# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 23:01:45 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 5-[2-(3,4-difluorophenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(CCc2ccc(F)c(F)c2)C(=O)NC(=O)N1
#
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
 QRO  QRO  '5-[2-(3,4-difluorophenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  30  21  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QRO
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
 QRO  OAA  O  O      0  -0.541   0.6711   2.3537  -0.0586
 QRO  CAN  C  C      0   0.417   1.9016   2.2408  -0.0123
 QRO  OAD  O  OC    -1  -0.584   2.7596   3.1408  -0.0446
 QRO  CAR  C  CR6    0   0.204   2.4884   0.8175   0.0765
 QRO  NAL  N  NR16   0  -0.706   3.8387   0.8100  -0.1420
 QRO  CAT  C  CR6    0   0.656   4.6277  -0.2944  -0.1575
 QRO  OAB  O  O      0  -0.492   5.8280  -0.2682  -0.3569
 QRO  NAM  N  NR16   0  -0.714   3.9347  -1.4541   0.0711
 QRO  CAU  C  CR6    0   0.564   2.5795  -1.5787   0.3154
 QRO  OAC  O  O      0  -0.466   2.0994  -2.6864   0.4944
 QRO  CAS  C  CR6    0  -0.159   1.8213  -0.3347   0.3318
 QRO  CAK  C  CH2    0  -0.480   0.3498  -0.4496   0.5934
 QRO  CAJ  C  CH2    0  -0.495  -0.4501  -0.6748  -0.6975
 QRO  CAO  C  CR6    0   0.123  -1.9307  -0.6386  -0.4514
 QRO  CAI  C  CR16   0  -0.458  -2.5557   0.5853  -0.2080
 QRO  CAQ  C  CR6    0   0.413  -3.9090   0.6296   0.0415
 QRO  FAF  F  F      0  -0.309  -4.5175   1.8001   0.2699
 QRO  CAP  C  CR6    0   0.376  -4.6645  -0.5316   0.0572
 QRO  FAE  F  F      0  -0.310  -5.9795  -0.4507   0.2988
 QRO  CAH  C  CR16   0  -0.390  -4.0656  -1.7495  -0.1775
 QRO  CAG  C  CR16   0  -0.318  -2.6991  -1.7968  -0.4307
 QRO  H2   H  HNR6   0   0.420   4.4756  -2.3093   0.0517
 QRO  H4   H  HCH2   0   0.242   0.1720  -1.2861   1.2717
 QRO  H5   H  HCH2   0   0.257  -0.0117   0.4472   1.0879
 QRO  H6   H  HCH2   0   0.252  -0.1815   0.1012  -1.4157
 QRO  H7   H  HCH2   0   0.246  -0.1704  -1.6331  -1.1391
 QRO  H8   H  HCR6   0   0.285  -1.9813   1.5045  -0.2162
 QRO  H9   H  HCR6   0   0.288  -4.6622  -2.6524  -0.1644
 QRO  H10  H  HCR6   0   0.261  -2.2333  -2.7553  -0.6207
 QRO  H11  H  HNR6   0   0.417   4.2621   1.7197  -0.2863

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
 QRO  CAG  CAO  aromatic  1.390  0.020  1.390
 QRO  CAG  CAH  aromatic  1.391  0.020  1.391
 QRO  CAJ  CAO  single    1.501  0.020  1.501
 QRO  CAJ  CAK  single    1.535  0.020  1.535
 QRO  CAO  CAI  aromatic  1.396  0.020  1.396
 QRO  CAH  CAP  aromatic  1.377  0.020  1.377
 QRO  CAI  CAQ  aromatic  1.377  0.020  1.377
