# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 18:09:33 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 6-(2,4-difluorophenoxy)-8-methyl-2-(tetrahydro-2H-pyran-4-ylamino)pyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C(=Cc2cnc(NC3CCOCC3)nc12)Oc4ccc(F)cc4F
#
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
 3FN  3FN  6-(2,4-difluorophenoxy)-8-methyl-2-(tetrahydro-2H-pyran-4-ylamino)pyrido[2,3-d]pyrimidin-7(8H)-one  ligand  46  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3FN
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
 3FN  C1    C  CH2   0  -0.473  -6.5425  -0.8414  -0.2715
 3FN  C2    C  CH2   0  -0.183  -7.8444  -0.2428   0.2383
 3FN  C4    C  CH2   0  -0.187  -7.0366   1.9467   0.0832
 3FN  C5    C  CH2   0  -0.456  -5.6815   1.4900  -0.4364
 3FN  C24   C  CR16  0  -0.560   6.4840   0.1976  -0.0109
 3FN  O3    O  O2    0  -0.483  -8.0677   1.0521  -0.2735
 3FN  C15   C  CR6   0   0.529   1.6429  -1.2442  -0.3301
 3FN  C25   C  CR6   0   0.488   5.4127  -0.2926   0.7038
 3FN  C8    C  CR6   0   0.618  -2.9224  -0.2490  -0.0017
 3FN  C6    C  CH1   0  -0.059  -5.3758   0.0798   0.0667
 3FN  C10   C  CR66  0  -0.116  -0.4518   0.1206   0.9702
 3FN  C17   C  CR16  0  -0.230   0.8765   0.2762   1.4459
 3FN  C23   C  CR6   0   0.528   6.2351   1.1795  -0.9528
 3FN  C22   C  CR16  0  -0.415   4.9674   1.6711  -1.1815
 3FN  C21   C  CR16  0  -0.310   3.9083   1.1652  -0.4380
 3FN  C9    C  CR66  0   0.555  -0.7055  -0.6891  -0.1516
 3FN  C11   C  CR16  0  -0.033  -1.5773   0.7207   1.5317
 3FN  C16   C  CR6   0   0.138   1.8723  -0.3811   0.8272
 3FN  C20   C  CR6   0   0.219   4.1196   0.1762   0.5084
 3FN  F1    F  F     0  -0.312   7.2670   1.6641  -1.6591
 3FN  O26   O  O2    0  -0.491   3.1473  -0.3433   1.3071
 3FN  N7    N  N     0  -0.469  -2.7948   0.5546   1.0712
 3FN  O19   O  O     0  -0.454   2.5504  -1.8522  -0.8696
 3FN  N14   N  NR6   0  -0.587   0.3319  -1.3289  -0.7765
 3FN  N12   N  N     0  -0.503  -1.9195  -0.8686  -0.6316
 3FN  N13   N  NH1   0  -0.657  -4.1522  -0.4635  -0.4820
 3FN  H1    H  HCH2  0   0.251  -6.3956  -1.8276   0.1754
 3FN  H1A   H  HCH2  0   0.233  -6.6040  -0.9801  -1.3561
 3FN  H2    H  HCH2  0   0.241  -8.6914  -0.8592  -0.0670
 3FN  H2A   H  HCH2  0   0.201  -7.8314  -0.2235   1.3381
 3FN  H4    H  HCH2  0   0.200  -6.9924   2.0625   1.1767
 3FN  H4A   H  HCH2  0   0.240  -7.2984   2.9195  -0.3352
 3FN  H5    H  HCH2  0   0.228  -5.6805   1.4957  -1.5307
 3FN  H5A   H  HCH2  0   0.244  -4.9116   2.1892  -0.1030
 3FN  H24   H  HCR6  0   0.308   7.4821  -0.1849   0.1583
 3FN  H6    H  HCH1  0   0.246  -5.2670   0.1161   1.1541
 3FN  H17   H  HCR6  0   0.292   1.0729   0.9015   2.3089
 3FN  H22   H  HCR6  0   0.290   4.8001   2.4418  -1.9214
 3FN  H21   H  HCR6  0   0.297   2.9133   1.5581  -0.6037
 3FN  H11   H  HCR6  0   0.281  -1.4621   1.3659   2.3974
 3FN  HN13  H  HNH1  0   0.396  -4.2123  -1.0364  -1.3095
