# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 13:27:36 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-[2-(6-methoxynaphthalen-1-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2c(CCC3=C(NC(=O)NC3=O)C(O)=O)cccc2c1
#
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
 W7L  W7L  '5-[2-(6-methoxynaphthalen-1-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  41  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W7L
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
 W7L  OAB  O  O     0  -0.394   2.6488  -2.6804   0.2471
 W7L  CAQ  C  C     0   0.522   3.5218  -1.8844   0.4598
 W7L  OAE  O  OH1   0  -0.591   4.7280  -2.1896   0.9020
 W7L  CAT  C  CR6   0   0.280   3.3845  -0.4084   0.2348
 W7L  NAN  N  NR16  0  -0.732   4.5658   0.2579   0.0259
 W7L  CAV  C  CR6   0   0.671   4.6592   1.5959  -0.2216
 W7L  OAC  O  O     0  -0.472   5.7124   2.1678  -0.4072
 W7L  NAO  N  NR16  0  -0.715   3.4462   2.2329  -0.2439
 W7L  CAW  C  CR6   0   0.590   2.2042   1.6696  -0.0492
 W7L  OAD  O  O     0  -0.439   1.2032   2.3567  -0.1112
 W7L  CAU  C  CR6   0  -0.118   2.1933   0.2299   0.2280
 W7L  CAM  C  CH2   0  -0.503   0.8504  -0.3888   0.4659
 W7L  CAL  C  CH2   0  -0.536   0.1643  -0.8081  -0.8449
 W7L  CAS  C  CR6   0   0.120  -1.1916  -1.4036  -0.5906
 W7L  CAG  C  CR16  0  -0.346  -1.3377  -2.7663  -0.5431
 W7L  CAF  C  CR16  0  -0.241  -2.5837  -3.3633  -0.2586
 W7L  CAI  C  CR16  0  -0.344  -3.6836  -2.5905  -0.0203
 W7L  CAX  C  CR66  0   0.141  -3.5859  -1.1772  -0.0593
 W7L  CAK  C  CR16  0  -0.430  -4.7115  -0.3656   0.1828
 W7L  CAY  C  CR66  0   0.061  -2.3285  -0.5776  -0.3467
 W7L  CAJ  C  CR16  0  -0.326  -2.2698   0.8335  -0.3745
 W7L  CAH  C  CR16  0  -0.374  -3.3732   1.6098  -0.1368
 W7L  CAR  C  CR6   0   0.393  -4.6186   1.0062   0.1472
 W7L  OAP  O  O2    0  -0.473  -5.7445   1.7042   0.3906
 W7L  CAA  C  CH3   0  -0.438  -5.6953   3.1171   0.3701
 W7L  H1   H  HOH1  0   0.504   4.8288  -3.1497   0.9960
 W7L  H2   H  HNR6  0   0.431   3.4710   3.2286  -0.4267
 W7L  H4   H  HCH2  0   0.267   0.9276  -1.2533   1.1214
 W7L  H5   H  HCH2  0   0.268   0.2254   0.3381   0.9868
 W7L  H6   H  HCH2  0   0.253   0.0931   0.0511  -1.5156
 W7L  H7   H  HCH2  0   0.268   0.7910  -1.5442  -1.3484
 W7L  H8   H  HCR6  0   0.245  -0.4761  -3.3983  -0.7228
 W7L  H9   H  HCR6  0   0.254  -2.6614  -4.4426  -0.2298
 W7L  H10  H  HCR6  0   0.250  -4.6405  -3.0470   0.2027
 W7L  H11  H  HCR6  0   0.257  -5.6644  -0.8330   0.4033
 W7L  H12  H  HCR6  0   0.259  -1.3325   1.3321  -0.5844
 W7L  H13  H  HCR6  0   0.281  -3.2690   2.6856  -0.1702
 W7L  H14  H  HCH3  0   0.229  -5.4056   3.5058  -0.6095
