# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 10:25:32 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  40  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 PERFECT
;

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  -0.438  -5.1887  -2.1653  -0.8921
 W6Y  CAQ  C  C     0   0.493  -5.6742  -1.1979  -0.3557
 W6Y  OAE  O  OH1   0  -0.590  -6.9362  -1.1664   0.0555
 W6Y  CAT  C  CR6   0  -0.093  -4.9637   0.0831  -0.1044
 W6Y  CAH  C  CR16  0  -0.270  -5.6937   1.2503  -0.1298
 W6Y  CAG  C  CR16  0  -0.250  -5.0739   2.5022   0.0134
 W6Y  CAJ  C  CR16  0  -0.304  -3.7231   2.5747   0.2027
 W6Y  CAY  C  CR66  0   0.124  -2.9367   1.4020   0.2593
 W6Y  CAL  C  CR16  0  -0.388  -1.5426   1.4941   0.4835
 W6Y  CAZ  C  CR66  0   0.119  -3.5499   0.1289   0.0984
 W6Y  CAK  C  CR16  0  -0.316  -2.7136  -1.0118   0.2016
 W6Y  CAI  C  CR16  0  -0.281  -1.3716  -0.8837   0.4279
 W6Y  CAS  C  CR6   0   0.132  -0.7532   0.3800   0.5672
 W6Y  CAM  C  CH2   0  -0.504   0.7300   0.4662   0.7745
 W6Y  CAN  C  CH2   0  -0.505   1.4933   0.1876  -0.5296
 W6Y  CAU  C  CR6   0  -0.119   2.9779   0.2001  -0.3321
 W6Y  CAX  C  CR6   0   0.587   3.6328   1.5104  -0.3989
 W6Y  OAD  O  O     0  -0.440   3.0405   2.5548  -0.5876
 W6Y  NAP  N  NR16  0  -0.717   5.0009   1.5051  -0.2305
 W6Y  CAW  C  CR6   0   0.671   5.8047   0.4193  -0.0015
 W6Y  OAC  O  O     0  -0.472   7.0061   0.5009   0.1424
 W6Y  NAO  N  NR16  0  -0.732   5.1227  -0.7609   0.0512
 W6Y  CAV  C  CR6   0   0.286   3.7633  -0.8732  -0.0954
 W6Y  CAR  C  C     0   0.520   3.2271  -2.2673   0.0298
 W6Y  OAF  O  O     0  -0.396   2.1088  -2.5277   0.3816
 W6Y  OAB  O  OH1   0  -0.588   4.1457  -3.1615  -0.2840
 W6Y  H1   H  HOH1  0   0.487  -7.3792  -1.9917  -0.1925
 W6Y  H2   H  HCR6  0   0.274  -6.7633   1.2215  -0.2839
 W6Y  H3   H  HCR6  0   0.267  -5.6739   3.4008  -0.0301
 W6Y  H4   H  HCR6  0   0.264  -3.2369   3.5359   0.3180
 W6Y  H5   H  HCR6  0   0.250  -1.1062   2.4800   0.6017
 W6Y  H6   H  HCR6  0   0.258  -3.1280  -2.0029   0.1075
 W6Y  H7   H  HCR6  0   0.254  -0.7630  -1.7767   0.5102
 W6Y  H8   H  HCH2  0   0.255   0.9960   1.4560   1.1497
 W6Y  H9   H  HCH2  0   0.258   1.0387  -0.2573   1.5317
 W6Y  H10  H  HCH2  0   0.266   1.1670  -0.7598  -0.9540
 W6Y  H11  H  HCH2  0   0.265   1.2373   0.9574  -1.2591
 W6Y  H12  H  HNR6  0   0.431   5.4678   2.4030  -0.2734
 W6Y  H13  H  HNR6  0   0.439   5.6767  -1.5863   0.2327
 W6Y  H14  H  HOH1  0   0.504   3.8058  -4.0621  -0.1628

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    1.213  0.020  1.213
 W6Y  CAW  NAO  single    1.364  0.020  1.364
 W6Y  CAW  NAP  single    1.370  0.020  1.370
 W6Y  NAO  CAV  single    1.372  0.020  1.372
 W6Y  OAF  CAR  double    1.201  0.020  1.201
 W6Y  OAB  CAR  single    1.320  0.020  1.320
 W6Y  CAR  CAV  single    1.499  0.020  1.499
 W6Y  NAP  CAX  single    1.378  0.020  1.378
 W6Y  CAV  CAU  double    1.351  0.020  1.351
 W6Y  CAX  CAU  single    1.466  0.020  1.466
 W6Y  CAX  OAD  double    1.215  0.020  1.215
 W6Y  CAU  CAN  single    1.498  0.020  1.498
 W6Y  CAN  CAM  single    1.536  0.020  1.536
 W6Y  OAA  CAQ  double    1.208  0.020  1.208
 W6Y  CAI  CAK  aromatic  1.367  0.020  1.367
 W6Y  CAI  CAS  aromatic  1.414  0.020  1.414
 W6Y  CAM  CAS  single    1.500  0.020  1.500
 W6Y  CAK  CAZ  aromatic  1.418  0.020  1.418
 W6Y  CAS  CAL  aromatic  1.368  0.020  1.368
 W6Y  CAQ  CAT  single    1.486  0.020  1.486
 W6Y  CAQ  OAE  single    1.328  0.020  1.328
 W6Y  CAZ  CAT  aromatic  1.429  0.020  1.429
 W6Y  CAZ  CAY  aromatic  1.422  0.020  1.422
 W6Y  CAL  CAY  aromatic  1.415  0.020  1.415
 W6Y  CAT  CAH  aromatic  1.377  0.020  1.377
 W6Y  CAY  CAJ  aromatic  1.413  0.020  1.413
 W6Y  CAH  CAG  aromatic  1.404  0.020  1.404
 W6Y  CAJ  CAG  aromatic  1.366  0.020  1.366
 W6Y  OAE  H1   single    0.850  0.020  0.980
 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
 W6Y  OAB  H14  single    0.850  0.020  0.980

