# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 06:12:03 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-[2-(8-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: COc1cccc2ccc(CCC3=C(NC(=O)NC3=O)C(O)=O)cc12
#
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
 W7D  W7D  '5-[2-(8-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_W7D
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
 W7D  O    O  O     0  -0.396   2.3574  -2.6549   0.2890
 W7D  C    C  C     0   0.523   3.3941  -2.1166   0.0109
 W7D  OXT  O  OH1   0  -0.591   4.5262  -2.7491  -0.2375
 W7D  CA   C  CR6   0   0.281   3.5719  -0.6309  -0.0829
 W7D  N    N  NR16  0  -0.732   4.8581  -0.1893   0.1021
 W7D  CAR  C  CR6   0   0.671   5.2301   1.1228   0.0813
 W7D  OAC  O  O     0  -0.472   6.3710   1.4941   0.2576
 W7D  ND2  N  NR16  0  -0.716   4.1898   1.9824  -0.1554
 W7D  CG   C  CR6   0   0.586   2.8669   1.6541  -0.3590
 W7D  OD1  O  O     0  -0.440   2.0402   2.5249  -0.5470
 W7D  CB   C  CR6   0  -0.119   2.5525   0.2218  -0.3276
 W7D  CAM  C  CH2   0  -0.503   1.1187  -0.1453  -0.5563
 W7D  CAL  C  CH2   0  -0.504   0.2896  -0.0783   0.7361
 W7D  CAT  C  CR6   0   0.131  -1.1272  -0.5161   0.5020
 W7D  CAK  C  CR16  0  -0.365  -2.1486   0.3924   0.3832
 W7D  CAW  C  CR66  0   0.013  -3.4785  -0.0203   0.1333
 W7D  CAH  C  CR16  0  -0.293  -1.4188  -1.8935   0.3670
 W7D  CAJ  C  CR16  0  -0.304  -2.6930  -2.3222   0.1238
 W7D  CAV  C  CR66  0   0.109  -3.7604  -1.4025  -0.0014
 W7D  CAI  C  CR16  0  -0.344  -5.0858  -1.8333  -0.2494
 W7D  CAF  C  CR16  0  -0.248  -6.0892  -0.9141  -0.3571
 W7D  CAG  C  CR16  0  -0.410  -5.8324   0.4665  -0.2246
 W7D  CAU  C  CR6   0   0.355  -4.5547   0.9113   0.0160
 W7D  OAP  O  O2    0  -0.463  -4.2135   2.2030   0.1576
 W7D  CAA  C  CH3   0  -0.436  -5.2308   3.1828   0.0953
 W7D  H1   H  HOH1  0   0.504   4.4155  -3.7076  -0.1366
 W7D  H2   H  HNR6  0   0.439   5.5954  -0.8562   0.2819
 W7D  H3   H  HNR6  0   0.431   4.4227   2.9683  -0.1733
 W7D  H4   H  HCH2  0   0.263   0.6947   0.5507  -1.2817
 W7D  H5   H  HCH2  0   0.266   1.0351  -1.1363  -0.9955
 W7D  H6   H  HCH2  0   0.255   0.7543  -0.7174   1.4896
 W7D  H7   H  HCH2  0   0.253   0.3058   0.9411   1.1256
 W7D  H8   H  HCR6  0   0.245  -1.9273   1.4468   0.4893
 W7D  H9   H  HCR6  0   0.251  -0.6170  -2.6161   0.4638
 W7D  H10  H  HCR6  0   0.252  -2.9020  -3.3809   0.0274
 W7D  H11  H  HCR6  0   0.249  -5.2886  -2.8920  -0.3514
 W7D  H12  H  HCR6  0   0.258  -7.1048  -1.2360  -0.5473
 W7D  H13  H  HCR6  0   0.280  -6.6592   1.1570  -0.3150
 W7D  H14  H  HCH3  0   0.230  -5.7212   3.1981  -0.8813
