# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:28:37 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7,8-trimethyl-7,8-dihydropteridin-6(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N(C)c2nc(Nc3cc(F)c(O)c(F)c3)ncc2N(C)C1=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
 E1D  E1D  (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7,8-trimethyl-7,8-dihydropteridin-6(5H)-one  ligand  39  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_E1D
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
 E1D  C4   C  CR66  0   0.188  -2.4296  -0.8606  -0.0929
 E1D  C14  C  CR6   0   0.519   4.1839  -1.0969  -0.0975
 E1D  C5   C  CR66  0   0.540  -2.3023   0.5355   0.1014
 E1D  C6   C  CR6   0   0.568  -4.8168  -0.7116  -0.1984
 E1D  C11  C  CR16  0  -0.535   3.4534   1.5153   0.2700
 E1D  C7   C  CR16  0  -0.210  -4.6025   0.7732  -0.4931
 E1D  C10  C  CH3   0  -0.698  -5.8614   1.5601  -0.1763
 E1D  C12  C  CR6   0   0.482   4.7773   1.1469   0.2212
 E1D  C13  C  CR6   0   0.039   5.2004  -0.1641   0.0416
 E1D  N2   N  N     0  -0.487  -0.0511  -0.9840  -0.1606
 E1D  C3   C  CR16  0  -0.069  -1.2573  -1.5590  -0.2287
 E1D  N3   N  N     0  -0.520  -1.1135   1.1000   0.1862
 E1D  C1   C  CR6   0   0.389   2.4566   0.5452   0.1191
 E1D  C2   C  CR6   0   0.596  -0.0394   0.3153   0.0627
 E1D  N4   N  NR6   0  -0.566  -3.6932  -1.4542  -0.0448
 E1D  N5   N  NR6   0  -0.495  -3.4276   1.2771   0.2218
 E1D  O1   O  O     0  -0.467  -5.9329  -1.1941  -0.1564
 E1D  C15  C  CR16  0  -0.515   2.8404  -0.7833  -0.0718
 E1D  O2   O  OH1   0  -0.626   6.4887  -0.5550  -0.0323
 E1D  F2   F  F     0  -0.317   5.7235   2.0896   0.3638
 E1D  H1   H  HCR6  0   0.296   3.2017   2.5577   0.4219
 E1D  H2   H  HCR6  0   0.282  -4.4233   0.8484  -1.5780
 E1D  H9   H  HCH3  0   0.242  -6.0741   1.5684   0.8928
 E1D  H10  H  HCH3  0   0.255  -5.7787   2.5868  -0.5255
 E1D  H11  H  HCH3  0   0.262  -6.7077   1.1138  -0.6911
 E1D  H13  H  HCR6  0   0.284  -1.2588  -2.6310  -0.3852
 E1D  H14  H  HCR6  0   0.311   2.1080  -1.5651  -0.1906
 E1D  H15  H  HOH1  0   0.479   7.0657   0.0850   0.3995
 E1D  C8   C  CH3   0  -0.559  -3.7784  -2.8895   0.1500
 E1D  C9   C  CH3   0  -0.541  -3.2980   2.7083   0.4146
 E1D  N1   N  NH1   0  -0.777   1.1458   0.9884   0.1756
 E1D  F1   F  F     0  -0.313   4.5401  -2.3766  -0.2750
 E1D  H3   H  HCH3  0   0.257  -3.1556  -3.1884   0.9927
 E1D  H4   H  HCH3  0   0.278  -4.8052  -3.1656   0.3599
 E1D  H5   H  HCH3  0   0.256  -3.4486  -3.4276  -0.7393
 E1D  H6   H  HCH3  0   0.235  -3.1569   3.2428  -0.5293
 E1D  H7   H  HCH3  0   0.261  -4.1831   3.0989   0.9080
 E1D  H8   H  HCH3  0   0.265  -2.4437   2.9103   1.0526
 E1D  H12  H  HNH1  0   0.411   1.0280   1.9792   0.3213

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
 E1D  F2   C12  single    1.343  0.020  1.343
 E1D  N2   C3   aromatic  1.338  0.020  1.338
 E1D  N2   C2   aromatic  1.318  0.020  1.318
 E1D  C11  C12  aromatic  1.375  0.020  1.375
 E1D  C11  C1   aromatic  1.399  0.020  1.399
 E1D  N1   C2   single    1.368  0.020  1.368
 E1D  N1   C1   single    1.385  0.020  1.385
 E1D  C3   C4   aromatic  1.371  0.020  1.371
 E1D  C12  C13  aromatic  1.389  0.020  1.389
 E1D  C2   N3   aromatic  1.336  0.020  1.336
