# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 02:11:37 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-amino-N,N-dimethyl-5-(1H-pyrrolo[2,3-b]pyridin-5-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)c1cc(ccc1N)c2cnc3[nH]ccc3c2
#
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
 2YE  2YE  "2-amino-N,N-dimethyl-5-(1H-pyrrolo[2,3-b]pyridin-5-yl)benzamide"  ligand  37  21  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2YE
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
 2YE  C4   C  C     0   0.511  -36.2872  -15.9426  -17.8655
 2YE  C6   C  CR6   0  -0.110  -34.9215  -15.4965  -17.4562
 2YE  C7   C  CR16  0  -0.322  -34.2205  -14.6170  -18.2749
 2YE  C8   C  CR6   0   0.082  -32.9831  -14.0910  -17.9202
 2YE  C10  C  CR16  0  -0.312  -33.1401  -15.3443  -15.8526
 2YE  C13  C  CR6   0  -0.019  -32.2643  -13.1582  -18.8064
 2YE  C15  C  CR56  0   0.034  -30.9086  -11.2291  -19.1974
 2YE  C17  C  CR15  0   0.002  -29.7845   -9.7073  -20.3896
 2YE  C20  C  CR56  0   0.456  -31.0152  -11.5482  -20.5706
 2YE  C22  C  CR16  0  -0.131  -32.2734  -13.3579  -20.2011
 2YE  C1   C  CH3   0  -0.524  -37.7634  -16.7280  -19.6069
 2YE  C11  C  CR6   0   0.280  -34.3959  -15.8615  -16.2031
 2YE  C14  C  CR16  0  -0.283  -31.5625  -12.0691  -18.3019
 2YE  C16  C  CR15  0  -0.448  -30.1169  -10.0443  -19.1096
 2YE  C3   C  CH3   0  -0.531  -35.3518  -16.9617  -19.9254
 2YE  C9   C  CR16  0  -0.306  -32.4559  -14.4853  -16.6875
 2YE  N18  N  NR15  0  -0.664  -30.3216  -10.6083  -21.2680
 2YE  N2   N  NT    0  -0.432  -36.4332  -16.4580  -19.1017
 2YE  N21  N  N     0  -0.417  -31.6701  -12.5774  -21.0816
 2YE  O5   O  O     0  -0.496  -37.2386  -15.7982  -17.1010
 2YE  H1   H  HCR6  0   0.260  -34.6750  -14.3171  -19.2123
 2YE  H2   H  HCR6  0   0.259  -32.7005  -15.6276  -14.9032
 2YE  H3   H  HNH2  0   0.382  -34.6979  -16.7725  -14.4222
 2YE  H4   H  HNH2  0   0.383  -36.0347  -16.7824  -15.4313
 2YE  H5   H  HCR5  0   0.287  -29.1957   -8.8797  -20.7508
 2YE  H6   H  HCR6  0   0.250  -32.7951  -14.2175  -20.6100
 2YE  H7   H  HCH3  0   0.254  -38.4916  -16.0623  -19.1536
 2YE  H8   H  HCH3  0   0.245  -37.7735  -16.5672  -20.6845
 2YE  H9   H  HCH3  0   0.239  -38.0663  -17.7601  -19.4134
 2YE  H10  H  HCR6  0   0.255  -31.5414  -11.8698  -17.2369
 2YE  H11  H  HCR5  0   0.251  -29.8291   -9.5122  -18.2174
 2YE  H12  H  HCH3  0   0.265  -34.4249  -17.0287  -19.3653
 2YE  H13  H  HCH3  0   0.254  -35.6055  -17.9649  -20.2715
 2YE  H14  H  HCH3  0   0.243  -35.1868  -16.3319  -20.8016
 2YE  H15  H  HCR6  0   0.252  -31.4845  -14.1208  -16.3754
 2YE  H16  H  HNR5  0   0.409  -30.2255  -10.5767  -22.2701
 2YE  N12  N  NH2   0  -0.859  -35.0301  -16.7506  -15.3728

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
 2YE  N18  C20  aromatic  1.360  0.020  1.360
 2YE  N18  C17  aromatic  1.368  0.020  1.368
 2YE  N21  C20  aromatic  1.323  0.020  1.323