 QRO  CAP  CAQ  aromatic  1.385  0.020  1.385
 QRO  CAP  FAE  single    1.339  0.020  1.339
 QRO  CAQ  FAF  single    1.339  0.020  1.339
 QRO  CAK  CAS  single    1.499  0.020  1.499
 QRO  OAC  CAU  double    1.220  0.020  1.220
 QRO  CAS  CAU  single    1.457  0.020  1.457
 QRO  CAS  CAR  double    1.356  0.020  1.356
 QRO  CAU  NAM  single    1.383  0.020  1.383
 QRO  CAR  CAN  single    1.542  0.020  1.542
 QRO  CAR  NAL  single    1.368  0.020  1.368
 QRO  OAA  CAN  deloc     1.237  0.020  1.237
 QRO  NAM  CAT  single    1.370  0.020  1.370
 QRO  CAN  OAD  deloc     1.244  0.020  1.244
 QRO  CAT  NAL  single    1.357  0.020  1.357
 QRO  CAT  OAB  double    1.217  0.020  1.217
 QRO  NAM  H2   single    0.860  0.020  1.020
 QRO  CAK  H4   single    0.970  0.020  1.090
 QRO  CAK  H5   single    0.970  0.020  1.090
 QRO  CAJ  H6   single    0.970  0.020  1.090
 QRO  CAJ  H7   single    0.970  0.020  1.090
 QRO  CAI  H8   single    0.930  0.020  1.080
 QRO  CAH  H9   single    0.930  0.020  1.080
 QRO  CAG  H10  single    0.930  0.020  1.080
 QRO  NAL  H11  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
 QRO  CAR  CAN  OAD  114.01  3.000
 QRO  OAD  CAN  OAA  128.27  3.000
 QRO  CAR  CAN  OAA  117.71  3.000
 QRO  CAS  CAR  NAL  120.74  3.000
 QRO  NAL  CAR  CAN  111.81  3.000
 QRO  CAS  CAR  CAN  127.45  3.000
 QRO  H11  NAL  CAT  119.06  3.000
 QRO  H11  NAL  CAR  115.47  3.000
 QRO  CAT  NAL  CAR  125.46  3.000
 QRO  NAM  CAT  OAB  122.98  3.000
 QRO  OAB  CAT  NAL  123.89  3.000
 QRO  NAM  CAT  NAL  113.13  3.000
 QRO  H2   NAM  CAU  116.81  3.000
 QRO  H2   NAM  CAT  116.21  3.000
 QRO  CAU  NAM  CAT  126.97  3.000
 QRO  CAS  CAU  OAC  124.65  3.000
 QRO  CAS  CAU  NAM  115.79  3.000
 QRO  OAC  CAU  NAM  119.56  3.000
 QRO  CAK  CAS  CAU  116.58  3.000
 QRO  CAU  CAS  CAR  117.87  3.000
 QRO  CAK  CAS  CAR  125.53  3.000
 QRO  H5   CAK  H4   107.20  3.000
 QRO  H5   CAK  CAJ  109.30  3.000
 QRO  H4   CAK  CAJ  108.98  3.000
 QRO  H5   CAK  CAS  110.05  3.000
 QRO  H4   CAK  CAS  109.09  3.000
 QRO  CAJ  CAK  CAS  112.09  3.000
 QRO  H7   CAJ  H6   107.16  3.000
 QRO  H7   CAJ  CAO  109.89  3.000
 QRO  H6   CAJ  CAO  109.49  3.000
 QRO  H7   CAJ  CAK  109.60  3.000
 QRO  H6   CAJ  CAK  108.72  3.000
 QRO  CAO  CAJ  CAK  111.87  3.000
 QRO  CAG  CAO  CAI  118.72  3.000
 QRO  CAI  CAO  CAJ  119.43  3.000
 QRO  CAG  CAO  CAJ  121.84  3.000
 QRO  H8   CAI  CAQ  119.67  3.000
 QRO  H8   CAI  CAO  120.34  3.000
 QRO  CAQ  CAI  CAO  119.99  3.000
 QRO  CAP  CAQ  FAF  118.88  3.000
 QRO  FAF  CAQ  CAI  120.39  3.000