 W7L  H15  H  HCH3  0   0.260  -6.7013   3.4618   0.5958
 W7L  H16  H  HCH3  0   0.229  -5.0131   3.5169   1.1248
 W7L  H17  H  HNR6  0   0.439   5.4376  -0.2525   0.0439

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
 W7L  CAA  OAP  single    1.414  0.020  1.414
 W7L  CAI  CAF  aromatic  1.365  0.020  1.365
 W7L  CAI  CAX  aromatic  1.417  0.020  1.417
 W7L  CAF  CAG  aromatic  1.411  0.020  1.411
 W7L  CAK  CAX  aromatic  1.409  0.020  1.409
 W7L  CAK  CAR  aromatic  1.375  0.020  1.375
 W7L  CAX  CAY  aromatic  1.422  0.020  1.422
 W7L  OAP  CAR  single    1.347  0.020  1.347
 W7L  CAG  CAS  aromatic  1.371  0.020  1.371
 W7L  CAR  CAH  aromatic  1.413  0.020  1.413
 W7L  CAY  CAS  aromatic  1.426  0.020  1.426
 W7L  CAY  CAJ  aromatic  1.413  0.020  1.413
 W7L  CAS  CAL  single    1.503  0.020  1.503
 W7L  CAH  CAJ  aromatic  1.370  0.020  1.370
 W7L  CAL  CAM  single    1.538  0.020  1.538
 W7L  CAM  CAU  single    1.498  0.020  1.498
 W7L  OAD  CAW  double    1.216  0.020  1.216
 W7L  CAU  CAW  single    1.466  0.020  1.466
 W7L  CAU  CAT  double    1.351  0.020  1.351
 W7L  CAW  NAO  single    1.378  0.020  1.378
 W7L  CAT  CAQ  single    1.499  0.020  1.499
 W7L  CAT  NAN  single    1.372  0.020  1.372
 W7L  CAQ  OAB  double    1.200  0.020  1.200
 W7L  CAQ  OAE  single    1.320  0.020  1.320
 W7L  NAO  CAV  single    1.370  0.020  1.370
 W7L  NAN  CAV  single    1.364  0.020  1.364
 W7L  CAV  OAC  double    1.213  0.020  1.213
 W7L  OAE  H1   single    0.850  0.020  0.980
 W7L  NAO  H2   single    0.860  0.020  1.020
 W7L  CAM  H4   single    0.970  0.020  1.090
 W7L  CAM  H5   single    0.970  0.020  1.090
 W7L  CAL  H6   single    0.970  0.020  1.090
 W7L  CAL  H7   single    0.970  0.020  1.090
 W7L  CAG  H8   single    0.930  0.020  1.080
 W7L  CAF  H9   single    0.930  0.020  1.080
 W7L  CAI  H10  single    0.930  0.020  1.080
 W7L  CAK  H11  single    0.930  0.020  1.080
 W7L  CAJ  H12  single    0.930  0.020  1.080
 W7L  CAH  H13  single    0.930  0.020  1.080
 W7L  CAA  H14  single    0.970  0.020  1.090
 W7L  CAA  H15  single    0.970  0.020  1.090
 W7L  CAA  H16  single    0.970  0.020  1.090
 W7L  NAN  H17  single    0.860  0.020  1.020

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
 W7L  CAT  CAQ  OAE  111.19  3.000
 W7L  OAE  CAQ  OAB  124.78  3.000
 W7L  CAT  CAQ  OAB  124.03  3.000
 W7L  H1   OAE  CAQ  110.86  3.000
 W7L  CAU  CAT  NAN  121.92  3.000
 W7L  NAN  CAT  CAQ  114.96  3.000
 W7L  CAU  CAT  CAQ  123.12  3.000
 W7L  H17  NAN  CAV  116.09  3.000
 W7L  H17  NAN  CAT  119.65  3.000
 W7L  CAV  NAN  CAT  124.26  3.000
 W7L  NAO  CAV  OAC  123.16  3.000
 W7L  OAC  CAV  NAN  123.36  3.000
