# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 12:26:27 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-[6-chloro-3-{[2,2-difluoro-2-(1-oxidopyridin-2-yl)ethyl]amino}-2-oxopyrazin-1(2H)-yl]-N-(2-fluorobenzyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][n+]1ccccc1C(F)(F)CNC2=NC=C(Cl)N(CC(=O)NCc3ccccc3F)C2=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
 CDD  CDD  2-[6-chloro-3-{[2,2-difluoro-2-(1-oxidopyridin-2-yl)ethyl]amino}-2-oxopyrazin-1(2H)-yl]-N-(2-fluorobenzyl)acetamide  ligand  49  32  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CDD
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
 CDD  C1    C   CR16   0  -0.025   7.8407  -1.3942  -0.7978
 CDD  N2    N   NR6    1  -0.066   6.5422  -1.5251  -0.4355
 CDD  C3    C   CR6    0   0.167   5.9555  -0.5414   0.3002
 CDD  C4    C   CR16   0  -0.367   6.6690   0.5897   0.6504
 CDD  C5    C   CR16   0  -0.129   7.9944   0.7327   0.2795
 CDD  C6    C   CR16   0  -0.346   8.5782  -0.2864  -0.4547
 CDD  C11   C   CT     0   0.792   4.5043  -0.7275   0.6781
 CDD  C12   C   CH2    0  -0.393   3.5344  -0.6602  -0.4959
 CDD  F13   F   F      0  -0.337   4.3411  -1.8908   1.3636
 CDD  F14   F   F      0  -0.327   4.1794   0.2512   1.5675
 CDD  N15   N   NH1    0  -0.662   2.1727  -0.7901  -0.0758
 CDD  C18   C   CR6    0   0.394   1.3548   0.2558   0.1441
 CDD  C19   C   CR6    0   0.513  -0.0263  -0.1205   0.5211
 CDD  N20   N   NR6    0  -0.504  -0.8561   0.9386   0.7658
 CDD  C21   C   CR6    0   0.226  -0.4195   2.2351   0.5713
 CDD  C22   C   CR16   0  -0.139   0.8512   2.4800   0.2048
 CDD  N23   N   N      0  -0.426   1.7481   1.4794   0.0021
 CDD  C24   C   CH2    0  -0.483  -2.2344   0.6612   1.1063
 CDD  C25   C   C      0   0.555  -3.1315   0.8353  -0.1137
 CDD  N28   N   NH1    0  -0.625  -4.4232   1.0125   0.1913
 CDD  C29   C   CH2    0  -0.359  -5.4904   1.0740  -0.7830
 CDD  C30   C   CR6    0  -0.090  -6.4955  -0.0294  -0.5899
 CDD  C33   C   CR16   0  -0.288  -7.8078   0.2426  -0.2168
 CDD  C34   C   CR16   0  -0.255  -8.7323  -0.7771  -0.0304
 CDD  C35   C   CR16   0  -0.249  -8.3481  -2.0974  -0.2138
 CDD  C2    C   CR16   0  -0.399  -7.0439  -2.3990  -0.5853
 CDD  C37   C   CR6    0   0.533  -6.1511  -1.3624  -0.7653
 CDD  O42   O   OC     0  -0.471  -0.3782  -1.2861   0.6186
 CDD  CL43  CL  CL     0  -0.061  -1.5454   3.5057   0.8175
 CDD  O44   O   O      0  -0.472  -2.6767   0.7848  -1.2418
 CDD  F1    F   F      0  -0.309  -4.8911  -1.6548  -1.1291
 CDD  O1    O   O     -1  -0.554   5.8936  -2.5597  -0.7829
 CDD  H1    H   HCR6   0   0.319   8.2382  -2.2177  -1.3709
 CDD  H4    H   HCR6   0   0.298   6.1813   1.3662   1.2201
 CDD  H5    H   HCR6   0   0.288   8.5520   1.6148   0.5579
