# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 23:24:11 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: N-[2-(carbamimidamidooxy)ethyl]-2-{3-[(2,2-difluoro-2-phenylethyl)amino]-6-methyl-2-oxopyrazin-1(2H)-yl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN=C(NCC(F)(F)c2ccccc2)C(=O)N1CC(=O)NCCONC(N)=N
#
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
 NLI  NLI  N-[2-(carbamimidamidooxy)ethyl]-2-{3-[(2,2-difluoro-2-phenylethyl)amino]-6-methyl-2-oxopyrazin-1(2H)-yl}acetamide  ligand  53  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NLI
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
 NLI  C01   C  CH3   0  -0.751   1.4834  -3.9602  -0.5439
 NLI  C02   C  CR6   0   0.324   0.5888  -2.7715  -0.4480
 NLI  C03   C  CR16  0  -0.221  -0.7479  -2.8461  -0.6341
 NLI  N04   N  N     0  -0.419  -1.5863  -1.7768  -0.5563
 NLI  C05   C  CR6   0   0.379  -1.0733  -0.6141  -0.3205
 NLI  N06   N  NH1   0  -0.665  -1.8239   0.5086  -0.2654
 NLI  C07   C  CH2   0  -0.392  -3.2442   0.5186  -0.4265
 NLI  C08   C  CT    0   0.773  -4.0023   0.4360   0.8927
 NLI  F09   F  F     0  -0.334  -3.5881  -0.6580   1.5910
 NLI  F10   F  F     0  -0.347  -3.6590   1.5104   1.6670
 NLI  C11   C  CR6   0  -0.090  -5.4916   0.3983   0.6991
 NLI  C12   C  CR16  0  -0.289  -6.2065   1.5857   0.5734
 NLI  C13   C  CR16  0  -0.238  -7.5740   1.5526   0.3401
 NLI  C14   C  CR16  0  -0.254  -8.2341   0.3363   0.2305
 NLI  C15   C  CR16  0  -0.238  -7.5205  -0.8485   0.3485
 NLI  C16   C  CR16  0  -0.292  -6.1525  -0.8202   0.5805
 NLI  C17   C  CR6   0   0.494   0.3717  -0.3955  -0.1365
 NLI  O18   O  O     0  -0.494   0.8546   0.7206   0.0303
 NLI  N19   N  NR6   0  -0.515   1.1266  -1.5275  -0.1568
 NLI  C20   C  CH2   0  -0.471   2.5529  -1.3346  -0.0054
 NLI  C21   C  C     0   0.542   3.1718  -0.8454  -1.3131
 NLI  O22   O  O     0  -0.501   2.6239  -1.0574  -2.3865
 NLI  N23   N  NH1   0  -0.671   4.3395  -0.2286  -1.1590
 NLI  C24   C  CH2   0  -0.297   5.1294   0.2416  -2.2750
 NLI  C25   C  CH2   0  -0.184   6.0975   1.3069  -1.8112
 NLI  O26   O  O2    0  -0.403   6.9787   0.7211  -0.8548
 NLI  N27   N  NH1   0  -0.382   7.2443   1.5635   0.1976
 NLI  C28   C  C     0   0.593   6.5825   1.2328   1.3743
 NLI  N29   N  N     0  -0.712   5.5614   0.4626   1.3558
 NLI  N30   N  NH2   0  -0.833   7.1458   1.8247   2.4688
 NLI  HN29  H  H     0   0.341   5.1363   0.3883   2.2717
 NLI  H01   H  HCH3  0   0.260   1.9772  -4.1884   0.4030
 NLI  H01A  H  HCH3  0   0.271   0.8943  -4.8309  -0.8240
 NLI  H4    H  HCH3  0   0.257   2.2589  -3.8253  -1.2995
 NLI  H03   H  HCR6  0   0.254  -1.2038  -3.8007  -0.8603
 NLI  H6    H  HNH1  0   0.403  -1.3477   1.3729  -0.0675
 NLI  H07   H  HCH2  0   0.289  -3.5466   1.4375  -0.9318
 NLI  H07A  H  HCH2  0   0.276  -3.5514  -0.3126  -1.0616
 NLI  H12   H  HCR6  0   0.264  -5.7071   2.5424   0.6548
 NLI  H13   H  HCR6  0   0.263  -8.1238   2.4796   0.2449
 NLI  H14   H  HCR6  0   0.263  -9.3012   0.3118   0.0527
 NLI  H15   H  HCR6  0   0.263  -8.0287  -1.7997   0.2604
 NLI  H16   H  HCR6  0   0.263  -5.6108  -1.7530   0.6666
 NLI  H20   H  HCH2  0   0.295   2.7444  -0.6350   0.8073