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  112.43  3.000
 W6Y  OAE  CAQ  OAA  122.59  3.000
 W6Y  CAT  CAQ  OAA  124.97  3.000
 W6Y  H1   OAE  CAQ  109.58  3.000
 W6Y  CAZ  CAT  CAH  120.00  3.000
 W6Y  CAH  CAT  CAQ  118.30  3.000
 W6Y  CAZ  CAT  CAQ  121.64  3.000
 W6Y  H2   CAH  CAG  118.36  3.000
 W6Y  H2   CAH  CAT  120.31  3.000
 W6Y  CAG  CAH  CAT  121.32  3.000
 W6Y  H3   CAG  CAJ  120.67  3.000
 W6Y  H3   CAG  CAH  119.46  3.000
 W6Y  CAJ  CAG  CAH  119.87  3.000
 W6Y  H4   CAJ  CAY  118.83  3.000
 W6Y  H4   CAJ  CAG  120.38  3.000
 W6Y  CAY  CAJ  CAG  120.79  3.000
 W6Y  CAZ  CAY  CAL  120.06  3.000
 W6Y  CAL  CAY  CAJ  120.04  3.000
 W6Y  CAZ  CAY  CAJ  119.89  3.000
 W6Y  H5   CAL  CAS  120.09  3.000
 W6Y  H5   CAL  CAY  118.22  3.000
 W6Y  CAS  CAL  CAY  121.68  3.000
 W6Y  CAK  CAZ  CAY  117.23  3.000
 W6Y  CAY  CAZ  CAT  118.12  3.000
 W6Y  CAK  CAZ  CAT  124.61  3.000
 W6Y  H6   CAK  CAI  118.55  3.000
 W6Y  H6   CAK  CAZ  120.42  3.000
 W6Y  CAI  CAK  CAZ  121.03  3.000
 W6Y  H7   CAI  CAS  118.90  3.000
 W6Y  H7   CAI  CAK  119.12  3.000
 W6Y  CAS  CAI  CAK  121.98  3.000
 W6Y  CAM  CAS  CAI  119.84  3.000
 W6Y  CAM  CAS  CAL  122.15  3.000
 W6Y  CAI  CAS  CAL  118.00  3.000
 W6Y  H9   CAM  H8   107.08  3.000
 W6Y  H9   CAM  CAN  109.15  3.000
 W6Y  H8   CAM  CAN  109.59  3.000
 W6Y  H9   CAM  CAS  109.71  3.000
 W6Y  H8   CAM  CAS  109.91  3.000
 W6Y  CAN  CAM  CAS  111.31  3.000
 W6Y  H11  CAN  H10  106.45  3.000
 W6Y  H11  CAN  CAU  108.35  3.000
 W6Y  H10  CAN  CAU  110.85  3.000
 W6Y  H11  CAN  CAM  108.84  3.000
 W6Y  H10  CAN  CAM  109.87  3.000
 W6Y  CAU  CAN  CAM  112.27  3.000
 W6Y  CAV  CAU  CAX  117.28  3.000
 W6Y  CAX  CAU  CAN  116.37  3.000
 W6Y  CAV  CAU  CAN  126.35  3.000
 W6Y  NAP  CAX  OAD  120.39  3.000
 W6Y  OAD  CAX  CAU  123.87  3.000
 W6Y  NAP  CAX  CAU  115.74  3.000
 W6Y  H12  NAP  CAW  116.04  3.000
 W6Y  H12  NAP  CAX  116.68  3.000
 W6Y  CAW  NAP  CAX  127.28  3.000
 W6Y  NAO  CAW  OAC  123.29  3.000
 W6Y  NAO  CAW  NAP  113.50  3.000
 W6Y  OAC  CAW  NAP  123.21  3.000
 W6Y  H13  NAO  CAV  119.71  3.000
 W6Y  H13  NAO  CAW  116.07  3.000
 W6Y  CAV  NAO  CAW  124.20  3.000
 W6Y  CAR  CAV  NAO  114.94  3.000
 W6Y  CAR  CAV  CAU  123.07  3.000
 W6Y  NAO  CAV  CAU  121.99  3.000
 W6Y  OAB  CAR  OAF  124.81  3.000
 W6Y  OAB  CAR  CAV  111.18  3.000
 W6Y  OAF  CAR  CAV  124.01  3.000
 W6Y  H14  OAB  CAR  110.81  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  CONST_38  H1   OAE  CAQ  CAT   180.00   0.0  0
 W6Y  CONST_39  H14  OAB  CAR  CAV   180.00   0.0  0
 W6Y  Var_01    CAZ  CAT  CAQ  OAA   -29.09  30.0  2
 W6Y  Var_02    CAN  CAM  CAS  CAL  -103.86  30.0  1
 W6Y  Var_03    CAU  CAN  CAM  CAS  -177.12  30.0  1
 W6Y  Var_04    CAV  CAU  CAN  CAM    94.58  30.0  2
 W6Y  Var_05    OAF  CAR  CAV  CAU   -26.28  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-3  H1   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
 W6Y  plan-4  H14  0.020

