# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 14:53:00 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 6-(2,4-difluorophenoxy)-8-methyl-2-[(1-methylethyl)amino]pyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Nc1ncc2C=C(Oc3ccc(F)cc3F)C(=O)N(C)c2n1
#
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
 FLY  FLY  6-(2,4-difluorophenoxy)-8-methyl-2-[(1-methylethyl)amino]pyrido[2,3-d]pyrimidin-7(8H)-one  ligand  41  25  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FLY
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
 FLY  C2    C  CR16  0  -0.031  -2.4762  -1.3391  -1.2577
 FLY  C3    C  CR66  0   0.563  -1.7059   0.1520   0.4088
 FLY  N1    N  N     0  -0.467  -3.6970  -0.8746  -1.1454
 FLY  C4    C  CR66  0  -0.128  -1.3991  -0.8760  -0.5026
 FLY  C5    C  CR16  0  -0.231  -0.0716  -1.3674  -0.6091
 FLY  C6    C  CR6   0   0.141   0.8822  -0.8526   0.1856
 FLY  C7    C  CR6   0   0.538   0.5988   0.2064   1.1488
 FLY  C9    C  CR6   0   0.624  -3.8793   0.1072  -0.2407
 FLY  C11   C  CH1   0  -0.085  -6.2988   0.1187  -0.7819
 FLY  C13   C  CH3   0  -0.650  -6.8378  -1.1449  -0.1199
 FLY  C14   C  CH3   0  -0.672  -7.3403   1.2269  -0.8077
 FLY  C17   C  CR6   0   0.217   3.1687  -0.5206  -0.1639
 FLY  C18   C  CR16  0  -0.311   3.0479   0.5314  -1.0569
 FLY  C19   C  CR16  0  -0.415   4.1516   1.3064  -1.3911
 FLY  C20   C  CR6   0   0.528   5.3723   1.0034  -0.8262
 FLY  C21   C  CR16  0  -0.560   5.5311  -0.0442   0.0630
 FLY  C22   C  CR6   0   0.489   4.4172  -0.7893   0.3832
 FLY  F24   F  F     0  -0.312   6.4469   1.7412  -1.1414
 FLY  F23   F  F     0  -0.300   4.5331  -1.8039   1.2451
 FLY  O16   O  O2    0  -0.492   2.1500  -1.3523   0.1878
 FLY  O15   O  O     0  -0.460   1.4536   0.6703   1.8831
 FLY  N8    N  NR6   0  -0.589  -0.7065   0.6689   1.1931
 FLY  C25   C  CH3   0  -0.543  -0.9794   1.7372   2.1473
 FLY  N10   N  N     0  -0.508  -2.9269   0.6323   0.5351
 FLY  N12   N  NH1   0  -0.642  -5.1094   0.6139  -0.1078
 FLY  H2    H  HCR6  0   0.280  -2.3158  -2.1298  -1.9844
 FLY  H5    H  HCR6  0   0.292   0.1546  -2.1594  -1.3135
 FLY  H11   H  HCH1  0   0.245  -6.0172  -0.1191  -1.8090
 FLY  H13   H  HCH3  0   0.228  -7.7152  -1.5073  -0.6568
 FLY  H13A  H  HCH3  0   0.235  -6.0913  -1.9391  -0.1208
 FLY  H13B  H  HCH3  0   0.221  -7.1304  -0.9494   0.9133
 FLY  H14   H  HCH3  0   0.227  -7.6374   1.5150   0.2031
 FLY  H14A  H  HCH3  0   0.241  -6.9664   2.1136  -1.3203
 FLY  H14B  H  HCH3  0   0.241  -8.2342   0.8883  -1.3305
 FLY  H18   H  HCR6  0   0.298   2.0895   0.7571  -1.5067
 FLY  H19   H  HCR6  0   0.291   4.0534   2.1285  -2.0866
