# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 19:36:03 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 4-(benzylamino)-6-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cnc(Nc2ccc3NC(=O)Cc3c2)cc1NCc4ccccc4
#
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
 9YY  9YY  4-(benzylamino)-6-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]pyridine-3-carboxamide  ligand  47  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9YY
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
 9YY  C13  C  CR6   0   0.077   4.9555  -1.4675  -0.1721
 9YY  C18  C  CR16  0  -0.307   5.7010  -2.0177  -1.2082
 9YY  C17  C  CR16  0  -0.240   7.0684  -2.2240  -1.0656
 9YY  C16  C  CR16  0  -0.265   7.7042  -1.8746   0.1168
 9YY  C15  C  CR16  0  -0.241   6.9663  -1.3215   1.1574
 9YY  C19  C  CR6   0   0.372  -2.9076  -0.2044  -0.0000
 9YY  C20  C  CR16  0  -0.448  -3.7212  -1.3508  -0.0498
 9YY  C21  C  CR56  0   0.023  -5.0848  -1.2261   0.0544
 9YY  C22  C  CR56  0   0.393  -5.6685   0.0303   0.2075
 9YY  C23  C  CR16  0  -0.294  -4.8952   1.1691   0.2564
 9YY  C24  C  CR16  0  -0.333  -3.5098   1.0469   0.1516
 9YY  C12  C  CH2   0  -0.335   3.4762  -1.2383  -0.3240
 9YY  C1   C  CR6   0  -0.255   1.7121   2.0874  -0.0437
 9YY  C2   C  CR16  0  -0.066   0.3936   2.5086  -0.0084
 9YY  N3   N  N     0  -0.498  -0.6777   1.7316  -0.0302
 9YY  C4   C  CR6   0   0.573  -0.4675   0.4158  -0.0912
 9YY  C5   C  CR16  0  -0.562   0.8107  -0.1458  -0.1632
 9YY  C6   C  CR6   0   0.506   1.9366   0.6773  -0.1522
 9YY  N7   N  NH1   0  -0.696   3.1802   0.1701  -0.2111
 9YY  C9   C  C     0   0.517   2.8311   3.0530  -0.0034
 9YY  N10  N  NH2   0  -0.813   2.5666   4.2774   0.4861
 9YY  O11  O  O     0  -0.509   3.9583   2.7633  -0.4106
 9YY  C14  C  CR16  0  -0.285   5.6017  -1.1206   1.0136
 9YY  C25  C  CH2   0  -0.621  -6.1761  -2.2484   0.0381
 9YY  C26  C  CR5   0   0.511  -7.4408  -1.4157   0.1956
 9YY  N27  N  NR15  0  -0.740  -7.0518  -0.1156   0.2874
 9YY  O28  O  O     0  -0.464  -8.5849  -1.8213   0.2345
 9YY  H1   H  HCR6  0   0.255   5.2103  -2.2895  -2.1353
 9YY  H2   H  HCR6  0   0.257   7.6344  -2.6539  -1.8819
 9YY  H3   H  HCR6  0   0.257   8.7690  -2.0320   0.2298
 9YY  H4   H  HCR6  0   0.258   7.4551  -1.0472   2.0834
 9YY  H5   H  HCR6  0   0.266  -3.2728  -2.3312  -0.1712
 9YY  H6   H  HCR6  0   0.265  -5.3368   2.1499   0.3760
 9YY  H7   H  HCR6  0   0.288  -2.8980   1.9328   0.1876
 9YY  H8   H  HCH2  0   0.250   3.1348  -1.6468  -1.2826
 9YY  H9   H  HCH2  0   0.253   2.9416  -1.7877   0.4575
 9YY  H10  H  HCR6  0   0.256   0.1736   3.5711   0.0159
 9YY  H11  H  HCR6  0   0.284   0.9117  -1.2201  -0.2377
 9YY  H12  H  HNH1  0   0.405   3.9228   0.8365  -0.3695
 9YY  H13  H  HNH1  0   0.413  -1.2900  -1.4059  -0.1801
 9YY  H14  H  HNH2  0   0.410   1.7392   4.4796   1.0186
 9YY  H15  H  HNH2  0   0.404   3.3205   4.9408   0.5594
 9YY  H16  H  HCR6  0   0.255   5.0350  -0.6924   1.8321
 9YY  H17  H  HCH2  0   0.303  -6.2177  -2.8226  -0.8905
 9YY  H18  H  HCH2  0   0.303  -6.1026  -2.9698   0.8554
 9YY  H19  H  HNR5  0   0.410  -7.7016   0.6467   0.4065
