# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:50:22 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: 3-[(4-fluorophenyl)methyl]-5-(1-piperidin-4-ylpyrazol-4-yl)-1~{H}-pyrrolo[2,3-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(Cc2c[nH]c3ncc(cc23)c4cnn(c4)C5CCNCC5)cc1
#
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
 SW5  SW5  3-[(4-fluorophenyl)methyl]-5-(1-piperidin-4-ylpyrazol-4-yl)-1~{H}-pyrrolo[2,3-b]pyridine  ligand  50  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SW5
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
 SW5  C1   C  CR16  0  -0.398  29.2753  193.8720  77.4310
 SW5  C2   C  CR16  0  -0.290  29.5978  195.0118  78.1575
 SW5  C3   C  CR6   0   0.087  29.4930  196.2801  77.5969
 SW5  C7   C  CR56  0   0.459  27.2093  199.7656  79.8631
 SW5  C8   C  CR16  0  -0.151  27.6810  201.7704  80.7353
 SW5  C9   C  CR6   0   0.002  29.0589  201.6338  80.4763
 SW5  C10  C  CR16  0  -0.332  29.4971  200.4635  79.8645
 SW5  C11  C  CR56  0   0.025  28.5567  199.4945  79.5372
 SW5  C12  C  CR5   0  -0.154  29.9931  202.6985  80.8365
 SW5  C13  C  CR15  0  -0.096  31.3594  202.8049  80.5050
 SW5  C14  C  CR15  0   0.021  29.7564  203.8441  81.5752
 SW5  C15  C  CH1   0  -0.067  31.1515  205.7861  82.3192
 SW5  C16  C  CH2   0  -0.439  32.1070  205.6146  83.4957
 SW5  C19  C  CH2   0  -0.441  31.6648  206.8532  81.3592
 SW5  C20  C  CR16  0  -0.273  29.0496  196.3877  76.2804
 SW5  C21  C  CR16  0  -0.398  28.7218  195.2645  75.5359
 SW5  C    C  CR6   0   0.509  28.8417  194.0220  76.1296
 SW5  C4   C  CH2   0  -0.569  29.8130  197.5122  78.3974
 SW5  C5   C  CR5   0  -0.061  28.5906  198.2077  78.9120
 SW5  N    N  NR15  0  -0.674  26.4673  198.6999  79.4631
 SW5  C6   C  CR15  0  -0.030  27.2963  197.7702  78.8908
 SW5  N1   N  N     0  -0.417  26.7614  200.8651  80.4459
 SW5  N3   N  NR5   0  -0.287  30.9129  204.5241  81.6363
 SW5  N2   N  N     0  -0.279  31.8961  203.9059  80.9944
 SW5  C18  C  CH2   0  -0.322  31.9269  208.1544  82.1186
 SW5  N4   N  NH1   0  -0.574  32.8160  208.0030  83.2580
 SW5  C17  C  CH2   0  -0.322  32.3559  206.9668  84.1660
 SW5  H1   H  HCR6  0   0.278  29.3652  192.8877  77.8720
 SW5  H2   H  HCR6  0   0.260  29.9394  194.9028  79.1798
 SW5  H3   H  HCR6  0   0.246  27.3131  202.6781  81.2017
 SW5  H4   H  HCR6  0   0.249  30.5477  200.3072  79.6506
 SW5  H5   H  HCR5  0   0.256  31.9636  202.1242  79.9234
 SW5  H6   H  HCR5  0   0.288  28.8649  204.2156  82.0548
 SW5  H7   H  HCH1  0   0.255  30.1743  206.0970  82.7001
 SW5  H8   H  HCH2  0   0.240  31.6917  204.9086  84.2193
 SW5  H9   H  HCH2  0   0.232  33.0534  205.1996  83.1370
 SW5  H10  H  HCH2  0   0.241  30.9393  207.0195  80.5593
 SW5  H11  H  HCH2  0   0.232  32.5930  206.5086  80.8949
