# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 16:29:01 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 5-[2-(4-methoxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CCC2=C(NC(=O)NC2=O)C(O)=O)cc1
#
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
 VRO  VRO  '5-[2-(4-methoxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  34  21  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VRO
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
 VRO  OAB  O  O      0  -0.540   1.0052   2.5225   0.0053
 VRO  CAO  C  C      0   0.416   2.2113   2.2526  -0.0157
 VRO  OAE  O  OC    -1  -0.586   3.1735   3.0351  -0.1194
 VRO  CAR  C  CR6    0   0.201   2.6182   0.7679   0.0792
 VRO  NAL  N  NR16   0  -0.707   3.9551   0.5946  -0.1566
 VRO  CAT  C  CR6    0   0.656   4.6058  -0.5956  -0.1712
 VRO  OAC  O  O      0  -0.493   5.7976  -0.7159  -0.3885
 VRO  NAM  N  NR16   0  -0.715   3.7823  -1.6610   0.0817
 VRO  CAU  C  CR6    0   0.564   2.4255  -1.6190   0.3440
 VRO  OAD  O  O      0  -0.467   1.8202  -2.6600   0.5433
 VRO  CAS  C  CR6    0  -0.159   1.8197  -0.2928   0.3538
 VRO  CAK  C  CH2    0  -0.476   0.3446  -0.2360   0.6155
 VRO  CAJ  C  CH2    0  -0.493  -0.4748  -0.3958  -0.6732
 VRO  CAP  C  CR6    0   0.103  -1.9495  -0.2456  -0.4320
 VRO  CAF  C  CR16   0  -0.290  -2.5000   1.0135  -0.1797
 VRO  CAH  C  CR16   0  -0.328  -3.8502   1.1757   0.0644
 VRO  CAQ  C  CR6    0   0.362  -4.7029   0.0687   0.0639
 VRO  OAN  O  O2     0  -0.474  -6.0073   0.3185   0.3036
 VRO  CAA  C  CH3    0  -0.435  -6.9148  -0.7630   0.2731
 VRO  CAI  C  CR16   0  -0.370  -4.1734  -1.1940  -0.1798
 VRO  CAG  C  CR16   0  -0.310  -2.8091  -1.3345  -0.4227
 VRO  H2   H  HNR6   0   0.419   4.2147  -2.5759   0.0668
 VRO  H4   H  HCH2   0   0.236   0.0755  -1.0349   1.3090
 VRO  H5   H  HCH2   0   0.254   0.0849   0.7057   1.0885
 VRO  H6   H  HCH2   0   0.242  -0.1390   0.3559  -1.3904
 VRO  H7   H  HCH2   0   0.237  -0.2683  -1.3725  -1.1156
 VRO  H8   H  HCR6   0   0.251  -1.8532   1.8836  -0.1786
 VRO  H9   H  HCR6   0   0.256  -4.2575   2.1617   0.2526
 VRO  H10  H  HCH3   0   0.226  -6.6930  -1.5079   1.0423
 VRO  H11  H  HCH3   0   0.258  -7.9008  -0.3467   0.4648
 VRO  H12  H  HCH3   0   0.226  -6.9273  -1.2597  -0.7010
 VRO  H13  H  HCR6   0   0.274  -4.7995  -2.0763  -0.1879
 VRO  H14  H  HCR6   0   0.246  -2.4179  -2.3270  -0.6153
 VRO  H15  H  HNR6   0   0.416   4.4786   1.4471  -0.3214

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
 VRO  CAA  OAN  single    1.412  0.020  1.412
 VRO  CAI  CAG  aromatic  1.393  0.020  1.393
 VRO  CAI  CAQ  aromatic  1.391  0.020  1.391
 VRO  CAG  CAP  aromatic  1.387  0.020  1.387
 VRO  OAN  CAQ  single    1.350  0.020  1.350
 VRO  CAQ  CAH  aromatic  1.397  0.020  1.397
 VRO  CAP  CAJ  single    1.502  0.020  1.502
