# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 06:07:53 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-[2-(5-methoxynaphthalen-2-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc2cc(CCC3=C(NC(=O)NC3=O)C(O)=O)ccc12
#
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
 W7C  W7C  '5-[2-(5-methoxynaphthalen-2-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_W7C
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
 W7C  OAB  O  O     0  -0.396   2.0002   2.5914  -0.3791
 W7C  CAQ  C  C     0   0.521   3.1121   2.2777  -0.0514
 W7C  OAE  O  OH1   0  -0.590   4.0831   3.1279   0.2266
 W7C  CAT  C  CR6   0   0.284   3.5802   0.8597   0.0794
 W7C  NAN  N  NR16  0  -0.732   4.9319   0.6798  -0.0746
 W7C  CAV  C  CR6   0   0.671   5.5566  -0.5314  -0.0168
 W7C  OAC  O  O     0  -0.472   6.7512  -0.6728  -0.1710
 W7C  NAO  N  NR16  0  -0.716   4.7034  -1.5746   0.2308
 W7C  CAW  C  CR6   0   0.586   3.3380  -1.5119   0.4075
 W7C  OAD  O  O     0  -0.440   2.6979  -2.5251   0.6102
 W7C  CAU  C  CR6   0  -0.118   2.7455  -0.1726   0.3304
 W7C  CAM  C  CH2   0  -0.504   1.2633  -0.0916   0.5278
 W7C  CAL  C  CH2   0  -0.505   0.4904  -0.3435  -0.7763
 W7C  CAR  C  CR6   0   0.138  -0.9912  -0.2309  -0.5650
 W7C  CAK  C  CR16  0  -0.400  -1.7954  -1.3384  -0.4950
 W7C  CAH  C  CR16  0  -0.299  -1.5803   1.0441  -0.3992
 W7C  CAJ  C  CR16  0  -0.272  -2.9219   1.1836  -0.1735
 W7C  CAY  C  CR66  0  -0.029  -3.7622   0.0483  -0.0982
 W7C  CAX  C  CR66  0   0.152  -3.1871  -1.2365  -0.2633
 W7C  CAI  C  CR16  0  -0.349  -4.0097  -2.3872  -0.1951
 W7C  CAF  C  CR16  0  -0.246  -5.3492  -2.2527   0.0312
 W7C  CAG  C  CR16  0  -0.412  -5.9415  -0.9834   0.1959
 W7C  CAS  C  CR6   0   0.361  -5.1671   0.1501   0.1320
 W7C  OAP  O  O2    0  -0.463  -5.6365   1.4008   0.2723
 W7C  CAA  C  CH3   0  -0.435  -7.0217   1.5827   0.4899
 W7C  H1   H  HOH1  0   0.504   3.7857   4.0429   0.1012
 W7C  H2   H  HNR6  0   0.439   5.5232   1.4757  -0.2691
 W7C  H3   H  HNR6  0   0.431   5.1260  -2.4939   0.2791
 W7C  H4   H  HCH2  0   0.264   0.9724  -0.8456   1.2606
 W7C  H5   H  HCH2  0   0.266   0.9791   0.8714   0.9464
 W7C  H6   H  HCH2  0   0.256   0.8133   0.3796  -1.5279
 W7C  H7   H  HCH2  0   0.253   0.7360  -1.3352  -1.1604
 W7C  H8   H  HCR6  0   0.244  -1.3664  -2.3265  -0.6239
 W7C  H9   H  HCR6  0   0.250  -0.9529   1.9259  -0.4587
 W7C  H10  H  HCR6  0   0.252  -3.3380   2.1746  -0.0540
 W7C  H11  H  HCR6  0   0.248  -3.5656  -3.3661  -0.3259
 W7C  H12  H  HCR6  0   0.258  -5.9821  -3.1288   0.0880
 W7C  H13  H  HCR6  0   0.280  -7.0069  -0.9275   0.3707
 W7C  H14  H  HCH3  0   0.261  -7.1832   2.6541   0.5764