 W7L  NAO  CAV  NAN  113.48  3.000
 W7L  H2   NAO  CAW  116.72  3.000
 W7L  H2   NAO  CAV  116.00  3.000
 W7L  CAW  NAO  CAV  127.28  3.000
 W7L  CAU  CAW  OAD  123.95  3.000
 W7L  CAU  CAW  NAO  115.78  3.000
 W7L  OAD  CAW  NAO  120.27  3.000
 W7L  CAM  CAU  CAW  116.25  3.000
 W7L  CAW  CAU  CAT  117.27  3.000
 W7L  CAM  CAU  CAT  126.48  3.000
 W7L  H5   CAM  H4   106.41  3.000
 W7L  H5   CAM  CAL  109.46  3.000
 W7L  H4   CAM  CAL  109.19  3.000
 W7L  H5   CAM  CAU  108.32  3.000
 W7L  H4   CAM  CAU  111.12  3.000
 W7L  CAL  CAM  CAU  112.17  3.000
 W7L  H7   CAL  H6   106.56  3.000
 W7L  H7   CAL  CAS  109.23  3.000
 W7L  H6   CAL  CAS  110.91  3.000
 W7L  H7   CAL  CAM  108.74  3.000
 W7L  H6   CAL  CAM  109.75  3.000
 W7L  CAS  CAL  CAM  111.50  3.000
 W7L  CAY  CAS  CAG  118.98  3.000
 W7L  CAY  CAS  CAL  121.25  3.000
 W7L  CAG  CAS  CAL  119.73  3.000
 W7L  H8   CAG  CAF  119.27  3.000
 W7L  H8   CAG  CAS  119.28  3.000
 W7L  CAF  CAG  CAS  121.45  3.000
 W7L  H9   CAF  CAI  120.13  3.000
 W7L  H9   CAF  CAG  119.39  3.000
 W7L  CAI  CAF  CAG  120.48  3.000
 W7L  H10  CAI  CAX  119.13  3.000
 W7L  H10  CAI  CAF  120.60  3.000
 W7L  CAX  CAI  CAF  120.27  3.000
 W7L  CAY  CAX  CAK  119.89  3.000
 W7L  CAY  CAX  CAI  119.14  3.000
 W7L  CAK  CAX  CAI  120.98  3.000
 W7L  H11  CAK  CAR  119.65  3.000
 W7L  H11  CAK  CAX  119.28  3.000
 W7L  CAR  CAK  CAX  121.08  3.000
 W7L  CAJ  CAY  CAX  117.50  3.000
 W7L  CAJ  CAY  CAS  122.82  3.000
 W7L  CAX  CAY  CAS  119.68  3.000
 W7L  H12  CAJ  CAH  118.05  3.000
 W7L  H12  CAJ  CAY  120.00  3.000
 W7L  CAH  CAJ  CAY  121.95  3.000
 W7L  H13  CAH  CAR  121.07  3.000
 W7L  H13  CAH  CAJ  118.74  3.000
 W7L  CAR  CAH  CAJ  120.19  3.000
 W7L  OAP  CAR  CAH  123.49  3.000
 W7L  CAH  CAR  CAK  119.39  3.000
 W7L  OAP  CAR  CAK  117.11  3.000
 W7L  CAA  OAP  CAR  119.09  3.000
 W7L  H16  CAA  H15  108.56  3.000
 W7L  H16  CAA  H14  108.86  3.000
 W7L  H15  CAA  H14  108.58  3.000
 W7L  H16  CAA  OAP  112.16  3.000
 W7L  H15  CAA  OAP  106.36  3.000
 W7L  H14  CAA  OAP  112.18  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
 W7L  CONST_01  CAI  CAF  CAG  CAS     0.00   0.0  0
 W7L  CONST_02  CAI  CAX  CAY  CAS     0.00   0.0  0
 W7L  CONST_03  CAK  CAX  CAY  CAS   180.00   0.0  0
 W7L  CONST_04  CAH  CAJ  CAY  CAS   180.00   0.0  0
 W7L  CONST_05  CAX  CAI  CAF  CAG     0.00   0.0  0
 W7L  CONST_06  CAX  CAY  CAS  CAG     0.00   0.0  0
 W7L  CONST_07  CAJ  CAY  CAS  CAG   180.00   0.0  0
 W7L  CONST_08  CAK  CAX  CAI  CAF   180.00   0.0  0
 W7L  CONST_09  CAY  CAX  CAI  CAF     0.00   0.0  0
 W7L  CONST_10  CAY  CAS  CAG  CAF     0.00   0.0  0