 FLY  H21   H  HCR6  0   0.308   6.4927  -0.2696   0.5051
 FLY  H25   H  HCH3  0   0.258  -0.7538   1.4071   3.1591
 FLY  H25A  H  HCH3  0   0.258  -0.3705   2.6087   1.9162
 FLY  H25B  H  HCH3  0   0.278  -2.0259   2.0058   2.0837
 FLY  HN12  H  HNH1  0   0.394  -5.2279   1.3030   0.6188

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
 FLY  C2   N1    aromatic  1.311  0.020  1.311
 FLY  C2   C4    aromatic  1.394  0.020  1.394
 FLY  C3   C4    aromatic  1.408  0.020  1.408
 FLY  C3   N8    single    1.372  0.020  1.372
 FLY  C3   N10   aromatic  1.318  0.020  1.318
 FLY  N1   C9    aromatic  1.348  0.020  1.348
 FLY  C4   C5    single    1.420  0.020  1.420
 FLY  C5   C6    double    1.344  0.020  1.344
 FLY  C6   C7    single    1.459  0.020  1.459
 FLY  C6   O16   single    1.363  0.020  1.363
 FLY  C7   O15   double    1.219  0.020  1.219
 FLY  C7   N8    single    1.385  0.020  1.385
 FLY  C9   N10   aromatic  1.336  0.020  1.336
 FLY  C9   N12   single    1.337  0.020  1.337
 FLY  C11  C13   single    1.525  0.020  1.525
 FLY  C11  C14   single    1.521  0.020  1.521
 FLY  C11  N12   single    1.454  0.020  1.454
 FLY  C17  C18   aromatic  1.385  0.020  1.385
 FLY  C17  C22   aromatic  1.389  0.020  1.389
 FLY  C17  O16   single    1.361  0.020  1.361
 FLY  C18  C19   aromatic  1.389  0.020  1.389
 FLY  C19  C20   aromatic  1.379  0.020  1.379
 FLY  C20  C21   aromatic  1.383  0.020  1.383
 FLY  C20  F24   single    1.341  0.020  1.341
 FLY  C21  C22   aromatic  1.378  0.020  1.378
 FLY  C22  F23   single    1.336  0.020  1.336
 FLY  N8   C25   single    1.458  0.020  1.458
 FLY  C2   H2    single    0.930  0.020  1.080
 FLY  C5   H5    single    0.930  0.020  1.080
 FLY  C11  H11   single    0.970  0.020  1.090
 FLY  C13  H13   single    0.970  0.020  1.090
 FLY  C13  H13A  single    0.970  0.020  1.090
 FLY  C13  H13B  single    0.970  0.020  1.090
 FLY  C14  H14   single    0.970  0.020  1.090
 FLY  C14  H14A  single    0.970  0.020  1.090
 FLY  C14  H14B  single    0.970  0.020  1.090
 FLY  C18  H18   single    0.930  0.020  1.080
 FLY  C19  H19   single    0.930  0.020  1.080
 FLY  C21  H21   single    0.930  0.020  1.080
 FLY  C25  H25   single    0.970  0.020  1.090
 FLY  C25  H25A  single    0.970  0.020  1.090
 FLY  C25  H25B  single    0.970  0.020  1.090
 FLY  N12  HN12  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
 FLY  H2    C2   C4    119.35  3.000
 FLY  H2    C2   N1    116.92  3.000
 FLY  C4    C2   N1    123.73  3.000
 FLY  N10   C3   N8    118.87  3.000
 FLY  N10   C3   C4    122.01  3.000
 FLY  N8    C3   C4    119.12  3.000
