# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 06:06:12 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 5-[2-(4-tert-butylphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1ccc(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
 2RO  2RO  '5-[2-(4-tert-butylphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  43  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2RO
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
 2RO  OAD  O  O     0  -0.396   1.5133   2.5129  -0.2199
 2RO  CAP  C  C     0   0.519   2.6354   2.2161   0.0876
 2RO  OAG  O  OH1   0  -0.589   3.5714   3.0774   0.4422
 2RO  CAS  C  CR6   0   0.283   3.1588   0.8119   0.1025
 2RO  NAN  N  NR16  0  -0.732   4.5138   0.6989  -0.0832
 2RO  CAU  C  CR6   0   0.671   5.1830  -0.4882  -0.1390
 2RO  OAE  O  O     0  -0.473   6.3785  -0.5708  -0.3255
 2RO  NAO  N  NR16  0  -0.716   4.3738  -1.5804   0.0348
 2RO  CAV  C  CR6   0   0.587   3.0110  -1.5857   0.2405
 2RO  OAF  O  O     0  -0.440   2.4138  -2.6359   0.3739
 2RO  CAT  C  CR6   0  -0.120   2.3675  -0.2687   0.2788
 2RO  CAM  C  CH2   0  -0.499   0.8856  -0.2581   0.4966
 2RO  CAL  C  CH2   0  -0.503   0.1053  -0.4651  -0.8110
 2RO  CAQ  C  CR6   0   0.105  -1.3769  -0.3768  -0.5866
 2RO  CAH  C  CR16  0  -0.291  -2.0099   0.8630  -0.5008
 2RO  CAJ  C  CR16  0  -0.297  -3.3709   0.9556  -0.2658
 2RO  CAR  C  CR6   0   0.182  -4.1657  -0.1829  -0.1015
 2RO  CAW  C  CT    0  -0.169  -5.6637  -0.0329   0.1400
 2RO  CAB  C  CH3   0  -0.633  -5.8983   0.8293   1.3874
 2RO  CAC  C  CH3   0  -0.629  -6.3030   0.6472  -1.0785
 2RO  CAA  C  CH3   0  -0.666  -6.3542  -1.3802   0.3523
 2RO  CAK  C  CR16  0  -0.326  -3.5271  -1.4167  -0.1832
 2RO  CAI  C  CR16  0  -0.294  -2.1594  -1.5113  -0.4220
 2RO  H1   H  HOH1  0   0.504   3.2396   3.9874   0.3886
 2RO  H2   H  HNR6  0   0.439   5.0719   1.5307  -0.2160
 2RO  H3   H  HNR6  0   0.431   4.8312  -2.4831  -0.0092
 2RO  H4   H  HCH2  0   0.261   0.6334  -1.0610   1.1914
 2RO  H5   H  HCH2  0   0.264   0.5666   0.6695   0.9657
 2RO  H6   H  HCH2  0   0.252   0.4160   0.2906  -1.5346
 2RO  H7   H  HCH2  0   0.250   0.3607  -1.4380  -1.2354
 2RO  H8   H  HCR6  0   0.242  -1.4267   1.7689  -0.6239
 2RO  H9   H  HCR6  0   0.242  -3.8192   1.9410  -0.2145
 2RO  H10  H  HCH3  0   0.227  -5.5011   1.8387   1.2711
 2RO  H11  H  HCH3  0   0.226  -6.9678   0.9206   1.5884
 2RO  H12  H  HCH3  0   0.228  -5.4298   0.3854   2.2672
 2RO  H13  H  HCH3  0   0.226  -6.1882   0.0339  -1.9744
 2RO  H14  H  HCH3  0   0.225  -7.3719   0.8003  -0.9143