 NLI  H20A  H  HCH2  0   0.321   3.0197  -2.2765   0.2759
 NLI  HN23  H  HNH1  0   0.448   4.7324  -0.0852  -0.2144
 NLI  H24   H  HCH2  0   0.242   5.6716  -0.5820  -2.7509
 NLI  H24A  H  HCH2  0   0.248   4.4854   0.6795  -3.0396
 NLI  H25   H  HCH2  0   0.239   6.6652   1.6870  -2.6661
 NLI  H25A  H  HCH2  0   0.235   5.5550   2.1424  -1.3641
 NLI  HN27  H  HNH1  0   0.398   8.2466   1.6725   0.2918
 NLI  HN30  H  HNH2  0   0.396   7.6761   2.6691   2.3178
 NLI  HN3A  H  HNH2  0   0.399   6.5722   1.8690   3.2953

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
 NLI  C01  C02   single    1.491  0.020  1.491
 NLI  C02  N19   single    1.386  0.020  1.386
 NLI  C02  C03   double    1.352  0.020  1.352
 NLI  C03  N04   single    1.361  0.020  1.361
 NLI  N04  C05   double    1.292  0.020  1.292
 NLI  C05  N06   single    1.352  0.020  1.352
 NLI  N06  C07   single    1.429  0.020  1.429
 NLI  C07  C08   single    1.524  0.020  1.524
 NLI  C08  F10   single    1.368  0.020  1.368
 NLI  C08  F09   single    1.362  0.020  1.362
 NLI  C11  C08   single    1.502  0.020  1.502
 NLI  C11  C16   aromatic  1.391  0.020  1.391
 NLI  C12  C11   aromatic  1.392  0.020  1.392
 NLI  C13  C12   aromatic  1.388  0.020  1.388
 NLI  C13  C14   aromatic  1.388  0.020  1.388
 NLI  C14  C15   aromatic  1.388  0.020  1.388
 NLI  C15  C16   aromatic  1.388  0.020  1.388
 NLI  C17  C05   single    1.473  0.020  1.473
 NLI  C17  O18   double    1.227  0.020  1.227
 NLI  N19  C17   single    1.361  0.020  1.361
 NLI  C20  N19   single    1.447  0.020  1.447
 NLI  C21  C20   single    1.527  0.020  1.527
 NLI  C21  N23   single    1.330  0.020  1.330
 NLI  O22  C21   double    1.224  0.020  1.224
 NLI  C24  N23   single    1.446  0.020  1.446
 NLI  C24  C25   single    1.512  0.020  1.512
 NLI  C25  O26   single    1.426  0.020  1.426
 NLI  O26  N27   single    1.374  0.020  1.374
 NLI  N27  C28   single    1.390  0.020  1.390
 NLI  C28  N29   double    1.279  0.020  1.279
 NLI  C28  N30   single    1.366  0.020  1.366
 NLI  N29  HN29  single    0.890  0.020  1.040
 NLI  C01  H01   single    0.970  0.020  1.090
 NLI  C01  H01A  single    0.970  0.020  1.090
 NLI  C01  H4    single    0.970  0.020  1.090
 NLI  C03  H03   single    0.930  0.020  1.080
 NLI  N06  H6    single    0.860  0.020  1.020
 NLI  C07  H07   single    0.970  0.020  1.090
 NLI  C07  H07A  single    0.970  0.020  1.090
 NLI  C12  H12   single    0.930  0.020  1.080
 NLI  C13  H13   single    0.930  0.020  1.080
 NLI  C14  H14   single    0.930  0.020  1.080
 NLI  C15  H15   single    0.930  0.020  1.080
 NLI  C16  H16   single    0.930  0.020  1.080
 NLI  C20  H20   single    0.970  0.020  1.090
 NLI  C20  H20A  single    0.970  0.020  1.090
 NLI  N23  HN23  single    0.860  0.020  1.020
 NLI  C24  H24   single    0.970  0.020  1.090
 NLI  C24  H24A  single    0.970  0.020  1.090
 NLI  C25  H25   single    0.970  0.020  1.090
 NLI  C25  H25A  single    0.970  0.020  1.090
 NLI  N27  HN27  single    0.890  0.020  1.040
 NLI  N30  HN30  single    0.890  0.020  1.040
 NLI  N30  HN3A  single    0.890  0.020  1.040

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
