# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 10:25:05 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 6-phenyl-1~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=O)C=C(N1)c2ccccc2
#
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
 M3E  M3E  6-phenyl-1~{H}-pyrimidine-2,4-dione  ligand  22  14  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_M3E
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
 M3E  CAC  C  CR16  0  -0.249   4.1104   0.0031  -0.0177
 M3E  CAD  C  CR16  0  -0.239   3.3927   1.1237  -0.4135
 M3E  CAE  C  CR16  0  -0.239   3.4361  -1.1417   0.3875
 M3E  CAF  C  CR16  0  -0.294   2.0065   1.1037  -0.4021
 M3E  CAG  C  CR16  0  -0.286   2.0509  -1.1676   0.3961
 M3E  CAH  C  CR16  0  -0.543  -0.8541  -1.1824  -0.3540
 M3E  CAK  C  CR6   0   0.051   1.3245  -0.0451   0.0001
 M3E  CAL  C  CR6   0   0.438  -0.1458  -0.0860  -0.0021
 M3E  CAM  C  CR6   0   0.583  -2.2950  -1.1514  -0.3474
 M3E  CAN  C  CR6   0   0.669  -2.1568   1.2009   0.3863
 M3E  NAI  N  NR16  0  -0.731  -0.7930   1.0637   0.3549
 M3E  NAJ  N  NR16  0  -0.716  -2.8382   0.0716   0.0202
 M3E  OAA  O  O     0  -0.467  -3.0224  -2.0834  -0.6409
 M3E  OAB  O  O     0  -0.473  -2.7050   2.2315   0.7162
 M3E  H1   H  HCR6  0   0.268   5.1922   0.0221  -0.0238
 M3E  H2   H  HCR6  0   0.269   3.9111   2.0158  -0.7382
 M3E  H3   H  HCR6  0   0.268   3.9887  -2.0153   0.7065
 M3E  H4   H  HCR6  0   0.271   1.4641   1.9795  -0.7361
 M3E  H5   H  HCR6  0   0.269   1.5333  -2.0562   0.7330
 M3E  H8   H  HNR6  0   0.427  -3.8482   0.1415   0.0315
 M3E  H7   H  HNR6  0   0.436  -0.2607   1.8561   0.6861
 M3E  H6   H  HCR6  0   0.289  -0.3580  -2.0851  -0.6753

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
 M3E  OAB  CAN  double    1.213  0.020  1.213
 M3E  CAN  NAJ  single    1.369  0.020  1.369
 M3E  CAN  NAI  single    1.371  0.020  1.371
 M3E  NAJ  CAM  single    1.388  0.020  1.388
 M3E  NAI  CAL  single    1.367  0.020  1.367
 M3E  CAM  OAA  double    1.218  0.020  1.218
 M3E  CAM  CAH  single    1.441  0.020  1.441
 M3E  CAL  CAH  double    1.352  0.020  1.352
 M3E  CAL  CAK  single    1.471  0.020  1.471
 M3E  CAF  CAK  aromatic  1.395  0.020  1.395
 M3E  CAF  CAD  aromatic  1.386  0.020  1.386
 M3E  CAK  CAG  aromatic  1.394  0.020  1.394
 M3E  CAD  CAC  aromatic  1.388  0.020  1.388
 M3E  CAG  CAE  aromatic  1.386  0.020  1.386
 M3E  CAC  CAE  aromatic  1.389  0.020  1.389
 M3E  CAC  H1   single    0.930  0.020  1.080
 M3E  CAD  H2   single    0.930  0.020  1.080
 M3E  CAE  H3   single    0.930  0.020  1.080
 M3E  CAF  H4   single    0.930  0.020  1.080
 M3E  CAG  H5   single    0.930  0.020  1.080
 M3E  CAH  H6   single    0.930  0.020  1.080
 M3E  NAJ  H8   single    0.860  0.020  1.020
 M3E  NAI  H7   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
 M3E  H1   CAC  CAE  120.10  3.000
 M3E  H1   CAC  CAD  120.07  3.000
 M3E  CAE  CAC  CAD  119.83  3.000
 M3E  H2   CAD  CAF  119.57  3.000