 VRO  CAP  CAF  aromatic  1.397  0.020  1.397
 VRO  CAJ  CAK  single    1.535  0.020  1.535
 VRO  CAF  CAH  aromatic  1.382  0.020  1.382
 VRO  CAK  CAS  single    1.499  0.020  1.499
 VRO  OAD  CAU  double    1.221  0.020  1.221
 VRO  CAS  CAU  single    1.458  0.020  1.458
 VRO  CAS  CAR  double    1.356  0.020  1.356
 VRO  CAU  NAM  single    1.383  0.020  1.383
 VRO  CAR  CAO  single    1.542  0.020  1.542
 VRO  CAR  NAL  single    1.368  0.020  1.368
 VRO  OAB  CAO  deloc     1.236  0.020  1.236
 VRO  NAM  CAT  single    1.370  0.020  1.370
 VRO  CAO  OAE  deloc     1.245  0.020  1.245
 VRO  NAL  CAT  single    1.357  0.020  1.357
 VRO  CAT  OAC  double    1.217  0.020  1.217
 VRO  NAM  H2   single    0.860  0.020  1.020
 VRO  CAK  H4   single    0.970  0.020  1.090
 VRO  CAK  H5   single    0.970  0.020  1.090
 VRO  CAJ  H6   single    0.970  0.020  1.090
 VRO  CAJ  H7   single    0.970  0.020  1.090
 VRO  CAF  H8   single    0.930  0.020  1.080
 VRO  CAH  H9   single    0.930  0.020  1.080
 VRO  CAA  H10  single    0.970  0.020  1.090
 VRO  CAA  H11  single    0.970  0.020  1.090
 VRO  CAA  H12  single    0.970  0.020  1.090
 VRO  CAI  H13  single    0.930  0.020  1.080
 VRO  CAG  H14  single    0.930  0.020  1.080
 VRO  NAL  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
 VRO  CAR  CAO  OAE  113.98  3.000
 VRO  OAE  CAO  OAB  128.21  3.000
 VRO  CAR  CAO  OAB  117.81  3.000
 VRO  CAS  CAR  NAL  120.74  3.000
 VRO  NAL  CAR  CAO  111.65  3.000
 VRO  CAS  CAR  CAO  127.60  3.000
 VRO  H15  NAL  CAT  119.23  3.000
 VRO  H15  NAL  CAR  115.21  3.000
 VRO  CAT  NAL  CAR  125.56  3.000
 VRO  NAM  CAT  OAC  122.99  3.000
 VRO  OAC  CAT  NAL  123.94  3.000
 VRO  NAM  CAT  NAL  113.07  3.000
 VRO  H2   NAM  CAU  116.71  3.000
 VRO  H2   NAM  CAT  116.33  3.000
 VRO  CAU  NAM  CAT  126.96  3.000
 VRO  CAS  CAU  OAD  124.65  3.000
 VRO  CAS  CAU  NAM  115.89  3.000
 VRO  OAD  CAU  NAM  119.46  3.000
 VRO  CAK  CAS  CAU  116.39  3.000
 VRO  CAU  CAS  CAR  117.74  3.000
 VRO  CAK  CAS  CAR  125.82  3.000
 VRO  H5   CAK  H4   107.40  3.000
 VRO  H5   CAK  CAJ  109.16  3.000
 VRO  H4   CAK  CAJ  109.00  3.000
 VRO  H5   CAK  CAS  110.14  3.000
 VRO  H4   CAK  CAS  109.01  3.000
 VRO  CAJ  CAK  CAS  112.00  3.000
 VRO  H7   CAJ  H6   106.95  3.000
 VRO  H7   CAJ  CAP  109.89  3.000
 VRO  H6   CAJ  CAP  109.79  3.000
 VRO  H7   CAJ  CAK  109.40  3.000
 VRO  H6   CAJ  CAK  108.40  3.000
 VRO  CAP  CAJ  CAK  112.26  3.000
 VRO  CAG  CAP  CAF  117.52  3.000
 VRO  CAF  CAP  CAJ  120.40  3.000
 VRO  CAG  CAP  CAJ  122.07  3.000
 VRO  H8   CAF  CAH  119.25  3.000
 VRO  H8   CAF  CAP  119.23  3.000
 VRO  CAH  CAF  CAP  121.52  3.000
 VRO  H9   CAH  CAQ  119.45  3.000
 VRO  H9   CAH  CAF  120.33  3.000
 VRO  CAQ  CAH  CAF  120.21  3.000
 VRO  CAI  CAQ  OAN  124.55  3.000
