# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 21:41:39 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 6-(ethylcarbamoylamino)-4-[(4-methoxyphenyl)amino]-~{N}-pyridin-3-yl-pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)Nc1cc(Nc2ccc(OC)cc2)c(cn1)C(=O)Nc3cccnc3
#
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
 D0K  D0K  6-(ethylcarbamoylamino)-4-[(4-methoxyphenyl)amino]-~{N}-pyridin-3-yl-pyridine-3-carboxamide  ligand  52  30  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D0K
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
 D0K  CBD  C  CH3   0  -0.438    5.9160   1.9079  -0.6102
 D0K  OBC  O  O2    0  -0.470    4.7321   1.9934  -1.3771
 D0K  CAZ  C  CR6   0   0.397    3.5536   2.0576  -0.7345
 D0K  CBA  C  CR16  0  -0.372    3.4147   2.1501   0.6476
 D0K  CBB  C  CR16  0  -0.245    2.1471   2.1662   1.2158
 D0K  CAY  C  CR16  0  -0.345    2.4104   2.0194  -1.5372
 D0K  CAX  C  CR16  0  -0.235    1.1572   2.0451  -0.9600
 D0K  CAW  C  CR6   0   0.174    1.0121   2.0997   0.4261
 D0K  NAK  N  NH1   0  -0.756   -0.2818   2.0445   1.0168
 D0K  CAJ  C  CR6   0   0.458   -1.1086   0.9862   0.7469
 D0K  CAI  C  CR16  0  -0.525   -2.4802   1.1691   0.6051
 D0K  CAH  C  CR6   0   0.543   -3.2936   0.0774   0.3032
 D0K  NAL  N  NH1   0  -0.776   -4.6425   0.3157   0.1134
 D0K  CAM  C  C     0   0.722   -5.6805  -0.6012   0.1762
 D0K  OAO  O  O     0  -0.504   -5.5571  -1.7432   0.5803
 D0K  NAN  N  NH1   0  -0.675   -6.8607  -0.0757  -0.2238
 D0K  CAP  C  CH2   0  -0.260   -8.0801  -0.8571  -0.2507
 D0K  CAQ  C  CH3   0  -0.692   -9.2884   0.0559  -0.3447
 D0K  NAG  N  N     0  -0.448   -2.8243  -1.1500   0.1257
 D0K  CAF  C  CR16  0  -0.071   -1.5199  -1.3246   0.2951
 D0K  CAE  C  CR6   0  -0.209   -0.6158  -0.3286   0.6110
 D0K  CAC  C  C     0   0.476    0.7835  -0.7040   0.9851
 D0K  OAD  O  O     0  -0.438    1.1460  -0.6982   2.1459
 D0K  NAB  N  NH1   0  -0.708    1.5610  -1.0801  -0.0604
 D0K  CAA  C  CR6   0   0.296    2.9233  -1.3748  -0.0536
 D0K  CAR  C  CR16  0  -0.202    3.6691  -1.6928   1.0780
 D0K  CAS  C  CR16  0  -0.315    5.0198  -1.9613   0.9178
 D0K  CAT  C  CR16  0  -0.088    5.5823  -1.9151  -0.3464
 D0K  NAU  N  N     0  -0.387    4.8721  -1.6217  -1.4310
 D0K  CAV  C  CR16  0  -0.133    3.5872  -1.3577  -1.2838
 D0K  H1   H  HCH3  0   0.229    6.0767   2.8030  -0.0040
 D0K  H2   H  HCH3  0   0.228    5.9138   1.0318   0.0434
 D0K  H3   H  HCH3  0   0.259    6.7368   1.8138  -1.3168
 D0K  H4   H  HCR6  0   0.277    4.2746   2.1819   1.3019
 D0K  H5   H  HCR6  0   0.261    2.0470   2.2050   2.2923
 D0K  H6   H  HCR6  0   0.267    2.5144   1.9612  -2.6136
 D0K  H7   H  HCR6  0   0.268    0.2801   2.0026  -1.5946