 9YY  N8   N  NH1   0  -0.790  -1.5362  -0.4316  -0.1021

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
 9YY  N3   C2   aromatic  1.324  0.020  1.324
 9YY  N3   C4   aromatic  1.334  0.020  1.334
 9YY  C2   C1   aromatic  1.385  0.020  1.385
 9YY  N10  C9   single    1.345  0.020  1.345
 9YY  N8   C4   single    1.364  0.020  1.364
 9YY  N8   C19  single    1.394  0.020  1.394
 9YY  C4   C5   aromatic  1.398  0.020  1.398
 9YY  C9   C1   single    1.479  0.020  1.479
 9YY  C9   O11  double    1.233  0.020  1.233
 9YY  C1   C6   aromatic  1.432  0.020  1.432
 9YY  C24  C19  aromatic  1.397  0.020  1.397
 9YY  C24  C23  aromatic  1.395  0.020  1.395
 9YY  C19  C20  aromatic  1.407  0.020  1.407
 9YY  C5   C6   aromatic  1.395  0.020  1.395
 9YY  C6   N7   single    1.344  0.020  1.344
 9YY  C23  C22  aromatic  1.377  0.020  1.377
 9YY  C20  C21  aromatic  1.373  0.020  1.373
 9YY  N7   C12  single    1.444  0.020  1.444
 9YY  C22  C21  aromatic  1.394  0.020  1.394
 9YY  C22  N27  single    1.393  0.020  1.393
 9YY  C21  C25  single    1.495  0.020  1.495
 9YY  C12  C13  single    1.505  0.020  1.505
 9YY  N27  C26  single    1.360  0.020  1.360
 9YY  C18  C13  aromatic  1.390  0.020  1.390
 9YY  C18  C17  aromatic  1.390  0.020  1.390
 9YY  C25  C26  single    1.522  0.020  1.522
 9YY  C13  C14  aromatic  1.394  0.020  1.394
 9YY  C17  C16  aromatic  1.387  0.020  1.387
 9YY  C26  O28  double    1.214  0.020  1.214
 9YY  C14  C15  aromatic  1.387  0.020  1.387
 9YY  C16  C15  aromatic  1.390  0.020  1.390
 9YY  C18  H1   single    0.930  0.020  1.080
 9YY  C17  H2   single    0.930  0.020  1.080
 9YY  C16  H3   single    0.930  0.020  1.080
 9YY  C15  H4   single    0.930  0.020  1.080
 9YY  C20  H5   single    0.930  0.020  1.080
 9YY  C23  H6   single    0.930  0.020  1.080
 9YY  C24  H7   single    0.930  0.020  1.080
 9YY  C12  H8   single    0.970  0.020  1.090
 9YY  C12  H9   single    0.970  0.020  1.090
 9YY  C2   H10  single    0.930  0.020  1.080
 9YY  C5   H11  single    0.930  0.020  1.080
 9YY  N7   H12  single    0.860  0.020  1.020
 9YY  N8   H13  single    0.860  0.020  1.020
 9YY  N10  H14  single    0.860  0.020  1.020
 9YY  N10  H15  single    0.860  0.020  1.020
 9YY  C14  H16  single    0.930  0.020  1.080
 9YY  C25  H17  single    0.970  0.020  1.090
 9YY  C25  H18  single    0.970  0.020  1.090
 9YY  N27  H19  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
 9YY  C14  C13  C12  120.24  3.000
 9YY  C14  C13  C18  118.94  3.000
 9YY  C12  C13  C18  120.82  3.000
 9YY  H1   C18  C17  119.73  3.000
 9YY  H1   C18  C13  119.62  3.000
 9YY  C17  C18  C13  120.65  3.000
 9YY  H2   C17  C16  120.21  3.000
 9YY  H2   C17  C18  119.73  3.000
 9YY  C16  C17  C18  120.05  3.000
 9YY  H3   C16  C15  120.12  3.000
 9YY  H3   C16  C17  120.22  3.000
 9YY  C15  C16  C17  119.66  3.000
 9YY  H4   C15  C14  119.76  3.000
 9YY  H4   C15  C16  120.09  3.000
 9YY  C14  C15  C16  120.15  3.000
 9YY  N8   C19  C24  125.31  3.000
 9YY  C24  C19  C20  118.99  3.000
 9YY  N8   C19  C20  115.70  3.000
 9YY  H5   C20  C21  120.07  3.000
