# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 11:56:09 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (7S)-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
 7DZ  7DZ  (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one  ligand  51  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7DZ
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
 7DZ  C18  C  CH3   0  -0.560  -2.1172  -4.1848   0.8903
 7DZ  C16  C  CR6   0   0.516   5.1079  -0.4430   0.2713
 7DZ  C17  C  CR16  0  -0.511   3.7296  -0.4900   0.2461
 7DZ  C15  C  CR6   0   0.042   5.8508   0.6922  -0.0166
 7DZ  C14  C  CR6   0   0.479   5.1049   1.8192  -0.3358
 7DZ  N1   N  N     0  -0.488   1.0025  -1.4714   0.1663
 7DZ  C13  C  CR16  0  -0.533   3.7302   1.8312  -0.3756
 7DZ  C12  C  CR6   0   0.387   3.0171   0.6645  -0.0827
 7DZ  C11  C  CH3   0  -0.662  -4.4137   3.8972  -1.0487
 7DZ  C10  C  CH3   0  -0.649  -6.0589   3.5654   0.8101
 7DZ  C8   C  CH2   0  -0.451  -4.5061   1.6975   0.2130
 7DZ  C7   C  CH2   0  -0.279  -3.1067   1.2796  -0.2176
 7DZ  C6   C  CR6   0   0.538  -1.5746  -0.5832   0.0181
 7DZ  C5   C  CR6   0   0.595   0.6695  -0.2074  -0.0006
 7DZ  C4   C  CR16  0  -0.078  -0.0123  -2.3381   0.2750
 7DZ  C3   C  CR6   0   0.197  -1.3304  -1.9663   0.2118
 7DZ  C2   C  C     0   0.544  -3.6692  -2.4743   0.1219
 7DZ  C1   C  CH1   0  -0.253  -3.8612  -1.0904  -0.4730
 7DZ  N2   N  N     0  -0.524  -0.5750   0.2719  -0.0825
 7DZ  F1   F  F     0  -0.318   5.7792   2.9462  -0.6217
 7DZ  F    F  F     0  -0.314   5.7836  -1.5540   0.6005
 7DZ  N4   N  NH1   0  -0.777   1.6352   0.7524  -0.1268
 7DZ  N    N  NT    0  -0.559  -2.3993  -2.8471   0.4066
 7DZ  O    O  O     0  -0.470  -4.6303  -3.2081   0.2687
 7DZ  N3   N  NT    0  -0.495  -2.8503  -0.1449  -0.0316
 7DZ  C    C  CH3   0  -0.655  -3.9449  -1.1926  -1.9982
 7DZ  H1   H  HCH3  0   0.278  -3.0502  -4.6915   1.1073
 7DZ  H2   H  HCH3  0   0.257  -1.5717  -4.7622   0.1430
 7DZ  H3   H  HCH3  0   0.258  -1.5221  -4.1375   1.8020
 7DZ  H4   H  HCR6  0   0.309   3.2233  -1.4127   0.4807
 7DZ  H5   H  HCR6  0   0.297   3.2182   2.7486  -0.6386
 7DZ  H6   H  HCH3  0   0.230  -4.5957   4.9710  -0.9803
 7DZ  H7   H  HCH3  0   0.231  -3.3892   3.7650  -1.3990
 7DZ  H8   H  HCH3  0   0.215  -5.0807   3.4975  -1.8171
 7DZ  H9   H  HCH1  0   0.221  -3.9324   3.5953   1.0159
 7DZ  H10  H  HCH3  0   0.225  -6.2545   3.1070   1.7810
 7DZ  H11  H  HCH3  0   0.227  -6.1798   4.6442   0.9213
 7DZ  H12  H  HCH3  0   0.214  -6.8284   3.2164   0.1171
 7DZ  H13  H  HCH2  0   0.239  -4.7217   1.2631   1.1943
 7DZ  H14  H  HCH2  0   0.224  -5.2626   1.3092  -0.4776
 7DZ  H15  H  HCH2  0   0.236  -2.9208   1.5634  -1.2588
 7DZ  H16  H  HCH2  0   0.258  -2.3768   1.8199   0.3843
 7DZ  H17  H  HCR6  0   0.284   0.2714  -3.3717   0.4324
 7DZ  H18  H  HOH1  0   0.479   7.5791   1.4806  -0.2468
 7DZ  H19  H  HCH1  0   0.300  -4.8248  -0.7544  -0.0933
 7DZ  H20  H  HNH1  0   0.410   1.2628   1.6720  -0.3077
