# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 12:53:40 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 5-[2-(4-methylphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(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
 LRO  LRO  '5-[2-(4-methylphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  34  20  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LRO
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
 LRO  OAB  O  OH1   0  -0.589  -2.6305  -3.0836   0.3791
 LRO  CAN  C  C     0   0.518  -1.6771  -2.2318   0.0487
 LRO  OAE  O  O     0  -0.396  -0.5557  -2.5410  -0.2494
 LRO  CAQ  C  CR6   0   0.284  -2.1789  -0.8200   0.0781
 LRO  NAL  N  NR16  0  -0.732  -3.5293  -0.6818  -0.1231
 LRO  CAS  C  CR6   0   0.671  -4.1800   0.5162  -0.1630
 LRO  OAC  O  O     0  -0.472  -5.3727   0.6203  -0.3570
 LRO  NAM  N  NR16  0  -0.716  -3.3553   1.5926   0.0341
 LRO  CAT  C  CR6   0   0.586  -1.9959   1.5722   0.2608
 LRO  OAD  O  O     0  -0.440  -1.3848   2.6103   0.4231
 LRO  CAR  C  CR6   0  -0.120  -1.3735   0.2446   0.2854
 LRO  CAK  C  CH2   0  -0.499   0.1036   0.2078   0.5296
 LRO  CAJ  C  CH2   0  -0.502   0.9134   0.4146  -0.7603
 LRO  CAP  C  CR6   0   0.108   2.3902   0.3328  -0.4981
 LRO  CAH  C  CR16  0  -0.290   3.0227  -0.9019  -0.3808
 LRO  CAF  C  CR16  0  -0.289   4.3791  -0.9868  -0.0985
 LRO  CAO  C  CR6   0   0.081   5.1512   0.1592   0.0749
 LRO  CAA  C  CH3   0  -0.723   6.6243   0.0723   0.3524
 LRO  CAG  C  CR16  0  -0.281   4.5162   1.3946  -0.0390
 LRO  CAI  C  CR16  0  -0.301   3.1600   1.4795  -0.3202
 LRO  H1   H  HOH1  0   0.504  -2.3108  -3.9977   0.3202
 LRO  H2   H  HNR6  0   0.431  -3.7980   2.5033   0.0070
 LRO  H4   H  HCH2  0   0.261   0.3548   1.0005   1.2361
 LRO  H5   H  HCH2  0   0.264   0.3988  -0.7291   0.9962
 LRO  H6   H  HCH2  0   0.253   0.6222  -0.3439  -1.4889
 LRO  H7   H  HCH2  0   0.249   0.6649   1.3859  -1.1924
 LRO  H8   H  HCR6  0   0.244   2.4462  -1.8111  -0.5112
 LRO  H9   H  HCR6  0   0.243   4.8436  -1.9624  -0.0116
 LRO  H10  H  HCH3  0   0.246   7.2074   0.3301  -0.5341
 LRO  H11  H  HCH3  0   0.243   6.9250   0.7603   1.1431
 LRO  H12  H  HCH3  0   0.242   6.9154  -0.9332   0.6537
 LRO  H13  H  HCR6  0   0.243   5.0899   2.3048   0.0938
 LRO  H14  H  HCR6  0   0.242   2.6935   2.4545  -0.4063
 LRO  H15  H  HNR6  0   0.439  -4.0988  -1.5017  -0.2790

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
 LRO  CAG  CAO  aromatic  1.394  0.020  1.394
 LRO  CAG  CAI  aromatic  1.388  0.020  1.388
 LRO  CAA  CAO  single    1.501  0.020  1.501
 LRO  CAO  CAF  aromatic  1.393  0.020  1.393
 LRO  CAI  CAP  aromatic  1.392  0.020  1.392
 LRO  CAP  CAH  aromatic  1.392  0.020  1.392
 LRO  CAP  CAJ  single    1.502  0.020  1.502
 LRO  CAF  CAH  aromatic  1.388  0.020  1.388