 2YE  N21  C22  aromatic  1.322  0.020  1.322
 2YE  C20  C15  aromatic  1.414  0.020  1.414
 2YE  C17  C16  aromatic  1.365  0.020  1.365
 2YE  C22  C13  aromatic  1.409  0.020  1.409
 2YE  C3   N2   single    1.450  0.020  1.450
 2YE  C1   N2   single    1.448  0.020  1.448
 2YE  C15  C16  aromatic  1.428  0.020  1.428
 2YE  C15  C14  aromatic  1.391  0.020  1.391
 2YE  N2   C4   single    1.347  0.020  1.347
 2YE  C13  C14  aromatic  1.390  0.020  1.390
 2YE  C13  C8   single    1.474  0.020  1.474
 2YE  C7   C8   aromatic  1.391  0.020  1.391
 2YE  C7   C6   aromatic  1.391  0.020  1.391
 2YE  C4   C6   single    1.494  0.020  1.494
 2YE  C4   O5   double    1.229  0.020  1.229
 2YE  C8   C9   aromatic  1.397  0.020  1.397
 2YE  C6   C11  aromatic  1.407  0.020  1.407
 2YE  C9   C10  aromatic  1.380  0.020  1.380
 2YE  C11  C10  aromatic  1.403  0.020  1.403
 2YE  C11  N12  single    1.372  0.020  1.372
 2YE  C7   H1   single    0.930  0.020  1.080
 2YE  C10  H2   single    0.930  0.020  1.080
 2YE  N12  H3   single    0.890  0.020  1.040
 2YE  N12  H4   single    0.890  0.020  1.040
 2YE  C17  H5   single    0.930  0.020  1.080
 2YE  C22  H6   single    0.930  0.020  1.080
 2YE  C1   H7   single    0.970  0.020  1.090
 2YE  C1   H8   single    0.970  0.020  1.090
 2YE  C1   H9   single    0.970  0.020  1.090
 2YE  C14  H10  single    0.930  0.020  1.080
 2YE  C16  H11  single    0.930  0.020  1.080
 2YE  C3   H12  single    0.970  0.020  1.090
 2YE  C3   H13  single    0.970  0.020  1.090
 2YE  C3   H14  single    0.970  0.020  1.090
 2YE  C9   H15  single    0.930  0.020  1.080
 2YE  N18  H16  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
 2YE  O5   C4   N2   122.13  3.000
 2YE  O5   C4   C6   120.14  3.000
 2YE  N2   C4   C6   117.69  3.000
 2YE  C11  C6   C7   120.00  3.000
 2YE  C11  C6   C4   120.53  3.000
 2YE  C7   C6   C4   119.23  3.000
 2YE  H1   C7   C8   119.27  3.000
 2YE  H1   C7   C6   118.20  3.000
 2YE  C8   C7   C6   122.51  3.000
 2YE  C9   C8   C13  121.67  3.000
 2YE  C9   C8   C7   117.00  3.000
 2YE  C13  C8   C7   121.33  3.000
 2YE  H2   C10  C9   119.46  3.000
 2YE  H2   C10  C11  119.05  3.000
 2YE  C9   C10  C11  121.49  3.000
 2YE  C14  C13  C22  118.26  3.000
 2YE  C14  C13  C8   121.59  3.000
 2YE  C22  C13  C8   120.15  3.000
 2YE  C16  C15  C14  136.24  3.000
 2YE  C14  C15  C20  116.97  3.000
 2YE  C16  C15  C20  106.79  3.000
 2YE  H5   C17  N18  120.33  3.000
 2YE  H5   C17  C16  129.56  3.000
 2YE  N18  C17  C16  110.12  3.000
 2YE  N21  C20  N18  126.30  3.000
 2YE  N21  C20  C15  126.03  3.000
 2YE  N18  C20  C15  107.67  3.000
 2YE  H6   C22  N21  115.84  3.000
 2YE  H6   C22  C13  119.23  3.000
 2YE  N21  C22  C13  124.92  3.000
 2YE  H9   C1   H8   108.17  3.000
 2YE  H9   C1   H7   108.61  3.000
 2YE  H8   C1   H7   108.44  3.000
 2YE  H9   C1   N2   111.64  3.000
 2YE  H8   C1   N2   109.02  3.000
 2YE  H7   C1   N2   110.86  3.000
