# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 09:25:25 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-{3-[(2,2-difluoro-2-pyridin-2-ylethyl)amino]-6-methyl-2-oxopyrazin-1(2H)-yl}-N-[(3-fluoropyridin-2-yl)methyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN=C(NCC(F)(F)c2ccccn2)C(=O)N1CC(=O)NCc3ncccc3F
#
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
 CDA  CDA  2-{3-[(2,2-difluoro-2-pyridin-2-ylethyl)amino]-6-methyl-2-oxopyrazin-1(2H)-yl}-N-[(3-fluoropyridin-2-yl)methyl]acetamide  ligand  50  31  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CDA
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
 CDA  N1    N  N     0  -0.413   1.2563  -0.3829  -6.3077
 CDA  C2    C  CR6   0   0.078   0.0041   0.0408  -6.1896
 CDA  C3    C  CR16  0  -0.331  -0.9012   0.0467  -7.2395
 CDA  C4    C  CR16  0  -0.144  -0.4632  -0.4003  -8.4789
 CDA  C5    C  CR16  0  -0.315   0.8445  -0.8336  -8.6139
 CDA  C6    C  CR16  0  -0.075   1.6651  -0.8070  -7.4940
 CDA  C11   C  CT    0   0.777  -0.3722   0.4871  -4.7982
 CDA  C12   C  CH2   0  -0.394  -0.4254  -0.6627  -3.8033
 CDA  F13   F  F     0  -0.340  -1.5839   1.1145  -4.8233
 CDA  F1    F  F     0  -0.338   0.5171   1.4259  -4.3725
 CDA  N18   N  NH1   0  -0.668  -0.7368  -0.2314  -2.4764
 CDA  C21   C  CR6   0   0.382   0.1962   0.0026  -1.5280
 CDA  C22   C  CR6   0   0.493  -0.3467   0.4393  -0.2291
 CDA  N23   N  NR6   0  -0.517   0.5932   0.6997   0.7207
 CDA  C24   C  CR6   0   0.322   1.9430   0.4544   0.5168
 CDA  C25   C  CR16  0  -0.218   2.3211   0.0304  -0.7089
 CDA  N26   N  N     0  -0.421   1.4577  -0.1800  -1.7402
 CDA  O28   O  OC    0  -0.491  -1.5491   0.5710  -0.0259
 CDA  C29   C  CH3   0  -0.748   2.9096   0.6556   1.6337
 CDA  C33   C  CH2   0  -0.479   0.0890   1.1198   2.0075
 CDA  C34   C  C     0   0.563  -0.3879  -0.0790   2.8193
 CDA  N37   N  NH1   0  -0.631  -1.1210   0.2563   3.8913
 CDA  O38   O  O     0  -0.475  -0.0887  -1.2173   2.5097
 CDA  C39   C  CH2   0  -0.369  -1.5686  -0.6812   4.8942
 CDA  C40   C  CR6   0   0.074  -0.9330  -0.4264   6.2364
 CDA  C43   C  CR6   0   0.477   0.4440  -0.4744   6.4181
 CDA  C44   C  CR16  0  -0.293   1.0118  -0.2276   7.6483
 CDA  C45   C  CR16  0  -0.306   0.1552   0.0640   8.6993
 CDA  N46   N  N     0  -0.406  -1.7331  -0.1465   7.2568
 CDA  F47   F  F     0  -0.299   1.2299  -0.7721   5.3755
 CDA  C50   C  CR16  0  -0.085  -1.2081   0.0887   8.4534
 CDA  H3    H  HCR6  0   0.279  -1.9185   0.3868  -7.1106
 CDA  H4    H  HCR6  0   0.282  -1.1387  -0.4067  -9.3236
 CDA  H5    H  HCR6  0   0.278   1.2263  -1.1883  -9.5608
 CDA  H6    H  HCR6  0   0.272   2.6933  -1.1434  -7.5600
