# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 13:53:29 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 6-{4-[(furo[3,2-c]pyridin-4-yl)oxy]-2-methylphenyl}-1,5-dimethylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)NC(=O)C(=C1c2ccc(Oc3nccc4occc34)cc2C)C
#
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
 VFP  VFP  6-{4-[(furo[3,2-c]pyridin-4-yl)oxy]-2-methylphenyl}-1,5-dimethylpyrimidine-2,4(1H,3H)-dione  ligand  44  27  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VFP
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
 VFP  C5   C  CR56  0   0.462  -15.0545  -78.4402  -42.5750
 VFP  C6   C  CR15  0   0.020  -14.4547  -76.5153  -43.3847
 VFP  N1   N  N     0  -0.453  -14.0260  -80.9551  -42.7685
 VFP  C2   C  CR6   0   0.447  -13.4347  -79.9689  -43.3875
 VFP  N3   N  NR16  0  -0.721   -9.1470  -87.8232  -44.5697
 VFP  C4   C  CR16  0  -0.419  -15.7115  -79.4648  -41.9037
 VFP  C1   C  CR56  0  -0.092  -13.9074  -78.6547  -43.3282
 VFP  C10  C  CR6   0   0.111  -11.7381  -83.5825  -45.3466
 VFP  C11  C  CR6   0  -0.069  -10.7410  -83.9888  -44.4536
 VFP  C12  C  CR16  0  -0.240  -10.2946  -83.1303  -43.4569
 VFP  C13  C  CR16  0  -0.321  -10.8317  -81.8603  -43.3223
 VFP  C14  C  CH3   0  -0.747  -12.2197  -84.4907  -46.4388
 VFP  C15  C  CR6   0   0.696  -10.1148  -87.5642  -43.6367
 VFP  C16  C  CR6   0   0.566   -8.6312  -86.9583  -45.5123
 VFP  C17  C  CR6   0  -0.195   -9.1748  -85.6162  -45.4636
 VFP  C18  C  CR6   0   0.373  -10.1449  -85.3427  -44.5613
 VFP  C3   C  CR16  0  -0.076  -15.1321  -80.7067  -42.0471
 VFP  C7   C  CR15  0  -0.372  -13.5282  -77.3746  -43.8504
 VFP  C8   C  CR6   0   0.385  -11.8224  -81.4640  -44.2018
 VFP  C9   C  CR16  0  -0.357  -12.2736  -82.3073  -45.2026
 VFP  N2   N  NR6   0  -0.557  -10.6356  -86.2924  -43.6848
 VFP  O1   O  O     0  -0.422  -15.3874  -77.1424  -42.6117
 VFP  O2   O  O2    0  -0.512  -12.3247  -80.1855  -44.1186
 VFP  O3   O  O     0  -0.451   -7.7811  -87.3370  -46.2983
 VFP  O4   O  O     0  -0.477  -10.4773  -88.4080  -42.8413
 VFP  H1   H  HCR5  0   0.294  -14.5852  -75.4527  -43.5112
 VFP  H2   H  HNR6  0   0.421   -8.7714  -88.7636  -44.5564
 VFP  H3   H  HCR6  0   0.283  -16.6033  -79.3149  -41.3126
 VFP  H4   H  HCR6  0   0.268   -9.5188  -83.4558  -42.7751
 VFP  H5   H  HCR6  0   0.274  -10.4809  -81.1916  -42.5471
 VFP  H6   H  HCH3  0   0.260  -11.4541  -84.6250  -47.2055
 VFP  H7   H  HCH3  0   0.252  -12.4694  -85.4828  -46.0600
 VFP  H8   H  HCH3  0   0.260  -13.1050  -84.0852  -46.9254
 VFP  H9   H  HCH3  0   0.252   -9.0542  -83.6359  -46.2970
 VFP  H10  H  HCH3  0   0.251   -7.5392  -84.5297  -46.3232
 VFP  H11  H  HCH3  0   0.246   -8.8103  -84.9325  -47.4630
 VFP  H12  H  HCH3  0   0.277  -12.1546  -86.8837  -42.3892
 VFP  H13  H  HCH3  0   0.262  -11.3417  -85.3915  -41.9062
 VFP  H14  H  HCH3  0   0.268  -12.4813  -85.3903  -43.2613
 VFP  H15  H  HCR6  0   0.272  -15.5744  -81.5653  -41.5569
 VFP  H16  H  HCR5  0   0.273  -12.6888  -77.1319  -44.4805
