# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 03:17:29 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: ~{N}-[(1~{S})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H](NC(=O)c1scc(c1)c2c[nH]c3ncccc23)c4ccccc4
#
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
 9JN  9JN  ~{N}-[(1~{S})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide  ligand  44  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9JN
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
 9JN  C1   C  CR16  0  -0.270   6.3533  -1.1112   1.7838
 9JN  C2   C  CR16  0  -0.243   6.4099   0.2755   1.8145
 9JN  C3   C  CR16  0  -0.244   5.4608  -1.7412   0.9248
 9JN  C4   C  CR16  0  -0.338  -6.5166  -0.1774  -1.3594
 9JN  C5   C  CR16  0  -0.265  -5.1377  -0.1935  -1.2417
 9JN  C6   C  CR16  0  -0.319   5.5757   1.0236   0.9936
 9JN  C7   C  CR16  0  -0.298   4.6334  -0.9902   0.1016
 9JN  C8   C  CR15  0  -0.239  -0.8073   0.2113   0.5217
 9JN  C9   C  CR16  0  -0.091  -7.3161  -0.2673  -0.2148
 9JN  C10  C  CR15  0  -0.050  -3.4743  -0.4159   1.9716
 9JN  C11  C  CR15  0  -0.598  -1.7751  -0.7359  -1.3446
 9JN  C12  C  CR56  0  -0.018  -4.5995  -0.3050   0.0385
 9JN  C13  C  CR5   0   0.184  -2.0020  -0.2938  -0.0669
 9JN  C14  C  CR5   0  -0.019  -3.2865  -0.3360   0.6153
 9JN  C15  C  CR6   0   0.155   4.6812   0.4005   0.1316
 9JN  C16  C  CR5   0  -0.319   0.2750   0.1477  -0.3051
 9JN  C17  C  CR56  0   0.477  -5.5202  -0.3725   1.1098
 9JN  C19  C  CH2   0  -0.299   4.5046   1.2693  -2.1910
 9JN  C20  C  CH1   0  -0.134   3.8433   1.2324  -0.8075
 9JN  N21  N  N     0  -0.423  -6.8392  -0.3602   1.0180
 9JN  N22  N  NR15  0  -0.664  -4.8040  -0.4391   2.2653
 9JN  N23  N  NH1   0  -0.678   2.5051   0.7134  -0.9808
 9JN  N24  N  NH2   0  -0.802   3.6456   1.9374  -3.1507
 9JN  O25  O  O     0  -0.469   1.9224   0.8865   1.1979
 9JN  S26  S  S2    0   0.258  -0.1482  -0.5459  -1.8244
 9JN  H1   H  HCR6  0   0.253   6.9970  -1.6987   2.4256
 9JN  H2   H  HCR6  0   0.253   7.0985   0.7778   2.4820
 9JN  H3   H  HCR6  0   0.253   5.4087  -2.8223   0.8954
 9JN  H5   H  HCR6  0   0.259  -4.5096  -0.1137  -2.1198
 9JN  H6   H  HCR6  0   0.247   5.6178   2.1063   1.0282
 9JN  H7   H  HCR6  0   0.246   3.9386  -1.4921  -0.5616
 9JN  H8   H  HCR5  0   0.267  -0.7573   0.6291   1.5177
 9JN  H9   H  HCR6  0   0.258  -8.3955  -0.2581  -0.3132
 9JN  H10  H  HCR5  0   0.297  -2.7398  -0.4708   2.7593
 9JN  H11  H  HCR5  0   0.296  -2.4768  -1.2010  -2.0200
 9JN  H12  H  HCH2  0   0.230   5.4970   1.7208  -2.0766
 9JN  H13  H  HCH2  0   0.238   4.6617   0.2425  -2.5298
 9JN  H14  H  HCH1  0   0.258   3.7973   2.2577  -0.4183
 9JN  H15  H  HNR5  0   0.415  -5.1941  -0.5032   3.1918
 9JN  H16  H  HNH1  0   0.395   2.1623   0.7950  -1.9312
 9JN  H17  H  HNH2  0   0.353   3.6858   2.9402  -3.0189
 9JN  H18  H  HNH2  0   0.363   3.9708   1.7579  -4.0907
 9JN  C18  C  C     0   0.561   1.6340   0.6203   0.0411
 9JN  H4   H  HCR6  0   0.266  -6.9870  -0.0920  -2.3292

