# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 16:08:42 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: ~{N}-(pyridin-2-ylmethyl)-2-(2-thiophen-2-ylindol-1-yl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cn1c2ccccc2cc1c3sccc3)NCc4ccccn4
#
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
 6UF  6UF  ~{N}-(pyridin-2-ylmethyl)-2-(2-thiophen-2-ylindol-1-yl)ethanamide  ligand  42  25  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6UF
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
 6UF  C2   C  CR16  0  -0.309  -0.5705   1.8378  -1.5028
 6UF  C3   C  CR56  0   0.362  -1.3976   0.9841  -0.7745
 6UF  C5   C  CR16  0  -0.353  -2.9341   2.7838  -0.2502
 6UF  C7   C  CR5   0   0.399  -2.3074  -0.7571   0.2889
 6UF  C9   C  C     0   0.570   1.0719  -0.9729  -0.2782
 6UF  C10  C  CH2   0  -0.352   3.4793  -0.7536  -0.4174
 6UF  C11  C  CR6   0   0.249   3.6178   0.7065  -0.0503
 6UF  C12  C  CR16  0  -0.075   3.1385   2.8779  -0.5580
 6UF  C13  C  CR16  0  -0.329   3.8568   3.3587   0.5260
 6UF  C15  C  CR16  0  -0.338   4.3578   1.0880   1.0631
 6UF  C18  C  CR15  0  -0.179  -3.5118  -4.0938   1.4181
 6UF  O    O  O     0  -0.468   1.0498  -0.7826   0.9248
 6UF  N1   N  NH1   0  -0.624   2.1981  -1.0607  -0.9986
 6UF  C14  C  CR16  0  -0.151   4.4824   2.4371   1.3527
 6UF  N2   N  N     0  -0.411   3.0240   1.5873  -0.8458
 6UF  N    N  NR5   0  -0.565  -1.2684  -0.3556  -0.5234
 6UF  C1   C  CR16  0  -0.281  -0.9538   3.1625  -1.5974
 6UF  C6   C  CR15  0  -0.454  -3.1298   0.3106   0.5344
 6UF  C4   C  CR56  0   0.077  -2.5721   1.4362  -0.1374
 6UF  C    C  CR16  0  -0.271  -2.1253   3.6316  -0.9808
 6UF  C16  C  CR5   0  -0.275  -2.4742  -2.1133   0.7792
 6UF  C19  C  CR15  0  -0.221  -3.6393  -2.8299   0.7873
 6UF  C17  C  CR15  0  -0.463  -2.2510  -4.3190   1.8799
 6UF  S    S  S2    0   0.230  -1.2109  -2.9961   1.5688
 6UF  H1   H  HCR6  0   0.258   0.3540   1.4985  -1.9537
 6UF  H2   H  HCR6  0   0.248  -3.8312   3.1545   0.2296
 6UF  H3   H  HCH2  0   0.285   4.2424  -1.0182  -1.1510
 6UF  H4   H  HCH2  0   0.264   3.6579  -1.3772   0.4593
 6UF  H5   H  HCR6  0   0.257   2.6306   3.5662  -1.2250
 6UF  H6   H  HCR6  0   0.269   3.9173   4.4212   0.7165
 6UF  H7   H  HCR6  0   0.266   4.8196   0.3395   1.6942
 6UF  H8   H  HCR5  0   0.270  -4.3196  -4.8044   1.5140
 6UF  H9   H  HNH1  0   0.406   2.1328  -1.0731  -2.0028
 6UF  H10  H  HCR6  0   0.273   5.0478   2.7628   2.2161
 6UF  H11  H  HCH2  0   0.292  -0.0818  -0.9168  -2.1240
 6UF  H12  H  HCH2  0   0.317  -0.5013  -2.2140  -1.0361
 6UF  H13  H  HCR6  0   0.249  -0.3345   3.8539  -2.1539
 6UF  H14  H  HCR5  0   0.253  -4.0080   0.2910   1.1601
 6UF  H15  H  HCR6  0   0.248  -2.3904   4.6766  -1.0761
 6UF  H16  H  HCR5  0   0.264  -4.5536  -2.4621   0.3431
 6UF  H17  H  HCR5  0   0.298  -1.8754  -5.1965   2.3836
 6UF  C8   C  CH2   0  -0.485  -0.2160  -1.1613  -1.0686

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
