# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 10:21:59 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N(CC#C)c2nc(Nc3cc(F)c(O)c(F)c3)ncc2N(CC#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
 F7D  F7D  (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one  ligand  43  28  .  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_F7D
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
 F7D  C4   C  CR6   0   0.210  -2.0780  -0.7163  -0.5663
 F7D  C14  C  CR6   0   0.389   2.8269   0.4776   0.0826
 F7D  C5   C  CR6   0   0.606   0.3339   0.3512  -0.1494
 F7D  C6   C  CR16  0  -0.037  -0.9170  -1.4598  -0.6646
 F7D  C11  C  CSP   0   0.301  -2.4677   2.5066   1.9524
 F7D  C9   C  CSP   0   0.259  -3.2215  -3.0987   0.8865
 F7D  C12  C  CSP1  0  -0.535  -1.6898   3.0888   2.6576
 F7D  C13  C  CSP1  0  -0.494  -2.9419  -3.4438   2.0022
 F7D  N1   N  NT    0  -0.480  -3.0308   1.4644  -0.1888
 F7D  N2   N  NT    0  -0.577  -3.3679  -1.2554  -0.6661
 F7D  C3   C  CR6   0   0.436  -1.9067   0.6421  -0.2601
 F7D  N3   N  N     0  -0.443  -0.7210   1.1636  -0.0573
 F7D  C1   C  C     0   0.569  -4.4484  -0.4433  -0.8653
 F7D  C2   C  CH1   0  -0.269  -4.0703   1.0121  -1.1143
 F7D  N4   N  N     0  -0.465   0.2849  -0.9357  -0.4595
 F7D  O1   O  O     0  -0.450  -5.5909  -0.8536  -0.8703
 F7D  N5   N  NH1   0  -0.779   1.5278   0.9624   0.0946
 F7D  C15  C  CR16  0  -0.531   3.8407   1.4018   0.3516
 F7D  C16  C  CR6   0   0.479   5.1532   0.9920   0.3596
 F7D  C17  C  CR6   0   0.044   5.5474  -0.3159   0.1090
 F7D  C18  C  CR6   0   0.518   4.5135  -1.2025  -0.1529
 F7D  C19  C  CR16  0  -0.510   3.1803  -0.8483  -0.1726
 F7D  F1   F  F     0  -0.313   4.8432  -2.4773  -0.4022
 F7D  O2   O  OH1   0  -0.621   6.8198  -0.7543   0.1058
 F7D  F2   F  F     0  -0.318   6.1180   1.8903   0.6205
 F7D  H1   H  HCR6  0   0.289  -0.9371  -2.5187  -0.8942
 F7D  H2   H  HCH3  0   0.257  -4.9534   2.9598  -1.2684
 F7D  H3   H  HCH3  0   0.265  -5.8988   1.6795  -2.0132
 F7D  H4   H  HCH3  0   0.244  -5.9041   1.8512  -0.2657
 F7D  H5   H  HCH2  0   0.305  -2.9576  -3.2421  -1.1951
 F7D  H6   H  HCH2  0   0.320  -4.5957  -2.9197  -0.6906
 F7D  H7   H  HCH2  0   0.271  -3.8148   0.9295   1.7276
 F7D  H8   H  HCH2  0   0.302  -4.3387   2.4708   1.0771
 F7D  H9   H  H     0   0.279  -0.9860   3.6024   3.2714
 F7D  H10  H  H     0   0.285  -2.7040  -3.7420   2.9978
 F7D  H11  H  HCH1  0   0.316  -3.6096   1.0379  -2.1094
 F7D  H12  H  HNH1  0   0.415   1.4324   1.9443   0.3051
 F7D  H13  H  HCR6  0   0.298   3.6122   2.4405   0.5563
 F7D  H14  H  HCR6  0   0.311   2.4355  -1.5982  -0.3852