 CDD  H6    H   HCR6   0   0.298   9.6097  -0.2359  -0.7725
 CDD  H121  H   HCH2   0   0.282   3.6729   0.2924  -1.0082
 CDD  H122  H   HCH2   0   0.297   3.7715  -1.4548  -1.1998
 CDD  H15   H   HNH1   0   0.411   1.7858  -1.7128   0.0385
 CDD  H22   H   HCR6   0   0.284   1.1950   3.4943   0.0593
 CDD  H241  H   HCH2   0   0.330  -2.3012  -0.3735   1.4392
 CDD  H242  H   HCH2   0   0.312  -2.5492   1.2824   1.9438
 CDD  H28   H   HNH1   0   0.409  -4.6863   1.0841   1.1622
 CDD  H291  H   HCH2   0   0.276  -5.9995   2.0361  -0.7032
 CDD  H292  H   HCH2   0   0.276  -5.0462   1.0333  -1.7764
 CDD  H33   H   HCR6   0   0.266  -8.1052   1.2736  -0.0680
 CDD  H34   H   HCR6   0   0.263  -9.7468  -0.5390   0.2593
 CDD  H35   H   HCR6   0   0.269  -9.0592  -2.8996  -0.0690
 CDD  H2    H   HCR6   0   0.280  -6.7259  -3.4223  -0.7361

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
 CDD  C1   N2    aromatic  1.354  0.020  1.354
 CDD  C1   C6    aromatic  1.374  0.020  1.374
 CDD  C1   H1    single    0.930  0.020  1.080
 CDD  N2   C3    aromatic  1.361  0.020  1.361
 CDD  N2   O1    single    1.270  0.020  1.270
 CDD  C3   C4    aromatic  1.382  0.020  1.382
 CDD  C3   C11   single    1.511  0.020  1.511
 CDD  C4   C5    aromatic  1.384  0.020  1.384
 CDD  C4   H4    single    0.930  0.020  1.080
 CDD  C5   C6    aromatic  1.385  0.020  1.385
 CDD  C5   H5    single    0.930  0.020  1.080
 CDD  C6   H6    single    0.930  0.020  1.080
 CDD  C11  C12   single    1.524  0.020  1.524
 CDD  C11  F13   single    1.360  0.020  1.360
 CDD  C11  F14   single    1.362  0.020  1.362
 CDD  C12  N15   single    1.431  0.020  1.431
 CDD  C12  H121  single    0.970  0.020  1.090
 CDD  C12  H122  single    0.970  0.020  1.090
 CDD  N15  C18   single    1.346  0.020  1.346
 CDD  N15  H15   single    0.860  0.020  1.020
 CDD  C18  C19   aromatic  1.480  0.020  1.480
 CDD  C18  N23   aromatic  1.293  0.020  1.293
 CDD  C19  N20   aromatic  1.367  0.020  1.367
 CDD  C19  O42   double    1.221  0.020  1.221
 CDD  N20  C21   aromatic  1.382  0.020  1.382
 CDD  N20  C24   single    1.447  0.020  1.447
 CDD  C21  C22   aromatic  1.345  0.020  1.345
 CDD  C21  CL43  single    1.715  0.020  1.715
 CDD  C22  N23   aromatic  1.359  0.020  1.359
 CDD  C22  H22   single    0.930  0.020  1.080
 CDD  C24  C25   single    1.524  0.020  1.524
 CDD  C24  H241  single    0.970  0.020  1.090
 CDD  C24  H242  single    0.970  0.020  1.090
 CDD  C25  N28   single    1.339  0.020  1.339
 CDD  C25  O44   double    1.217  0.020  1.217
 CDD  N28  C29   single    1.446  0.020  1.446
 CDD  N28  H28   single    0.860  0.020  1.020
 CDD  C29  C30   single    1.505  0.020  1.505