 9YY  H5   C20  C19  120.09  3.000
 9YY  C21  C20  C19  119.84  3.000
 9YY  C25  C21  C22  108.17  3.000
 9YY  C25  C21  C20  131.43  3.000
 9YY  C22  C21  C20  120.40  3.000
 9YY  N27  C22  C23  129.93  3.000
 9YY  N27  C22  C21  109.13  3.000
 9YY  C23  C22  C21  120.94  3.000
 9YY  H6   C23  C24  119.54  3.000
 9YY  H6   C23  C22  121.61  3.000
 9YY  C24  C23  C22  118.85  3.000
 9YY  H7   C24  C23  119.31  3.000
 9YY  H7   C24  C19  119.70  3.000
 9YY  C23  C24  C19  120.99  3.000
 9YY  H9   C12  H8   106.56  3.000
 9YY  H9   C12  N7   109.49  3.000
 9YY  H8   C12  N7   111.60  3.000
 9YY  H9   C12  C13  109.36  3.000
 9YY  H8   C12  C13  109.73  3.000
 9YY  N7   C12  C13  110.01  3.000
 9YY  C9   C1   C6   121.77  3.000
 9YY  C6   C1   C2   116.79  3.000
 9YY  C9   C1   C2   121.42  3.000
 9YY  H10  C2   N3   114.27  3.000
 9YY  H10  C2   C1   119.43  3.000
 9YY  N3   C2   C1   126.29  3.000
 9YY  C4   N3   C2   116.89  3.000
 9YY  N8   C4   C5   117.80  3.000
 9YY  C5   C4   N3   122.87  3.000
 9YY  N8   C4   N3   119.33  3.000
 9YY  H11  C5   C6   120.76  3.000
 9YY  H11  C5   C4   119.20  3.000
 9YY  C6   C5   C4   120.04  3.000
 9YY  N7   C6   C5   121.58  3.000
 9YY  N7   C6   C1   121.32  3.000
 9YY  C5   C6   C1   117.08  3.000
 9YY  H12  N7   C6   115.98  3.000
 9YY  H12  N7   C12  118.72  3.000
 9YY  C6   N7   C12  124.14  3.000
 9YY  O11  C9   N10  120.93  3.000
 9YY  O11  C9   C1   121.97  3.000
 9YY  N10  C9   C1   117.10  3.000
 9YY  H15  N10  H14  116.46  3.000
 9YY  H15  N10  C9   118.62  3.000
 9YY  H14  N10  C9   122.56  3.000
 9YY  H16  C14  C15  119.57  3.000
 9YY  H16  C14  C13  119.88  3.000
 9YY  C15  C14  C13  120.55  3.000
 9YY  H18  C25  H17  106.93  3.000
 9YY  H18  C25  C26  109.86  3.000
 9YY  H17  C25  C26  110.11  3.000
 9YY  H18  C25  C21  113.21  3.000
 9YY  H17  C25  C21  113.35  3.000
 9YY  C26  C25  C21  103.37  3.000
 9YY  O28  C26  N27  125.91  3.000
 9YY  O28  C26  C25  127.11  3.000
 9YY  N27  C26  C25  106.99  3.000
 9YY  H19  N27  C26  123.10  3.000
 9YY  H19  N27  C22  124.55  3.000
 9YY  C26  N27  C22  112.34  3.000
 9YY  H13  N8   C4   114.20  3.000
 9YY  H13  N8   C19  113.80  3.000
 9YY  C4   N8   C19  131.99  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
 9YY  CONST_01  C16  C17  C18  C13     0.00   0.0  0
 9YY  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 9YY  CONST_03  C15  C14  C13  C18     0.00   0.0  0
 9YY  CONST_04  C15  C16  C17  C18     0.00   0.0  0
 9YY  CONST_05  C14  C13  C18  C17     0.00   0.0  0
 9YY  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 9YY  CONST_07  C22  C23  C24  C19     0.00   0.0  0
 9YY  CONST_08  C22  C21  C20  C19     0.00   0.0  0
 9YY  CONST_09  C23  C24  C19  C20     0.00   0.0  0
 9YY  CONST_10  C23  C22  C21  C20     0.00   0.0  0
 9YY  CONST_11  C24  C19  C20  C21     0.00   0.0  0
 9YY  CONST_12  C24  C23  C22  C21     0.00   0.0  0
 9YY  CONST_13  C4   N3   C2   C1      0.00   0.0  0
 9YY  CONST_14  C4   C5   C6   C1      0.00   0.0  0
 9YY  CONST_15  C5   C4   N3   C2      0.00   0.0  0
 9YY  CONST_16  C5   C6   C1   C2      0.00   0.0  0