 2YE  N12  C11  C10  120.11  3.000
 2YE  N12  C11  C6   122.31  3.000
 2YE  C10  C11  C6   117.47  3.000
 2YE  H10  C14  C15  120.83  3.000
 2YE  H10  C14  C13  120.69  3.000
 2YE  C15  C14  C13  118.47  3.000
 2YE  H11  C16  C17  126.11  3.000
 2YE  H11  C16  C15  127.49  3.000
 2YE  C17  C16  C15  106.40  3.000
 2YE  H14  C3   H13  108.13  3.000
 2YE  H14  C3   H12  108.71  3.000
 2YE  H13  C3   H12  107.79  3.000
 2YE  H14  C3   N2   111.61  3.000
 2YE  H13  C3   N2   109.04  3.000
 2YE  H12  C3   N2   111.43  3.000
 2YE  H15  C9   C10  118.67  3.000
 2YE  H15  C9   C8   119.83  3.000
 2YE  C10  C9   C8   121.50  3.000
 2YE  H16  N18  C20  125.47  3.000
 2YE  H16  N18  C17  125.50  3.000
 2YE  C20  N18  C17  109.02  3.000
 2YE  C3   N2   C1   114.97  3.000
 2YE  C1   N2   C4   119.40  3.000
 2YE  C3   N2   C4   124.99  3.000
 2YE  C22  N21  C20  115.34  3.000
 2YE  H4   N12  H3   112.54  3.000
 2YE  H4   N12  C11  116.52  3.000
 2YE  H3   N12  C11  115.65  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
 2YE  CONST_01  C13  C8   C7   C6    180.00   0.0  0
 2YE  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 2YE  CONST_03  C9   C10  C11  C6      0.00   0.0  0
 2YE  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 2YE  CONST_07  C10  C11  C6   C7      0.00   0.0  0
 2YE  CONST_08  N21  C22  C13  C8    180.00   0.0  0
 2YE  CONST_09  C15  C14  C13  C8    180.00   0.0  0
 2YE  CONST_10  C11  C6   C7   C8      0.00   0.0  0
 2YE  CONST_11  C11  C10  C9   C8      0.00   0.0  0
 2YE  CONST_12  C13  C8   C9   C10   180.00   0.0  0
 2YE  CONST_13  C20  N21  C22  C13     0.00   0.0  0
 2YE  CONST_14  C20  C15  C14  C13     0.00   0.0  0
 2YE  CONST_15  C16  C15  C14  C13   180.00   0.0  0
 2YE  CONST_16  C17  N18  C20  C15     0.00   0.0  0
 2YE  CONST_17  C22  N21  C20  C15     0.00   0.0  0
 2YE  CONST_18  N18  C17  C16  C15     0.00   0.0  0
 2YE  CONST_19  C22  C13  C14  C15     0.00   0.0  0
 2YE  CONST_20  N21  C20  N18  C17   180.00   0.0  0
 2YE  CONST_21  C20  C15  C16  C17     0.00   0.0  0
 2YE  CONST_22  C14  C15  C16  C17   180.00   0.0  0
 2YE  CONST_23  C16  C17  N18  C20     0.00   0.0  0
 2YE  CONST_24  N18  C20  N21  C22   180.00   0.0  0
 2YE  CONST_26  N18  C20  C15  C14   180.00   0.0  0
 2YE  CONST_27  N21  C20  C15  C14     0.00   0.0  0
 2YE  CONST_28  N21  C22  C13  C14     0.00   0.0  0
 2YE  CONST_30  N18  C20  C15  C16     0.00   0.0  0
 2YE  CONST_31  N21  C20  C15  C16   180.00   0.0  0
 2YE  CONST_32  C8   C7   C6   C4    180.00   0.0  0
 2YE  CONST_33  C10  C11  C6   C4    180.00   0.0  0
 2YE  CONST_34  N12  C11  C6   C7    180.00   0.0  0
 2YE  CONST_35  C9   C10  C11  N12   180.00   0.0  0
 2YE  CONST_36  H2   C10  C11  C6    180.00   0.0  0
 2YE  CONST_37  H15  C9   C8   C7    180.00   0.0  0
 2YE  CONST_38  H6   C22  C13  C8      0.00   0.0  0
 2YE  CONST_39  H10  C14  C13  C8      0.00   0.0  0
 2YE  CONST_40  H2   C10  C9   C8    180.00   0.0  0