 F7D  H15  H  HOH1  0   0.480   7.4321  -0.0312   0.2832
 F7D  C7   C  CH3   0  -0.701  -5.2789   1.9264  -1.1539
 F7D  C8   C  CH2   0  -0.481  -3.5560  -2.6837  -0.4723
 F7D  C10  C  CH2   0  -0.445  -3.4764   1.8101   1.1647

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
 F7D  F1   C18  single    1.340  0.020  1.340
 F7D  N4   C6   aromatic  1.327  0.020  1.327
 F7D  N4   C5   aromatic  1.325  0.020  1.325
 F7D  C19  C18  aromatic  1.380  0.020  1.380
 F7D  C19  C14  aromatic  1.396  0.020  1.396
 F7D  C13  C9   triple    1.201  0.020  1.201
 F7D  N5   C5   single    1.363  0.020  1.363
 F7D  N5   C14  single    1.387  0.020  1.387
 F7D  C6   C4   aromatic  1.382  0.020  1.382
 F7D  C18  C17  aromatic  1.387  0.020  1.387
 F7D  C9   C8   single    1.460  0.020  1.460
 F7D  C5   N3   aromatic  1.335  0.020  1.335
 F7D  C14  C15  aromatic  1.398  0.020  1.398
 F7D  C8   N2   single    1.454  0.020  1.454
 F7D  C4   N2   single    1.402  0.020  1.402
 F7D  C4   C3   aromatic  1.403  0.020  1.403
 F7D  C17  O2   single    1.346  0.020  1.346
 F7D  C17  C16  aromatic  1.389  0.020  1.389
 F7D  N3   C3   aromatic  1.311  0.020  1.311
 F7D  C15  C16  aromatic  1.375  0.020  1.375
 F7D  N2   C1   single    1.366  0.020  1.366
 F7D  C3   N1   single    1.395  0.020  1.395
 F7D  C16  F2   single    1.344  0.020  1.344
 F7D  C1   O1   double    1.214  0.020  1.214
 F7D  C1   C2   single    1.524  0.020  1.524
 F7D  N1   C2   single    1.463  0.020  1.463
 F7D  N1   C10  single    1.466  0.020  1.466
 F7D  C2   C7   single    1.516  0.020  1.516
 F7D  C10  C11  single    1.457  0.020  1.457
 F7D  C11  C12  triple    1.201  0.020  1.201
 F7D  C6   H1   single    0.929  0.020  1.085
 F7D  C7   H2   single    0.939  0.020  1.096
 F7D  C7   H3   single    0.939  0.020  1.096
 F7D  C7   H4   single    0.939  0.020  1.096
 F7D  C8   H5   single    0.939  0.020  1.096
 F7D  C8   H6   single    0.939  0.020  1.096
 F7D  C10  H7   single    0.939  0.020  1.096
 F7D  C10  H8   single    0.939  0.020  1.096
 F7D  C12  H9   single    0.913  0.020  1.066
 F7D  C13  H10  single    0.913  0.020  1.066
 F7D  C2   H11  single    0.939  0.020  1.096
 F7D  N5   H12  single    0.868  0.020  1.013
 F7D  C15  H13  single    0.929  0.020  1.085
 F7D  C19  H14  single    0.929  0.020  1.085
 F7D  O2   H15  single    0.832  0.020  0.971

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
 F7D  C3   C4   N2   120.02  3.000
 F7D  C3   C4   C6   115.71  3.000
 F7D  N2   C4   C6   124.14  3.000
 F7D  C19  C14  C15  118.66  3.000
 F7D  C15  C14  N5   116.52  3.000