 W7D  H15  H  HCH3  0   0.230  -5.9887   3.0292   0.8676
 W7D  H16  H  HCH3  0   0.261  -4.7469   4.1419   0.2603

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
 W7D  CAA  OAP  single    1.414  0.020  1.414
 W7D  OAP  CAU  single    1.343  0.020  1.343
 W7D  CAU  CAG  aromatic  1.374  0.020  1.374
 W7D  CAU  CAW  aromatic  1.428  0.020  1.428
 W7D  CAG  CAF  aromatic  1.411  0.020  1.411
 W7D  CAK  CAW  aromatic  1.415  0.020  1.415
 W7D  CAK  CAT  aromatic  1.372  0.020  1.372
 W7D  CAW  CAV  aromatic  1.417  0.020  1.417
 W7D  CAF  CAI  aromatic  1.365  0.020  1.365
 W7D  CAL  CAT  single    1.501  0.020  1.501
 W7D  CAL  CAM  single    1.537  0.020  1.537
 W7D  CAT  CAH  aromatic  1.414  0.020  1.414
 W7D  CAV  CAI  aromatic  1.416  0.020  1.416
 W7D  CAV  CAJ  aromatic  1.414  0.020  1.414
 W7D  CAH  CAJ  aromatic  1.366  0.020  1.366
 W7D  CAM  CB   single    1.498  0.020  1.498
 W7D  OD1  CG   double    1.215  0.020  1.215
 W7D  CB   CG   single    1.467  0.020  1.467
 W7D  CB   CA   double    1.351  0.020  1.351
 W7D  CG   ND2  single    1.378  0.020  1.378
 W7D  O    C    double    1.201  0.020  1.201
 W7D  C    CA   single    1.499  0.020  1.499
 W7D  C    OXT  single    1.320  0.020  1.320
 W7D  CA   N    single    1.372  0.020  1.372
 W7D  ND2  CAR  single    1.370  0.020  1.370
 W7D  N    CAR  single    1.364  0.020  1.364
 W7D  CAR  OAC  double    1.213  0.020  1.213
 W7D  OXT  H1   single    0.850  0.020  0.980
 W7D  N    H2   single    0.860  0.020  1.020
 W7D  ND2  H3   single    0.860  0.020  1.020
 W7D  CAM  H4   single    0.970  0.020  1.090
 W7D  CAM  H5   single    0.970  0.020  1.090
 W7D  CAL  H6   single    0.970  0.020  1.090
 W7D  CAL  H7   single    0.970  0.020  1.090
 W7D  CAK  H8   single    0.930  0.020  1.080
 W7D  CAH  H9   single    0.930  0.020  1.080
 W7D  CAJ  H10  single    0.930  0.020  1.080
 W7D  CAI  H11  single    0.930  0.020  1.080
 W7D  CAF  H12  single    0.930  0.020  1.080
 W7D  CAG  H13  single    0.930  0.020  1.080
 W7D  CAA  H14  single    0.970  0.020  1.090
 W7D  CAA  H15  single    0.970  0.020  1.090
 W7D  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
 W7D  CA   C    OXT  111.17  3.000
 W7D  OXT  C    O    124.69  3.000
 W7D  CA   C    O    124.14  3.000
 W7D  H1   OXT  C    110.85  3.000
 W7D  CB   CA   N    121.89  3.000
 W7D  N    CA   C    114.94  3.000
 W7D  CB   CA   C    123.17  3.000
 W7D  H2   N    CAR  116.02  3.000
 W7D  H2   N    CA   119.70  3.000
 W7D  CAR  N    CA   124.27  3.000
 W7D  ND2  CAR  OAC  123.18  3.000
 W7D  OAC  CAR  N    123.30  3.000
 W7D  ND2  CAR  N    113.52  3.000