 7DZ  H21  H  HCH3  0   0.253  -4.7236  -1.8945  -2.2934
 7DZ  H22  H  HCH3  0   0.252  -4.1946  -0.2229  -2.4304
 7DZ  H23  H  HCH3  0   0.240  -2.9988  -1.5225  -2.4299
 7DZ  O1   O  OH1   0  -0.622   7.1956   0.6406   0.0298
 7DZ  C9   C  CH1   0  -0.237  -4.6666   3.2172   0.2945

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
 7DZ  C10  C9   single    1.525  0.020  1.525
 7DZ  C9   C8   single    1.530  0.020  1.530
 7DZ  C9   C11  single    1.527  0.020  1.527
 7DZ  C8   C7   single    1.523  0.020  1.523
 7DZ  O    C2   double    1.218  0.020  1.218
 7DZ  C2   C1   single    1.519  0.020  1.519
 7DZ  C2   N    single    1.354  0.020  1.354
 7DZ  C1   N3   single    1.453  0.020  1.453
 7DZ  C1   C    single    1.531  0.020  1.531
 7DZ  C7   N3   single    1.459  0.020  1.459
 7DZ  N3   C6   single    1.350  0.020  1.350
 7DZ  N    C18  single    1.450  0.020  1.450
 7DZ  N    C3   single    1.399  0.020  1.399
 7DZ  C6   C3   aromatic  1.418  0.020  1.418
 7DZ  C6   N2   aromatic  1.319  0.020  1.319
 7DZ  C3   C4   aromatic  1.371  0.020  1.371
 7DZ  N2   C5   aromatic  1.336  0.020  1.336
 7DZ  O1   C15  single    1.347  0.020  1.347
 7DZ  C4   N1   aromatic  1.339  0.020  1.339
 7DZ  F    C16  single    1.341  0.020  1.341
 7DZ  C16  C15  aromatic  1.387  0.020  1.387
 7DZ  C16  C17  aromatic  1.379  0.020  1.379
 7DZ  C15  C14  aromatic  1.389  0.020  1.389
 7DZ  C5   N1   aromatic  1.318  0.020  1.318
 7DZ  C5   N4   single    1.367  0.020  1.367
 7DZ  C17  C12  aromatic  1.396  0.020  1.396
 7DZ  C14  C13  aromatic  1.375  0.020  1.375
 7DZ  C14  F1   single    1.344  0.020  1.344
 7DZ  C12  C13  aromatic  1.398  0.020  1.398
 7DZ  C12  N4   single    1.385  0.020  1.385
 7DZ  C18  H1   single    0.970  0.020  1.090
 7DZ  C18  H2   single    0.970  0.020  1.090
 7DZ  C18  H3   single    0.970  0.020  1.090
 7DZ  C17  H4   single    0.930  0.020  1.080
 7DZ  C13  H5   single    0.930  0.020  1.080
 7DZ  C11  H6   single    0.970  0.020  1.090
 7DZ  C11  H7   single    0.970  0.020  1.090
 7DZ  C11  H8   single    0.970  0.020  1.090
 7DZ  C9   H9   single    0.970  0.020  1.090
 7DZ  C10  H10  single    0.970  0.020  1.090
 7DZ  C10  H11  single    0.970  0.020  1.090
 7DZ  C10  H12  single    0.970  0.020  1.090
 7DZ  C8   H13  single    0.970  0.020  1.090
 7DZ  C8   H14  single    0.970  0.020  1.090
 7DZ  C7   H15  single    0.970  0.020  1.090
 7DZ  C7   H16  single    0.970  0.020  1.090
 7DZ  C4   H17  single    0.930  0.020  1.080
 7DZ  O1   H18  single    0.850  0.020  0.980
 7DZ  C1   H19  single    0.970  0.020  1.090
 7DZ  N4   H20  single    0.860  0.020  1.020
 7DZ  C    H21  single    0.970  0.020  1.090
 7DZ  C    H22  single    0.970  0.020  1.090
 7DZ  C    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
 7DZ  H3   C18  H2   108.85  3.000
 7DZ  H3   C18  H1   108.84  3.000
 7DZ  H2   C18  H1   108.68  3.000
 7DZ  H3   C18  N    110.19  3.000
 7DZ  H2   C18  N    110.92  3.000
