# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 07:32:49 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5-{4-[5-(methoxycarbonyl)naphthalen-2-yl]butyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1cccc2cc(CCCCC3=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
 W87  W87  '5-{4-[5-(methoxycarbonyl)naphthalen-2-yl]butyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  48  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W87
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
 W87  OAB  O  OC    -1  -0.587  -5.9676  -2.7590   0.8085
 W87  CAT  C  C      0   0.413  -4.9780  -2.0057   0.7544
 W87  OAF  O  O      0  -0.542  -3.7867  -2.2966   0.9052
 W87  CAX  C  CR6    0   0.198  -5.3230  -0.5364   0.4393
 W87  NAQ  N  NR16   0  -0.707  -6.6462  -0.3870   0.1225
 W87  CAZ  C  CR6    0   0.655  -7.2480   0.7787  -0.2208
 W87  OAD  O  O      0  -0.494  -8.4301   0.8796  -0.4944
 W87  NAR  N  NR16   0  -0.714  -6.3860   1.8435  -0.2341
 W87  CBA  C  CR6    0   0.561  -5.0364   1.8251   0.0659
 W87  OAE  O  O      0  -0.468  -4.3940   2.8607  -0.0043
 W87  CAY  C  CR6    0  -0.152  -4.4856   0.5299   0.4478
 W87  CAP  C  CH2    0  -0.475  -3.0214   0.5015   0.7743
 W87  CAN  C  CH2    0  -0.410  -2.1498   0.2442  -0.4545
 W87  CAM  C  CH2    0  -0.421  -0.6680   0.1978  -0.1104
 W87  CAO  C  CH2    0  -0.506   0.2133  -0.0532  -1.3362
 W87  CAV  C  CR6    0   0.147   1.6707  -0.1036  -0.9818
 W87  CAL  C  CR16   0  -0.396   2.3595  -1.2840  -0.9098
 W87  CAI  C  CR16   0  -0.285   2.3675   1.0877  -0.6733
 W87  CAK  C  CR16   0  -0.321   3.6803   1.0818  -0.2911
 W87  CBC  C  CR66   0   0.119   4.4070  -0.1317  -0.1912
 W87  CBB  C  CR66   0   0.129   3.7213  -1.3306  -0.5290
 W87  CAJ  C  CR16   0  -0.307   4.4043  -2.5671  -0.4868
 W87  CAG  C  CR16   0  -0.250   5.7245  -2.6250  -0.1413
 W87  CAH  C  CR16   0  -0.280   6.4163  -1.4459   0.1820
 W87  CAW  C  CR6    0  -0.082   5.7844  -0.2232   0.1760
 W87  CAU  C  C      0   0.542   6.5500   0.9716   0.6218
 W87  OAC  O  O      0  -0.446   6.0795   1.9079   1.2224
 W87  OAS  O  O2     0  -0.451   7.8335   0.8852   0.3059
 W87  CAA  C  CH3    0  -0.423   8.6948   1.9313   0.7564
 W87  H2   H  HNR6   0   0.419  -6.7814   2.7366  -0.4986
 W87  H4   H  HCH2   0   0.227  -2.7452   1.4638   1.2111
 W87  H5   H  HCH2   0   0.240  -2.8176  -0.2598   1.5219
 W87  H6   H  HCH2   0   0.222  -2.4503  -0.7055  -0.9031
 W87  H7   H  HCH2   0   0.214  -2.3282   1.0216  -1.2041
 W87  H8   H  HCH2   0   0.221  -0.3701   1.1385   0.3639
 W87  H9   H  HCH2   0   0.223  -0.4893  -0.5904   0.6276
 W87  H10  H  HCH2   0   0.239  -0.0838  -0.9925  -1.8091
 W87  H11  H  HCH2   0   0.239   0.0394   0.7381  -2.0717
 W87  H12  H  HCR6   0   0.249   1.8643  -2.2177  -1.1538
 W87  H13  H  HCR6   0   0.252   1.8464   2.0354  -0.7485
 W87  H14  H  HCR6   0   0.256   4.1576   2.0237  -0.0715
 W87  H15  H  HCR6   0   0.263   3.8635  -3.4716  -0.7373
 W87  H16  H  HCR6   0   0.266   6.2440  -3.5731  -0.1084