 VFP  H17  H  HCR6  0   0.269  -13.0487  -81.9680  -45.8793
 VFP  C19  C  CH3   0  -0.724   -8.6205  -84.6231  -46.4338
 VFP  C20  C  CH3   0  -0.534  -11.7118  -85.9648  -42.7549

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
 VFP  O3   C16  double    1.218  0.020  1.218
 VFP  C19  C17  single    1.495  0.020  1.495
 VFP  C14  C10  single    1.500  0.020  1.500
 VFP  C16  C17  single    1.449  0.020  1.449
 VFP  C16  N3   single    1.379  0.020  1.379
 VFP  C17  C18  double    1.353  0.020  1.353
 VFP  C10  C9   aromatic  1.390  0.020  1.390
 VFP  C10  C11  aromatic  1.399  0.020  1.399
 VFP  C9   C8   aromatic  1.384  0.020  1.384
 VFP  N3   C15  single    1.369  0.020  1.369
 VFP  C18  C11  single    1.483  0.020  1.483
 VFP  C18  N2   single    1.382  0.020  1.382
 VFP  C11  C12  aromatic  1.389  0.020  1.389
 VFP  C8   O2   single    1.376  0.020  1.376
 VFP  C8   C13  aromatic  1.383  0.020  1.383
 VFP  O2   C2   single    1.347  0.020  1.347
 VFP  C15  N2   single    1.375  0.020  1.375
 VFP  C15  O4   double    1.215  0.020  1.215
 VFP  N2   C20  single    1.460  0.020  1.460
 VFP  C12  C13  aromatic  1.386  0.020  1.386
 VFP  C7   C1   aromatic  1.434  0.020  1.434
 VFP  C7   C6   aromatic  1.347  0.020  1.347
 VFP  C2   C1   aromatic  1.398  0.020  1.398
 VFP  C2   N1   aromatic  1.306  0.020  1.306
 VFP  C1   C5   aromatic  1.389  0.020  1.389
 VFP  C6   O1   aromatic  1.364  0.020  1.364
 VFP  N1   C3   aromatic  1.344  0.020  1.344
 VFP  C5   O1   aromatic  1.340  0.020  1.340
 VFP  C5   C4   aromatic  1.390  0.020  1.390
 VFP  C3   C4   aromatic  1.378  0.020  1.378
 VFP  C6   H1   single    0.930  0.020  1.080
 VFP  N3   H2   single    0.860  0.020  1.020
 VFP  C4   H3   single    0.930  0.020  1.080
 VFP  C12  H4   single    0.930  0.020  1.080
 VFP  C13  H5   single    0.930  0.020  1.080
 VFP  C14  H6   single    0.970  0.020  1.090
 VFP  C14  H7   single    0.970  0.020  1.090
 VFP  C14  H8   single    0.970  0.020  1.090
 VFP  C19  H9   single    0.970  0.020  1.090
 VFP  C19  H10  single    0.970  0.020  1.090
 VFP  C19  H11  single    0.970  0.020  1.090
 VFP  C20  H12  single    0.970  0.020  1.090
 VFP  C20  H13  single    0.970  0.020  1.090
 VFP  C20  H14  single    0.970  0.020  1.090
 VFP  C3   H15  single    0.930  0.020  1.080
 VFP  C7   H16  single    0.930  0.020  1.080
 VFP  C9   H17  single    0.930  0.020  1.080

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
 VFP  O1   C5   C1   109.87  3.000
 VFP  O1   C5   C4   127.56  3.000
 VFP  C1   C5   C4   122.57  3.000
 VFP  H1   C6   O1   115.91  3.000
 VFP  H1   C6   C7   132.19  3.000
 VFP  O1   C6   C7   111.90  3.000
 VFP  C3   N1   C2   119.19  3.000
 VFP  O2   C2   C1   116.93  3.000
 VFP  C1   C2   N1   122.46  3.000
 VFP  O2   C2   N1   120.60  3.000
 VFP  H2   N3   C16  116.90  3.000
 VFP  H2   N3   C15  115.40  3.000
 VFP  C16  N3   C15  127.70  3.000
 VFP  H3   C4   C3   121.94  3.000
 VFP  H3   C4   C5   123.51  3.000