 6UF  C    C1   aromatic  1.405  0.020  1.405
 6UF  C    C5   aromatic  1.381  0.020  1.381
 6UF  C1   C2   aromatic  1.382  0.020  1.382
 6UF  C5   C4   aromatic  1.400  0.020  1.400
 6UF  C2   C3   aromatic  1.394  0.020  1.394
 6UF  C4   C3   aromatic  1.411  0.020  1.411
 6UF  C4   C6   aromatic  1.425  0.020  1.425
 6UF  C3   N    aromatic  1.369  0.020  1.369
 6UF  C14  C13  aromatic  1.387  0.020  1.387
 6UF  C14  C15  aromatic  1.385  0.020  1.385
 6UF  C13  C12  aromatic  1.386  0.020  1.386
 6UF  O    C9   double    1.218  0.020  1.218
 6UF  C15  C11  aromatic  1.390  0.020  1.390
 6UF  C12  N2   aromatic  1.327  0.020  1.327
 6UF  C6   C7   aromatic  1.370  0.020  1.370
 6UF  N    C8   single    1.433  0.020  1.433
 6UF  N    C7   aromatic  1.379  0.020  1.379
 6UF  C9   C8   single    1.523  0.020  1.523
 6UF  C9   N1   single    1.340  0.020  1.340
 6UF  C11  N2   aromatic  1.327  0.020  1.327
 6UF  C11  C10  single    1.512  0.020  1.512
 6UF  C7   C16  single    1.452  0.020  1.452
 6UF  C10  N1   single    1.440  0.020  1.440
 6UF  C16  C19  aromatic  1.368  0.020  1.368
 6UF  C16  S    aromatic  1.732  0.020  1.732
 6UF  C19  C18  aromatic  1.418  0.020  1.418
 6UF  S    C17  aromatic  1.711  0.020  1.711
 6UF  C18  C17  aromatic  1.362  0.020  1.362
 6UF  C2   H1   single    0.930  0.020  1.080
 6UF  C5   H2   single    0.930  0.020  1.080
 6UF  C10  H3   single    0.970  0.020  1.090
 6UF  C10  H4   single    0.970  0.020  1.090
 6UF  C12  H5   single    0.930  0.020  1.080
 6UF  C13  H6   single    0.930  0.020  1.080
 6UF  C15  H7   single    0.930  0.020  1.080
 6UF  C18  H8   single    0.930  0.020  1.080
 6UF  N1   H9   single    0.860  0.020  1.020
 6UF  C14  H10  single    0.930  0.020  1.080
 6UF  C8   H11  single    0.970  0.020  1.090
 6UF  C8   H12  single    0.970  0.020  1.090
 6UF  C1   H13  single    0.930  0.020  1.080
 6UF  C6   H14  single    0.930  0.020  1.080
 6UF  C    H15  single    0.930  0.020  1.080
 6UF  C19  H16  single    0.930  0.020  1.080
 6UF  C17  H17  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
 6UF  H1   C2   C1   120.56  3.000
 6UF  H1   C2   C3   122.14  3.000
 6UF  C1   C2   C3   117.27  3.000
 6UF  C4   C3   N    108.02  3.000
 6UF  N    C3   C2   129.72  3.000
 6UF  C4   C3   C2   122.25  3.000
 6UF  H2   C5   C    120.63  3.000
 6UF  H2   C5   C4   120.54  3.000
 6UF  C    C5   C4   118.83  3.000
 6UF  C16  C7   C6   126.77  3.000
 6UF  C16  C7   N    123.90  3.000
 6UF  C6   C7   N    109.33  3.000
 6UF  C8   C9   N1   115.07  3.000
 6UF  N1   C9   O    123.82  3.000
 6UF  C8   C9   O    121.10  3.000
 6UF  H4   C10  H3   106.70  3.000
 6UF  H4   C10  N1   110.38  3.000
 6UF  H3   C10  N1   107.41  3.000
 6UF  H4   C10  C11  110.00  3.000
 6UF  H3   C10  C11  109.47  3.000
 6UF  N1   C10  C11  112.67  3.000
 6UF  N2   C11  C15  122.42  3.000
 6UF  N2   C11  C10  117.03  3.000