 W7D  H3   ND2  CG   116.74  3.000
 W7D  H3   ND2  CAR  116.04  3.000
 W7D  CG   ND2  CAR  127.22  3.000
 W7D  CB   CG   OD1  123.87  3.000
 W7D  CB   CG   ND2  115.80  3.000
 W7D  OD1  CG   ND2  120.34  3.000
 W7D  CAM  CB   CG   116.18  3.000
 W7D  CG   CB   CA   117.29  3.000
 W7D  CAM  CB   CA   126.53  3.000
 W7D  H5   CAM  H4   106.44  3.000
 W7D  H5   CAM  CAL  109.75  3.000
 W7D  H4   CAM  CAL  108.76  3.000
 W7D  H5   CAM  CB   111.02  3.000
 W7D  H4   CAM  CB   108.50  3.000
 W7D  CAL  CAM  CB   112.17  3.000
 W7D  H7   CAL  H6   107.11  3.000
 W7D  H7   CAL  CAT  110.00  3.000
 W7D  H6   CAL  CAT  109.79  3.000
 W7D  H7   CAL  CAM  109.44  3.000
 W7D  H6   CAL  CAM  108.98  3.000
 W7D  CAT  CAL  CAM  111.42  3.000
 W7D  CAH  CAT  CAK  118.89  3.000
 W7D  CAH  CAT  CAL  119.57  3.000
 W7D  CAK  CAT  CAL  121.53  3.000
 W7D  H8   CAK  CAW  119.58  3.000
 W7D  H8   CAK  CAT  118.96  3.000
 W7D  CAW  CAK  CAT  121.46  3.000
 W7D  CAU  CAW  CAV  118.59  3.000
 W7D  CAV  CAW  CAK  119.23  3.000
 W7D  CAU  CAW  CAK  122.18  3.000
 W7D  H9   CAH  CAJ  119.78  3.000
 W7D  H9   CAH  CAT  119.23  3.000
 W7D  CAJ  CAH  CAT  120.99  3.000
 W7D  H10  CAJ  CAV  118.81  3.000
 W7D  H10  CAJ  CAH  120.16  3.000
 W7D  CAV  CAJ  CAH  121.03  3.000
 W7D  CAI  CAV  CAJ  121.62  3.000
 W7D  CAJ  CAV  CAW  118.40  3.000
 W7D  CAI  CAV  CAW  119.98  3.000
 W7D  H11  CAI  CAF  120.88  3.000
 W7D  H11  CAI  CAV  119.30  3.000
 W7D  CAF  CAI  CAV  119.82  3.000
 W7D  H12  CAF  CAG  118.59  3.000
 W7D  H12  CAF  CAI  120.23  3.000
 W7D  CAG  CAF  CAI  121.19  3.000
 W7D  H13  CAG  CAU  121.27  3.000
 W7D  H13  CAG  CAF  118.56  3.000
 W7D  CAU  CAG  CAF  120.17  3.000
 W7D  OAP  CAU  CAG  124.45  3.000
 W7D  CAG  CAU  CAW  120.26  3.000
 W7D  OAP  CAU  CAW  115.29  3.000
 W7D  CAA  OAP  CAU  118.62  3.000
 W7D  H16  CAA  H15  108.99  3.000
 W7D  H16  CAA  H14  108.85  3.000
 W7D  H15  CAA  H14  108.79  3.000
 W7D  H16  CAA  OAP  106.53  3.000
 W7D  H15  CAA  OAP  111.75  3.000
 W7D  H14  CAA  OAP  111.84  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
 W7D  CONST_01  CAU  CAW  CAK  CAT   180.00   0.0  0
 W7D  CONST_02  CAV  CAW  CAK  CAT     0.00   0.0  0
 W7D  CONST_03  CAV  CAJ  CAH  CAT     0.00   0.0  0
 W7D  CONST_04  CAG  CAU  CAW  CAK   180.00   0.0  0
 W7D  CONST_05  CAI  CAV  CAW  CAK   180.00   0.0  0
 W7D  CONST_06  CAJ  CAV  CAW  CAK     0.00   0.0  0
 W7D  CONST_07  CAJ  CAH  CAT  CAK     0.00   0.0  0
 W7D  CONST_08  CAF  CAG  CAU  CAW     0.00   0.0  0
 W7D  CONST_09  CAH  CAT  CAK  CAW     0.00   0.0  0
 W7D  CONST_10  CAF  CAI  CAV  CAW     0.00   0.0  0
 W7D  CONST_11  CAH  CAJ  CAV  CAW     0.00   0.0  0