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
 9JN  C1   C3   aromatic  1.390  0.020  1.390
 9JN  C1   C2   aromatic  1.388  0.020  1.388
 9JN  C3   C7   aromatic  1.388  0.020  1.388
 9JN  C2   C6   aromatic  1.389  0.020  1.389
 9JN  C7   C15  aromatic  1.392  0.020  1.392
 9JN  C6   C15  aromatic  1.390  0.020  1.390
 9JN  C15  C20  single    1.509  0.020  1.509
 9JN  O25  C18  double    1.222  0.020  1.222
 9JN  C18  C16  single    1.480  0.020  1.480
 9JN  C18  N23  single    1.346  0.020  1.346
 9JN  S26  C16  aromatic  1.723  0.020  1.723
 9JN  S26  C11  aromatic  1.707  0.020  1.707
 9JN  C20  N23  single    1.446  0.020  1.446
 9JN  C20  C19  single    1.534  0.020  1.534
 9JN  C16  C8   aromatic  1.363  0.020  1.363
 9JN  C11  C13  aromatic  1.371  0.020  1.371
 9JN  C8   C13  aromatic  1.424  0.020  1.424
 9JN  C19  N24  single    1.451  0.020  1.451
 9JN  C13  C14  single    1.455  0.020  1.455
 9JN  C14  C10  aromatic  1.372  0.020  1.372
 9JN  C14  C12  aromatic  1.434  0.020  1.434
 9JN  C10  N22  aromatic  1.362  0.020  1.362
 9JN  C12  C5   aromatic  1.393  0.020  1.393
 9JN  C12  C17  aromatic  1.414  0.020  1.414
 9JN  C5   C4   aromatic  1.384  0.020  1.384
 9JN  N22  C17  aromatic  1.361  0.020  1.361
 9JN  C17  N21  aromatic  1.322  0.020  1.322
 9JN  C4   C9   aromatic  1.399  0.020  1.399
 9JN  N21  C9   aromatic  1.325  0.020  1.325
 9JN  C1   H1   single    0.930  0.020  1.080
 9JN  C2   H2   single    0.930  0.020  1.080
 9JN  C3   H3   single    0.930  0.020  1.080
 9JN  C4   H4   single    0.930  0.020  1.080
 9JN  C5   H5   single    0.930  0.020  1.080
 9JN  C6   H6   single    0.930  0.020  1.080
 9JN  C7   H7   single    0.930  0.020  1.080
 9JN  C8   H8   single    0.930  0.020  1.080
 9JN  C9   H9   single    0.930  0.020  1.080
 9JN  C10  H10  single    0.930  0.020  1.080
 9JN  C11  H11  single    0.930  0.020  1.080
 9JN  C19  H12  single    0.970  0.020  1.090
 9JN  C19  H13  single    0.970  0.020  1.090
 9JN  C20  H14  single    0.970  0.020  1.090
 9JN  N22  H15  single    0.860  0.020  1.020
 9JN  N23  H16  single    0.890  0.020  1.040
 9JN  N24  H17  single    0.890  0.020  1.040
 9JN  N24  H18  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
 9JN  H1   C1   C3   120.16  3.000
 9JN  H1   C1   C2   120.32  3.000
 9JN  C3   C1   C2   119.52  3.000
 9JN  H2   C2   C6   119.77  3.000
 9JN  H2   C2   C1   120.20  3.000
 9JN  C6   C2   C1   120.03  3.000
 9JN  H3   C3   C7   119.70  3.000
 9JN  H3   C3   C1   120.02  3.000
 9JN  C7   C3   C1   120.28  3.000
 9JN  H4   C4   C9   119.36  3.000
 9JN  H4   C4   C5   120.71  3.000
 9JN  C9   C4   C5   119.93  3.000
 9JN  H5   C5   C12  121.81  3.000
 9JN  H5   C5   C4   120.54  3.000
 9JN  C12  C5   C4   117.64  3.000
 9JN  H6   C6   C15  119.51  3.000
 9JN  H6   C6   C2   119.72  3.000
 9JN  C15  C6   C2   120.77  3.000
 9JN  H7   C7   C15  119.87  3.000
 9JN  H7   C7   C3   119.64  3.000
 9JN  C15  C7   C3   120.49  3.000