 6UF  C15  C11  C10  120.54  3.000
 6UF  H5   C12  N2   116.32  3.000
 6UF  H5   C12  C13  120.22  3.000
 6UF  N2   C12  C13  123.46  3.000
 6UF  H6   C13  C14  121.51  3.000
 6UF  H6   C13  C12  120.50  3.000
 6UF  C14  C13  C12  117.99  3.000
 6UF  H7   C15  C14  120.86  3.000
 6UF  H7   C15  C11  120.29  3.000
 6UF  C14  C15  C11  118.85  3.000
 6UF  H8   C18  C17  123.61  3.000
 6UF  H8   C18  C19  123.96  3.000
 6UF  C17  C18  C19  112.43  3.000
 6UF  H9   N1   C10  117.59  3.000
 6UF  H9   N1   C9   118.87  3.000
 6UF  C10  N1   C9   121.12  3.000
 6UF  H10  C14  C15  120.46  3.000
 6UF  H10  C14  C13  120.73  3.000
 6UF  C15  C14  C13  118.80  3.000
 6UF  C12  N2   C11  118.48  3.000
 6UF  C8   N    C7   127.87  3.000
 6UF  C7   N    C3   108.78  3.000
 6UF  C8   N    C3   123.34  3.000
 6UF  H13  C1   C    119.32  3.000
 6UF  H13  C1   C2   119.26  3.000
 6UF  C    C1   C2   121.42  3.000
 6UF  H14  C6   C4   127.35  3.000
 6UF  H14  C6   C7   125.35  3.000
 6UF  C4   C6   C7   107.24  3.000
 6UF  C6   C4   C5   134.22  3.000
 6UF  C6   C4   C3   106.60  3.000
 6UF  C5   C4   C3   119.17  3.000
 6UF  H15  C    C1   119.22  3.000
 6UF  H15  C    C5   119.73  3.000
 6UF  C1   C    C5   121.05  3.000
 6UF  S    C16  C19  110.58  3.000
 6UF  S    C16  C7   123.12  3.000
 6UF  C19  C16  C7   126.11  3.000
 6UF  H16  C19  C16  122.66  3.000
 6UF  H16  C19  C18  124.19  3.000
 6UF  C16  C19  C18  113.14  3.000
 6UF  H17  C17  S    120.13  3.000
 6UF  H17  C17  C18  127.96  3.000
 6UF  S    C17  C18  111.92  3.000
 6UF  C17  S    C16   91.93  3.000
 6UF  H12  C8   H11  106.08  3.000
 6UF  H12  C8   N    109.82  3.000
 6UF  H11  C8   N    109.40  3.000
 6UF  H12  C8   C9   108.96  3.000
 6UF  H11  C8   C9   111.73  3.000
 6UF  N    C8   C9   110.73  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
 6UF  CONST_01  C5   C    C1   C2     0.00   0.0  0
 6UF  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 6UF  CONST_03  C6   C4   C3   C2   180.00   0.0  0
 6UF  CONST_04  C7   N    C3   C2   180.00   0.0  0
 6UF  CONST_05  C    C1   C2   C3     0.00   0.0  0
 6UF  CONST_06  C    C5   C4   C3     0.00   0.0  0
 6UF  CONST_07  C7   C6   C4   C3     0.00   0.0  0
 6UF  CONST_08  C6   C7   N    C3     0.00   0.0  0
 6UF  CONST_09  C16  C7   N    C3   180.00   0.0  0
 6UF  CONST_10  N    C3   C4   C5   180.00   0.0  0
 6UF  CONST_11  C7   C6   C4   C5   180.00   0.0  0
 6UF  CONST_12  C4   C3   N    C7     0.00   0.0  0
 6UF  CONST_13  C18  C19  C16  C7   180.00   0.0  0
 6UF  CONST_14  C17  S    C16  C7   180.00   0.0  0
 6UF  CONST_15  C13  C14  C15  C11    0.00   0.0  0
 6UF  CONST_16  C13  C12  N2   C11    0.00   0.0  0
 6UF  CONST_17  C15  C14  C13  C12    0.00   0.0  0
 6UF  CONST_18  C15  C11  N2   C12    0.00   0.0  0
 6UF  CONST_19  S    C16  C19  C18    0.00   0.0  0
 6UF  CONST_20  C16  S    C17  C18    0.00   0.0  0
 6UF  CONST_21  N2   C12  C13  C14    0.00   0.0  0
 6UF  CONST_22  N2   C11  C15  C14    0.00   0.0  0
