# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 10:59:36 2021
#   Inital geometry file: a 94 line input string
#   Ligand name: 5-[2-(4-fluoro-3-methylphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(CCC2=C(NC(=O)NC2=O)C(O)=O)ccc1F
#
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
 KRO  KRO  '5-[2-(4-fluoro-3-methylphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  34  21  .  2021-08-12  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KRO
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
 KRO  OAB  O  O     0  -0.398  7.5581  18.3758  13.5763
 KRO  CAN  C  C     0   0.510  6.6594  17.5892  13.6919
 KRO  OAE  O  OH1   0  -0.576  5.3762  17.8882  13.6254
 KRO  CAR  C  CR6   0   0.310  6.8551  16.1295  13.9856
 KRO  NAL  N  NR16  0  -0.728  5.9608  15.6109  14.8862
 KRO  CAT  C  CR6   0   0.669  5.9668  14.3124  15.3081
 KRO  OAC  O  O     0  -0.472  5.1761  13.8719  16.1151
 KRO  NAM  N  NR16  0  -0.716  6.9526  13.5565  14.7315
 KRO  CAU  C  CR6   0   0.584  7.8912  13.9689  13.8072
 KRO  OAD  O  O     0  -0.443  8.6981  13.1767  13.3601
 KRO  CAS  C  CR6   0  -0.131  7.8310  15.3807  13.4289
 KRO  CAK  C  CH2   0  -0.522  8.7617  15.8253  12.3437
 KRO  CAJ  C  CH2   0  -0.509  8.1910  15.5213  10.9435
 KRO  CAP  C  CR6   0   0.107  6.8828  16.2182  10.7012
 KRO  CAI  C  CR16  0  -0.326  6.8507  17.5696  10.3617
 KRO  CAO  C  CR6   0  -0.085  5.6608  18.2689  10.1954
 KRO  CAA  C  CH3   0  -0.715  5.6370  19.7281   9.8527
 KRO  CAQ  C  CR6   0   0.500  4.4862  17.5522  10.3776
 KRO  FAF  F  F     0  -0.316  3.3150  18.2001  10.2251
 KRO  CAH  C  CR16  0  -0.384  4.4656  16.2139  10.7060
 KRO  CAG  C  CR16  0  -0.303  5.6742  15.5515  10.8719
 KRO  H1   H  HOH1  0   0.498  5.2535  18.8413  13.4923
 KRO  H2   H  HNR6  0   0.431  6.9886  12.5843  15.0134
 KRO  H4   H  HCH2  0   0.265  9.7127  15.3040  12.4550
 KRO  H5   H  HCH2  0   0.270  8.9781  16.8868  12.4235
 KRO  H6   H  HCH2  0   0.252  8.0670  14.4433  10.8251
 KRO  H7   H  HCH2  0   0.259  8.9311  15.8375  10.2051
 KRO  H8   H  HCR6  0   0.252  7.7857  18.1030  10.2262
 KRO  H9   H  HCH3  0   0.250  5.0262  19.9317   8.9726
 KRO  H10  H  HCH3  0   0.249  5.2299  20.3242  10.6715
 KRO  H11  H  HCH3  0   0.249  6.6433  20.0904   9.6504
 KRO  H12  H  HCR6  0   0.273  3.5240  15.6966  10.8377
 KRO  H13  H  HCR6  0   0.256  5.6692  14.5000  11.1328
 KRO  H14  H  HNR6  0   0.438  5.2500  16.2041  15.2911

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
 KRO  CAA  CAO  single    1.499  0.020  1.499
 KRO  CAO  CAI  aromatic  1.390  0.020  1.390
 KRO  CAO  CAQ  aromatic  1.388  0.020  1.388
 KRO  FAF  CAQ  single    1.347  0.020  1.347
 KRO  CAI  CAP  aromatic  1.394  0.020  1.394
 KRO  CAQ  CAH  aromatic  1.378  0.020  1.378
 KRO  CAP  CAJ  single    1.502  0.020  1.502