 CDA  H121  H  HCH2  0   0.277   0.5359  -1.1763  -3.8089
 CDA  H122  H  HCH2  0   0.291  -1.1778  -1.3773  -4.1428
 CDA  H18   H  HNH1  0   0.404  -1.6981  -0.0652  -2.2297
 CDA  H25   H  HCR6  0   0.256   3.3668  -0.1609  -0.9091
 CDA  H291  H  HCH3  0   0.273   3.9039   0.3673   1.2997
 CDA  H292  H  HCH3  0   0.261   2.9640   1.6954   1.9619
 CDA  H293  H  HCH3  0   0.253   2.6617   0.0432   2.5030
 CDA  H331  H  HCH2  0   0.326   0.8726   1.6348   2.5612
 CDA  H332  H  HCH2  0   0.313  -0.7165   1.8399   1.8663
 CDA  H37   H  HNH1  0   0.411  -1.3351   1.2294   4.0461
 CDA  H391  H  HCH2  0   0.280  -2.6496  -0.6068   5.0168
 CDA  H392  H  HCH2  0   0.279  -1.3472  -1.6895   4.5453
 CDA  H44   H  HCR6  0   0.299   2.0851  -0.2660   7.7809
 CDA  H45   H  HCR6  0   0.283   0.5405   0.2679   9.6884
 CDA  H50   H  HCR6  0   0.270  -1.9055   0.3101   9.2524

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
 CDA  N1   C2    aromatic  1.327  0.020  1.327
 CDA  N1   C6    aromatic  1.324  0.020  1.324
 CDA  C2   C3    aromatic  1.386  0.020  1.386
 CDA  C2   C11   single    1.509  0.020  1.509
 CDA  C3   C4    aromatic  1.388  0.020  1.388
 CDA  C3   H3    single    0.930  0.020  1.080
 CDA  C4   C5    aromatic  1.384  0.020  1.384
 CDA  C4   H4    single    0.930  0.020  1.080
 CDA  C5   C6    aromatic  1.389  0.020  1.389
 CDA  C5   H5    single    0.930  0.020  1.080
 CDA  C6   H6    single    0.930  0.020  1.080
 CDA  C11  C12   single    1.521  0.020  1.521
 CDA  C11  F13   single    1.365  0.020  1.365
 CDA  C11  F1    single    1.361  0.020  1.361
 CDA  C12  N18   single    1.430  0.020  1.430
 CDA  C12  H121  single    0.970  0.020  1.090
 CDA  C12  H122  single    0.970  0.020  1.090
 CDA  N18  C21   single    1.351  0.020  1.351
 CDA  N18  H18   single    0.860  0.020  1.020
 CDA  C21  C22   aromatic  1.474  0.020  1.474
 CDA  C21  N26   aromatic  1.292  0.020  1.292
 CDA  C22  N23   aromatic  1.361  0.020  1.361
 CDA  C22  O28   double    1.227  0.020  1.227
 CDA  N23  C24   aromatic  1.387  0.020  1.387
 CDA  N23  C33   single    1.445  0.020  1.445
 CDA  C24  C25   aromatic  1.351  0.020  1.351
 CDA  C24  C29   single    1.491  0.020  1.491
 CDA  C25  N26   aromatic  1.361  0.020  1.361
 CDA  C25  H25   single    0.930  0.020  1.080
 CDA  C29  H291  single    0.970  0.020  1.090
 CDA  C29  H292  single    0.970  0.020  1.090
 CDA  C29  H293  single    0.970  0.020  1.090
 CDA  C33  C34   single    1.524  0.020  1.524
 CDA  C33  H331  single    0.970  0.020  1.090
 CDA  C33  H332  single    0.970  0.020  1.090
 CDA  C34  N37   single    1.341  0.020  1.341
 CDA  C34  O38   double    1.217  0.020  1.217
 CDA  N37  C39   single    1.444  0.020  1.444
