# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 01:12:56 2020
#   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  33  21  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.540   1.0468  -2.5674   0.0486
 KRO  CAN  C  C      0   0.417   2.2421  -2.2535   0.0781
 KRO  OAE  O  OC    -1  -0.585   3.2303  -2.9963   0.2208
 KRO  CAR  C  CR6    0   0.200   2.5966  -0.7582  -0.0584
 KRO  NAL  N  NR16   0  -0.707   3.9255  -0.5304   0.1743
 KRO  CAT  C  CR6    0   0.656   4.5330   0.6828   0.1576
 KRO  OAC  O  O      0  -0.493   5.7192   0.8517   0.3727
 KRO  NAM  N  NR16   0  -0.715   3.6721   1.7106  -0.1243
 KRO  CAU  C  CR6    0   0.564   2.3180   1.6126  -0.3861
 KRO  OAD  O  O      0  -0.467   1.6749   2.6252  -0.6115
 KRO  CAS  C  CR6    0  -0.158   1.7610   0.2654  -0.3625
 KRO  CAK  C  CH2    0  -0.477   0.2902   0.1477  -0.6258
 KRO  CAJ  C  CH2    0  -0.496  -0.5375   0.3003   0.6584
 KRO  CAP  C  CR6    0   0.129  -2.0046   0.0969   0.4095
 KRO  CAI  C  CR16   0  -0.352  -2.8843   1.1734   0.3411
 KRO  CAO  C  CR6    0  -0.076  -4.2443   1.0139   0.0845
 KRO  CAA  C  CH3    0  -0.716  -5.1870   2.1787   0.0252
 KRO  CAQ  C  CR6    0   0.493  -4.6923  -0.2840  -0.1063
 KRO  FAF  F  F      0  -0.318  -6.0037  -0.4791  -0.3506
 KRO  CAH  C  CR16   0  -0.390  -3.8584  -1.3828  -0.0526
 KRO  CAG  C  CR16   0  -0.308  -2.5104  -1.1848   0.2063
 KRO  H2   H  HNR6   0   0.420   4.0714   2.6407  -0.1353
 KRO  H4   H  HCH2   0   0.238  -0.0080   0.9218  -1.3352
 KRO  H5   H  HCH2   0   0.255   0.0670  -0.8125  -1.0802
 KRO  H6   H  HCH2   0   0.246  -0.1818  -0.4302   1.3872
 KRO  H7   H  HCH2   0   0.240  -0.3659   1.2897   1.0871
 KRO  H8   H  HCR6   0   0.247  -2.5050   2.1772   0.5003
 KRO  H9   H  HCH3   0   0.249  -5.7165   2.2225  -0.9274
 KRO  H10  H  HCH3   0   0.250  -5.9409   2.1246   0.8118
 KRO  H11  H  HCH3   0   0.248  -4.6476   3.1162   0.1478
 KRO  H12  H  HCR6   0   0.271  -4.2567  -2.3772  -0.2083
 KRO  H13  H  HCR6   0   0.258  -1.8433  -2.0373   0.2514
 KRO  H14  H  HNR6   0   0.416   4.4786  -1.3589   0.3634

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    1.500  0.020  1.500
 KRO  CAO  CAI  aromatic  1.393  0.020  1.393
 KRO  CAO  CAQ  aromatic  1.386  0.020  1.386
 KRO  FAF  CAQ  single    1.348  0.020  1.348
 KRO  CAI  CAP  aromatic  1.392  0.020  1.392
 KRO  CAQ  CAH  aromatic  1.381  0.020  1.381
 KRO  CAP  CAJ  single    1.502  0.020  1.502
 KRO  CAP  CAG  aromatic  1.393  0.020  1.393
 KRO  CAH  CAG  aromatic  1.387  0.020  1.387
 KRO  CAJ  CAK  single    1.535  0.020  1.535
 KRO  CAK  CAS  single    1.499  0.020  1.499
 KRO  OAD  CAU  double    1.221  0.020  1.221
 KRO  CAS  CAU  single    1.458  0.020  1.458
 KRO  CAS  CAR  double    1.356  0.020  1.356