 6UF  CONST_23  C1   C2   C3   N    180.00   0.0  0
 6UF  CONST_24  C6   C4   C3   N      0.00   0.0  0
 6UF  CONST_25  C4   C6   C7   N      0.00   0.0  0
 6UF  CONST_28  C4   C5   C    C1     0.00   0.0  0
 6UF  CONST_29  C4   C3   C2   C1     0.00   0.0  0
 6UF  CONST_30  C    C5   C4   C6   180.00   0.0  0
 6UF  CONST_33  C16  C7   C6   C4   180.00   0.0  0
 6UF  CONST_34  C17  C18  C19  C16    0.00   0.0  0
 6UF  CONST_35  C17  S    C16  C19    0.00   0.0  0
 6UF  CONST_36  S    C17  C18  C19    0.00   0.0  0
 6UF  CONST_37  C8   N    C3   C2     0.00   0.0  0
 6UF  CONST_38  C14  C15  C11  C10  180.00   0.0  0
 6UF  CONST_39  C12  N2   C11  C10  180.00   0.0  0
 6UF  CONST_40  C4   C3   N    C8   180.00   0.0  0
 6UF  CONST_41  C6   C7   N    C8   180.00   0.0  0
 6UF  CONST_42  C16  C7   N    C8     0.00   0.0  0
 6UF  CONST_43  H15  C    C1   C2   180.00   0.0  0
 6UF  CONST_44  H13  C1   C2   C3   180.00   0.0  0
 6UF  CONST_45  H2   C5   C4   C3   180.00   0.0  0
 6UF  CONST_46  H14  C6   C4   C3   180.00   0.0  0
 6UF  CONST_47  H16  C19  C16  C7     0.00   0.0  0
 6UF  CONST_48  H10  C14  C15  C11  180.00   0.0  0
 6UF  CONST_49  H5   C12  N2   C11  180.00   0.0  0
 6UF  CONST_50  H7   C15  C14  C13  180.00   0.0  0
 6UF  CONST_51  H6   C13  C14  C15  180.00   0.0  0
 6UF  CONST_52  H1   C2   C3   N      0.00   0.0  0
 6UF  CONST_53  H8   C18  C19  C16  180.00   0.0  0
 6UF  CONST_54  H17  C17  S    C16  180.00   0.0  0
 6UF  CONST_55  O    C9   N1   C10    0.00   0.0  0
 6UF  CONST_56  C8   C9   N1   C10  180.00   0.0  0
 6UF  CONST_57  H9   N1   C9   O    180.00   0.0  0
 6UF  Var_01    C9   C8   N    C3    79.64  30.0  2
 6UF  Var_02    N1   C10  C11  C15  146.08  30.0  2
 6UF  Var_03    C11  C10  N1   C9   -66.42  30.0  1
 6UF  Var_04    N    C8   C9   O     34.52  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
 6UF  plan-1  C7   0.020
 6UF  plan-1  C18  0.020
 6UF  plan-1  C16  0.020
 6UF  plan-1  C19  0.020
 6UF  plan-1  C17  0.020
 6UF  plan-1  S    0.020
 6UF  plan-1  H8   0.020
 6UF  plan-1  H16  0.020
 6UF  plan-1  H17  0.020
 6UF  plan-2  C10  0.020
 6UF  plan-2  C11  0.020
 6UF  plan-2  C12  0.020
 6UF  plan-2  C13  0.020
 6UF  plan-2  C15  0.020
 6UF  plan-2  C14  0.020
 6UF  plan-2  N2   0.020
 6UF  plan-2  H5   0.020
 6UF  plan-2  H6   0.020
 6UF  plan-2  H7   0.020
 6UF  plan-2  H10  0.020
 6UF  plan-3  C2   0.020
 6UF  plan-3  C3   0.020
 6UF  plan-3  C5   0.020
 6UF  plan-3  C7   0.020
 6UF  plan-3  N    0.020
 6UF  plan-3  C1   0.020
 6UF  plan-3  C6   0.020
 6UF  plan-3  C4   0.020
 6UF  plan-3  C    0.020
 6UF  plan-3  C16  0.020
 6UF  plan-3  H1   0.020
 6UF  plan-3  H2   0.020
 6UF  plan-3  H13  0.020
 6UF  plan-3  H14  0.020
 6UF  plan-3  H15  0.020
 6UF  plan-3  C8   0.020
 6UF  plan-4  C9   0.020
 6UF  plan-4  C10  0.020
 6UF  plan-4  O    0.020
 6UF  plan-4  N1   0.020
 6UF  plan-4  H9   0.020
 6UF  plan-4  C8   0.020