 D0K  H8   H  HNH1  0   0.396   -0.7525   2.9337   1.1079
 D0K  H9   H  HCR6  0   0.280   -2.9074   2.1601   0.7037
 D0K  H10  H  HNH1  0   0.413   -4.9000   1.2868   0.0277
 D0K  H11  H  HNH1  0   0.396   -6.8618   0.7920  -0.7378
 D0K  H12  H  HCH2  0   0.228   -8.0766  -1.5587  -1.0908
 D0K  H13  H  HCH2  0   0.238   -8.1359  -1.4533   0.6599
 D0K  H14  H  HCH3  0   0.231   -9.2623   0.6603  -1.2529
 D0K  H15  H  HCH3  0   0.242  -10.2031  -0.5350  -0.3693
 D0K  H16  H  HCH3  0   0.233   -9.3420   0.7281   0.5118
 D0K  H17  H  HCR6  0   0.267   -1.1631  -2.3435   0.1768
 D0K  H18  H  HNH1  0   0.419    1.1524  -0.9546  -0.9748
 D0K  H19  H  HCR6  0   0.289    3.2221  -1.7293   2.0577
 D0K  H20  H  HCR6  0   0.272    5.6291  -2.2095   1.7762
 D0K  H21  H  HCR6  0   0.263    6.6361  -2.1219  -0.4924
 D0K  H22  H  HCR6  0   0.268    3.0330  -1.1157  -2.1867

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
 D0K  CBD  OBC  single    1.413  0.020  1.413
 D0K  OBC  CAZ  single    1.344  0.020  1.344
 D0K  CAQ  CAP  single    1.517  0.020  1.517
 D0K  CAP  NAN  single    1.448  0.020  1.448
 D0K  CAZ  CAY  aromatic  1.397  0.020  1.397
 D0K  CAZ  CBA  aromatic  1.392  0.020  1.392
 D0K  NAN  CAM  single    1.352  0.020  1.352
 D0K  CAY  CAX  aromatic  1.380  0.020  1.380
 D0K  OAO  CAM  double    1.218  0.020  1.218
 D0K  CBA  CBB  aromatic  1.389  0.020  1.389
 D0K  CAM  NAL  single    1.386  0.020  1.386
 D0K  CAX  CAW  aromatic  1.395  0.020  1.395
 D0K  CBB  CAW  aromatic  1.384  0.020  1.384
 D0K  NAL  CAH  single    1.383  0.020  1.383
 D0K  CAW  NAK  single    1.423  0.020  1.423
 D0K  CAI  CAH  aromatic  1.395  0.020  1.395
 D0K  CAI  CAJ  aromatic  1.391  0.020  1.391
 D0K  CAH  NAG  aromatic  1.326  0.020  1.326
 D0K  NAK  CAJ  single    1.370  0.020  1.370
 D0K  CAJ  CAE  aromatic  1.411  0.020  1.411
 D0K  NAG  CAF  aromatic  1.327  0.020  1.327
 D0K  CAE  CAF  aromatic  1.382  0.020  1.382
 D0K  CAE  CAC  single    1.496  0.020  1.496
 D0K  OAD  CAC  double    1.216  0.020  1.216
 D0K  CAC  NAB  single    1.356  0.020  1.356
 D0K  NAB  CAA  single    1.394  0.020  1.394
 D0K  CAA  CAR  aromatic  1.392  0.020  1.392
 D0K  CAA  CAV  aromatic  1.398  0.020  1.398
 D0K  CAR  CAS  aromatic  1.386  0.020  1.386
 D0K  CAV  NAU  aromatic  1.320  0.020  1.320
 D0K  CAS  CAT  aromatic  1.385  0.020  1.385
 D0K  NAU  CAT  aromatic  1.329  0.020  1.329
 D0K  CBD  H1   single    0.970  0.020  1.090
 D0K  CBD  H2   single    0.970  0.020  1.090
 D0K  CBD  H3   single    0.970  0.020  1.090
 D0K  CBA  H4   single    0.930  0.020  1.080
 D0K  CBB  H5   single    0.930  0.020  1.080
 D0K  CAY  H6   single    0.930  0.020  1.080
