# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 09:41:18 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 5-{2-[3-(methoxycarbonyl)phenyl]ethyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1cccc(CCC2=C(NC(=O)NC2=O)C(O)=O)c1
#
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
 W85  W85  '5-{2-[3-(methoxycarbonyl)phenyl]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_W85
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
 W85  OAB  O  OH1   0  -0.591  -4.2838  -2.6248   0.4317
 W85  CAP  C  C     0   0.525  -3.1275  -2.0583   0.1393
 W85  OAF  O  O     0  -0.396  -2.1103  -2.6560  -0.0840
 W85  CAT  C  CR6   0   0.281  -3.2492  -0.5642   0.1051
 W85  NAM  N  NR16  0  -0.732  -4.5209  -0.0907  -0.0996
 W85  CAV  C  CR6   0   0.671  -4.8429   1.2316  -0.1873
 W85  OAD  O  O     0  -0.472  -5.9713   1.6302  -0.3833
 W85  NAN  N  NR16  0  -0.716  -3.7678   2.0677  -0.0361
 W85  CAW  C  CR6   0   0.586  -2.4540   1.7072   0.1709
 W85  OAE  O  O     0  -0.440  -1.5913   2.5581   0.2670
 W85  CAU  C  CR6   0  -0.120  -2.1945   0.2664   0.2603
 W85  CAL  C  CH2   0  -0.501  -0.7725  -0.1368   0.5019
 W85  CAK  C  CH2   0  -0.504   0.0278  -0.2535  -0.8039
 W85  CAR  C  CR6   0   0.143   1.4416  -0.6846  -0.5402
 W85  CAJ  C  CR16  0  -0.326   2.4605   0.2488  -0.4032
 W85  CAH  C  CR16  0  -0.295   1.7537  -2.0345  -0.3900
 W85  CAG  C  CR16  0  -0.226   3.0523  -2.4389  -0.1179
 W85  CAI  C  CR16  0  -0.286   4.0652  -1.5007   0.0112
 W85  CAS  C  CR6   0  -0.063   3.7691  -0.1466  -0.1316
 W85  CAQ  C  C     0   0.596   4.8057   0.9104  -0.0120
 W85  OAC  O  O     0  -0.449   4.5737   2.0926  -0.1012
 W85  OAO  O  O2    0  -0.457   6.0157   0.4191   0.1998
 W85  CAA  C  CH3   0  -0.424   7.0941   1.3466   0.3187
 W85  H1   H  HOH1  0   0.504  -4.2106  -3.5919   0.4066
 W85  H2   H  HNR6  0   0.431  -3.9643   3.0598  -0.0968
 W85  H4   H  HCH2  0   0.265  -0.3036   0.6169   1.1359
 W85  H5   H  HCH2  0   0.267  -0.7204  -1.0756   1.0488
 W85  H6   H  HCH2  0   0.259  -0.4611  -0.9722  -1.4628
 W85  H7   H  HCH2  0   0.255   0.0230   0.7079  -1.3210
 W85  H8   H  HCR6  0   0.253   2.2344   1.3017  -0.5197
 W85  H9   H  HCR6  0   0.258   0.9697  -2.7760  -0.4900
 W85  H10  H  HCR6  0   0.263   3.2783  -3.4913  -0.0088
 W85  H11  H  HCR6  0   0.264   5.0727  -1.8314   0.2199
 W85  H12  H  HCH3  0   0.241   6.9556   2.0102   1.1717
 W85  H13  H  HCH3  0   0.254   7.9870   0.7472   0.4692
 W85  H14  H  HCH3  0   0.241   7.2071   1.9423  -0.5868
 W85  H15  H  HNR6  0   0.439  -5.2852  -0.7413  -0.2140

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
 W85  CAA  OAO  single    1.427  0.020  1.427
 W85  OAO  CAQ  single    1.323  0.020  1.323
 W85  CAQ  OAC  double    1.208  0.020  1.208
 W85  CAQ  CAS  single    1.485  0.020  1.485
 W85  CAS  CAJ  aromatic  1.394  0.020  1.394
 W85  CAS  CAI  aromatic  1.393  0.020  1.393
 W85  CAJ  CAR  aromatic  1.388  0.020  1.388
 W85  CAI  CAG  aromatic  1.387  0.020  1.387