 CDA  N37  H37   single    0.860  0.020  1.020
 CDA  C39  C40   single    1.507  0.020  1.507
 CDA  C39  H391  single    0.970  0.020  1.090
 CDA  C39  H392  single    0.970  0.020  1.090
 CDA  C40  C43   aromatic  1.390  0.020  1.390
 CDA  C40  N46   aromatic  1.326  0.020  1.326
 CDA  C43  C44   aromatic  1.377  0.020  1.377
 CDA  C43  F47   single    1.339  0.020  1.339
 CDA  C44  C45   aromatic  1.387  0.020  1.387
 CDA  C44  H44   single    0.930  0.020  1.080
 CDA  C45  C50   aromatic  1.386  0.020  1.386
 CDA  C45  H45   single    0.930  0.020  1.080
 CDA  N46  C50   aromatic  1.328  0.020  1.328
 CDA  C50  H50   single    0.930  0.020  1.080

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
 CDA  C6    N1   C2    118.23  3.000
 CDA  C11   C2   C3    122.29  3.000
 CDA  C11   C2   N1    114.32  3.000
 CDA  C3    C2   N1    123.37  3.000
 CDA  H3    C3   C4    120.32  3.000
 CDA  H3    C3   C2    121.73  3.000
 CDA  C4    C3   C2    117.95  3.000
 CDA  H4    C4   C5    120.79  3.000
 CDA  H4    C4   C3    120.14  3.000
 CDA  C5    C4   C3    119.07  3.000
 CDA  H5    C5   C6    120.27  3.000
 CDA  H5    C5   C4    121.46  3.000
 CDA  C6    C5   C4    118.27  3.000
 CDA  H6    C6   C5    120.37  3.000
 CDA  H6    C6   N1    116.53  3.000
 CDA  C5    C6   N1    123.10  3.000
 CDA  F1    C11  F13   105.59  3.000
 CDA  F1    C11  C12   109.85  3.000
 CDA  F13   C11  C12   109.17  3.000
 CDA  F1    C11  C2    109.23  3.000
 CDA  F13   C11  C2    109.90  3.000
 CDA  C12   C11  C2    112.84  3.000
 CDA  H122  C12  H121  107.32  3.000
 CDA  H122  C12  N18   109.63  3.000
 CDA  H121  C12  N18   109.82  3.000
 CDA  H122  C12  C11   108.39  3.000
 CDA  H121  C12  C11   108.78  3.000
 CDA  N18   C12  C11   112.74  3.000
 CDA  H18   N18  C21   117.33  3.000
 CDA  H18   N18  C12   119.04  3.000
 CDA  C21   N18  C12   123.61  3.000
 CDA  N26   C21  C22   123.11  3.000
 CDA  N26   C21  N18   122.31  3.000
 CDA  C22   C21  N18   114.56  3.000
 CDA  O28   C22  N23   122.73  3.000
 CDA  O28   C22  C21   122.61  3.000
 CDA  N23   C22  C21   114.66  3.000
 CDA  C33   N23  C24   121.47  3.000
 CDA  C33   N23  C22   115.86  3.000
 CDA  C24   N23  C22   122.38  3.000
 CDA  C29   C24  C25   122.73  3.000
 CDA  C29   C24  N23   119.80  3.000
 CDA  C25   C24  N23   117.47  3.000
 CDA  H25   C25  N26   116.46  3.000
 CDA  H25   C25  C24   119.60  3.000
 CDA  N26   C25  C24   123.94  3.000
 CDA  C25   N26  C21   118.22  3.000
 CDA  H293  C29  H292  107.83  3.000
 CDA  H293  C29  H291  107.66  3.000
 CDA  H292  C29  H291  107.41  3.000
 CDA  H293  C29  C24   111.94  3.000
 CDA  H292  C29  C24   112.71  3.000
 CDA  H291  C29  C24   109.08  3.000
 CDA  H332  C33  H331  106.58  3.000
