# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 03:26:33 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (7S)-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
 E5M  E5M  (7S)-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_E5M
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
 E5M  C4   C  CR66  0   0.184   2.4732  -0.9774  -0.1612
 E5M  C14  C  CR6   0   0.479  -4.7012   1.1034   0.3524
 E5M  C5   C  CR66  0   0.537   2.3676   0.3754   0.2414
 E5M  C6   C  CR6   0   0.566   4.8658  -0.8743  -0.1871
 E5M  C11  C  CR16  0  -0.514  -2.7963  -0.7932  -0.2248
 E5M  C7   C  CR16  0  -0.206   4.7030   0.6454  -0.2175
 E5M  C10  C  CH3   0  -0.694   5.9591   1.3141   0.3145
 E5M  C12  C  CR6   0   0.519  -4.1445  -1.0714  -0.3149
 E5M  C13  C  CR6   0   0.040  -5.1461  -0.1536  -0.0358
 E5M  N2   N  N     0  -0.487   0.0948  -1.0352  -0.3102
 E5M  C3   C  CR16  0  -0.074   1.2925  -1.6181  -0.4369
 E5M  N3   N  N     0  -0.515   1.1864   0.9450   0.3809
 E5M  C1   C  CR6   0   0.385  -2.3906   0.4825   0.1719
 E5M  C2   C  CR6   0   0.589   0.1014   0.2131   0.1139
 E5M  N4   N  NR6   0  -0.566   3.7229  -1.6015  -0.1792
 E5M  N5   N  NR6   0  -0.494   3.5006   1.0660   0.5045
 E5M  O1   O  O     0  -0.468   5.9683  -1.3883  -0.2191
 E5M  C15  C  CR16  0  -0.536  -3.3716   1.4366   0.4610
 E5M  O2   O  OH1   0  -0.622  -6.4377  -0.5164  -0.1514
 E5M  F2   F  F     0  -0.314  -4.5232  -2.2998  -0.6955
 E5M  H1   H  HCR6  0   0.311  -2.0770  -1.5615  -0.4586
 E5M  H2   H  HCR6  0   0.279   4.5972   0.9187  -1.2800
 E5M  H9   H  HCH3  0   0.241   6.0977   1.1183   1.3779
 E5M  H10  H  HCH3  0   0.260   6.8271   0.9377  -0.2195
 E5M  H11  H  HCH3  0   0.254   5.9274   2.3898   0.1579
 E5M  H13  H  HCR6  0   0.281   1.2810  -2.6512  -0.7631
 E5M  H14  H  HCR6  0   0.296  -3.1022   2.4375   0.7744
 E5M  H15  H  HOH1  0   0.478  -7.0199   0.2104   0.0970
 E5M  C8   C  CH3   0  -0.558   3.7737  -3.0506  -0.2341
 E5M  C9   C  CH3   0  -0.581   3.3973   2.4622   0.8839
 E5M  N1   N  NH1   0  -0.783  -1.0727   0.8861   0.3091
 E5M  F1   F  F     0  -0.319  -5.6340   2.0289   0.6357
 E5M  H3   H  HCH3  0   0.278   4.7803  -3.3867  -0.0138
 E5M  H4   H  HCH3  0   0.256   3.0944  -3.4721   0.5055
 E5M  H5   H  HCH3  0   0.255   3.4919  -3.4195  -1.2211
 E5M  H6   H  HCH3  0   0.255   3.3967   3.1240   0.0129
 E5M  H7   H  HCH3  0   0.287   2.4758   2.6194   1.4341
 E5M  H8   H  HCH3  0   0.271   4.2273   2.7360   1.5292
 E5M  H12  H  HNH1  0   0.430  -0.9389   1.8358   0.6202

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
 E5M  C9   N5   single    1.451  0.020  1.451
 E5M  C10  C7   single    1.519  0.020  1.519
 E5M  F1   C14  single    1.344  0.020  1.344
 E5M  C7   N5   single    1.464  0.020  1.464
 E5M  C7   C6   single    1.529  0.020  1.529
 E5M  N5   C5   single    1.353  0.020  1.353
 E5M  O1   C6   double    1.217  0.020  1.217
 E5M  C6   N4   single    1.355  0.020  1.355
 E5M  C14  C15  aromatic  1.375  0.020  1.375
 E5M  C14  C13  aromatic  1.389  0.020  1.389
 E5M  O2   C13  single    1.347  0.020  1.347
 E5M  C15  C1   aromatic  1.399  0.020  1.399
 E5M  C13  C12  aromatic  1.387  0.020  1.387
 E5M  C5   N3   aromatic  1.319  0.020  1.319