 E1D  C1   C15  aromatic  1.396  0.020  1.396
 E1D  C8   N4   single    1.451  0.020  1.451
 E1D  C4   N4   single    1.397  0.020  1.397
 E1D  C4   C5   aromatic  1.415  0.020  1.415
 E1D  C13  O2   single    1.348  0.020  1.348
 E1D  C13  C14  aromatic  1.387  0.020  1.387
 E1D  N3   C5   aromatic  1.319  0.020  1.319
 E1D  N4   C6   single    1.356  0.020  1.356
 E1D  C15  C14  aromatic  1.380  0.020  1.380
 E1D  C5   N5   single    1.353  0.020  1.353
 E1D  C14  F1   single    1.340  0.020  1.340
 E1D  C6   O1   double    1.217  0.020  1.217
 E1D  C6   C7   single    1.529  0.020  1.529
 E1D  N5   C7   single    1.465  0.020  1.465
 E1D  N5   C9   single    1.450  0.020  1.450
 E1D  C7   C10  single    1.518  0.020  1.518
 E1D  C11  H1   single    0.930  0.020  1.080
 E1D  C7   H2   single    0.970  0.020  1.090
 E1D  C8   H3   single    0.970  0.020  1.090
 E1D  C8   H4   single    0.970  0.020  1.090
 E1D  C8   H5   single    0.970  0.020  1.090
 E1D  C9   H6   single    0.970  0.020  1.090
 E1D  C9   H7   single    0.970  0.020  1.090
 E1D  C9   H8   single    0.970  0.020  1.090
 E1D  C10  H9   single    0.970  0.020  1.090
 E1D  C10  H10  single    0.970  0.020  1.090
 E1D  C10  H11  single    0.970  0.020  1.090
 E1D  N1   H12  single    0.860  0.020  1.020
 E1D  C3   H13  single    0.930  0.020  1.080
 E1D  C15  H14  single    0.930  0.020  1.080
 E1D  O2   H15  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
 E1D  N4   C4   C3   124.07  3.000
 E1D  N4   C4   C5   119.72  3.000
 E1D  C3   C4   C5   116.05  3.000
 E1D  F1   C14  C15  118.57  3.000
 E1D  F1   C14  C13  117.44  3.000
 E1D  C15  C14  C13  123.99  3.000
 E1D  N5   C5   N3   120.62  3.000
 E1D  N5   C5   C4   118.56  3.000
 E1D  N3   C5   C4   120.81  3.000
 E1D  O1   C6   N4   122.63  3.000
 E1D  O1   C6   C7   121.36  3.000
 E1D  N4   C6   C7   115.95  3.000
 E1D  H1   C11  C1   121.12  3.000
 E1D  H1   C11  C12  119.11  3.000
 E1D  C1   C11  C12  119.76  3.000
 E1D  H2   C7   N5   109.06  3.000
 E1D  H2   C7   C10  107.75  3.000
 E1D  N5   C7   C10  112.64  3.000
 E1D  H2   C7   C6   106.19  3.000
 E1D  C10  C7   C6   110.30  3.000
 E1D  N5   C7   C6   110.64  3.000
 E1D  H11  C10  H10  107.15  3.000
 E1D  H11  C10  H9   108.41  3.000
 E1D  H10  C10  H9   108.82  3.000
 E1D  H11  C10  C7   109.52  3.000
 E1D  H10  C10  C7   111.06  3.000
 E1D  H9   C10  C7   111.74  3.000
 E1D  F2   C12  C13  117.48  3.000
 E1D  C13  C12  C11  123.41  3.000
 E1D  F2   C12  C11  119.11  3.000
 E1D  O2   C13  C12  124.86  3.000
 E1D  O2   C13  C14  119.99  3.000
 E1D  C12  C13  C14  115.12  3.000
 E1D  C2   N2   C3   116.12  3.000
 E1D  H13  C3   N2   115.72  3.000
 E1D  H13  C3   C4   121.14  3.000
 E1D  N2   C3   C4   123.14  3.000
 E1D  C2   N3   C5   117.87  3.000
 E1D  C15  C1   N1   124.78  3.000
 E1D  C15  C1   C11  118.61  3.000
 E1D  N1   C1   C11  116.62  3.000
 E1D  N3   C2   N2   125.97  3.000
 E1D  N3   C2   N1   113.58  3.000
 E1D  N2   C2   N1   120.45  3.000
 E1D  C8   N4   C6   120.56  3.000
 E1D  C6   N4   C4   120.87  3.000
 E1D  C8   N4   C4   118.56  3.000
 E1D  C9   N5   C7   118.44  3.000
 E1D  C9   N5   C5   118.59  3.000
 E1D  C7   N5   C5   115.79  3.000
 E1D  H14  C15  C1   121.24  3.000
 E1D  H14  C15  C14  119.66  3.000
 E1D  C1   C15  C14  119.11  3.000
