# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 07:59:58 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 5-[2-(2-methoxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1CCC2=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
 W7G  W7G  '5-[2-(2-methoxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  34  21  .  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_W7G
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
 W7G  OAB  O  OC    -1  -0.590  -2.7639  -3.0354   0.1369
 W7G  CAO  C  C      0   0.410  -1.8045  -2.2424   0.1881
 W7G  OAE  O  O      0  -0.532  -0.5990  -2.5011   0.2424
 W7G  CAR  C  CR6    0   0.195  -2.2186  -0.7567   0.1622
 W7G  NAL  N  NR16   0  -0.707  -3.5567  -0.6135  -0.0880
 W7G  CAT  C  CR6    0   0.655  -4.2201   0.5648  -0.1918
 W7G  OAC  O  O      0  -0.494  -5.4123   0.6562  -0.4210
 W7G  NAM  N  NR16   0  -0.715  -3.4088   1.6541  -0.0132
 W7G  CAU  C  CR6    0   0.566  -2.0529   1.6446   0.2566
 W7G  OAD  O  O      0  -0.467  -1.4617   2.7037   0.3937
 W7G  CAS  C  CR6    0  -0.160  -1.4294   0.3288   0.3544
 W7G  CAK  C  CH2    0  -0.473   0.0458   0.3274   0.6262
 W7G  CAJ  C  CH2    0  -0.485   0.8645   0.5400  -0.6573
 W7G  CAP  C  CR6    0   0.021   2.3210   0.7726  -0.3685
 W7G  CAH  C  CR16   0  -0.296   2.8106   2.0660  -0.2477
 W7G  CAF  C  CR16   0  -0.272   4.1423   2.3255   0.0579
 W7G  CAG  C  CR16   0  -0.258   5.0075   1.2617   0.2469
 W7G  CAI  C  CR16   0  -0.383   4.5491  -0.0467   0.1366
 W7G  CAQ  C  CR6    0   0.342   3.2118  -0.2942  -0.1659
 W7G  OAN  O  O2     0  -0.455   2.6884  -1.5295  -0.2829
 W7G  CAA  C  CH3    0  -0.433   3.5164  -2.6489  -0.0606
 W7G  H2   H  HNR6   0   0.419  -3.8511   2.5610  -0.0909
 W7G  H4   H  HCH2   0   0.234   0.2687   1.1386   1.3224
 W7G  H5   H  HCH2   0   0.262   0.3485  -0.6041   1.0920
 W7G  H6   H  HCH2   0   0.243   0.7227  -0.3242  -1.3072
 W7G  H7   H  HCH2   0   0.240   0.4753   1.4086  -1.1924
 W7G  H8   H  HCR6   0   0.242   2.1247   2.8927  -0.3957
 W7G  H9   H  HCR6   0   0.246   4.4939   3.3452   0.1443
 W7G  H10  H  HCR6   0   0.253   6.0496   1.4380   0.4811
 W7G  H11  H  HCR6   0   0.274   5.2467  -0.8596   0.2875
 W7G  H12  H  HCH3   0   0.224   3.9352  -2.6557   0.9495
 W7G  H13  H  HCH3   0   0.256   2.8863  -3.5266  -0.1825
 W7G  H14  H  HCH3   0   0.223   4.3392  -2.7039  -0.7790
 W7G  H15  H  HNR6   0   0.416  -4.0694  -1.4821  -0.1929

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
 W7G  CAH  CAF  aromatic  1.391  0.020  1.391
 W7G  CAH  CAP  aromatic  1.388  0.020  1.388
 W7G  CAF  CAG  aromatic  1.384  0.020  1.384
 W7G  CAJ  CAP  single    1.503  0.020  1.503
 W7G  CAJ  CAK  single    1.537  0.020  1.537
 W7G  CAP  CAQ  aromatic  1.405  0.020  1.405
 W7G  CAG  CAI  aromatic  1.391  0.020  1.391
