# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 11:08:08 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCN1[C@H](C)C(=O)N(C)c2cnc(Nc3cc(F)c(O)c(F)c3)nc12
#
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
 584  584  (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one  ligand  51  28  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_584
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
 584  C1   C  CR6   0   0.604   0.3592   0.3925   0.1460
 584  C2   C  CR6   0   0.553  -1.9066   0.5110   0.3335
 584  C3   C  CR6   0   0.205  -1.8394   1.9098   0.0983
 584  O2   O  OH1   0  -0.612   6.9144   0.2510  -0.4305
 584  C11  C  CH3   0  -0.634  -2.8682  -4.7443  -1.2738
 584  C12  C  CH3   0  -0.644  -2.1354  -4.3757   1.0955
 584  C14  C  CR6   0   0.402   2.7892  -0.2250   0.0422
 584  C15  C  CR16  0  -0.514   3.6429  -1.3197   0.2083
 584  C16  C  CR6   0   0.483   4.9994  -1.1567   0.0493
 584  C17  C  CR6   0   0.037   5.5898   0.0581  -0.2681
 584  C18  C  CR6   0   0.530   4.7135   1.1218  -0.4262
 584  C19  C  CR16  0  -0.515   3.3457   1.0132  -0.2836
 584  N1   N  N     0  -0.489   0.5267   1.6676  -0.1315
 584  N2   N  N     0  -0.524  -0.8047  -0.2155   0.3777
 584  C4   C  CR16  0  -0.068  -0.5875   2.4134  -0.1376
 584  N3   N  NH1   0  -0.773   1.4345  -0.4533   0.2131
 584  N4   N  NT    0  -0.495  -3.0907  -0.0845   0.5390
 584  C5   C  CH2   0  -0.295  -3.1525  -1.5058   0.8478
 584  C6   C  CH2   0  -0.411  -2.8919  -2.4269  -0.3415
 584  C7   C  CH1   0  -0.234  -3.0741  -3.9093  -0.0143
 584  C8   C  CH1   0  -0.203  -4.3389   0.6272   0.3401
 584  C9   C  C     0   0.525  -4.2202   2.1436   0.3779
 584  N5   N  NT    0  -0.571  -2.9928   2.6938   0.1780
 584  C10  C  CH3   0  -0.643  -5.0463   0.2305  -0.9584
 584  F1   F  F     0  -0.317   5.8125  -2.2145   0.2102
 584  F2   F  F     0  -0.302   5.2363   2.3121  -0.7352
 584  H1   H  HOH1  0   0.459   7.4016  -0.5422  -0.1889
 584  H2   H  HCH3  0   0.222  -3.0561  -5.8020  -1.0836
 584  H3   H  HCH3  0   0.220  -3.5362  -4.4288  -2.0771
 584  H4   H  HCH3  0   0.208  -1.8438  -4.6503  -1.6421
 584  H5   H  HCH3  0   0.205  -1.0955  -4.1480   0.8473
 584  H6   H  HCH3  0   0.223  -2.3571  -3.9041   2.0533
 584  H7   H  HCH3  0   0.227  -2.2111  -5.4539   1.2443
 584  H8   H  HCH3  0   0.291  -3.8270   4.5903   0.2607
 584  H9   H  HCH3  0   0.236  -2.1695   4.4934   0.8702
 584  H10  H  HCH3  0   0.234  -2.4804   4.4334  -0.8749
 584  H11  H  HCR6  0   0.257   3.2622  -2.3006   0.4630
 584  H12  H  HCR6  0   0.308   2.7218   1.8819  -0.4208
 584  H13  H  HCR6  0   0.253  -0.4339   3.4672  -0.3338
 584  H14  H  HNH1  0   0.382   1.1711  -1.3994   0.4335
 584  H15  H  HCH2  0   0.253  -2.4347  -1.7110   1.6426
 584  H16  H  HCH2  0   0.232  -4.1449  -1.7008   1.2623
 584  H17  H  HCH2  0   0.223  -3.5609  -2.1611  -1.1636
 584  H18  H  HCH2  0   0.232  -1.8743  -2.2591  -0.7021
 584  H19  H  HCH1  0   0.208  -4.1063  -4.0620   0.3238
 584  H20  H  HCH1  0   0.274  -4.9983   0.3789   1.1766
