# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 11:54:40 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-ethyl-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1[C@H](C)C(=O)N(CC#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
 F8Y  F8Y  (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-ethyl-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one  ligand  44  27  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F8Y
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
 F8Y  C4   C  CR6   0   0.507  -4.5708  -0.9892   0.0781
 F8Y  C14  C  CH2   0  -0.289   2.8407   2.9724  -0.3006
 F8Y  C5   C  CR16  0  -0.514  -3.2316  -0.6562   0.0648
 F8Y  C6   C  CR6   0   0.386  -2.8734   0.6891  -0.0165
 F8Y  C11  C  CH1   0  -0.261   4.2037   0.8821  -0.5171
 F8Y  C7   C  CR6   0   0.598  -0.3744   0.5058   0.0386
 F8Y  C8   C  CR6   0   0.541   1.8836   0.7733   0.0444
 F8Y  C9   C  CR6   0   0.188   2.0329  -0.6155   0.2822
 F8Y  C10  C  CR16  0  -0.058   0.8764  -1.3497   0.3150
 F8Y  C12  C  C     0   0.559   4.4257  -0.4517   0.1701
 F8Y  C13  C  CH3   0  -0.656   4.2339   0.6860  -2.0343
 F8Y  N1   N  NH1   0  -0.776  -1.5705   1.1604  -0.0468
 F8Y  N2   N  N     0  -0.520   0.6853   1.3141  -0.0573
 F8Y  C3   C  CR6   0   0.044  -5.6047  -0.0690   0.0146
 F8Y  N3   N  N     0  -0.489  -0.3386  -0.8040   0.1896
 F8Y  C1   C  CR16  0  -0.533  -3.8890   1.6505  -0.0809
 F8Y  C2   C  CR6   0   0.490  -5.2073   1.2606  -0.0648
 F8Y  F1   F  F     0  -0.321  -4.9110  -2.2885   0.1557
 F8Y  O1   O  OH1   0  -0.623  -6.9168  -0.3709   0.0275
 F8Y  F2   F  F     0  -0.310  -6.1665   2.1932  -0.1254
 F8Y  N4   N  NT    0  -0.487   2.9909   1.5397  -0.0568
 F8Y  N5   N  NT    0  -0.562   3.3096  -1.1352   0.5289
 F8Y  O2   O  O     0  -0.459   5.5474  -0.8897   0.3366
 F8Y  C15  C  CH3   0  -0.708   4.1037   3.7652  -0.0161
 F8Y  C16  C  CH2   0  -0.489   3.4451  -2.4485   1.1337
 F8Y  C17  C  CSP   0   0.263   3.3823  -3.5243   0.1480
 F8Y  C18  C  CSP1  0  -0.500   3.3241  -4.4063  -0.6652
 F8Y  H1   H  HCH2  0   0.238   2.5104   3.1546  -1.3289
 F8Y  H2   H  HCH2  0   0.260   2.0421   3.3267   0.3481
 F8Y  H3   H  HCR6  0   0.312  -2.4871  -1.4339   0.1153
 F8Y  H4   H  HCH1  0   0.306   5.0526   1.4969  -0.2223
 F8Y  H5   H  HCR6  0   0.279   0.8965  -2.4243   0.4573
 F8Y  H6   H  HCH3  0   0.240   3.4234   0.0382  -2.3719
 F8Y  H7   H  HCH3  0   0.257   4.1353   1.6446  -2.5429
 F8Y  H8   H  HCH3  0   0.255   5.1797   0.2425  -2.3431
 F8Y  H9   H  HNH1  0   0.412  -1.4717   2.1591  -0.1462
 F8Y  H10  H  HCR6  0   0.295  -3.6551   2.7061  -0.1439
 F8Y  H11  H  HOH1  0   0.479  -7.0458  -1.3256   0.0608
