# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 18:40:38 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 5-{2-[4-(cyanomethyl)phenyl]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(CCc2ccc(CC#N)cc2)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
 XRO  XRO  '5-{2-[4-(cyanomethyl)phenyl]ethyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  34  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XRO
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
 XRO  OAB  O  OC    -1  -0.585  -3.2465  -3.0617  -0.0560
 XRO  CAP  C  C      0   0.417  -2.3065  -2.2464  -0.0448
 XRO  OAE  O  O      0  -0.541  -1.0975  -2.4722  -0.1694
 XRO  CAS  C  CR6    0   0.202  -2.7490  -0.7794   0.1311
 XRO  NAN  N  NR16   0  -0.707  -4.1091  -0.6496   0.0649
 XRO  CAU  C  CR6    0   0.656  -4.7952   0.5174   0.1565
 XRO  OAC  O  O      0  -0.493  -6.0082   0.5984   0.0952
 XRO  NAO  N  NR16   0  -0.715  -3.9824   1.6075   0.3226
 XRO  CAV  C  CR6    0   0.564  -2.6026   1.6094   0.4121
 XRO  OAD  O  O      0  -0.466  -2.0106   2.6675   0.5524
 XRO  CAT  C  CR6    0  -0.158  -1.9580   0.3046   0.3249
 XRO  CAM  C  CH2    0  -0.477  -0.4621   0.2920   0.4203
 XRO  CAL  C  CH2    0  -0.496   0.2076   0.4754  -0.9485
 XRO  CAR  C  CR6    0   0.117   1.7024   0.3853  -0.8449
 XRO  CAI  C  CR16   0  -0.305   2.5023   1.5235  -0.8453
 XRO  CAG  C  CR16   0  -0.273   3.8810   1.4286  -0.7069
 XRO  CAQ  C  CR6    0   0.091   4.4893   0.1885  -0.5659
 XRO  CAK  C  CH2    0  -0.629   5.9874   0.0832  -0.4005
 XRO  CAF  C  CSP    0   0.139   6.3586   0.0224   1.0067
 XRO  NAA  N  NS     0  -0.276   6.6339  -0.0256   2.1229
 XRO  CAH  C  CR16   0  -0.268   3.6972  -0.9557  -0.5652
 XRO  CAJ  C  CR16   0  -0.291   2.3222  -0.8560  -0.7030
 XRO  H2   H  HNR6   0   0.420  -4.4441   2.5057   0.3870
 XRO  H4   H  HCH2   0   0.240  -0.1411   1.0982   1.0825
 XRO  H5   H  HCH2   0   0.256  -0.1230  -0.6417   0.8592
 XRO  H6   H  HCH2   0   0.248  -0.1652  -0.2980  -1.6213
 XRO  H7   H  HCH2   0   0.241  -0.0805   1.4400  -1.3718
 XRO  H8   H  HCR6   0   0.248   2.0463   2.4996  -0.9623
 XRO  H9   H  HCR6   0   0.256   4.4854   2.3281  -0.7139
 XRO  H10  H  HCH2   0   0.329   6.3789  -0.8102  -0.8903
 XRO  H11  H  HCH2   0   0.329   6.4958   0.9401  -0.8462
 XRO  H12  H  HCR6   0   0.256   4.1568  -1.9313  -0.4612
 XRO  H13  H  HCR6   0   0.254   1.7143  -1.7535  -0.7026
 XRO  H14  H  HNR6   0   0.416  -4.6224  -1.5160  -0.0540

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
 XRO  CAI  CAG  aromatic  1.389  0.020  1.389
 XRO  CAI  CAR  aromatic  1.391  0.020  1.391
 XRO  CAG  CAQ  aromatic  1.388  0.020  1.388
 XRO  CAR  CAL  single    1.501  0.020  1.501
 XRO  CAR  CAJ  aromatic  1.395  0.020  1.395
 XRO  CAL  CAM  single    1.535  0.020  1.535
