# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 15:29:49 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}naphthalene-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=O)N(CCOc2ccccc2Oc3cccc4cc(ccc34)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
 3LQ  3LQ  5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}naphthalene-2-carbonitrile  ligand  47  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3LQ
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
 3LQ  C00  C  CR16  0  -0.386   3.0364  -3.2360   0.0368
 3LQ  C01  C  CR16  0  -0.245   3.0317  -4.3273   0.8994
 3LQ  C02  C  CR16  0  -0.281   1.9958  -4.5159   1.7984
 3LQ  C03  C  CR16  0  -0.308   0.9492  -3.6009   1.8370
 3LQ  C04  C  CR6   0   0.230   0.9540  -2.5117   0.9893
 3LQ  C05  C  CR6   0   0.365   1.9939  -2.3164   0.0712
 3LQ  O0A  O  O2    0  -0.503  -0.0382  -1.5719   1.0910
 3LQ  O0B  O  O2    0  -0.451   1.8851  -1.2384  -0.7201
 3LQ  C0D  C  CH2   0  -0.194   2.9846  -0.8650  -1.5227
 3LQ  C0E  C  CH2   0  -0.364   2.6269   0.4415  -2.2016
 3LQ  N0H  N  NR6   0  -0.520   2.1788   1.4434  -1.2438
 3LQ  C0K  C  CR6   0   0.740   0.8316   1.7315  -1.1432
 3LQ  N0M  N  NR16  0  -0.733   0.5167   2.6081  -0.1344
 3LQ  C0N  C  CR6   0   0.564   1.3651   3.2090   0.7805
 3LQ  C0O  C  CR16  0  -0.509   2.7500   2.8539   0.5938
 3LQ  C0P  C  CR16  0   0.101   3.0823   2.0009  -0.3900
 3LQ  O0Q  O  O     0  -0.460  -0.0107   1.2744  -1.8825
 3LQ  O0S  O  O     0  -0.467   0.9247   3.9581   1.6337
 3LQ  CAH  C  CR6   0   0.366  -0.9988  -1.5008   0.1372
 3LQ  CAI  C  CR66  0   0.040  -1.8682  -0.3834   0.2407
 3LQ  CAY  C  CR16  0  -0.284  -1.7343   0.5869   1.2610
 3LQ  CAZ  C  CR16  0  -0.265  -2.5879   1.6503   1.3325
 3LQ  CBA  C  CR6   0   0.010  -3.6183   1.7862   0.3722
 3LQ  CBC  C  CSP   0   0.053  -4.5088   2.8981   0.4509
 3LQ  NBD  N  NS    0  -0.251  -5.2286   3.7951   0.5257
 3LQ  CBB  C  CR16  0  -0.315  -3.7732   0.8587  -0.6298
 3LQ  CAJ  C  CR66  0   0.149  -2.9045  -0.2472  -0.7179
 3LQ  CAK  C  CR16  0  -0.335  -3.0570  -1.2133  -1.7386
 3LQ  CAL  C  CR16  0  -0.250  -2.2060  -2.2796  -1.7924
 3LQ  CAM  C  CR16  0  -0.347  -1.1704  -2.4335  -0.8505
 3LQ  H1   H  HCR6  0   0.288   3.8568  -3.1146  -0.6577
 3LQ  H2   H  HCR6  0   0.264   3.8525  -5.0309   0.8594
 3LQ  H3   H  HCR6  0   0.262   1.9943  -5.3665   2.4660
 3LQ  H4   H  HCR6  0   0.274   0.1318  -3.7229   2.5365
 3LQ  H5   H  HCH2  0   0.238   3.8855  -0.7537  -0.9090