 W7G  CAQ  CAI  aromatic  1.393  0.020  1.393
 W7G  CAQ  OAN  single    1.347  0.020  1.347
 W7G  OAN  CAA  single    1.410  0.020  1.410
 W7G  CAK  CAS  single    1.500  0.020  1.500
 W7G  OAD  CAU  double    1.221  0.020  1.221
 W7G  CAS  CAU  single    1.459  0.020  1.459
 W7G  CAS  CAR  double    1.356  0.020  1.356
 W7G  CAU  NAM  single    1.383  0.020  1.383
 W7G  CAR  CAO  single    1.543  0.020  1.543
 W7G  CAR  NAL  single    1.369  0.020  1.369
 W7G  OAE  CAO  deloc     1.234  0.020  1.234
 W7G  CAO  OAB  deloc     1.246  0.020  1.246
 W7G  NAM  CAT  single    1.370  0.020  1.370
 W7G  NAL  CAT  single    1.356  0.020  1.356
 W7G  CAT  OAC  double    1.217  0.020  1.217
 W7G  NAM  H2   single    0.860  0.020  1.020
 W7G  CAK  H4   single    0.970  0.020  1.090
 W7G  CAK  H5   single    0.970  0.020  1.090
 W7G  CAJ  H6   single    0.970  0.020  1.090
 W7G  CAJ  H7   single    0.970  0.020  1.090
 W7G  CAH  H8   single    0.930  0.020  1.080
 W7G  CAF  H9   single    0.930  0.020  1.080
 W7G  CAG  H10  single    0.930  0.020  1.080
 W7G  CAI  H11  single    0.930  0.020  1.080
 W7G  CAA  H12  single    0.970  0.020  1.090
 W7G  CAA  H13  single    0.970  0.020  1.090
 W7G  CAA  H14  single    0.970  0.020  1.090
 W7G  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
 W7G  CAR  CAO  OAE  117.70  3.000
 W7G  OAE  CAO  OAB  128.36  3.000
 W7G  CAR  CAO  OAB  113.93  3.000
 W7G  CAS  CAR  NAL  120.74  3.000
 W7G  NAL  CAR  CAO  111.48  3.000
 W7G  CAS  CAR  CAO  127.77  3.000
 W7G  H15  NAL  CAT  119.27  3.000
 W7G  H15  NAL  CAR  115.07  3.000
 W7G  CAT  NAL  CAR  125.67  3.000
 W7G  NAM  CAT  OAC  123.01  3.000
 W7G  OAC  CAT  NAL  123.97  3.000
 W7G  NAM  CAT  NAL  113.03  3.000
 W7G  H2   NAM  CAU  116.73  3.000
 W7G  H2   NAM  CAT  116.34  3.000
 W7G  CAU  NAM  CAT  126.93  3.000
 W7G  CAS  CAU  OAD  124.60  3.000
 W7G  CAS  CAU  NAM  115.99  3.000
 W7G  OAD  CAU  NAM  119.40  3.000
 W7G  CAK  CAS  CAU  115.67  3.000
 W7G  CAU  CAS  CAR  117.63  3.000
 W7G  CAK  CAS  CAR  126.68  3.000
 W7G  H5   CAK  H4   107.90  3.000
 W7G  H5   CAK  CAJ  109.19  3.000
 W7G  H4   CAK  CAJ  108.72  3.000
 W7G  H5   CAK  CAS  110.67  3.000
 W7G  H4   CAK  CAS  108.39  3.000
 W7G  CAJ  CAK  CAS  111.86  3.000
 W7G  H7   CAJ  H6   106.98  3.000
 W7G  H7   CAJ  CAP  108.45  3.000
 W7G  H6   CAJ  CAP  111.29  3.000
 W7G  H7   CAJ  CAK  109.23  3.000
 W7G  H6   CAJ  CAK  108.59  3.000
 W7G  CAP  CAJ  CAK  112.15  3.000
 W7G  CAQ  CAP  CAH  118.13  3.000
 W7G  CAQ  CAP  CAJ  121.65  3.000
 W7G  CAH  CAP  CAJ  120.18  3.000
 W7G  H8   CAH  CAF  119.57  3.000
 W7G  H8   CAH  CAP  118.38  3.000
 W7G  CAF  CAH  CAP  122.05  3.000
 W7G  H9   CAF  CAG  120.68  3.000
 W7G  H9   CAF  CAH  120.30  3.000
 W7G  CAG  CAF  CAH  119.02  3.000