 W7L  CONST_11  CAR  CAK  CAX  CAI   180.00   0.0  0
 W7L  CONST_12  CAJ  CAY  CAX  CAI   180.00   0.0  0
 W7L  CONST_13  CAH  CAR  CAK  CAX     0.00   0.0  0
 W7L  CONST_14  CAH  CAJ  CAY  CAX     0.00   0.0  0
 W7L  CONST_15  CAJ  CAY  CAX  CAK     0.00   0.0  0
 W7L  CONST_16  CAJ  CAH  CAR  CAK     0.00   0.0  0
 W7L  CONST_17  CAR  CAK  CAX  CAY     0.00   0.0  0
 W7L  CONST_18  CAR  CAH  CAJ  CAY     0.00   0.0  0
 W7L  CONST_19  NAO  CAV  NAN  CAT     0.00   0.0  0
 W7L  CONST_20  CAW  NAO  CAV  NAN     0.00   0.0  0
 W7L  CONST_21  CAU  CAW  NAO  CAV     0.00   0.0  0
 W7L  CONST_22  CAF  CAG  CAS  CAL   180.00   0.0  0
 W7L  CONST_23  CAX  CAY  CAS  CAL   180.00   0.0  0
 W7L  CONST_24  CAJ  CAY  CAS  CAL     0.00   0.0  0
 W7L  CONST_25  OAP  CAR  CAK  CAX   180.00   0.0  0
 W7L  CONST_26  OAP  CAR  CAH  CAJ   180.00   0.0  0
 W7L  CONST_27  OAC  CAV  NAN  CAT   180.00   0.0  0
 W7L  CONST_28  OAD  CAW  NAO  CAV   180.00   0.0  0
 W7L  CONST_29  CAW  NAO  CAV  OAC   180.00   0.0  0
 W7L  CONST_30  H9   CAF  CAG  CAS   180.00   0.0  0
 W7L  CONST_31  H12  CAJ  CAY  CAS     0.00   0.0  0
 W7L  CONST_32  H10  CAI  CAF  CAG   180.00   0.0  0
 W7L  CONST_33  H8   CAG  CAF  CAI   180.00   0.0  0
 W7L  CONST_34  H11  CAK  CAX  CAI     0.00   0.0  0
 W7L  CONST_35  H13  CAH  CAR  CAK   180.00   0.0  0
 W7L  CONST_36  H2   NAO  CAV  NAN   180.00   0.0  0
 W7L  CONST_37  H17  NAN  CAV  NAO   180.00   0.0  0
 W7L  CONST_38  H1   OAE  CAQ  CAT   180.00   0.0  0
 W7L  Var_01    CAU  CAT  CAQ  OAB    23.92  30.0  2
 W7L  Var_02    CAL  CAM  CAU  CAT   -93.42  30.0  2
 W7L  Var_03    CAS  CAL  CAM  CAU  -178.96  30.0  1
 W7L  Var_04    CAG  CAS  CAL  CAM   -97.63  30.0  1
 W7L  Var_05    H14  CAA  OAP  CAR    61.77  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
 W7L  plan-1  CAQ  0.020
 W7L  plan-1  CAT  0.020
 W7L  plan-1  NAN  0.020
 W7L  plan-1  CAV  0.020
 W7L  plan-1  OAC  0.020
 W7L  plan-1  NAO  0.020
 W7L  plan-1  CAW  0.020
 W7L  plan-1  OAD  0.020
 W7L  plan-1  CAU  0.020
 W7L  plan-1  CAM  0.020
 W7L  plan-1  H2   0.020
 W7L  plan-1  H17  0.020
 W7L  plan-2  CAL  0.020
 W7L  plan-2  CAS  0.020
 W7L  plan-2  CAG  0.020
 W7L  plan-2  CAF  0.020
 W7L  plan-2  CAI  0.020
 W7L  plan-2  CAX  0.020
 W7L  plan-2  CAK  0.020
 W7L  plan-2  CAY  0.020
 W7L  plan-2  CAJ  0.020
 W7L  plan-2  CAH  0.020
 W7L  plan-2  CAR  0.020
 W7L  plan-2  OAP  0.020
 W7L  plan-2  H8   0.020
 W7L  plan-2  H9   0.020
 W7L  plan-2  H10  0.020
 W7L  plan-2  H11  0.020
 W7L  plan-2  H12  0.020
 W7L  plan-2  H13  0.020
 W7L  plan-3  OAB  0.020
 W7L  plan-3  CAQ  0.020
 W7L  plan-3  OAE  0.020
 W7L  plan-3  CAT  0.020
 W7L  plan-3  H1   0.020

