# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 21:36:07 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  31  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 PERFECT
;

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  -0.396   0.7606   2.4386  -0.2033
 QRO  CAN  C  C     0   0.519   1.8992   2.2043   0.0976
 QRO  OAD  O  OH1   0  -0.588   2.7899   3.1140   0.4459
 QRO  CAR  C  CR6   0   0.286   2.4978   0.8299   0.1079
 QRO  NAL  N  NR16  0  -0.731   3.8537   0.7871  -0.0958
 QRO  CAT  C  CR6   0   0.671   4.5840  -0.3638  -0.1523
 QRO  OAB  O  O     0  -0.472   5.7811  -0.3841  -0.3444
 QRO  NAM  N  NR16  0  -0.716   3.8336  -1.4968   0.0255
 QRO  CAU  C  CR6   0   0.587   2.4756  -1.5722   0.2497
 QRO  OAC  O  O     0  -0.440   1.9339  -2.6512   0.3891
 QRO  CAS  C  CR6   0  -0.120   1.7672  -0.2900   0.2987
 QRO  CAK  C  CH2   0  -0.502   0.2921  -0.3531   0.5484
 QRO  CAJ  C  CH2   0  -0.504  -0.5054  -0.5916  -0.7430
 QRO  CAO  C  CR6   0   0.125  -1.9830  -0.5971  -0.4755
 QRO  CAI  C  CR16  0  -0.453  -2.6713   0.6095  -0.3539
 QRO  CAQ  C  CR6   0   0.412  -4.0197   0.6074  -0.0714
 QRO  FAF  F  F     0  -0.308  -4.6882   1.7611   0.0423
 QRO  CAP  C  CR6   0   0.378  -4.7050  -0.5841   0.0974
 QRO  FAE  F  F     0  -0.308  -6.0154  -0.5502   0.3689
 QRO  CAH  C  CR16  0  -0.390  -4.0415  -1.7864  -0.0166
 QRO  CAG  C  CR16  0  -0.308  -2.6818  -1.7867  -0.3026
 QRO  H1   H  HOH1  0   0.504   2.4099   4.0054   0.3957
 QRO  H2   H  HNR6  0   0.431   4.3369  -2.3745  -0.0228
 QRO  H4   H  HCH2  0   0.265   0.0940  -1.1709   1.2432
 QRO  H5   H  HCH2  0   0.267  -0.0601   0.5552   1.0320
 QRO  H6   H  HCH2  0   0.261  -0.2632   0.1887  -1.4657
 QRO  H7   H  HCH2  0   0.258  -0.2071  -1.5435  -1.1854
 QRO  H8   H  HCR6  0   0.281  -2.1567   1.5546  -0.4827
 QRO  H9   H  HCR6  0   0.290  -4.5836  -2.7136   0.1160
 QRO  H10  H  HCR6  0   0.262  -2.1637  -2.7327  -0.3971
 QRO  H11  H  HNR6  0   0.439   4.3667   1.6466  -0.2343

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  1.389  0.020  1.389
 QRO  CAJ  CAO  single    1.502  0.020  1.502
 QRO  CAJ  CAK  single    1.536  0.020  1.536
 QRO  CAO  CAI  aromatic  1.394  0.020  1.394
 QRO  CAH  CAP  aromatic  1.378  0.020  1.378
 QRO  CAI  CAQ  aromatic  1.378  0.020  1.378
 QRO  CAP  CAQ  aromatic  1.385  0.020  1.385
 QRO  CAP  FAE  single    1.339  0.020  1.339
 QRO  CAQ  FAF  single    1.338  0.020  1.338
 QRO  CAK  CAS  single    1.497  0.020  1.497
 QRO  OAC  CAU  double    1.215  0.020  1.215
 QRO  CAS  CAU  single    1.466  0.020  1.466
 QRO  CAS  CAR  double    1.351  0.020  1.351
