# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 16:55:54 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2,6-dioxo-5-(2-phenylethyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(CCc2ccccc2)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
 MRO  MRO  '2,6-dioxo-5-(2-phenylethyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  31  19  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MRO
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
 MRO  OAA  O  O     0  -0.396   0.2064   2.5210  -0.1958
 MRO  CAN  C  C     0   0.518   1.3320   2.2115   0.0857
 MRO  OAD  O  OH1   0  -0.589   2.2885   3.0618   0.4104
 MRO  CAQ  C  CR6   0   0.284   1.8364   0.8002   0.0955
 MRO  NAL  N  NR16  0  -0.732   3.1832   0.6663  -0.1310
 MRO  CAR  C  CR6   0   0.671   3.8341  -0.5306  -0.1965
 MRO  OAB  O  O     0  -0.472   5.0227  -0.6313  -0.4149
 MRO  NAM  N  NR16  0  -0.716   3.0145  -1.6098   0.0068
 MRO  CAS  C  CR6   0   0.586   1.6593  -1.5938   0.2577
 MRO  OAC  O  O     0  -0.440   1.0523  -2.6343   0.4196
 MRO  CAP  C  CR6   0  -0.120   1.0362  -0.2674   0.3066
 MRO  CAK  C  CH2   0  -0.499  -0.4368  -0.2344   0.5746
 MRO  CAJ  C  CH2   0  -0.503  -1.2649  -0.4378  -0.7042
 MRO  CAO  C  CR6   0   0.124  -2.7375  -0.3551  -0.4189
 MRO  CAH  C  CR16  0  -0.314  -3.4985  -1.5040  -0.2201
 MRO  CAF  C  CR16  0  -0.241  -4.8525  -1.4192   0.0806
 MRO  CAE  C  CR16  0  -0.272  -5.4656  -0.1783   0.1882
 MRO  CAG  C  CR16  0  -0.241  -4.7159   0.9757  -0.0060
 MRO  CAI  C  CR16  0  -0.305  -3.3642   0.8855  -0.3065
 MRO  H1   H  HOH1  0   0.504   1.9680   3.9761   0.3595
 MRO  H2   H  HNR6  0   0.431   3.4573  -2.5195  -0.0418
 MRO  H4   H  HCH2  0   0.262  -0.6757  -1.0303   1.2819
 MRO  H5   H  HCH2  0   0.264  -0.7266   0.6998   1.0496
 MRO  H6   H  HCH2  0   0.255  -0.9852   0.3223  -1.4356
 MRO  H7   H  HCH2  0   0.251  -1.0237  -1.4085  -1.1412
 MRO  H8   H  HCR6  0   0.245  -3.0285  -2.4770  -0.3079
 MRO  H9   H  HCR6  0   0.253  -5.4289  -2.3236   0.2287
 MRO  H10  H  HCR6  0   0.253  -6.5212  -0.1096   0.4176
 MRO  H11  H  HCR6  0   0.252  -5.1860   1.9477   0.0747
 MRO  H12  H  HCR6  0   0.247  -2.7851   1.7893  -0.4587
 MRO  H13  H  HNR6  0   0.439   3.7486   1.4891  -0.2870

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
 MRO  CAF  CAH  aromatic  1.390  0.020  1.390
 MRO  CAF  CAE  aromatic  1.388  0.020  1.388
 MRO  CAH  CAO  aromatic  1.392  0.020  1.392
 MRO  CAE  CAG  aromatic  1.390  0.020  1.390
 MRO  CAO  CAJ  single    1.502  0.020  1.502
 MRO  CAO  CAI  aromatic  1.394  0.020  1.394
 MRO  CAJ  CAK  single    1.537  0.020  1.537