 XRO  CAQ  CAK  single    1.511  0.020  1.511
 XRO  CAQ  CAH  aromatic  1.392  0.020  1.392
 XRO  CAK  CAF  single    1.457  0.020  1.457
 XRO  CAJ  CAH  aromatic  1.386  0.020  1.386
 XRO  CAF  NAA  triple    1.151  0.020  1.151
 XRO  CAM  CAT  single    1.499  0.020  1.499
 XRO  OAD  CAV  double    1.221  0.020  1.221
 XRO  CAT  CAV  single    1.458  0.020  1.458
 XRO  CAT  CAS  double    1.356  0.020  1.356
 XRO  CAV  NAO  single    1.383  0.020  1.383
 XRO  OAE  CAP  deloc     1.236  0.020  1.236
 XRO  CAS  CAP  single    1.542  0.020  1.542
 XRO  CAS  NAN  single    1.368  0.020  1.368
 XRO  CAP  OAB  deloc     1.244  0.020  1.244
 XRO  NAO  CAU  single    1.370  0.020  1.370
 XRO  NAN  CAU  single    1.357  0.020  1.357
 XRO  CAU  OAC  double    1.217  0.020  1.217
 XRO  NAO  H2   single    0.860  0.020  1.020
 XRO  CAM  H4   single    0.970  0.020  1.090
 XRO  CAM  H5   single    0.970  0.020  1.090
 XRO  CAL  H6   single    0.970  0.020  1.090
 XRO  CAL  H7   single    0.970  0.020  1.090
 XRO  CAI  H8   single    0.930  0.020  1.080
 XRO  CAG  H9   single    0.930  0.020  1.080
 XRO  CAK  H10  single    0.970  0.020  1.090
 XRO  CAK  H11  single    0.970  0.020  1.090
 XRO  CAH  H12  single    0.930  0.020  1.080
 XRO  CAJ  H13  single    0.930  0.020  1.080
 XRO  NAN  H14  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
 XRO  CAS  CAP  OAE  117.76  3.000
 XRO  CAS  CAP  OAB  114.04  3.000
 XRO  OAE  CAP  OAB  128.19  3.000
 XRO  CAT  CAS  NAN  120.74  3.000
 XRO  NAN  CAS  CAP  111.72  3.000
 XRO  CAT  CAS  CAP  127.54  3.000
 XRO  H14  NAN  CAU  119.13  3.000
 XRO  H14  NAN  CAS  115.34  3.000
 XRO  CAU  NAN  CAS  125.53  3.000
 XRO  NAO  CAU  OAC  122.99  3.000
 XRO  OAC  CAU  NAN  123.90  3.000
 XRO  NAO  CAU  NAN  113.11  3.000
 XRO  H2   NAO  CAV  116.74  3.000
 XRO  H2   NAO  CAU  116.32  3.000
 XRO  CAV  NAO  CAU  126.94  3.000
 XRO  CAT  CAV  OAD  124.63  3.000
 XRO  CAT  CAV  NAO  115.86  3.000
 XRO  OAD  CAV  NAO  119.51  3.000
 XRO  CAM  CAT  CAV  116.42  3.000
 XRO  CAV  CAT  CAS  117.78  3.000
 XRO  CAM  CAT  CAS  125.77  3.000
 XRO  H5   CAM  H4   107.34  3.000
 XRO  H5   CAM  CAL  109.08  3.000
 XRO  H4   CAM  CAL  108.93  3.000
 XRO  H5   CAM  CAT  110.15  3.000
 XRO  H4   CAM  CAT  109.02  3.000
 XRO  CAL  CAM  CAT  112.19  3.000
 XRO  H7   CAL  H6   107.28  3.000
 XRO  H7   CAL  CAR  110.03  3.000
 XRO  H6   CAL  CAR  109.90  3.000
 XRO  H7   CAL  CAM  109.64  3.000
 XRO  H6   CAL  CAM  108.43  3.000
 XRO  CAR  CAL  CAM  111.46  3.000
 XRO  CAJ  CAR  CAI  118.21  3.000
 XRO  CAJ  CAR  CAL  120.20  3.000
 XRO  CAI  CAR  CAL  121.57  3.000
 XRO  H8   CAI  CAG  119.34  3.000
 XRO  H8   CAI  CAR  119.67  3.000
 XRO  CAG  CAI  CAR  120.99  3.000
 XRO  H9   CAG  CAQ  119.84  3.000
 XRO  H9   CAG  CAI  119.76  3.000
 XRO  CAQ  CAG  CAI  120.40  3.000