 F8Y  H12  H  HCH3  0   0.256   3.8605   4.8266  -0.0475
 F8Y  H13  H  HCH3  0   0.239   4.5042   3.5427   0.9734
 F8Y  H14  H  HCH3  0   0.237   4.8875   3.5951  -0.7542
 F8Y  H15  H  HCH2  0   0.319   4.3939  -2.4903   1.6669
 F8Y  H16  H  HCH2  0   0.309   2.6602  -2.5752   1.8816
 F8Y  H17  H  H     0   0.285   3.2765  -5.1906  -1.3858

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
 F8Y  C18  C17  triple    1.201  0.020  1.201
 F8Y  N3   C10  aromatic  1.338  0.020  1.338
 F8Y  N3   C7   aromatic  1.319  0.020  1.319
 F8Y  C17  C16  single    1.460  0.020  1.460
 F8Y  C10  C9   aromatic  1.370  0.020  1.370
 F8Y  N1   C7   single    1.366  0.020  1.366
 F8Y  N1   C6   single    1.386  0.020  1.386
 F8Y  C5   C6   aromatic  1.395  0.020  1.395
 F8Y  C5   C4   aromatic  1.380  0.020  1.380
 F8Y  C7   N2   aromatic  1.336  0.020  1.336
 F8Y  C16  N5   single    1.452  0.020  1.452
 F8Y  C6   C1   aromatic  1.400  0.020  1.400
 F8Y  F1   C4   single    1.345  0.020  1.345
 F8Y  C4   C3   aromatic  1.386  0.020  1.386
 F8Y  C9   N5   single    1.400  0.020  1.400
 F8Y  C9   C8   aromatic  1.417  0.020  1.417
 F8Y  N5   C12  single    1.357  0.020  1.357
 F8Y  N2   C8   aromatic  1.319  0.020  1.319
 F8Y  C1   C2   aromatic  1.375  0.020  1.375
 F8Y  C8   N4   single    1.350  0.020  1.350
 F8Y  C3   C2   aromatic  1.390  0.020  1.390
 F8Y  C3   O1   single    1.346  0.020  1.346
 F8Y  C2   F2   single    1.339  0.020  1.339
 F8Y  C12  O2   double    1.216  0.020  1.216
 F8Y  C12  C11  single    1.517  0.020  1.517
 F8Y  N4   C11  single    1.454  0.020  1.454
 F8Y  N4   C14  single    1.461  0.020  1.461
 F8Y  C11  C13  single    1.530  0.020  1.530
 F8Y  C14  C15  single    1.518  0.020  1.518
 F8Y  C14  H1   single    0.939  0.020  1.096
 F8Y  C14  H2   single    0.939  0.020  1.096
 F8Y  C5   H3   single    0.929  0.020  1.085
 F8Y  C11  H4   single    0.939  0.020  1.096
 F8Y  C10  H5   single    0.929  0.020  1.085
 F8Y  C13  H6   single    0.939  0.020  1.096
 F8Y  C13  H7   single    0.939  0.020  1.096
 F8Y  C13  H8   single    0.939  0.020  1.096
 F8Y  N1   H9   single    0.868  0.020  1.013
 F8Y  C1   H10  single    0.929  0.020  1.085
 F8Y  O1   H11  single    0.832  0.020  0.971
 F8Y  C15  H12  single    0.939  0.020  1.096
 F8Y  C15  H13  single    0.939  0.020  1.096
 F8Y  C15  H14  single    0.939  0.020  1.096
 F8Y  C16  H15  single    0.939  0.020  1.096
 F8Y  C16  H16  single    0.939  0.020  1.096
 F8Y  C18  H17  single    0.913  0.020  1.066

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
 F8Y  F1   C4   C3   117.08  3.000
 F8Y  C3   C4   C5   124.29  3.000
 F8Y  F1   C4   C5   118.62  3.000
 F8Y  H2   C14  H1   106.50  3.000
