# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:10:26 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-phenyl-7,8-dihydropteridin-6(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1c(F)cc(Nc2ncc3NC(=O)CN(c4ccccc4)c3n2)cc1F
#
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
 E8D  E8D  2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-phenyl-7,8-dihydropteridin-6(5H)-one  ligand  40  27  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_E8D
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
 E8D  C4   C  CR66  0   0.190   1.7140  -2.1415  -0.2371
 E8D  C14  C  CR16  0  -0.301   4.4700   1.5193   0.9743
 E8D  C5   C  CR66  0   0.523   1.9719  -0.7704  -0.0363
 E8D  C6   C  CR6   0   0.506   4.0583  -2.7045  -0.2094
 E8D  C11  C  CR6   0   0.044  -5.4336   0.5722   0.1846
 E8D  C7   C  C     0  -0.436   4.2825  -1.3296   0.3869
 E8D  C8   C  CR6   0   0.328   3.6168   1.0097   0.0019
 E8D  C9   C  CR16  0  -0.513  -3.3319  -0.6547  -0.0517
 E8D  C10  C  CR6   0   0.507  -4.7102  -0.5879  -0.0391
 E8D  C12  C  CR6   0   0.490  -4.6693   1.7113   0.4093
 E8D  C13  C  CR16  0  -0.534  -3.2946   1.7035   0.4115
 E8D  N2   N  N     0  -0.482  -0.6071  -1.6422  -0.1282
 E8D  C3   C  CR16  0  -0.060   0.3953  -2.5127  -0.2655
 E8D  N3   N  N     0  -0.496   0.9877   0.0916   0.1015
 E8D  C1   C  CR6   0   0.386  -2.6005   0.5104   0.1771
 E8D  C2   C  CR6   0   0.603  -0.2610  -0.3781   0.0415
 E8D  N4   N  NR16  0  -0.719   2.7721  -3.0183  -0.4588
 E8D  N5   N  NR6   0  -0.611   3.2696  -0.3599   0.0026
 E8D  O1   O  O     0  -0.461   4.9837  -3.4703  -0.3988
 E8D  O2   O  OH1   0  -0.623  -6.7772   0.6590   0.2019
 E8D  F2   F  F     0  -0.321  -5.4119  -1.7142  -0.2614
 E8D  C15  C  CR16  0  -0.253   4.8449   2.8568   0.9396
 E8D  C16  C  CR16  0  -0.261   4.3634   3.6946  -0.0541
 E8D  C17  C  CR16  0  -0.259   3.5096   3.1828  -1.0252
 E8D  C18  C  CR16  0  -0.265   3.1428   1.8477  -1.0059
 E8D  H1   H  HCR6  0   0.272   4.8474   0.8845   1.7658
 E8D  H2   H  H     0   0.290   4.3408  -1.4485   1.4765
 E8D  H3   H  H     0   0.299   5.2531  -0.9756   0.0450
 E8D  H4   H  HCR6  0   0.312  -2.8444  -1.5985  -0.2365
 E8D  H5   H  HCR6  0   0.296  -2.7631   2.6286   0.5982
 E8D  H6   H  HNH1  0   0.412  -0.8330   1.5092   0.3270
 E8D  H7   H  HCR6  0   0.285   0.1222  -3.5507  -0.4258
 E8D  H8   H  HNR6  0   0.416   2.5689  -3.9429  -0.8141
 E8D  H9   H  HOH1  0   0.479  -7.1751  -0.1868  -0.0332
 E8D  H10  H  HCR6  0   0.261   5.5101   3.2413   1.7016
 E8D  H11  H  HCR6  0   0.259   4.6545   4.7362  -0.0790
 E8D  H12  H  HCR6  0   0.260   3.1355   3.8245  -1.8122
 E8D  H13  H  HCR6  0   0.265   2.4963   1.4545  -1.7788