 NLI  H4    C01  H01A  107.78  3.000
 NLI  H4    C01  H01   107.76  3.000
 NLI  H01A  C01  H01   107.51  3.000
 NLI  H4    C01  C02   111.87  3.000
 NLI  H01A  C01  C02   109.25  3.000
 NLI  H01   C01  C02   112.47  3.000
 NLI  N19   C02  C03   117.52  3.000
 NLI  C03   C02  C01   122.72  3.000
 NLI  N19   C02  C01   119.75  3.000
 NLI  H03   C03  N04   116.46  3.000
 NLI  H03   C03  C02   119.62  3.000
 NLI  N04   C03  C02   123.92  3.000
 NLI  C05   N04  C03   118.20  3.000
 NLI  C17   C05  N06   114.60  3.000
 NLI  C17   C05  N04   123.07  3.000
 NLI  N06   C05  N04   122.29  3.000
 NLI  H6    N06  C07   119.10  3.000
 NLI  H6    N06  C05   117.29  3.000
 NLI  C07   N06  C05   123.57  3.000
 NLI  H07A  C07  H07   107.10  3.000
 NLI  H07A  C07  C08   108.83  3.000
 NLI  H07   C07  C08   107.97  3.000
 NLI  H07A  C07  N06   109.89  3.000
 NLI  H07   C07  N06   109.48  3.000
 NLI  C08   C07  N06   113.36  3.000
 NLI  C11   C08  F10   109.96  3.000
 NLI  C11   C08  F09   110.33  3.000
 NLI  F10   C08  F09   105.32  3.000
 NLI  C11   C08  C07   112.52  3.000
 NLI  F09   C08  C07   109.63  3.000
 NLI  F10   C08  C07   108.82  3.000
 NLI  C16   C11  C12   119.71  3.000
 NLI  C12   C11  C08   119.96  3.000
 NLI  C16   C11  C08   120.26  3.000
 NLI  H12   C12  C13   119.24  3.000
 NLI  H12   C12  C11   120.69  3.000
 NLI  C13   C12  C11   120.07  3.000
 NLI  H13   C13  C14   120.14  3.000
 NLI  H13   C13  C12   119.68  3.000
 NLI  C14   C13  C12   120.18  3.000
 NLI  H14   C14  C15   120.10  3.000
 NLI  H14   C14  C13   120.12  3.000
 NLI  C15   C14  C13   119.78  3.000
 NLI  H15   C15  C16   119.64  3.000
 NLI  H15   C15  C14   120.13  3.000
 NLI  C16   C15  C14   120.23  3.000
 NLI  H16   C16  C15   119.29  3.000
 NLI  H16   C16  C11   120.69  3.000
 NLI  C15   C16  C11   120.02  3.000
 NLI  N19   C17  O18   122.69  3.000
 NLI  N19   C17  C05   114.76  3.000
 NLI  O18   C17  C05   122.54  3.000
 NLI  C20   N19  C17   115.74  3.000
 NLI  C20   N19  C02   121.60  3.000
 NLI  C17   N19  C02   122.31  3.000
 NLI  H20A  C20  H20   106.71  3.000
 NLI  H20A  C20  C21   108.95  3.000
 NLI  H20   C20  C21   111.22  3.000
 NLI  H20A  C20  N19   109.54  3.000
 NLI  H20   C20  N19   109.69  3.000
 NLI  C21   C20  N19   110.64  3.000
 NLI  N23   C21  O22   125.12  3.000
 NLI  O22   C21  C20   120.94  3.000
 NLI  N23   C21  C20   113.91  3.000
 NLI  HN23  N23  C24   116.93  3.000
 NLI  HN23  N23  C21   120.29  3.000
 NLI  C24   N23  C21   122.76  3.000
 NLI  H24A  C24  H24   106.82  3.000
 NLI  H24A  C24  C25   108.06  3.000
 NLI  H24   C24  C25   110.25  3.000
 NLI  H24A  C24  N23   110.42  3.000
 NLI  H24   C24  N23   111.19  3.000
 NLI  C25   C24  N23   110.00  3.000
 NLI  H25A  C25  H25   108.17  3.000
 NLI  H25A  C25  O26   110.29  3.000
 NLI  H25   C25  O26   110.24  3.000
 NLI  H25A  C25  C24   110.27  3.000
 NLI  H25   C25  C24   109.71  3.000
 NLI  O26   C25  C24   108.16  3.000
 NLI  N27   O26  C25   112.40  3.000
 NLI  HN27  N27  C28   114.72  3.000
 NLI  HN27  N27  O26   109.18  3.000
 NLI  C28   N27  O26   114.24  3.000
 NLI  N30   C28  N29   127.00  3.000
 NLI  N30   C28  N27   112.27  3.000
 NLI  N29   C28  N27   120.74  3.000
