# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 17:09:22 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 5-{2-[2-(hydroxymethyl)phenyl]ethyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccccc1CCC2=C(NC(=O)NC2=O)C(O)=O
#
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
 JDM  JDM  '5-{2-[2-(hydroxymethyl)phenyl]ethyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  34  21  .  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_JDM
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
 JDM  OAJ  O  OC    -1  -0.585  -3.2485  -2.8933   0.0870
 JDM  CAI  C  C      0   0.416  -2.1668  -2.2906  -0.0380
 JDM  OAK  O  O      0  -0.541  -1.0276  -2.7667  -0.0955
 JDM  C4   C  C      0   0.199  -2.3093  -0.7558  -0.1087
 JDM  N3   N  NH1    0  -0.706  -3.5970  -0.3586   0.1252
 JDM  C2   C  C      0   0.656  -4.0342   0.9257   0.1511
 JDM  O2   O  O      0  -0.492  -5.1896   1.2460   0.3608
 JDM  N1   N  NH1    0  -0.714  -3.0377   1.8373  -0.0801
 JDM  C6   C  C      0   0.565  -1.7044   1.5663  -0.3262
 JDM  O6   O  O      0  -0.464  -0.9260   2.4917  -0.4949
 JDM  C5   C  C      0  -0.158  -1.3377   0.1558  -0.3606
 JDM  CAL  C  CH2    0  -0.475   0.1067  -0.1463  -0.6219
 JDM  CAM  C  CH2    0  -0.521   0.9299  -0.2013   0.6728
 JDM  CAN  C  CR6    0   0.105   2.3868  -0.4419   0.3887
 JDM  CAO  C  CR16   0  -0.304   2.8385  -1.7514   0.2529
 JDM  CAP  C  CR16   0  -0.257   4.1624  -2.0313  -0.0550
 JDM  CAQ  C  CR16   0  -0.260   5.0543  -0.9846  -0.2318
 JDM  CAR  C  CR16   0  -0.295   4.6179   0.3277  -0.1008
 JDM  CAS  C  CR6    0  -0.013   3.2900   0.6141   0.2039
 JDM  CAT  C  CH2    0  -0.206   2.8201   2.0372   0.3683
 JDM  OAU  O  OH1    0  -0.668   3.8240   2.9335  -0.0345
 JDM  H2   H  HNH1   0   0.417  -4.2592  -1.1117   0.2763
 JDM  H3   H  HNH1   0   0.420  -3.3081   2.8124  -0.0567
 JDM  H4   H  HCH2   0   0.256   0.2080  -1.0962  -1.1379
 JDM  H5   H  HCH2   0   0.242   0.5165   0.6209  -1.2810
 JDM  H6   H  HCH2   0   0.241   0.7872   0.7169   1.2463
 JDM  H7   H  HCH2   0   0.255   0.5374  -1.0128   1.2859
 JDM  H8   H  HCR6   0   0.243   2.1313  -2.5624   0.3875
 JDM  H9   H  HCR6   0   0.248   4.4925  -3.0574  -0.1545
 JDM  H10  H  HCR6   0   0.248   6.0917  -1.1850  -0.4679
 JDM  H11  H  HCR6   0   0.250   5.3271   1.1323  -0.2382
 JDM  H12  H  HCH2   0   0.220   1.8985   2.1894  -0.2076
 JDM  H13  H  HCH2   0   0.216   2.5450   2.1961   1.4211
 JDM  H14  H  HOH1   0   0.461   3.5056   3.8260   0.1265

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
 JDM  O2   C2   double    1.217  0.020  1.217
 JDM  N3   C2   single    1.357  0.020  1.357
 JDM  N3   C4   single    1.368  0.020  1.368
 JDM  C2   N1   single    1.370  0.020  1.370
 JDM  OAK  CAI  deloc     1.236  0.020  1.236
 JDM  OAJ  CAI  deloc     1.245  0.020  1.245
