# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 20:07:51 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 1-[(2-hydroxyethoxy)methyl]-5-(phenylselanyl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCOCN1C=C([Se]c2ccccc2)C(=O)NC1=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
 182  182  1-[(2-hydroxyethoxy)methyl]-5-(phenylselanyl)pyrimidine-2,4(1H,3H)-dione  ligand  34  20  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_182
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
 182  OAC   O   OH1   0  -0.658   7.3851  160.2559  11.5740
 182  CAJ   C   CH2   0  -0.181   6.2787  160.9293  11.0198
 182  CAK   C   CH2   0  -0.186   6.3333  162.3800  11.4209
 182  OAN   O   O2    0  -0.470   6.1706  162.4777  12.8257
 182  CAL   C   CH2   0  -0.064   6.3243  163.7511  13.3434
 182  NAT   N   NR6   0  -0.550   7.7260  164.1819  13.2740
 182  CAS   C   CR6   0   0.723   8.0912  165.2631  12.4930
 182  OAB   O   OC    0  -0.463   7.2911  165.9717  11.9237
 182  NAM   N   NR16  0  -0.727   9.4425  165.4718  12.4145
 182  CAR   C   CR6   0   0.597  10.4634  164.7183  12.9718
 182  OAA   O   OC    0  -0.432  11.6237  165.0099  12.7776
 182  CAI   C   CR16  0   0.124   8.6590  163.3953  13.8762
 182  CAQ   C   CR6   0  -0.434   9.9868  163.6009  13.7695
 182  SE    SE  SE    0   0.180  11.2289  162.4610  14.6148
 182  CAP   C   CR6   0  -0.135  11.7274  161.4258  13.0811
 182  CAH   C   CR16  0  -0.272  13.0738  161.1601  12.8576
 182  CAF   C   CR16  0  -0.242  13.4519  160.3727  11.7763
 182  CAD   C   CR16  0  -0.262  12.4933  159.8659  10.9099
 182  CAE   C   CR16  0  -0.244  11.1493  160.1381  11.1354
 182  CAG   C   CR16  0  -0.253  10.7621  160.9066  12.2236
 182  HAC   H   HOH1  0   0.458   7.3507  159.3368  11.2953
 182  HAJ1  H   HCH2  0   0.209   6.2810  160.8952   9.9237
 182  HAJ2  H   HCH2  0   0.206   5.3276  160.4928  11.3510
 182  HAK1  H   HCH2  0   0.219   7.2922  162.8075  11.1024
 182  HAK2  H   HCH2  0   0.230   5.5380  162.9279  10.9023
 182  HAL1  H   HCH2  0   0.263   5.7241  164.5032  12.8288
 182  HAL2  H   HCH2  0   0.281   6.0277  163.7130  14.3906
 182  HAM   H   HNR6  0   0.431   9.7238  166.2672  11.8534
 182  HAI   H   HCR6  0   0.333   8.2622  162.5685  14.4503
 182  HAH   H   HCR6  0   0.266  13.8335  161.5678  13.5130
 182  HAF   H   HCR6  0   0.262  14.5009  160.1695  11.6048
 182  HAD   H   HCR6  0   0.261  12.7912  159.2632  10.0619
 182  HAE   H   HCR6  0   0.257  10.3926  159.7456  10.4683
 182  HAG   H   HCR6  0   0.272   9.7078  161.0888  12.3888

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
 182  OAC  CAJ   single    1.409  0.020  1.409
 182  OAC  HAC   single    0.850  0.020  0.980
 182  CAJ  CAK   single    1.506  0.020  1.506
 182  CAJ  HAJ1  single    0.970  0.020  1.090
 182  CAJ  HAJ2  single    0.970  0.020  1.090
 182  CAK  OAN   single    1.418  0.020  1.418
 182  CAK  HAK1  single    0.970  0.020  1.090