 VFP  C3   C4   C5   114.55  3.000
 VFP  C7   C1   C2   137.27  3.000
 VFP  C2   C1   C5   116.58  3.000
 VFP  C7   C1   C5   106.14  3.000
 VFP  C9   C10  C14  120.47  3.000
 VFP  C9   C10  C11  118.34  3.000
 VFP  C14  C10  C11  121.19  3.000
 VFP  C18  C11  C12  119.14  3.000
 VFP  C12  C11  C10  120.51  3.000
 VFP  C18  C11  C10  120.35  3.000
 VFP  H4   C12  C13  119.48  3.000
 VFP  H4   C12  C11  119.75  3.000
 VFP  C13  C12  C11  120.77  3.000
 VFP  H5   C13  C8   120.72  3.000
 VFP  H5   C13  C12  120.68  3.000
 VFP  C8   C13  C12  118.60  3.000
 VFP  H8   C14  H7   107.93  3.000
 VFP  H8   C14  H6   107.59  3.000
 VFP  H7   C14  H6   107.01  3.000
 VFP  H8   C14  C10  111.16  3.000
 VFP  H7   C14  C10  111.80  3.000
 VFP  H6   C14  C10  111.14  3.000
 VFP  O4   C15  N2   123.52  3.000
 VFP  O4   C15  N3   121.72  3.000
 VFP  N2   C15  N3   114.76  3.000
 VFP  O3   C16  C17  124.85  3.000
 VFP  C17  C16  N3   114.68  3.000
 VFP  O3   C16  N3   120.47  3.000
 VFP  C19  C17  C18  124.36  3.000
 VFP  C18  C17  C16  118.61  3.000
 VFP  C19  C17  C16  117.03  3.000
 VFP  N2   C18  C17  122.58  3.000
 VFP  N2   C18  C11  116.00  3.000
 VFP  C17  C18  C11  121.41  3.000
 VFP  H15  C3   C4   119.71  3.000
 VFP  H15  C3   N1   115.64  3.000
 VFP  C4   C3   N1   124.65  3.000
 VFP  H16  C7   C1   128.34  3.000
 VFP  H16  C7   C6   126.48  3.000
 VFP  C1   C7   C6   105.18  3.000
 VFP  O2   C8   C9   119.39  3.000
 VFP  O2   C8   C13  119.29  3.000
 VFP  C9   C8   C13  121.25  3.000
 VFP  H17  C9   C8   119.60  3.000
 VFP  H17  C9   C10  119.87  3.000
 VFP  C8   C9   C10  120.53  3.000
 VFP  C20  N2   C18  120.77  3.000
 VFP  C20  N2   C15  117.68  3.000
 VFP  C18  N2   C15  121.54  3.000
 VFP  C6   O1   C5   106.91  3.000
 VFP  C8   O2   C2   118.89  3.000
 VFP  H11  C19  H10  106.99  3.000
 VFP  H11  C19  H9   107.87  3.000
 VFP  H10  C19  H9   107.76  3.000
 VFP  H11  C19  C17  111.05  3.000
 VFP  H10  C19  C17  111.01  3.000
 VFP  H9   C19  C17  111.95  3.000
 VFP  H14  C20  H13  109.01  3.000
 VFP  H14  C20  H12  108.45  3.000
 VFP  H13  C20  H12  108.81  3.000
 VFP  H14  C20  N2   110.13  3.000
 VFP  H13  C20  N2   111.35  3.000
 VFP  H12  C20  N2   109.03  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
 VFP  CONST_01  C6   C7   C1   C5      0.00   0.0  0
 VFP  CONST_02  N1   C2   C1   C5      0.00   0.0  0
 VFP  CONST_03  C7   C6   O1   C5      0.00   0.0  0
 VFP  CONST_04  N1   C3   C4   C5      0.00   0.0  0
 VFP  CONST_05  C2   C1   C7   C6    180.00   0.0  0
 VFP  CONST_06  C1   C5   O1   C6      0.00   0.0  0
 VFP  CONST_07  C4   C5   O1   C6    180.00   0.0  0
 VFP  CONST_08  C7   C1   C2   N1    180.00   0.0  0
 VFP  CONST_09  O1   C5   C1   C2    180.00   0.0  0
 VFP  CONST_10  C4   C5   C1   C2      0.00   0.0  0
 VFP  CONST_11  C4   C3   N1   C2      0.00   0.0  0
 VFP  CONST_12  C7   C1   C5   C4    180.00   0.0  0
 VFP  CONST_13  O1   C6   C7   C1      0.00   0.0  0
 VFP  CONST_14  C3   N1   C2   C1      0.00   0.0  0