 W85  CAR  CAK  single    1.501  0.020  1.501
 W85  CAR  CAH  aromatic  1.394  0.020  1.394
 W85  CAK  CAL  single    1.536  0.020  1.536
 W85  CAH  CAG  aromatic  1.387  0.020  1.387
 W85  CAL  CAU  single    1.498  0.020  1.498
 W85  OAE  CAW  double    1.215  0.020  1.215
 W85  CAU  CAW  single    1.467  0.020  1.467
 W85  CAU  CAT  double    1.351  0.020  1.351
 W85  CAW  NAN  single    1.378  0.020  1.378
 W85  CAT  CAP  single    1.499  0.020  1.499
 W85  CAT  NAM  single    1.372  0.020  1.372
 W85  OAF  CAP  double    1.201  0.020  1.201
 W85  NAN  CAV  single    1.370  0.020  1.370
 W85  CAP  OAB  single    1.320  0.020  1.320
 W85  NAM  CAV  single    1.364  0.020  1.364
 W85  CAV  OAD  double    1.213  0.020  1.213
 W85  OAB  H1   single    0.850  0.020  0.980
 W85  NAN  H2   single    0.860  0.020  1.020
 W85  CAL  H4   single    0.970  0.020  1.090
 W85  CAL  H5   single    0.970  0.020  1.090
 W85  CAK  H6   single    0.970  0.020  1.090
 W85  CAK  H7   single    0.970  0.020  1.090
 W85  CAJ  H8   single    0.930  0.020  1.080
 W85  CAH  H9   single    0.930  0.020  1.080
 W85  CAG  H10  single    0.930  0.020  1.080
 W85  CAI  H11  single    0.930  0.020  1.080
 W85  CAA  H12  single    0.970  0.020  1.090
 W85  CAA  H13  single    0.970  0.020  1.090
 W85  CAA  H14  single    0.970  0.020  1.090
 W85  NAM  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
 W85  H1   OAB  CAP  110.85  3.000
 W85  CAT  CAP  OAF  124.09  3.000
 W85  OAF  CAP  OAB  124.71  3.000
 W85  CAT  CAP  OAB  111.19  3.000
 W85  CAU  CAT  NAM  121.89  3.000
 W85  NAM  CAT  CAP  114.99  3.000
 W85  CAU  CAT  CAP  123.12  3.000
 W85  H15  NAM  CAV  116.01  3.000
 W85  H15  NAM  CAT  119.72  3.000
 W85  CAV  NAM  CAT  124.26  3.000
 W85  NAN  CAV  OAD  123.18  3.000
 W85  OAD  CAV  NAM  123.29  3.000
 W85  NAN  CAV  NAM  113.53  3.000
 W85  H2   NAN  CAW  116.75  3.000
 W85  H2   NAN  CAV  116.02  3.000
 W85  CAW  NAN  CAV  127.23  3.000
 W85  CAU  CAW  OAE  123.86  3.000
 W85  CAU  CAW  NAN  115.77  3.000
 W85  OAE  CAW  NAN  120.36  3.000
 W85  CAL  CAU  CAW  116.25  3.000
 W85  CAW  CAU  CAT  117.30  3.000
 W85  CAL  CAU  CAT  126.45  3.000
 W85  H5   CAL  H4   106.47  3.000
 W85  H5   CAL  CAK  109.68  3.000
 W85  H4   CAL  CAK  108.83  3.000
 W85  H5   CAL  CAU  111.03  3.000
 W85  H4   CAL  CAU  108.42  3.000
 W85  CAK  CAL  CAU  112.21  3.000
 W85  H7   CAK  H6   106.98  3.000
 W85  H7   CAK  CAR  109.88  3.000
 W85  H6   CAK  CAR  109.82  3.000
 W85  H7   CAK  CAL  109.48  3.000
 W85  H6   CAK  CAL  109.28  3.000
 W85  CAR  CAK  CAL  111.29  3.000
 W85  CAH  CAR  CAJ  118.44  3.000
 W85  CAH  CAR  CAK  120.52  3.000
 W85  CAJ  CAR  CAK  121.02  3.000
 W85  H8   CAJ  CAS  119.51  3.000
 W85  H8   CAJ  CAR  119.32  3.000
 W85  CAS  CAJ  CAR  121.16  3.000
 W85  H9   CAH  CAG  119.73  3.000
 W85  H9   CAH  CAR  119.39  3.000
 W85  CAG  CAH  CAR  120.87  3.000
 W85  H10  CAG  CAI  119.75  3.000
 W85  H10  CAG  CAH  119.93  3.000
 W85  CAI  CAG  CAH  120.33  3.000