 FLY  C9    N1   C2    116.20  3.000
 FLY  C5    C4   C3    120.35  3.000
 FLY  C5    C4   C2    124.52  3.000
 FLY  C3    C4   C2    115.13  3.000
 FLY  H5    C5   C6    121.07  3.000
 FLY  H5    C5   C4    119.80  3.000
 FLY  C6    C5   C4    119.12  3.000
 FLY  O16   C6   C7    116.47  3.000
 FLY  O16   C6   C5    121.38  3.000
 FLY  C7    C6   C5    122.04  3.000
 FLY  N8    C7   O15   120.96  3.000
 FLY  N8    C7   C6    116.51  3.000
 FLY  O15   C7   C6    122.53  3.000
 FLY  N12   C9   N10   116.69  3.000
 FLY  N12   C9   N1    117.86  3.000
 FLY  N10   C9   N1    125.44  3.000
 FLY  H11   C11  N12   107.43  3.000
 FLY  H11   C11  C14   108.63  3.000
 FLY  N12   C11  C14   108.65  3.000
 FLY  H11   C11  C13   108.62  3.000
 FLY  N12   C11  C13   111.72  3.000
 FLY  C14   C11  C13   111.66  3.000
 FLY  H13B  C13  H13A  108.36  3.000
 FLY  H13B  C13  H13   108.05  3.000
 FLY  H13A  C13  H13   107.96  3.000
 FLY  H13B  C13  C11   110.93  3.000
 FLY  H13A  C13  C11   111.19  3.000
 FLY  H13   C13  C11   110.24  3.000
 FLY  H14B  C14  H14A  107.97  3.000
 FLY  H14B  C14  H14   107.63  3.000
 FLY  H14A  C14  H14   108.29  3.000
 FLY  H14B  C14  C11   110.09  3.000
 FLY  H14A  C14  C11   111.45  3.000
 FLY  H14   C14  C11   111.27  3.000
 FLY  O16   C17  C22   116.91  3.000
 FLY  O16   C17  C18   124.42  3.000
 FLY  C22   C17  C18   118.63  3.000
 FLY  H18   C18  C19   119.15  3.000
 FLY  H18   C18  C17   120.23  3.000
 FLY  C19   C18  C17   120.62  3.000
 FLY  H19   C19  C20   120.74  3.000
 FLY  H19   C19  C18   120.44  3.000
 FLY  C20   C19  C18   118.83  3.000
 FLY  F24   C20  C21   118.41  3.000
 FLY  F24   C20  C19   119.49  3.000
 FLY  C21   C20  C19   122.10  3.000
 FLY  H21   C21  C22   120.71  3.000
 FLY  H21   C21  C20   121.50  3.000
 FLY  C22   C21  C20   117.79  3.000
 FLY  F23   C22  C21   119.37  3.000
 FLY  F23   C22  C17   118.61  3.000
 FLY  C21   C22  C17   122.03  3.000
 FLY  C17   O16  C6    118.15  3.000
 FLY  C25   N8   C7    116.22  3.000
 FLY  C25   N8   C3    120.93  3.000
 FLY  C7    N8   C3    122.85  3.000
 FLY  H25B  C25  H25A  109.26  3.000
 FLY  H25B  C25  H25   109.30  3.000
 FLY  H25A  C25  H25   108.94  3.000
 FLY  H25B  C25  N8    108.92  3.000
 FLY  H25A  C25  N8    110.07  3.000
 FLY  H25   C25  N8    110.33  3.000
 FLY  C9    N10  C3    117.48  3.000
 FLY  HN12  N12  C11   118.08  3.000
 FLY  HN12  N12  C9    116.02  3.000
 FLY  C11   N12  C9    125.27  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
 FLY  CONST_01  N10   C9   N1   C2     0.00   0.0  0
 FLY  CONST_02  N10   C3   C4   C2     0.00   0.0  0
 FLY  CONST_03  N1    C2   C4   C3     0.00   0.0  0
