# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 17:26:34 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-[2-(7-methoxynaphthalen-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: COc1ccc2ccc(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
 JDB  JDB  '5-[2-(7-methoxynaphthalen-2-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  40  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JDB
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
 JDB  OAJ  O  OC    -1  -0.585  -4.7598  -2.6735  -0.2011
 JDB  CAI  C  C      0   0.417  -3.6697  -2.0848  -0.0823
 JDB  OAK  O  O      0  -0.540  -2.5338  -2.5721  -0.0763
 JDB  C4   C  CR6    0   0.201  -3.7960  -0.5538   0.0558
 JDB  N3   N  NR16   0  -0.707  -5.0827  -0.1347  -0.1436
 JDB  C2   C  CR6    0   0.656  -5.5065   1.1538  -0.1118
 JDB  O2   O  O      0  -0.492  -6.6609   1.4940  -0.2942
 JDB  N1   N  NR16   0  -0.715  -4.4977   2.0449   0.1438
 JDB  C6   C  CR6    0   0.563  -3.1652   1.7503   0.3672
 JDB  O6   O  O      0  -0.466  -2.3766   2.6590   0.5719
 JDB  C5   C  CR6    0  -0.157  -2.8117   0.3364   0.3331
 JDB  CAL  C  CH2    0  -0.478  -1.3676   0.0063   0.5639
 JDB  CAM  C  CH2    0  -0.496  -0.5591   0.0147  -0.7411
 JDB  CAN  C  CR6    0   0.129   0.8682  -0.3887  -0.5138
 JDB  CAS  C  CR16   0  -0.406   1.8827   0.5313  -0.5009
 JDB  CAR  C  CR66   0   0.166   3.2270   0.1523  -0.2566
 JDB  CAT  C  CR16   0  -0.437   4.2742   1.0940  -0.2460
 JDB  CAW  C  CR6    0   0.394   5.5731   0.7035  -0.0090
 JDB  OAX  O  O2     0  -0.474   6.5111   1.6710  -0.0199
 JDB  CAY  C  CH3    0  -0.438   7.8591   1.3256   0.2279
 JDB  CAV  C  CR16   0  -0.382   5.8656  -0.6596   0.2298
 JDB  CAU  C  CR16   0  -0.294   4.8561  -1.5861   0.2215
 JDB  CAQ  C  CR66   0   0.076   3.5175  -1.2159  -0.0192
 JDB  CAP  C  CR16   0  -0.293   2.4573  -2.1545  -0.0353
 JDB  CAO  C  CR16   0  -0.311   1.1741  -1.7539  -0.2733
 JDB  H2   H  HNR6   0   0.420  -4.7583   3.0228   0.1671
 JDB  H4   H  HCH2   0   0.240  -0.9383   0.7409   1.2471
 JDB  H5   H  HCH2   0   0.255  -1.2739  -0.9665   1.0368
 JDB  H6   H  HCH2   0   0.246  -1.0303  -0.6759  -1.4432
 JDB  H7   H  HCH2   0   0.241  -0.5986   1.0095  -1.1896
 JDB  H8   H  HCR6   0   0.240   1.6631   1.5779  -0.6837
 JDB  H9   H  HCR6   0   0.255   4.0539   2.1398  -0.4274
 JDB  H10  H  HCH3   0   0.229   7.9976   0.8952   1.2230
 JDB  H11  H  HCH3   0   0.229   8.2489   0.6265  -0.5163
 JDB  H12  H  HCH3   0   0.260   8.4286   2.2499   0.1670
 JDB  H13  H  HCR6   0   0.281   6.8781  -0.9885   0.4191
 JDB  H14  H  HCR6   0   0.259   5.0907  -2.6277   0.4050