 D0K  CAX  H7   single    0.930  0.020  1.080
 D0K  NAK  H8   single    0.890  0.020  1.040
 D0K  CAI  H9   single    0.930  0.020  1.080
 D0K  NAL  H10  single    0.860  0.020  1.020
 D0K  NAN  H11  single    0.860  0.020  1.020
 D0K  CAP  H12  single    0.970  0.020  1.090
 D0K  CAP  H13  single    0.970  0.020  1.090
 D0K  CAQ  H14  single    0.970  0.020  1.090
 D0K  CAQ  H15  single    0.970  0.020  1.090
 D0K  CAQ  H16  single    0.970  0.020  1.090
 D0K  CAF  H17  single    0.930  0.020  1.080
 D0K  NAB  H18  single    0.860  0.020  1.020
 D0K  CAR  H19  single    0.930  0.020  1.080
 D0K  CAS  H20  single    0.930  0.020  1.080
 D0K  CAT  H21  single    0.930  0.020  1.080
 D0K  CAV  H22  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
 D0K  H3   CBD  H2   108.72  3.000
 D0K  H3   CBD  H1   108.69  3.000
 D0K  H2   CBD  H1   108.97  3.000
 D0K  H3   CBD  OBC  106.56  3.000
 D0K  H2   CBD  OBC  111.79  3.000
 D0K  H1   CBD  OBC  112.00  3.000
 D0K  CAZ  OBC  CBD  118.56  3.000
 D0K  CAY  CAZ  CBA  119.37  3.000
 D0K  CBA  CAZ  OBC  124.43  3.000
 D0K  CAY  CAZ  OBC  116.19  3.000
 D0K  H4   CBA  CBB  118.55  3.000
 D0K  H4   CBA  CAZ  121.56  3.000
 D0K  CBB  CBA  CAZ  119.86  3.000
 D0K  H5   CBB  CAW  119.57  3.000
 D0K  H5   CBB  CBA  119.47  3.000
 D0K  CAW  CBB  CBA  120.95  3.000
 D0K  H6   CAY  CAX  120.26  3.000
 D0K  H6   CAY  CAZ  119.59  3.000
 D0K  CAX  CAY  CAZ  120.14  3.000
 D0K  H7   CAX  CAW  119.96  3.000
 D0K  H7   CAX  CAY  119.30  3.000
 D0K  CAW  CAX  CAY  120.73  3.000
 D0K  NAK  CAW  CAX  120.36  3.000
 D0K  NAK  CAW  CBB  120.70  3.000
 D0K  CAX  CAW  CBB  118.91  3.000
 D0K  H8   NAK  CAJ  114.62  3.000
 D0K  H8   NAK  CAW  115.26  3.000
 D0K  CAJ  NAK  CAW  119.80  3.000
 D0K  CAE  CAJ  CAI  117.21  3.000
 D0K  CAE  CAJ  NAK  121.88  3.000
 D0K  CAI  CAJ  NAK  120.91  3.000
 D0K  H9   CAI  CAH  120.37  3.000
 D0K  H9   CAI  CAJ  119.98  3.000
 D0K  CAH  CAI  CAJ  119.62  3.000
 D0K  NAG  CAH  NAL  119.10  3.000
 D0K  NAG  CAH  CAI  123.18  3.000
 D0K  NAL  CAH  CAI  117.63  3.000
 D0K  H10  NAL  CAM  116.72  3.000
 D0K  H10  NAL  CAH  115.26  3.000
 D0K  CAM  NAL  CAH  127.60  3.000
 D0K  NAN  CAM  OAO  123.44  3.000
 D0K  OAO  CAM  NAL  124.01  3.000
 D0K  NAN  CAM  NAL  112.52  3.000
 D0K  H11  NAN  CAP  116.98  3.000
 D0K  H11  NAN  CAM  119.08  3.000
 D0K  CAP  NAN  CAM  122.04  3.000
 D0K  H13  CAP  H12  106.91  3.000
 D0K  H13  CAP  CAQ  109.88  3.000
 D0K  H12  CAP  CAQ  109.92  3.000
 D0K  H13  CAP  NAN  108.83  3.000
 D0K  H12  CAP  NAN  110.94  3.000
 D0K  CAQ  CAP  NAN  110.30  3.000
 D0K  H16  CAQ  H15  108.12  3.000
 D0K  H16  CAQ  H14  108.27  3.000
 D0K  H15  CAQ  H14  107.57  3.000