 SW5  H12  H  HCR6  0   0.261  28.9558  197.3655  75.8234
 SW5  H13  H  HCR6  0   0.278  28.3824  195.3553  74.5122
 SW5  H14  H  HCH2  0   0.259  30.4664  197.2452  79.2335
 SW5  H15  H  HCH2  0   0.256  30.3886  198.2107  77.7824
 SW5  H16  H  HNR5  0   0.409  25.4690  198.6120  79.5567
 SW5  H17  H  HCR5  0   0.285  26.8917  196.8511  78.4983
 SW5  H18  H  HCH2  0   0.243  32.3475  208.8980  81.4393
 SW5  H19  H  HCH2  0   0.220  30.9763  208.5635  82.4781
 SW5  H20  H  HNH1  0   0.341  33.7424  207.7634  82.9232
 SW5  H22  H  HCH2  0   0.243  33.0839  206.8524  84.9707
 SW5  H23  H  HCH2  0   0.220  31.4271  207.3129  84.6329
 SW5  F    F  F     0  -0.318  28.5310  192.9260  75.4152

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
 SW5  F    C    single    1.345  0.020  1.345
 SW5  C21  C    aromatic  1.382  0.020  1.382
 SW5  C21  C20  aromatic  1.387  0.020  1.387
 SW5  C    C1   aromatic  1.380  0.020  1.380
 SW5  C20  C3   aromatic  1.393  0.020  1.393
 SW5  C1   C2   aromatic  1.390  0.020  1.390
 SW5  C3   C2   aromatic  1.391  0.020  1.391
 SW5  C3   C4   single    1.504  0.020  1.504
 SW5  C4   C5   single    1.498  0.020  1.498
 SW5  C6   C5   aromatic  1.366  0.020  1.366
 SW5  C6   N    aromatic  1.371  0.020  1.371
 SW5  C5   C11  aromatic  1.431  0.020  1.431
 SW5  N    C7   aromatic  1.359  0.020  1.359
 SW5  C11  C10  aromatic  1.389  0.020  1.389
 SW5  C11  C7   aromatic  1.412  0.020  1.412
 SW5  C10  C9   aromatic  1.391  0.020  1.391
 SW5  C7   N1   aromatic  1.323  0.020  1.323
 SW5  C13  C12  aromatic  1.410  0.020  1.410
 SW5  C13  N2   aromatic  1.319  0.020  1.319
 SW5  N1   C8   aromatic  1.322  0.020  1.322
 SW5  C9   C8   aromatic  1.409  0.020  1.409
 SW5  C9   C12  single    1.461  0.020  1.461
 SW5  C12  C14  aromatic  1.384  0.020  1.384
 SW5  N2   N3   aromatic  1.327  0.020  1.327
 SW5  C19  C18  single    1.529  0.020  1.529
 SW5  C19  C15  single    1.524  0.020  1.524
 SW5  C14  N3   aromatic  1.343  0.020  1.343
 SW5  N3   C15  single    1.455  0.020  1.455
 SW5  C18  N4   single    1.453  0.020  1.453
 SW5  C15  C16  single    1.525  0.020  1.525
 SW5  N4   C17  single    1.453  0.020  1.453
 SW5  C16  C17  single    1.530  0.020  1.530
 SW5  C1   H1   single    0.930  0.020  1.080
 SW5  C2   H2   single    0.930  0.020  1.080
 SW5  C8   H3   single    0.930  0.020  1.080
 SW5  C10  H4   single    0.930  0.020  1.080
 SW5  C13  H5   single    0.930  0.020  1.080
 SW5  C14  H6   single    0.930  0.020  1.080
 SW5  C15  H7   single    0.970  0.020  1.090
 SW5  C16  H8   single    0.970  0.020  1.090
 SW5  C16  H9   single    0.970  0.020  1.090
 SW5  C19  H10  single    0.970  0.020  1.090
 SW5  C19  H11  single    0.970  0.020  1.090