 F8Y  H2   C14  C15  109.20  3.000
 F8Y  H1   C14  C15  109.88  3.000
 F8Y  H2   C14  N4   107.17  3.000
 F8Y  H1   C14  N4   110.53  3.000
 F8Y  C15  C14  N4   113.28  3.000
 F8Y  H3   C5   C6   121.42  3.000
 F8Y  H3   C5   C4   119.72  3.000
 F8Y  C6   C5   C4   118.86  3.000
 F8Y  C1   C6   N1   116.58  3.000
 F8Y  C1   C6   C5   118.60  3.000
 F8Y  N1   C6   C5   124.81  3.000
 F8Y  H4   C11  N4   108.01  3.000
 F8Y  H4   C11  C13  108.99  3.000
 F8Y  N4   C11  C13  112.85  3.000
 F8Y  H4   C11  C12  105.06  3.000
 F8Y  C13  C11  C12  109.49  3.000
 F8Y  N4   C11  C12  112.10  3.000
 F8Y  N3   C7   N2   125.97  3.000
 F8Y  N2   C7   N1   113.58  3.000
 F8Y  N3   C7   N1   120.45  3.000
 F8Y  N4   C8   N2   120.44  3.000
 F8Y  N4   C8   C9   118.85  3.000
 F8Y  N2   C8   C9   120.71  3.000
 F8Y  N5   C9   C10  124.50  3.000
 F8Y  N5   C9   C8   119.30  3.000
 F8Y  C10  C9   C8   116.13  3.000
 F8Y  H5   C10  N3   115.68  3.000
 F8Y  H5   C10  C9   121.24  3.000
 F8Y  N3   C10  C9   123.07  3.000
 F8Y  O2   C12  N5   122.77  3.000
 F8Y  O2   C12  C11  120.92  3.000
 F8Y  N5   C12  C11  116.25  3.000
 F8Y  H8   C13  H7   107.72  3.000
 F8Y  H8   C13  H6   108.40  3.000
 F8Y  H7   C13  H6   108.10  3.000
 F8Y  H8   C13  C11  110.51  3.000
 F8Y  H7   C13  C11  110.38  3.000
 F8Y  H6   C13  C11  111.61  3.000
 F8Y  H9   N1   C7   113.26  3.000
 F8Y  H9   N1   C6   115.54  3.000
 F8Y  C7   N1   C6   131.21  3.000
 F8Y  C8   N2   C7   117.85  3.000
 F8Y  O1   C3   C2   119.58  3.000
 F8Y  O1   C3   C4   125.30  3.000
 F8Y  C2   C3   C4   115.12  3.000
 F8Y  C10  N3   C7   116.13  3.000
 F8Y  H10  C1   C2   118.96  3.000
 F8Y  H10  C1   C6   121.01  3.000
 F8Y  C2   C1   C6   120.03  3.000
 F8Y  F2   C2   C1   119.26  3.000
 F8Y  F2   C2   C3   117.64  3.000
 F8Y  C1   C2   C3   123.10  3.000
 F8Y  H11  O1   C3   110.66  3.000
 F8Y  C8   N4   C11  116.80  3.000
 F8Y  C11  N4   C14  118.44  3.000
 F8Y  C8   N4   C14  118.99  3.000
 F8Y  C16  N5   C12  119.27  3.000
 F8Y  C12  N5   C9   121.09  3.000
 F8Y  C16  N5   C9   119.61  3.000
 F8Y  H14  C15  H13  108.57  3.000
 F8Y  H14  C15  H12  107.04  3.000
 F8Y  H13  C15  H12  107.87  3.000
 F8Y  H14  C15  C14  112.95  3.000
 F8Y  H13  C15  C14  111.66  3.000
 F8Y  H12  C15  C14  108.52  3.000
 F8Y  H16  C16  H15  106.65  3.000
 F8Y  H16  C16  C17  110.25  3.000
 F8Y  H15  C16  C17  109.85  3.000
 F8Y  H16  C16  N5   108.86  3.000
 F8Y  H15  C16  N5   108.65  3.000
 F8Y  C17  C16  N5   112.40  3.000
 F8Y  C18  C17  C16  180.00  3.000
 F8Y  H17  C18  C17  180.00  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