 9JN  H8   C8   C16  122.68  3.000
 9JN  H8   C8   C13  123.81  3.000
 9JN  C16  C8   C13  113.49  3.000
 9JN  H9   C9   N21  116.32  3.000
 9JN  H9   C9   C4   119.62  3.000
 9JN  N21  C9   C4   124.06  3.000
 9JN  H10  C10  N22  120.43  3.000
 9JN  H10  C10  C14  129.20  3.000
 9JN  N22  C10  C14  110.36  3.000
 9JN  H11  C11  S26  119.46  3.000
 9JN  H11  C11  C13  127.92  3.000
 9JN  S26  C11  C13  112.57  3.000
 9JN  C17  C12  C14  106.88  3.000
 9JN  C17  C12  C5   116.64  3.000
 9JN  C14  C12  C5   136.45  3.000
 9JN  C14  C13  C11  125.01  3.000
 9JN  C14  C13  C8   123.85  3.000
 9JN  C11  C13  C8   111.14  3.000
 9JN  C13  C14  C12  128.24  3.000
 9JN  C12  C14  C10  105.88  3.000
 9JN  C13  C14  C10  125.89  3.000
 9JN  C20  C15  C7   121.23  3.000
 9JN  C20  C15  C6   119.76  3.000
 9JN  C7   C15  C6   118.91  3.000
 9JN  S26  C16  C18  124.08  3.000
 9JN  S26  C16  C8   111.01  3.000
 9JN  C18  C16  C8   124.90  3.000
 9JN  N22  C17  N21  125.75  3.000
 9JN  N21  C17  C12  126.61  3.000
 9JN  N22  C17  C12  107.63  3.000
 9JN  H13  C19  H12  106.81  3.000
 9JN  H13  C19  N24  108.23  3.000
 9JN  H12  C19  N24  114.54  3.000
 9JN  H13  C19  C20  108.60  3.000
 9JN  H12  C19  C20  107.82  3.000
 9JN  N24  C19  C20  110.64  3.000
 9JN  H14  C20  N23  109.82  3.000
 9JN  H14  C20  C19  108.38  3.000
 9JN  N23  C20  C19  107.43  3.000
 9JN  H14  C20  C15  108.51  3.000
 9JN  C19  C20  C15  109.59  3.000
 9JN  N23  C20  C15  113.00  3.000
 9JN  C17  N21  C9   115.10  3.000
 9JN  H15  N22  C17  125.46  3.000
 9JN  H15  N22  C10  125.28  3.000
 9JN  C17  N22  C10  109.26  3.000
 9JN  H16  N23  C20  113.36  3.000
 9JN  H16  N23  C18  119.91  3.000
 9JN  C20  N23  C18  122.20  3.000
 9JN  H18  N24  H17  106.51  3.000
 9JN  H18  N24  C19  110.05  3.000
 9JN  H17  N24  C19  110.28  3.000
 9JN  C16  S26  C11   91.78  3.000
 9JN  O25  C18  N23  123.44  3.000
 9JN  N23  C18  C16  116.03  3.000
 9JN  O25  C18  C16  120.52  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
 9JN  CONST_01  C15  C7   C3   C1     0.00   0.0  0
 9JN  CONST_02  C15  C6   C2   C1     0.00   0.0  0
 9JN  CONST_03  C7   C3   C1   C2     0.00   0.0  0
 9JN  CONST_04  C7   C15  C6   C2     0.00   0.0  0
 9JN  CONST_05  C6   C2   C1   C3     0.00   0.0  0
 9JN  CONST_06  C6   C15  C7   C3     0.00   0.0  0
 9JN  CONST_07  C14  C12  C5   C4   180.00   0.0  0
 9JN  CONST_08  C17  C12  C5   C4     0.00   0.0  0
 9JN  CONST_09  C17  N21  C9   C4     0.00   0.0  0
 9JN  CONST_10  C13  C14  C12  C5     0.00   0.0  0
 9JN  CONST_11  C10  C14  C12  C5   180.00   0.0  0
 9JN  CONST_12  N22  C17  C12  C5   180.00   0.0  0
 9JN  CONST_13  N21  C17  C12  C5     0.00   0.0  0
 9JN  CONST_14  N21  C9   C4   C5     0.00   0.0  0
 9JN  CONST_15  C11  S26  C16  C8     0.00   0.0  0
 9JN  CONST_16  S26  C11  C13  C8     0.00   0.0  0
 9JN  CONST_19  C12  C5   C4   C9     0.00   0.0  0
 9JN  CONST_20  C12  C17  N21  C9     0.00   0.0  0
 9JN  CONST_21  N22  C17  N21  C9   180.00   0.0  0
