# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 07:00:37 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 5-[2-(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: OC(=O)C1=C(CCc2ccc3ccccc3c2)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
 W7H  W7H  '5-[2-(naphthalen-2-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  37  23  .  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_W7H
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
 W7H  OAA  O  OH1   0  -0.589  -3.8041  -2.9271   0.3080
 W7H  CAP  C  C     0   0.520  -2.7476  -2.1956   0.0047
 W7H  OAD  O  O     0  -0.396  -1.6752  -2.6372  -0.3060
 W7H  CAS  C  CR6   0   0.283  -3.0622  -0.7316   0.0791
 W7H  NAN  N  NR16  0  -0.732  -4.3844  -0.4127  -0.1037
 W7H  CAT  C  CR6   0   0.671  -4.8727   0.8609  -0.1079
 W7H  OAB  O  O     0  -0.472  -6.0428   1.1251  -0.2863
 W7H  NAO  N  NR16  0  -0.716  -3.9129   1.8152   0.1064
 W7H  CAU  C  CR6   0   0.587  -2.5658   1.6113   0.3149
 W7H  OAC  O  O     0  -0.440  -1.8221   2.5565   0.4901
 W7H  CAR  C  CR6   0  -0.117  -2.1232   0.2135   0.3036
 W7H  CAM  C  CH2   0  -0.504  -0.6616  -0.0183   0.5313
 W7H  CAL  C  CH2   0  -0.505   0.1563   0.1289  -0.7617
 W7H  CAQ  C  CR6   0   0.131   1.6182  -0.1038  -0.5144
 W7H  CAK  C  CR16  0  -0.394   2.5141   0.9325  -0.4799
 W7H  CAW  C  CR66  0   0.139   3.8869   0.7162  -0.2125
 W7H  CAI  C  CR16  0  -0.316   4.8196   1.7799  -0.1788
 W7H  CAF  C  CR16  0  -0.259   6.1417   1.5410   0.0826
 W7H  CAE  C  CR16  0  -0.261   6.5951   0.2266   0.3227
 W7H  CAH  C  CR16  0  -0.309   5.7152  -0.8217   0.2966
 W7H  CAV  C  CR66  0   0.096   4.3436  -0.6049   0.0292
 W7H  CAJ  C  CR16  0  -0.299   3.4050  -1.6641  -0.0100
 W7H  CAG  C  CR16  0  -0.298   2.0870  -1.4197  -0.2734
 W7H  H1   H  HOH1  0   0.504  -3.6049  -3.8726   0.2210
 W7H  H2   H  HNR6  0   0.431  -4.2335   2.7763   0.1053
 W7H  H4   H  HCH2  0   0.264  -0.3056   0.7145   1.2573
 W7H  H5   H  HCH2  0   0.266  -0.4851  -0.9971   0.9703
 W7H  H6   H  HCH2  0   0.255  -0.2162  -0.5831  -1.5012
 W7H  H7   H  HCH2  0   0.254   0.0055   1.1274  -1.1748
 W7H  H8   H  HCR6  0   0.245   2.1746   1.9462  -0.6643
 W7H  H9   H  HCR6  0   0.253   4.4722   2.7892  -0.3645
 W7H  H10  H  HCR6  0   0.257   6.8468   2.3615   0.1065
 W7H  H11  H  HCR6  0   0.257   7.6433   0.0509   0.5264
 W7H  H12  H  HCR6  0   0.254   6.0609  -1.8317   0.4817
 W7H  H13  H  HCR6  0   0.253   3.7465  -2.6764   0.1703