 584  H21  H  HCH3  0   0.237  -5.3027  -0.8278  -0.9502
 584  H22  H  HCH3  0   0.262  -5.9726   0.7904  -1.0696
 584  H23  H  HCH3  0   0.229  -4.4128   0.4226  -1.8249
 584  O1   O  O     0  -0.420  -5.2250   2.8036   0.5297
 584  C13  C  CH3   0  -0.548  -2.8570   4.1326   0.1039

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
 584  C12  C7   single    1.527  0.020  1.527
 584  C10  C8   single    1.531  0.020  1.531
 584  C7   C11  single    1.525  0.020  1.525
 584  C7   C6   single    1.529  0.020  1.529
 584  C5   C6   single    1.527  0.020  1.527
 584  C5   N4   single    1.456  0.020  1.456
 584  C8   N4   single    1.451  0.020  1.451
 584  C8   C9   single    1.521  0.020  1.521
 584  N4   C2   single    1.341  0.020  1.341
 584  O1   C9   double    1.212  0.020  1.212
 584  O2   C17  single    1.348  0.020  1.348
 584  C9   N5   single    1.360  0.020  1.360
 584  F2   C18  single    1.336  0.020  1.336
 584  C17  C18  aromatic  1.387  0.020  1.387
 584  C17  C16  aromatic  1.387  0.020  1.387
 584  C18  C19  aromatic  1.380  0.020  1.380
 584  C2   N2   aromatic  1.321  0.020  1.321
 584  C2   C3   aromatic  1.420  0.020  1.420
 584  N2   C1   aromatic  1.333  0.020  1.333
 584  N5   C3   single    1.397  0.020  1.397
 584  N5   C13  single    1.447  0.020  1.447
 584  C16  F1   single    1.344  0.020  1.344
 584  C16  C15  aromatic  1.375  0.020  1.375
 584  C19  C14  aromatic  1.396  0.020  1.396
 584  C3   C4   aromatic  1.370  0.020  1.370
 584  C15  C14  aromatic  1.398  0.020  1.398
 584  C14  N3   single    1.384  0.020  1.384
 584  C1   N3   single    1.370  0.020  1.370
 584  C1   N1   aromatic  1.316  0.020  1.316
 584  C4   N1   aromatic  1.341  0.020  1.341
 584  O2   H1   single    0.850  0.020  0.980
 584  C11  H2   single    0.970  0.020  1.090
 584  C11  H3   single    0.970  0.020  1.090
 584  C11  H4   single    0.970  0.020  1.090
 584  C12  H5   single    0.970  0.020  1.090
 584  C12  H6   single    0.970  0.020  1.090
 584  C12  H7   single    0.970  0.020  1.090
 584  C13  H8   single    0.970  0.020  1.090
 584  C13  H9   single    0.970  0.020  1.090
 584  C13  H10  single    0.970  0.020  1.090
 584  C15  H11  single    0.930  0.020  1.080
 584  C19  H12  single    0.930  0.020  1.080
 584  C4   H13  single    0.930  0.020  1.080
 584  N3   H14  single    0.860  0.020  1.020
 584  C5   H15  single    0.970  0.020  1.090
 584  C5   H16  single    0.970  0.020  1.090
 584  C6   H17  single    0.970  0.020  1.090
 584  C6   H18  single    0.970  0.020  1.090
 584  C7   H19  single    0.970  0.020  1.090
 584  C8   H20  single    0.970  0.020  1.090
 584  C10  H21  single    0.970  0.020  1.090
 584  C10  H22  single    0.970  0.020  1.090
 584  C10  H23  single    0.970  0.020  1.090

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
 584  N3   C1   N2   113.27  3.000
 584  N3   C1   N1   120.59  3.000
 584  N2   C1   N1   126.14  3.000
 584  N4   C2   N2   119.16  3.000
 584  N2   C2   C3   120.53  3.000