 3FN  C18   C  CH3   0  -0.537   0.0313  -2.1668  -1.9308
 3FN  F2    F  F     0  -0.301   5.6159  -1.2463   1.6179
 3FN  H18   H  HCH3  0   0.270   0.9570  -2.5595  -2.3319
 3FN  H18A  H  HCH3  0   0.260  -0.6133  -2.9940  -1.6412
 3FN  H18B  H  HCH3  0   0.261  -0.4726  -1.5824  -2.6964

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
 3FN  C1   C2    single    1.521  0.020  1.521
 3FN  C1   C6    single    1.525  0.020  1.525
 3FN  C2   O3    single    1.410  0.020  1.410
 3FN  C4   C5    single    1.521  0.020  1.521
 3FN  C4   O3    single    1.411  0.020  1.411
 3FN  C5   C6    single    1.528  0.020  1.528
 3FN  C24  C25   aromatic  1.378  0.020  1.378
 3FN  C24  C23   aromatic  1.383  0.020  1.383
 3FN  C15  C16   single    1.462  0.020  1.462
 3FN  C15  O19   double    1.218  0.020  1.218
 3FN  C15  N14   single    1.388  0.020  1.388
 3FN  C25  C20   aromatic  1.389  0.020  1.389
 3FN  C25  F2    single    1.337  0.020  1.337
 3FN  C8   N7    aromatic  1.346  0.020  1.346
 3FN  C8   N12   aromatic  1.337  0.020  1.337
 3FN  C8   N13   single    1.338  0.020  1.338
 3FN  C6   N13   single    1.447  0.020  1.447
 3FN  C10  C17   single    1.419  0.020  1.419
 3FN  C10  C9    aromatic  1.407  0.020  1.407
 3FN  C10  C11   aromatic  1.394  0.020  1.394
 3FN  C17  C16   double    1.344  0.020  1.344
 3FN  C23  C22   aromatic  1.379  0.020  1.379
 3FN  C23  F1    single    1.341  0.020  1.341
 3FN  C22  C21   aromatic  1.389  0.020  1.389
 3FN  C21  C20   aromatic  1.385  0.020  1.385
 3FN  C9   N14   single    1.370  0.020  1.370
 3FN  C9   N12   aromatic  1.318  0.020  1.318
 3FN  C11  N7    aromatic  1.312  0.020  1.312
 3FN  C16  O26   single    1.363  0.020  1.363
 3FN  C20  O26   single    1.361  0.020  1.361
 3FN  C18  N14   single    1.458  0.020  1.458
 3FN  C1   H1    single    0.970  0.020  1.090
 3FN  C1   H1A   single    0.970  0.020  1.090
 3FN  C2   H2    single    0.970  0.020  1.090
 3FN  C2   H2A   single    0.970  0.020  1.090
 3FN  C4   H4    single    0.970  0.020  1.090
 3FN  C4   H4A   single    0.970  0.020  1.090
 3FN  C5   H5    single    0.970  0.020  1.090
 3FN  C5   H5A   single    0.970  0.020  1.090
 3FN  C24  H24   single    0.930  0.020  1.080
 3FN  C6   H6    single    0.970  0.020  1.090
 3FN  C17  H17   single    0.930  0.020  1.080
 3FN  C22  H22   single    0.930  0.020  1.080
 3FN  C21  H21   single    0.930  0.020  1.080
 3FN  C11  H11   single    0.930  0.020  1.080
 3FN  C18  H18   single    0.970  0.020  1.090
 3FN  C18  H18A  single    0.970  0.020  1.090
 3FN  C18  H18B  single    0.970  0.020  1.090
 3FN  N13  HN13  single    0.860  0.020  1.020

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
 3FN  H1A   C1   H1    107.36  3.000
 3FN  H1A   C1   C6    109.83  3.000
 3FN  H1    C1   C6    110.60  3.000
 3FN  H1A   C1   C2    109.49  3.000
 3FN  H1    C1   C2    109.47  3.000
 3FN  C6    C1   C2    110.05  3.000