 W7G  H10  CAG  CAI  119.19  3.000
 W7G  H10  CAG  CAF  120.40  3.000
 W7G  CAI  CAG  CAF  120.41  3.000
 W7G  H11  CAI  CAQ  121.05  3.000
 W7G  H11  CAI  CAG  118.90  3.000
 W7G  CAQ  CAI  CAG  120.05  3.000
 W7G  OAN  CAQ  CAI  123.71  3.000
 W7G  OAN  CAQ  CAP  115.95  3.000
 W7G  CAI  CAQ  CAP  120.34  3.000
 W7G  CAA  OAN  CAQ  119.09  3.000
 W7G  H14  CAA  H13  108.77  3.000
 W7G  H14  CAA  H12  108.56  3.000
 W7G  H13  CAA  H12  108.69  3.000
 W7G  H14  CAA  OAN  112.22  3.000
 W7G  H13  CAA  OAN  106.43  3.000
 W7G  H12  CAA  OAN  112.05  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
 W7G  CONST_01  CAG  CAF  CAH  CAP    0.00   0.0  0
 W7G  CONST_02  CAG  CAI  CAQ  CAP    0.00   0.0  0
 W7G  CONST_03  CAI  CAG  CAF  CAH    0.00   0.0  0
 W7G  CONST_04  CAI  CAQ  CAP  CAH    0.00   0.0  0
 W7G  CONST_05  CAQ  CAP  CAH  CAF    0.00   0.0  0
 W7G  CONST_06  CAQ  CAI  CAG  CAF    0.00   0.0  0
 W7G  CONST_07  NAM  CAT  NAL  CAR    0.00   0.0  0
 W7G  CONST_08  CAU  NAM  CAT  NAL    0.00   0.0  0
 W7G  CONST_09  CAS  CAU  NAM  CAT    0.00   0.0  0
 W7G  CONST_10  CAF  CAH  CAP  CAJ  180.00   0.0  0
 W7G  CONST_11  CAI  CAQ  CAP  CAJ  180.00   0.0  0
 W7G  CONST_12  OAN  CAQ  CAP  CAH  180.00   0.0  0
 W7G  CONST_13  OAN  CAQ  CAI  CAG  180.00   0.0  0
 W7G  CONST_14  OAC  CAT  NAL  CAR  180.00   0.0  0
 W7G  CONST_15  OAD  CAU  NAM  CAT  180.00   0.0  0
 W7G  CONST_16  CAU  NAM  CAT  OAC  180.00   0.0  0
 W7G  CONST_17  H9   CAF  CAH  CAP  180.00   0.0  0
 W7G  CONST_18  H11  CAI  CAQ  CAP  180.00   0.0  0
 W7G  CONST_19  H10  CAG  CAF  CAH  180.00   0.0  0
 W7G  CONST_20  H8   CAH  CAF  CAG  180.00   0.0  0
 W7G  CONST_21  H2   NAM  CAT  NAL  180.00   0.0  0
 W7G  CONST_22  H15  NAL  CAT  NAM  180.00   0.0  0
 W7G  Var_01    CAS  CAR  CAO  OAB  171.92  30.0  2
 W7G  Var_02    CAJ  CAK  CAS  CAR   96.17  30.0  1
 W7G  Var_03    CAP  CAJ  CAK  CAS  170.31  30.0  2
 W7G  Var_04    CAH  CAP  CAJ  CAK  -93.90  30.0  2
 W7G  Var_05    H12  CAA  OAN  CAQ   59.92  30.0  3

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
 W7G  plan-1  CAO  0.020
 W7G  plan-1  CAR  0.020
 W7G  plan-1  NAL  0.020
 W7G  plan-1  CAT  0.020
 W7G  plan-1  OAC  0.020
 W7G  plan-1  NAM  0.020
 W7G  plan-1  CAU  0.020
 W7G  plan-1  OAD  0.020
 W7G  plan-1  CAS  0.020
 W7G  plan-1  CAK  0.020
 W7G  plan-1  H2   0.020
 W7G  plan-1  H15  0.020
 W7G  plan-2  CAJ  0.020
 W7G  plan-2  CAP  0.020
 W7G  plan-2  CAH  0.020
 W7G  plan-2  CAF  0.020
 W7G  plan-2  CAG  0.020
 W7G  plan-2  CAI  0.020
 W7G  plan-2  CAQ  0.020
 W7G  plan-2  OAN  0.020
 W7G  plan-2  H8   0.020
 W7G  plan-2  H9   0.020
 W7G  plan-2  H10  0.020
 W7G  plan-2  H11  0.020
 W7G  plan-3  OAB  0.020
 W7G  plan-3  CAO  0.020
 W7G  plan-3  OAE  0.020
 W7G  plan-3  CAR  0.020

