# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 01:01:42 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 5-benzyl-1-[(2-hydroxyethoxy)methyl]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCOCN1C=C(Cc2ccccc2)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
 BAU  BAU  5-benzyl-1-[(2-hydroxyethoxy)methyl]pyrimidine-2,4(1H,3H)-dione  ligand  36  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BAU
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
 BAU  OAC   O  OH1   0  -0.670   3.2212  -2.9146   1.3330
 BAU  CAJ   C  CH2   0  -0.181   3.1564  -3.0970  -0.0616
 BAU  CAK   C  CH2   0  -0.184   2.5225  -1.8861  -0.6952
 BAU  OAO   O  O2    0  -0.462   3.3648  -0.7634  -0.5193
 BAU  CAM   C  CH2   0  -0.055   2.9502   0.3770  -1.1840
 BAU  NAT   N  NR6   0  -0.546   1.7437   0.9645  -0.6120
 BAU  CAS   C  CR6   0   0.735   1.8525   1.6627   0.5709
 BAU  OAB   O  OC    0  -0.478   2.9103   1.8563   1.1312
 BAU  NAN   N  NR16  0  -0.732   0.6626   2.1328   1.0612
 BAU  CAR   C  CR6   0   0.570  -0.6029   1.9759   0.5223
 BAU  OAA   O  OC    0  -0.446  -1.5736   2.4631   1.0697
 BAU  CAI   C  CR16  0   0.024   0.5274   0.7635  -1.2078
 BAU  CAQ   C  CR6   0  -0.139  -0.6368   1.2148  -0.7113
 BAU  CAL   C  CH2   0  -0.591  -1.9577   0.9501  -1.3663
 BAU  CG    C  CR6   0   0.149  -2.7921  -0.0407  -0.5888
 BAU  CD2   C  CR16  0  -0.313  -3.9885   0.3393   0.0094
 BAU  CE2   C  CR16  0  -0.243  -4.7509  -0.5799   0.7198
 BAU  CZ    C  CR16  0  -0.272  -4.3210  -1.8937   0.8455
 BAU  CE1   C  CR16  0  -0.241  -3.1260  -2.2833   0.2524
 BAU  CD1   C  CR16  0  -0.289  -2.3695  -1.3620  -0.4575
 BAU  HAC   H  HOH1  0   0.457   3.6226  -3.6982   1.7188
 BAU  HAJ1  H  HCH2  0   0.205   4.1489  -3.2607  -0.5006
 BAU  HAJ2  H  HCH2  0   0.207   2.5399  -3.9624  -0.3358
 BAU  HAK1  H  HCH2  0   0.220   2.3681  -2.0913  -1.7625
 BAU  HAK2  H  HCH2  0   0.217   1.5342  -1.7159  -0.2478
 BAU  HAM1  H  HCH2  0   0.271   3.7571   1.1028  -1.1241
 BAU  HAM2  H  HCH2  0   0.248   2.7311   0.1860  -2.2397
 BAU  HAN   H  HNR6  0   0.426   0.7275   2.6631   1.9218
 BAU  HAI   H  HCR6  0   0.319   0.5617   0.2052  -2.1351
 BAU  HAL1  H  HCH2  0   0.271  -2.5104   1.8845  -1.4810
 BAU  HAL2  H  HCH2  0   0.273  -1.7821   0.5682  -2.3748
 BAU  HD2   H  HCR6  0   0.246  -4.3276   1.3640  -0.0804
 BAU  HE2   H  HCR6  0   0.253  -5.6801  -0.2674   1.1789
 BAU  HZ    H  HCR6  0   0.254  -4.9121  -2.6099   1.4016
 BAU  HE1   H  HCR6  0   0.254  -2.7841  -3.3066   0.3412
 BAU  HD1   H  HCR6  0   0.241  -1.4384  -1.6766  -0.9157

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
 BAU  OAC  CAJ   single    1.408  0.020  1.408
 BAU  OAC  HAC   single    0.850  0.020  0.980
 BAU  CAJ  CAK   single    1.507  0.020  1.507
 BAU  CAJ  HAJ1  single    0.970  0.020  1.090
 BAU  CAJ  HAJ2  single    0.970  0.020  1.090
 BAU  CAK  OAO   single    1.415  0.020  1.415
 BAU  CAK  HAK1  single    0.970  0.020  1.090
 BAU  CAK  HAK2  single    0.970  0.020  1.090
 BAU  OAO  CAM   single    1.384  0.020  1.384