 W87  H17  H  HCR6   0   0.270   7.4585  -1.5203   0.4603
 W87  H18  H  HCH3   0   0.241   8.7039   1.9991   1.8439
 W87  H19  H  HCH3   0   0.254   9.6876   1.6709   0.4025
 W87  H20  H  HCH3   0   0.241   8.4023   2.8937   0.3379
 W87  H21  H  HNR6   0   0.416  -7.2002  -1.2347   0.1736

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
 W87  OAD  CAZ  double    1.218  0.020  1.218
 W87  CAZ  NAQ  single    1.356  0.020  1.356
 W87  CAZ  NAR  single    1.370  0.020  1.370
 W87  NAQ  CAX  single    1.369  0.020  1.369
 W87  NAR  CBA  single    1.383  0.020  1.383
 W87  CAX  CAT  single    1.542  0.020  1.542
 W87  CAX  CAY  double    1.356  0.020  1.356
 W87  CAT  OAF  deloc     1.236  0.020  1.236
 W87  CAT  OAB  deloc     1.245  0.020  1.245
 W87  CBA  CAY  single    1.458  0.020  1.458
 W87  CBA  OAE  double    1.221  0.020  1.221
 W87  CAY  CAP  single    1.500  0.020  1.500
 W87  CAP  CAN  single    1.528  0.020  1.528
 W87  CAN  CAM  single    1.522  0.020  1.522
 W87  CAM  CAO  single    1.530  0.020  1.530
 W87  OAC  CAU  double    1.208  0.020  1.208
 W87  CAA  OAS  single    1.428  0.020  1.428
 W87  CAI  CAK  aromatic  1.367  0.020  1.367
 W87  CAI  CAV  aromatic  1.414  0.020  1.414
 W87  CAK  CBC  aromatic  1.418  0.020  1.418
 W87  CAU  OAS  single    1.325  0.020  1.325
 W87  CAU  CAW  single    1.487  0.020  1.487
 W87  CAO  CAV  single    1.501  0.020  1.501
 W87  CAV  CAL  aromatic  1.369  0.020  1.369
 W87  CBC  CAW  aromatic  1.428  0.020  1.428
 W87  CBC  CBB  aromatic  1.422  0.020  1.422
 W87  CAW  CAH  aromatic  1.376  0.020  1.376
 W87  CAL  CBB  aromatic  1.415  0.020  1.415
 W87  CBB  CAJ  aromatic  1.413  0.020  1.413
 W87  CAH  CAG  aromatic  1.405  0.020  1.405
 W87  CAJ  CAG  aromatic  1.366  0.020  1.366
 W87  NAR  H2   single    0.860  0.020  1.020
 W87  CAP  H4   single    0.970  0.020  1.090
 W87  CAP  H5   single    0.970  0.020  1.090
 W87  CAN  H6   single    0.970  0.020  1.090
 W87  CAN  H7   single    0.970  0.020  1.090
 W87  CAM  H8   single    0.970  0.020  1.090
 W87  CAM  H9   single    0.970  0.020  1.090
 W87  CAO  H10  single    0.970  0.020  1.090
 W87  CAO  H11  single    0.970  0.020  1.090
 W87  CAL  H12  single    0.930  0.020  1.080
 W87  CAI  H13  single    0.930  0.020  1.080
 W87  CAK  H14  single    0.930  0.020  1.080
 W87  CAJ  H15  single    0.930  0.020  1.080
 W87  CAG  H16  single    0.930  0.020  1.080
 W87  CAH  H17  single    0.930  0.020  1.080
 W87  CAA  H18  single    0.970  0.020  1.090
 W87  CAA  H19  single    0.970  0.020  1.090
 W87  CAA  H20  single    0.970  0.020  1.090
 W87  NAQ  H21  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
 W87  CAX  CAT  OAF  117.72  3.000
 W87  OAF  CAT  OAB  128.22  3.000
 W87  CAX  CAT  OAB  114.06  3.000
 W87  CAY  CAX  NAQ  120.84  3.000
 W87  CAY  CAX  CAT  127.59  3.000
 W87  NAQ  CAX  CAT  111.57  3.000
 W87  H21  NAQ  CAZ  119.27  3.000
 W87  H21  NAQ  CAX  115.17  3.000
 W87  CAZ  NAQ  CAX  125.55  3.000
 W87  NAR  CAZ  OAD  122.98  3.000