 W7H  H14  H  HCR6  0   0.251   1.3819  -2.2422  -0.3040
 W7H  H15  H  HNR6  0   0.439  -5.0588  -1.1470  -0.2677

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
 W7H  CAI  CAF  aromatic  1.369  0.020  1.369
 W7H  CAI  CAW  aromatic  1.415  0.020  1.415
 W7H  CAF  CAE  aromatic  1.411  0.020  1.411
 W7H  CAE  CAH  aromatic  1.369  0.020  1.369
 W7H  CAW  CAK  aromatic  1.415  0.020  1.415
 W7H  CAW  CAV  aromatic  1.419  0.020  1.419
 W7H  CAK  CAQ  aromatic  1.370  0.020  1.370
 W7H  CAH  CAV  aromatic  1.414  0.020  1.414
 W7H  CAV  CAJ  aromatic  1.416  0.020  1.416
 W7H  CAQ  CAL  single    1.501  0.020  1.501
 W7H  CAQ  CAG  aromatic  1.418  0.020  1.418
 W7H  CAL  CAM  single    1.537  0.020  1.537
 W7H  CAJ  CAG  aromatic  1.366  0.020  1.366
 W7H  CAM  CAR  single    1.497  0.020  1.497
 W7H  OAC  CAU  double    1.215  0.020  1.215
 W7H  CAR  CAU  single    1.466  0.020  1.466
 W7H  CAR  CAS  double    1.351  0.020  1.351
 W7H  CAU  NAO  single    1.378  0.020  1.378
 W7H  OAD  CAP  double    1.201  0.020  1.201
 W7H  CAS  CAP  single    1.499  0.020  1.499
 W7H  CAS  NAN  single    1.372  0.020  1.372
 W7H  CAP  OAA  single    1.320  0.020  1.320
 W7H  NAO  CAT  single    1.370  0.020  1.370
 W7H  NAN  CAT  single    1.364  0.020  1.364
 W7H  CAT  OAB  double    1.213  0.020  1.213
 W7H  OAA  H1   single    0.850  0.020  0.980
 W7H  NAO  H2   single    0.860  0.020  1.020
 W7H  CAM  H4   single    0.970  0.020  1.090
 W7H  CAM  H5   single    0.970  0.020  1.090
 W7H  CAL  H6   single    0.970  0.020  1.090
 W7H  CAL  H7   single    0.970  0.020  1.090
 W7H  CAK  H8   single    0.930  0.020  1.080
 W7H  CAI  H9   single    0.930  0.020  1.080
 W7H  CAF  H10  single    0.930  0.020  1.080
 W7H  CAE  H11  single    0.930  0.020  1.080
 W7H  CAH  H12  single    0.930  0.020  1.080
 W7H  CAJ  H13  single    0.930  0.020  1.080
 W7H  CAG  H14  single    0.930  0.020  1.080
 W7H  NAN  H15  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
 W7H  H1   OAA  CAP  110.80  3.000
 W7H  CAS  CAP  OAD  124.01  3.000
 W7H  CAS  CAP  OAA  111.20  3.000
 W7H  OAD  CAP  OAA  124.78  3.000
 W7H  CAR  CAS  NAN  121.95  3.000
 W7H  NAN  CAS  CAP  114.99  3.000
 W7H  CAR  CAS  CAP  123.06  3.000
 W7H  H15  NAN  CAT  116.05  3.000
 W7H  H15  NAN  CAS  119.72  3.000
 W7H  CAT  NAN  CAS  124.22  3.000
 W7H  NAO  CAT  OAB  123.17  3.000
 W7H  OAB  CAT  NAN  123.32  3.000
 W7H  NAO  CAT  NAN  113.52  3.000