 BAU  CAM  NAT   single    1.459  0.020  1.459
 BAU  CAM  HAM1  single    0.970  0.020  1.090
 BAU  CAM  HAM2  single    0.970  0.020  1.090
 BAU  NAT  CAS   aromatic  1.378  0.020  1.378
 BAU  NAT  CAI   aromatic  1.369  0.020  1.369
 BAU  CAS  OAB   double    1.213  0.020  1.213
 BAU  CAS  NAN   aromatic  1.370  0.020  1.370
 BAU  NAN  CAR   aromatic  1.384  0.020  1.384
 BAU  NAN  HAN   single    0.860  0.020  1.020
 BAU  CAR  OAA   double    1.216  0.020  1.216
 BAU  CAR  CAQ   aromatic  1.450  0.020  1.450
 BAU  CAI  CAQ   aromatic  1.344  0.020  1.344
 BAU  CAI  HAI   single    0.930  0.020  1.080
 BAU  CAQ  CAL   single    1.498  0.020  1.498
 BAU  CAL  CG    single    1.511  0.020  1.511
 BAU  CAL  HAL1  single    0.970  0.020  1.090
 BAU  CAL  HAL2  single    0.970  0.020  1.090
 BAU  CG   CD2   aromatic  1.391  0.020  1.391
 BAU  CG   CD1   aromatic  1.394  0.020  1.394
 BAU  CD2  CE2   aromatic  1.390  0.020  1.390
 BAU  CD2  HD2   single    0.930  0.020  1.080
 BAU  CE2  CZ    aromatic  1.388  0.020  1.388
 BAU  CE2  HE2   single    0.930  0.020  1.080
 BAU  CZ   CE1   aromatic  1.390  0.020  1.390
 BAU  CZ   HZ    single    0.930  0.020  1.080
 BAU  CE1  CD1   aromatic  1.387  0.020  1.387
 BAU  CE1  HE1   single    0.930  0.020  1.080
 BAU  CD1  HD1   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
 BAU  HAC   OAC  CAJ   108.13  3.000
 BAU  HAJ2  CAJ  HAJ1  106.89  3.000
 BAU  HAJ2  CAJ  CAK   107.00  3.000
 BAU  HAJ1  CAJ  CAK   109.40  3.000
 BAU  HAJ2  CAJ  OAC   112.06  3.000
 BAU  HAJ1  CAJ  OAC   111.96  3.000
 BAU  CAK   CAJ  OAC   109.38  3.000
 BAU  HAK2  CAK  HAK1  107.36  3.000
 BAU  HAK2  CAK  OAO   111.24  3.000
 BAU  HAK1  CAK  OAO   110.67  3.000
 BAU  HAK2  CAK  CAJ   109.38  3.000
 BAU  HAK1  CAK  CAJ   108.53  3.000
 BAU  OAO   CAK  CAJ   109.58  3.000
 BAU  CAM   OAO  CAK   114.58  3.000
 BAU  HAM2  CAM  HAM1  108.55  3.000
 BAU  HAM2  CAM  NAT   106.43  3.000
 BAU  HAM1  CAM  NAT   108.87  3.000
 BAU  HAM2  CAM  OAO   112.30  3.000
 BAU  HAM1  CAM  OAO   107.54  3.000
 BAU  NAT   CAM  OAO   113.05  3.000
 BAU  CAI   NAT  CAS   121.21  3.000
 BAU  CAI   NAT  CAM   120.33  3.000
 BAU  CAS   NAT  CAM   118.38  3.000
 BAU  NAN   CAS  OAB   122.52  3.000
 BAU  NAN   CAS  NAT   114.36  3.000
 BAU  OAB   CAS  NAT   123.13  3.000
 BAU  HAN   NAN  CAR   116.66  3.000
 BAU  HAN   NAN  CAS   115.34  3.000
 BAU  CAR   NAN  CAS   128.00  3.000
 BAU  CAQ   CAR  OAA   125.06  3.000
 BAU  CAQ   CAR  NAN   114.34  3.000
 BAU  OAA   CAR  NAN   120.60  3.000
 BAU  HAI   CAI  CAQ   121.13  3.000
 BAU  HAI   CAI  NAT   114.84  3.000
 BAU  CAQ   CAI  NAT   124.03  3.000
 BAU  CAL   CAQ  CAI   122.89  3.000
 BAU  CAL   CAQ  CAR   119.04  3.000
 BAU  CAI   CAQ  CAR   118.06  3.000
 BAU  HAL2  CAL  HAL1  106.47  3.000
 BAU  HAL2  CAL  CG    109.55  3.000
 BAU  HAL1  CAL  CG    109.63  3.000
 BAU  HAL2  CAL  CAQ   108.88  3.000
 BAU  HAL1  CAL  CAQ   109.94  3.000
 BAU  CG    CAL  CAQ   112.20  3.000
 BAU  CD1   CG   CD2   118.65  3.000
 BAU  CD1   CG   CAL   120.19  3.000
 BAU  CD2   CG   CAL   121.16  3.000