 KRO  CAP  CAG  aromatic  1.391  0.020  1.391
 KRO  CAH  CAG  aromatic  1.388  0.020  1.388
 KRO  CAJ  CAK  single    1.542  0.020  1.542
 KRO  CAK  CAS  single    1.497  0.020  1.497
 KRO  OAD  CAU  double    1.216  0.020  1.216
 KRO  CAS  CAU  single    1.463  0.020  1.463
 KRO  CAS  CAR  double    1.350  0.020  1.350
 KRO  CAU  NAM  single    1.380  0.020  1.380
 KRO  OAB  CAN  double    1.200  0.020  1.200
 KRO  CAN  CAR  single    1.502  0.020  1.502
 KRO  CAN  OAE  single    1.319  0.020  1.319
 KRO  CAR  NAL  single    1.371  0.020  1.371
 KRO  NAM  CAT  single    1.370  0.020  1.370
 KRO  NAL  CAT  single    1.365  0.020  1.365
 KRO  CAT  OAC  double    1.213  0.020  1.213
 KRO  OAE  H1   single    0.850  0.020  0.980
 KRO  NAM  H2   single    0.860  0.020  1.020
 KRO  CAK  H4   single    0.970  0.020  1.090
 KRO  CAK  H5   single    0.970  0.020  1.090
 KRO  CAJ  H6   single    0.970  0.020  1.090
 KRO  CAJ  H7   single    0.970  0.020  1.090
 KRO  CAI  H8   single    0.930  0.020  1.080
 KRO  CAA  H9   single    0.970  0.020  1.090
 KRO  CAA  H10  single    0.970  0.020  1.090
 KRO  CAA  H11  single    0.970  0.020  1.090
 KRO  CAH  H12  single    0.930  0.020  1.080
 KRO  CAG  H13  single    0.930  0.020  1.080
 KRO  NAL  H14  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
 KRO  CAR  CAN  OAE  110.91  3.000
 KRO  OAE  CAN  OAB  125.10  3.000
 KRO  CAR  CAN  OAB  123.95  3.000
 KRO  H1   OAE  CAN  110.65  3.000
 KRO  CAS  CAR  NAL  122.18  3.000
 KRO  NAL  CAR  CAN  114.28  3.000
 KRO  CAS  CAR  CAN  123.54  3.000
 KRO  H14  NAL  CAT  115.95  3.000
 KRO  H14  NAL  CAR  120.00  3.000
 KRO  CAT  NAL  CAR  124.05  3.000
 KRO  NAM  CAT  OAC  123.30  3.000
 KRO  OAC  CAT  NAL  123.25  3.000
 KRO  NAM  CAT  NAL  113.46  3.000
 KRO  H2   NAM  CAU  116.68  3.000
 KRO  H2   NAM  CAT  115.99  3.000
 KRO  CAU  NAM  CAT  127.33  3.000
 KRO  CAS  CAU  OAD  124.13  3.000
 KRO  CAS  CAU  NAM  115.69  3.000
 KRO  OAD  CAU  NAM  120.19  3.000
 KRO  CAK  CAS  CAU  116.64  3.000
 KRO  CAU  CAS  CAR  117.28  3.000
 KRO  CAK  CAS  CAR  125.70  3.000
 KRO  H5   CAK  H4   106.62  3.000
 KRO  H5   CAK  CAJ  109.45  3.000
 KRO  H4   CAK  CAJ  108.74  3.000
 KRO  H5   CAK  CAS  111.15  3.000
 KRO  H4   CAK  CAS  109.04  3.000
 KRO  CAJ  CAK  CAS  111.69  3.000
 KRO  H7   CAJ  H6   106.83  3.000
 KRO  H7   CAJ  CAP  110.29  3.000
 KRO  H6   CAJ  CAP  109.98  3.000
 KRO  H7   CAJ  CAK  107.82  3.000
 KRO  H6   CAJ  CAK  109.58  3.000
 KRO  CAP  CAJ  CAK  112.17  3.000
 KRO  CAG  CAP  CAI  118.34  3.000
 KRO  CAG  CAP  CAJ  120.98  3.000
 KRO  CAI  CAP  CAJ  120.61  3.000
 KRO  H8   CAI  CAO  118.38  3.000
 KRO  H8   CAI  CAP  119.16  3.000
 KRO  CAO  CAI  CAP  122.45  3.000
 KRO  CAQ  CAO  CAA  121.28  3.000
 KRO  CAQ  CAO  CAI  116.67  3.000
 KRO  CAA  CAO  CAI  122.04  3.000
 KRO  H11  CAA  H10  107.60  3.000