 W7C  H15  H  HCH3  0   0.230  -7.6162   1.2006  -0.3440
 W7C  H16  H  HCH3  0   0.230  -7.3540   1.0982   1.4112

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
 W7C  CAF  CAI  aromatic  1.365  0.020  1.365
 W7C  CAF  CAG  aromatic  1.410  0.020  1.410
 W7C  CAI  CAX  aromatic  1.416  0.020  1.416
 W7C  CAG  CAS  aromatic  1.374  0.020  1.374
 W7C  CAX  CAK  aromatic  1.415  0.020  1.415
 W7C  CAX  CAY  aromatic  1.417  0.020  1.417
 W7C  CAK  CAR  aromatic  1.371  0.020  1.371
 W7C  CAS  CAY  aromatic  1.427  0.020  1.427
 W7C  CAS  OAP  single    1.343  0.020  1.343
 W7C  CAY  CAJ  aromatic  1.414  0.020  1.414
 W7C  CAR  CAL  single    1.501  0.020  1.501
 W7C  CAR  CAH  aromatic  1.414  0.020  1.414
 W7C  CAL  CAM  single    1.537  0.020  1.537
 W7C  CAA  OAP  single    1.414  0.020  1.414
 W7C  CAJ  CAH  aromatic  1.368  0.020  1.368
 W7C  CAM  CAU  single    1.497  0.020  1.497
 W7C  OAD  CAW  double    1.215  0.020  1.215
 W7C  CAU  CAW  single    1.467  0.020  1.467
 W7C  CAU  CAT  double    1.351  0.020  1.351
 W7C  CAW  NAO  single    1.378  0.020  1.378
 W7C  CAT  CAQ  single    1.499  0.020  1.499
 W7C  CAT  NAN  single    1.372  0.020  1.372
 W7C  CAQ  OAB  double    1.201  0.020  1.201
 W7C  CAQ  OAE  single    1.320  0.020  1.320
 W7C  NAO  CAV  single    1.370  0.020  1.370
 W7C  NAN  CAV  single    1.364  0.020  1.364
 W7C  CAV  OAC  double    1.213  0.020  1.213
 W7C  OAE  H1   single    0.850  0.020  0.980
 W7C  NAN  H2   single    0.860  0.020  1.020
 W7C  NAO  H3   single    0.860  0.020  1.020
 W7C  CAM  H4   single    0.970  0.020  1.090
 W7C  CAM  H5   single    0.970  0.020  1.090
 W7C  CAL  H6   single    0.970  0.020  1.090
 W7C  CAL  H7   single    0.970  0.020  1.090
 W7C  CAK  H8   single    0.930  0.020  1.080
 W7C  CAH  H9   single    0.930  0.020  1.080
 W7C  CAJ  H10  single    0.930  0.020  1.080
 W7C  CAI  H11  single    0.930  0.020  1.080
 W7C  CAF  H12  single    0.930  0.020  1.080
 W7C  CAG  H13  single    0.930  0.020  1.080
 W7C  CAA  H14  single    0.970  0.020  1.090
 W7C  CAA  H15  single    0.970  0.020  1.090
 W7C  CAA  H16  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
 W7C  CAT  CAQ  OAE  111.17  3.000
 W7C  OAE  CAQ  OAB  124.76  3.000
 W7C  CAT  CAQ  OAB  124.06  3.000
 W7C  H1   OAE  CAQ  110.77  3.000
 W7C  CAU  CAT  NAN  121.95  3.000
 W7C  NAN  CAT  CAQ  114.95  3.000
 W7C  CAU  CAT  CAQ  123.10  3.000
 W7C  H2   NAN  CAV  116.08  3.000
 W7C  H2   NAN  CAT  119.65  3.000
 W7C  CAV  NAN  CAT  124.25  3.000
 W7C  NAO  CAV  OAC  123.20  3.000
 W7C  OAC  CAV  NAN  123.32  3.000
 W7C  NAO  CAV  NAN  113.48  3.000