 584  N4   C2   C3   120.30  3.000
 584  N5   C3   C4   123.92  3.000
 584  C4   C3   C2   115.71  3.000
 584  N5   C3   C2   120.29  3.000
 584  H1   O2   C17  110.45  3.000
 584  H4   C11  H3   107.51  3.000
 584  H4   C11  H2   107.68  3.000
 584  H3   C11  H2   107.65  3.000
 584  H4   C11  C7   110.97  3.000
 584  H3   C11  C7   111.53  3.000
 584  H2   C11  C7   111.32  3.000
 584  H7   C12  H6   107.07  3.000
 584  H7   C12  H5   107.63  3.000
 584  H6   C12  H5   107.63  3.000
 584  H7   C12  C7   111.00  3.000
 584  H6   C12  C7   112.42  3.000
 584  H5   C12  C7   110.87  3.000
 584  N3   C14  C19  124.41  3.000
 584  N3   C14  C15  116.98  3.000
 584  C19  C14  C15  118.60  3.000
 584  H11  C15  C16  118.78  3.000
 584  H11  C15  C14  121.51  3.000
 584  C16  C15  C14  119.71  3.000
 584  F1   C16  C17  117.33  3.000
 584  F1   C16  C15  119.31  3.000
 584  C17  C16  C15  123.36  3.000
 584  C18  C17  C16  115.38  3.000
 584  C16  C17  O2   124.81  3.000
 584  C18  C17  O2   119.81  3.000
 584  F2   C18  C19  118.81  3.000
 584  C19  C18  C17  123.66  3.000
 584  F2   C18  C17  117.53  3.000
 584  H12  C19  C18  119.81  3.000
 584  H12  C19  C14  120.91  3.000
 584  C18  C19  C14  119.29  3.000
 584  C4   N1   C1   115.74  3.000
 584  C2   N2   C1   118.14  3.000
 584  H13  C4   N1   115.11  3.000
 584  H13  C4   C3   121.24  3.000
 584  N1   C4   C3   123.66  3.000
 584  H14  N3   C14  115.99  3.000
 584  H14  N3   C1   112.69  3.000
 584  C14  N3   C1   131.32  3.000
 584  C8   N4   C5   118.14  3.000
 584  C8   N4   C2   121.39  3.000
 584  C5   N4   C2   120.23  3.000
 584  H16  C5   H15  106.72  3.000
 584  H16  C5   C6   110.04  3.000
 584  H15  C5   C6   109.99  3.000
 584  H16  C5   N4   107.05  3.000
 584  H15  C5   N4   108.09  3.000
 584  C6   C5   N4   114.62  3.000
 584  H18  C6   H17  106.54  3.000
 584  H18  C6   C7   109.30  3.000
 584  H17  C6   C7   108.90  3.000
 584  H18  C6   C5   108.87  3.000
 584  H17  C6   C5   109.56  3.000
 584  C7   C6   C5   113.45  3.000
 584  H19  C7   C6   108.24  3.000
 584  H19  C7   C12  108.18  3.000
 584  C6   C7   C12  112.24  3.000
 584  H19  C7   C11  107.78  3.000
 584  C6   C7   C11  109.76  3.000
 584  C12  C7   C11  110.49  3.000
 584  H20  C8   C10  108.13  3.000
 584  H20  C8   C9   104.73  3.000
 584  C10  C8   C9   108.38  3.000
 584  H20  C8   N4   107.61  3.000
 584  C9   C8   N4   114.74  3.000
 584  C10  C8   N4   112.76  3.000
 584  N5   C9   C8   118.03  3.000
 584  N5   C9   O1   123.13  3.000
 584  C8   C9   O1   118.77  3.000
 584  C9   N5   C13  119.63  3.000
 584  C13  N5   C3   118.53  3.000
 584  C9   N5   C3   121.78  3.000
 584  H23  C10  H22  108.83  3.000
 584  H23  C10  H21  108.30  3.000
 584  H22  C10  H21  107.48  3.000
 584  H23  C10  C8   111.09  3.000
 584  H22  C10  C8   110.29  3.000
 584  H21  C10  C8   110.75  3.000
 584  H10  C13  H9   108.75  3.000
 584  H10  C13  H8   108.80  3.000
 584  H9   C13  H8   108.82  3.000
 584  H10  C13  N5   110.64  3.000
