# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 11:43:21 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 5-{2-[7-(methoxymethoxy)naphthalen-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: COCOc1ccc2ccc(CCC3=C(NC(=O)NC3=O)C(O)=O)cc2c1
#
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
 W83  W83  '5-{2-[7-(methoxymethoxy)naphthalen-2-yl]ethyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  45  27  .  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_W83
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
 W83  OAB  O  OH1   0  -0.590  -5.5106  -2.6061   0.0978
 W83  CAS  C  C     0   0.522  -4.3637  -1.9887  -0.1181
 W83  OAE  O  O     0  -0.396  -3.3339  -2.5376  -0.4005
 W83  CAV  C  CR6   0   0.282  -4.5147  -0.5034   0.0198
 W83  NAO  N  NR16  0  -0.732  -5.7879  -0.0307  -0.1773
 W83  CAX  C  CR6   0   0.671  -6.1348   1.2872  -0.1207
 W83  OAC  O  O     0  -0.472  -7.2640   1.6873  -0.3089
 W83  NAP  N  NR16  0  -0.716  -5.0835   2.1174   0.1671
 W83  CAY  C  CR6   0   0.586  -3.7729   1.7559   0.3925
 W83  OAD  O  O     0  -0.440  -2.9355   2.6026   0.6355
 W83  CAW  C  CR6   0  -0.119  -3.4845   0.3199   0.3143
 W83  CAM  C  CH2   0  -0.503  -2.0628  -0.0830   0.5588
 W83  CAL  C  CH2   0  -0.504  -1.2072   0.0143  -0.7140
 W83  CAT  C  CR6   0   0.129   0.1979  -0.4533  -0.4676
 W83  CAJ  C  CR16  0  -0.400   1.2302   0.4321  -0.3036
 W83  CBA  C  CR66  0   0.166   2.5517  -0.0105  -0.0457
 W83  CAK  C  CR16  0  -0.439   3.6206   0.8933   0.1175
 W83  CAF  C  CR16  0  -0.307   0.4616  -1.8439  -0.3720
 W83  CAH  C  CR16  0  -0.293   1.7226  -2.3045  -0.1221
 W83  CAZ  C  CR66  0   0.079   2.7998  -1.4031   0.0486
 W83  CAI  C  CR16  0  -0.295   4.1183  -1.8349   0.3017
 W83  CAG  C  CR16  0  -0.368   5.1494  -0.9465   0.4511
 W83  CAU  C  CR6   0   0.397   4.8962   0.4431   0.3629
 W83  OAR  O  O2    0  -0.494   5.8495   1.3950   0.5085
 W83  CAN  C  CH2   0   0.015   7.1699   1.0340   0.8422
 W83  OAQ  O  O2    0  -0.481   7.8418   0.4041  -0.1862
 W83  CAA  C  CH3   0  -0.411   8.0960   1.2224  -1.3115
 W83  H1   H  HOH1  0   0.504  -5.4175  -3.5631  -0.0314
 W83  H2   H  HNR6  0   0.439  -6.5341  -0.6770  -0.3928
 W83  H3   H  HNR6  0   0.431  -5.2985   3.1062   0.2167
 W83  H4   H  HCH2  0   0.263  -1.6419   0.5808   1.3155
 W83  H5   H  HCH2  0   0.267  -2.0062  -1.0897   0.9657
 W83  H6   H  HCH2  0   0.255  -1.6651  -0.5935  -1.4969
 W83  H7   H  HCH2  0   0.253  -1.2008   1.0460  -1.0699
 W83  H8   H  HCR6  0   0.242   1.0439   1.4984  -0.3761
 W83  H9   H  HCR6  0   0.257   3.4333   1.9588   0.0492
 W83  H10  H  HCR6  0   0.249  -0.3531  -2.5457  -0.5058
 W83  H11  H  HCR6  0   0.252   1.9119  -3.3695  -0.0573
 W83  H12  H  HCR6  0   0.260   4.3198  -2.8971   0.3707
 W83  H13  H  HCR6  0   0.283   6.1440  -1.3311   0.6247