 SW5  C20  H12  single    0.930  0.020  1.080
 SW5  C21  H13  single    0.930  0.020  1.080
 SW5  C4   H14  single    0.970  0.020  1.090
 SW5  C4   H15  single    0.970  0.020  1.090
 SW5  N    H16  single    0.860  0.020  1.020
 SW5  C6   H17  single    0.930  0.020  1.080
 SW5  C18  H18  single    0.970  0.020  1.090
 SW5  C18  H19  single    0.970  0.020  1.090
 SW5  N4   H20  single    0.890  0.020  1.040
 SW5  C17  H22  single    0.970  0.020  1.090
 SW5  C17  H23  single    0.970  0.020  1.090

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
 SW5  H1   C1   C    120.61  3.000
 SW5  H1   C1   C2   120.91  3.000
 SW5  C    C1   C2   118.48  3.000
 SW5  H2   C2   C3   119.73  3.000
 SW5  H2   C2   C1   118.95  3.000
 SW5  C3   C2   C1   121.32  3.000
 SW5  C4   C3   C20  120.49  3.000
 SW5  C4   C3   C2   121.11  3.000
 SW5  C20  C3   C2   118.38  3.000
 SW5  N1   C7   N    126.64  3.000
 SW5  N1   C7   C11  125.75  3.000
 SW5  N    C7   C11  107.60  3.000
 SW5  H3   C8   N1   115.54  3.000
 SW5  H3   C8   C9   119.47  3.000
 SW5  N1   C8   C9   125.00  3.000
 SW5  C12  C9   C10  121.31  3.000
 SW5  C12  C9   C8   120.62  3.000
 SW5  C10  C9   C8   118.07  3.000
 SW5  H4   C10  C11  120.61  3.000
 SW5  H4   C10  C9   120.90  3.000
 SW5  C11  C10  C9   118.49  3.000
 SW5  C5   C11  C10  135.56  3.000
 SW5  C10  C11  C7   117.22  3.000
 SW5  C5   C11  C7   107.22  3.000
 SW5  C14  C12  C13  103.23  3.000
 SW5  C14  C12  C9   128.71  3.000
 SW5  C13  C12  C9   128.06  3.000
 SW5  H5   C13  N2   119.88  3.000
 SW5  H5   C13  C12  128.40  3.000
 SW5  N2   C13  C12  111.72  3.000
 SW5  H6   C14  N3   121.15  3.000
 SW5  H6   C14  C12  131.62  3.000
 SW5  N3   C14  C12  107.23  3.000
 SW5  H7   C15  N3   105.28  3.000
 SW5  H7   C15  C19  108.73  3.000
 SW5  N3   C15  C19  111.52  3.000
 SW5  H7   C15  C16  108.84  3.000
 SW5  N3   C15  C16  111.55  3.000
 SW5  C19  C15  C16  110.70  3.000
 SW5  H9   C16  H8   107.50  3.000
 SW5  H9   C16  C17  109.77  3.000
 SW5  H8   C16  C17  110.04  3.000
 SW5  H9   C16  C15  109.37  3.000
 SW5  H8   C16  C15  110.20  3.000
 SW5  C17  C16  C15  109.91  3.000
 SW5  H11  C19  H10  107.50  3.000
 SW5  H11  C19  C18  109.48  3.000
 SW5  H10  C19  C18  110.35  3.000
 SW5  H11  C19  C15  109.42  3.000
 SW5  H10  C19  C15  110.12  3.000
 SW5  C18  C19  C15  109.91  3.000
 SW5  H12  C20  C21  118.95  3.000
 SW5  H12  C20  C3   119.72  3.000
 SW5  C21  C20  C3   121.33  3.000
 SW5  H13  C21  C    120.59  3.000
 SW5  H13  C21  C20  120.93  3.000
 SW5  C    C21  C20  118.49  3.000
 SW5  F    C    C21  118.97  3.000
 SW5  C21  C    C1   122.00  3.000
 SW5  F    C    C1   119.02  3.000
 SW5  H15  C4   H14  105.73  3.000
 SW5  H15  C4   C5   109.03  3.000