 FLY  CONST_04  N1    C9   N10  C3     0.00   0.0  0
 FLY  CONST_05  C9    N1   C2   C4     0.00   0.0  0
 FLY  CONST_06  C9    N10  C3   C4     0.00   0.0  0
 FLY  CONST_07  C20   C19  C18  C17    0.00   0.0  0
 FLY  CONST_08  C20   C21  C22  C17    0.00   0.0  0
 FLY  CONST_09  C21   C22  C17  C18    0.00   0.0  0
 FLY  CONST_10  C21   C20  C19  C18    0.00   0.0  0
 FLY  CONST_11  C22   C17  C18  C19    0.00   0.0  0
 FLY  CONST_12  C22   C21  C20  C19    0.00   0.0  0
 FLY  CONST_13  C6    C7   N8   C3     0.00   0.0  0
 FLY  CONST_14  N12   C9   N1   C2   180.00   0.0  0
 FLY  CONST_15  N12   C9   N10  C3   180.00   0.0  0
 FLY  CONST_16  F23   C22  C17  C18  180.00   0.0  0
 FLY  CONST_17  F24   C20  C19  C18  180.00   0.0  0
 FLY  CONST_18  O16   C17  C18  C19  180.00   0.0  0
 FLY  CONST_19  F23   C22  C21  C20  180.00   0.0  0
 FLY  CONST_20  O16   C17  C22  C21  180.00   0.0  0
 FLY  CONST_21  F24   C20  C21  C22  180.00   0.0  0
 FLY  CONST_22  O15   C7   N8   C3   180.00   0.0  0
 FLY  CONST_23  C25   N8   C7   C6   180.00   0.0  0
 FLY  CONST_24  H2    C2   C4   C3   180.00   0.0  0
 FLY  CONST_25  H19   C19  C18  C17  180.00   0.0  0
 FLY  CONST_26  H21   C21  C22  C17  180.00   0.0  0
 FLY  CONST_27  H18   C18  C19  C20  180.00   0.0  0
 FLY  CONST_28  C11   N12  C9   N1     0.00   0.0  0
 FLY  CONST_29  N10   C9   N12  C11  180.00   0.0  0
 FLY  CONST_30  C25   N8   C7   O15    0.00   0.0  0
 FLY  CONST_31  HN12  N12  C9   N1   180.00   0.0  0
 FLY  Var_01    C18   C17  O16  C6   -30.40  30.0  2
 FLY  Var_02    H25   C25  N8   C3   119.00  30.0  3
 FLY  Var_03    C13   C11  N12  C9    77.87  30.0  2
 FLY  Var_04    H14   C14  C11  C13   61.50  30.0  3
 FLY  Var_05    H13   C13  C11  C14   59.33  30.0  3

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
 FLY  plan-1  C17   0.020
 FLY  plan-1  C18   0.020
 FLY  plan-1  C19   0.020
 FLY  plan-1  C20   0.020
 FLY  plan-1  C21   0.020
 FLY  plan-1  C22   0.020
 FLY  plan-1  F24   0.020
 FLY  plan-1  F23   0.020
 FLY  plan-1  O16   0.020
 FLY  plan-1  H18   0.020
 FLY  plan-1  H19   0.020
 FLY  plan-1  H21   0.020
 FLY  plan-2  C2    0.020
 FLY  plan-2  C3    0.020
 FLY  plan-2  N1    0.020
 FLY  plan-2  C4    0.020
 FLY  plan-2  C5    0.020
 FLY  plan-2  C6    0.020
 FLY  plan-2  C7    0.020
 FLY  plan-2  C9    0.020
 FLY  plan-2  O16   0.020
 FLY  plan-2  O15   0.020
 FLY  plan-2  N8    0.020
 FLY  plan-2  C25   0.020
 FLY  plan-2  N10   0.020
 FLY  plan-2  N12   0.020
 FLY  plan-2  H2    0.020
 FLY  plan-2  H5    0.020
 FLY  plan-3  C9    0.020
 FLY  plan-3  C11   0.020
 FLY  plan-3  N12   0.020
 FLY  plan-3  HN12  0.020