 E5M  C5   C4   aromatic  1.415  0.020  1.415
 E5M  N3   C2   aromatic  1.336  0.020  1.336
 E5M  N4   C4   single    1.397  0.020  1.397
 E5M  N4   C8   single    1.451  0.020  1.451
 E5M  C4   C3   aromatic  1.371  0.020  1.371
 E5M  C1   C11  aromatic  1.396  0.020  1.396
 E5M  C1   N1   single    1.385  0.020  1.385
 E5M  C12  F2   single    1.341  0.020  1.341
 E5M  C12  C11  aromatic  1.380  0.020  1.380
 E5M  C2   N1   single    1.367  0.020  1.367
 E5M  C2   N2   aromatic  1.318  0.020  1.318
 E5M  C3   N2   aromatic  1.338  0.020  1.338
 E5M  C11  H1   single    0.930  0.020  1.080
 E5M  C7   H2   single    0.970  0.020  1.090
 E5M  C8   H3   single    0.970  0.020  1.090
 E5M  C8   H4   single    0.970  0.020  1.090
 E5M  C8   H5   single    0.970  0.020  1.090
 E5M  C9   H6   single    0.970  0.020  1.090
 E5M  C9   H7   single    0.970  0.020  1.090
 E5M  C9   H8   single    0.970  0.020  1.090
 E5M  C10  H9   single    0.970  0.020  1.090
 E5M  C10  H10  single    0.970  0.020  1.090
 E5M  C10  H11  single    0.970  0.020  1.090
 E5M  N1   H12  single    0.860  0.020  1.020
 E5M  C3   H13  single    0.930  0.020  1.080
 E5M  C15  H14  single    0.930  0.020  1.080
 E5M  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
 E5M  N4   C4   C3   123.98  3.000
 E5M  C3   C4   C5   116.07  3.000
 E5M  N4   C4   C5   119.83  3.000
 E5M  F1   C14  C15  119.18  3.000
 E5M  C15  C14  C13  123.45  3.000
 E5M  F1   C14  C13  117.37  3.000
 E5M  N5   C5   N3   120.60  3.000
 E5M  N3   C5   C4   120.65  3.000
 E5M  N5   C5   C4   118.74  3.000
 E5M  O1   C6   N4   122.54  3.000
 E5M  N4   C6   C7   116.35  3.000
 E5M  O1   C6   C7   121.06  3.000
 E5M  H1   C11  C1   121.25  3.000
 E5M  H1   C11  C12  119.62  3.000
 E5M  C1   C11  C12  119.13  3.000
 E5M  H2   C7   N5   108.98  3.000
 E5M  H2   C7   C10  107.92  3.000
 E5M  N5   C7   C10  112.32  3.000
 E5M  H2   C7   C6   106.01  3.000
 E5M  N5   C7   C6   111.30  3.000
 E5M  C10  C7   C6   110.03  3.000
 E5M  H11  C10  H10  107.17  3.000
 E5M  H11  C10  H9   108.78  3.000
 E5M  H10  C10  H9   108.40  3.000
 E5M  H11  C10  C7   111.16  3.000
 E5M  H10  C10  C7   109.63  3.000
 E5M  H9   C10  C7   111.57  3.000
 E5M  F2   C12  C13  117.35  3.000
 E5M  F2   C12  C11  118.65  3.000
 E5M  C13  C12  C11  124.00  3.000
 E5M  O2   C13  C12  119.81  3.000
 E5M  C12  C13  C14  115.08  3.000
 E5M  O2   C13  C14  125.11  3.000
 E5M  C2   N2   C3   116.00  3.000
 E5M  H13  C3   N2   115.74  3.000
 E5M  H13  C3   C4   121.01  3.000
 E5M  N2   C3   C4   123.24  3.000
 E5M  C2   N3   C5   118.01  3.000
 E5M  C15  C1   N1   116.62  3.000
 E5M  N1   C1   C11  124.81  3.000
 E5M  C15  C1   C11  118.57  3.000
 E5M  N3   C2   N2   125.96  3.000
 E5M  N2   C2   N1   120.50  3.000
 E5M  N3   C2   N1   113.53  3.000
 E5M  C8   N4   C6   120.42  3.000
 E5M  C8   N4   C4   118.55  3.000
 E5M  C6   N4   C4   121.00  3.000
 E5M  C9   N5   C7   117.65  3.000
 E5M  C7   N5   C5   116.44  3.000
 E5M  C9   N5   C5   118.86  3.000
 E5M  H14  C15  C1   121.06  3.000
 E5M  H14  C15  C14  119.17  3.000
 E5M  C1   C15  C14  119.77  3.000
 E5M  H15  O2   C13  110.74  3.000
 E5M  H5   C8   H4   108.81  3.000
 E5M  H5   C8   H3   108.60  3.000