 QRO  CAP  CAQ  CAI  120.74  3.000
 QRO  CAH  CAP  FAE  120.73  3.000
 QRO  FAE  CAP  CAQ  119.13  3.000
 QRO  CAH  CAP  CAQ  120.14  3.000
 QRO  H9   CAH  CAG  121.03  3.000
 QRO  H9   CAH  CAP  119.73  3.000
 QRO  CAG  CAH  CAP  119.23  3.000
 QRO  H10  CAG  CAH  119.01  3.000
 QRO  H10  CAG  CAO  119.82  3.000
 QRO  CAH  CAG  CAO  121.17  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
 QRO  CONST_01  CAP  CAH  CAG  CAO     0.00   0.0  0
 QRO  CONST_02  CAP  CAQ  CAI  CAO     0.00   0.0  0
 QRO  CONST_03  CAH  CAG  CAO  CAI     0.00   0.0  0
 QRO  CONST_04  CAH  CAP  CAQ  CAI     0.00   0.0  0
 QRO  CONST_05  CAG  CAO  CAI  CAQ     0.00   0.0  0
 QRO  CONST_06  CAG  CAH  CAP  CAQ     0.00   0.0  0
 QRO  CONST_07  NAM  CAT  NAL  CAR     0.00   0.0  0
 QRO  CONST_08  CAU  NAM  CAT  NAL     0.00   0.0  0
 QRO  CONST_09  CAS  CAU  NAM  CAT     0.00   0.0  0
 QRO  CONST_10  CAH  CAG  CAO  CAJ   180.00   0.0  0
 QRO  CONST_11  CAQ  CAI  CAO  CAJ   180.00   0.0  0
 QRO  CONST_12  FAF  CAQ  CAI  CAO   180.00   0.0  0
 QRO  CONST_13  FAE  CAP  CAQ  CAI   180.00   0.0  0
 QRO  CONST_14  CAH  CAP  CAQ  FAF   180.00   0.0  0
 QRO  CONST_15  CAG  CAH  CAP  FAE   180.00   0.0  0
 QRO  CONST_16  OAB  CAT  NAL  CAR   180.00   0.0  0
 QRO  CONST_17  OAC  CAU  NAM  CAT   180.00   0.0  0
 QRO  CONST_18  CAU  NAM  CAT  OAB   180.00   0.0  0
 QRO  CONST_19  H9   CAH  CAG  CAO   180.00   0.0  0
 QRO  CONST_20  H10  CAG  CAO  CAI   180.00   0.0  0
 QRO  CONST_21  H8   CAI  CAQ  CAP   180.00   0.0  0
 QRO  CONST_22  H2   NAM  CAT  NAL   180.00   0.0  0
 QRO  CONST_23  H11  NAL  CAT  NAM   180.00   0.0  0
 QRO  Var_01    CAS  CAR  CAN  OAA   -11.85  30.0  2
 QRO  Var_02    CAJ  CAK  CAS  CAR    90.32  30.0  2
 QRO  Var_03    CAO  CAJ  CAK  CAS  -173.74  30.0  1
 QRO  Var_04    CAG  CAO  CAJ  CAK  -104.79  30.0  2

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
 QRO  plan-1  CAN  0.020
 QRO  plan-1  CAR  0.020
 QRO  plan-1  NAL  0.020
 QRO  plan-1  CAT  0.020
 QRO  plan-1  OAB  0.020
 QRO  plan-1  NAM  0.020
 QRO  plan-1  CAU  0.020
 QRO  plan-1  OAC  0.020
 QRO  plan-1  CAS  0.020
 QRO  plan-1  CAK  0.020
 QRO  plan-1  H2   0.020
 QRO  plan-1  H11  0.020
 QRO  plan-2  CAJ  0.020
 QRO  plan-2  CAO  0.020
 QRO  plan-2  CAI  0.020
 QRO  plan-2  CAQ  0.020
 QRO  plan-2  FAF  0.020
 QRO  plan-2  CAP  0.020
 QRO  plan-2  FAE  0.020
 QRO  plan-2  CAH  0.020
 QRO  plan-2  CAG  0.020
 QRO  plan-2  H8   0.020
 QRO  plan-2  H9   0.020
 QRO  plan-2  H10  0.020
 QRO  plan-3  OAA  0.020
 QRO  plan-3  CAN  0.020
 QRO  plan-3  OAD  0.020
 QRO  plan-3  CAR  0.020