 VRO  OAN  CAQ  CAH  116.30  3.000
 VRO  CAI  CAQ  CAH  119.15  3.000
 VRO  CAA  OAN  CAQ  118.39  3.000
 VRO  H12  CAA  H11  108.70  3.000
 VRO  H12  CAA  H10  108.63  3.000
 VRO  H11  CAA  H10  108.70  3.000
 VRO  H12  CAA  OAN  112.00  3.000
 VRO  H11  CAA  OAN  106.60  3.000
 VRO  H10  CAA  OAN  112.10  3.000
 VRO  H13  CAI  CAG  118.90  3.000
 VRO  H13  CAI  CAQ  121.43  3.000
 VRO  CAG  CAI  CAQ  119.67  3.000
 VRO  H14  CAG  CAI  118.48  3.000
 VRO  H14  CAG  CAP  119.59  3.000
 VRO  CAI  CAG  CAP  121.93  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
 VRO  CONST_01  CAQ  CAI  CAG  CAP     0.00   0.0  0
 VRO  CONST_02  CAQ  CAH  CAF  CAP     0.00   0.0  0
 VRO  CONST_03  CAI  CAG  CAP  CAF     0.00   0.0  0
 VRO  CONST_04  CAI  CAQ  CAH  CAF     0.00   0.0  0
 VRO  CONST_05  CAG  CAI  CAQ  CAH     0.00   0.0  0
 VRO  CONST_06  CAG  CAP  CAF  CAH     0.00   0.0  0
 VRO  CONST_07  NAM  CAT  NAL  CAR     0.00   0.0  0
 VRO  CONST_08  CAU  NAM  CAT  NAL     0.00   0.0  0
 VRO  CONST_09  CAS  CAU  NAM  CAT     0.00   0.0  0
 VRO  CONST_10  CAI  CAG  CAP  CAJ   180.00   0.0  0
 VRO  CONST_11  CAH  CAF  CAP  CAJ   180.00   0.0  0
 VRO  CONST_12  OAN  CAQ  CAH  CAF   180.00   0.0  0
 VRO  CONST_13  CAG  CAI  CAQ  OAN   180.00   0.0  0
 VRO  CONST_14  OAC  CAT  NAL  CAR   180.00   0.0  0
 VRO  CONST_15  OAD  CAU  NAM  CAT   180.00   0.0  0
 VRO  CONST_16  CAU  NAM  CAT  OAC   180.00   0.0  0
 VRO  CONST_17  H13  CAI  CAG  CAP   180.00   0.0  0
 VRO  CONST_18  H9   CAH  CAF  CAP   180.00   0.0  0
 VRO  CONST_19  H14  CAG  CAP  CAF   180.00   0.0  0
 VRO  CONST_20  H8   CAF  CAH  CAQ   180.00   0.0  0
 VRO  CONST_21  H2   NAM  CAT  NAL   180.00   0.0  0
 VRO  CONST_22  H15  NAL  CAT  NAM   180.00   0.0  0
 VRO  Var_01    CAS  CAR  CAO  OAB    -9.08  30.0  3
 VRO  Var_02    CAJ  CAK  CAS  CAR    90.49  30.0  2
 VRO  Var_03    CAP  CAJ  CAK  CAS  -176.07  30.0  1
 VRO  Var_04    CAG  CAP  CAJ  CAK  -105.19  30.0  2
 VRO  Var_05    CAI  CAQ  OAN  CAA    -1.77  30.0  2
 VRO  Var_06    H10  CAA  OAN  CAQ    62.53  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
 VRO  plan-1  CAO  0.020
 VRO  plan-1  CAR  0.020
 VRO  plan-1  NAL  0.020
 VRO  plan-1  CAT  0.020
 VRO  plan-1  OAC  0.020
 VRO  plan-1  NAM  0.020
 VRO  plan-1  CAU  0.020
 VRO  plan-1  OAD  0.020
 VRO  plan-1  CAS  0.020
 VRO  plan-1  CAK  0.020
 VRO  plan-1  H2   0.020
 VRO  plan-1  H15  0.020
 VRO  plan-2  CAJ  0.020
 VRO  plan-2  CAP  0.020
 VRO  plan-2  CAF  0.020
 VRO  plan-2  CAH  0.020
 VRO  plan-2  CAQ  0.020
 VRO  plan-2  OAN  0.020
 VRO  plan-2  CAI  0.020
 VRO  plan-2  CAG  0.020
 VRO  plan-2  H8   0.020
 VRO  plan-2  H9   0.020
 VRO  plan-2  H13  0.020
 VRO  plan-2  H14  0.020
 VRO  plan-3  OAB  0.020
 VRO  plan-3  CAO  0.020
 VRO  plan-3  OAE  0.020
 VRO  plan-3  CAR  0.020