 JDB  H15  H  HCR6   0   0.250   2.6794  -3.2005   0.1414
 JDB  H16  H  HCR6   0   0.251   0.3702  -2.4803  -0.2846
 JDB  H17  H  HNR6   0   0.417  -5.7550  -0.8748  -0.3130

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
 JDB  CAY  OAX  single    1.413  0.020  1.413
 JDB  OAX  CAW  single    1.348  0.020  1.348
 JDB  CAW  CAT  aromatic  1.377  0.020  1.377
 JDB  CAW  CAV  aromatic  1.414  0.020  1.414
 JDB  CAT  CAR  aromatic  1.408  0.020  1.408
 JDB  CAR  CAS  aromatic  1.418  0.020  1.418
 JDB  CAR  CAQ  aromatic  1.419  0.020  1.419
 JDB  CAV  CAU  aromatic  1.370  0.020  1.370
 JDB  CAS  CAN  aromatic  1.370  0.020  1.370
 JDB  CAU  CAQ  aromatic  1.410  0.020  1.410
 JDB  CAQ  CAP  aromatic  1.416  0.020  1.416
 JDB  CAN  CAM  single    1.500  0.020  1.500
 JDB  CAN  CAO  aromatic  1.420  0.020  1.420
 JDB  CAM  CAL  single    1.535  0.020  1.535
 JDB  CAP  CAO  aromatic  1.365  0.020  1.365
 JDB  CAL  C5   single    1.499  0.020  1.499
 JDB  O6   C6   double    1.220  0.020  1.220
 JDB  C5   C6   single    1.458  0.020  1.458
 JDB  C5   C4   double    1.356  0.020  1.356
 JDB  C6   N1   single    1.383  0.020  1.383
 JDB  OAK  CAI  deloc     1.236  0.020  1.236
 JDB  C4   CAI  single    1.542  0.020  1.542
 JDB  C4   N3   single    1.368  0.020  1.368
 JDB  CAI  OAJ  deloc     1.245  0.020  1.245
 JDB  N1   C2   single    1.370  0.020  1.370
 JDB  N3   C2   single    1.357  0.020  1.357
 JDB  C2   O2   double    1.217  0.020  1.217
 JDB  N1   H2   single    0.860  0.020  1.020
 JDB  CAL  H4   single    0.970  0.020  1.090
 JDB  CAL  H5   single    0.970  0.020  1.090
 JDB  CAM  H6   single    0.970  0.020  1.090
 JDB  CAM  H7   single    0.970  0.020  1.090
 JDB  CAS  H8   single    0.930  0.020  1.080
 JDB  CAT  H9   single    0.930  0.020  1.080
 JDB  CAY  H10  single    0.970  0.020  1.090
 JDB  CAY  H11  single    0.970  0.020  1.090
 JDB  CAY  H12  single    0.970  0.020  1.090
 JDB  CAV  H13  single    0.930  0.020  1.080
 JDB  CAU  H14  single    0.930  0.020  1.080
 JDB  CAP  H15  single    0.930  0.020  1.080
 JDB  CAO  H16  single    0.930  0.020  1.080
 JDB  N3   H17  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
 JDB  C4   CAI  OAK  117.78  3.000
 JDB  C4   CAI  OAJ  113.98  3.000
 JDB  OAK  CAI  OAJ  128.24  3.000
 JDB  C5   C4   N3   120.77  3.000
 JDB  N3   C4   CAI  111.59  3.000
 JDB  C5   C4   CAI  127.63  3.000
 JDB  H17  N3   C2   119.33  3.000
 JDB  H17  N3   C4   115.11  3.000
 JDB  C2   N3   C4   125.55  3.000
 JDB  N1   C2   O2   123.00  3.000
 JDB  O2   C2   N3   123.92  3.000
 JDB  N1   C2   N3   113.08  3.000