 3LQ  H6   H  HCH2  0   0.258   3.1980  -1.6131  -2.2929
 3LQ  H7   H  HCH2  0   0.291   3.5033   0.8180  -2.7293
 3LQ  H8   H  HCH2  0   0.292   1.8403   0.2935  -2.9354
 3LQ  H9   H  HNR6  0   0.421  -0.4688   2.8255  -0.0530
 3LQ  H10  H  HCR6  0   0.292   3.5056   3.2725   1.2398
 3LQ  H11  H  HCR6  0   0.322   4.1125   1.7164  -0.5571
 3LQ  H12  H  HCR6  0   0.273  -0.9454   0.4967   1.9939
 3LQ  H13  H  HCR6  0   0.284  -2.4821   2.3875   2.1166
 3LQ  H14  H  HCR6  0   0.281  -4.5657   0.9681  -1.3589
 3LQ  H15  H  HCR6  0   0.260  -3.8517  -1.0986  -2.4639
 3LQ  H16  H  HCR6  0   0.267  -2.3190  -3.0277  -2.5656
 3LQ  H17  H  HCR6  0   0.281  -0.5193  -3.2949  -0.9209

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
 3LQ  C01  C00  aromatic  1.391  0.020  1.391
 3LQ  C01  C02  aromatic  1.385  0.020  1.385
 3LQ  C00  C05  aromatic  1.391  0.020  1.391
 3LQ  C02  C03  aromatic  1.391  0.020  1.391
 3LQ  O0Q  C0K  double    1.210  0.020  1.210
 3LQ  C0D  O0B  single    1.412  0.020  1.412
 3LQ  C0D  C0E  single    1.515  0.020  1.515
 3LQ  C05  O0B  single    1.342  0.020  1.342
 3LQ  C05  C04  aromatic  1.401  0.020  1.401
 3LQ  C03  C04  aromatic  1.380  0.020  1.380
 3LQ  C04  O0A  single    1.370  0.020  1.370
 3LQ  C0E  N0H  single    1.457  0.020  1.457
 3LQ  C0K  N0H  single    1.381  0.020  1.381
 3LQ  C0K  N0M  single    1.373  0.020  1.373
 3LQ  N0H  C0P  single    1.362  0.020  1.362
 3LQ  N0M  C0N  single    1.385  0.020  1.385
 3LQ  O0A  CAH  single    1.356  0.020  1.356
 3LQ  CAM  CAH  aromatic  1.369  0.020  1.369
 3LQ  CAM  CAL  aromatic  1.408  0.020  1.408
 3LQ  C0P  C0O  double    1.344  0.020  1.344
 3LQ  C0N  O0S  double    1.218  0.020  1.218
 3LQ  C0N  C0O  single    1.442  0.020  1.442
 3LQ  CAH  CAI  aromatic  1.420  0.020  1.420
 3LQ  CAL  CAK  aromatic  1.365  0.020  1.365
 3LQ  CAI  CAY  aromatic  1.414  0.020  1.414
 3LQ  CAI  CAJ  aromatic  1.418  0.020  1.418
 3LQ  CAY  CAZ  aromatic  1.366  0.020  1.366
 3LQ  CAK  CAJ  aromatic  1.414  0.020  1.414
 3LQ  CAJ  CBB  aromatic  1.409  0.020  1.409
 3LQ  CAZ  CBA  aromatic  1.415  0.020  1.415
 3LQ  CBB  CBA  aromatic  1.374  0.020  1.374
 3LQ  CBA  CBC  single    1.427  0.020  1.427
 3LQ  CBC  NBD  triple    1.152  0.020  1.152
 3LQ  C00  H1   single    0.930  0.020  1.080
 3LQ  C01  H2   single    0.930  0.020  1.080
 3LQ  C02  H3   single    0.930  0.020  1.080
 3LQ  C03  H4   single    0.930  0.020  1.080
 3LQ  C0D  H5   single    0.970  0.020  1.090
 3LQ  C0D  H6   single    0.970  0.020  1.090