 JDM  N1   C6   single    1.383  0.020  1.383
 JDM  C4   CAI  single    1.543  0.020  1.543
 JDM  C4   C5   double    1.356  0.020  1.356
 JDM  C6   C5   single    1.458  0.020  1.458
 JDM  C6   O6   double    1.221  0.020  1.221
 JDM  C5   CAL  single    1.499  0.020  1.499
 JDM  CAL  CAM  single    1.535  0.020  1.535
 JDM  CAM  CAN  single    1.504  0.020  1.504
 JDM  CAT  OAU  single    1.405  0.020  1.405
 JDM  CAT  CAS  single    1.508  0.020  1.508
 JDM  CAN  CAS  aromatic  1.402  0.020  1.402
 JDM  CAN  CAO  aromatic  1.392  0.020  1.392
 JDM  CAS  CAR  aromatic  1.392  0.020  1.392
 JDM  CAO  CAP  aromatic  1.388  0.020  1.388
 JDM  CAR  CAQ  aromatic  1.389  0.020  1.389
 JDM  CAP  CAQ  aromatic  1.386  0.020  1.386
 JDM  N3   H2   single    0.860  0.020  1.020
 JDM  N1   H3   single    0.860  0.020  1.020
 JDM  CAL  H4   single    0.970  0.020  1.090
 JDM  CAL  H5   single    0.970  0.020  1.090
 JDM  CAM  H6   single    0.970  0.020  1.090
 JDM  CAM  H7   single    0.970  0.020  1.090
 JDM  CAO  H8   single    0.930  0.020  1.080
 JDM  CAP  H9   single    0.930  0.020  1.080
 JDM  CAQ  H10  single    0.930  0.020  1.080
 JDM  CAR  H11  single    0.930  0.020  1.080
 JDM  CAT  H12  single    0.970  0.020  1.090
 JDM  CAT  H13  single    0.970  0.020  1.090
 JDM  OAU  H14  single    0.850  0.020  0.980

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
 JDM  C4   CAI  OAK  117.78  3.000
 JDM  C4   CAI  OAJ  113.96  3.000
 JDM  OAK  CAI  OAJ  128.26  3.000
 JDM  C5   C4   N3   120.74  3.000
 JDM  C5   C4   CAI  127.67  3.000
 JDM  N3   C4   CAI  111.59  3.000
 JDM  H2   N3   C2   119.32  3.000
 JDM  H2   N3   C4   115.12  3.000
 JDM  C2   N3   C4   125.56  3.000
 JDM  N1   C2   O2   122.98  3.000
 JDM  N1   C2   N3   113.09  3.000
 JDM  O2   C2   N3   123.93  3.000
 JDM  H3   N1   C6   116.78  3.000
 JDM  H3   N1   C2   116.28  3.000
 JDM  C6   N1   C2   126.94  3.000
 JDM  C5   C6   O6   124.73  3.000
 JDM  O6   C6   N1   119.40  3.000
 JDM  C5   C6   N1   115.88  3.000
 JDM  CAL  C5   C6   116.21  3.000
 JDM  CAL  C5   C4   125.98  3.000
 JDM  C6   C5   C4   117.77  3.000
 JDM  H5   CAL  H4   107.03  3.000
 JDM  H5   CAL  CAM  109.46  3.000
 JDM  H4   CAL  CAM  108.62  3.000
 JDM  H5   CAL  C5   109.00  3.000
 JDM  H4   CAL  C5   110.44  3.000
 JDM  CAM  CAL  C5   112.15  3.000
 JDM  H7   CAM  H6   106.47  3.000
 JDM  H7   CAM  CAN  109.63  3.000
 JDM  H6   CAM  CAN  111.13  3.000
 JDM  H7   CAM  CAL  107.93  3.000
 JDM  H6   CAM  CAL  110.04  3.000
 JDM  CAN  CAM  CAL  111.46  3.000
 JDM  CAS  CAN  CAO  119.13  3.000
 JDM  CAO  CAN  CAM  118.91  3.000
 JDM  CAS  CAN  CAM  121.91  3.000
 JDM  H8   CAO  CAP  119.92  3.000
 JDM  H8   CAO  CAN  118.68  3.000
 JDM  CAP  CAO  CAN  121.40  3.000
 JDM  H9   CAP  CAQ  120.51  3.000
 JDM  H9   CAP  CAO  120.17  3.000