 MRO  CAG  CAI  aromatic  1.388  0.020  1.388
 MRO  CAK  CAP  single    1.498  0.020  1.498
 MRO  OAC  CAS  double    1.215  0.020  1.215
 MRO  CAP  CAS  single    1.466  0.020  1.466
 MRO  CAP  CAQ  double    1.351  0.020  1.351
 MRO  CAS  NAM  single    1.378  0.020  1.378
 MRO  CAQ  CAN  single    1.499  0.020  1.499
 MRO  CAQ  NAL  single    1.372  0.020  1.372
 MRO  CAN  OAA  double    1.201  0.020  1.201
 MRO  CAN  OAD  single    1.320  0.020  1.320
 MRO  NAM  CAR  single    1.370  0.020  1.370
 MRO  NAL  CAR  single    1.364  0.020  1.364
 MRO  CAR  OAB  double    1.213  0.020  1.213
 MRO  OAD  H1   single    0.850  0.020  0.980
 MRO  NAM  H2   single    0.860  0.020  1.020
 MRO  CAK  H4   single    0.970  0.020  1.090
 MRO  CAK  H5   single    0.970  0.020  1.090
 MRO  CAJ  H6   single    0.970  0.020  1.090
 MRO  CAJ  H7   single    0.970  0.020  1.090
 MRO  CAH  H8   single    0.930  0.020  1.080
 MRO  CAF  H9   single    0.930  0.020  1.080
 MRO  CAE  H10  single    0.930  0.020  1.080
 MRO  CAG  H11  single    0.930  0.020  1.080
 MRO  CAI  H12  single    0.930  0.020  1.080
 MRO  NAL  H13  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
 MRO  CAQ  CAN  OAD  111.16  3.000
 MRO  OAD  CAN  OAA  124.80  3.000
 MRO  CAQ  CAN  OAA  124.04  3.000
 MRO  H1   OAD  CAN  110.78  3.000
 MRO  CAP  CAQ  NAL  122.01  3.000
 MRO  NAL  CAQ  CAN  114.90  3.000
 MRO  CAP  CAQ  CAN  123.08  3.000
 MRO  H13  NAL  CAR  116.11  3.000
 MRO  H13  NAL  CAQ  119.69  3.000
 MRO  CAR  NAL  CAQ  124.18  3.000
 MRO  NAM  CAR  OAB  123.19  3.000
 MRO  OAB  CAR  NAL  123.32  3.000
 MRO  NAM  CAR  NAL  113.49  3.000
 MRO  H2   NAM  CAS  116.68  3.000
 MRO  H2   NAM  CAR  116.03  3.000
 MRO  CAS  NAM  CAR  127.29  3.000
 MRO  CAP  CAS  OAC  123.90  3.000
 MRO  CAP  CAS  NAM  115.75  3.000
 MRO  OAC  CAS  NAM  120.36  3.000
 MRO  CAK  CAP  CAS  116.36  3.000
 MRO  CAS  CAP  CAQ  117.26  3.000
 MRO  CAK  CAP  CAQ  126.38  3.000
 MRO  H5   CAK  H4   106.57  3.000
 MRO  H5   CAK  CAJ  109.49  3.000
 MRO  H4   CAK  CAJ  108.95  3.000
 MRO  H5   CAK  CAP  111.06  3.000
 MRO  H4   CAK  CAP  108.37  3.000
 MRO  CAJ  CAK  CAP  112.21  3.000
 MRO  H7   CAJ  H6   107.12  3.000
 MRO  H7   CAJ  CAO  109.98  3.000
 MRO  H6   CAJ  CAO  109.89  3.000
 MRO  H7   CAJ  CAK  109.38  3.000
 MRO  H6   CAJ  CAK  109.11  3.000
 MRO  CAO  CAJ  CAK  111.27  3.000
 MRO  CAI  CAO  CAH  118.49  3.000
 MRO  CAI  CAO  CAJ  120.32  3.000
 MRO  CAH  CAO  CAJ  121.16  3.000
 MRO  H8   CAH  CAF  119.65  3.000
 MRO  H8   CAH  CAO  119.47  3.000
 MRO  CAF  CAH  CAO  120.87  3.000