 W83  H14  H  HCH2  0   0.243   7.6462   1.9810   1.1176
 W83  H15  H  HCH2  0   0.240   7.1873   0.3569   1.7007
 W83  H16  H  HCH3  0   0.240   8.7631   0.6704  -1.9707
 W83  H17  H  HCH3  0   0.222   7.1850   1.4647  -1.8645
 W83  H18  H  HCH3  0   0.213   8.5856   2.1594  -1.0252

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
 W83  CAA  OAQ  single    1.414  0.020  1.414
 W83  OAQ  CAN  single    1.381  0.020  1.381
 W83  CAN  OAR  single    1.409  0.020  1.409
 W83  OAR  CAU  single    1.355  0.020  1.355
 W83  CAU  CAK  aromatic  1.375  0.020  1.375
 W83  CAU  CAG  aromatic  1.415  0.020  1.415
 W83  CAK  CBA  aromatic  1.409  0.020  1.409
 W83  CAG  CAI  aromatic  1.369  0.020  1.369
 W83  CBA  CAJ  aromatic  1.417  0.020  1.417
 W83  CBA  CAZ  aromatic  1.418  0.020  1.418
 W83  CAJ  CAT  aromatic  1.370  0.020  1.370
 W83  CAI  CAZ  aromatic  1.410  0.020  1.410
 W83  CAZ  CAH  aromatic  1.415  0.020  1.415
 W83  CAT  CAL  single    1.501  0.020  1.501
 W83  CAT  CAF  aromatic  1.419  0.020  1.419
 W83  CAL  CAM  single    1.537  0.020  1.537
 W83  CAH  CAF  aromatic  1.365  0.020  1.365
 W83  CAM  CAW  single    1.498  0.020  1.498
 W83  OAD  CAY  double    1.215  0.020  1.215
 W83  CAW  CAY  single    1.467  0.020  1.467
 W83  CAW  CAV  double    1.351  0.020  1.351
 W83  CAY  NAP  single    1.378  0.020  1.378
 W83  OAE  CAS  double    1.201  0.020  1.201
 W83  CAS  OAB  single    1.320  0.020  1.320
 W83  CAS  CAV  single    1.499  0.020  1.499
 W83  CAV  NAO  single    1.372  0.020  1.372
 W83  NAP  CAX  single    1.370  0.020  1.370
 W83  NAO  CAX  single    1.364  0.020  1.364
 W83  CAX  OAC  double    1.213  0.020  1.213
 W83  OAB  H1   single    0.850  0.020  0.980
 W83  NAO  H2   single    0.860  0.020  1.020
 W83  NAP  H3   single    0.860  0.020  1.020
 W83  CAM  H4   single    0.970  0.020  1.090
 W83  CAM  H5   single    0.970  0.020  1.090
 W83  CAL  H6   single    0.970  0.020  1.090
 W83  CAL  H7   single    0.970  0.020  1.090
 W83  CAJ  H8   single    0.930  0.020  1.080
 W83  CAK  H9   single    0.930  0.020  1.080
 W83  CAF  H10  single    0.930  0.020  1.080
 W83  CAH  H11  single    0.930  0.020  1.080
 W83  CAI  H12  single    0.930  0.020  1.080
 W83  CAG  H13  single    0.930  0.020  1.080
 W83  CAN  H14  single    0.970  0.020  1.090
 W83  CAN  H15  single    0.970  0.020  1.090
 W83  CAA  H16  single    0.970  0.020  1.090
 W83  CAA  H17  single    0.970  0.020  1.090
 W83  CAA  H18  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
 W83  H1   OAB  CAS  110.86  3.000
 W83  CAV  CAS  OAE  124.12  3.000
 W83  CAV  CAS  OAB  111.15  3.000
 W83  OAE  CAS  OAB  124.73  3.000
 W83  CAW  CAV  NAO  121.92  3.000
 W83  NAO  CAV  CAS  114.93  3.000
 W83  CAW  CAV  CAS  123.16  3.000
 W83  H2   NAO  CAX  116.04  3.000
 W83  H2   NAO  CAV  119.70  3.000