 W7C  H3   NAO  CAW  116.65  3.000
 W7C  H3   NAO  CAV  116.09  3.000
 W7C  CAW  NAO  CAV  127.26  3.000
 W7C  CAU  CAW  OAD  123.86  3.000
 W7C  CAU  CAW  NAO  115.79  3.000
 W7C  OAD  CAW  NAO  120.35  3.000
 W7C  CAM  CAU  CAW  116.26  3.000
 W7C  CAW  CAU  CAT  117.25  3.000
 W7C  CAM  CAU  CAT  126.49  3.000
 W7C  H5   CAM  H4   106.48  3.000
 W7C  H5   CAM  CAL  109.89  3.000
 W7C  H4   CAM  CAL  108.82  3.000
 W7C  H5   CAM  CAU  110.93  3.000
 W7C  H4   CAM  CAU  108.37  3.000
 W7C  CAL  CAM  CAU  112.15  3.000
 W7C  H7   CAL  H6   107.03  3.000
 W7C  H7   CAL  CAR  109.87  3.000
 W7C  H6   CAL  CAR  109.83  3.000
 W7C  H7   CAL  CAM  109.54  3.000
 W7C  H6   CAL  CAM  109.08  3.000
 W7C  CAR  CAL  CAM  111.39  3.000
 W7C  CAH  CAR  CAK  118.57  3.000
 W7C  CAH  CAR  CAL  119.69  3.000
 W7C  CAK  CAR  CAL  121.73  3.000
 W7C  H8   CAK  CAX  118.30  3.000
 W7C  H8   CAK  CAR  119.86  3.000
 W7C  CAX  CAK  CAR  121.83  3.000
 W7C  H9   CAH  CAJ  119.60  3.000
 W7C  H9   CAH  CAR  119.08  3.000
 W7C  CAJ  CAH  CAR  121.33  3.000
 W7C  H10  CAJ  CAY  120.07  3.000
 W7C  H10  CAJ  CAH  119.28  3.000
 W7C  CAY  CAJ  CAH  120.64  3.000
 W7C  CAS  CAY  CAX  118.87  3.000
 W7C  CAS  CAY  CAJ  122.42  3.000
 W7C  CAX  CAY  CAJ  118.71  3.000
 W7C  CAI  CAX  CAY  119.69  3.000
 W7C  CAY  CAX  CAK  118.92  3.000
 W7C  CAI  CAX  CAK  121.39  3.000
 W7C  H11  CAI  CAF  120.76  3.000
 W7C  H11  CAI  CAX  119.38  3.000
 W7C  CAF  CAI  CAX  119.86  3.000
 W7C  H12  CAF  CAG  118.48  3.000
 W7C  H12  CAF  CAI  120.18  3.000
 W7C  CAG  CAF  CAI  121.34  3.000
 W7C  H13  CAG  CAS  121.35  3.000
 W7C  H13  CAG  CAF  118.64  3.000
 W7C  CAS  CAG  CAF  120.02  3.000
 W7C  OAP  CAS  CAG  124.49  3.000
 W7C  OAP  CAS  CAY  115.29  3.000
 W7C  CAG  CAS  CAY  120.22  3.000
 W7C  CAA  OAP  CAS  118.56  3.000
 W7C  H16  CAA  H15  108.83  3.000
 W7C  H16  CAA  H14  108.95  3.000
 W7C  H15  CAA  H14  108.94  3.000
 W7C  H16  CAA  OAP  111.76  3.000
 W7C  H15  CAA  OAP  111.75  3.000
 W7C  H14  CAA  OAP  106.53  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
 W7C  CONST_01  CAI  CAX  CAK  CAR   180.00   0.0  0
 W7C  CONST_02  CAY  CAX  CAK  CAR     0.00   0.0  0
 W7C  CONST_03  CAY  CAJ  CAH  CAR     0.00   0.0  0
 W7C  CONST_04  CAF  CAI  CAX  CAK   180.00   0.0  0
 W7C  CONST_05  CAS  CAY  CAX  CAK   180.00   0.0  0
 W7C  CONST_06  CAJ  CAY  CAX  CAK     0.00   0.0  0
 W7C  CONST_07  CAJ  CAH  CAR  CAK     0.00   0.0  0
 W7C  CONST_08  CAX  CAK  CAR  CAH     0.00   0.0  0
 W7C  CONST_09  CAX  CAY  CAJ  CAH     0.00   0.0  0
 W7C  CONST_10  CAS  CAY  CAJ  CAH   180.00   0.0  0
 W7C  CONST_11  CAI  CAX  CAY  CAJ   180.00   0.0  0