 3LQ  C0E  H7   single    0.970  0.020  1.090
 3LQ  C0E  H8   single    0.970  0.020  1.090
 3LQ  N0M  H9   single    0.860  0.020  1.020
 3LQ  C0O  H10  single    0.930  0.020  1.080
 3LQ  C0P  H11  single    0.930  0.020  1.080
 3LQ  CAY  H12  single    0.930  0.020  1.080
 3LQ  CAZ  H13  single    0.930  0.020  1.080
 3LQ  CBB  H14  single    0.930  0.020  1.080
 3LQ  CAK  H15  single    0.930  0.020  1.080
 3LQ  CAL  H16  single    0.930  0.020  1.080
 3LQ  CAM  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
 3LQ  H1   C00  C05  120.68  3.000
 3LQ  H1   C00  C01  119.25  3.000
 3LQ  C05  C00  C01  120.07  3.000
 3LQ  H2   C01  C02  120.21  3.000
 3LQ  H2   C01  C00  119.00  3.000
 3LQ  C02  C01  C00  120.80  3.000
 3LQ  H3   C02  C03  119.96  3.000
 3LQ  H3   C02  C01  120.60  3.000
 3LQ  C03  C02  C01  119.44  3.000
 3LQ  H4   C03  C04  119.23  3.000
 3LQ  H4   C03  C02  120.79  3.000
 3LQ  C04  C03  C02  119.97  3.000
 3LQ  O0A  C04  C05  119.37  3.000
 3LQ  O0A  C04  C03  119.55  3.000
 3LQ  C05  C04  C03  121.00  3.000
 3LQ  O0B  C05  C04  116.00  3.000
 3LQ  C04  C05  C00  118.72  3.000
 3LQ  O0B  C05  C00  125.28  3.000
 3LQ  CAH  O0A  C04  119.79  3.000
 3LQ  C0D  O0B  C05  118.99  3.000
 3LQ  H6   C0D  H5   107.65  3.000
 3LQ  H6   C0D  C0E  108.67  3.000
 3LQ  H5   C0D  C0E  110.94  3.000
 3LQ  H6   C0D  O0B  111.78  3.000
 3LQ  H5   C0D  O0B  110.42  3.000
 3LQ  C0E  C0D  O0B  107.40  3.000
 3LQ  H8   C0E  H7   107.60  3.000
 3LQ  H8   C0E  N0H  108.37  3.000
 3LQ  H7   C0E  N0H  109.15  3.000
 3LQ  H8   C0E  C0D  110.87  3.000
 3LQ  H7   C0E  C0D  108.96  3.000
 3LQ  N0H  C0E  C0D  111.78  3.000
 3LQ  C0P  N0H  C0K  121.05  3.000
 3LQ  C0P  N0H  C0E  119.31  3.000
 3LQ  C0K  N0H  C0E  119.43  3.000
 3LQ  O0Q  C0K  N0M  122.03  3.000
 3LQ  N0M  C0K  N0H  114.22  3.000
 3LQ  O0Q  C0K  N0H  123.74  3.000
 3LQ  H9   N0M  C0N  116.75  3.000
 3LQ  H9   N0M  C0K  114.79  3.000
 3LQ  C0N  N0M  C0K  128.45  3.000
 3LQ  O0S  C0N  C0O  126.12  3.000
 3LQ  C0O  C0N  N0M  113.33  3.000
 3LQ  O0S  C0N  N0M  120.54  3.000
 3LQ  H10  C0O  C0P  120.77  3.000
 3LQ  H10  C0O  C0N  119.98  3.000
 3LQ  C0P  C0O  C0N  119.25  3.000
 3LQ  H11  C0P  C0O  121.03  3.000
 3LQ  H11  C0P  N0H  115.28  3.000
 3LQ  C0O  C0P  N0H  123.68  3.000
 3LQ  CAM  CAH  CAI  120.80  3.000
 3LQ  CAI  CAH  O0A  115.09  3.000
 3LQ  CAM  CAH  O0A  124.10  3.000
 3LQ  CAJ  CAI  CAY  119.40  3.000
 3LQ  CAJ  CAI  CAH  118.28  3.000
 3LQ  CAY  CAI  CAH  122.32  3.000