 W83  CAX  NAO  CAV  124.25  3.000
 W83  NAP  CAX  OAC  123.17  3.000
 W83  OAC  CAX  NAO  123.31  3.000
 W83  NAP  CAX  NAO  113.52  3.000
 W83  H3   NAP  CAY  116.73  3.000
 W83  H3   NAP  CAX  116.03  3.000
 W83  CAY  NAP  CAX  127.24  3.000
 W83  CAW  CAY  OAD  123.86  3.000
 W83  CAW  CAY  NAP  115.79  3.000
 W83  OAD  CAY  NAP  120.35  3.000
 W83  CAM  CAW  CAY  116.19  3.000
 W83  CAY  CAW  CAV  117.27  3.000
 W83  CAM  CAW  CAV  126.53  3.000
 W83  H5   CAM  H4   106.48  3.000
 W83  H5   CAM  CAL  109.85  3.000
 W83  H4   CAM  CAL  108.73  3.000
 W83  H5   CAM  CAW  111.08  3.000
 W83  H4   CAM  CAW  108.40  3.000
 W83  CAL  CAM  CAW  112.10  3.000
 W83  H7   CAL  H6   107.15  3.000
 W83  H7   CAL  CAT  110.03  3.000
 W83  H6   CAL  CAT  109.68  3.000
 W83  H7   CAL  CAM  109.47  3.000
 W83  H6   CAL  CAM  108.97  3.000
 W83  CAT  CAL  CAM  111.43  3.000
 W83  CAF  CAT  CAJ  119.04  3.000
 W83  CAF  CAT  CAL  119.37  3.000
 W83  CAJ  CAT  CAL  121.57  3.000
 W83  H8   CAJ  CBA  118.63  3.000
 W83  H8   CAJ  CAT  119.86  3.000
 W83  CBA  CAJ  CAT  121.50  3.000
 W83  CAZ  CBA  CAK  119.31  3.000
 W83  CAZ  CBA  CAJ  118.82  3.000
 W83  CAK  CBA  CAJ  121.87  3.000
 W83  H9   CAK  CAU  119.57  3.000
 W83  H9   CAK  CBA  119.47  3.000
 W83  CAU  CAK  CBA  120.96  3.000
 W83  H10  CAF  CAH  119.90  3.000
 W83  H10  CAF  CAT  119.13  3.000
 W83  CAH  CAF  CAT  120.97  3.000
 W83  H11  CAH  CAZ  119.07  3.000
 W83  H11  CAH  CAF  120.25  3.000
 W83  CAZ  CAH  CAF  120.68  3.000
 W83  CAI  CAZ  CAH  122.57  3.000
 W83  CAH  CAZ  CBA  118.98  3.000
 W83  CAI  CAZ  CBA  118.45  3.000
 W83  H12  CAI  CAG  119.28  3.000
 W83  H12  CAI  CAZ  119.05  3.000
 W83  CAG  CAI  CAZ  121.67  3.000
 W83  H13  CAG  CAU  121.62  3.000
 W83  H13  CAG  CAI  118.68  3.000
 W83  CAU  CAG  CAI  119.70  3.000
 W83  OAR  CAU  CAG  123.86  3.000
 W83  CAG  CAU  CAK  119.92  3.000
 W83  OAR  CAU  CAK  116.22  3.000
 W83  CAN  OAR  CAU  120.31  3.000
 W83  H15  CAN  H14  109.34  3.000
 W83  H15  CAN  OAQ  107.13  3.000
 W83  H14  CAN  OAQ  111.73  3.000
 W83  H15  CAN  OAR  111.07  3.000
 W83  H14  CAN  OAR  104.21  3.000
 W83  OAQ  CAN  OAR  113.36  3.000
 W83  CAA  OAQ  CAN  114.59  3.000
 W83  H18  CAA  H17  108.38  3.000
 W83  H18  CAA  H16  108.56  3.000
 W83  H17  CAA  H16  108.48  3.000
 W83  H18  CAA  OAQ  111.55  3.000
 W83  H17  CAA  OAQ  112.39  3.000
 W83  H16  CAA  OAQ  107.37  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
 W83  CONST_01  CAK  CBA  CAJ  CAT   180.00   0.0  0
 W83  CONST_02  CAZ  CBA  CAJ  CAT     0.00   0.0  0
 W83  CONST_03  CAZ  CAH  CAF  CAT     0.00   0.0  0
 W83  CONST_04  CAU  CAK  CBA  CAJ   180.00   0.0  0
 W83  CONST_05  CAI  CAZ  CBA  CAJ   180.00   0.0  0
 W83  CONST_06  CAH  CAZ  CBA  CAJ     0.00   0.0  0
 W83  CONST_07  CAH  CAF  CAT  CAJ     0.00   0.0  0