 W7H  H2   NAO  CAU  116.73  3.000
 W7H  H2   NAO  CAT  116.03  3.000
 W7H  CAU  NAO  CAT  127.24  3.000
 W7H  CAR  CAU  OAC  123.91  3.000
 W7H  CAR  CAU  NAO  115.78  3.000
 W7H  OAC  CAU  NAO  120.32  3.000
 W7H  CAM  CAR  CAU  116.17  3.000
 W7H  CAU  CAR  CAS  117.28  3.000
 W7H  CAM  CAR  CAS  126.54  3.000
 W7H  H5   CAM  H4   106.44  3.000
 W7H  H5   CAM  CAL  109.85  3.000
 W7H  H4   CAM  CAL  108.77  3.000
 W7H  H5   CAM  CAR  111.06  3.000
 W7H  H4   CAM  CAR  108.40  3.000
 W7H  CAL  CAM  CAR  112.13  3.000
 W7H  H7   CAL  H6   107.05  3.000
 W7H  H7   CAL  CAQ  109.81  3.000
 W7H  H6   CAL  CAQ  110.04  3.000
 W7H  H7   CAL  CAM  109.42  3.000
 W7H  H6   CAL  CAM  109.01  3.000
 W7H  CAQ  CAL  CAM  111.40  3.000
 W7H  CAG  CAQ  CAK  118.78  3.000
 W7H  CAG  CAQ  CAL  119.61  3.000
 W7H  CAK  CAQ  CAL  121.58  3.000
 W7H  H8   CAK  CAW  118.58  3.000
 W7H  H8   CAK  CAQ  119.85  3.000
 W7H  CAW  CAK  CAQ  121.56  3.000
 W7H  CAV  CAW  CAI  118.94  3.000
 W7H  CAV  CAW  CAK  119.13  3.000
 W7H  CAI  CAW  CAK  121.94  3.000
 W7H  H9   CAI  CAF  120.33  3.000
 W7H  H9   CAI  CAW  119.00  3.000
 W7H  CAF  CAI  CAW  120.67  3.000
 W7H  H10  CAF  CAE  119.55  3.000
 W7H  H10  CAF  CAI  120.09  3.000
 W7H  CAE  CAF  CAI  120.36  3.000
 W7H  H11  CAE  CAH  120.12  3.000
 W7H  H11  CAE  CAF  119.64  3.000
 W7H  CAH  CAE  CAF  120.24  3.000
 W7H  H12  CAH  CAV  118.99  3.000
 W7H  H12  CAH  CAE  120.37  3.000
 W7H  CAV  CAH  CAE  120.64  3.000
 W7H  CAJ  CAV  CAH  122.24  3.000
 W7H  CAJ  CAV  CAW  118.60  3.000
 W7H  CAH  CAV  CAW  119.16  3.000
 W7H  H13  CAJ  CAG  120.22  3.000
 W7H  H13  CAJ  CAV  119.04  3.000
 W7H  CAG  CAJ  CAV  120.74  3.000
 W7H  H14  CAG  CAJ  119.83  3.000
 W7H  H14  CAG  CAQ  118.98  3.000
 W7H  CAJ  CAG  CAQ  121.19  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
 W7H  CONST_01  CAI  CAW  CAK  CAQ   180.00   0.0  0
 W7H  CONST_02  CAV  CAW  CAK  CAQ     0.00   0.0  0
 W7H  CONST_03  CAV  CAJ  CAG  CAQ     0.00   0.0  0
 W7H  CONST_04  CAF  CAI  CAW  CAK   180.00   0.0  0
 W7H  CONST_05  CAH  CAV  CAW  CAK   180.00   0.0  0
 W7H  CONST_06  CAJ  CAV  CAW  CAK     0.00   0.0  0
 W7H  CONST_07  CAJ  CAG  CAQ  CAK     0.00   0.0  0
 W7H  CONST_08  CAE  CAF  CAI  CAW     0.00   0.0  0
 W7H  CONST_09  CAG  CAQ  CAK  CAW     0.00   0.0  0
 W7H  CONST_10  CAE  CAH  CAV  CAW     0.00   0.0  0
 W7H  CONST_11  CAG  CAJ  CAV  CAW     0.00   0.0  0