 W87  NAR  CAZ  NAQ  113.04  3.000
 W87  OAD  CAZ  NAQ  123.98  3.000
 W87  H2   NAR  CBA  116.73  3.000
 W87  H2   NAR  CAZ  116.27  3.000
 W87  CBA  NAR  CAZ  126.99  3.000
 W87  CAY  CBA  OAE  124.74  3.000
 W87  OAE  CBA  NAR  119.33  3.000
 W87  CAY  CBA  NAR  115.93  3.000
 W87  CAP  CAY  CBA  116.25  3.000
 W87  CAP  CAY  CAX  126.10  3.000
 W87  CBA  CAY  CAX  117.62  3.000
 W87  H5   CAP  H4   107.15  3.000
 W87  H5   CAP  CAN  109.17  3.000
 W87  H4   CAP  CAN  109.00  3.000
 W87  H5   CAP  CAY  110.25  3.000
 W87  H4   CAP  CAY  108.49  3.000
 W87  CAN  CAP  CAY  112.62  3.000
 W87  H7   CAN  H6   106.95  3.000
 W87  H7   CAN  CAM  109.58  3.000
 W87  H6   CAN  CAM  109.52  3.000
 W87  H7   CAN  CAP  109.76  3.000
 W87  H6   CAN  CAP  108.64  3.000
 W87  CAM  CAN  CAP  112.25  3.000
 W87  H9   CAM  H8   106.39  3.000
 W87  H9   CAM  CAO  109.15  3.000
 W87  H8   CAM  CAO  109.35  3.000
 W87  H9   CAM  CAN  109.47  3.000
 W87  H8   CAM  CAN  109.68  3.000
 W87  CAO  CAM  CAN  112.62  3.000
 W87  H11  CAO  H10  106.71  3.000
 W87  H11  CAO  CAV  109.71  3.000
 W87  H10  CAO  CAV  109.71  3.000
 W87  H11  CAO  CAM  109.17  3.000
 W87  H10  CAO  CAM  109.33  3.000
 W87  CAV  CAO  CAM  112.06  3.000
 W87  CAI  CAV  CAL  117.85  3.000
 W87  CAL  CAV  CAO  122.02  3.000
 W87  CAI  CAV  CAO  120.11  3.000
 W87  H12  CAL  CBB  118.14  3.000
 W87  H12  CAL  CAV  120.05  3.000
 W87  CBB  CAL  CAV  121.80  3.000
 W87  H13  CAI  CAK  118.99  3.000
 W87  H13  CAI  CAV  118.98  3.000
 W87  CAK  CAI  CAV  122.03  3.000
 W87  H14  CAK  CBC  120.42  3.000
 W87  H14  CAK  CAI  118.56  3.000
 W87  CBC  CAK  CAI  121.03  3.000
 W87  CAW  CBC  CBB  118.17  3.000
 W87  CBB  CBC  CAK  117.24  3.000
 W87  CAW  CBC  CAK  124.54  3.000
 W87  CAJ  CBB  CBC  119.84  3.000
 W87  CAJ  CBB  CAL  120.13  3.000
 W87  CBC  CBB  CAL  120.02  3.000
 W87  H15  CAJ  CAG  120.37  3.000
 W87  H15  CAJ  CBB  118.85  3.000
 W87  CAG  CAJ  CBB  120.78  3.000
 W87  H16  CAG  CAH  119.48  3.000
 W87  H16  CAG  CAJ  120.61  3.000
 W87  CAH  CAG  CAJ  119.91  3.000
 W87  H17  CAH  CAW  120.32  3.000
 W87  H17  CAH  CAG  118.43  3.000
 W87  CAW  CAH  CAG  121.23  3.000
 W87  CAU  CAW  CAH  118.42  3.000
 W87  CAH  CAW  CBC  120.05  3.000
 W87  CAU  CAW  CBC  121.46  3.000
 W87  OAS  CAU  OAC  123.13  3.000
 W87  OAS  CAU  CAW  112.02  3.000
 W87  OAC  CAU  CAW  124.84  3.000
 W87  CAA  OAS  CAU  117.48  3.000
 W87  H20  CAA  H19  109.40  3.000
 W87  H20  CAA  H18  109.31  3.000
 W87  H19  CAA  H18  109.43  3.000
 W87  H20  CAA  OAS  111.35  3.000
 W87  H19  CAA  OAS  105.84  3.000
 W87  H18  CAA  OAS  111.44  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
 W87  CONST_01  CBC  CAK  CAI  CAV     0.00   0.0  0
 W87  CONST_02  CBC  CBB  CAL  CAV     0.00   0.0  0
 W87  CONST_03  CAJ  CBB  CAL  CAV   180.00   0.0  0
 W87  CONST_04  CAK  CAI  CAV  CAL     0.00   0.0  0
 W87  CONST_05  CAK  CBC  CBB  CAL     0.00   0.0  0
 W87  CONST_06  CAW  CBC  CBB  CAL   180.00   0.0  0
 W87  CONST_07  CAG  CAJ  CBB  CAL   180.00   0.0  0