 LRO  CAJ  CAK  single    1.537  0.020  1.537
 LRO  CAK  CAR  single    1.498  0.020  1.498
 LRO  OAD  CAT  double    1.216  0.020  1.216
 LRO  CAR  CAT  single    1.466  0.020  1.466
 LRO  CAR  CAQ  double    1.351  0.020  1.351
 LRO  CAT  NAM  single    1.378  0.020  1.378
 LRO  OAE  CAN  double    1.201  0.020  1.201
 LRO  CAN  CAQ  single    1.499  0.020  1.499
 LRO  CAN  OAB  single    1.320  0.020  1.320
 LRO  CAQ  NAL  single    1.372  0.020  1.372
 LRO  NAM  CAS  single    1.370  0.020  1.370
 LRO  NAL  CAS  single    1.364  0.020  1.364
 LRO  CAS  OAC  double    1.213  0.020  1.213
 LRO  OAB  H1   single    0.850  0.020  0.980
 LRO  NAM  H2   single    0.860  0.020  1.020
 LRO  CAK  H4   single    0.970  0.020  1.090
 LRO  CAK  H5   single    0.970  0.020  1.090
 LRO  CAJ  H6   single    0.970  0.020  1.090
 LRO  CAJ  H7   single    0.970  0.020  1.090
 LRO  CAH  H8   single    0.930  0.020  1.080
 LRO  CAF  H9   single    0.930  0.020  1.080
 LRO  CAA  H10  single    0.970  0.020  1.090
 LRO  CAA  H11  single    0.970  0.020  1.090
 LRO  CAA  H12  single    0.970  0.020  1.090
 LRO  CAG  H13  single    0.930  0.020  1.080
 LRO  CAI  H14  single    0.930  0.020  1.080
 LRO  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
 LRO  H1   OAB  CAN  110.77  3.000
 LRO  CAQ  CAN  OAE  124.06  3.000
 LRO  CAQ  CAN  OAB  111.17  3.000
 LRO  OAE  CAN  OAB  124.77  3.000
 LRO  CAR  CAQ  NAL  121.99  3.000
 LRO  NAL  CAQ  CAN  114.93  3.000
 LRO  CAR  CAQ  CAN  123.08  3.000
 LRO  H15  NAL  CAS  116.07  3.000
 LRO  H15  NAL  CAQ  119.71  3.000
 LRO  CAS  NAL  CAQ  124.21  3.000
 LRO  NAM  CAS  OAC  123.19  3.000
 LRO  OAC  CAS  NAL  123.31  3.000
 LRO  NAM  CAS  NAL  113.49  3.000
 LRO  H2   NAM  CAT  116.67  3.000
 LRO  H2   NAM  CAS  116.06  3.000
 LRO  CAT  NAM  CAS  127.27  3.000
 LRO  CAR  CAT  OAD  123.88  3.000
 LRO  CAR  CAT  NAM  115.77  3.000
 LRO  OAD  CAT  NAM  120.35  3.000
 LRO  CAK  CAR  CAT  116.34  3.000
 LRO  CAT  CAR  CAQ  117.24  3.000
 LRO  CAK  CAR  CAQ  126.42  3.000
 LRO  H5   CAK  H4   106.59  3.000
 LRO  H5   CAK  CAJ  109.45  3.000
 LRO  H4   CAK  CAJ  108.92  3.000
 LRO  H5   CAK  CAR  111.03  3.000
 LRO  H4   CAK  CAR  108.35  3.000
 LRO  CAJ  CAK  CAR  112.30  3.000
 LRO  H7   CAJ  H6   107.06  3.000
 LRO  H7   CAJ  CAP  109.96  3.000
 LRO  H6   CAJ  CAP  109.94  3.000
 LRO  H7   CAJ  CAK  109.38  3.000
 LRO  H6   CAJ  CAK  109.04  3.000
 LRO  CAP  CAJ  CAK  111.36  3.000
 LRO  CAI  CAP  CAH  117.93  3.000
 LRO  CAH  CAP  CAJ  120.64  3.000
 LRO  CAI  CAP  CAJ  121.40  3.000
 LRO  H8   CAH  CAF  119.51  3.000
 LRO  H8   CAH  CAP  119.47  3.000
 LRO  CAF  CAH  CAP  121.02  3.000
 LRO  H9   CAF  CAO  119.54  3.000
 LRO  H9   CAF  CAH  119.35  3.000
 LRO  CAO  CAF  CAH  121.11  3.000
 LRO  CAG  CAO  CAA  120.89  3.000