 D0K  H16  CAQ  CAP  111.19  3.000
 D0K  H15  CAQ  CAP  110.10  3.000
 D0K  H14  CAQ  CAP  111.45  3.000
 D0K  CAF  NAG  CAH  116.91  3.000
 D0K  H17  CAF  CAE  119.09  3.000
 D0K  H17  CAF  NAG  115.63  3.000
 D0K  CAE  CAF  NAG  125.28  3.000
 D0K  CAC  CAE  CAF  119.22  3.000
 D0K  CAC  CAE  CAJ  122.44  3.000
 D0K  CAF  CAE  CAJ  117.73  3.000
 D0K  NAB  CAC  OAD  124.49  3.000
 D0K  NAB  CAC  CAE  114.39  3.000
 D0K  OAD  CAC  CAE  121.08  3.000
 D0K  H18  NAB  CAA  115.24  3.000
 D0K  H18  NAB  CAC  115.58  3.000
 D0K  CAA  NAB  CAC  127.97  3.000
 D0K  CAV  CAA  CAR  117.62  3.000
 D0K  CAV  CAA  NAB  117.21  3.000
 D0K  CAR  CAA  NAB  125.16  3.000
 D0K  H19  CAR  CAS  120.18  3.000
 D0K  H19  CAR  CAA  121.64  3.000
 D0K  CAS  CAR  CAA  118.18  3.000
 D0K  H20  CAS  CAT  120.23  3.000
 D0K  H20  CAS  CAR  120.11  3.000
 D0K  CAT  CAS  CAR  119.66  3.000
 D0K  H21  CAT  NAU  116.86  3.000
 D0K  H21  CAT  CAS  120.78  3.000
 D0K  NAU  CAT  CAS  122.36  3.000
 D0K  CAV  NAU  CAT  118.25  3.000
 D0K  H22  CAV  NAU  116.64  3.000
 D0K  H22  CAV  CAA  119.45  3.000
 D0K  NAU  CAV  CAA  123.91  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
 D0K  CONST_01  CAW  CAX  CAY  CAZ     0.00   0.0  0
 D0K  CONST_02  CAW  CBB  CBA  CAZ     0.00   0.0  0
 D0K  CONST_03  CAX  CAY  CAZ  CBA     0.00   0.0  0
 D0K  CONST_04  CAX  CAW  CBB  CBA     0.00   0.0  0
 D0K  CONST_05  CAY  CAZ  CBA  CBB     0.00   0.0  0
 D0K  CONST_06  CAY  CAX  CAW  CBB     0.00   0.0  0
 D0K  CONST_07  NAG  CAH  CAI  CAJ     0.00   0.0  0
 D0K  CONST_08  NAG  CAF  CAE  CAJ     0.00   0.0  0
 D0K  CONST_09  CAF  NAG  CAH  CAI     0.00   0.0  0
 D0K  CONST_10  CAF  CAE  CAJ  CAI     0.00   0.0  0
 D0K  CONST_11  CAE  CAJ  CAI  CAH     0.00   0.0  0
 D0K  CONST_12  CAE  CAF  NAG  CAH     0.00   0.0  0
 D0K  CONST_13  CAT  CAS  CAR  CAA     0.00   0.0  0
 D0K  CONST_14  CAT  NAU  CAV  CAA     0.00   0.0  0
 D0K  CONST_15  NAU  CAV  CAA  CAR     0.00   0.0  0
 D0K  CONST_16  NAU  CAT  CAS  CAR     0.00   0.0  0
 D0K  CONST_17  CAV  CAA  CAR  CAS     0.00   0.0  0
 D0K  CONST_18  CAV  NAU  CAT  CAS     0.00   0.0  0
 D0K  CONST_19  CAX  CAY  CAZ  OBC   180.00   0.0  0
 D0K  CONST_20  CBB  CBA  CAZ  OBC   180.00   0.0  0
 D0K  CONST_21  NAK  CAW  CBB  CBA   180.00   0.0  0
 D0K  CONST_22  NAK  CAW  CAX  CAY   180.00   0.0  0
 D0K  CONST_23  CAH  CAI  CAJ  NAK   180.00   0.0  0
 D0K  CONST_24  CAF  CAE  CAJ  NAK   180.00   0.0  0
 D0K  CONST_25  NAL  CAH  CAI  CAJ   180.00   0.0  0
 D0K  CONST_26  CAC  CAE  CAJ  CAI   180.00   0.0  0
 D0K  CONST_27  CAF  NAG  CAH  NAL   180.00   0.0  0
 D0K  CONST_28  CAC  CAE  CAF  NAG   180.00   0.0  0
 D0K  CONST_29  CAS  CAR  CAA  NAB   180.00   0.0  0