 W83  CONST_08  CAG  CAU  CAK  CBA     0.00   0.0  0
 W83  CONST_09  CAF  CAT  CAJ  CBA     0.00   0.0  0
 W83  CONST_10  CAG  CAI  CAZ  CBA     0.00   0.0  0
 W83  CONST_11  CAF  CAH  CAZ  CBA     0.00   0.0  0
 W83  CONST_12  CAI  CAG  CAU  CAK     0.00   0.0  0
 W83  CONST_13  CAI  CAZ  CBA  CAK     0.00   0.0  0
 W83  CONST_14  CAH  CAZ  CBA  CAK   180.00   0.0  0
 W83  CONST_15  CAI  CAZ  CAH  CAF   180.00   0.0  0
 W83  CONST_16  CAG  CAI  CAZ  CAH   180.00   0.0  0
 W83  CONST_17  CAU  CAK  CBA  CAZ     0.00   0.0  0
 W83  CONST_18  CAU  CAG  CAI  CAZ     0.00   0.0  0
 W83  CONST_19  NAP  CAX  NAO  CAV     0.00   0.0  0
 W83  CONST_20  CAY  NAP  CAX  NAO     0.00   0.0  0
 W83  CONST_21  CAW  CAY  NAP  CAX     0.00   0.0  0
 W83  CONST_22  CBA  CAJ  CAT  CAL   180.00   0.0  0
 W83  CONST_23  CAH  CAF  CAT  CAL   180.00   0.0  0
 W83  CONST_24  OAR  CAU  CAK  CBA   180.00   0.0  0
 W83  CONST_25  OAR  CAU  CAG  CAI   180.00   0.0  0
 W83  CONST_26  OAC  CAX  NAO  CAV   180.00   0.0  0
 W83  CONST_27  OAD  CAY  NAP  CAX   180.00   0.0  0
 W83  CONST_28  CAY  NAP  CAX  OAC   180.00   0.0  0
 W83  CONST_29  H11  CAH  CAF  CAT   180.00   0.0  0
 W83  CONST_30  H9   CAK  CBA  CAJ     0.00   0.0  0
 W83  CONST_31  H10  CAF  CAT  CAJ   180.00   0.0  0
 W83  CONST_32  H12  CAI  CAZ  CBA   180.00   0.0  0
 W83  CONST_33  H13  CAG  CAU  CAK   180.00   0.0  0
 W83  CONST_34  H8   CAJ  CBA  CAK     0.00   0.0  0
 W83  CONST_35  H3   NAP  CAX  NAO   180.00   0.0  0
 W83  CONST_36  H2   NAO  CAX  NAP   180.00   0.0  0
 W83  CONST_37  H1   OAB  CAS  CAV   180.00   0.0  0
 W83  Var_01    CAW  CAV  CAS  OAB   156.17  30.0  2
 W83  Var_02    CAL  CAM  CAW  CAV    94.51  30.0  2
 W83  Var_03    CAT  CAL  CAM  CAW  -177.35  30.0  1
 W83  Var_04    CAJ  CAT  CAL  CAM  -102.38  30.0  1
 W83  Var_05    OAQ  CAN  OAR  CAU    70.98  30.0  1
 W83  Var_06    H16  CAA  OAQ  CAN   170.85  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
 W83  plan-1  CAS  0.020
 W83  plan-1  CAV  0.020
 W83  plan-1  NAO  0.020
 W83  plan-1  CAX  0.020
 W83  plan-1  OAC  0.020
 W83  plan-1  NAP  0.020
 W83  plan-1  CAY  0.020
 W83  plan-1  OAD  0.020
 W83  plan-1  CAW  0.020
 W83  plan-1  CAM  0.020
 W83  plan-1  H2   0.020
 W83  plan-1  H3   0.020
 W83  plan-2  CAL  0.020
 W83  plan-2  CAT  0.020
 W83  plan-2  CAJ  0.020
 W83  plan-2  CBA  0.020
 W83  plan-2  CAK  0.020
 W83  plan-2  CAF  0.020
 W83  plan-2  CAH  0.020
 W83  plan-2  CAZ  0.020
 W83  plan-2  CAI  0.020
 W83  plan-2  CAG  0.020
 W83  plan-2  CAU  0.020
 W83  plan-2  OAR  0.020
 W83  plan-2  H8   0.020
 W83  plan-2  H9   0.020
 W83  plan-2  H10  0.020
 W83  plan-2  H11  0.020
 W83  plan-2  H12  0.020
 W83  plan-2  H13  0.020
 W83  plan-3  OAB  0.020
 W83  plan-3  CAS  0.020
 W83  plan-3  OAE  0.020
 W83  plan-3  CAV  0.020
 W83  plan-3  H1   0.020