 SW5  H14  C4   C5   109.76  3.000
 SW5  H15  C4   C3   109.62  3.000
 SW5  H14  C4   C3   109.50  3.000
 SW5  C5   C4   C3   112.94  3.000
 SW5  C6   C5   C4   128.25  3.000
 SW5  C6   C5   C11  105.80  3.000
 SW5  C4   C5   C11  125.95  3.000
 SW5  H16  N    C6   125.41  3.000
 SW5  H16  N    C7   125.65  3.000
 SW5  C6   N    C7   108.94  3.000
 SW5  H17  C6   N    120.21  3.000
 SW5  H17  C6   C5   129.35  3.000
 SW5  N    C6   C5   110.44  3.000
 SW5  C8   N1   C7   115.47  3.000
 SW5  N2   N3   C15  120.65  3.000
 SW5  C15  N3   C14  127.01  3.000
 SW5  N2   N3   C14  112.34  3.000
 SW5  N3   N2   C13  105.48  3.000
 SW5  H19  C18  H18  106.51  3.000
 SW5  H19  C18  N4   108.21  3.000
 SW5  H18  C18  N4   108.86  3.000
 SW5  H19  C18  C19  109.39  3.000
 SW5  H18  C18  C19  109.67  3.000
 SW5  N4   C18  C19  113.93  3.000
 SW5  H20  N4   C17  109.10  3.000
 SW5  H20  N4   C18  108.96  3.000
 SW5  C17  N4   C18  111.76  3.000
 SW5  H23  C17  H22  106.52  3.000
 SW5  H23  C17  N4   108.04  3.000
 SW5  H22  C17  N4   108.94  3.000
 SW5  H23  C17  C16  109.15  3.000
 SW5  H22  C17  C16  109.82  3.000
 SW5  N4   C17  C16  114.09  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
 SW5  CONST_01  C20  C21  C    C1      0.00   0.0  0
 SW5  CONST_02  C20  C3   C2   C1      0.00   0.0  0
 SW5  CONST_03  C21  C    C1   C2      0.00   0.0  0
 SW5  CONST_04  C21  C20  C3   C2      0.00   0.0  0
 SW5  CONST_05  C    C21  C20  C3      0.00   0.0  0
 SW5  CONST_06  C    C1   C2   C3      0.00   0.0  0
 SW5  CONST_07  C5   C6   N    C7      0.00   0.0  0
 SW5  CONST_08  C6   C5   C11  C7      0.00   0.0  0
 SW5  CONST_09  C9   C10  C11  C7      0.00   0.0  0
 SW5  CONST_10  C9   C8   N1   C7      0.00   0.0  0
 SW5  CONST_11  N    C7   N1   C8    180.00   0.0  0
 SW5  CONST_12  C11  C7   N1   C8      0.00   0.0  0
 SW5  CONST_13  C11  C10  C9   C8      0.00   0.0  0
 SW5  CONST_14  C13  C12  C9   C8    180.00   0.0  0
 SW5  CONST_15  C14  C12  C9   C8      0.00   0.0  0
 SW5  CONST_16  C5   C11  C10  C9    180.00   0.0  0
 SW5  CONST_17  N2   C13  C12  C9    180.00   0.0  0
 SW5  CONST_18  N3   C14  C12  C9    180.00   0.0  0
 SW5  CONST_19  C6   C5   C11  C10   180.00   0.0  0
 SW5  CONST_20  N    C7   C11  C10   180.00   0.0  0
 SW5  CONST_21  N1   C7   C11  C10     0.00   0.0  0
 SW5  CONST_22  N1   C8   C9   C10     0.00   0.0  0
 SW5  CONST_23  C13  C12  C9   C10     0.00   0.0  0
 SW5  CONST_24  C14  C12  C9   C10   180.00   0.0  0
 SW5  CONST_25  N    C6   C5   C11     0.00   0.0  0
 SW5  CONST_26  C12  C9   C10  C11   180.00   0.0  0
 SW5  CONST_27  C6   N    C7   C11     0.00   0.0  0
 SW5  CONST_28  N3   N2   C13  C12     0.00   0.0  0
 SW5  CONST_29  N1   C8   C9   C12   180.00   0.0  0