 KRO  CAU  NAM  single    1.383  0.020  1.383
 KRO  OAB  CAN  deloc     1.236  0.020  1.236
 KRO  CAN  CAR  single    1.543  0.020  1.543
 KRO  CAN  OAE  deloc     1.244  0.020  1.244
 KRO  CAR  NAL  single    1.368  0.020  1.368
 KRO  NAM  CAT  single    1.370  0.020  1.370
 KRO  NAL  CAT  single    1.357  0.020  1.357
 KRO  CAT  OAC  double    1.217  0.020  1.217
 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  113.97  3.000
 KRO  OAE  CAN  OAB  128.24  3.000
 KRO  CAR  CAN  OAB  117.79  3.000
 KRO  CAS  CAR  NAL  120.73  3.000
 KRO  NAL  CAR  CAN  111.69  3.000
 KRO  CAS  CAR  CAN  127.58  3.000
 KRO  H14  NAL  CAT  119.26  3.000
 KRO  H14  NAL  CAR  115.18  3.000
 KRO  CAT  NAL  CAR  125.57  3.000
 KRO  NAM  CAT  OAC  123.00  3.000
 KRO  OAC  CAT  NAL  123.93  3.000
 KRO  NAM  CAT  NAL  113.08  3.000
 KRO  H2   NAM  CAU  116.71  3.000
 KRO  H2   NAM  CAT  116.34  3.000
 KRO  CAU  NAM  CAT  126.95  3.000
 KRO  CAS  CAU  OAD  124.63  3.000
 KRO  CAS  CAU  NAM  115.89  3.000
 KRO  OAD  CAU  NAM  119.48  3.000
 KRO  CAK  CAS  CAU  116.40  3.000
 KRO  CAU  CAS  CAR  117.76  3.000
 KRO  CAK  CAS  CAR  125.79  3.000
 KRO  H5   CAK  H4   107.40  3.000
 KRO  H5   CAK  CAJ  109.10  3.000
 KRO  H4   CAK  CAJ  109.02  3.000
 KRO  H5   CAK  CAS  110.17  3.000
 KRO  H4   CAK  CAS  109.05  3.000
 KRO  CAJ  CAK  CAS  111.97  3.000
 KRO  H7   CAJ  H6   107.04  3.000
 KRO  H7   CAJ  CAP  109.96  3.000
 KRO  H6   CAJ  CAP  109.77  3.000
 KRO  H7   CAJ  CAK  109.50  3.000
 KRO  H6   CAJ  CAK  108.44  3.000
 KRO  CAP  CAJ  CAK  111.99  3.000
 KRO  CAG  CAP  CAI  118.36  3.000
 KRO  CAG  CAP  CAJ  120.24  3.000
 KRO  CAI  CAP  CAJ  121.38  3.000
 KRO  H8   CAI  CAO  118.32  3.000
 KRO  H8   CAI  CAP  119.17  3.000
 KRO  CAO  CAI  CAP  122.51  3.000
 KRO  CAQ  CAO  CAA  121.24  3.000
 KRO  CAQ  CAO  CAI  116.62  3.000
 KRO  CAA  CAO  CAI  122.14  3.000
 KRO  H11  CAA  H10  107.69  3.000
 KRO  H11  CAA  H9   107.72  3.000
 KRO  H10  CAA  H9   107.23  3.000
 KRO  H11  CAA  CAO  110.68  3.000
 KRO  H10  CAA  CAO  111.56  3.000
 KRO  H9   CAA  CAO  111.77  3.000
 KRO  CAH  CAQ  FAF  118.65  3.000
 KRO  CAH  CAQ  CAO  123.00  3.000
 KRO  FAF  CAQ  CAO  118.35  3.000
 KRO  H12  CAH  CAG  121.04  3.000
 KRO  H12  CAH  CAQ  120.22  3.000
 KRO  CAG  CAH  CAQ  118.73  3.000
 KRO  H13  CAG  CAH  119.60  3.000
 KRO  H13  CAG  CAP  119.63  3.000
 KRO  CAH  CAG  CAP  120.77  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  Var_01    CAS  CAR  CAN  OAB    -8.23  30.0  2
 KRO  Var_02    CAJ  CAK  CAS  CAR    90.06  30.0  2
 KRO  Var_03    CAP  CAJ  CAK  CAS  -176.42  30.0  2
 KRO  Var_04    CAI  CAP  CAJ  CAK  -103.25  30.0  2
 KRO  Var_05    H9   CAA  CAO  CAI   123.40  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