 2RO  H15  H  HCH3  0   0.227  -5.8586   1.6220  -1.2830
 2RO  H16  H  HCH3  0   0.229  -5.9616  -1.9094   1.2229
 2RO  H17  H  HCH3  0   0.236  -7.4211  -1.2242   0.5201
 2RO  H18  H  HCH3  0   0.229  -6.2525  -2.0339  -0.5157
 2RO  H19  H  HCR6  0   0.247  -4.0898  -2.3327  -0.0654
 2RO  H20  H  HCR6  0   0.240  -1.7011  -2.4920  -0.4866

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
 2RO  CAA  CAW  single    1.529  0.020  1.529
 2RO  CAK  CAI  aromatic  1.392  0.020  1.392
 2RO  CAK  CAR  aromatic  1.392  0.020  1.392
 2RO  CAB  CAW  single    1.534  0.020  1.534
 2RO  CAI  CAQ  aromatic  1.388  0.020  1.388
 2RO  CAR  CAW  single    1.525  0.020  1.525
 2RO  CAR  CAJ  aromatic  1.398  0.020  1.398
 2RO  CAW  CAC  single    1.535  0.020  1.535
 2RO  CAQ  CAL  single    1.502  0.020  1.502
 2RO  CAQ  CAH  aromatic  1.395  0.020  1.395
 2RO  CAL  CAM  single    1.537  0.020  1.537
 2RO  CAJ  CAH  aromatic  1.384  0.020  1.384
 2RO  CAM  CAT  single    1.498  0.020  1.498
 2RO  OAF  CAV  double    1.215  0.020  1.215
 2RO  CAT  CAV  single    1.466  0.020  1.466
 2RO  CAT  CAS  double    1.351  0.020  1.351
 2RO  CAV  NAO  single    1.378  0.020  1.378
 2RO  OAD  CAP  double    1.201  0.020  1.201
 2RO  CAS  CAP  single    1.499  0.020  1.499
 2RO  CAS  NAN  single    1.372  0.020  1.372
 2RO  CAP  OAG  single    1.320  0.020  1.320
 2RO  NAO  CAU  single    1.370  0.020  1.370
 2RO  NAN  CAU  single    1.364  0.020  1.364
 2RO  CAU  OAE  double    1.213  0.020  1.213
 2RO  OAG  H1   single    0.850  0.020  0.980
 2RO  NAN  H2   single    0.860  0.020  1.020
 2RO  NAO  H3   single    0.860  0.020  1.020
 2RO  CAM  H4   single    0.970  0.020  1.090
 2RO  CAM  H5   single    0.970  0.020  1.090
 2RO  CAL  H6   single    0.970  0.020  1.090
 2RO  CAL  H7   single    0.970  0.020  1.090
 2RO  CAH  H8   single    0.930  0.020  1.080
 2RO  CAJ  H9   single    0.930  0.020  1.080
 2RO  CAB  H10  single    0.970  0.020  1.090
 2RO  CAB  H11  single    0.970  0.020  1.090
 2RO  CAB  H12  single    0.970  0.020  1.090
 2RO  CAC  H13  single    0.970  0.020  1.090
 2RO  CAC  H14  single    0.970  0.020  1.090
 2RO  CAC  H15  single    0.970  0.020  1.090
 2RO  CAA  H16  single    0.970  0.020  1.090
 2RO  CAA  H17  single    0.970  0.020  1.090
 2RO  CAA  H18  single    0.970  0.020  1.090
 2RO  CAK  H19  single    0.930  0.020  1.080
 2RO  CAI  H20  single    0.930  0.020  1.080

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
 2RO  CAS  CAP  OAG  111.16  3.000