 7DZ  H1   C18  N    109.30  3.000
 7DZ  F    C16  C15  117.32  3.000
 7DZ  C15  C16  C17  124.01  3.000
 7DZ  F    C16  C17  118.67  3.000
 7DZ  H4   C17  C12  121.28  3.000
 7DZ  H4   C17  C16  119.63  3.000
 7DZ  C12  C17  C16  119.09  3.000
 7DZ  O1   C15  C14  125.13  3.000
 7DZ  C14  C15  C16  115.11  3.000
 7DZ  O1   C15  C16  119.76  3.000
 7DZ  F1   C14  C13  119.20  3.000
 7DZ  F1   C14  C15  117.38  3.000
 7DZ  C13  C14  C15  123.41  3.000
 7DZ  C4   N1   C5   116.09  3.000
 7DZ  H5   C13  C12  121.09  3.000
 7DZ  H5   C13  C14  119.15  3.000
 7DZ  C12  C13  C14  119.76  3.000
 7DZ  N4   C12  C13  116.68  3.000
 7DZ  N4   C12  C17  124.69  3.000
 7DZ  C13  C12  C17  118.63  3.000
 7DZ  H8   C11  H7   107.65  3.000
 7DZ  H8   C11  H6   107.58  3.000
 7DZ  H7   C11  H6   107.22  3.000
 7DZ  H8   C11  C9   110.76  3.000
 7DZ  H7   C11  C9   112.59  3.000
 7DZ  H6   C11  C9   110.82  3.000
 7DZ  H12  C10  H11  107.60  3.000
 7DZ  H12  C10  H10  107.68  3.000
 7DZ  H11  C10  H10  107.75  3.000
 7DZ  H12  C10  C9   110.83  3.000
 7DZ  H11  C10  C9   111.18  3.000
 7DZ  H10  C10  C9   111.63  3.000
 7DZ  H14  C8   H13  106.77  3.000
 7DZ  H14  C8   C7   111.05  3.000
 7DZ  H13  C8   C7   109.00  3.000
 7DZ  H14  C8   C9   108.25  3.000
 7DZ  H13  C8   C9   109.01  3.000
 7DZ  C7   C8   C9   112.58  3.000
 7DZ  H16  C7   H15  106.44  3.000
 7DZ  H16  C7   N3   107.21  3.000
 7DZ  H15  C7   N3   110.14  3.000
 7DZ  H16  C7   C8   108.87  3.000
 7DZ  H15  C7   C8   110.72  3.000
 7DZ  N3   C7   C8   113.16  3.000
 7DZ  N3   C6   N2   120.19  3.000
 7DZ  N2   C6   C3   120.81  3.000
 7DZ  N3   C6   C3   118.99  3.000
 7DZ  N4   C5   N2   113.59  3.000
 7DZ  N4   C5   N1   120.44  3.000
 7DZ  N2   C5   N1   125.96  3.000
 7DZ  H17  C4   C3   121.15  3.000
 7DZ  H17  C4   N1   115.52  3.000
 7DZ  C3   C4   N1   123.32  3.000
 7DZ  N    C3   C4   123.89  3.000
 7DZ  C4   C3   C6   115.88  3.000
 7DZ  N    C3   C6   120.11  3.000
 7DZ  O    C2   N    123.29  3.000
 7DZ  N    C2   C1   116.87  3.000
 7DZ  O    C2   C1   119.77  3.000
 7DZ  H19  C1   C    108.64  3.000
 7DZ  H19  C1   N3   107.99  3.000
 7DZ  C    C1   N3   112.59  3.000
 7DZ  H19  C1   C2   104.86  3.000
 7DZ  C    C1   C2   109.66  3.000
 7DZ  N3   C1   C2   112.71  3.000
 7DZ  C5   N2   C6   117.94  3.000
 7DZ  H20  N4   C5   113.32  3.000
 7DZ  H20  N4   C12  115.59  3.000
 7DZ  C5   N4   C12  131.07  3.000
 7DZ  C2   N    C3   120.94  3.000
 7DZ  C3   N    C18  118.60  3.000
 7DZ  C2   N    C18  120.44  3.000
 7DZ  C1   N3   C6   117.22  3.000
 7DZ  C6   N3   C7   119.19  3.000
 7DZ  C1   N3   C7   118.31  3.000
 7DZ  H23  C    H22  108.10  3.000
 7DZ  H23  C    H21  108.54  3.000
 7DZ  H22  C    H21  107.57  3.000
 7DZ  H23  C    C1   111.53  3.000
 7DZ  H22  C    C1   110.36  3.000
 7DZ  H21  C    C1   110.62  3.000
 7DZ  H18  O1   C15  110.73  3.000
 7DZ  H9   C9   C8   107.89  3.000
 7DZ  H9   C9   C10  108.07  3.000
 7DZ  C8   C9   C10  109.91  3.000