 3LQ  H12  CAY  CAZ  119.07  3.000
 3LQ  H12  CAY  CAI  120.08  3.000
 3LQ  CAZ  CAY  CAI  120.86  3.000
 3LQ  H13  CAZ  CBA  119.86  3.000
 3LQ  H13  CAZ  CAY  120.51  3.000
 3LQ  CBA  CAZ  CAY  119.63  3.000
 3LQ  CBB  CBA  CBC  119.73  3.000
 3LQ  CBC  CBA  CAZ  119.46  3.000
 3LQ  CBB  CBA  CAZ  120.80  3.000
 3LQ  NBD  CBC  CBA  180.00  3.000
 3LQ  H14  CBB  CAJ  119.25  3.000
 3LQ  H14  CBB  CBA  120.36  3.000
 3LQ  CAJ  CBB  CBA  120.39  3.000
 3LQ  CAK  CAJ  CBB  121.00  3.000
 3LQ  CBB  CAJ  CAI  118.92  3.000
 3LQ  CAK  CAJ  CAI  120.08  3.000
 3LQ  H15  CAK  CAL  120.94  3.000
 3LQ  H15  CAK  CAJ  119.40  3.000
 3LQ  CAL  CAK  CAJ  119.66  3.000
 3LQ  H16  CAL  CAM  118.64  3.000
 3LQ  H16  CAL  CAK  120.21  3.000
 3LQ  CAM  CAL  CAK  121.15  3.000
 3LQ  H17  CAM  CAL  119.07  3.000
 3LQ  H17  CAM  CAH  120.91  3.000
 3LQ  CAL  CAM  CAH  120.01  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
 3LQ  CONST_01  C03  C02  C01  C00     0.00   0.0  0
 3LQ  CONST_02  C03  C04  C05  C00     0.00   0.0  0
 3LQ  CONST_03  C04  C05  C00  C01     0.00   0.0  0
 3LQ  CONST_04  C04  C03  C02  C01     0.00   0.0  0
 3LQ  CONST_05  C05  C00  C01  C02     0.00   0.0  0
 3LQ  CONST_06  C05  C04  C03  C02     0.00   0.0  0
 3LQ  CONST_07  CAK  CAL  CAM  CAH     0.00   0.0  0
 3LQ  CONST_08  CAZ  CAY  CAI  CAH   180.00   0.0  0
 3LQ  CONST_09  CAK  CAJ  CAI  CAH     0.00   0.0  0
 3LQ  CONST_10  CBB  CAJ  CAI  CAH   180.00   0.0  0
 3LQ  CONST_11  CAL  CAM  CAH  CAI     0.00   0.0  0
 3LQ  CONST_12  CBA  CAZ  CAY  CAI     0.00   0.0  0
 3LQ  CONST_13  CAL  CAK  CAJ  CAI     0.00   0.0  0
 3LQ  CONST_14  CBA  CBB  CAJ  CAI     0.00   0.0  0
 3LQ  CONST_15  CAM  CAH  CAI  CAY   180.00   0.0  0
 3LQ  CONST_16  CAK  CAJ  CAI  CAY   180.00   0.0  0
 3LQ  CONST_17  CBB  CAJ  CAI  CAY     0.00   0.0  0
 3LQ  CONST_18  CBB  CBA  CAZ  CAY     0.00   0.0  0
 3LQ  CONST_19  CAJ  CAI  CAY  CAZ     0.00   0.0  0
 3LQ  CONST_20  CAJ  CBB  CBA  CAZ     0.00   0.0  0
 3LQ  CONST_21  CAK  CAJ  CBB  CBA   180.00   0.0  0
 3LQ  CONST_22  CAL  CAK  CAJ  CBB   180.00   0.0  0
 3LQ  CONST_23  CAM  CAH  CAI  CAJ     0.00   0.0  0
 3LQ  CONST_24  CAM  CAL  CAK  CAJ     0.00   0.0  0
 3LQ  CONST_25  C0N  N0M  C0K  N0H     0.00   0.0  0
 3LQ  CONST_26  C0O  C0N  N0M  C0K     0.00   0.0  0
 3LQ  CONST_27  C0P  N0H  C0K  N0M     0.00   0.0  0
 3LQ  CONST_28  O0A  C04  C05  C00   180.00   0.0  0
 3LQ  CONST_29  O0B  C05  C00  C01   180.00   0.0  0
 3LQ  CONST_30  O0A  C04  C03  C02   180.00   0.0  0
