# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 22:38:04 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  33  20  .  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_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  OC    -1  -0.586  -2.6722  -3.0815  -0.0841
 LRO  CAN  C  C      0   0.415  -1.7305  -2.2704  -0.0200
 LRO  OAE  O  O      0  -0.541  -0.5169  -2.5044  -0.0478
 LRO  CAQ  C  CR6    0   0.203  -2.1755  -0.7991   0.0904
 LRO  NAL  N  NR16   0  -0.707  -3.5189  -0.6581  -0.1283
 LRO  CAS  C  CR6    0   0.656  -4.2002   0.5156  -0.1196
 LRO  OAC  O  O      0  -0.493  -5.3981   0.6070  -0.3151
 LRO  NAM  N  NR16   0  -0.715  -3.4001   1.5995   0.1293
 LRO  CAT  C  CR6    0   0.564  -2.0393   1.5899   0.3736
 LRO  OAD  O  O      0  -0.467  -1.4575   2.6439   0.5739
 LRO  CAR  C  CR6    0  -0.159  -1.4007   0.2794   0.3642
 LRO  CAK  C  CH2    0  -0.476   0.0774   0.2564   0.6141
 LRO  CAJ  C  CH2    0  -0.495   0.8842   0.4477  -0.6781
 LRO  CAP  C  C      0   0.108   2.3629   0.3403  -0.4386
 LRO  CAH  C  C1     0  -0.293   2.9532  -0.9054  -0.2251
 LRO  CAF  C  C1     0  -0.282   4.3105  -1.0199   0.0294
 LRO  CAO  C  C      0   0.080   5.1319   0.1068   0.0797
 LRO  CAA  C  CH3    0  -0.723   6.6074  -0.0253   0.3246
 LRO  CAG  C  C1     0  -0.288   4.5416   1.3494  -0.1285
 LRO  CAI  C  C1     0  -0.307   3.1797   1.4641  -0.3834
 LRO  H2   H  HNR6   0   0.420  -3.8569   2.5026   0.1311
 LRO  H4   H  HCH2   0   0.237   0.3314   1.0557   1.3130
 LRO  H5   H  HCH2   0   0.254   0.3648  -0.6824   1.0777
 LRO  H6   H  HCH2   0   0.243   0.5703  -0.3120  -1.3963
 LRO  H7   H  HCH2   0   0.238   0.6467   1.4201  -1.1147
 LRO  H8   H  H      0   0.246   2.3350  -1.7959  -0.2588
 LRO  H9   H  H      0   0.241   4.7402  -2.0020   0.1921
 LRO  H10  H  HCH3   0   0.245   7.1301  -0.3373  -0.5823
 LRO  H11  H  HCH3   0   0.241   7.0467   0.9196   0.6430
 LRO  H12  H  HCH3   0   0.241   6.8222  -0.7717   1.0898
 LRO  H13  H  H      0   0.242   5.1534   2.2437  -0.0904
 LRO  H14  H  H      0   0.240   2.7503   2.4466  -0.5442
 LRO  H15  H  HNR6   0   0.416  -4.0259  -1.5212  -0.2886

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  1.391  0.020  1.391
 LRO  CAG  CAI  aromatic  1.390  0.020  1.390
 LRO  CAA  CAO  single    1.502  0.020  1.502
 LRO  CAO  CAF  aromatic  1.395  0.020  1.395
 LRO  CAI  CAP  aromatic  1.390  0.020  1.390
 LRO  CAP  CAH  aromatic  1.395  0.020  1.395
 LRO  CAP  CAJ  single    1.502  0.020  1.502
 LRO  CAF  CAH  aromatic  1.386  0.020  1.386
 LRO  CAJ  CAK  single    1.535  0.020  1.535
 LRO  CAK  CAR  single    1.499  0.020  1.499
 LRO  OAD  CAT  double    1.221  0.020  1.221
 LRO  CAR  CAT  single    1.458  0.020  1.458
 LRO  CAR  CAQ  double    1.356  0.020  1.356