 JDM  CAQ  CAP  CAO  119.32  3.000
 JDM  H10  CAQ  CAR  119.76  3.000
 JDM  H10  CAQ  CAP  120.30  3.000
 JDM  CAR  CAQ  CAP  119.94  3.000
 JDM  H11  CAR  CAS  120.03  3.000
 JDM  H11  CAR  CAQ  119.00  3.000
 JDM  CAS  CAR  CAQ  120.97  3.000
 JDM  CAT  CAS  CAR  121.02  3.000
 JDM  CAR  CAS  CAN  119.24  3.000
 JDM  CAT  CAS  CAN  119.73  3.000
 JDM  H13  CAT  H12  105.80  3.000
 JDM  H13  CAT  OAU  111.17  3.000
 JDM  H12  CAT  OAU  111.18  3.000
 JDM  H13  CAT  CAS  108.59  3.000
 JDM  H12  CAT  CAS  109.60  3.000
 JDM  OAU  CAT  CAS  110.38  3.000
 JDM  H14  OAU  CAT  107.92  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
 JDM  CONST_01  CAQ  CAR  CAS  CAN     0.00   0.0  0
 JDM  CONST_02  CAQ  CAP  CAO  CAN     0.00   0.0  0
 JDM  CONST_03  CAR  CAS  CAN  CAO     0.00   0.0  0
 JDM  CONST_04  CAR  CAQ  CAP  CAO     0.00   0.0  0
 JDM  CONST_05  CAS  CAN  CAO  CAP     0.00   0.0  0
 JDM  CONST_06  CAS  CAR  CAQ  CAP     0.00   0.0  0
 JDM  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 JDM  CONST_08  C6   N1   C2   N3      0.00   0.0  0
 JDM  CONST_09  C5   C6   N1   C2      0.00   0.0  0
 JDM  CONST_10  CAR  CAS  CAN  CAM   180.00   0.0  0
 JDM  CONST_11  CAP  CAO  CAN  CAM   180.00   0.0  0
 JDM  CONST_12  CAT  CAS  CAN  CAO   180.00   0.0  0
 JDM  CONST_13  CAT  CAS  CAR  CAQ   180.00   0.0  0
 JDM  CONST_14  O2   C2   N3   C4    180.00   0.0  0
 JDM  CONST_15  O6   C6   N1   C2    180.00   0.0  0
 JDM  CONST_16  C6   N1   C2   O2    180.00   0.0  0
 JDM  CONST_17  H11  CAR  CAS  CAN   180.00   0.0  0
 JDM  CONST_18  H9   CAP  CAO  CAN   180.00   0.0  0
 JDM  CONST_19  H10  CAQ  CAP  CAO   180.00   0.0  0
 JDM  CONST_20  H8   CAO  CAP  CAQ   180.00   0.0  0
 JDM  CONST_21  H3   N1   C2   N3    180.00   0.0  0
 JDM  CONST_22  H2   N3   C2   N1    180.00   0.0  0
 JDM  Var_01    N3   C4   CAI  OAJ     6.52  30.0  2
 JDM  Var_02    CAM  CAL  C5   C4    -88.62  30.0  3
 JDM  Var_03    CAN  CAM  CAL  C5   -177.36  30.0  3
 JDM  Var_04    CAS  CAN  CAM  CAL    91.01  30.0  2
 JDM  Var_05    OAU  CAT  CAS  CAN  -172.04  30.0  1

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
 JDM  plan-1  CAI  0.020
 JDM  plan-1  C4   0.020
 JDM  plan-1  N3   0.020
 JDM  plan-1  C2   0.020
 JDM  plan-1  O2   0.020
 JDM  plan-1  N1   0.020
 JDM  plan-1  C6   0.020
 JDM  plan-1  O6   0.020
 JDM  plan-1  C5   0.020
 JDM  plan-1  CAL  0.020
 JDM  plan-1  H2   0.020
 JDM  plan-1  H3   0.020
 JDM  plan-2  CAM  0.020
 JDM  plan-2  CAN  0.020
 JDM  plan-2  CAO  0.020
 JDM  plan-2  CAP  0.020
 JDM  plan-2  CAQ  0.020
 JDM  plan-2  CAR  0.020
 JDM  plan-2  CAS  0.020
 JDM  plan-2  CAT  0.020
 JDM  plan-2  H8   0.020
 JDM  plan-2  H9   0.020
 JDM  plan-2  H10  0.020
 JDM  plan-2  H11  0.020
 JDM  plan-3  OAJ  0.020
 JDM  plan-3  CAI  0.020
 JDM  plan-3  OAK  0.020
 JDM  plan-3  C4   0.020