 M3E  H2   CAD  CAC  120.24  3.000
 M3E  CAF  CAD  CAC  120.19  3.000
 M3E  H3   CAE  CAG  119.59  3.000
 M3E  H3   CAE  CAC  120.24  3.000
 M3E  CAG  CAE  CAC  120.17  3.000
 M3E  H4   CAF  CAK  120.67  3.000
 M3E  H4   CAF  CAD  119.11  3.000
 M3E  CAK  CAF  CAD  120.20  3.000
 M3E  H5   CAG  CAK  120.02  3.000
 M3E  H5   CAG  CAE  119.70  3.000
 M3E  CAK  CAG  CAE  120.26  3.000
 M3E  H6   CAH  CAM  118.62  3.000
 M3E  H6   CAH  CAL  121.01  3.000
 M3E  CAM  CAH  CAL  120.35  3.000
 M3E  CAL  CAK  CAG  119.92  3.000
 M3E  CAG  CAK  CAF  119.35  3.000
 M3E  CAL  CAK  CAF  120.73  3.000
 M3E  NAI  CAL  CAK  116.72  3.000
 M3E  CAK  CAL  CAH  123.14  3.000
 M3E  NAI  CAL  CAH  120.14  3.000
 M3E  OAA  CAM  NAJ  120.29  3.000
 M3E  OAA  CAM  CAH  125.41  3.000
 M3E  NAJ  CAM  CAH  114.30  3.000
 M3E  OAB  CAN  NAJ  123.27  3.000
 M3E  NAJ  CAN  NAI  113.99  3.000
 M3E  OAB  CAN  NAI  122.74  3.000
 M3E  H7   NAI  CAN  115.97  3.000
 M3E  H7   NAI  CAL  119.73  3.000
 M3E  CAN  NAI  CAL  124.14  3.000
 M3E  H8   NAJ  CAN  115.89  3.000
 M3E  H8   NAJ  CAM  117.02  3.000
 M3E  CAN  NAJ  CAM  127.09  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
 M3E  CONST_01  CAK  CAF  CAD  CAC    0.00   0.0  0
 M3E  CONST_02  CAK  CAG  CAE  CAC    0.00   0.0  0
 M3E  CONST_03  CAG  CAK  CAF  CAD    0.00   0.0  0
 M3E  CONST_04  CAG  CAE  CAC  CAD    0.00   0.0  0
 M3E  CONST_05  CAF  CAK  CAG  CAE    0.00   0.0  0
 M3E  CONST_06  CAF  CAD  CAC  CAE    0.00   0.0  0
 M3E  CONST_07  CAL  CAK  CAF  CAD  180.00   0.0  0
 M3E  CONST_08  CAL  CAK  CAG  CAE  180.00   0.0  0
 M3E  CONST_09  CAN  NAJ  CAM  CAH    0.00   0.0  0
 M3E  CONST_10  NAJ  CAN  NAI  CAL    0.00   0.0  0
 M3E  CONST_11  NAI  CAN  NAJ  CAM    0.00   0.0  0
 M3E  CONST_12  OAB  CAN  NAI  CAL  180.00   0.0  0
 M3E  CONST_13  OAB  CAN  NAJ  CAM  180.00   0.0  0
 M3E  CONST_14  OAA  CAM  NAJ  CAN  180.00   0.0  0
 M3E  CONST_15  H4   CAF  CAD  CAC  180.00   0.0  0
 M3E  CONST_16  H5   CAG  CAE  CAC  180.00   0.0  0
 M3E  CONST_17  H3   CAE  CAC  CAD  180.00   0.0  0
 M3E  CONST_18  H2   CAD  CAC  CAE  180.00   0.0  0
 M3E  CONST_19  H1   CAC  CAD  CAF  180.00   0.0  0
 M3E  CONST_20  H8   NAJ  CAM  CAH  180.00   0.0  0
 M3E  CONST_21  H7   NAI  CAN  NAJ  180.00   0.0  0
 M3E  Var_01    NAI  CAL  CAK  CAF  -36.70  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
 M3E  plan-1  CAC  0.020
 M3E  plan-1  CAD  0.020
 M3E  plan-1  CAE  0.020
 M3E  plan-1  CAF  0.020
 M3E  plan-1  CAG  0.020
 M3E  plan-1  CAK  0.020
 M3E  plan-1  CAL  0.020
 M3E  plan-1  H1   0.020
 M3E  plan-1  H2   0.020
 M3E  plan-1  H3   0.020
 M3E  plan-1  H4   0.020
 M3E  plan-1  H5   0.020
 M3E  plan-2  CAH  0.020
 M3E  plan-2  CAK  0.020
 M3E  plan-2  CAL  0.020
 M3E  plan-2  CAM  0.020
 M3E  plan-2  CAN  0.020
 M3E  plan-2  NAI  0.020
 M3E  plan-2  NAJ  0.020
 M3E  plan-2  OAA  0.020
 M3E  plan-2  OAB  0.020
 M3E  plan-2  H8   0.020
 M3E  plan-2  H7   0.020
 M3E  plan-2  H6   0.020

