# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 00:41:31 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 5-[2-(3-chlorophenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(CCc2cccc(Cl)c2)C(=O)NC(=O)N1
#
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
 3RO  3RO  '5-[2-(3-chlorophenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  30  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3RO
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
 3RO  OAA  O   OC    -1  -0.585  -3.5395  -2.7945   0.0277
 3RO  CAN  C   C      0   0.417  -2.4638  -2.1750   0.1172
 3RO  OAD  O   O      0  -0.540  -1.3171  -2.6337   0.1595
 3RO  CAQ  C   CR6    0   0.202  -2.6259  -0.6413   0.1597
 3RO  NAL  N   NR16   0  -0.707  -3.9248  -0.2656  -0.0444
 3RO  CAS  C   CR6    0   0.657  -4.3800   1.0122  -0.0812
 3RO  OAB  O   O      0  -0.492  -5.5458   1.3132  -0.2580
 3RO  NAM  N   NR16   0  -0.715  -3.3884   1.9407   0.0976
 3RO  CAT  C   CR6    0   0.562  -2.0453   1.6918   0.3131
 3RO  OAC  O   O      0  -0.466  -1.2750   2.6296   0.4421
 3RO  CAR  C   CR6    0  -0.159  -1.6591   0.2870   0.3645
 3RO  CAK  C   CH2    0  -0.475  -0.2048   0.0031   0.5942
 3RO  CAJ  C   CH2    0  -0.498   0.5768  -0.1107  -0.7210
 3RO  CAP  C   C      0   0.117   2.0205  -0.4387  -0.4740
 3RO  CAI  C   C1     0  -0.275   2.9728   0.5724  -0.3841
 3RO  CAO  C   C      0  -0.021   4.2942   0.2523  -0.1132
 3RO  CL1  CL  CL     0  -0.137   5.4681   1.5287  -0.0104
 3RO  CAG  C   C1     0  -0.235   4.7013  -1.0587   0.0732
 3RO  CAF  C   C1     0  -0.245   3.7479  -2.0648  -0.0140
 3RO  CAH  C   C1     0  -0.297   2.4222  -1.7592  -0.2819
 3RO  H2   H   HNR6   0   0.420  -3.6716   2.9119   0.0640
 3RO  H4   H   HCH2   0   0.242   0.2249   0.8090   1.1910
 3RO  H5   H   HCH2   0   0.255  -0.0850  -0.9158   1.1607
 3RO  H6   H   HCH2   0   0.252   0.1208  -0.8908  -1.3312
 3RO  H7   H   HCH2   0   0.244   0.4961   0.8248  -1.2788
 3RO  H8   H   H      0   0.268   2.6828   1.6055  -0.5315
 3RO  H9   H   H      0   0.276   5.7365  -1.2930   0.2800
 3RO  H10  H   H      0   0.264   4.0485  -3.0944   0.1288
 3RO  H11  H   H      0   0.254   1.6844  -2.5502  -0.3418
 3RO  H12  H   HNR6   0   0.417  -4.5800  -1.0308  -0.1617

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
 3RO  CL1  CAO  single    1.737  0.020  1.737
 3RO  CAO  CAI  aromatic  1.386  0.020  1.386
 3RO  CAO  CAG  aromatic  1.385  0.020  1.385
 3RO  CAI  CAP  aromatic  1.392  0.020  1.392
 3RO  CAG  CAF  aromatic  1.389  0.020  1.389
 3RO  CAP  CAJ  single    1.501  0.020  1.501