 2RO  OAG  CAP  OAD  124.75  3.000
 2RO  CAS  CAP  OAD  124.09  3.000
 2RO  H1   OAG  CAP  110.76  3.000
 2RO  CAT  CAS  NAN  122.02  3.000
 2RO  NAN  CAS  CAP  114.87  3.000
 2RO  CAT  CAS  CAP  123.11  3.000
 2RO  H2   NAN  CAU  116.11  3.000
 2RO  H2   NAN  CAS  119.69  3.000
 2RO  CAU  NAN  CAS  124.17  3.000
 2RO  NAO  CAU  OAE  123.18  3.000
 2RO  OAE  CAU  NAN  123.31  3.000
 2RO  NAO  CAU  NAN  113.51  3.000
 2RO  H3   NAO  CAV  116.71  3.000
 2RO  H3   NAO  CAU  115.99  3.000
 2RO  CAV  NAO  CAU  127.29  3.000
 2RO  CAT  CAV  OAF  123.89  3.000
 2RO  CAT  CAV  NAO  115.75  3.000
 2RO  OAF  CAV  NAO  120.36  3.000
 2RO  CAM  CAT  CAV  116.38  3.000
 2RO  CAV  CAT  CAS  117.26  3.000
 2RO  CAM  CAT  CAS  126.36  3.000
 2RO  H5   CAM  H4   106.57  3.000
 2RO  H5   CAM  CAL  109.45  3.000
 2RO  H4   CAM  CAL  108.99  3.000
 2RO  H5   CAM  CAT  111.04  3.000
 2RO  H4   CAM  CAT  108.42  3.000
 2RO  CAL  CAM  CAT  112.19  3.000
 2RO  H7   CAL  H6   107.02  3.000
 2RO  H7   CAL  CAQ  109.97  3.000
 2RO  H6   CAL  CAQ  109.84  3.000
 2RO  H7   CAL  CAM  109.38  3.000
 2RO  H6   CAL  CAM  109.05  3.000
 2RO  CAQ  CAL  CAM  111.47  3.000
 2RO  CAI  CAQ  CAH  117.61  3.000
 2RO  CAH  CAQ  CAL  120.63  3.000
 2RO  CAI  CAQ  CAL  121.74  3.000
 2RO  H8   CAH  CAJ  119.48  3.000
 2RO  H8   CAH  CAQ  119.44  3.000
 2RO  CAJ  CAH  CAQ  121.08  3.000
 2RO  H9   CAJ  CAR  119.97  3.000
 2RO  H9   CAJ  CAH  118.40  3.000
 2RO  CAR  CAJ  CAH  121.63  3.000
 2RO  CAK  CAR  CAW  123.18  3.000
 2RO  CAW  CAR  CAJ  119.80  3.000
 2RO  CAK  CAR  CAJ  117.01  3.000
 2RO  CAA  CAW  CAC  108.22  3.000
 2RO  CAC  CAW  CAB  109.44  3.000
 2RO  CAA  CAW  CAB  108.26  3.000
 2RO  CAC  CAW  CAR  109.09  3.000
 2RO  CAB  CAW  CAR  109.53  3.000
 2RO  CAA  CAW  CAR  112.27  3.000
 2RO  H12  CAB  H11  107.83  3.000
 2RO  H12  CAB  H10  107.82  3.000
 2RO  H11  CAB  H10  107.39  3.000
 2RO  H12  CAB  CAW  111.18  3.000
 2RO  H11  CAB  CAW  110.26  3.000
 2RO  H10  CAB  CAW  112.18  3.000
 2RO  H15  CAC  H14  107.56  3.000
 2RO  H15  CAC  H13  107.77  3.000
 2RO  H14  CAC  H13  107.76  3.000
 2RO  H15  CAC  CAW  112.03  3.000
 2RO  H14  CAC  CAW  110.51  3.000
 2RO  H13  CAC  CAW  111.03  3.000
 2RO  H18  CAA  H17  107.40  3.000
 2RO  H18  CAA  H16  108.08  3.000
 2RO  H17  CAA  H16  107.35  3.000
 2RO  H18  CAA  CAW  112.04  3.000
 2RO  H17  CAA  CAW  109.69  3.000
 2RO  H16  CAA  CAW  112.06  3.000
 2RO  H19  CAK  CAI  118.19  3.000
 2RO  H19  CAK  CAR  120.38  3.000
 2RO  CAI  CAK  CAR  121.42  3.000
 2RO  H20  CAI  CAK  119.15  3.000