 9JN  CONST_23  C17  C12  C14  C10    0.00   0.0  0
 9JN  CONST_24  C12  C17  N22  C10    0.00   0.0  0
 9JN  CONST_25  N21  C17  N22  C10  180.00   0.0  0
 9JN  CONST_26  C16  C8   C13  C11    0.00   0.0  0
 9JN  CONST_28  N22  C10  C14  C12    0.00   0.0  0
 9JN  CONST_29  C16  S26  C11  C13    0.00   0.0  0
 9JN  CONST_30  S26  C16  C8   C13    0.00   0.0  0
 9JN  CONST_31  N22  C10  C14  C13  180.00   0.0  0
 9JN  CONST_32  C17  C12  C14  C13  180.00   0.0  0
 9JN  CONST_33  S26  C11  C13  C14  180.00   0.0  0
 9JN  CONST_34  C16  C8   C13  C14  180.00   0.0  0
 9JN  CONST_35  C17  N22  C10  C14    0.00   0.0  0
 9JN  CONST_36  N22  C17  C12  C14    0.00   0.0  0
 9JN  CONST_37  N21  C17  C12  C14  180.00   0.0  0
 9JN  CONST_38  C20  C15  C6   C2   180.00   0.0  0
 9JN  CONST_39  C20  C15  C7   C3   180.00   0.0  0
 9JN  CONST_40  C18  C16  S26  C11  180.00   0.0  0
 9JN  CONST_41  C18  C16  C8   C13  180.00   0.0  0
 9JN  CONST_42  H7   C7   C3   C1   180.00   0.0  0
 9JN  CONST_43  H6   C6   C2   C1   180.00   0.0  0
 9JN  CONST_44  H3   C3   C1   C2   180.00   0.0  0
 9JN  CONST_45  H2   C2   C1   C3   180.00   0.0  0
 9JN  CONST_46  H9   C9   C4   C5   180.00   0.0  0
 9JN  CONST_47  H1   C1   C2   C6   180.00   0.0  0
 9JN  CONST_48  H11  C11  C13  C8   180.00   0.0  0
 9JN  CONST_49  H5   C5   C4   C9   180.00   0.0  0
 9JN  CONST_50  H8   C8   C13  C11  180.00   0.0  0
 9JN  CONST_51  H10  C10  C14  C12  180.00   0.0  0
 9JN  CONST_52  H4   C4   C5   C12  180.00   0.0  0
 9JN  CONST_53  H15  N22  C17  C12  180.00   0.0  0
 9JN  CONST_54  C20  N23  C18  C16  180.00   0.0  0
 9JN  CONST_56  O25  C18  N23  C20    0.00   0.0  0
 9JN  Var_01    O25  C18  C16  C8    13.26  30.0  2
 9JN  Var_02    H17  N24  C19  C20   76.93  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 9JN  chir_01  C20  C15  N23  C19  positiv

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
 9JN  plan-1  C8   0.020
 9JN  plan-1  C11  0.020
 9JN  plan-1  C13  0.020
 9JN  plan-1  C14  0.020
 9JN  plan-1  C16  0.020
 9JN  plan-1  S26  0.020
 9JN  plan-1  H8   0.020
 9JN  plan-1  H11  0.020
 9JN  plan-1  C18  0.020
 9JN  plan-2  C1   0.020
 9JN  plan-2  C2   0.020
 9JN  plan-2  C3   0.020
 9JN  plan-2  C6   0.020
 9JN  plan-2  C7   0.020
 9JN  plan-2  C15  0.020
 9JN  plan-2  C20  0.020
 9JN  plan-2  H1   0.020
 9JN  plan-2  H2   0.020
 9JN  plan-2  H3   0.020
 9JN  plan-2  H6   0.020
 9JN  plan-2  H7   0.020
 9JN  plan-3  C4   0.020
 9JN  plan-3  C5   0.020
 9JN  plan-3  C9   0.020
 9JN  plan-3  C10  0.020
 9JN  plan-3  C12  0.020
 9JN  plan-3  C13  0.020
 9JN  plan-3  C14  0.020
 9JN  plan-3  C17  0.020
 9JN  plan-3  N21  0.020
 9JN  plan-3  N22  0.020
 9JN  plan-3  H5   0.020
 9JN  plan-3  H9   0.020
 9JN  plan-3  H10  0.020
 9JN  plan-3  H15  0.020
 9JN  plan-3  H4   0.020
 9JN  plan-4  C16  0.020
 9JN  plan-4  C20  0.020
 9JN  plan-4  N23  0.020
 9JN  plan-4  O25  0.020
 9JN  plan-4  H16  0.020
 9JN  plan-4  C18  0.020