 W7H  CONST_12  CAH  CAE  CAF  CAI     0.00   0.0  0
 W7H  CONST_13  CAH  CAV  CAW  CAI     0.00   0.0  0
 W7H  CONST_14  CAJ  CAV  CAW  CAI   180.00   0.0  0
 W7H  CONST_15  CAV  CAW  CAI  CAF     0.00   0.0  0
 W7H  CONST_16  CAV  CAH  CAE  CAF     0.00   0.0  0
 W7H  CONST_17  CAJ  CAV  CAH  CAE   180.00   0.0  0
 W7H  CONST_18  CAG  CAJ  CAV  CAH   180.00   0.0  0
 W7H  CONST_19  NAO  CAT  NAN  CAS     0.00   0.0  0
 W7H  CONST_20  CAU  NAO  CAT  NAN     0.00   0.0  0
 W7H  CONST_21  CAR  CAU  NAO  CAT     0.00   0.0  0
 W7H  CONST_22  CAW  CAK  CAQ  CAL   180.00   0.0  0
 W7H  CONST_23  CAJ  CAG  CAQ  CAL   180.00   0.0  0
 W7H  CONST_24  OAB  CAT  NAN  CAS   180.00   0.0  0
 W7H  CONST_25  OAC  CAU  NAO  CAT   180.00   0.0  0
 W7H  CONST_26  CAU  NAO  CAT  OAB   180.00   0.0  0
 W7H  CONST_27  H13  CAJ  CAG  CAQ   180.00   0.0  0
 W7H  CONST_28  H9   CAI  CAW  CAK     0.00   0.0  0
 W7H  CONST_29  H14  CAG  CAQ  CAK   180.00   0.0  0
 W7H  CONST_30  H10  CAF  CAI  CAW   180.00   0.0  0
 W7H  CONST_31  H12  CAH  CAV  CAW   180.00   0.0  0
 W7H  CONST_32  H11  CAE  CAF  CAI   180.00   0.0  0
 W7H  CONST_33  H8   CAK  CAW  CAI     0.00   0.0  0
 W7H  CONST_34  H2   NAO  CAT  NAN   180.00   0.0  0
 W7H  CONST_35  H15  NAN  CAT  NAO   180.00   0.0  0
 W7H  CONST_36  H1   OAA  CAP  CAS   180.00   0.0  0
 W7H  Var_01    CAR  CAS  CAP  OAA   155.01  30.0  2
 W7H  Var_02    CAL  CAM  CAR  CAS    95.61  30.0  2
 W7H  Var_03    CAQ  CAL  CAM  CAR   179.88  30.0  1
 W7H  Var_04    CAK  CAQ  CAL  CAM  -105.20  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
 W7H  plan-1  CAP  0.020
 W7H  plan-1  CAS  0.020
 W7H  plan-1  NAN  0.020
 W7H  plan-1  CAT  0.020
 W7H  plan-1  OAB  0.020
 W7H  plan-1  NAO  0.020
 W7H  plan-1  CAU  0.020
 W7H  plan-1  OAC  0.020
 W7H  plan-1  CAR  0.020
 W7H  plan-1  CAM  0.020
 W7H  plan-1  H2   0.020
 W7H  plan-1  H15  0.020
 W7H  plan-2  CAL  0.020
 W7H  plan-2  CAQ  0.020
 W7H  plan-2  CAK  0.020
 W7H  plan-2  CAW  0.020
 W7H  plan-2  CAI  0.020
 W7H  plan-2  CAF  0.020
 W7H  plan-2  CAE  0.020
 W7H  plan-2  CAH  0.020
 W7H  plan-2  CAV  0.020
 W7H  plan-2  CAJ  0.020
 W7H  plan-2  CAG  0.020
 W7H  plan-2  H8   0.020
 W7H  plan-2  H9   0.020
 W7H  plan-2  H10  0.020
 W7H  plan-2  H11  0.020
 W7H  plan-2  H12  0.020
 W7H  plan-2  H13  0.020
 W7H  plan-2  H14  0.020
 W7H  plan-3  OAA  0.020
 W7H  plan-3  CAP  0.020
 W7H  plan-3  OAD  0.020
 W7H  plan-3  CAS  0.020
 W7H  plan-3  H1   0.020