 3FN  H2A   C2   H2    107.39  3.000
 3FN  H2A   C2   O3    110.40  3.000
 3FN  H2    C2   O3    107.11  3.000
 3FN  H2A   C2   C1    109.38  3.000
 3FN  H2    C2   C1    110.39  3.000
 3FN  O3    C2   C1    112.05  3.000
 3FN  H4A   C4   H4    107.27  3.000
 3FN  H4A   C4   O3    107.04  3.000
 3FN  H4    C4   O3    110.32  3.000
 3FN  H4A   C4   C5    110.51  3.000
 3FN  H4    C4   C5    109.59  3.000
 3FN  O3    C4   C5    111.98  3.000
 3FN  H5A   C5   H5    107.54  3.000
 3FN  H5A   C5   C6    110.44  3.000
 3FN  H5    C5   C6    109.51  3.000
 3FN  H5A   C5   C4    109.35  3.000
 3FN  H5    C5   C4    109.92  3.000
 3FN  C6    C5   C4    110.04  3.000
 3FN  H24   C24  C23   121.55  3.000
 3FN  H24   C24  C25   120.68  3.000
 3FN  C23   C24  C25   117.77  3.000
 3FN  C4    O3   C2    112.01  3.000
 3FN  N14   C15  O19   122.06  3.000
 3FN  N14   C15  C16   116.04  3.000
 3FN  O19   C15  C16   121.90  3.000
 3FN  F2    C25  C20   118.59  3.000
 3FN  F2    C25  C24   119.37  3.000
 3FN  C20   C25  C24   122.05  3.000
 3FN  N13   C8   N12   116.50  3.000
 3FN  N13   C8   N7    117.97  3.000
 3FN  N12   C8   N7    125.53  3.000
 3FN  H6    C6   N13   107.78  3.000
 3FN  H6    C6   C5    108.47  3.000
 3FN  N13   C6   C5    113.01  3.000
 3FN  H6    C6   C1    108.47  3.000
 3FN  N13   C6   C1    109.64  3.000
 3FN  C5    C6   C1    109.36  3.000
 3FN  C11   C10  C9    115.06  3.000
 3FN  C11   C10  C17   125.00  3.000
 3FN  C9    C10  C17   119.94  3.000
 3FN  H17   C17  C16   120.96  3.000
 3FN  H17   C17  C10   119.98  3.000
 3FN  C16   C17  C10   119.04  3.000
 3FN  F1    C23  C22   119.42  3.000
 3FN  F1    C23  C24   118.47  3.000
 3FN  C22   C23  C24   122.10  3.000
 3FN  H22   C22  C21   120.51  3.000
 3FN  H22   C22  C23   120.65  3.000
 3FN  C21   C22  C23   118.84  3.000
 3FN  H21   C21  C20   120.26  3.000
 3FN  H21   C21  C22   119.12  3.000
 3FN  C20   C21  C22   120.62  3.000
 3FN  N12   C9   N14   117.90  3.000
 3FN  N12   C9   C10   122.35  3.000
 3FN  N14   C9   C10   119.75  3.000
 3FN  H11   C11  N7    116.97  3.000
 3FN  H11   C11  C10   119.43  3.000
 3FN  N7    C11  C10   123.60  3.000
 3FN  O26   C16  C17   121.17  3.000
 3FN  O26   C16  C15   116.23  3.000
 3FN  C17   C16  C15   122.48  3.000
 3FN  O26   C20  C21   124.37  3.000
 3FN  O26   C20  C25   116.97  3.000
 3FN  C21   C20  C25   118.62  3.000
 3FN  C20   O26  C16   118.18  3.000
 3FN  C11   N7   C8    116.30  3.000
 3FN  C18   N14  C9    118.27  3.000
 3FN  C18   N14  C15   118.99  3.000
 3FN  C9    N14  C15   122.71  3.000
 3FN  C9    N12  C8    117.16  3.000
 3FN  HN13  N13  C6    118.31  3.000
 3FN  HN13  N13  C8    116.15  3.000
 3FN  C6    N13  C8    125.53  3.000
 3FN  H18B  C18  H18A  108.76  3.000
 3FN  H18B  C18  H18   109.30  3.000
 3FN  H18A  C18  H18   109.23  3.000
 3FN  H18B  C18  N14   110.13  3.000
 3FN  H18A  C18  N14   110.39  3.000
