# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:10:22 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 5-[2-(5-carboxynaphthalen-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: OC(=O)C1=C(CCc2ccc3c(cccc3C(O)=O)c2)C(=O)NC(=O)N1
#
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
 W6Y  W6Y  '5-[2-(5-carboxynaphthalen-2-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  38  26  .  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_W6Y
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
 W6Y  OAA  O  O      0  -0.590  -5.0565  -2.2162  -0.8171
 W6Y  CAQ  C  C      0   0.374  -5.6731  -1.2707  -0.2885
 W6Y  OAE  O  OC    -1  -0.592  -6.8641  -1.2785   0.0756
 W6Y  CAT  C  CR6    0  -0.119  -4.9218   0.0479  -0.0976
 W6Y  CAH  C  CR16   0  -0.307  -5.6615   1.2071  -0.1436
 W6Y  CAG  C  CR16   0  -0.250  -5.0695   2.4785  -0.0427
 W6Y  CAJ  C  CR16   0  -0.330  -3.7201   2.5911   0.1396
 W6Y  CAY  C  CR66   0   0.122  -2.9144   1.4332   0.2262
 W6Y  CAL  C  CR16   0  -0.396  -1.5200   1.5521   0.4466
 W6Y  CAZ  C  CR66   0   0.077  -3.5090   0.1450   0.0979
 W6Y  CAK  C  CR16   0  -0.314  -2.6470  -0.9769   0.2297
 W6Y  CAI  C  CR16   0  -0.293  -1.3068  -0.8237   0.4500
 W6Y  CAS  C  CR6    0   0.122  -0.7098   0.4550   0.5569
 W6Y  CAM  C  CH2    0  -0.495   0.7736   0.5717   0.7473
 W6Y  CAN  C  CH2    0  -0.477   1.5356   0.3263  -0.5633
 W6Y  CAU  C  C      0  -0.158   3.0194   0.2594  -0.3552
 W6Y  CAX  C  C      0   0.564   3.7375   1.5271  -0.3925
 W6Y  OAD  O  O      0  -0.467   3.2150   2.6156  -0.5703
 W6Y  NAP  N  NH1    0  -0.715   5.1057   1.4505  -0.2062
 W6Y  CAW  C  C      0   0.656   5.8437   0.3195   0.0243
 W6Y  OAC  O  O      0  -0.493   7.0510   0.3361   0.1788
 W6Y  NAO  N  NH1    0  -0.706   5.0910  -0.8090   0.0636
 W6Y  CAV  C  C      0   0.203   3.7339  -0.8645  -0.1024
 W6Y  CAR  C  C      0   0.415   3.1987  -2.3031   0.0430
 W6Y  OAF  O  O      0  -0.540   1.9767  -2.4516   0.1548
 W6Y  OAB  O  OC    -1  -0.586   4.0855  -3.1759   0.0511
 W6Y  H2   H  HCR6   0   0.246  -6.7335   1.1381  -0.2692
 W6Y  H3   H  HCR6   0   0.249  -5.6900   3.3634  -0.1066
 W6Y  H4   H  HCR6   0   0.248  -3.2533   3.5653   0.2273
 W6Y  H5   H  HCR6   0   0.237  -1.0989   2.5483   0.5384
 W6Y  H6   H  HCR6   0   0.250  -3.0614  -1.9687   0.1436
 W6Y  H7   H  HCR6   0   0.249  -0.6749  -1.7000   0.5398
 W6Y  H8   H  HCH2   0   0.238   1.0229   1.5615   1.1357
 W6Y  H9   H  HCH2   0   0.244   1.1097  -0.1587   1.4856
 W6Y  H10  H  HCH2   0   0.256   1.1782  -0.5918  -1.0213
