# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 01:24:36 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 4-[3-(2-amino-4-hydroxy-6-oxo-1,6-dihydropyrimidin-5-yl)propyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=C(CCCc2ccc(cc2)C(O)=O)C(=O)N1)O
#
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
 EJ5  EJ5  '4-[3-(2-amino-4-hydroxy-6-oxo-1,6-dihydropyrimidin-5-yl)propyl]benzoic acid'  ligand  36  21  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EJ5
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
 EJ5  CAF   C  CR16  0  -0.297  -2.6346   1.0271  -0.8829
 EJ5  CAH   C  CR16  0  -0.240  -3.8395   1.1459  -0.2137
 EJ5  CAR   C  CR6   0  -0.101  -4.5083   0.0107   0.2423
 EJ5  CAO   C  C     0   0.528  -5.7991   0.1858   0.9462
 EJ5  OAD   O  OH1   0  -0.595  -6.3250  -0.9589   1.3631
 EJ5  OAB   O  O     0  -0.443  -6.3279   1.2574   1.1291
 EJ5  CAI   C  CR16  0  -0.242  -3.9451  -1.2442   0.0145
 EJ5  CAG   C  CR16  0  -0.301  -2.7387  -1.3531  -0.6573
 EJ5  CAQ   C  CR6   0   0.147  -2.0653  -0.2239  -1.1188
 EJ5  CAK   C  CH2   0  -0.514  -0.7418  -0.3480  -1.8134
 EJ5  CAJ   C  CH2   0  -0.407   0.4318  -0.1858  -0.8450
 EJ5  CAL   C  CH2   0  -0.480   1.7808  -0.3605  -1.5446
 EJ5  CAT   C  CR6   0  -0.250   2.9464  -0.1318  -0.6319
 EJ5  CAS   C  CR6   0   0.478   3.4715  -1.1087   0.1837
 EJ5  OAE   O  OH1   0  -0.603   2.9430  -2.3295   0.1413
 EJ5  NAM   N  N     0  -0.541   4.4904  -0.9543   1.0424
 EJ5  CAP   C  CR6   0   0.703   5.0296   0.2390   1.1178
 EJ5  NAA   N  NH2   0  -0.824   6.0512   0.4556   1.9458
 EJ5  NAN   N  NR16  0  -0.713   4.5799   1.2695   0.3706
 EJ5  CAU   C  CR6   0   0.528   3.5186   1.1682  -0.5340
 EJ5  OAC   O  O     0  -0.502   3.1763   2.1712  -1.1533
 EJ5  HAF   H  HCR6  0   0.254  -2.1305   1.9203  -1.2320
 EJ5  HAH   H  HCR6  0   0.263  -4.2637   2.1270  -0.0469
 EJ5  HOAD  H  HOH1  0   0.487  -7.1660  -0.7902   1.8129
 EJ5  HAG   H  HCR6  0   0.255  -2.3169  -2.3354  -0.8327
 EJ5  HAK   H  HCH2  0   0.244  -0.6740  -1.3230  -2.3037
 EJ5  HAKA  H  HCH2  0   0.245  -0.6635   0.4073  -2.6001
 EJ5  HAJ   H  HCH2  0   0.229   0.3890   0.8039  -0.3814
 EJ5  HAJA  H  HCH2  0   0.230   0.3415  -0.9146  -0.0348
 EJ5  HAL   H  HCH2  0   0.234   1.8281  -1.3587  -1.9873
 EJ5  HNAA  H  HNH2  0   0.416   6.3735  -0.2946   2.5314
 EJ5  HNAB  H  HNH2  0   0.420   6.4813   1.3578   2.0506
 EJ5  HAI   H  HCR6  0   0.265  -4.4409  -2.1446   0.3502
 EJ5  H13   H  HCH2  0   0.234   1.8386   0.3414  -2.3802
 EJ5  H14   H  HOH1  0   0.474   3.4158  -2.8956   0.7659
 EJ5  HNAN  H  HNR6  0   0.420   5.0118   2.1797   0.4615

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
 EJ5  CAF  CAH   aromatic  1.383  0.020  1.383
 EJ5  CAF  HAF   single    0.930  0.020  1.080
 EJ5  CAH  CAR   aromatic  1.394  0.020  1.394
 EJ5  CAH  HAH   single    0.930  0.020  1.080
 EJ5  CAR  CAO   single    1.481  0.020  1.481
 EJ5  CAO  OAD   single    1.327  0.020  1.327
 EJ5  OAD  HOAD  single    0.850  0.020  0.980
 EJ5  OAB  CAO   double    1.209  0.020  1.209