 F7D  C19  C14  N5   124.82  3.000
 F7D  N5   C5   N4   120.66  3.000
 F7D  N5   C5   N3   114.01  3.000
 F7D  N4   C5   N3   125.33  3.000
 F7D  H1   C6   N4   115.81  3.000
 F7D  H1   C6   C4   121.67  3.000
 F7D  N4   C6   C4   122.50  3.000
 F7D  C12  C11  C10  180.00  3.000
 F7D  C13  C9   C8   180.00  3.000
 F7D  H9   C12  C11  180.00  3.000
 F7D  H10  C13  C9   180.00  3.000
 F7D  C2   N1   C3   110.98  3.000
 F7D  C2   N1   C10  116.15  3.000
 F7D  C3   N1   C10  115.54  3.000
 F7D  C1   N2   C8   120.08  3.000
 F7D  C1   N2   C4   120.64  3.000
 F7D  C8   N2   C4   119.17  3.000
 F7D  N3   C3   N1   119.11  3.000
 F7D  N1   C3   C4   118.93  3.000
 F7D  N3   C3   C4   121.96  3.000
 F7D  C3   N3   C5   117.52  3.000
 F7D  O1   C1   C2   123.75  3.000
 F7D  C2   C1   N2   113.28  3.000
 F7D  O1   C1   N2   122.96  3.000
 F7D  H11  C2   C1   105.95  3.000
 F7D  H11  C2   N1   105.55  3.000
 F7D  C1   C2   N1   111.59  3.000
 F7D  H11  C2   C7   107.28  3.000
 F7D  N1   C2   C7   113.36  3.000
 F7D  C1   C2   C7   112.48  3.000
 F7D  C6   N4   C5   116.96  3.000
 F7D  H12  N5   C5   113.02  3.000
 F7D  H12  N5   C14  115.52  3.000
 F7D  C5   N5   C14  131.46  3.000
 F7D  H13  C15  C16  119.08  3.000
 F7D  H13  C15  C14  121.16  3.000
 F7D  C16  C15  C14  119.75  3.000
 F7D  F2   C16  C17  117.43  3.000
 F7D  F2   C16  C15  119.16  3.000
 F7D  C17  C16  C15  123.41  3.000
 F7D  O2   C17  C18  119.75  3.000
 F7D  O2   C17  C16  125.14  3.000
 F7D  C18  C17  C16  115.11  3.000
 F7D  F1   C18  C19  118.64  3.000
 F7D  C19  C18  C17  123.99  3.000
 F7D  F1   C18  C17  117.37  3.000
 F7D  H14  C19  C18  119.46  3.000
 F7D  H14  C19  C14  121.46  3.000
 F7D  C18  C19  C14  119.08  3.000
 F7D  H15  O2   C17  110.84  3.000
 F7D  H4   C7   H3   107.54  3.000
 F7D  H4   C7   H2   108.83  3.000
 F7D  H3   C7   H2   107.60  3.000
 F7D  H4   C7   C2   113.26  3.000
 F7D  H3   C7   C2   109.76  3.000
 F7D  H2   C7   C2   109.68  3.000
 F7D  H6   C8   H5   106.25  3.000
 F7D  H6   C8   N2   108.05  3.000
 F7D  H5   C8   N2   110.08  3.000
 F7D  H6   C8   C9   110.12  3.000
 F7D  H5   C8   C9   110.20  3.000
 F7D  N2   C8   C9   111.96  3.000
 F7D  H8   C10  H7   106.46  3.000
 F7D  H8   C10  N1   108.01  3.000
 F7D  H7   C10  N1   112.19  3.000
 F7D  H8   C10  C11  107.54  3.000
 F7D  H7   C10  C11  108.62  3.000
 F7D  N1   C10  C11  113.66  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
 F7D  CONST_01  C5   N4   C6   C4      0.00   0.0  0
 F7D  CONST_02  C5   N3   C3   C4      0.00   0.0  0
 F7D  CONST_03  C17  C18  C19  C14     0.00   0.0  0