 QRO  CAU  NAM  single    1.378  0.020  1.378
 QRO  CAR  CAN  single    1.499  0.020  1.499
 QRO  CAR  NAL  single    1.372  0.020  1.372
 QRO  OAA  CAN  double    1.201  0.020  1.201
 QRO  NAM  CAT  single    1.371  0.020  1.371
 QRO  CAN  OAD  single    1.320  0.020  1.320
 QRO  CAT  NAL  single    1.364  0.020  1.364
 QRO  CAT  OAB  double    1.213  0.020  1.213
 QRO  OAD  H1   single    0.850  0.020  0.980
 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  111.14  3.000
 QRO  OAD  CAN  OAA  124.85  3.000
 QRO  CAR  CAN  OAA  124.01  3.000
 QRO  H1   OAD  CAN  110.81  3.000
 QRO  CAS  CAR  NAL  121.99  3.000
 QRO  NAL  CAR  CAN  114.98  3.000
 QRO  CAS  CAR  CAN  123.03  3.000
 QRO  H11  NAL  CAT  116.11  3.000
 QRO  H11  NAL  CAR  119.71  3.000
 QRO  CAT  NAL  CAR  124.16  3.000
 QRO  NAM  CAT  OAB  123.18  3.000
 QRO  OAB  CAT  NAL  123.31  3.000
 QRO  NAM  CAT  NAL  113.51  3.000
 QRO  H2   NAM  CAU  116.74  3.000
 QRO  H2   NAM  CAT  115.98  3.000
 QRO  CAU  NAM  CAT  127.28  3.000
 QRO  CAS  CAU  OAC  123.87  3.000
 QRO  CAS  CAU  NAM  115.71  3.000
 QRO  OAC  CAU  NAM  120.42  3.000
 QRO  CAK  CAS  CAU  116.41  3.000
 QRO  CAU  CAS  CAR  117.33  3.000
 QRO  CAK  CAS  CAR  126.25  3.000
 QRO  H5   CAK  H4   106.49  3.000
 QRO  H5   CAK  CAJ  109.59  3.000
 QRO  H4   CAK  CAJ  108.94  3.000
 QRO  H5   CAK  CAS  110.98  3.000
 QRO  H4   CAK  CAS  108.46  3.000
 QRO  CAJ  CAK  CAS  112.19  3.000
 QRO  H7   CAJ  H6   107.14  3.000
 QRO  H7   CAJ  CAO  109.76  3.000
 QRO  H6   CAJ  CAO  109.83  3.000
 QRO  H7   CAJ  CAK  109.52  3.000
 QRO  H6   CAJ  CAK  109.31  3.000
 QRO  CAO  CAJ  CAK  111.20  3.000
 QRO  CAG  CAO  CAI  118.78  3.000
 QRO  CAI  CAO  CAJ  119.87  3.000
 QRO  CAG  CAO  CAJ  121.32  3.000
 QRO  H8   CAI  CAQ  119.37  3.000
 QRO  H8   CAI  CAO  120.65  3.000
 QRO  CAQ  CAI  CAO  119.98  3.000
 QRO  CAP  CAQ  FAF  118.96  3.000
 QRO  FAF  CAQ  CAI  120.33  3.000
 QRO  CAP  CAQ  CAI  120.71  3.000
 QRO  CAH  CAP  FAE  120.68  3.000
 QRO  FAE  CAP  CAQ  119.16  3.000
 QRO  CAH  CAP  CAQ  120.16  3.000
 QRO  H9   CAH  CAG  121.01  3.000
 QRO  H9   CAH  CAP  119.75  3.000
 QRO  CAG  CAH  CAP  119.24  3.000
 QRO  H10  CAG  CAH  119.11  3.000
 QRO  H10  CAG  CAO  119.75  3.000
 QRO  CAH  CAG  CAO  121.14  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  CONST_24  H1   OAD  CAN  CAR   180.00   0.0  0
 QRO  Var_01    CAS  CAR  CAN  OAA   -26.76  30.0  2
 QRO  Var_02    CAJ  CAK  CAS  CAR    95.18  30.0  2
 QRO  Var_03    CAO  CAJ  CAK  CAS  -177.77  30.0  1
 QRO  Var_04    CAG  CAO  CAJ  CAK   -97.30  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
 QRO  plan-3  H1   0.020