 3RO  CAP  CAH  aromatic  1.394  0.020  1.394
 3RO  CAJ  CAK  single    1.534  0.020  1.534
 3RO  CAF  CAH  aromatic  1.387  0.020  1.387
 3RO  CAK  CAR  single    1.499  0.020  1.499
 3RO  OAC  CAT  double    1.220  0.020  1.220
 3RO  CAR  CAT  single    1.458  0.020  1.458
 3RO  CAR  CAQ  double    1.356  0.020  1.356
 3RO  CAT  NAM  single    1.383  0.020  1.383
 3RO  CAN  OAD  deloc     1.236  0.020  1.236
 3RO  CAN  CAQ  single    1.543  0.020  1.543
 3RO  CAN  OAA  deloc     1.245  0.020  1.245
 3RO  CAQ  NAL  single    1.368  0.020  1.368
 3RO  NAM  CAS  single    1.370  0.020  1.370
 3RO  NAL  CAS  single    1.357  0.020  1.357
 3RO  CAS  OAB  double    1.217  0.020  1.217
 3RO  NAM  H2   single    0.860  0.020  1.020
 3RO  CAK  H4   single    0.970  0.020  1.090
 3RO  CAK  H5   single    0.970  0.020  1.090
 3RO  CAJ  H6   single    0.970  0.020  1.090
 3RO  CAJ  H7   single    0.970  0.020  1.090
 3RO  CAI  H8   single    0.930  0.020  1.080
 3RO  CAG  H9   single    0.930  0.020  1.080
 3RO  CAF  H10  single    0.930  0.020  1.080
 3RO  CAH  H11  single    0.930  0.020  1.080
 3RO  NAL  H12  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
 3RO  CAQ  CAN  OAD  117.74  3.000
 3RO  CAQ  CAN  OAA  113.96  3.000
 3RO  OAD  CAN  OAA  128.29  3.000
 3RO  CAR  CAQ  NAL  120.78  3.000
 3RO  NAL  CAQ  CAN  111.64  3.000
 3RO  CAR  CAQ  CAN  127.58  3.000
 3RO  H12  NAL  CAS  119.38  3.000
 3RO  H12  NAL  CAQ  115.07  3.000
 3RO  CAS  NAL  CAQ  125.55  3.000
 3RO  NAM  CAS  OAB  123.00  3.000
 3RO  OAB  CAS  NAL  123.93  3.000
 3RO  NAM  CAS  NAL  113.07  3.000
 3RO  H2   NAM  CAT  116.72  3.000
 3RO  H2   NAM  CAS  116.32  3.000
 3RO  CAT  NAM  CAS  126.97  3.000
 3RO  CAR  CAT  OAC  124.72  3.000
 3RO  CAR  CAT  NAM  115.86  3.000
 3RO  OAC  CAT  NAM  119.42  3.000
 3RO  CAK  CAR  CAT  116.41  3.000
 3RO  CAT  CAR  CAQ  117.75  3.000
 3RO  CAK  CAR  CAQ  125.80  3.000
 3RO  H5   CAK  H4   107.23  3.000
 3RO  H5   CAK  CAJ  109.16  3.000
 3RO  H4   CAK  CAJ  108.85  3.000
 3RO  H5   CAK  CAR  110.31  3.000
 3RO  H4   CAK  CAR  109.02  3.000
 3RO  CAJ  CAK  CAR  112.14  3.000
 3RO  H7   CAJ  H6   107.23  3.000
 3RO  H7   CAJ  CAP  110.02  3.000
 3RO  H6   CAJ  CAP  109.76  3.000
 3RO  H7   CAJ  CAK  109.67  3.000
 3RO  H6   CAJ  CAK  108.65  3.000
 3RO  CAP  CAJ  CAK  111.42  3.000
 3RO  CAH  CAP  CAI  118.83  3.000
 3RO  CAH  CAP  CAJ  120.47  3.000
 3RO  CAI  CAP  CAJ  120.66  3.000
 3RO  H8   CAI  CAO  120.14  3.000
 3RO  H8   CAI  CAP  120.06  3.000
 3RO  CAO  CAI  CAP  119.80  3.000
 3RO  CAG  CAO  CL1  119.26  3.000
