0  0
 7AX  CONST_19  C03  C02  C01  C00     0.00   0.0  0
 7AX  CONST_20  C03  C04  C05  C00     0.00   0.0  0
 7AX  CONST_21  C04  C05  C00  C01     0.00   0.0  0
 7AX  CONST_22  C04  C03  C02  C01     0.00   0.0  0
 7AX  CONST_23  C05  C00  C01  C02     0.00   0.0  0
 7AX  CONST_24  C05  C04  C03  C02     0.00   0.0  0
 7AX  CONST_25  N0M  C0K  N0H  C0P     0.00   0.0  0
 7AX  CONST_26  C0O  C0N  N0M  C0K     0.00   0.0  0
 7AX  CONST_27  N0H  C0K  N0M  C0N     0.00   0.0  0
 7AX  CONST_28  O0A  CAL  CAM  CAH   180.00   0.0  0
 7AX  CONST_29  O0A  CAL  CAK  CAJ   180.00   0.0  0
 7AX  CONST_30  CBC  CBA  CBB  CAJ   180.00   0.0  0
 7AX  CONST_31  CBC  CBA  CAZ  CAY   180.00   0.0  0
 7AX  CONST_32  O0A  C04  C05  C00   180.00   0.0  0
 7AX  CONST_33  C02  C03  C04  O0A   180.00   0.0  0
 7AX  CONST_34  C01  C00  C05  O0B   180.00   0.0  0
 7AX  CONST_35  C03  C04  C05  O0B   180.00   0.0  0
 7AX  CONST_36  O0Q  C0K  N0H  C0P   180.00   0.0  0
 7AX  CONST_37  N0M  C0K  N0H  C0E   180.00   0.0  0
 7AX  CONST_38  O0S  C0N  N0M  C0K   180.00   0.0  0
 7AX  CONST_39  O0Q  C0K  N0M  C0N   180.00   0.0  0
 7AX  CONST_40  H4   CAY  CAI  CAH     0.00   0.0  0
 7AX  CONST_41  H2   CAK  CAJ  CAI   180.00   0.0  0
 7AX  CONST_42  H6   CBB  CAJ  CAI   180.00   0.0  0
 7AX  CONST_43  H3   CAM  CAH  CAI   180.00   0.0  0
 7AX  CONST_44  H5   CAZ  CAY  CAI   180.00   0.0  0
 7AX  CONST_45  H1   CAH  CAI  CAJ   180.00   0.0  0
 7AX  CONST_46  H16  C02  C01  C00   180.00   0.0  0
 7AX  CONST_47  H17  C03  C02  C01   180.00   0.0  0
 7AX  CONST_48  H8   C00  C01  C02   180.00   0.0  0
 7AX  CONST_49  H15  C01  C02  C03   180.00   0.0  0
 7AX  CONST_50  H14  N0M  C0N  C0O   180.00   0.0  0
 7AX  CONST_51  O0Q  C0K  N0H  C0E     0.00   0.0  0
 7AX  Var_01    C05  C04  O0A  CAL   -78.94  30.0  1
 7AX  Var_02    C0D  C0E  N0H  C0P  -105.02  30.0  2
 7AX  Var_03    C04  C05  O0B  C0D   173.67  30.0  1
 7AX  Var_04    O0B  C0D  C0E  N0H    61.26  30.0  2

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
 7AX  plan-1  C0P  0.020
 7AX  plan-1  C0E  0.020
 7AX  plan-1  C0K  0.020
 7AX  plan-1  C0N  0.020
 7AX  plan-1  C0O  0.020
 7AX  plan-1  N0H  0.020
 7AX  plan-1  N0M  0.020
 7AX  plan-1  O0S  0.020
 7AX  plan-1  H7   0.020
 7AX  plan-1  H13  0.020
 7AX  plan-1  H14  0.020
 7AX  plan-1  O0Q  0.020
 7AX  plan-2  C00  0.020
 7AX  plan-2  O0A  0.020
 7AX  plan-2  O0B  0.020
 7AX  plan-2  C01  0.020
 7AX  plan-2  C02  0.020
 7AX  plan-2  C03  0.020
 7AX  plan-2  C04  0.020
 7AX  plan-2  C05  0.020
 7AX  plan-2  H8   0.020
 7AX  plan-2  H15  0.020
 7AX  plan-2  H16  0.020
 7AX  plan-2  H17  0.020
 7AX  plan-3  CAH  0.020
 7AX  plan-3  CAI  0.020
 7AX  plan-3  CAJ  0.020
 7AX  plan-3  CAK  0.020
 7AX  plan-3  CAL  0.020
 7AX  plan-3  CAM  0.020
 7AX  plan-3  CAY  0.020
 7AX  plan-3  CAZ  0.020
 7AX  plan-3  CBA  0.020
 7AX  plan-3  CBB  0.020
 7AX  plan-3  CBC  0.020
 7AX  plan-3  NBD  0.020
 7AX  plan-3  O0A  0.020
 7AX  plan-3  H1   0.020
 7AX  plan-3  H2   0.020
 7AX  plan-3  H3   0.020
 7AX  plan-3  H4   0.020
 7AX  plan-3  H5   0.020
 7AX  plan-3  H6   0.020