 E8D  N1   N  NH1   0  -0.778  -1.2169   0.5876   0.1841
 E8D  F1   F  F     0  -0.310  -5.3192   2.8598   0.6349

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
 E8D  C16  C15  aromatic  1.386  0.020  1.386
 E8D  C16  C17  aromatic  1.391  0.020  1.391
 E8D  C15  C14  aromatic  1.389  0.020  1.389
 E8D  C17  C18  aromatic  1.385  0.020  1.385
 E8D  C14  C8   aromatic  1.390  0.020  1.390
 E8D  C18  C8   aromatic  1.394  0.020  1.394
 E8D  C8   N5   single    1.413  0.020  1.413
 E8D  F2   C10  single    1.345  0.020  1.345
 E8D  C7   N5   single    1.454  0.020  1.454
 E8D  C7   C6   single    1.515  0.020  1.515
 E8D  N5   C5   single    1.362  0.020  1.362
 E8D  O1   C6   double    1.216  0.020  1.216
 E8D  C10  C9   aromatic  1.380  0.020  1.380
 E8D  C10  C11  aromatic  1.385  0.020  1.385
 E8D  O2   C11  single    1.346  0.020  1.346
 E8D  C6   N4   single    1.347  0.020  1.347
 E8D  C9   C1   aromatic  1.395  0.020  1.395
 E8D  C11  C12  aromatic  1.390  0.020  1.390
 E8D  C5   N3   aromatic  1.316  0.020  1.316
 E8D  C5   C4   aromatic  1.410  0.020  1.410
 E8D  N3   C2   aromatic  1.336  0.020  1.336
 E8D  N4   C4   single    1.392  0.020  1.392
 E8D  C4   C3   aromatic  1.370  0.020  1.370
 E8D  C1   C13  aromatic  1.400  0.020  1.400
 E8D  C1   N1   single    1.386  0.020  1.386
 E8D  C12  C13  aromatic  1.375  0.020  1.375
 E8D  C12  F1   single    1.339  0.020  1.339
 E8D  C2   N1   single    1.366  0.020  1.366
 E8D  C2   N2   aromatic  1.322  0.020  1.322
 E8D  C3   N2   aromatic  1.335  0.020  1.335
 E8D  C14  H1   single    0.930  0.020  1.080
 E8D  C7   H2   single    0.970  0.020  1.090
 E8D  C7   H3   single    0.970  0.020  1.090
 E8D  C9   H4   single    0.930  0.020  1.080
 E8D  C13  H5   single    0.930  0.020  1.080
 E8D  N1   H6   single    0.860  0.020  1.020
 E8D  C3   H7   single    0.930  0.020  1.080
 E8D  N4   H8   single    0.860  0.020  1.020
 E8D  O2   H9   single    0.850  0.020  0.980
 E8D  C15  H10  single    0.930  0.020  1.080
 E8D  C16  H11  single    0.930  0.020  1.080
 E8D  C17  H12  single    0.930  0.020  1.080
 E8D  C18  H13  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
 E8D  N4   C4   C3   123.89  3.000
 E8D  C3   C4   C5   116.27  3.000
 E8D  N4   C4   C5   119.76  3.000
 E8D  H1   C14  C15  119.25  3.000
 E8D  H1   C14  C8   120.69  3.000
 E8D  C15  C14  C8   120.06  3.000
 E8D  N5   C5   N3   120.83  3.000
 E8D  N3   C5   C4   121.02  3.000
 E8D  N5   C5   C4   118.14  3.000
 E8D  O1   C6   N4   123.44  3.000
 E8D  N4   C6   C7   115.18  3.000
 E8D  O1   C6   C7   121.34  3.000
 E8D  O2   C11  C12  119.59  3.000
 E8D  C12  C11  C10  115.16  3.000
 E8D  O2   C11  C10  125.25  3.000
 E8D  H3   C7   H2   107.44  3.000