 CDD  C29  H291  single    0.970  0.020  1.090
 CDD  C29  H292  single    0.970  0.020  1.090
 CDD  C30  C33   aromatic  1.391  0.020  1.391
 CDD  C30  C37   aromatic  1.388  0.020  1.388
 CDD  C33  C34   aromatic  1.389  0.020  1.389
 CDD  C33  H33   single    0.930  0.020  1.080
 CDD  C34  C35   aromatic  1.387  0.020  1.387
 CDD  C34  H34   single    0.930  0.020  1.080
 CDD  C35  C2    aromatic  1.389  0.020  1.389
 CDD  C35  H35   single    0.930  0.020  1.080
 CDD  C2   C37   aromatic  1.380  0.020  1.380
 CDD  C2   H2    single    0.930  0.020  1.080
 CDD  C37  F1    single    1.344  0.020  1.344

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
 CDD  H1    C1   C6    123.37  3.000
 CDD  H1    C1   N2    114.92  3.000
 CDD  C6    C1   N2    121.71  3.000
 CDD  O1    N2   C3    121.10  3.000
 CDD  O1    N2   C1    119.70  3.000
 CDD  C3    N2   C1    119.20  3.000
 CDD  C11   C3   C4    122.21  3.000
 CDD  C11   C3   N2    117.39  3.000
 CDD  C4    C3   N2    120.38  3.000
 CDD  H4    C4   C5    119.99  3.000
 CDD  H4    C4   C3    119.28  3.000
 CDD  C5    C4   C3    120.73  3.000
 CDD  H5    C5   C6    121.33  3.000
 CDD  H5    C5   C4    120.65  3.000
 CDD  C6    C5   C4    118.02  3.000
 CDD  H6    C6   C5    121.59  3.000
 CDD  H6    C6   C1    118.46  3.000
 CDD  C5    C6   C1    119.95  3.000
 CDD  F14   C11  F13   104.88  3.000
 CDD  F14   C11  C12   108.63  3.000
 CDD  F13   C11  C12   110.46  3.000
 CDD  F14   C11  C3    107.69  3.000
 CDD  F13   C11  C3    110.28  3.000
 CDD  C12   C11  C3    114.40  3.000
 CDD  H122  C12  H121  107.85  3.000
 CDD  H122  C12  N15   109.34  3.000
 CDD  H121  C12  N15   109.76  3.000
 CDD  H122  C12  C11   109.11  3.000
 CDD  H121  C12  C11   108.64  3.000
 CDD  N15   C12  C11   112.05  3.000
 CDD  H15   N15  C18   117.39  3.000
 CDD  H15   N15  C12   118.82  3.000
 CDD  C18   N15  C12   123.76  3.000
 CDD  N23   C18  C19   123.52  3.000
 CDD  N23   C18  N15   122.18  3.000
 CDD  C19   C18  N15   114.27  3.000
 CDD  O42   C19  N20   123.36  3.000
 CDD  O42   C19  C18   122.12  3.000
 CDD  N20   C19  C18   114.51  3.000
 CDD  C24   N20  C21   120.94  3.000
 CDD  C24   N20  C19   118.15  3.000
 CDD  C21   N20  C19   120.65  3.000
 CDD  CL43  C21  C22   121.62  3.000
 CDD  CL43  C21  N20   117.87  3.000
 CDD  C22   C21  N20   120.51  3.000
 CDD  H22   C22  N23   117.46  3.000
 CDD  H22   C22  C21   120.53  3.000
 CDD  N23   C22  C21   122.01  3.000
 CDD  C22   N23  C18   118.67  3.000
 CDD  H242  C24  H241  106.80  3.000
 CDD  H242  C24  C25   112.34  3.000
 CDD  H241  C24  C25   108.49  3.000
 CDD  H242  C24  N20   110.30  3.000
 CDD  H241  C24  N20   108.22  3.000
 CDD  C25   C24  N20   110.52  3.000
 CDD  O44   C25  N28   125.24  3.000