 7DZ  H9   C9   C11  108.32  3.000
 7DZ  C8   C9   C11  112.22  3.000
 7DZ  C10  C9   C11  110.31  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
 7DZ  CONST_01  C13  C14  C15  C16     0.00   0.0  0
 7DZ  CONST_02  C13  C12  C17  C16     0.00   0.0  0
 7DZ  CONST_03  C14  C15  C16  C17     0.00   0.0  0
 7DZ  CONST_04  C14  C13  C12  C17     0.00   0.0  0
 7DZ  CONST_05  C12  C17  C16  C15     0.00   0.0  0
 7DZ  CONST_06  C12  C13  C14  C15     0.00   0.0  0
 7DZ  CONST_07  C6   C3   C4   N1      0.00   0.0  0
 7DZ  CONST_08  C6   N2   C5   N1      0.00   0.0  0
 7DZ  CONST_09  C3   C6   N2   C5      0.00   0.0  0
 7DZ  CONST_10  C3   C4   N1   C5      0.00   0.0  0
 7DZ  CONST_11  N2   C6   C3   C4      0.00   0.0  0
 7DZ  CONST_12  N2   C5   N1   C4      0.00   0.0  0
 7DZ  CONST_13  C1   C2   N    C3      0.00   0.0  0
 7DZ  CONST_14  F1   C14  C15  C16   180.00   0.0  0
 7DZ  CONST_15  N4   C12  C17  C16   180.00   0.0  0
 7DZ  CONST_16  O1   C15  C16  C17   180.00   0.0  0
 7DZ  CONST_17  F    C16  C15  C14   180.00   0.0  0
 7DZ  CONST_18  N4   C12  C13  C14   180.00   0.0  0
 7DZ  CONST_19  O1   C15  C14  C13   180.00   0.0  0
 7DZ  CONST_20  F    C16  C17  C12   180.00   0.0  0
 7DZ  CONST_21  F1   C14  C13  C12   180.00   0.0  0
 7DZ  CONST_22  N4   C5   N2   C6    180.00   0.0  0
 7DZ  CONST_23  N4   C5   N1   C4    180.00   0.0  0
 7DZ  CONST_24  C1   C2   N    C18   180.00   0.0  0
 7DZ  CONST_25  O    C2   N    C3    180.00   0.0  0
 7DZ  CONST_26  H5   C13  C12  C17   180.00   0.0  0
 7DZ  CONST_27  H4   C17  C16  C15   180.00   0.0  0
 7DZ  CONST_28  H17  C4   C3   C6    180.00   0.0  0
 7DZ  CONST_29  O    C2   N    C18     0.00   0.0  0
 7DZ  Var_01    C2   N    C3   C6     14.91  30.0  1
 7DZ  Var_02    C1   N3   C6   C3    -26.66  30.0  1
 7DZ  Var_03    C5   N4   C12  C17    -6.70  30.0  2
 7DZ  Var_04    C12  N4   C5   N1     -1.73  30.0  2
 7DZ  Var_05    H1   C18  N    C3    172.79  30.0  3
 7DZ  Var_06    N3   C7   C8   C9    167.88  30.0  3
 7DZ  Var_07    C7   C8   C9   C11    60.26  30.0  3
 7DZ  Var_08    H10  C10  C9   C11  -178.79  30.0  3
 7DZ  Var_09    H6   C11  C9   C10    53.49  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
 7DZ  chir_01  C1  C2  N3  C  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
 7DZ  plan-1  C16  0.020
 7DZ  plan-1  C17  0.020
 7DZ  plan-1  C15  0.020
 7DZ  plan-1  C14  0.020
 7DZ  plan-1  C13  0.020
 7DZ  plan-1  C12  0.020
 7DZ  plan-1  F1   0.020
 7DZ  plan-1  F    0.020
 7DZ  plan-1  N4   0.020
 7DZ  plan-1  H4   0.020
 7DZ  plan-1  H5   0.020
 7DZ  plan-1  O1   0.020
 7DZ  plan-2  N1   0.020
 7DZ  plan-2  C6   0.020
 7DZ  plan-2  C5   0.020
 7DZ  plan-2  C4   0.020
 7DZ  plan-2  C3   0.020
 7DZ  plan-2  N2   0.020
 7DZ  plan-2  N4   0.020
 7DZ  plan-2  N    0.020
 7DZ  plan-2  N3   0.020
 7DZ  plan-2  H17  0.020
 7DZ  plan-3  C18  0.020
 7DZ  plan-3  C3   0.020
 7DZ  plan-3  C2   0.020
 7DZ  plan-3  C1   0.020
 7DZ  plan-3  N    0.020
 7DZ  plan-3  O    0.020