 NLI  HN29  N29  C28   111.49  3.000
 NLI  HN3A  N30  HN30  112.68  3.000
 NLI  HN3A  N30  C28   116.21  3.000
 NLI  HN30  N30  C28   117.37  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
 NLI  CONST_01  C14   C15  C16  C11     0.00   0.0  0
 NLI  CONST_02  C14   C13  C12  C11     0.00   0.0  0
 NLI  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 NLI  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 NLI  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 NLI  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 NLI  CONST_07  C05   C17  N19  C02     0.00   0.0  0
 NLI  CONST_08  C17   C05  N04  C03     0.00   0.0  0
 NLI  CONST_09  C15   C16  C11  C08   180.00   0.0  0
 NLI  CONST_10  C13   C12  C11  C08   180.00   0.0  0
 NLI  CONST_11  O18   C17  N19  C02   180.00   0.0  0
 NLI  CONST_12  N06   C05  N04  C03   180.00   0.0  0
 NLI  CONST_13  C20   N19  C17  C05   180.00   0.0  0
 NLI  CONST_14  H15   C15  C16  C11   180.00   0.0  0
 NLI  CONST_15  H13   C13  C12  C11   180.00   0.0  0
 NLI  CONST_16  H16   C16  C11  C12   180.00   0.0  0
 NLI  CONST_17  H14   C14  C13  C12   180.00   0.0  0
 NLI  CONST_18  H12   C12  C13  C14   180.00   0.0  0
 NLI  CONST_19  C07   N06  C05  N04     0.00   0.0  0
 NLI  CONST_20  C17   C05  N06  C07   180.00   0.0  0
 NLI  CONST_21  C20   N19  C17  O18     0.00   0.0  0
 NLI  CONST_22  H6    N06  C05  N04   180.00   0.0  0
 NLI  CONST_23  C24   N23  C21  C20   180.00   0.0  0
 NLI  CONST_24  C24   N23  C21  O22     0.00   0.0  0
 NLI  CONST_27  HN23  N23  C21  C20     0.00   0.0  0
 NLI  CONST_28  HN29  N29  C28  N27   180.00   0.0  0
 NLI  Var_01    C21   C20  N19  C02    95.76  30.0  2
 NLI  Var_02    C16   C11  C08  C07    91.23  30.0  2
 NLI  Var_03    H01   C01  C02  C03  -116.63  30.0  3
 NLI  Var_04    C08   C07  N06  C05    93.55  30.0  3
 NLI  Var_05    C11   C08  C07  N06  -177.95  30.0  3
 NLI  Var_06    N23   C21  C20  N19   158.62  30.0  2
 NLI  Var_07    C25   C24  N23  C21   159.35  30.0  2
 NLI  Var_08    O26   C25  C24  N23    61.92  30.0  3
 NLI  Var_09    C28   N27  O26  C25   104.76  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
 NLI  plan-1  C01   0.020
 NLI  plan-1  C02   0.020
 NLI  plan-1  C03   0.020
 NLI  plan-1  N04   0.020
 NLI  plan-1  C05   0.020
 NLI  plan-1  N06   0.020
 NLI  plan-1  C07   0.020
 NLI  plan-1  C17   0.020
 NLI  plan-1  O18   0.020
 NLI  plan-1  N19   0.020
 NLI  plan-1  C20   0.020
 NLI  plan-1  H03   0.020
 NLI  plan-1  H6    0.020
 NLI  plan-2  C08   0.020
 NLI  plan-2  C11   0.020
 NLI  plan-2  C12   0.020
 NLI  plan-2  C13   0.020
 NLI  plan-2  C14   0.020
 NLI  plan-2  C15   0.020
 NLI  plan-2  C16   0.020
 NLI  plan-2  H12   0.020
 NLI  plan-2  H13   0.020
 NLI  plan-2  H14   0.020
 NLI  plan-2  H15   0.020
 NLI  plan-2  H16   0.020
 NLI  plan-3  C20   0.020
 NLI  plan-3  C21   0.020
 NLI  plan-3  O22   0.020
 NLI  plan-3  N23   0.020
 NLI  plan-3  C24   0.020
 NLI  plan-3  HN23  0.020
 NLI  plan-4  O26   0.020
 NLI  plan-4  N27   0.020
 NLI  plan-4  C28   0.020
 NLI  plan-4  N29   0.020
 NLI  plan-4  N30   0.020
 NLI  plan-4  HN29  0.020
 NLI  plan-4  HN27  0.020
 NLI  plan-4  HN30  0.020
 NLI  plan-4  HN3A  0.020