 CDD  O44   C25  C24   121.13  3.000
 CDD  N28   C25  C24   113.62  3.000
 CDD  H28   N28  C29   116.94  3.000
 CDD  H28   N28  C25   118.71  3.000
 CDD  C29   N28  C25   124.33  3.000
 CDD  H292  C29  H291  106.85  3.000
 CDD  H292  C29  C30   111.23  3.000
 CDD  H291  C29  C30   108.99  3.000
 CDD  H292  C29  N28   108.17  3.000
 CDD  H291  C29  N28   109.42  3.000
 CDD  C30   C29  N28   112.03  3.000
 CDD  C37   C30  C33   117.12  3.000
 CDD  C37   C30  C29   121.48  3.000
 CDD  C33   C30  C29   121.40  3.000
 CDD  H33   C33  C34   119.84  3.000
 CDD  H33   C33  C30   118.81  3.000
 CDD  C34   C33  C30   121.35  3.000
 CDD  H34   C34  C35   120.31  3.000
 CDD  H34   C34  C33   119.91  3.000
 CDD  C35   C34  C33   119.78  3.000
 CDD  H35   C35  C2    119.47  3.000
 CDD  H35   C35  C34   120.40  3.000
 CDD  C2    C35  C34   120.13  3.000
 CDD  H2    C2   C37   120.14  3.000
 CDD  H2    C2   C35   121.22  3.000
 CDD  C37   C2   C35   118.64  3.000
 CDD  F1    C37  C2    118.59  3.000
 CDD  F1    C37  C30   118.42  3.000
 CDD  C2    C37  C30   122.99  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
 CDD  CONST_01  C4    C3   N2   C1      0.00   0.0  0
 CDD  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 CDD  CONST_03  C5    C6   C1   N2      0.00   0.0  0
 CDD  CONST_04  C5    C4   C3   N2      0.00   0.0  0
 CDD  CONST_05  C6    C1   N2   C3      0.00   0.0  0
 CDD  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 CDD  CONST_07  C21   N20  C19  C18     0.00   0.0  0
 CDD  CONST_08  C21   C22  N23  C18     0.00   0.0  0
 CDD  CONST_09  C22   N23  C18  C19     0.00   0.0  0
 CDD  CONST_10  C22   C21  N20  C19     0.00   0.0  0
 CDD  CONST_11  N23   C18  C19  N20     0.00   0.0  0
 CDD  CONST_12  N23   C22  C21  N20     0.00   0.0  0
 CDD  CONST_13  C35   C34  C33  C30     0.00   0.0  0
 CDD  CONST_14  C35   C2   C37  C30     0.00   0.0  0
 CDD  CONST_15  C2    C37  C30  C33     0.00   0.0  0
 CDD  CONST_16  C2    C35  C34  C33     0.00   0.0  0
 CDD  CONST_17  C37   C30  C33  C34     0.00   0.0  0
 CDD  CONST_18  C37   C2   C35  C34     0.00   0.0  0
 CDD  CONST_19  C11   C3   N2   C1    180.00   0.0  0
 CDD  CONST_20  O1    N2   C3   C4    180.00   0.0  0
 CDD  CONST_21  C11   C3   C4   C5    180.00   0.0  0
 CDD  CONST_22  O1    N2   C1   C6    180.00   0.0  0
 CDD  CONST_23  N20   C19  C18  N15   180.00   0.0  0
 CDD  CONST_24  C22   N23  C18  N15   180.00   0.0  0
 CDD  CONST_25  C24   N20  C19  C18   180.00   0.0  0
 CDD  CONST_26  CL43  C21  N20  C19   180.00   0.0  0
 CDD  CONST_27  O42   C19  N20  C21   180.00   0.0  0
 CDD  CONST_28  C24   N20  C21  C22   180.00   0.0  0
 CDD  CONST_29  O42   C19  C18  N23   180.00   0.0  0