 EJ5  CAI  CAR   aromatic  1.394  0.020  1.394
 EJ5  CAG  CAI   aromatic  1.385  0.020  1.385
 EJ5  CAG  HAG   single    0.930  0.020  1.080
 EJ5  CAQ  CAF   aromatic  1.395  0.020  1.395
 EJ5  CAQ  CAG   aromatic  1.393  0.020  1.393
 EJ5  CAK  CAQ   single    1.500  0.020  1.500
 EJ5  CAK  CAJ   single    1.530  0.020  1.530
 EJ5  CAK  HAK   single    0.970  0.020  1.090
 EJ5  CAK  HAKA  single    0.970  0.020  1.090
 EJ5  CAJ  CAL   single    1.530  0.020  1.530
 EJ5  CAJ  HAJ   single    0.970  0.020  1.090
 EJ5  CAJ  HAJA  single    0.970  0.020  1.090
 EJ5  CAL  CAT   single    1.498  0.020  1.498
 EJ5  CAL  HAL   single    0.970  0.020  1.090
 EJ5  CAT  CAU   single    1.424  0.020  1.424
 EJ5  CAS  CAT   double    1.377  0.020  1.377
 EJ5  CAS  NAM   single    1.341  0.020  1.341
 EJ5  OAE  CAS   single    1.331  0.020  1.331
 EJ5  NAM  CAP   double    1.312  0.020  1.312
 EJ5  CAP  NAN   single    1.350  0.020  1.350
 EJ5  CAP  NAA   single    1.333  0.020  1.333
 EJ5  NAA  HNAA  single    0.860  0.020  1.020
 EJ5  NAA  HNAB  single    0.860  0.020  1.020
 EJ5  CAU  NAN   single    1.398  0.020  1.398
 EJ5  CAU  OAC   double    1.228  0.020  1.228
 EJ5  CAI  HAI   single    0.930  0.020  1.080
 EJ5  CAL  H13   single    0.970  0.020  1.090
 EJ5  OAE  H14   single    0.850  0.020  0.980
 EJ5  NAN  HNAN  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
 EJ5  HAF   CAF  CAQ   119.68  3.000
 EJ5  CAQ   CAF  CAH   120.96  3.000
 EJ5  HAF   CAF  CAH   119.36  3.000
 EJ5  HAH   CAH  CAR   119.99  3.000
 EJ5  HAH   CAH  CAF   119.60  3.000
 EJ5  CAR   CAH  CAF   120.41  3.000
 EJ5  CAI   CAR  CAO   122.43  3.000
 EJ5  CAI   CAR  CAH   119.05  3.000
 EJ5  CAO   CAR  CAH   118.52  3.000
 EJ5  OAB   CAO  OAD   122.94  3.000
 EJ5  OAB   CAO  CAR   123.93  3.000
 EJ5  OAD   CAO  CAR   113.13  3.000
 EJ5  HOAD  OAD  CAO   109.87  3.000
 EJ5  HAI   CAI  CAG   118.98  3.000
 EJ5  HAI   CAI  CAR   120.90  3.000
 EJ5  CAG   CAI  CAR   120.12  3.000
 EJ5  HAG   CAG  CAQ   119.54  3.000
 EJ5  CAQ   CAG  CAI   121.19  3.000
 EJ5  HAG   CAG  CAI   119.27  3.000
 EJ5  CAK   CAQ  CAG   120.85  3.000
 EJ5  CAK   CAQ  CAF   120.85  3.000
 EJ5  CAG   CAQ  CAF   118.27  3.000
 EJ5  HAKA  CAK  HAK   106.79  3.000
 EJ5  HAKA  CAK  CAJ   109.09  3.000
 EJ5  HAK   CAK  CAJ   109.31  3.000
 EJ5  HAKA  CAK  CAQ   109.83  3.000
 EJ5  HAK   CAK  CAQ   109.64  3.000
 EJ5  CAJ   CAK  CAQ   112.02  3.000
 EJ5  HAJA  CAJ  HAJ   106.61  3.000
 EJ5  HAJA  CAJ  CAL   109.61  3.000
 EJ5  HAJ   CAJ  CAL   109.38  3.000
 EJ5  HAJA  CAJ  CAK   109.56  3.000
 EJ5  HAJ   CAJ  CAK   109.52  3.000
 EJ5  CAL   CAJ  CAK   112.02  3.000
 EJ5  H13   CAL  HAL   105.94  3.000
 EJ5  H13   CAL  CAT   109.07  3.000
 EJ5  HAL   CAL  CAT   110.64  3.000
 EJ5  H13   CAL  CAJ   108.84  3.000
 EJ5  HAL   CAL  CAJ   109.13  3.000
 EJ5  CAT   CAL  CAJ   112.96  3.000
 EJ5  CAU   CAT  CAS   116.99  3.000
 EJ5  CAS   CAT  CAL   123.33  3.000
 EJ5  CAU   CAT  CAL   119.60  3.000
 EJ5  NAM   CAS  OAE   115.32  3.000