 W6Y  H11  H  HCH2   0   0.238   1.3140   1.1390  -1.2578
 W6Y  H12  H  HNH1   0   0.420   5.6192   2.3222  -0.2328
 W6Y  H13  H  HNH1   0   0.416   5.5475  -1.6999   0.2229

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
 W6Y  OAC  CAW  double    1.217  0.020  1.217
 W6Y  CAW  NAO  single    1.357  0.020  1.357
 W6Y  CAW  NAP  single    1.370  0.020  1.370
 W6Y  NAO  CAV  single    1.368  0.020  1.368
 W6Y  OAF  CAR  deloc     1.236  0.020  1.236
 W6Y  OAB  CAR  deloc     1.244  0.020  1.244
 W6Y  CAR  CAV  single    1.542  0.020  1.542
 W6Y  NAP  CAX  single    1.383  0.020  1.383
 W6Y  CAV  CAU  double    1.356  0.020  1.356
 W6Y  CAX  CAU  single    1.457  0.020  1.457
 W6Y  CAX  OAD  double    1.220  0.020  1.220
 W6Y  CAU  CAN  single    1.500  0.020  1.500
 W6Y  CAN  CAM  single    1.536  0.020  1.536
 W6Y  OAA  CAQ  deloc     1.246  0.020  1.246
 W6Y  CAI  CAK  aromatic  1.367  0.020  1.367
 W6Y  CAI  CAS  aromatic  1.415  0.020  1.415
 W6Y  CAM  CAS  single    1.500  0.020  1.500
 W6Y  CAK  CAZ  aromatic  1.421  0.020  1.421
 W6Y  CAS  CAL  aromatic  1.368  0.020  1.368
 W6Y  CAQ  CAT  single    1.530  0.020  1.530
 W6Y  CAQ  OAE  deloc     1.245  0.020  1.245
 W6Y  CAZ  CAT  aromatic  1.430  0.020  1.430
 W6Y  CAZ  CAY  aromatic  1.425  0.020  1.425
 W6Y  CAL  CAY  aromatic  1.417  0.020  1.417
 W6Y  CAT  CAH  aromatic  1.376  0.020  1.376
 W6Y  CAY  CAJ  aromatic  1.413  0.020  1.413
 W6Y  CAH  CAG  aromatic  1.406  0.020  1.406
 W6Y  CAJ  CAG  aromatic  1.366  0.020  1.366
 W6Y  CAH  H2   single    0.930  0.020  1.080
 W6Y  CAG  H3   single    0.930  0.020  1.080
 W6Y  CAJ  H4   single    0.930  0.020  1.080
 W6Y  CAL  H5   single    0.930  0.020  1.080
 W6Y  CAK  H6   single    0.930  0.020  1.080
 W6Y  CAI  H7   single    0.930  0.020  1.080
 W6Y  CAM  H8   single    0.970  0.020  1.090
 W6Y  CAM  H9   single    0.970  0.020  1.090
 W6Y  CAN  H10  single    0.970  0.020  1.090
 W6Y  CAN  H11  single    0.970  0.020  1.090
 W6Y  NAP  H12  single    0.860  0.020  1.020
 W6Y  NAO  H13  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
 W6Y  CAT  CAQ  OAE  116.02  3.000
 W6Y  OAE  CAQ  OAA  126.32  3.000
 W6Y  CAT  CAQ  OAA  117.64  3.000
 W6Y  CAZ  CAT  CAH  118.60  3.000
 W6Y  CAH  CAT  CAQ  117.26  3.000
 W6Y  CAZ  CAT  CAQ  124.13  3.000
 W6Y  H2   CAH  CAG  118.90  3.000
 W6Y  H2   CAH  CAT  118.88  3.000
 W6Y  CAG  CAH  CAT  122.22  3.000
 W6Y  H3   CAG  CAJ  120.43  3.000
 W6Y  H3   CAG  CAH  119.58  3.000
 W6Y  CAJ  CAG  CAH  119.99  3.000
 W6Y  H4   CAJ  CAY  119.07  3.000
 W6Y  H4   CAJ  CAG  120.68  3.000