 CDA  H332  C33  C34   110.94  3.000
 CDA  H331  C33  C34   109.05  3.000
 CDA  H332  C33  N23   109.55  3.000
 CDA  H331  C33  N23   109.84  3.000
 CDA  C34   C33  N23   110.78  3.000
 CDA  O38   C34  N37   124.86  3.000
 CDA  O38   C34  C33   121.55  3.000
 CDA  N37   C34  C33   113.58  3.000
 CDA  H37   N37  C39   117.01  3.000
 CDA  H37   N37  C34   118.69  3.000
 CDA  C39   N37  C34   124.21  3.000
 CDA  H392  C39  H391  107.49  3.000
 CDA  H392  C39  C40   110.85  3.000
 CDA  H391  C39  C40   107.85  3.000
 CDA  H392  C39  N37   108.38  3.000
 CDA  H391  C39  N37   109.95  3.000
 CDA  C40   C39  N37   112.22  3.000
 CDA  N46   C40  C43   120.28  3.000
 CDA  N46   C40  C39   117.81  3.000
 CDA  C43   C40  C39   121.91  3.000
 CDA  F47   C43  C44   119.56  3.000
 CDA  F47   C43  C40   119.17  3.000
 CDA  C44   C43  C40   121.27  3.000
 CDA  H44   C44  C45   121.81  3.000
 CDA  H44   C44  C43   120.80  3.000
 CDA  C45   C44  C43   117.39  3.000
 CDA  H45   C45  C50   120.65  3.000
 CDA  H45   C45  C44   120.86  3.000
 CDA  C50   C45  C44   118.49  3.000
 CDA  C50   N46  C40   119.48  3.000
 CDA  H50   C50  N46   116.51  3.000
 CDA  H50   C50  C45   120.41  3.000
 CDA  N46   C50  C45   123.09  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
 CDA  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 CDA  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 CDA  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 CDA  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 CDA  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 CDA  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 CDA  CONST_07  C24   N23  C22  C21     0.00   0.0  0
 CDA  CONST_08  C24   C25  N26  C21     0.00   0.0  0
 CDA  CONST_09  C25   N26  C21  C22     0.00   0.0  0
 CDA  CONST_10  C25   C24  N23  C22     0.00   0.0  0
 CDA  CONST_11  N26   C21  C22  N23     0.00   0.0  0
 CDA  CONST_12  N26   C25  C24  N23     0.00   0.0  0
 CDA  CONST_13  C45   C44  C43  C40     0.00   0.0  0
 CDA  CONST_14  C45   C50  N46  C40     0.00   0.0  0
 CDA  CONST_15  C50   N46  C40  C43     0.00   0.0  0
 CDA  CONST_16  C50   C45  C44  C43     0.00   0.0  0
 CDA  CONST_17  N46   C40  C43  C44     0.00   0.0  0
 CDA  CONST_18  N46   C50  C45  C44     0.00   0.0  0
 CDA  CONST_19  C11   C2   C3   C4    180.00   0.0  0
 CDA  CONST_20  C11   C2   N1   C6    180.00   0.0  0
 CDA  CONST_21  N23   C22  C21  N18   180.00   0.0  0
 CDA  CONST_22  C25   N26  C21  N18   180.00   0.0  0
 CDA  CONST_23  C33   N23  C22  C21   180.00   0.0  0
 CDA  CONST_24  C29   C24  N23  C22   180.00   0.0  0
 CDA  CONST_25  O28   C22  N23  C24   180.00   0.0  0
 CDA  CONST_26  C33   N23  C24  C25   180.00   0.0  0