 MRO  H9   CAF  CAE  120.06  3.000
 MRO  H9   CAF  CAH  119.83  3.000
 MRO  CAE  CAF  CAH  120.11  3.000
 MRO  H10  CAE  CAG  120.20  3.000
 MRO  H10  CAE  CAF  120.25  3.000
 MRO  CAG  CAE  CAF  119.54  3.000
 MRO  H11  CAG  CAI  119.83  3.000
 MRO  H11  CAG  CAE  120.05  3.000
 MRO  CAI  CAG  CAE  120.12  3.000
 MRO  H12  CAI  CAG  119.77  3.000
 MRO  H12  CAI  CAO  119.36  3.000
 MRO  CAG  CAI  CAO  120.87  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
 MRO  CONST_01  CAE  CAF  CAH  CAO     0.00   0.0  0
 MRO  CONST_02  CAE  CAG  CAI  CAO     0.00   0.0  0
 MRO  CONST_03  CAG  CAE  CAF  CAH     0.00   0.0  0
 MRO  CONST_04  CAG  CAI  CAO  CAH     0.00   0.0  0
 MRO  CONST_05  CAI  CAO  CAH  CAF     0.00   0.0  0
 MRO  CONST_06  CAI  CAG  CAE  CAF     0.00   0.0  0
 MRO  CONST_07  NAM  CAR  NAL  CAQ     0.00   0.0  0
 MRO  CONST_08  CAS  NAM  CAR  NAL     0.00   0.0  0
 MRO  CONST_09  CAP  CAS  NAM  CAR     0.00   0.0  0
 MRO  CONST_10  CAF  CAH  CAO  CAJ   180.00   0.0  0
 MRO  CONST_11  CAG  CAI  CAO  CAJ   180.00   0.0  0
 MRO  CONST_12  OAB  CAR  NAL  CAQ   180.00   0.0  0
 MRO  CONST_13  OAC  CAS  NAM  CAR   180.00   0.0  0
 MRO  CONST_14  CAS  NAM  CAR  OAB   180.00   0.0  0
 MRO  CONST_15  H9   CAF  CAH  CAO   180.00   0.0  0
 MRO  CONST_16  H11  CAG  CAI  CAO   180.00   0.0  0
 MRO  CONST_17  H10  CAE  CAF  CAH   180.00   0.0  0
 MRO  CONST_18  H12  CAI  CAO  CAH   180.00   0.0  0
 MRO  CONST_19  H8   CAH  CAF  CAE   180.00   0.0  0
 MRO  CONST_20  H2   NAM  CAR  NAL   180.00   0.0  0
 MRO  CONST_21  H13  NAL  CAR  NAM   180.00   0.0  0
 MRO  CONST_22  H1   OAD  CAN  CAQ   180.00   0.0  0
 MRO  Var_01    CAP  CAQ  CAN  OAA   -26.66  30.0  2
 MRO  Var_02    CAJ  CAK  CAP  CAQ    95.35  30.0  2
 MRO  Var_03    CAO  CAJ  CAK  CAP  -178.10  30.0  1
 MRO  Var_04    CAH  CAO  CAJ  CAK   -97.00  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
 MRO  plan-1  CAN  0.020
 MRO  plan-1  CAQ  0.020
 MRO  plan-1  NAL  0.020
 MRO  plan-1  CAR  0.020
 MRO  plan-1  OAB  0.020
 MRO  plan-1  NAM  0.020
 MRO  plan-1  CAS  0.020
 MRO  plan-1  OAC  0.020
 MRO  plan-1  CAP  0.020
 MRO  plan-1  CAK  0.020
 MRO  plan-1  H2   0.020
 MRO  plan-1  H13  0.020
 MRO  plan-2  CAJ  0.020
 MRO  plan-2  CAO  0.020
 MRO  plan-2  CAH  0.020
 MRO  plan-2  CAF  0.020
 MRO  plan-2  CAE  0.020
 MRO  plan-2  CAG  0.020
 MRO  plan-2  CAI  0.020
 MRO  plan-2  H8   0.020
 MRO  plan-2  H9   0.020
 MRO  plan-2  H10  0.020
 MRO  plan-2  H11  0.020
 MRO  plan-2  H12  0.020
 MRO  plan-3  OAA  0.020
 MRO  plan-3  CAN  0.020
 MRO  plan-3  OAD  0.020
 MRO  plan-3  CAQ  0.020
 MRO  plan-3  H1   0.020