 182  CAK  HAK2  single    0.970  0.020  1.090
 182  OAN  CAL   single    1.383  0.020  1.383
 182  CAL  NAT   single    1.468  0.020  1.468
 182  CAL  HAL1  single    0.970  0.020  1.090
 182  CAL  HAL2  single    0.970  0.020  1.090
 182  NAT  CAS   aromatic  1.383  0.020  1.383
 182  NAT  CAI   aromatic  1.361  0.020  1.361
 182  CAS  OAB   double    1.211  0.020  1.211
 182  CAS  NAM   aromatic  1.370  0.020  1.370
 182  NAM  CAR   aromatic  1.386  0.020  1.386
 182  NAM  HAM   single    0.860  0.020  1.020
 182  CAR  OAA   double    1.212  0.020  1.212
 182  CAR  CAQ   aromatic  1.453  0.020  1.453
 182  CAI  CAQ   aromatic  1.348  0.020  1.348
 182  CAI  HAI   single    0.930  0.020  1.080
 182  CAQ  SE    single    1.886  0.020  1.886
 182  SE   CAP   single    1.916  0.020  1.916
 182  CAP  CAH   aromatic  1.391  0.020  1.391
 182  CAP  CAG   aromatic  1.392  0.020  1.392
 182  CAH  CAF   aromatic  1.390  0.020  1.390
 182  CAH  HAH   single    0.930  0.020  1.080
 182  CAF  CAD   aromatic  1.388  0.020  1.388
 182  CAF  HAF   single    0.930  0.020  1.080
 182  CAD  CAE   aromatic  1.390  0.020  1.390
 182  CAD  HAD   single    0.930  0.020  1.080
 182  CAE  CAG   aromatic  1.387  0.020  1.387
 182  CAE  HAE   single    0.930  0.020  1.080
 182  CAG  HAG   single    0.930  0.020  1.080

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
 182  HAC   OAC  CAJ   108.36  3.000
 182  HAJ2  CAJ  HAJ1  106.92  3.000
 182  HAJ2  CAJ  CAK   109.52  3.000
 182  HAJ1  CAJ  CAK   107.22  3.000
 182  HAJ2  CAJ  OAC   111.83  3.000
 182  HAJ1  CAJ  OAC   112.13  3.000
 182  CAK   CAJ  OAC   109.10  3.000
 182  HAK2  CAK  HAK1  107.58  3.000
 182  HAK2  CAK  OAN   110.56  3.000
 182  HAK1  CAK  OAN   111.17  3.000
 182  HAK2  CAK  CAJ   109.22  3.000
 182  HAK1  CAK  CAJ   109.25  3.000
 182  OAN   CAK  CAJ   109.04  3.000
 182  CAL   OAN  CAK   114.94  3.000
 182  HAL2  CAL  HAL1  109.13  3.000
 182  HAL2  CAL  NAT   108.40  3.000
 182  HAL1  CAL  NAT   107.50  3.000
 182  HAL2  CAL  OAN   107.30  3.000
 182  HAL1  CAL  OAN   113.39  3.000
 182  NAT   CAL  OAN   111.01  3.000
 182  CAI   NAT  CAS   121.38  3.000
 182  CAI   NAT  CAL   117.66  3.000
 182  CAS   NAT  CAL   120.55  3.000
 182  NAM   CAS  OAB   122.40  3.000
 182  NAM   CAS  NAT   114.34  3.000
 182  OAB   CAS  NAT   123.26  3.000
 182  HAM   NAM  CAR   116.42  3.000
 182  HAM   NAM  CAS   115.17  3.000
 182  CAR   NAM  CAS   128.39  3.000
 182  CAQ   CAR  OAA   125.93  3.000
 182  CAQ   CAR  NAM   113.40  3.000
 182  OAA   CAR  NAM   120.66  3.000
 182  HAI   CAI  CAQ   121.33  3.000
 182  HAI   CAI  NAT   115.15  3.000
 182  CAQ   CAI  NAT   123.52  3.000
 182  SE    CAQ  CAI   121.41  3.000
 182  SE    CAQ  CAR   119.66  3.000
 182  CAI   CAQ  CAR   118.93  3.000
 182  CAP   SE   CAQ    98.00  3.000
 182  CAG   CAP  CAH   120.09  3.000
 182  CAG   CAP  SE    120.95  3.000
 182  CAH   CAP  SE    118.93  3.000
 182  HAH   CAH  CAF   119.55  3.000
 182  HAH   CAH  CAP   120.66  3.000