 2RO  H20  CAI  CAQ  119.60  3.000
 2RO  CAK  CAI  CAQ  121.25  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
 2RO  CONST_01  CAR  CAK  CAI  CAQ     0.00   0.0  0
 2RO  CONST_02  CAR  CAJ  CAH  CAQ     0.00   0.0  0
 2RO  CONST_03  CAK  CAI  CAQ  CAH     0.00   0.0  0
 2RO  CONST_04  CAK  CAR  CAJ  CAH     0.00   0.0  0
 2RO  CONST_05  CAI  CAK  CAR  CAJ     0.00   0.0  0
 2RO  CONST_06  CAI  CAQ  CAH  CAJ     0.00   0.0  0
 2RO  CONST_07  NAO  CAU  NAN  CAS     0.00   0.0  0
 2RO  CONST_08  CAV  NAO  CAU  NAN     0.00   0.0  0
 2RO  CONST_09  CAT  CAV  NAO  CAU     0.00   0.0  0
 2RO  CONST_10  CAK  CAI  CAQ  CAL   180.00   0.0  0
 2RO  CONST_11  CAJ  CAH  CAQ  CAL   180.00   0.0  0
 2RO  CONST_12  CAW  CAR  CAJ  CAH   180.00   0.0  0
 2RO  CONST_13  CAI  CAK  CAR  CAW   180.00   0.0  0
 2RO  CONST_14  OAE  CAU  NAN  CAS   180.00   0.0  0
 2RO  CONST_15  OAF  CAV  NAO  CAU   180.00   0.0  0
 2RO  CONST_16  CAV  NAO  CAU  OAE   180.00   0.0  0
 2RO  CONST_17  H19  CAK  CAI  CAQ   180.00   0.0  0
 2RO  CONST_18  H9   CAJ  CAH  CAQ   180.00   0.0  0
 2RO  CONST_19  H20  CAI  CAQ  CAH   180.00   0.0  0
 2RO  CONST_20  H8   CAH  CAJ  CAR   180.00   0.0  0
 2RO  CONST_21  H3   NAO  CAU  NAN   180.00   0.0  0
 2RO  CONST_22  H2   NAN  CAU  NAO   180.00   0.0  0
 2RO  CONST_23  H1   OAG  CAP  CAS   180.00   0.0  0
 2RO  Var_01    CAT  CAS  CAP  OAD   -26.20  30.0  3
 2RO  Var_02    CAL  CAM  CAT  CAS    95.40  30.0  2
 2RO  Var_03    CAQ  CAL  CAM  CAT  -176.89  30.0  1
 2RO  Var_04    CAI  CAQ  CAL  CAM   -97.47  30.0  2
 2RO  Var_05    CAA  CAW  CAR  CAJ  -177.64  30.0  2
 2RO  Var_06    H16  CAA  CAW  CAR    60.91  30.0  3
 2RO  Var_07    H10  CAB  CAW  CAR    61.99  30.0  3
 2RO  Var_08    H13  CAC  CAW  CAR    62.60  30.0  3

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
 2RO  plan-1  CAP  0.020
 2RO  plan-1  CAS  0.020
 2RO  plan-1  NAN  0.020
 2RO  plan-1  CAU  0.020
 2RO  plan-1  OAE  0.020
 2RO  plan-1  NAO  0.020
 2RO  plan-1  CAV  0.020
 2RO  plan-1  OAF  0.020
 2RO  plan-1  CAT  0.020
 2RO  plan-1  CAM  0.020
 2RO  plan-1  H2   0.020
 2RO  plan-1  H3   0.020
 2RO  plan-2  CAL  0.020
 2RO  plan-2  CAQ  0.020
 2RO  plan-2  CAH  0.020
 2RO  plan-2  CAJ  0.020
 2RO  plan-2  CAR  0.020
 2RO  plan-2  CAW  0.020
 2RO  plan-2  CAK  0.020
 2RO  plan-2  CAI  0.020
 2RO  plan-2  H8   0.020
 2RO  plan-2  H9   0.020
 2RO  plan-2  H19  0.020
 2RO  plan-2  H20  0.020
 2RO  plan-3  OAD  0.020
 2RO  plan-3  CAP  0.020
 2RO  plan-3  OAG  0.020
 2RO  plan-3  CAS  0.020
 2RO  plan-3  H1   0.020