 E8D  H3   C7   N5   108.74  3.000
 E8D  H2   C7   N5   111.82  3.000
 E8D  H3   C7   C6   107.67  3.000
 E8D  H2   C7   C6   107.47  3.000
 E8D  N5   C7   C6   113.46  3.000
 E8D  C18  C8   N5   119.98  3.000
 E8D  N5   C8   C14  120.38  3.000
 E8D  C18  C8   C14  119.61  3.000
 E8D  H4   C9   C1   121.49  3.000
 E8D  H4   C9   C10  119.70  3.000
 E8D  C1   C9   C10  118.81  3.000
 E8D  F2   C10  C9   118.61  3.000
 E8D  C9   C10  C11  124.30  3.000
 E8D  F2   C10  C11  117.09  3.000
 E8D  F1   C12  C13  119.34  3.000
 E8D  F1   C12  C11  117.60  3.000
 E8D  C13  C12  C11  123.06  3.000
 E8D  H5   C13  C1   120.89  3.000
 E8D  H5   C13  C12  119.09  3.000
 E8D  C1   C13  C12  120.02  3.000
 E8D  C2   N2   C3   116.13  3.000
 E8D  H7   C3   N2   116.75  3.000
 E8D  H7   C3   C4   120.29  3.000
 E8D  N2   C3   C4   122.95  3.000
 E8D  C2   N3   C5   117.67  3.000
 E8D  N1   C1   C13  116.53  3.000
 E8D  N1   C1   C9   124.82  3.000
 E8D  C13  C1   C9   118.65  3.000
 E8D  N3   C2   N2   125.95  3.000
 E8D  N2   C2   N1   120.42  3.000
 E8D  N3   C2   N1   113.63  3.000
 E8D  H8   N4   C6   118.03  3.000
 E8D  H8   N4   C4   118.63  3.000
 E8D  C6   N4   C4   123.33  3.000
 E8D  C8   N5   C7   118.39  3.000
 E8D  C7   N5   C5   118.06  3.000
 E8D  C8   N5   C5   121.76  3.000
 E8D  H9   O2   C11  110.62  3.000
 E8D  H10  C15  C16  120.24  3.000
 E8D  H10  C15  C14  119.36  3.000
 E8D  C16  C15  C14  120.40  3.000
 E8D  H11  C16  C17  120.24  3.000
 E8D  H11  C16  C15  120.33  3.000
 E8D  C17  C16  C15  119.44  3.000
 E8D  H12  C17  C18  119.36  3.000
 E8D  H12  C17  C16  120.12  3.000
 E8D  C18  C17  C16  120.52  3.000
 E8D  H13  C18  C17  119.93  3.000
 E8D  H13  C18  C8   120.09  3.000
 E8D  C17  C18  C8   119.98  3.000
 E8D  H6   N1   C2   113.23  3.000
 E8D  H6   N1   C1   115.57  3.000
 E8D  C2   N1   C1   131.20  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
 E8D  CONST_01  C2   N3   C5   C4     0.00   0.0  0
 E8D  CONST_02  C2   N2   C3   C4     0.00   0.0  0
 E8D  CONST_03  C17  C16  C15  C14    0.00   0.0  0
 E8D  CONST_04  C17  C18  C8   C14    0.00   0.0  0
 E8D  CONST_05  N2   C2   N3   C5     0.00   0.0  0
 E8D  CONST_06  N2   C3   C4   C5     0.00   0.0  0
 E8D  CONST_07  C1   C9   C10  C11    0.00   0.0  0
 E8D  CONST_08  C1   C13  C12  C11    0.00   0.0  0
 E8D  CONST_09  C16  C15  C14  C8     0.00   0.0  0
 E8D  CONST_10  C16  C17  C18  C8     0.00   0.0  0
 E8D  CONST_11  C12  C11  C10  C9     0.00   0.0  0
 E8D  CONST_12  C12  C13  C1   C9     0.00   0.0  0
 E8D  CONST_13  C13  C1   C9   C10    0.00   0.0  0
 E8D  CONST_14  C13  C12  C11  C10    0.00   0.0  0
 E8D  CONST_15  N3   C5   C4   C3     0.00   0.0  0