 F8Y  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 F8Y  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 F8Y  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 F8Y  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 F8Y  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 F8Y  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 F8Y  CONST_07  C9   C10  N3   C7      0.00   0.0  0
 F8Y  CONST_08  C9   C8   N2   C7      0.00   0.0  0
 F8Y  CONST_09  N3   C10  C9   C8      0.00   0.0  0
 F8Y  CONST_10  N3   C7   N2   C8      0.00   0.0  0
 F8Y  CONST_11  N2   C7   N3   C10     0.00   0.0  0
 F8Y  CONST_12  N2   C8   C9   C10     0.00   0.0  0
 F8Y  CONST_13  C9   N5   C12  C11     0.00   0.0  0
 F8Y  CONST_14  N1   C6   C5   C4    180.00   0.0  0
 F8Y  CONST_15  F2   C2   C3   C4    180.00   0.0  0
 F8Y  CONST_16  O1   C3   C4   C5    180.00   0.0  0
 F8Y  CONST_17  F1   C4   C5   C6    180.00   0.0  0
 F8Y  CONST_18  F2   C2   C1   C6    180.00   0.0  0
 F8Y  CONST_19  N1   C7   N2   C8    180.00   0.0  0
 F8Y  CONST_20  N1   C7   N3   C10   180.00   0.0  0
 F8Y  CONST_21  C2   C1   C6   N1    180.00   0.0  0
 F8Y  CONST_22  O1   C3   C2   C1    180.00   0.0  0
 F8Y  CONST_23  F1   C4   C3   C2    180.00   0.0  0
 F8Y  CONST_24  C16  N5   C12  C11   180.00   0.0  0
 F8Y  CONST_25  O2   C12  N5   C9    180.00   0.0  0
 F8Y  CONST_26  H10  C1   C6   C5    180.00   0.0  0
 F8Y  CONST_27  H5   C10  N3   C7    180.00   0.0  0
 F8Y  CONST_28  H3   C5   C4   C3    180.00   0.0  0
 F8Y  CONST_29  C16  N5   C12  O2      0.00   0.0  0
 F8Y  Var_01    C9   C8   N4   C11    27.19  30.0  1
 F8Y  Var_02    C12  N5   C9   C8    -19.48  30.0  1
 F8Y  Var_03    C7   N1   C6   C5     -2.67  30.0  3
 F8Y  Var_04    N3   C7   N1   C6     -0.71  30.0  2
 F8Y  Var_05    C15  C14  N4   C11   -43.42  30.0  3
 F8Y  Var_06    C17  C16  N5   C9     84.79  30.0  2
 F8Y  Var_07    H12  C15  C14  N4   -169.95  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
 F8Y  chir_01  C11  C12  N4  C13  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
 F8Y  plan-1  C4   0.020
 F8Y  plan-1  C5   0.020
 F8Y  plan-1  C6   0.020
 F8Y  plan-1  N1   0.020
 F8Y  plan-1  C3   0.020
 F8Y  plan-1  C1   0.020
 F8Y  plan-1  C2   0.020
 F8Y  plan-1  F1   0.020
 F8Y  plan-1  O1   0.020
 F8Y  plan-1  F2   0.020
 F8Y  plan-1  H3   0.020
 F8Y  plan-1  H10  0.020
 F8Y  plan-2  C7   0.020
 F8Y  plan-2  C8   0.020
 F8Y  plan-2  C9   0.020
 F8Y  plan-2  C10  0.020
 F8Y  plan-2  N1   0.020
 F8Y  plan-2  N2   0.020
 F8Y  plan-2  N3   0.020
 F8Y  plan-2  N4   0.020
 F8Y  plan-2  N5   0.020
 F8Y  plan-2  H5   0.020
 F8Y  plan-3  C11  0.020
 F8Y  plan-3  C9   0.020
 F8Y  plan-3  C12  0.020
 F8Y  plan-3  N5   0.020
 F8Y  plan-3  O2   0.020
 F8Y  plan-3  C16  0.020