 E1D  H15  O2   C13  110.79  3.000
 E1D  H5   C8   H4   108.58  3.000
 E1D  H5   C8   H3   108.81  3.000
 E1D  H4   C8   H3   108.77  3.000
 E1D  H5   C8   N4   111.16  3.000
 E1D  H4   C8   N4   109.49  3.000
 E1D  H3   C8   N4   109.98  3.000
 E1D  H8   C9   H7   107.92  3.000
 E1D  H8   C9   H6   108.35  3.000
 E1D  H7   C9   H6   108.75  3.000
 E1D  H8   C9   N5   109.40  3.000
 E1D  H7   C9   N5   110.03  3.000
 E1D  H6   C9   N5   112.28  3.000
 E1D  H12  N1   C2   113.22  3.000
 E1D  H12  N1   C1   115.53  3.000
 E1D  C2   N1   C1   131.25  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
 E1D  CONST_01  C2   N2   C3   C4     0.00   0.0  0
 E1D  CONST_02  C2   N3   C5   C4     0.00   0.0  0
 E1D  CONST_03  C11  C12  C13  C14    0.00   0.0  0
 E1D  CONST_04  C11  C1   C15  C14    0.00   0.0  0
 E1D  CONST_05  N2   C3   C4   C5     0.00   0.0  0
 E1D  CONST_06  N2   C2   N3   C5     0.00   0.0  0
 E1D  CONST_07  C15  C1   C11  C12    0.00   0.0  0
 E1D  CONST_08  C15  C14  C13  C12    0.00   0.0  0
 E1D  CONST_09  C1   C11  C12  C13    0.00   0.0  0
 E1D  CONST_10  C1   C15  C14  C13    0.00   0.0  0
 E1D  CONST_11  N3   C2   N2   C3     0.00   0.0  0
 E1D  CONST_12  N3   C5   C4   C3     0.00   0.0  0
 E1D  CONST_13  C7   C6   N4   C4     0.00   0.0  0
 E1D  CONST_14  F2   C12  C13  C14  180.00   0.0  0
 E1D  CONST_15  N1   C1   C15  C14  180.00   0.0  0
 E1D  CONST_16  N1   C2   N3   C5   180.00   0.0  0
 E1D  CONST_17  O2   C13  C12  C11  180.00   0.0  0
 E1D  CONST_18  N1   C1   C11  C12  180.00   0.0  0
 E1D  CONST_19  F1   C14  C13  C12  180.00   0.0  0
 E1D  CONST_20  C3   N2   C2   N1   180.00   0.0  0
 E1D  CONST_21  F2   C12  C11  C1   180.00   0.0  0
 E1D  CONST_22  F1   C14  C15  C1   180.00   0.0  0
 E1D  CONST_23  O2   C13  C14  C15  180.00   0.0  0
 E1D  CONST_24  O1   C6   N4   C4   180.00   0.0  0
 E1D  CONST_25  C8   N4   C6   C7   180.00   0.0  0
 E1D  CONST_26  H13  C3   C4   C5   180.00   0.0  0
 E1D  CONST_27  H14  C15  C1   C11  180.00   0.0  0
 E1D  CONST_28  H1   C11  C12  C13  180.00   0.0  0
 E1D  CONST_29  O1   C6   N4   C8     0.00   0.0  0
 E1D  Var_01    C7   N5   C5   C4   -29.75  30.0  1
 E1D  Var_02    C6   N4   C4   C5    19.04  30.0  1
 E1D  Var_03    C2   N1   C1   C11  179.74  30.0  3
 E1D  Var_04    C1   N1   C2   N2    -1.24  30.0  1
 E1D  Var_05    H3   C8   N4   C4    49.41  30.0  3
 E1D  Var_06    H6   C9   N5   C5    83.10  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 E1D  chir_01  C7  C6  N5  C10  positiv

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
 E1D  plan-1  C14  0.020
 E1D  plan-1  C11  0.020
 E1D  plan-1  C12  0.020
 E1D  plan-1  C13  0.020
 E1D  plan-1  C1   0.020
 E1D  plan-1  C15  0.020
 E1D  plan-1  O2   0.020
 E1D  plan-1  F2   0.020
 E1D  plan-1  H1   0.020
 E1D  plan-1  H14  0.020
 E1D  plan-1  N1   0.020
 E1D  plan-1  F1   0.020
 E1D  plan-2  C4   0.020
 E1D  plan-2  C5   0.020
 E1D  plan-2  N2   0.020
 E1D  plan-2  C3   0.020
 E1D  plan-2  N3   0.020
 E1D  plan-2  C2   0.020
 E1D  plan-2  N4   0.020
 E1D  plan-2  N5   0.020
 E1D  plan-2  H13  0.020
 E1D  plan-2  N1   0.020
 E1D  plan-3  C4   0.020
 E1D  plan-3  C6   0.020
 E1D  plan-3  C7   0.020
 E1D  plan-3  N4   0.020
 E1D  plan-3  O1   0.020
 E1D  plan-3  C8   0.020