 JDB  H2   N1   C6   116.75  3.000
 JDB  H2   N1   C2   116.30  3.000
 JDB  C6   N1   C2   126.95  3.000
 JDB  C5   C6   O6   124.71  3.000
 JDB  C5   C6   N1   115.88  3.000
 JDB  O6   C6   N1   119.41  3.000
 JDB  CAL  C5   C6   116.33  3.000
 JDB  C6   C5   C4   117.74  3.000
 JDB  CAL  C5   C4   125.89  3.000
 JDB  H5   CAL  H4   107.25  3.000
 JDB  H5   CAL  CAM  109.25  3.000
 JDB  H4   CAL  CAM  108.74  3.000
 JDB  H5   CAL  C5   110.33  3.000
 JDB  H4   CAL  C5   109.09  3.000
 JDB  CAM  CAL  C5   112.04  3.000
 JDB  H7   CAM  H6   107.25  3.000
 JDB  H7   CAM  CAN  109.97  3.000
 JDB  H6   CAM  CAN  109.75  3.000
 JDB  H7   CAM  CAL  109.58  3.000
 JDB  H6   CAM  CAL  108.41  3.000
 JDB  CAN  CAM  CAL  111.76  3.000
 JDB  CAO  CAN  CAS  119.00  3.000
 JDB  CAO  CAN  CAM  119.29  3.000
 JDB  CAS  CAN  CAM  121.70  3.000
 JDB  H8   CAS  CAR  118.61  3.000
 JDB  H8   CAS  CAN  119.77  3.000
 JDB  CAR  CAS  CAN  121.62  3.000
 JDB  CAQ  CAR  CAT  119.43  3.000
 JDB  CAQ  CAR  CAS  118.74  3.000
 JDB  CAT  CAR  CAS  121.84  3.000
 JDB  H9   CAT  CAW  119.61  3.000
 JDB  H9   CAT  CAR  119.51  3.000
 JDB  CAW  CAT  CAR  120.87  3.000
 JDB  CAV  CAW  OAX  123.32  3.000
 JDB  CAV  CAW  CAT  119.83  3.000
 JDB  OAX  CAW  CAT  116.85  3.000
 JDB  CAY  OAX  CAW  119.14  3.000
 JDB  H12  CAY  H11  108.59  3.000
 JDB  H12  CAY  H10  108.62  3.000
 JDB  H11  CAY  H10  108.83  3.000
 JDB  H12  CAY  OAX  106.38  3.000
 JDB  H11  CAY  OAX  112.15  3.000
 JDB  H10  CAY  OAX  112.13  3.000
 JDB  H13  CAV  CAU  119.03  3.000
 JDB  H13  CAV  CAW  121.08  3.000
 JDB  CAU  CAV  CAW  119.88  3.000
 JDB  H14  CAU  CAQ  119.15  3.000
 JDB  H14  CAU  CAV  119.31  3.000
 JDB  CAQ  CAU  CAV  121.54  3.000
 JDB  CAP  CAQ  CAU  122.61  3.000
 JDB  CAP  CAQ  CAR  118.95  3.000
 JDB  CAU  CAQ  CAR  118.44  3.000
 JDB  H15  CAP  CAO  120.28  3.000
 JDB  H15  CAP  CAQ  118.98  3.000
 JDB  CAO  CAP  CAQ  120.74  3.000
 JDB  H16  CAO  CAP  120.16  3.000
 JDB  H16  CAO  CAN  118.88  3.000
 JDB  CAP  CAO  CAN  120.95  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
 JDB  CONST_01  CAT  CAR  CAS  CAN   180.00   0.0  0
 JDB  CONST_02  CAQ  CAR  CAS  CAN     0.00   0.0  0
 JDB  CONST_03  CAQ  CAP  CAO  CAN     0.00   0.0  0
 JDB  CONST_04  CAW  CAT  CAR  CAS   180.00   0.0  0
 JDB  CONST_05  CAU  CAQ  CAR  CAS   180.00   0.0  0
 JDB  CONST_06  CAP  CAQ  CAR  CAS     0.00   0.0  0
 JDB  CONST_07  CAP  CAO  CAN  CAS     0.00   0.0  0
 JDB  CONST_08  CAV  CAW  CAT  CAR     0.00   0.0  0
 JDB  CONST_09  CAO  CAN  CAS  CAR     0.00   0.0  0
 JDB  CONST_10  CAV  CAU  CAQ  CAR     0.00   0.0  0