 CDD  CONST_30  CL43  C21  C22  N23   180.00   0.0  0
 CDD  CONST_31  C34   C33  C30  C29   180.00   0.0  0
 CDD  CONST_32  C2    C37  C30  C29   180.00   0.0  0
 CDD  CONST_33  F1    C37  C30  C33   180.00   0.0  0
 CDD  CONST_34  F1    C37  C2   C35   180.00   0.0  0
 CDD  CONST_35  H5    C5   C6   C1    180.00   0.0  0
 CDD  CONST_36  H6    C6   C1   N2    180.00   0.0  0
 CDD  CONST_37  H4    C4   C3   N2    180.00   0.0  0
 CDD  CONST_38  H1    C1   N2   C3    180.00   0.0  0
 CDD  CONST_39  H22   C22  N23  C18   180.00   0.0  0
 CDD  CONST_40  H34   C34  C33  C30   180.00   0.0  0
 CDD  CONST_41  H2    C2   C37  C30   180.00   0.0  0
 CDD  CONST_42  H35   C35  C34  C33   180.00   0.0  0
 CDD  CONST_43  H33   C33  C34  C35   180.00   0.0  0
 CDD  CONST_44  O42   C19  N20  C24     0.00   0.0  0
 CDD  CONST_45  C19   C18  N15  C12   180.00   0.0  0
 CDD  CONST_46  N23   C18  N15  C12     0.00   0.0  0
 CDD  CONST_47  H15   N15  C18  C19     0.00   0.0  0
 CDD  CONST_48  C29   N28  C25  C24   180.00   0.0  0
 CDD  CONST_49  O44   C25  N28  C29     0.00   0.0  0
 CDD  CONST_50  H28   N28  C25  C24     0.00   0.0  0
 CDD  Var_01    C12   C11  C3   N2    -68.21  30.0  2
 CDD  Var_02    C25   C24  N20  C19   -99.55  30.0  2
 CDD  Var_03    C33   C30  C29  N28   114.51  30.0  2
 CDD  Var_04    N15   C12  C11  C3   -177.72  30.0  3
 CDD  Var_05    C18   N15  C12  C11    96.45  30.0  3
 CDD  Var_06    N28   C25  C24  N20  -160.12  30.0  3
 CDD  Var_07    C30   C29  N28  C25   118.47  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
 CDD  plan-1  C1    0.020
 CDD  plan-1  N2    0.020
 CDD  plan-1  C3    0.020
 CDD  plan-1  C4    0.020
 CDD  plan-1  C5    0.020
 CDD  plan-1  C6    0.020
 CDD  plan-1  C11   0.020
 CDD  plan-1  O1    0.020
 CDD  plan-1  H1    0.020
 CDD  plan-1  H4    0.020
 CDD  plan-1  H5    0.020
 CDD  plan-1  H6    0.020
 CDD  plan-2  N15   0.020
 CDD  plan-2  C18   0.020
 CDD  plan-2  C19   0.020
 CDD  plan-2  N20   0.020
 CDD  plan-2  C21   0.020
 CDD  plan-2  C22   0.020
 CDD  plan-2  N23   0.020
 CDD  plan-2  C24   0.020
 CDD  plan-2  O42   0.020
 CDD  plan-2  CL43  0.020
 CDD  plan-2  H22   0.020
 CDD  plan-3  C29   0.020
 CDD  plan-3  C30   0.020
 CDD  plan-3  C33   0.020
 CDD  plan-3  C34   0.020
 CDD  plan-3  C35   0.020
 CDD  plan-3  C2    0.020
 CDD  plan-3  C37   0.020
 CDD  plan-3  F1    0.020
 CDD  plan-3  H33   0.020
 CDD  plan-3  H34   0.020
 CDD  plan-3  H35   0.020
 CDD  plan-3  H2    0.020
 CDD  plan-4  C24   0.020
 CDD  plan-4  C25   0.020
 CDD  plan-4  N28   0.020
 CDD  plan-4  C29   0.020
 CDD  plan-4  O44   0.020
 CDD  plan-4  H28   0.020
 CDD  plan-5  C12   0.020
 CDD  plan-5  N15   0.020
 CDD  plan-5  C18   0.020
 CDD  plan-5  H15   0.020