 W87  CONST_08  CAW  CBC  CAK  CAI   180.00   0.0  0
 W87  CONST_09  CBB  CBC  CAK  CAI     0.00   0.0  0
 W87  CONST_10  CBB  CAL  CAV  CAI     0.00   0.0  0
 W87  CONST_11  CAH  CAW  CBC  CAK   180.00   0.0  0
 W87  CONST_12  CAJ  CBB  CBC  CAK   180.00   0.0  0
 W87  CONST_13  CAG  CAH  CAW  CBC     0.00   0.0  0
 W87  CONST_14  CAG  CAJ  CBB  CBC     0.00   0.0  0
 W87  CONST_15  CAH  CAW  CBC  CBB     0.00   0.0  0
 W87  CONST_16  CAH  CAG  CAJ  CBB     0.00   0.0  0
 W87  CONST_17  CAW  CBC  CBB  CAJ     0.00   0.0  0
 W87  CONST_18  CAW  CAH  CAG  CAJ     0.00   0.0  0
 W87  CONST_19  NAR  CAZ  NAQ  CAX     0.00   0.0  0
 W87  CONST_20  CBA  NAR  CAZ  NAQ     0.00   0.0  0
 W87  CONST_21  CAY  CBA  NAR  CAZ     0.00   0.0  0
 W87  CONST_22  CAK  CAI  CAV  CAO   180.00   0.0  0
 W87  CONST_23  CBB  CAL  CAV  CAO   180.00   0.0  0
 W87  CONST_24  CAU  CAW  CBC  CAK     0.00   0.0  0
 W87  CONST_25  CAU  CAW  CBC  CBB   180.00   0.0  0
 W87  CONST_26  CAU  CAW  CAH  CAG   180.00   0.0  0
 W87  CONST_27  OAD  CAZ  NAQ  CAX   180.00   0.0  0
 W87  CONST_28  OAE  CBA  NAR  CAZ   180.00   0.0  0
 W87  CONST_29  CBA  NAR  CAZ  OAD   180.00   0.0  0
 W87  CONST_30  H14  CAK  CAI  CAV   180.00   0.0  0
 W87  CONST_31  H13  CAI  CAV  CAL   180.00   0.0  0
 W87  CONST_32  H15  CAJ  CBB  CAL     0.00   0.0  0
 W87  CONST_33  H12  CAL  CAV  CAI   180.00   0.0  0
 W87  CONST_34  H17  CAH  CAW  CBC   180.00   0.0  0
 W87  CONST_35  H16  CAG  CAJ  CBB   180.00   0.0  0
 W87  CONST_36  H2   NAR  CAZ  NAQ   180.00   0.0  0
 W87  CONST_37  H21  NAQ  CAZ  NAR   180.00   0.0  0
 W87  Var_01    NAQ  CAX  CAT  OAB    -7.34  30.0  2
 W87  Var_02    CAN  CAP  CAY  CAX    89.09  30.0  3
 W87  Var_03    CAI  CAV  CAO  CAM   -74.25  30.0  2
 W87  Var_04    OAC  CAU  CAW  CBC    31.71  30.0  2
 W87  Var_05    CAM  CAN  CAP  CAY  -179.20  30.0  3
 W87  Var_06    CAV  CAO  CAM  CAN  -179.70  30.0  3
 W87  Var_07    CAO  CAM  CAN  CAP  -179.74  30.0  3
 W87  Var_08    H18  CAA  OAS  CAU    60.82  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
 W87  plan-1  CAT  0.020
 W87  plan-1  CAX  0.020
 W87  plan-1  NAQ  0.020
 W87  plan-1  CAZ  0.020
 W87  plan-1  OAD  0.020
 W87  plan-1  NAR  0.020
 W87  plan-1  CBA  0.020
 W87  plan-1  OAE  0.020
 W87  plan-1  CAY  0.020
 W87  plan-1  CAP  0.020
 W87  plan-1  H2   0.020
 W87  plan-1  H21  0.020
 W87  plan-2  CAW  0.020
 W87  plan-2  CAU  0.020
 W87  plan-2  OAC  0.020
 W87  plan-2  OAS  0.020
 W87  plan-3  CAO  0.020
 W87  plan-3  CAV  0.020
 W87  plan-3  CAL  0.020
 W87  plan-3  CAI  0.020
 W87  plan-3  CAK  0.020
 W87  plan-3  CBC  0.020
 W87  plan-3  CBB  0.020
 W87  plan-3  CAJ  0.020
 W87  plan-3  CAG  0.020
 W87  plan-3  CAH  0.020
 W87  plan-3  CAW  0.020
 W87  plan-3  CAU  0.020
 W87  plan-3  H12  0.020
 W87  plan-3  H13  0.020
 W87  plan-3  H14  0.020
 W87  plan-3  H15  0.020
 W87  plan-3  H16  0.020
 W87  plan-3  H17  0.020
 W87  plan-4  OAB  0.020
 W87  plan-4  CAT  0.020
 W87  plan-4  OAF  0.020
 W87  plan-4  CAX  0.020