 VFP  CONST_15  C3   C4   C5   C1      0.00   0.0  0
 VFP  CONST_16  C13  C8   C9   C10     0.00   0.0  0
 VFP  CONST_17  C13  C12  C11  C10     0.00   0.0  0
 VFP  CONST_18  C8   C9   C10  C11     0.00   0.0  0
 VFP  CONST_19  C8   C13  C12  C11     0.00   0.0  0
 VFP  CONST_20  C9   C10  C11  C12     0.00   0.0  0
 VFP  CONST_21  C9   C8   C13  C12     0.00   0.0  0
 VFP  CONST_22  O1   C5   C4   C3    180.00   0.0  0
 VFP  CONST_23  O1   C5   C1   C7      0.00   0.0  0
 VFP  CONST_24  C18  C11  C12  C13   180.00   0.0  0
 VFP  CONST_25  C9   C10  C11  C18   180.00   0.0  0
 VFP  CONST_26  C18  N2   C15  N3      0.00   0.0  0
 VFP  CONST_27  N2   C15  N3   C16     0.00   0.0  0
 VFP  CONST_28  O2   C2   C1   C5    180.00   0.0  0
 VFP  CONST_29  O2   C8   C9   C10   180.00   0.0  0
 VFP  CONST_30  C14  C10  C11  C12   180.00   0.0  0
 VFP  CONST_31  O2   C8   C13  C12   180.00   0.0  0
 VFP  CONST_32  C8   C9   C10  C14   180.00   0.0  0
 VFP  CONST_33  C18  C11  C10  C14     0.00   0.0  0
 VFP  CONST_34  O2   C2   N1   C3    180.00   0.0  0
 VFP  CONST_35  O2   C2   C1   C7      0.00   0.0  0
 VFP  CONST_36  C20  N2   C15  N3    180.00   0.0  0
 VFP  CONST_37  O4   C15  N3   C16   180.00   0.0  0
 VFP  CONST_38  O4   C15  N2   C18   180.00   0.0  0
 VFP  CONST_39  H16  C7   C1   C5    180.00   0.0  0
 VFP  CONST_40  H1   C6   O1   C5    180.00   0.0  0
 VFP  CONST_41  H15  C3   C4   C5    180.00   0.0  0
 VFP  CONST_42  H3   C4   C3   N1    180.00   0.0  0
 VFP  CONST_43  H4   C12  C11  C10   180.00   0.0  0
 VFP  CONST_44  H17  C9   C10  C11   180.00   0.0  0
 VFP  CONST_45  H5   C13  C12  C11   180.00   0.0  0
 VFP  CONST_46  H2   N3   C15  N2    180.00   0.0  0
 VFP  CONST_47  O4   C15  N2   C20     0.00   0.0  0
 VFP  Var_01    C17  C18  C11  C10    80.68  30.0  2
 VFP  Var_02    C9   C8   O2   C2     88.85  30.0  2
 VFP  Var_03    H6   C14  C10  C11   -69.91  30.0  2
 VFP  Var_04    H12  C20  N2   C15   -18.74  30.0  3
 VFP  Var_05    H9   C19  C17  C16  -177.53  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
 VFP  plan-1  C10  0.020
 VFP  plan-1  C11  0.020
 VFP  plan-1  C12  0.020
 VFP  plan-1  C13  0.020
 VFP  plan-1  C14  0.020
 VFP  plan-1  C18  0.020
 VFP  plan-1  C8   0.020
 VFP  plan-1  C9   0.020
 VFP  plan-1  O2   0.020
 VFP  plan-1  H4   0.020
 VFP  plan-1  H5   0.020
 VFP  plan-1  H17  0.020
 VFP  plan-2  N3   0.020
 VFP  plan-2  C11  0.020
 VFP  plan-2  C15  0.020
 VFP  plan-2  C16  0.020
 VFP  plan-2  C17  0.020
 VFP  plan-2  C18  0.020
 VFP  plan-2  N2   0.020
 VFP  plan-2  O3   0.020
 VFP  plan-2  O4   0.020
 VFP  plan-2  H2   0.020
 VFP  plan-2  C19  0.020
 VFP  plan-2  C20  0.020
 VFP  plan-3  C5   0.020
 VFP  plan-3  C6   0.020
 VFP  plan-3  N1   0.020
 VFP  plan-3  C2   0.020
 VFP  plan-3  C4   0.020
 VFP  plan-3  C1   0.020
 VFP  plan-3  C3   0.020
 VFP  plan-3  C7   0.020
 VFP  plan-3  O1   0.020
 VFP  plan-3  O2   0.020
 VFP  plan-3  H1   0.020
 VFP  plan-3  H3   0.020
 VFP  plan-3  H15  0.020
 VFP  plan-3  H16  0.020