 KRO  H11  CAA  H9   107.80  3.000
 KRO  H10  CAA  H9   107.13  3.000
 KRO  H11  CAA  CAO  110.60  3.000
 KRO  H10  CAA  CAO  111.47  3.000
 KRO  H9   CAA  CAO  112.04  3.000
 KRO  CAH  CAQ  FAF  118.75  3.000
 KRO  CAH  CAQ  CAO  123.05  3.000
 KRO  FAF  CAQ  CAO  118.20  3.000
 KRO  H12  CAH  CAG  120.99  3.000
 KRO  H12  CAH  CAQ  120.40  3.000
 KRO  CAG  CAH  CAQ  118.61  3.000
 KRO  H13  CAG  CAH  119.20  3.000
 KRO  H13  CAG  CAP  119.92  3.000
 KRO  CAH  CAG  CAP  120.87  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
 KRO  CONST_01  CAQ  CAO  CAI  CAP    0.00   0.0  0
 KRO  CONST_02  CAQ  CAH  CAG  CAP    0.00   0.0  0
 KRO  CONST_03  CAH  CAQ  CAO  CAI    0.00   0.0  0
 KRO  CONST_04  CAH  CAG  CAP  CAI    0.00   0.0  0
 KRO  CONST_05  CAG  CAP  CAI  CAO    0.00   0.0  0
 KRO  CONST_06  CAG  CAH  CAQ  CAO    0.00   0.0  0
 KRO  CONST_07  NAM  CAT  NAL  CAR    0.00   0.0  0
 KRO  CONST_08  CAU  NAM  CAT  NAL    0.00   0.0  0
 KRO  CONST_09  CAS  CAU  NAM  CAT    0.00   0.0  0
 KRO  CONST_10  CAO  CAI  CAP  CAJ  180.00   0.0  0
 KRO  CONST_11  CAH  CAG  CAP  CAJ  180.00   0.0  0
 KRO  CONST_12  CAA  CAO  CAI  CAP  180.00   0.0  0
 KRO  CONST_13  FAF  CAQ  CAO  CAI  180.00   0.0  0
 KRO  CONST_14  CAH  CAQ  CAO  CAA  180.00   0.0  0
 KRO  CONST_15  CAG  CAH  CAQ  FAF  180.00   0.0  0
 KRO  CONST_16  OAC  CAT  NAL  CAR  180.00   0.0  0
 KRO  CONST_17  OAD  CAU  NAM  CAT  180.00   0.0  0
 KRO  CONST_18  CAU  NAM  CAT  OAC  180.00   0.0  0
 KRO  CONST_19  H12  CAH  CAG  CAP  180.00   0.0  0
 KRO  CONST_20  H13  CAG  CAP  CAI  180.00   0.0  0
 KRO  CONST_21  H8   CAI  CAO  CAQ  180.00   0.0  0
 KRO  CONST_22  H2   NAM  CAT  NAL  180.00   0.0  0
 KRO  CONST_23  H14  NAL  CAT  NAM  180.00   0.0  0
 KRO  CONST_24  H1   OAE  CAN  CAR  180.00   0.0  0
 KRO  Var_01    CAS  CAR  CAN  OAB  -40.46  30.0  2
 KRO  Var_02    CAJ  CAK  CAS  CAR  -90.05  30.0  2
 KRO  Var_03    CAP  CAJ  CAK  CAS   60.31  30.0  3
 KRO  Var_04    CAI  CAP  CAJ  CAK   78.89  30.0  2
 KRO  Var_05    H9   CAA  CAO  CAI  126.82  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
 KRO  plan-1  CAN  0.020
 KRO  plan-1  CAR  0.020
 KRO  plan-1  NAL  0.020
 KRO  plan-1  CAT  0.020
 KRO  plan-1  OAC  0.020
 KRO  plan-1  NAM  0.020
 KRO  plan-1  CAU  0.020
 KRO  plan-1  OAD  0.020
 KRO  plan-1  CAS  0.020
 KRO  plan-1  CAK  0.020
 KRO  plan-1  H2   0.020
 KRO  plan-1  H14  0.020
 KRO  plan-2  CAJ  0.020
 KRO  plan-2  CAP  0.020
 KRO  plan-2  CAI  0.020
 KRO  plan-2  CAO  0.020
 KRO  plan-2  CAA  0.020
 KRO  plan-2  CAQ  0.020
 KRO  plan-2  FAF  0.020
 KRO  plan-2  CAH  0.020
 KRO  plan-2  CAG  0.020
 KRO  plan-2  H8   0.020
 KRO  plan-2  H12  0.020
 KRO  plan-2  H13  0.020
 KRO  plan-3  OAB  0.020
 KRO  plan-3  CAN  0.020
 KRO  plan-3  OAE  0.020
 KRO  plan-3  CAR  0.020
 KRO  plan-3  H1   0.020