 182  CAF   CAH  CAP   119.78  3.000
 182  HAF   CAF  CAD   120.13  3.000
 182  HAF   CAF  CAH   119.56  3.000
 182  CAD   CAF  CAH   120.31  3.000
 182  HAD   CAD  CAE   120.16  3.000
 182  HAD   CAD  CAF   120.16  3.000
 182  CAE   CAD  CAF   119.68  3.000
 182  HAE   CAE  CAG   119.29  3.000
 182  HAE   CAE  CAD   120.33  3.000
 182  CAG   CAE  CAD   120.38  3.000
 182  HAG   CAG  CAE   118.99  3.000
 182  HAG   CAG  CAP   121.24  3.000
 182  CAE   CAG  CAP   119.76  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
 182  CONST_01  CAR  NAM  CAS  NAT    0.00   0.0  0
 182  CONST_02  CAR  CAQ  CAI  NAT    0.00   0.0  0
 182  CONST_03  CAQ  CAI  NAT  CAS    0.00   0.0  0
 182  CONST_04  CAQ  CAR  NAM  CAS    0.00   0.0  0
 182  CONST_05  CAI  NAT  CAS  NAM    0.00   0.0  0
 182  CONST_06  CAI  CAQ  CAR  NAM    0.00   0.0  0
 182  CONST_07  CAD  CAF  CAH  CAP    0.00   0.0  0
 182  CONST_08  CAD  CAE  CAG  CAP    0.00   0.0  0
 182  CONST_09  CAE  CAG  CAP  CAH    0.00   0.0  0
 182  CONST_10  CAE  CAD  CAF  CAH    0.00   0.0  0
 182  CONST_11  CAG  CAP  CAH  CAF    0.00   0.0  0
 182  CONST_12  CAG  CAE  CAD  CAF    0.00   0.0  0
 182  CONST_13  NAM  CAS  NAT  CAL  180.00   0.0  0
 182  CONST_14  CAQ  CAI  NAT  CAL  180.00   0.0  0
 182  CONST_15  SE   CAQ  CAI  NAT  180.00   0.0  0
 182  CONST_16  OAA  CAR  NAM  CAS  180.00   0.0  0
 182  CONST_17  CAI  NAT  CAS  OAB  180.00   0.0  0
 182  CONST_18  CAR  NAM  CAS  OAB  180.00   0.0  0
 182  CONST_19  SE   CAQ  CAR  NAM  180.00   0.0  0
 182  CONST_20  CAI  CAQ  CAR  OAA  180.00   0.0  0
 182  CONST_21  CAF  CAH  CAP  SE   180.00   0.0  0
 182  CONST_22  CAE  CAG  CAP  SE   180.00   0.0  0
 182  CONST_23  HAM  NAM  CAS  NAT  180.00   0.0  0
 182  CONST_24  HAI  CAI  NAT  CAS  180.00   0.0  0
 182  CONST_25  HAF  CAF  CAH  CAP  180.00   0.0  0
 182  CONST_26  HAE  CAE  CAG  CAP  180.00   0.0  0
 182  CONST_27  HAG  CAG  CAP  CAH  180.00   0.0  0
 182  CONST_28  HAD  CAD  CAF  CAH  180.00   0.0  0
 182  CONST_29  HAH  CAH  CAF  CAD  180.00   0.0  0
 182  CONST_30  OAB  CAS  NAT  CAL    0.00   0.0  0
 182  Var_01    CAH  CAP  SE   CAQ  135.10  30.0  2
 182  Var_02    CAS  NAT  CAL  OAN  116.25  30.0  2
 182  Var_03    NAT  CAL  OAN  CAK  -70.16  30.0  3
 182  Var_04    OAN  CAK  CAJ  OAC  -65.29  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
 182  plan-1  CAL  0.020
 182  plan-1  NAT  0.020
 182  plan-1  CAS  0.020
 182  plan-1  OAB  0.020
 182  plan-1  NAM  0.020
 182  plan-1  CAR  0.020
 182  plan-1  OAA  0.020
 182  plan-1  CAI  0.020
 182  plan-1  CAQ  0.020
 182  plan-1  SE   0.020
 182  plan-1  HAM  0.020
 182  plan-1  HAI  0.020
 182  plan-2  SE   0.020
 182  plan-2  CAP  0.020
 182  plan-2  CAH  0.020
 182  plan-2  CAF  0.020
 182  plan-2  CAD  0.020
 182  plan-2  CAE  0.020
 182  plan-2  CAG  0.020
 182  plan-2  HAH  0.020
 182  plan-2  HAF  0.020
 182  plan-2  HAD  0.020
 182  plan-2  HAE  0.020
 182  plan-2  HAG  0.020