 W6Y  CAY  CAJ  CAG  120.25  3.000
 W6Y  CAZ  CAY  CAL  120.05  3.000
 W6Y  CAL  CAY  CAJ  120.12  3.000
 W6Y  CAZ  CAY  CAJ  119.83  3.000
 W6Y  H5   CAL  CAS  119.96  3.000
 W6Y  H5   CAL  CAY  118.17  3.000
 W6Y  CAS  CAL  CAY  121.87  3.000
 W6Y  CAK  CAZ  CAY  116.90  3.000
 W6Y  CAY  CAZ  CAT  119.09  3.000
 W6Y  CAK  CAZ  CAT  123.96  3.000
 W6Y  H6   CAK  CAI  119.52  3.000
 W6Y  H6   CAK  CAZ  119.06  3.000
 W6Y  CAI  CAK  CAZ  121.42  3.000
 W6Y  H7   CAI  CAS  118.57  3.000
 W6Y  H7   CAI  CAK  119.63  3.000
 W6Y  CAS  CAI  CAK  121.81  3.000
 W6Y  CAM  CAS  CAI  119.81  3.000
 W6Y  CAM  CAS  CAL  122.23  3.000
 W6Y  CAI  CAS  CAL  117.94  3.000
 W6Y  H9   CAM  H8   107.20  3.000
 W6Y  H9   CAM  CAN  108.51  3.000
 W6Y  H8   CAM  CAN  109.58  3.000
 W6Y  H9   CAM  CAS  109.77  3.000
 W6Y  H8   CAM  CAS  109.96  3.000
 W6Y  CAN  CAM  CAS  111.71  3.000
 W6Y  H11  CAN  H10  107.10  3.000
 W6Y  H11  CAN  CAU  108.80  3.000
 W6Y  H10  CAN  CAU  110.26  3.000
 W6Y  H11  CAN  CAM  108.86  3.000
 W6Y  H10  CAN  CAM  109.36  3.000
 W6Y  CAU  CAN  CAM  112.31  3.000
 W6Y  CAV  CAU  CAX  117.79  3.000
 W6Y  CAX  CAU  CAN  116.43  3.000
 W6Y  CAV  CAU  CAN  125.76  3.000
 W6Y  NAP  CAX  OAD  119.51  3.000
 W6Y  OAD  CAX  CAU  124.65  3.000
 W6Y  NAP  CAX  CAU  115.84  3.000
 W6Y  H12  NAP  CAW  116.24  3.000
 W6Y  H12  NAP  CAX  116.79  3.000
 W6Y  CAW  NAP  CAX  126.96  3.000
 W6Y  NAO  CAW  OAC  123.91  3.000
 W6Y  NAO  CAW  NAP  113.11  3.000
 W6Y  OAC  CAW  NAP  122.98  3.000
 W6Y  H13  NAO  CAV  115.48  3.000
 W6Y  H13  NAO  CAW  119.05  3.000
 W6Y  CAV  NAO  CAW  125.48  3.000
 W6Y  CAR  CAV  NAO  111.76  3.000
 W6Y  CAR  CAV  CAU  127.46  3.000
 W6Y  NAO  CAV  CAU  120.78  3.000
 W6Y  OAB  CAR  OAF  128.30  3.000
 W6Y  OAB  CAR  CAV  114.06  3.000
 W6Y  OAF  CAR  CAV  117.63  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
 W6Y  CONST_01  CAI  CAK  CAZ  CAT   180.00   0.0  0
 W6Y  CONST_02  CAL  CAY  CAZ  CAT   180.00   0.0  0
 W6Y  CONST_03  CAJ  CAY  CAZ  CAT     0.00   0.0  0
 W6Y  CONST_04  CAJ  CAG  CAH  CAT     0.00   0.0  0
 W6Y  CONST_05  CAK  CAZ  CAT  CAH   180.00   0.0  0
 W6Y  CONST_06  CAY  CAZ  CAT  CAH     0.00   0.0  0
 W6Y  CONST_07  CAY  CAJ  CAG  CAH     0.00   0.0  0
 W6Y  CONST_08  CAZ  CAT  CAH  CAG     0.00   0.0  0
 W6Y  CONST_09  CAZ  CAY  CAJ  CAG     0.00   0.0  0
 W6Y  CONST_10  CAL  CAY  CAJ  CAG   180.00   0.0  0
 W6Y  CONST_11  CAK  CAZ  CAY  CAJ   180.00   0.0  0
 W6Y  CONST_12  CAS  CAL  CAY  CAJ   180.00   0.0  0
 W6Y  CONST_13  CAI  CAK  CAZ  CAY     0.00   0.0  0