 3RO  CAG  CAO  CAI  121.66  3.000
 3RO  CL1  CAO  CAI  119.08  3.000
 3RO  H9   CAG  CAF  120.81  3.000
 3RO  H9   CAG  CAO  120.80  3.000
 3RO  CAF  CAG  CAO  118.39  3.000
 3RO  H10  CAF  CAH  120.05  3.000
 3RO  H10  CAF  CAG  119.36  3.000
 3RO  CAH  CAF  CAG  120.58  3.000
 3RO  H11  CAH  CAF  120.06  3.000
 3RO  H11  CAH  CAP  119.20  3.000
 3RO  CAF  CAH  CAP  120.74  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
 3RO  CONST_01  CAG  CAO  CAI  CAP     0.00   0.0  0
 3RO  CONST_02  CAG  CAF  CAH  CAP     0.00   0.0  0
 3RO  CONST_03  CAF  CAG  CAO  CAI     0.00   0.0  0
 3RO  CONST_04  CAF  CAH  CAP  CAI     0.00   0.0  0
 3RO  CONST_05  CAH  CAP  CAI  CAO     0.00   0.0  0
 3RO  CONST_06  CAH  CAF  CAG  CAO     0.00   0.0  0
 3RO  CONST_07  NAM  CAS  NAL  CAQ     0.00   0.0  0
 3RO  CONST_08  CAT  NAM  CAS  NAL     0.00   0.0  0
 3RO  CONST_09  CAR  CAT  NAM  CAS     0.00   0.0  0
 3RO  CONST_10  CAO  CAI  CAP  CAJ   180.00   0.0  0
 3RO  CONST_11  CAF  CAH  CAP  CAJ   180.00   0.0  0
 3RO  CONST_12  CL1  CAO  CAI  CAP   180.00   0.0  0
 3RO  CONST_13  CAF  CAG  CAO  CL1   180.00   0.0  0
 3RO  CONST_14  OAB  CAS  NAL  CAQ   180.00   0.0  0
 3RO  CONST_15  OAC  CAT  NAM  CAS   180.00   0.0  0
 3RO  CONST_16  CAT  NAM  CAS  OAB   180.00   0.0  0
 3RO  CONST_17  H10  CAF  CAH  CAP   180.00   0.0  0
 3RO  CONST_18  H9   CAG  CAO  CAI   180.00   0.0  0
 3RO  CONST_19  H11  CAH  CAP  CAI   180.00   0.0  0
 3RO  CONST_20  H8   CAI  CAO  CAG   180.00   0.0  0
 3RO  CONST_21  H2   NAM  CAS  NAL   180.00   0.0  0
 3RO  CONST_22  H12  NAL  CAS  NAM   180.00   0.0  0
 3RO  Var_01    CAR  CAQ  CAN  OAA   174.05  30.0  2
 3RO  Var_02    CAJ  CAK  CAR  CAQ    87.14  30.0  2
 3RO  Var_03    CAP  CAJ  CAK  CAR  -178.16  30.0  1
 3RO  Var_04    CAI  CAP  CAJ  CAK   -93.80  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
 3RO  plan-1  CAN  0.020
 3RO  plan-1  CAQ  0.020
 3RO  plan-1  NAL  0.020
 3RO  plan-1  CAS  0.020
 3RO  plan-1  OAB  0.020
 3RO  plan-1  NAM  0.020
 3RO  plan-1  CAT  0.020
 3RO  plan-1  OAC  0.020
 3RO  plan-1  CAR  0.020
 3RO  plan-1  CAK  0.020
 3RO  plan-1  H2   0.020
 3RO  plan-1  H12  0.020
 3RO  plan-2  CAJ  0.020
 3RO  plan-2  CAP  0.020
 3RO  plan-2  CAI  0.020
 3RO  plan-2  CAO  0.020
 3RO  plan-2  CL1  0.020
 3RO  plan-2  CAG  0.020
 3RO  plan-2  CAF  0.020
 3RO  plan-2  CAH  0.020
 3RO  plan-2  H8   0.020
 3RO  plan-2  H9   0.020
 3RO  plan-2  H10  0.020
 3RO  plan-2  H11  0.020
 3RO  plan-3  OAA  0.020
 3RO  plan-3  CAN  0.020
 3RO  plan-3  OAD  0.020
 3RO  plan-3  CAQ  0.020