 EJ5  OAE   CAS  CAT   118.71  3.000
 EJ5  NAM   CAS  CAT   125.97  3.000
 EJ5  H14   OAE  CAS   108.80  3.000
 EJ5  CAP   NAM  CAS   116.99  3.000
 EJ5  NAN   CAP  NAA   118.37  3.000
 EJ5  NAA   CAP  NAM   119.91  3.000
 EJ5  NAN   CAP  NAM   121.72  3.000
 EJ5  HNAB  NAA  HNAA  118.18  3.000
 EJ5  HNAB  NAA  CAP   122.60  3.000
 EJ5  HNAA  NAA  CAP   119.12  3.000
 EJ5  HNAN  NAN  CAU   116.58  3.000
 EJ5  HNAN  NAN  CAP   119.67  3.000
 EJ5  CAU   NAN  CAP   123.75  3.000
 EJ5  OAC   CAU  NAN   118.61  3.000
 EJ5  OAC   CAU  CAT   126.82  3.000
 EJ5  NAN   CAU  CAT   114.56  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
 EJ5  CONST_01  CAI   CAR  CAH  CAF     0.00   0.0  0
 EJ5  CONST_02  CAI   CAG  CAQ  CAF     0.00   0.0  0
 EJ5  CONST_03  CAG   CAQ  CAF  CAH     0.00   0.0  0
 EJ5  CONST_04  CAG   CAI  CAR  CAH     0.00   0.0  0
 EJ5  CONST_05  CAQ   CAF  CAH  CAR     0.00   0.0  0
 EJ5  CONST_06  CAQ   CAG  CAI  CAR     0.00   0.0  0
 EJ5  CONST_07  CAP   NAN  CAU  CAT     0.00   0.0  0
 EJ5  CONST_08  NAN   CAP  NAM  CAS     0.00   0.0  0
 EJ5  CONST_09  CAU   NAN  CAP  NAM     0.00   0.0  0
 EJ5  CONST_10  CAO   CAR  CAH  CAF   180.00   0.0  0
 EJ5  CONST_11  CAK   CAQ  CAF  CAH   180.00   0.0  0
 EJ5  CONST_12  CAG   CAI  CAR  CAO   180.00   0.0  0
 EJ5  CONST_13  CAK   CAQ  CAG  CAI   180.00   0.0  0
 EJ5  CONST_14  NAA   CAP  NAM  CAS   180.00   0.0  0
 EJ5  CONST_15  OAC   CAU  NAN  CAP   180.00   0.0  0
 EJ5  CONST_16  CAU   NAN  CAP  NAA   180.00   0.0  0
 EJ5  CONST_17  HAG   CAG  CAQ  CAF   180.00   0.0  0
 EJ5  CONST_18  HAI   CAI  CAR  CAH   180.00   0.0  0
 EJ5  CONST_19  HAF   CAF  CAH  CAR   180.00   0.0  0
 EJ5  CONST_20  HAH   CAH  CAR  CAI   180.00   0.0  0
 EJ5  CONST_21  HNAN  NAN  CAU  CAT   180.00   0.0  0
 EJ5  CONST_22  HNAA  NAA  CAP  NAM     0.00   0.0  0
 EJ5  CONST_23  HNAB  NAA  CAP  NAM   180.00   0.0  0
 EJ5  CONST_24  HOAD  OAD  CAO  CAR   180.00   0.0  0
 EJ5  Var_01    CAJ   CAK  CAQ  CAF    84.13  30.0  2
 EJ5  Var_02    OAD   CAO  CAR  CAH  -178.38  30.0  2
 EJ5  Var_03    CAU   CAT  CAL  CAJ   -91.85  30.0  3
 EJ5  Var_04    CAL   CAJ  CAK  CAQ   178.02  30.0  3
 EJ5  Var_05    CAT   CAL  CAJ  CAK   176.85  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
 EJ5  plan-1  CAF   0.020
 EJ5  plan-1  CAH   0.020
 EJ5  plan-1  CAR   0.020
 EJ5  plan-1  CAO   0.020
 EJ5  plan-1  CAI   0.020
 EJ5  plan-1  CAG   0.020
 EJ5  plan-1  CAQ   0.020
 EJ5  plan-1  CAK   0.020
 EJ5  plan-1  HAF   0.020
 EJ5  plan-1  HAH   0.020
 EJ5  plan-1  HAG   0.020
 EJ5  plan-1  HAI   0.020
 EJ5  plan-2  CAL   0.020
 EJ5  plan-2  CAT   0.020
 EJ5  plan-2  CAS   0.020
 EJ5  plan-2  OAE   0.020
 EJ5  plan-2  NAM   0.020
 EJ5  plan-2  CAP   0.020
 EJ5  plan-2  NAA   0.020
 EJ5  plan-2  NAN   0.020
 EJ5  plan-2  CAU   0.020
 EJ5  plan-2  OAC   0.020
 EJ5  plan-2  HNAA  0.020
 EJ5  plan-2  HNAB  0.020
 EJ5  plan-2  HNAN  0.020
 EJ5  plan-3  CAR   0.020
 EJ5  plan-3  CAO   0.020
 EJ5  plan-3  OAD   0.020
 EJ5  plan-3  OAB   0.020
 EJ5  plan-3  HOAD  0.020