 2YE  CONST_41  H1   C7   C8   C13     0.00   0.0  0
 2YE  CONST_42  H15  C9   C8   C13     0.00   0.0  0
 2YE  CONST_43  H16  N18  C20  C15   180.00   0.0  0
 2YE  CONST_44  H5   C17  C16  C15   180.00   0.0  0
 2YE  CONST_45  H5   C17  N18  C20   180.00   0.0  0
 2YE  CONST_46  H6   C22  N21  C20   180.00   0.0  0
 2YE  CONST_47  H11  C16  C15  C20   180.00   0.0  0
 2YE  CONST_48  H10  C14  C15  C20   180.00   0.0  0
 2YE  CONST_49  H10  C14  C13  C22   180.00   0.0  0
 2YE  CONST_50  H1   C7   C6   C11   180.00   0.0  0
 2YE  CONST_51  H15  C9   C10  C11   180.00   0.0  0
 2YE  CONST_52  H11  C16  C15  C14     0.00   0.0  0
 2YE  CONST_53  H6   C22  C13  C14   180.00   0.0  0
 2YE  CONST_54  H16  N18  C17  C16   180.00   0.0  0
 2YE  CONST_55  H10  C14  C15  C16     0.00   0.0  0
 2YE  CONST_56  H1   C7   C8   C9    180.00   0.0  0
 2YE  CONST_57  H11  C16  C17  N18   180.00   0.0  0
 2YE  CONST_58  H16  N18  C20  N21     0.00   0.0  0
 2YE  CONST_59  H3   N12  C11  C6    180.00   0.0  0
 2YE  CONST_64  C1   N2   C4   C6    180.00   0.0  0
 2YE  CONST_65  O5   C4   N2   C1      0.00   0.0  0
 2YE  Var_01    N2   C4   C6   C7     52.50  30.0  2
 2YE  Var_02    O5   C4   C6   C7   -125.35  30.0  2
 2YE  Var_03    N2   C4   C6   C11  -133.22  30.0  2
 2YE  Var_04    O5   C4   C6   C11    48.92  30.0  2
 2YE  Var_05    H12  C3   N2   C4      9.52  30.0  3
 2YE  Var_06    H13  C3   N2   C4    128.38  30.0  3
 2YE  Var_07    H14  C3   N2   C4   -112.23  30.0  3
 2YE  Var_08    H7   C1   N2   C4     27.86  30.0  3
 2YE  Var_09    H8   C1   N2   C4    147.16  30.0  3
 2YE  Var_10    H9   C1   N2   C4    -93.38  30.0  3
 2YE  Var_11    H12  C3   N2   C1   -161.22  30.0  3
 2YE  Var_12    H13  C3   N2   C1    -42.35  30.0  3
 2YE  Var_13    H14  C3   N2   C1     77.04  30.0  3
 2YE  Var_14    H7   C1   N2   C3   -160.85  30.0  3
 2YE  Var_15    H8   C1   N2   C3    -41.55  30.0  3
 2YE  Var_16    H9   C1   N2   C3     77.91  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
 2YE  plan-1  C4   0.020
 2YE  plan-1  C6   0.020
 2YE  plan-1  C7   0.020
 2YE  plan-1  C8   0.020
 2YE  plan-1  C10  0.020
 2YE  plan-1  C13  0.020
 2YE  plan-1  C11  0.020
 2YE  plan-1  C9   0.020
 2YE  plan-1  H1   0.020
 2YE  plan-1  H2   0.020
 2YE  plan-1  H15  0.020
 2YE  plan-1  N12  0.020
 2YE  plan-2  C8   0.020
 2YE  plan-2  C13  0.020
 2YE  plan-2  C15  0.020
 2YE  plan-2  C17  0.020
 2YE  plan-2  C20  0.020
 2YE  plan-2  C22  0.020
 2YE  plan-2  C14  0.020
 2YE  plan-2  C16  0.020
 2YE  plan-2  N18  0.020
 2YE  plan-2  N21  0.020
 2YE  plan-2  H5   0.020
 2YE  plan-2  H6   0.020
 2YE  plan-2  H10  0.020
 2YE  plan-2  H11  0.020
 2YE  plan-2  H16  0.020
 2YE  plan-3  C4   0.020
 2YE  plan-3  C6   0.020
 2YE  plan-3  C1   0.020
 2YE  plan-3  C3   0.020
 2YE  plan-3  N2   0.020
 2YE  plan-3  O5   0.020
 2YE  plan-4  C11  0.020
 2YE  plan-4  H3   0.020
 2YE  plan-4  H4   0.020
 2YE  plan-4  N12  0.020