 LRO  CAT  NAM  single    1.383  0.020  1.383
 LRO  OAE  CAN  deloc     1.236  0.020  1.236
 LRO  CAN  CAQ  single    1.541  0.020  1.541
 LRO  CAN  OAB  deloc     1.245  0.020  1.245
 LRO  CAQ  NAL  single    1.368  0.020  1.368
 LRO  NAM  CAS  single    1.370  0.020  1.370
 LRO  NAL  CAS  single    1.357  0.020  1.357
 LRO  CAS  OAC  double    1.217  0.020  1.217
 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  CAQ  CAN  OAE  117.76  3.000
 LRO  CAQ  CAN  OAB  114.05  3.000
 LRO  OAE  CAN  OAB  128.19  3.000
 LRO  CAR  CAQ  NAL  120.75  3.000
 LRO  NAL  CAQ  CAN  111.74  3.000
 LRO  CAR  CAQ  CAN  127.51  3.000
 LRO  H15  NAL  CAS  119.09  3.000
 LRO  H15  NAL  CAQ  115.38  3.000
 LRO  CAS  NAL  CAQ  125.52  3.000
 LRO  NAM  CAS  OAC  123.00  3.000
 LRO  OAC  CAS  NAL  123.91  3.000
 LRO  NAM  CAS  NAL  113.09  3.000
 LRO  H2   NAM  CAT  116.75  3.000
 LRO  H2   NAM  CAS  116.28  3.000
 LRO  CAT  NAM  CAS  126.97  3.000
 LRO  CAR  CAT  OAD  124.65  3.000
 LRO  CAR  CAT  NAM  115.86  3.000
 LRO  OAD  CAT  NAM  119.49  3.000
 LRO  CAK  CAR  CAT  116.40  3.000
 LRO  CAT  CAR  CAQ  117.78  3.000
 LRO  CAK  CAR  CAQ  125.79  3.000
 LRO  H5   CAK  H4   107.35  3.000
 LRO  H5   CAK  CAJ  109.15  3.000
 LRO  H4   CAK  CAJ  108.98  3.000
 LRO  H5   CAK  CAR  110.20  3.000
 LRO  H4   CAK  CAR  108.95  3.000
 LRO  CAJ  CAK  CAR  112.08  3.000
 LRO  H7   CAJ  H6   107.10  3.000
 LRO  H7   CAJ  CAP  109.97  3.000
 LRO  H6   CAJ  CAP  109.77  3.000
 LRO  H7   CAJ  CAK  109.46  3.000
 LRO  H6   CAJ  CAK  108.42  3.000
 LRO  CAP  CAJ  CAK  111.98  3.000
 LRO  CAI  CAP  CAH  117.85  3.000
 LRO  CAH  CAP  CAJ  120.32  3.000
 LRO  CAI  CAP  CAJ  121.80  3.000
 LRO  H8   CAH  CAF  119.75  3.000
 LRO  H8   CAH  CAP  119.17  3.000
 LRO  CAF  CAH  CAP  121.09  3.000
 LRO  H9   CAF  CAO  119.52  3.000
 LRO  H9   CAF  CAH  119.38  3.000
 LRO  CAO  CAF  CAH  121.10  3.000
 LRO  CAG  CAO  CAA  121.32  3.000
 LRO  CAA  CAO  CAF  120.89  3.000
 LRO  CAG  CAO  CAF  117.78  3.000
 LRO  H12  CAA  H11  108.01  3.000
 LRO  H12  CAA  H10  107.03  3.000
 LRO  H11  CAA  H10  107.30  3.000
 LRO  H12  CAA  CAO  111.60  3.000
 LRO  H11  CAA  CAO  111.57  3.000
 LRO  H10  CAA  CAO  111.10  3.000
 LRO  H13  CAG  CAI  119.42  3.000
 LRO  H13  CAG  CAO  119.48  3.000
 LRO  CAI  CAG  CAO  121.11  3.000
 LRO  H14  CAI  CAG  119.34  3.000
 LRO  H14  CAI  CAP  119.60  3.000
 LRO  CAG  CAI  CAP  121.07  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  Var_01    CAR  CAQ  CAN  OAB   169.86  30.0  2
 LRO  Var_02    CAJ  CAK  CAR  CAQ    90.73  30.0  2
 LRO  Var_03    CAP  CAJ  CAK  CAR  -176.50  30.0  2
 LRO  Var_04    CAI  CAP  CAJ  CAK  -103.12  30.0  2
 LRO  Var_05    H10  CAA  CAO  CAF    78.20  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