 3FN  H18   C18  N14   109.00  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
 3FN  CONST_01  C21   C20  C25  C24    0.00   0.0  0
 3FN  CONST_02  C21   C22  C23  C24    0.00   0.0  0
 3FN  CONST_03  C22   C23  C24  C25    0.00   0.0  0
 3FN  CONST_04  C22   C21  C20  C25    0.00   0.0  0
 3FN  CONST_05  C10   C11  N7   C8     0.00   0.0  0
 3FN  CONST_06  C10   C9   N12  C8     0.00   0.0  0
 3FN  CONST_07  C20   C25  C24  C23    0.00   0.0  0
 3FN  CONST_08  C20   C21  C22  C23    0.00   0.0  0
 3FN  CONST_09  N7    C11  C10  C9     0.00   0.0  0
 3FN  CONST_10  N7    C8   N12  C9     0.00   0.0  0
 3FN  CONST_11  N12   C9   C10  C11    0.00   0.0  0
 3FN  CONST_12  N12   C8   N7   C11    0.00   0.0  0
 3FN  CONST_13  C16   C15  N14  C9     0.00   0.0  0
 3FN  CONST_14  O26   C20  C25  C24  180.00   0.0  0
 3FN  CONST_15  F1    C23  C24  C25  180.00   0.0  0
 3FN  CONST_16  F2    C25  C24  C23  180.00   0.0  0
 3FN  CONST_17  O26   C20  C21  C22  180.00   0.0  0
 3FN  CONST_18  F1    C23  C22  C21  180.00   0.0  0
 3FN  CONST_19  F2    C25  C20  C21  180.00   0.0  0
 3FN  CONST_20  N13   C8   N12  C9   180.00   0.0  0
 3FN  CONST_21  N13   C8   N7   C11  180.00   0.0  0
 3FN  CONST_22  N7    C8   N13  C6     0.00   0.0  0
 3FN  CONST_23  N12   C8   N13  C6   180.00   0.0  0
 3FN  CONST_24  O19   C15  N14  C9   180.00   0.0  0
 3FN  CONST_25  C18   N14  C15  C16  180.00   0.0  0
 3FN  CONST_26  H22   C22  C23  C24  180.00   0.0  0
 3FN  CONST_27  H21   C21  C20  C25  180.00   0.0  0
 3FN  CONST_28  H11   C11  N7   C8   180.00   0.0  0
 3FN  CONST_29  H24   C24  C23  C22  180.00   0.0  0
 3FN  CONST_30  O19   C15  N14  C18    0.00   0.0  0
 3FN  CONST_31  HN13  N13  C8   N7   180.00   0.0  0
 3FN  Var_01    C5    C4   O3   C2    59.76  30.0  1
 3FN  Var_02    C6    C1   C2   O3    56.40  30.0  1
 3FN  Var_03    C6    C5   C4   O3   -56.26  30.0  1
 3FN  Var_04    H2    C2   O3   C4   178.98  30.0  1
 3FN  Var_05    H18   C18  N14  C15   -4.58  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
 3FN  chir_01  C6  C1  C5  N13  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
 3FN  plan-1  C24   0.020
 3FN  plan-1  C25   0.020
 3FN  plan-1  C23   0.020
 3FN  plan-1  C22   0.020
 3FN  plan-1  C21   0.020
 3FN  plan-1  C20   0.020
 3FN  plan-1  F1    0.020
 3FN  plan-1  O26   0.020
 3FN  plan-1  H24   0.020
 3FN  plan-1  H22   0.020
 3FN  plan-1  H21   0.020
 3FN  plan-1  F2    0.020
 3FN  plan-2  C15   0.020
 3FN  plan-2  C8    0.020
 3FN  plan-2  C10   0.020
 3FN  plan-2  C17   0.020
 3FN  plan-2  C9    0.020
 3FN  plan-2  C11   0.020
 3FN  plan-2  C16   0.020
 3FN  plan-2  O26   0.020
 3FN  plan-2  N7    0.020
 3FN  plan-2  O19   0.020
 3FN  plan-2  N14   0.020
 3FN  plan-2  N12   0.020
 3FN  plan-2  N13   0.020
 3FN  plan-2  H17   0.020
 3FN  plan-2  H11   0.020
 3FN  plan-2  C18   0.020
 3FN  plan-3  C8    0.020
 3FN  plan-3  C6    0.020
 3FN  plan-3  N13   0.020
 3FN  plan-3  HN13  0.020