 JDB  CONST_11  CAO  CAP  CAQ  CAR     0.00   0.0  0
 JDB  CONST_12  CAU  CAV  CAW  CAT     0.00   0.0  0
 JDB  CONST_13  CAU  CAQ  CAR  CAT     0.00   0.0  0
 JDB  CONST_14  CAP  CAQ  CAR  CAT   180.00   0.0  0
 JDB  CONST_15  CAQ  CAR  CAT  CAW     0.00   0.0  0
 JDB  CONST_16  CAQ  CAU  CAV  CAW     0.00   0.0  0
 JDB  CONST_17  CAP  CAQ  CAU  CAV   180.00   0.0  0
 JDB  CONST_18  CAO  CAP  CAQ  CAU   180.00   0.0  0
 JDB  CONST_19  N1   C2   N3   C4      0.00   0.0  0
 JDB  CONST_20  C6   N1   C2   N3      0.00   0.0  0
 JDB  CONST_21  C5   C6   N1   C2      0.00   0.0  0
 JDB  CONST_22  CAR  CAS  CAN  CAM   180.00   0.0  0
 JDB  CONST_23  CAP  CAO  CAN  CAM   180.00   0.0  0
 JDB  CONST_24  OAX  CAW  CAT  CAR   180.00   0.0  0
 JDB  CONST_25  CAU  CAV  CAW  OAX   180.00   0.0  0
 JDB  CONST_26  O2   C2   N3   C4    180.00   0.0  0
 JDB  CONST_27  O6   C6   N1   C2    180.00   0.0  0
 JDB  CONST_28  C6   N1   C2   O2    180.00   0.0  0
 JDB  CONST_29  H15  CAP  CAO  CAN   180.00   0.0  0
 JDB  CONST_30  H9   CAT  CAR  CAS     0.00   0.0  0
 JDB  CONST_31  H16  CAO  CAN  CAS   180.00   0.0  0
 JDB  CONST_32  H14  CAU  CAQ  CAR   180.00   0.0  0
 JDB  CONST_33  H13  CAV  CAW  CAT   180.00   0.0  0
 JDB  CONST_34  H8   CAS  CAR  CAT     0.00   0.0  0
 JDB  CONST_35  H2   N1   C2   N3    180.00   0.0  0
 JDB  CONST_36  H17  N3   C2   N1    180.00   0.0  0
 JDB  Var_01    C5   C4   CAI  OAJ   172.77  30.0  2
 JDB  Var_02    CAM  CAL  C5   C4     89.40  30.0  3
 JDB  Var_03    CAN  CAM  CAL  C5   -176.92  30.0  1
 JDB  Var_04    CAS  CAN  CAM  CAL  -103.99  30.0  2
 JDB  Var_05    CAV  CAW  OAX  CAY    -0.50  30.0  2
 JDB  Var_06    H10  CAY  OAX  CAW   -61.56  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
 JDB  plan-1  CAI  0.020
 JDB  plan-1  C4   0.020
 JDB  plan-1  N3   0.020
 JDB  plan-1  C2   0.020
 JDB  plan-1  O2   0.020
 JDB  plan-1  N1   0.020
 JDB  plan-1  C6   0.020
 JDB  plan-1  O6   0.020
 JDB  plan-1  C5   0.020
 JDB  plan-1  CAL  0.020
 JDB  plan-1  H2   0.020
 JDB  plan-1  H17  0.020
 JDB  plan-2  CAM  0.020
 JDB  plan-2  CAN  0.020
 JDB  plan-2  CAS  0.020
 JDB  plan-2  CAR  0.020
 JDB  plan-2  CAT  0.020
 JDB  plan-2  CAW  0.020
 JDB  plan-2  OAX  0.020
 JDB  plan-2  CAV  0.020
 JDB  plan-2  CAU  0.020
 JDB  plan-2  CAQ  0.020
 JDB  plan-2  CAP  0.020
 JDB  plan-2  CAO  0.020
 JDB  plan-2  H8   0.020
 JDB  plan-2  H9   0.020
 JDB  plan-2  H13  0.020
 JDB  plan-2  H14  0.020
 JDB  plan-2  H15  0.020
 JDB  plan-2  H16  0.020
 JDB  plan-3  OAJ  0.020
 JDB  plan-3  CAI  0.020
 JDB  plan-3  OAK  0.020
 JDB  plan-3  C4   0.020