 W85  H11  CAI  CAS  121.01  3.000
 W85  H11  CAI  CAG  119.47  3.000
 W85  CAS  CAI  CAG  119.52  3.000
 W85  CAQ  CAS  CAI  122.34  3.000
 W85  CAI  CAS  CAJ  119.68  3.000
 W85  CAQ  CAS  CAJ  117.98  3.000
 W85  OAO  CAQ  OAC  123.43  3.000
 W85  OAC  CAQ  CAS  123.81  3.000
 W85  OAO  CAQ  CAS  112.76  3.000
 W85  CAA  OAO  CAQ  117.58  3.000
 W85  H14  CAA  H13  109.37  3.000
 W85  H14  CAA  H12  109.31  3.000
 W85  H13  CAA  H12  109.40  3.000
 W85  H14  CAA  OAO  111.37  3.000
 W85  H13  CAA  OAO  105.91  3.000
 W85  H12  CAA  OAO  111.40  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
 W85  CONST_01  CAI  CAS  CAJ  CAR     0.00   0.0  0
 W85  CONST_02  CAI  CAG  CAH  CAR     0.00   0.0  0
 W85  CONST_03  CAG  CAI  CAS  CAJ     0.00   0.0  0
 W85  CONST_04  CAG  CAH  CAR  CAJ     0.00   0.0  0
 W85  CONST_05  CAS  CAJ  CAR  CAH     0.00   0.0  0
 W85  CONST_06  CAS  CAI  CAG  CAH     0.00   0.0  0
 W85  CONST_07  NAN  CAV  NAM  CAT     0.00   0.0  0
 W85  CONST_08  CAW  NAN  CAV  NAM     0.00   0.0  0
 W85  CONST_09  CAU  CAW  NAN  CAV     0.00   0.0  0
 W85  CONST_10  CAS  CAJ  CAR  CAK   180.00   0.0  0
 W85  CONST_11  CAG  CAH  CAR  CAK   180.00   0.0  0
 W85  CONST_12  CAQ  CAS  CAJ  CAR   180.00   0.0  0
 W85  CONST_13  CAQ  CAS  CAI  CAG   180.00   0.0  0
 W85  CONST_14  OAD  CAV  NAM  CAT   180.00   0.0  0
 W85  CONST_15  OAE  CAW  NAN  CAV   180.00   0.0  0
 W85  CONST_16  CAW  NAN  CAV  OAD   180.00   0.0  0
 W85  CONST_17  H10  CAG  CAH  CAR   180.00   0.0  0
 W85  CONST_18  H11  CAI  CAS  CAJ   180.00   0.0  0
 W85  CONST_19  H9   CAH  CAR  CAJ   180.00   0.0  0
 W85  CONST_20  H8   CAJ  CAR  CAH   180.00   0.0  0
 W85  CONST_21  H2   NAN  CAV  NAM   180.00   0.0  0
 W85  CONST_22  H15  NAM  CAV  NAN   180.00   0.0  0
 W85  CONST_23  H1   OAB  CAP  CAT   180.00   0.0  0
 W85  Var_01    CAU  CAT  CAP  OAB   158.03  30.0  2
 W85  Var_02    CAK  CAL  CAU  CAT    92.90  30.0  1
 W85  Var_03    CAR  CAK  CAL  CAU  -178.88  30.0  1
 W85  Var_04    CAJ  CAR  CAK  CAL   -94.32  30.0  3
 W85  Var_05    OAO  CAQ  CAS  CAJ  -177.79  30.0  2
 W85  Var_06    H12  CAA  OAO  CAQ    62.11  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
 W85  plan-1  CAP  0.020
 W85  plan-1  CAT  0.020
 W85  plan-1  NAM  0.020
 W85  plan-1  CAV  0.020
 W85  plan-1  OAD  0.020
 W85  plan-1  NAN  0.020
 W85  plan-1  CAW  0.020
 W85  plan-1  OAE  0.020
 W85  plan-1  CAU  0.020
 W85  plan-1  CAL  0.020
 W85  plan-1  H2   0.020
 W85  plan-1  H15  0.020
 W85  plan-2  CAK  0.020
 W85  plan-2  CAR  0.020
 W85  plan-2  CAJ  0.020
 W85  plan-2  CAH  0.020
 W85  plan-2  CAG  0.020
 W85  plan-2  CAI  0.020
 W85  plan-2  CAS  0.020
 W85  plan-2  CAQ  0.020
 W85  plan-2  H8   0.020
 W85  plan-2  H9   0.020
 W85  plan-2  H10  0.020
 W85  plan-2  H11  0.020
 W85  plan-3  OAB  0.020
 W85  plan-3  CAP  0.020
 W85  plan-3  OAF  0.020
 W85  plan-3  CAT  0.020
 W85  plan-3  H1   0.020
 W85  plan-4  CAS  0.020
 W85  plan-4  CAQ  0.020
 W85  plan-4  OAC  0.020
 W85  plan-4  OAO  0.020