 W7D  CONST_12  CAI  CAV  CAJ  CAH   180.00   0.0  0
 W7D  CONST_13  CAU  CAW  CAV  CAJ   180.00   0.0  0
 W7D  CONST_14  CAF  CAI  CAV  CAJ   180.00   0.0  0
 W7D  CONST_15  CAG  CAU  CAW  CAV     0.00   0.0  0
 W7D  CONST_16  CAG  CAF  CAI  CAV     0.00   0.0  0
 W7D  CONST_17  CAU  CAG  CAF  CAI     0.00   0.0  0
 W7D  CONST_18  CAU  CAW  CAV  CAI     0.00   0.0  0
 W7D  CONST_19  ND2  CAR  N    CA      0.00   0.0  0
 W7D  CONST_20  CG   ND2  CAR  N       0.00   0.0  0
 W7D  CONST_21  CB   CG   ND2  CAR     0.00   0.0  0
 W7D  CONST_22  CAW  CAK  CAT  CAL   180.00   0.0  0
 W7D  CONST_23  CAJ  CAH  CAT  CAL   180.00   0.0  0
 W7D  CONST_24  OAP  CAU  CAW  CAK     0.00   0.0  0
 W7D  CONST_25  OAP  CAU  CAW  CAV   180.00   0.0  0
 W7D  CONST_26  OAP  CAU  CAG  CAF   180.00   0.0  0
 W7D  CONST_27  OAC  CAR  N    CA    180.00   0.0  0
 W7D  CONST_28  OD1  CG   ND2  CAR   180.00   0.0  0
 W7D  CONST_29  CG   ND2  CAR  OAC   180.00   0.0  0
 W7D  CONST_30  H10  CAJ  CAH  CAT   180.00   0.0  0
 W7D  CONST_31  H9   CAH  CAT  CAK   180.00   0.0  0
 W7D  CONST_32  H13  CAG  CAU  CAW   180.00   0.0  0
 W7D  CONST_33  H11  CAI  CAV  CAW   180.00   0.0  0
 W7D  CONST_34  H8   CAK  CAT  CAH   180.00   0.0  0
 W7D  CONST_35  H12  CAF  CAI  CAV   180.00   0.0  0
 W7D  CONST_36  H3   ND2  CAR  N     180.00   0.0  0
 W7D  CONST_37  H2   N    CAR  ND2   180.00   0.0  0
 W7D  CONST_38  H1   OXT  C    CA    180.00   0.0  0
 W7D  Var_01    CB   CA   C    O     -23.88  30.0  2
 W7D  Var_02    CAL  CAM  CB   CA     94.43  30.0  2
 W7D  Var_03    CAT  CAL  CAM  CB   -177.11  30.0  2
 W7D  Var_04    CAK  CAT  CAL  CAM  -102.11  30.0  2
 W7D  Var_05    H14  CAA  OAP  CAU   -62.77  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
 W7D  plan-1  C    0.020
 W7D  plan-1  CA   0.020
 W7D  plan-1  N    0.020
 W7D  plan-1  CAR  0.020
 W7D  plan-1  OAC  0.020
 W7D  plan-1  ND2  0.020
 W7D  plan-1  CG   0.020
 W7D  plan-1  OD1  0.020
 W7D  plan-1  CB   0.020
 W7D  plan-1  CAM  0.020
 W7D  plan-1  H2   0.020
 W7D  plan-1  H3   0.020
 W7D  plan-2  CAL  0.020
 W7D  plan-2  CAT  0.020
 W7D  plan-2  CAK  0.020
 W7D  plan-2  CAW  0.020
 W7D  plan-2  CAH  0.020
 W7D  plan-2  CAJ  0.020
 W7D  plan-2  CAV  0.020
 W7D  plan-2  CAI  0.020
 W7D  plan-2  CAF  0.020
 W7D  plan-2  CAG  0.020
 W7D  plan-2  CAU  0.020
 W7D  plan-2  OAP  0.020
 W7D  plan-2  H8   0.020
 W7D  plan-2  H9   0.020
 W7D  plan-2  H10  0.020
 W7D  plan-2  H11  0.020
 W7D  plan-2  H12  0.020
 W7D  plan-2  H13  0.020
 W7D  plan-3  O    0.020
 W7D  plan-3  C    0.020
 W7D  plan-3  OXT  0.020
 W7D  plan-3  CA   0.020
 W7D  plan-3  H1   0.020