 BAU  HD2   CD2  CE2   119.76  3.000
 BAU  HD2   CD2  CG    119.49  3.000
 BAU  CE2   CD2  CG    120.75  3.000
 BAU  HE2   CE2  CZ    120.05  3.000
 BAU  HE2   CE2  CD2   119.79  3.000
 BAU  CZ    CE2  CD2   120.16  3.000
 BAU  HZ    CZ   CE1   120.22  3.000
 BAU  HZ    CZ   CE2   120.24  3.000
 BAU  CE1   CZ   CE2   119.54  3.000
 BAU  HE1   CE1  CD1   119.83  3.000
 BAU  HE1   CE1  CZ    120.10  3.000
 BAU  CD1   CE1  CZ    120.07  3.000
 BAU  HD1   CD1  CE1   119.46  3.000
 BAU  HD1   CD1  CG    119.71  3.000
 BAU  CE1   CD1  CG    120.83  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
 BAU  CONST_01  CAR  NAN  CAS  NAT    0.00   0.0  0
 BAU  CONST_02  CAR  CAQ  CAI  NAT    0.00   0.0  0
 BAU  CONST_03  CAQ  CAI  NAT  CAS    0.00   0.0  0
 BAU  CONST_04  CAQ  CAR  NAN  CAS    0.00   0.0  0
 BAU  CONST_05  CAI  NAT  CAS  NAN    0.00   0.0  0
 BAU  CONST_06  CAI  CAQ  CAR  NAN    0.00   0.0  0
 BAU  CONST_07  CZ   CE2  CD2  CG     0.00   0.0  0
 BAU  CONST_08  CZ   CE1  CD1  CG     0.00   0.0  0
 BAU  CONST_09  CE1  CD1  CG   CD2    0.00   0.0  0
 BAU  CONST_10  CE1  CZ   CE2  CD2    0.00   0.0  0
 BAU  CONST_11  CD1  CG   CD2  CE2    0.00   0.0  0
 BAU  CONST_12  CD1  CE1  CZ   CE2    0.00   0.0  0
 BAU  CONST_13  NAN  CAS  NAT  CAM  180.00   0.0  0
 BAU  CONST_14  CAQ  CAI  NAT  CAM  180.00   0.0  0
 BAU  CONST_15  CAL  CAQ  CAI  NAT  180.00   0.0  0
 BAU  CONST_16  OAA  CAR  NAN  CAS  180.00   0.0  0
 BAU  CONST_17  CAI  NAT  CAS  OAB  180.00   0.0  0
 BAU  CONST_18  CAR  NAN  CAS  OAB  180.00   0.0  0
 BAU  CONST_19  CAL  CAQ  CAR  NAN  180.00   0.0  0
 BAU  CONST_20  CAI  CAQ  CAR  OAA  180.00   0.0  0
 BAU  CONST_21  CE2  CD2  CG   CAL  180.00   0.0  0
 BAU  CONST_22  CE1  CD1  CG   CAL  180.00   0.0  0
 BAU  CONST_23  HAN  NAN  CAS  NAT  180.00   0.0  0
 BAU  CONST_24  HAI  CAI  NAT  CAS  180.00   0.0  0
 BAU  CONST_25  HE2  CE2  CD2  CG   180.00   0.0  0
 BAU  CONST_26  HE1  CE1  CD1  CG   180.00   0.0  0
 BAU  CONST_27  HD1  CD1  CG   CD2  180.00   0.0  0
 BAU  CONST_28  HZ   CZ   CE2  CD2  180.00   0.0  0
 BAU  CONST_29  HD2  CD2  CE2  CZ   180.00   0.0  0
 BAU  CONST_30  OAB  CAS  NAT  CAM    0.00   0.0  0
 BAU  Var_01    CG   CAL  CAQ  CAR  -70.96  30.0  2
 BAU  Var_02    CD2  CG   CAL  CAQ  114.36  30.0  2
 BAU  Var_03    CAS  NAT  CAM  OAO   75.36  30.0  2
 BAU  Var_04    NAT  CAM  OAO  CAK   69.95  30.0  3
 BAU  Var_05    OAO  CAK  CAJ  OAC   65.78  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
 BAU  plan-1  CAM  0.020
 BAU  plan-1  NAT  0.020
 BAU  plan-1  CAS  0.020
 BAU  plan-1  OAB  0.020
 BAU  plan-1  NAN  0.020
 BAU  plan-1  CAR  0.020
 BAU  plan-1  OAA  0.020
 BAU  plan-1  CAI  0.020
 BAU  plan-1  CAQ  0.020
 BAU  plan-1  CAL  0.020
 BAU  plan-1  HAN  0.020
 BAU  plan-1  HAI  0.020
 BAU  plan-2  CAL  0.020
 BAU  plan-2  CG   0.020
 BAU  plan-2  CD2  0.020
 BAU  plan-2  CE2  0.020
 BAU  plan-2  CZ   0.020
 BAU  plan-2  CE1  0.020
 BAU  plan-2  CD1  0.020
 BAU  plan-2  HD2  0.020
 BAU  plan-2  HE2  0.020
 BAU  plan-2  HZ   0.020
 BAU  plan-2  HE1  0.020
 BAU  plan-2  HD1  0.020