 W6Y  CONST_14  CAI  CAS  CAL  CAY     0.00   0.0  0
 W6Y  CONST_15  CAK  CAI  CAS  CAL     0.00   0.0  0
 W6Y  CONST_16  CAK  CAZ  CAY  CAL     0.00   0.0  0
 W6Y  CONST_17  CAS  CAI  CAK  CAZ     0.00   0.0  0
 W6Y  CONST_18  CAS  CAL  CAY  CAZ     0.00   0.0  0
 W6Y  CONST_19  CAW  NAP  CAX  CAU     0.00   0.0  0
 W6Y  CONST_20  NAO  CAW  NAP  CAX     0.00   0.0  0
 W6Y  CONST_21  CAV  NAO  CAW  NAP     0.00   0.0  0
 W6Y  CONST_22  CAK  CAZ  CAT  CAQ     0.00   0.0  0
 W6Y  CONST_23  CAY  CAZ  CAT  CAQ   180.00   0.0  0
 W6Y  CONST_24  CAG  CAH  CAT  CAQ   180.00   0.0  0
 W6Y  CONST_25  CAM  CAS  CAL  CAY   180.00   0.0  0
 W6Y  CONST_26  CAM  CAS  CAI  CAK   180.00   0.0  0
 W6Y  CONST_27  OAC  CAW  NAP  CAX   180.00   0.0  0
 W6Y  CONST_28  CAW  NAP  CAX  OAD   180.00   0.0  0
 W6Y  CONST_29  CAV  NAO  CAW  OAC   180.00   0.0  0
 W6Y  CONST_30  H6   CAK  CAZ  CAT     0.00   0.0  0
 W6Y  CONST_31  H3   CAG  CAH  CAT   180.00   0.0  0
 W6Y  CONST_32  H4   CAJ  CAG  CAH   180.00   0.0  0
 W6Y  CONST_33  H5   CAL  CAY  CAJ     0.00   0.0  0
 W6Y  CONST_34  H2   CAH  CAG  CAJ   180.00   0.0  0
 W6Y  CONST_35  H7   CAI  CAS  CAL   180.00   0.0  0
 W6Y  CONST_36  H12  NAP  CAX  CAU   180.00   0.0  0
 W6Y  CONST_37  H13  NAO  CAW  NAP   180.00   0.0  0
 W6Y  Var_01    CAZ  CAT  CAQ  OAA   -29.28  30.0  2
 W6Y  Var_02    CAN  CAM  CAS  CAL  -101.44  30.0  2
 W6Y  Var_03    CAU  CAN  CAM  CAS  -172.42  30.0  1
 W6Y  Var_04    CAV  CAU  CAN  CAM    91.00  30.0  3
 W6Y  Var_05    OAF  CAR  CAV  CAU   -12.44  30.0  2

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
 W6Y  plan-1  CAN  0.020
 W6Y  plan-1  CAU  0.020
 W6Y  plan-1  CAX  0.020
 W6Y  plan-1  OAD  0.020
 W6Y  plan-1  NAP  0.020
 W6Y  plan-1  CAW  0.020
 W6Y  plan-1  OAC  0.020
 W6Y  plan-1  NAO  0.020
 W6Y  plan-1  CAV  0.020
 W6Y  plan-1  CAR  0.020
 W6Y  plan-1  H12  0.020
 W6Y  plan-1  H13  0.020
 W6Y  plan-2  CAQ  0.020
 W6Y  plan-2  CAT  0.020
 W6Y  plan-2  CAH  0.020
 W6Y  plan-2  CAG  0.020
 W6Y  plan-2  CAJ  0.020
 W6Y  plan-2  CAY  0.020
 W6Y  plan-2  CAL  0.020
 W6Y  plan-2  CAZ  0.020
 W6Y  plan-2  CAK  0.020
 W6Y  plan-2  CAI  0.020
 W6Y  plan-2  CAS  0.020
 W6Y  plan-2  CAM  0.020
 W6Y  plan-2  H2   0.020
 W6Y  plan-2  H3   0.020
 W6Y  plan-2  H4   0.020
 W6Y  plan-2  H5   0.020
 W6Y  plan-2  H6   0.020
 W6Y  plan-2  H7   0.020
 W6Y  plan-3  OAA  0.020
 W6Y  plan-3  CAQ  0.020
 W6Y  plan-3  OAE  0.020
 W6Y  plan-3  CAT  0.020
 W6Y  plan-4  CAV  0.020
 W6Y  plan-4  CAR  0.020
 W6Y  plan-4  OAF  0.020
 W6Y  plan-4  OAB  0.020