 3LQ  CONST_31  O0B  C05  C04  C03   180.00   0.0  0
 3LQ  CONST_32  CAL  CAM  CAH  O0A   180.00   0.0  0
 3LQ  CONST_33  CAY  CAI  CAH  O0A     0.00   0.0  0
 3LQ  CONST_34  CAJ  CAI  CAH  O0A   180.00   0.0  0
 3LQ  CONST_35  CBC  CBA  CAZ  CAY   180.00   0.0  0
 3LQ  CONST_36  CAJ  CBB  CBA  CBC   180.00   0.0  0
 3LQ  CONST_37  N0M  C0K  N0H  C0E   180.00   0.0  0
 3LQ  CONST_38  O0S  C0N  N0M  C0K   180.00   0.0  0
 3LQ  CONST_39  O0Q  C0K  N0M  C0N   180.00   0.0  0
 3LQ  CONST_40  O0Q  C0K  N0H  C0P   180.00   0.0  0
 3LQ  CONST_41  H3   C02  C01  C00   180.00   0.0  0
 3LQ  CONST_42  H4   C03  C02  C01   180.00   0.0  0
 3LQ  CONST_43  H1   C00  C01  C02   180.00   0.0  0
 3LQ  CONST_44  H2   C01  C02  C03   180.00   0.0  0
 3LQ  CONST_45  H16  CAL  CAM  CAH   180.00   0.0  0
 3LQ  CONST_46  H12  CAY  CAI  CAH     0.00   0.0  0
 3LQ  CONST_47  H17  CAM  CAH  CAI   180.00   0.0  0
 3LQ  CONST_48  H13  CAZ  CAY  CAI   180.00   0.0  0
 3LQ  CONST_49  H15  CAK  CAJ  CAI   180.00   0.0  0
 3LQ  CONST_50  H14  CBB  CAJ  CAI   180.00   0.0  0
 3LQ  CONST_51  H9   N0M  C0K  N0H   180.00   0.0  0
 3LQ  CONST_52  O0Q  C0K  N0H  C0E     0.00   0.0  0
 3LQ  Var_01    CAM  CAH  O0A  C04     9.65  30.0  2
 3LQ  Var_02    C0K  N0H  C0E  C0D  -103.96  30.0  3
 3LQ  Var_03    C0E  C0D  O0B  C05  -174.85  30.0  1
 3LQ  Var_04    N0H  C0E  C0D  O0B    52.25  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
 3LQ  plan-1  C00  0.020
 3LQ  plan-1  C01  0.020
 3LQ  plan-1  C02  0.020
 3LQ  plan-1  C03  0.020
 3LQ  plan-1  C04  0.020
 3LQ  plan-1  C05  0.020
 3LQ  plan-1  O0A  0.020
 3LQ  plan-1  O0B  0.020
 3LQ  plan-1  H1   0.020
 3LQ  plan-1  H2   0.020
 3LQ  plan-1  H3   0.020
 3LQ  plan-1  H4   0.020
 3LQ  plan-2  C0E  0.020
 3LQ  plan-2  N0H  0.020
 3LQ  plan-2  C0K  0.020
 3LQ  plan-2  N0M  0.020
 3LQ  plan-2  C0N  0.020
 3LQ  plan-2  C0O  0.020
 3LQ  plan-2  C0P  0.020
 3LQ  plan-2  O0Q  0.020
 3LQ  plan-2  O0S  0.020
 3LQ  plan-2  H9   0.020
 3LQ  plan-2  H10  0.020
 3LQ  plan-2  H11  0.020
 3LQ  plan-3  O0A  0.020
 3LQ  plan-3  CAH  0.020
 3LQ  plan-3  CAI  0.020
 3LQ  plan-3  CAY  0.020
 3LQ  plan-3  CAZ  0.020
 3LQ  plan-3  CBA  0.020
 3LQ  plan-3  CBC  0.020
 3LQ  plan-3  NBD  0.020
 3LQ  plan-3  CBB  0.020
 3LQ  plan-3  CAJ  0.020
 3LQ  plan-3  CAK  0.020
 3LQ  plan-3  CAL  0.020
 3LQ  plan-3  CAM  0.020
 3LQ  plan-3  H12  0.020
 3LQ  plan-3  H13  0.020
 3LQ  plan-3  H14  0.020
 3LQ  plan-3  H15  0.020
 3LQ  plan-3  H16  0.020
 3LQ  plan-3  H17  0.020