 9YY  CONST_17  C6   C1   C2   N3      0.00   0.0  0
 9YY  CONST_18  C6   C5   C4   N3      0.00   0.0  0
 9YY  CONST_19  C25  C26  N27  C22     0.00   0.0  0
 9YY  CONST_20  C12  C13  C18  C17   180.00   0.0  0
 9YY  CONST_21  C12  C13  C14  C15   180.00   0.0  0
 9YY  CONST_22  N8   C19  C20  C21   180.00   0.0  0
 9YY  CONST_23  N8   C19  C24  C23   180.00   0.0  0
 9YY  CONST_24  N8   C4   N3   C2    180.00   0.0  0
 9YY  CONST_25  N7   C6   C1   C2    180.00   0.0  0
 9YY  CONST_26  C9   C1   C2   N3    180.00   0.0  0
 9YY  CONST_27  N7   C6   C5   C4    180.00   0.0  0
 9YY  CONST_28  C9   C1   C6   C5    180.00   0.0  0
 9YY  CONST_29  N8   C4   C5   C6    180.00   0.0  0
 9YY  CONST_30  O28  C26  N27  C22   180.00   0.0  0
 9YY  CONST_31  H2   C17  C18  C13   180.00   0.0  0
 9YY  CONST_32  H4   C15  C14  C13   180.00   0.0  0
 9YY  CONST_33  H16  C14  C13  C18   180.00   0.0  0
 9YY  CONST_34  H3   C16  C17  C18   180.00   0.0  0
 9YY  CONST_35  H1   C18  C17  C16   180.00   0.0  0
 9YY  CONST_36  H6   C23  C24  C19   180.00   0.0  0
 9YY  CONST_37  H7   C24  C19  C20   180.00   0.0  0
 9YY  CONST_38  H5   C20  C21  C22   180.00   0.0  0
 9YY  CONST_39  H11  C5   C6   C1    180.00   0.0  0
 9YY  CONST_40  H10  C2   N3   C4    180.00   0.0  0
 9YY  CONST_41  H19  N27  C26  C25   180.00   0.0  0
 9YY  CONST_42  C1   C6   N7   C12   180.00   0.0  0
 9YY  CONST_43  C5   C6   N7   C12     0.00   0.0  0
 9YY  CONST_44  H12  N7   C6   C1      0.00   0.0  0
 9YY  CONST_46  H15  N10  C9   C1    180.00   0.0  0
 9YY  Var_01    N3   C4   N8   C19    -3.32  30.0  2
 9YY  Var_02    C4   N8   C19  C20  -179.87  30.0  2
 9YY  Var_03    H17  C25  C21  C20   -60.71  30.0  1
 9YY  Var_04    C6   N7   C12  C13  -172.17  30.0  1
 9YY  Var_05    N7   C12  C13  C18  -118.02  30.0  2
 9YY  Var_06    N10  C9   C1   C2     20.61  30.0  2

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
 9YY  plan-1  C13  0.020
 9YY  plan-1  C18  0.020
 9YY  plan-1  C17  0.020
 9YY  plan-1  C16  0.020
 9YY  plan-1  C15  0.020
 9YY  plan-1  C12  0.020
 9YY  plan-1  C14  0.020
 9YY  plan-1  H1   0.020
 9YY  plan-1  H2   0.020
 9YY  plan-1  H3   0.020
 9YY  plan-1  H4   0.020
 9YY  plan-1  H16  0.020
 9YY  plan-2  C1   0.020
 9YY  plan-2  C2   0.020
 9YY  plan-2  N3   0.020
 9YY  plan-2  C4   0.020
 9YY  plan-2  C5   0.020
 9YY  plan-2  C6   0.020
 9YY  plan-2  N7   0.020
 9YY  plan-2  C9   0.020
 9YY  plan-2  H10  0.020
 9YY  plan-2  H11  0.020
 9YY  plan-2  N8   0.020
 9YY  plan-3  C1   0.020
 9YY  plan-3  C9   0.020
 9YY  plan-3  N10  0.020
 9YY  plan-3  O11  0.020
 9YY  plan-3  H14  0.020
 9YY  plan-3  H15  0.020
 9YY  plan-4  C12  0.020
 9YY  plan-4  C6   0.020
 9YY  plan-4  N7   0.020
 9YY  plan-4  H12  0.020
 9YY  plan-5  C19  0.020
 9YY  plan-5  C20  0.020
 9YY  plan-5  C21  0.020
 9YY  plan-5  C22  0.020
 9YY  plan-5  C23  0.020
 9YY  plan-5  C24  0.020
 9YY  plan-5  C25  0.020
 9YY  plan-5  C26  0.020
 9YY  plan-5  N27  0.020
 9YY  plan-5  O28  0.020
 9YY  plan-5  H5   0.020
 9YY  plan-5  H6   0.020
 9YY  plan-5  H7   0.020
 9YY  plan-5  H19  0.020
 9YY  plan-5  N8   0.020