 W7C  CONST_12  CAG  CAS  CAY  CAJ   180.00   0.0  0
 W7C  CONST_13  CAF  CAI  CAX  CAY     0.00   0.0  0
 W7C  CONST_14  CAF  CAG  CAS  CAY     0.00   0.0  0
 W7C  CONST_15  CAG  CAF  CAI  CAX     0.00   0.0  0
 W7C  CONST_16  CAG  CAS  CAY  CAX     0.00   0.0  0
 W7C  CONST_17  CAS  CAG  CAF  CAI     0.00   0.0  0
 W7C  CONST_18  CAS  CAY  CAX  CAI     0.00   0.0  0
 W7C  CONST_19  NAO  CAV  NAN  CAT     0.00   0.0  0
 W7C  CONST_20  CAW  NAO  CAV  NAN     0.00   0.0  0
 W7C  CONST_21  CAU  CAW  NAO  CAV     0.00   0.0  0
 W7C  CONST_22  CAX  CAK  CAR  CAL   180.00   0.0  0
 W7C  CONST_23  CAJ  CAH  CAR  CAL   180.00   0.0  0
 W7C  CONST_24  OAP  CAS  CAY  CAJ     0.00   0.0  0
 W7C  CONST_25  OAP  CAS  CAY  CAX   180.00   0.0  0
 W7C  CONST_26  OAP  CAS  CAG  CAF   180.00   0.0  0
 W7C  CONST_27  OAC  CAV  NAN  CAT   180.00   0.0  0
 W7C  CONST_28  OAD  CAW  NAO  CAV   180.00   0.0  0
 W7C  CONST_29  CAW  NAO  CAV  OAC   180.00   0.0  0
 W7C  CONST_30  H10  CAJ  CAH  CAR   180.00   0.0  0
 W7C  CONST_31  H11  CAI  CAX  CAK     0.00   0.0  0
 W7C  CONST_32  H9   CAH  CAR  CAK   180.00   0.0  0
 W7C  CONST_33  H8   CAK  CAR  CAH   180.00   0.0  0
 W7C  CONST_34  H13  CAG  CAS  CAY   180.00   0.0  0
 W7C  CONST_35  H12  CAF  CAI  CAX   180.00   0.0  0
 W7C  CONST_36  H3   NAO  CAV  NAN   180.00   0.0  0
 W7C  CONST_37  H2   NAN  CAV  NAO   180.00   0.0  0
 W7C  CONST_38  H1   OAE  CAQ  CAT   180.00   0.0  0
 W7C  Var_01    CAU  CAT  CAQ  OAB   -25.27  30.0  2
 W7C  Var_02    CAL  CAM  CAU  CAT    94.17  30.0  2
 W7C  Var_03    CAR  CAL  CAM  CAU  -178.85  30.0  2
 W7C  Var_04    CAK  CAR  CAL  CAM  -104.07  30.0  2
 W7C  Var_05    H14  CAA  OAP  CAS   179.87  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
 W7C  plan-1  CAQ  0.020
 W7C  plan-1  CAT  0.020
 W7C  plan-1  NAN  0.020
 W7C  plan-1  CAV  0.020
 W7C  plan-1  OAC  0.020
 W7C  plan-1  NAO  0.020
 W7C  plan-1  CAW  0.020
 W7C  plan-1  OAD  0.020
 W7C  plan-1  CAU  0.020
 W7C  plan-1  CAM  0.020
 W7C  plan-1  H2   0.020
 W7C  plan-1  H3   0.020
 W7C  plan-2  CAL  0.020
 W7C  plan-2  CAR  0.020
 W7C  plan-2  CAK  0.020
 W7C  plan-2  CAH  0.020
 W7C  plan-2  CAJ  0.020
 W7C  plan-2  CAY  0.020
 W7C  plan-2  CAX  0.020
 W7C  plan-2  CAI  0.020
 W7C  plan-2  CAF  0.020
 W7C  plan-2  CAG  0.020
 W7C  plan-2  CAS  0.020
 W7C  plan-2  OAP  0.020
 W7C  plan-2  H8   0.020
 W7C  plan-2  H9   0.020
 W7C  plan-2  H10  0.020
 W7C  plan-2  H11  0.020
 W7C  plan-2  H12  0.020
 W7C  plan-2  H13  0.020
 W7C  plan-3  OAB  0.020
 W7C  plan-3  CAQ  0.020
 W7C  plan-3  OAE  0.020
 W7C  plan-3  CAT  0.020
 W7C  plan-3  H1   0.020