 D0K  CONST_30  NAU  CAV  CAA  NAB   180.00   0.0  0
 D0K  CONST_31  H7   CAX  CAY  CAZ   180.00   0.0  0
 D0K  CONST_32  H5   CBB  CBA  CAZ   180.00   0.0  0
 D0K  CONST_33  H6   CAY  CAZ  CBA   180.00   0.0  0
 D0K  CONST_34  H4   CBA  CAZ  CAY   180.00   0.0  0
 D0K  CONST_35  H17  CAF  CAE  CAJ   180.00   0.0  0
 D0K  CONST_36  H9   CAI  CAH  NAG   180.00   0.0  0
 D0K  CONST_37  H20  CAS  CAR  CAA   180.00   0.0  0
 D0K  CONST_38  H22  CAV  CAA  CAR   180.00   0.0  0
 D0K  CONST_39  H21  CAT  CAS  CAR   180.00   0.0  0
 D0K  CONST_40  H19  CAR  CAS  CAT   180.00   0.0  0
 D0K  CONST_41  CAA  NAB  CAC  CAE   180.00   0.0  0
 D0K  CONST_46  H10  NAL  CAH  CAI     0.00   0.0  0
 D0K  CONST_47  H18  NAB  CAA  CAR   180.00   0.0  0
 D0K  CONST_48  OAO  CAM  NAL  CAH     0.00   0.0  0
 D0K  CONST_49  CAA  NAB  CAC  OAD     0.00   0.0  0
 D0K  CONST_50  NAN  CAM  NAL  CAH   180.00   0.0  0
 D0K  CONST_51  CAP  NAN  CAM  OAO     0.00   0.0  0
 D0K  CONST_52  CAP  NAN  CAM  NAL   180.00   0.0  0
 D0K  CONST_53  H11  NAN  CAM  OAO   180.00   0.0  0
 D0K  Var_01    CAJ  NAK  CAW  CBB  -121.58  30.0  2
 D0K  Var_02    CAI  CAJ  NAK  CAW  -142.88  30.0  2
 D0K  Var_03    CAY  CAZ  OBC  CBD  -174.44  30.0  2
 D0K  Var_04    OAD  CAC  CAE  CAJ    68.14  30.0  2
 D0K  Var_05    H1   CBD  OBC  CAZ   -64.19  30.0  3
 D0K  Var_06    CAQ  CAP  NAN  CAM   163.68  30.0  2
 D0K  Var_07    H14  CAQ  CAP  NAN    60.46  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
 D0K  plan-1  OBC  0.020
 D0K  plan-1  CAZ  0.020
 D0K  plan-1  CBA  0.020
 D0K  plan-1  CBB  0.020
 D0K  plan-1  CAY  0.020
 D0K  plan-1  CAX  0.020
 D0K  plan-1  CAW  0.020
 D0K  plan-1  NAK  0.020
 D0K  plan-1  H4   0.020
 D0K  plan-1  H5   0.020
 D0K  plan-1  H6   0.020
 D0K  plan-1  H7   0.020
 D0K  plan-2  NAK  0.020
 D0K  plan-2  CAJ  0.020
 D0K  plan-2  CAI  0.020
 D0K  plan-2  CAH  0.020
 D0K  plan-2  NAL  0.020
 D0K  plan-2  NAG  0.020
 D0K  plan-2  CAF  0.020
 D0K  plan-2  CAE  0.020
 D0K  plan-2  CAC  0.020
 D0K  plan-2  H9   0.020
 D0K  plan-2  H17  0.020
 D0K  plan-3  NAB  0.020
 D0K  plan-3  CAA  0.020
 D0K  plan-3  CAR  0.020
 D0K  plan-3  CAS  0.020
 D0K  plan-3  CAT  0.020
 D0K  plan-3  NAU  0.020
 D0K  plan-3  CAV  0.020
 D0K  plan-3  H19  0.020
 D0K  plan-3  H20  0.020
 D0K  plan-3  H21  0.020
 D0K  plan-3  H22  0.020
 D0K  plan-4  CAH  0.020
 D0K  plan-4  NAL  0.020
 D0K  plan-4  CAM  0.020
 D0K  plan-4  OAO  0.020
 D0K  plan-4  NAN  0.020
 D0K  plan-4  CAP  0.020
 D0K  plan-4  H10  0.020
 D0K  plan-4  H11  0.020
 D0K  plan-5  CAE  0.020
 D0K  plan-5  CAC  0.020
 D0K  plan-5  OAD  0.020
 D0K  plan-5  NAB  0.020
 D0K  plan-5  CAA  0.020
 D0K  plan-5  H18  0.020