 584  H9   C13  N5   110.61  3.000
 584  H8   C13  N5   109.18  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
 584  CONST_01  C3   C2   N2   C1      0.00   0.0  0
 584  CONST_02  C3   C4   N1   C1      0.00   0.0  0
 584  CONST_03  N1   C1   N2   C2      0.00   0.0  0
 584  CONST_04  N1   C4   C3   C2      0.00   0.0  0
 584  CONST_05  C17  C18  C19  C14     0.00   0.0  0
 584  CONST_06  C17  C16  C15  C14     0.00   0.0  0
 584  CONST_07  C18  C17  C16  C15     0.00   0.0  0
 584  CONST_08  C18  C19  C14  C15     0.00   0.0  0
 584  CONST_09  C19  C18  C17  C16     0.00   0.0  0
 584  CONST_10  C19  C14  C15  C16     0.00   0.0  0
 584  CONST_11  C4   C3   C2   N2      0.00   0.0  0
 584  CONST_12  C4   N1   C1   N2      0.00   0.0  0
 584  CONST_13  C8   C9   N5   C3      0.00   0.0  0
 584  CONST_14  N3   C1   N2   C2    180.00   0.0  0
 584  CONST_15  C19  C18  C17  O2    180.00   0.0  0
 584  CONST_16  C15  C16  C17  O2    180.00   0.0  0
 584  CONST_17  F2   C18  C19  C14   180.00   0.0  0
 584  CONST_18  F1   C16  C15  C14   180.00   0.0  0
 584  CONST_19  F2   C18  C17  C16   180.00   0.0  0
 584  CONST_20  N3   C14  C15  C16   180.00   0.0  0
 584  CONST_21  F1   C16  C17  C18   180.00   0.0  0
 584  CONST_22  N3   C14  C19  C18   180.00   0.0  0
 584  CONST_23  N3   C1   N1   C4    180.00   0.0  0
 584  CONST_24  O1   C9   N5   C3    180.00   0.0  0
 584  CONST_25  C8   C9   N5   C13   180.00   0.0  0
 584  CONST_26  H13  C4   N1   C1    180.00   0.0  0
 584  CONST_27  H12  C19  C14  C15   180.00   0.0  0
 584  CONST_28  H11  C15  C16  C17   180.00   0.0  0
 584  CONST_29  C13  N5   C9   O1      0.00   0.0  0
 584  Var_01    C9   N5   C3   C2     -5.12  30.0  1
 584  Var_02    C8   N4   C2   C3      8.96  30.0  1
 584  Var_03    C19  C14  N3   C1     -1.44  30.0  2
 584  Var_04    N2   C1   N3   C14  -179.83  30.0  1
 584  Var_05    C6   C5   N4   C2    -74.35  30.0  2
 584  Var_06    H8   C13  N5   C3   -175.47  30.0  3
 584  Var_07    C7   C6   C5   N4   -175.34  30.0  3
 584  Var_08    C5   C6   C7   C11   176.96  30.0  3
 584  Var_09    H5   C12  C7   C11    68.09  30.0  3
 584  Var_10    H2   C11  C7   C12    59.39  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
 584  chir_01  C8  C10  N4  C9  negativ

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
 584  plan-1  O2   0.020
 584  plan-1  C14  0.020
 584  plan-1  C15  0.020
 584  plan-1  C16  0.020
 584  plan-1  C17  0.020
 584  plan-1  C18  0.020
 584  plan-1  C19  0.020
 584  plan-1  N3   0.020
 584  plan-1  F1   0.020
 584  plan-1  F2   0.020
 584  plan-1  H11  0.020
 584  plan-1  H12  0.020
 584  plan-2  C1   0.020
 584  plan-2  C2   0.020
 584  plan-2  C3   0.020
 584  plan-2  N1   0.020
 584  plan-2  N2   0.020
 584  plan-2  C4   0.020
 584  plan-2  N3   0.020
 584  plan-2  N4   0.020
 584  plan-2  N5   0.020
 584  plan-2  H13  0.020
 584  plan-3  C3   0.020
 584  plan-3  C8   0.020
 584  plan-3  C9   0.020
 584  plan-3  N5   0.020
 584  plan-3  O1   0.020
 584  plan-3  C13  0.020