 LRO  CAA  CAO  CAF  121.29  3.000
 LRO  CAG  CAO  CAF  117.81  3.000
 LRO  H12  CAA  H11  107.95  3.000
 LRO  H12  CAA  H10  107.44  3.000
 LRO  H11  CAA  H10  107.01  3.000
 LRO  H12  CAA  CAO  111.51  3.000
 LRO  H11  CAA  CAO  111.60  3.000
 LRO  H10  CAA  CAO  111.12  3.000
 LRO  H13  CAG  CAI  119.39  3.000
 LRO  H13  CAG  CAO  119.54  3.000
 LRO  CAI  CAG  CAO  121.07  3.000
 LRO  H14  CAI  CAG  119.45  3.000
 LRO  H14  CAI  CAP  119.50  3.000
 LRO  CAG  CAI  CAP  121.05  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
 LRO  CONST_01  CAO  CAG  CAI  CAP     0.00   0.0  0
 LRO  CONST_02  CAO  CAF  CAH  CAP     0.00   0.0  0
 LRO  CONST_03  CAG  CAI  CAP  CAH     0.00   0.0  0
 LRO  CONST_04  CAG  CAO  CAF  CAH     0.00   0.0  0
 LRO  CONST_05  CAI  CAG  CAO  CAF     0.00   0.0  0
 LRO  CONST_06  CAI  CAP  CAH  CAF     0.00   0.0  0
 LRO  CONST_07  NAM  CAS  NAL  CAQ     0.00   0.0  0
 LRO  CONST_08  CAT  NAM  CAS  NAL     0.00   0.0  0
 LRO  CONST_09  CAR  CAT  NAM  CAS     0.00   0.0  0
 LRO  CONST_10  CAG  CAI  CAP  CAJ   180.00   0.0  0
 LRO  CONST_11  CAF  CAH  CAP  CAJ   180.00   0.0  0
 LRO  CONST_12  CAA  CAO  CAF  CAH   180.00   0.0  0
 LRO  CONST_13  CAI  CAG  CAO  CAA   180.00   0.0  0
 LRO  CONST_14  OAC  CAS  NAL  CAQ   180.00   0.0  0
 LRO  CONST_15  OAD  CAT  NAM  CAS   180.00   0.0  0
 LRO  CONST_16  CAT  NAM  CAS  OAC   180.00   0.0  0
 LRO  CONST_17  H13  CAG  CAI  CAP   180.00   0.0  0
 LRO  CONST_18  H9   CAF  CAH  CAP   180.00   0.0  0
 LRO  CONST_19  H14  CAI  CAP  CAH   180.00   0.0  0
 LRO  CONST_20  H8   CAH  CAF  CAO   180.00   0.0  0
 LRO  CONST_21  H2   NAM  CAS  NAL   180.00   0.0  0
 LRO  CONST_22  H15  NAL  CAS  NAM   180.00   0.0  0
 LRO  CONST_23  H1   OAB  CAN  CAQ   180.00   0.0  0
 LRO  Var_01    CAR  CAQ  CAN  OAB   154.17  30.0  2
 LRO  Var_02    CAJ  CAK  CAR  CAQ    95.09  30.0  2
 LRO  Var_03    CAP  CAJ  CAK  CAR  -178.30  30.0  2
 LRO  Var_04    CAI  CAP  CAJ  CAK   -97.60  30.0  3
 LRO  Var_05    H10  CAA  CAO  CAF   104.69  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
 LRO  plan-1  CAN  0.020
 LRO  plan-1  CAQ  0.020
 LRO  plan-1  NAL  0.020
 LRO  plan-1  CAS  0.020
 LRO  plan-1  OAC  0.020
 LRO  plan-1  NAM  0.020
 LRO  plan-1  CAT  0.020
 LRO  plan-1  OAD  0.020
 LRO  plan-1  CAR  0.020
 LRO  plan-1  CAK  0.020
 LRO  plan-1  H2   0.020
 LRO  plan-1  H15  0.020
 LRO  plan-2  CAJ  0.020
 LRO  plan-2  CAP  0.020
 LRO  plan-2  CAH  0.020
 LRO  plan-2  CAF  0.020
 LRO  plan-2  CAO  0.020
 LRO  plan-2  CAA  0.020
 LRO  plan-2  CAG  0.020
 LRO  plan-2  CAI  0.020
 LRO  plan-2  H8   0.020
 LRO  plan-2  H9   0.020
 LRO  plan-2  H13  0.020
 LRO  plan-2  H14  0.020
 LRO  plan-3  OAB  0.020
 LRO  plan-3  CAN  0.020
 LRO  plan-3  OAE  0.020
 LRO  plan-3  CAQ  0.020
 LRO  plan-3  H1   0.020