 CDA  CONST_27  O28   C22  C21  N26   180.00   0.0  0
 CDA  CONST_28  C29   C24  C25  N26   180.00   0.0  0
 CDA  CONST_29  C44   C43  C40  C39   180.00   0.0  0
 CDA  CONST_30  C50   N46  C40  C39   180.00   0.0  0
 CDA  CONST_31  F47   C43  C44  C45   180.00   0.0  0
 CDA  CONST_32  F47   C43  C40  N46   180.00   0.0  0
 CDA  CONST_33  H3    C3   C2   N1    180.00   0.0  0
 CDA  CONST_34  H5    C5   C6   N1    180.00   0.0  0
 CDA  CONST_35  H6    C6   N1   C2    180.00   0.0  0
 CDA  CONST_36  H4    C4   C3   C2    180.00   0.0  0
 CDA  CONST_37  H25   C25  N26  C21   180.00   0.0  0
 CDA  CONST_38  H44   C44  C43  C40   180.00   0.0  0
 CDA  CONST_39  H50   C50  N46  C40   180.00   0.0  0
 CDA  CONST_40  H45   C45  C44  C43   180.00   0.0  0
 CDA  CONST_41  C33   N23  C22  O28     0.00   0.0  0
 CDA  CONST_42  C22   C21  N18  C12   180.00   0.0  0
 CDA  CONST_43  N26   C21  N18  C12     0.00   0.0  0
 CDA  CONST_44  H18   N18  C21  C22     0.00   0.0  0
 CDA  CONST_45  C39   N37  C34  C33   180.00   0.0  0
 CDA  CONST_46  C39   N37  C34  O38     0.00   0.0  0
 CDA  CONST_47  H37   N37  C34  C33     0.00   0.0  0
 CDA  Var_01    C12   C11  C2   N1    -68.34  30.0  2
 CDA  Var_02    C34   C33  N23  C22    79.75  30.0  2
 CDA  Var_03    C43   C40  C39  N37   -59.93  30.0  2
 CDA  Var_04    H291  C29  C24  N23   177.21  30.0  2
 CDA  Var_05    N18   C12  C11  C2    177.97  30.0  3
 CDA  Var_06    C21   N18  C12  C11   -96.73  30.0  3
 CDA  Var_07    N37   C34  C33  N23  -166.59  30.0  3
 CDA  Var_08    C40   C39  N37  C34   113.97  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
 CDA  plan-1  N1   0.020
 CDA  plan-1  C2   0.020
 CDA  plan-1  C3   0.020
 CDA  plan-1  C4   0.020
 CDA  plan-1  C5   0.020
 CDA  plan-1  C6   0.020
 CDA  plan-1  C11  0.020
 CDA  plan-1  H3   0.020
 CDA  plan-1  H4   0.020
 CDA  plan-1  H5   0.020
 CDA  plan-1  H6   0.020
 CDA  plan-2  N18  0.020
 CDA  plan-2  C21  0.020
 CDA  plan-2  C22  0.020
 CDA  plan-2  N23  0.020
 CDA  plan-2  C24  0.020
 CDA  plan-2  C25  0.020
 CDA  plan-2  N26  0.020
 CDA  plan-2  O28  0.020
 CDA  plan-2  C29  0.020
 CDA  plan-2  C33  0.020
 CDA  plan-2  H25  0.020
 CDA  plan-3  C39  0.020
 CDA  plan-3  C40  0.020
 CDA  plan-3  C43  0.020
 CDA  plan-3  C44  0.020
 CDA  plan-3  C45  0.020
 CDA  plan-3  N46  0.020
 CDA  plan-3  F47  0.020
 CDA  plan-3  C50  0.020
 CDA  plan-3  H44  0.020
 CDA  plan-3  H45  0.020
 CDA  plan-3  H50  0.020
 CDA  plan-4  C33  0.020
 CDA  plan-4  C34  0.020
 CDA  plan-4  N37  0.020
 CDA  plan-4  O38  0.020
 CDA  plan-4  C39  0.020
 CDA  plan-4  H37  0.020
 CDA  plan-5  C12  0.020
 CDA  plan-5  N18  0.020
 CDA  plan-5  C21  0.020
 CDA  plan-5  H18  0.020