 E8D  CONST_16  N3   C2   N2   C3     0.00   0.0  0
 E8D  CONST_17  C18  C17  C16  C15    0.00   0.0  0
 E8D  CONST_18  C18  C8   C14  C15    0.00   0.0  0
 E8D  CONST_19  C15  C14  C8   N5   180.00   0.0  0
 E8D  CONST_20  C17  C18  C8   N5   180.00   0.0  0
 E8D  CONST_21  C7   C6   N4   C4     0.00   0.0  0
 E8D  CONST_22  N1   C2   N3   C5   180.00   0.0  0
 E8D  CONST_23  O2   C11  C10  C9   180.00   0.0  0
 E8D  CONST_24  N1   C1   C9   C10  180.00   0.0  0
 E8D  CONST_25  F1   C12  C11  C10  180.00   0.0  0
 E8D  CONST_26  F2   C10  C11  C12  180.00   0.0  0
 E8D  CONST_27  N1   C1   C13  C12  180.00   0.0  0
 E8D  CONST_28  O2   C11  C12  C13  180.00   0.0  0
 E8D  CONST_29  C3   N2   C2   N1   180.00   0.0  0
 E8D  CONST_30  F2   C10  C9   C1   180.00   0.0  0
 E8D  CONST_31  F1   C12  C13  C1   180.00   0.0  0
 E8D  CONST_32  O1   C6   N4   C4   180.00   0.0  0
 E8D  CONST_33  H11  C16  C15  C14  180.00   0.0  0
 E8D  CONST_34  H13  C18  C8   C14  180.00   0.0  0
 E8D  CONST_35  H7   C3   C4   C5   180.00   0.0  0
 E8D  CONST_36  H4   C9   C10  C11  180.00   0.0  0
 E8D  CONST_37  H5   C13  C12  C11  180.00   0.0  0
 E8D  CONST_38  H10  C15  C14  C8   180.00   0.0  0
 E8D  CONST_39  H12  C17  C18  C8   180.00   0.0  0
 E8D  CONST_40  H1   C14  C8   N5     0.00   0.0  0
 E8D  CONST_41  H8   N4   C6   C7   180.00   0.0  0
 E8D  Var_01    C8   N5   C5   C4   170.53  30.0  1
 E8D  Var_02    C6   C7   N5   C5    40.78  30.0  1
 E8D  Var_03    C6   N4   C4   C5    15.05  30.0  1
 E8D  Var_04    N5   C7   C6   N4   -28.73  30.0  1
 E8D  Var_05    C2   N1   C1   C9    -3.09  30.0  2
 E8D  Var_06    C1   N1   C2   N2    -0.60  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
 E8D  plan-1  C11  0.020
 E8D  plan-1  C9   0.020
 E8D  plan-1  C10  0.020
 E8D  plan-1  C12  0.020
 E8D  plan-1  C13  0.020
 E8D  plan-1  C1   0.020
 E8D  plan-1  O2   0.020
 E8D  plan-1  F2   0.020
 E8D  plan-1  H4   0.020
 E8D  plan-1  H5   0.020
 E8D  plan-1  N1   0.020
 E8D  plan-1  F1   0.020
 E8D  plan-2  C14  0.020
 E8D  plan-2  C8   0.020
 E8D  plan-2  N5   0.020
 E8D  plan-2  C15  0.020
 E8D  plan-2  C16  0.020
 E8D  plan-2  C17  0.020
 E8D  plan-2  C18  0.020
 E8D  plan-2  H1   0.020
 E8D  plan-2  H10  0.020
 E8D  plan-2  H11  0.020
 E8D  plan-2  H12  0.020
 E8D  plan-2  H13  0.020
 E8D  plan-3  C4   0.020
 E8D  plan-3  C5   0.020
 E8D  plan-3  N2   0.020
 E8D  plan-3  C3   0.020
 E8D  plan-3  N3   0.020
 E8D  plan-3  C2   0.020
 E8D  plan-3  N4   0.020
 E8D  plan-3  N5   0.020
 E8D  plan-3  H7   0.020
 E8D  plan-3  N1   0.020
 E8D  plan-4  C4   0.020
 E8D  plan-4  C6   0.020
 E8D  plan-4  C7   0.020
 E8D  plan-4  N4   0.020
 E8D  plan-4  O1   0.020
 E8D  plan-4  H8   0.020