 E5M  H4   C8   H3   108.73  3.000
 E5M  H5   C8   N4   111.28  3.000
 E5M  H4   C8   N4   109.82  3.000
 E5M  H3   C8   N4   109.55  3.000
 E5M  H8   C9   H7   108.13  3.000
 E5M  H8   C9   H6   108.72  3.000
 E5M  H7   C9   H6   108.41  3.000
 E5M  H8   C9   N5   110.10  3.000
 E5M  H7   C9   N5   109.43  3.000
 E5M  H6   C9   N5   111.97  3.000
 E5M  H12  N1   C2   113.18  3.000
 E5M  H12  N1   C1   115.55  3.000
 E5M  C2   N1   C1   131.26  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
 E5M  CONST_01  C2   N3   C5   C4      0.00   0.0  0
 E5M  CONST_02  C2   N2   C3   C4      0.00   0.0  0
 E5M  CONST_03  C11  C1   C15  C14     0.00   0.0  0
 E5M  CONST_04  C11  C12  C13  C14     0.00   0.0  0
 E5M  CONST_05  N2   C2   N3   C5      0.00   0.0  0
 E5M  CONST_06  N2   C3   C4   C5      0.00   0.0  0
 E5M  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 E5M  CONST_08  C15  C1   C11  C12     0.00   0.0  0
 E5M  CONST_09  C1   C15  C14  C13     0.00   0.0  0
 E5M  CONST_10  C1   C11  C12  C13     0.00   0.0  0
 E5M  CONST_11  N3   C5   C4   C3      0.00   0.0  0
 E5M  CONST_12  N3   C2   N2   C3      0.00   0.0  0
 E5M  CONST_13  C7   C6   N4   C4      0.00   0.0  0
 E5M  CONST_14  N1   C1   C15  C14   180.00   0.0  0
 E5M  CONST_15  F2   C12  C13  C14   180.00   0.0  0
 E5M  CONST_16  N1   C2   N3   C5    180.00   0.0  0
 E5M  CONST_17  O2   C13  C12  C11   180.00   0.0  0
 E5M  CONST_18  F1   C14  C13  C12   180.00   0.0  0
 E5M  CONST_19  N1   C1   C11  C12   180.00   0.0  0
 E5M  CONST_20  C3   N2   C2   N1    180.00   0.0  0
 E5M  CONST_21  F1   C14  C15  C1    180.00   0.0  0
 E5M  CONST_22  F2   C12  C11  C1    180.00   0.0  0
 E5M  CONST_23  O2   C13  C14  C15   180.00   0.0  0
 E5M  CONST_24  O1   C6   N4   C4    180.00   0.0  0
 E5M  CONST_25  C8   N4   C6   C7    180.00   0.0  0
 E5M  CONST_26  H13  C3   C4   C5    180.00   0.0  0
 E5M  CONST_27  H14  C15  C1   C11   180.00   0.0  0
 E5M  CONST_28  H1   C11  C12  C13   180.00   0.0  0
 E5M  CONST_29  O1   C6   N4   C8      0.00   0.0  0
 E5M  Var_01    C7   N5   C5   C4     28.47  30.0  1
 E5M  Var_02    C6   N4   C4   C5    -18.64  30.0  1
 E5M  Var_03    C2   N1   C1   C11    -0.02  30.0  2
 E5M  Var_04    C1   N1   C2   N2      1.94  30.0  2
 E5M  Var_05    H3   C8   N4   C4   -167.08  30.0  3
 E5M  Var_06    H6   C9   N5   C5    -88.10  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
 E5M  chir_01  C7  C10  N5  C6  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
 E5M  plan-1  C14  0.020
 E5M  plan-1  C11  0.020
 E5M  plan-1  C12  0.020
 E5M  plan-1  C13  0.020
 E5M  plan-1  C1   0.020
 E5M  plan-1  C15  0.020
 E5M  plan-1  O2   0.020
 E5M  plan-1  F2   0.020
 E5M  plan-1  H1   0.020
 E5M  plan-1  H14  0.020
 E5M  plan-1  N1   0.020
 E5M  plan-1  F1   0.020
 E5M  plan-2  C4   0.020
 E5M  plan-2  C5   0.020
 E5M  plan-2  N2   0.020
 E5M  plan-2  C3   0.020
 E5M  plan-2  N3   0.020
 E5M  plan-2  C2   0.020
 E5M  plan-2  N4   0.020
 E5M  plan-2  N5   0.020
 E5M  plan-2  H13  0.020
 E5M  plan-2  N1   0.020
 E5M  plan-3  C4   0.020
 E5M  plan-3  C6   0.020
 E5M  plan-3  C7   0.020
 E5M  plan-3  N4   0.020
 E5M  plan-3  O1   0.020
 E5M  plan-3  C8   0.020