 SW5  CONST_30  N2   N3   C14  C12     0.00   0.0  0
 SW5  CONST_31  N3   C14  C12  C13     0.00   0.0  0
 SW5  CONST_32  C14  N3   N2   C13     0.00   0.0  0
 SW5  CONST_33  N2   C13  C12  C14     0.00   0.0  0
 SW5  CONST_34  N    C7   C11  C5      0.00   0.0  0
 SW5  CONST_35  N1   C7   C11  C5    180.00   0.0  0
 SW5  CONST_36  N1   C7   N    C6    180.00   0.0  0
 SW5  CONST_37  C15  N3   C14  C12   180.00   0.0  0
 SW5  CONST_38  C15  N3   N2   C13   180.00   0.0  0
 SW5  CONST_39  C4   C3   C2   C1    180.00   0.0  0
 SW5  CONST_40  F    C    C1   C2    180.00   0.0  0
 SW5  CONST_41  C4   C5   C11  C7    180.00   0.0  0
 SW5  CONST_42  C4   C5   C11  C10     0.00   0.0  0
 SW5  CONST_43  F    C    C21  C20   180.00   0.0  0
 SW5  CONST_44  C4   C3   C20  C21   180.00   0.0  0
 SW5  CONST_45  N    C6   C5   C4    180.00   0.0  0
 SW5  CONST_46  H13  C21  C    C1    180.00   0.0  0
 SW5  CONST_47  H12  C20  C3   C2    180.00   0.0  0
 SW5  CONST_48  H1   C1   C2   C3    180.00   0.0  0
 SW5  CONST_49  H17  C6   N    C7    180.00   0.0  0
 SW5  CONST_50  H4   C10  C11  C7    180.00   0.0  0
 SW5  CONST_51  H3   C8   N1   C7    180.00   0.0  0
 SW5  CONST_52  H5   C13  C12  C9      0.00   0.0  0
 SW5  CONST_53  H6   C14  C12  C9      0.00   0.0  0
 SW5  CONST_54  H16  N    C7   C11   180.00   0.0  0
 SW5  CONST_55  H2   C2   C3   C20   180.00   0.0  0
 SW5  Var_01    N4   C18  C19  C15    54.52  30.0  1
 SW5  Var_02    N4   C17  C16  C15   -54.13  30.0  1
 SW5  Var_03    C18  N4   C17  C16    53.67  30.0  1
 SW5  Var_04    C17  N4   C18  C19   -53.82  30.0  1
 SW5  Var_05    C5   C4   C3   C2   -100.61  30.0  2
 SW5  Var_06    C6   C5   C4   C3      9.40  30.0  2

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
 SW5  chir_01  C15  C19  N3  C16  negativ

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
 SW5  plan-1  C9   0.020
 SW5  plan-1  C12  0.020
 SW5  plan-1  C13  0.020
 SW5  plan-1  C14  0.020
 SW5  plan-1  C15  0.020
 SW5  plan-1  N3   0.020
 SW5  plan-1  N2   0.020
 SW5  plan-1  H5   0.020
 SW5  plan-1  H6   0.020
 SW5  plan-2  C1   0.020
 SW5  plan-2  C2   0.020
 SW5  plan-2  C3   0.020
 SW5  plan-2  C20  0.020
 SW5  plan-2  C21  0.020
 SW5  plan-2  C    0.020
 SW5  plan-2  C4   0.020
 SW5  plan-2  H1   0.020
 SW5  plan-2  H2   0.020
 SW5  plan-2  H12  0.020
 SW5  plan-2  H13  0.020
 SW5  plan-2  F    0.020
 SW5  plan-3  C7   0.020
 SW5  plan-3  C8   0.020
 SW5  plan-3  C9   0.020
 SW5  plan-3  C10  0.020
 SW5  plan-3  C11  0.020
 SW5  plan-3  C12  0.020
 SW5  plan-3  C4   0.020
 SW5  plan-3  C5   0.020
 SW5  plan-3  N    0.020
 SW5  plan-3  C6   0.020
 SW5  plan-3  N1   0.020
 SW5  plan-3  H3   0.020
 SW5  plan-3  H4   0.020
 SW5  plan-3  H16  0.020
 SW5  plan-3  H17  0.020