 XRO  CAH  CAQ  CAK  120.47  3.000
 XRO  CAH  CAQ  CAG  119.01  3.000
 XRO  CAK  CAQ  CAG  120.51  3.000
 XRO  H11  CAK  H10  106.99  3.000
 XRO  H11  CAK  CAF  107.98  3.000
 XRO  H10  CAK  CAF  107.93  3.000
 XRO  H11  CAK  CAQ  111.25  3.000
 XRO  H10  CAK  CAQ  111.32  3.000
 XRO  CAF  CAK  CAQ  111.19  3.000
 XRO  NAA  CAF  CAK  180.00  3.000
 XRO  H12  CAH  CAJ  119.69  3.000
 XRO  H12  CAH  CAQ  119.93  3.000
 XRO  CAJ  CAH  CAQ  120.38  3.000
 XRO  H13  CAJ  CAH  119.79  3.000
 XRO  H13  CAJ  CAR  119.19  3.000
 XRO  CAH  CAJ  CAR  121.01  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
 XRO  CONST_01  CAQ  CAG  CAI  CAR     0.00   0.0  0
 XRO  CONST_02  CAQ  CAH  CAJ  CAR     0.00   0.0  0
 XRO  CONST_03  CAH  CAQ  CAG  CAI     0.00   0.0  0
 XRO  CONST_04  CAH  CAJ  CAR  CAI     0.00   0.0  0
 XRO  CONST_05  CAJ  CAR  CAI  CAG     0.00   0.0  0
 XRO  CONST_06  CAJ  CAH  CAQ  CAG     0.00   0.0  0
 XRO  CONST_07  NAO  CAU  NAN  CAS     0.00   0.0  0
 XRO  CONST_08  CAV  NAO  CAU  NAN     0.00   0.0  0
 XRO  CONST_09  CAT  CAV  NAO  CAU     0.00   0.0  0
 XRO  CONST_10  CAG  CAI  CAR  CAL   180.00   0.0  0
 XRO  CONST_11  CAH  CAJ  CAR  CAL   180.00   0.0  0
 XRO  CONST_12  CAK  CAQ  CAG  CAI   180.00   0.0  0
 XRO  CONST_13  CAJ  CAH  CAQ  CAK   180.00   0.0  0
 XRO  CONST_14  OAC  CAU  NAN  CAS   180.00   0.0  0
 XRO  CONST_15  OAD  CAV  NAO  CAU   180.00   0.0  0
 XRO  CONST_16  CAV  NAO  CAU  OAC   180.00   0.0  0
 XRO  CONST_17  H9   CAG  CAI  CAR   180.00   0.0  0
 XRO  CONST_18  H12  CAH  CAJ  CAR   180.00   0.0  0
 XRO  CONST_19  H13  CAJ  CAR  CAI   180.00   0.0  0
 XRO  CONST_20  H8   CAI  CAG  CAQ   180.00   0.0  0
 XRO  CONST_21  H2   NAO  CAU  NAN   180.00   0.0  0
 XRO  CONST_22  H14  NAN  CAU  NAO   180.00   0.0  0
 XRO  Var_01    CAT  CAS  CAP  OAB   172.29  30.0  2
 XRO  Var_02    CAL  CAM  CAT  CAS    90.14  30.0  2
 XRO  Var_03    CAR  CAL  CAM  CAT  -176.89  30.0  1
 XRO  Var_04    CAI  CAR  CAL  CAM  -101.45  30.0  3
 XRO  Var_05    CAF  CAK  CAQ  CAG    94.54  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
 XRO  plan-1  CAP  0.020
 XRO  plan-1  CAS  0.020
 XRO  plan-1  NAN  0.020
 XRO  plan-1  CAU  0.020
 XRO  plan-1  OAC  0.020
 XRO  plan-1  NAO  0.020
 XRO  plan-1  CAV  0.020
 XRO  plan-1  OAD  0.020
 XRO  plan-1  CAT  0.020
 XRO  plan-1  CAM  0.020
 XRO  plan-1  H2   0.020
 XRO  plan-1  H14  0.020
 XRO  plan-2  CAL  0.020
 XRO  plan-2  CAR  0.020
 XRO  plan-2  CAI  0.020
 XRO  plan-2  CAG  0.020
 XRO  plan-2  CAQ  0.020
 XRO  plan-2  CAK  0.020
 XRO  plan-2  CAH  0.020
 XRO  plan-2  CAJ  0.020
 XRO  plan-2  H8   0.020
 XRO  plan-2  H9   0.020
 XRO  plan-2  H12  0.020
 XRO  plan-2  H13  0.020
 XRO  plan-3  OAB  0.020
 XRO  plan-3  CAP  0.020
 XRO  plan-3  OAE  0.020
 XRO  plan-3  CAS  0.020