 F7D  CONST_04  C17  C16  C15  C14     0.00   0.0  0
 F7D  CONST_05  N3   C5   N4   C6      0.00   0.0  0
 F7D  CONST_06  N3   C3   C4   C6      0.00   0.0  0
 F7D  CONST_07  N4   C6   C4   C3      0.00   0.0  0
 F7D  CONST_08  N4   C5   N3   C3      0.00   0.0  0
 F7D  CONST_09  C18  C19  C14  C15     0.00   0.0  0
 F7D  CONST_10  C18  C17  C16  C15     0.00   0.0  0
 F7D  CONST_11  C19  C18  C17  C16     0.00   0.0  0
 F7D  CONST_12  C19  C14  C15  C16     0.00   0.0  0
 F7D  CONST_13  C2   C1   N2   C4      0.00   0.0  0
 F7D  CONST_14  F1   C18  C19  C14   180.00   0.0  0
 F7D  CONST_15  F2   C16  C15  C14   180.00   0.0  0
 F7D  CONST_16  N5   C5   N4   C6    180.00   0.0  0
 F7D  CONST_17  N5   C5   N3   C3    180.00   0.0  0
 F7D  CONST_18  C18  C19  C14  N5    180.00   0.0  0
 F7D  CONST_19  C16  C15  C14  N5    180.00   0.0  0
 F7D  CONST_20  O2   C17  C16  C15   180.00   0.0  0
 F7D  CONST_21  F1   C18  C17  C16   180.00   0.0  0
 F7D  CONST_22  F2   C16  C17  C18   180.00   0.0  0
 F7D  CONST_23  O2   C17  C18  C19   180.00   0.0  0
 F7D  CONST_24  O1   C1   N2   C4    180.00   0.0  0
 F7D  CONST_25  C2   C1   N2   C8    180.00   0.0  0
 F7D  CONST_26  H1   C6   N4   C5    180.00   0.0  0
 F7D  CONST_27  H14  C19  C14  C15   180.00   0.0  0
 F7D  CONST_28  H13  C15  C16  C17   180.00   0.0  0
 F7D  CONST_29  O1   C1   N2   C8      0.00   0.0  0
 F7D  Var_01    C2   N1   C3   C4    -31.46  30.0  1
 F7D  Var_02    C1   N2   C4   C6   -164.93  30.0  1
 F7D  Var_03    N4   C5   N5   C14     0.21  30.0  2
 F7D  Var_04    C19  C14  N5   C5     -1.74  30.0  2
 F7D  Var_05    C9   C8   N2   C4     64.39  30.0  2
 F7D  Var_06    C3   N1   C10  C11    59.33  30.0  1
 F7D  Var_07    N1   C10  C11  C12   175.17  30.0  2
 F7D  Var_08    N2   C8   C9   C13  -117.60  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
 F7D  chir_01  C2  C1  N1  C7  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
 F7D  plan-1  C14  0.020
 F7D  plan-1  N5   0.020
 F7D  plan-1  C15  0.020
 F7D  plan-1  C16  0.020
 F7D  plan-1  C17  0.020
 F7D  plan-1  C18  0.020
 F7D  plan-1  C19  0.020
 F7D  plan-1  F1   0.020
 F7D  plan-1  O2   0.020
 F7D  plan-1  F2   0.020
 F7D  plan-1  H13  0.020
 F7D  plan-1  H14  0.020
 F7D  plan-2  C4   0.020
 F7D  plan-2  C5   0.020
 F7D  plan-2  C6   0.020
 F7D  plan-2  N1   0.020
 F7D  plan-2  N2   0.020
 F7D  plan-2  C3   0.020
 F7D  plan-2  N3   0.020
 F7D  plan-2  N4   0.020
 F7D  plan-2  N5   0.020
 F7D  plan-2  H1   0.020
 F7D  plan-3  C4   0.020
 F7D  plan-3  N2   0.020
 F7D  plan-3  C1   0.020
 F7D  plan-3  C2   0.020
 F7D  plan-3  O1   0.020
 F7D  plan-3  C8   0.020

