# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:53:48 2021
#   Inital geometry file: a 133 line input string
#   Ligand name: 4-~{tert}-butyl-~{N}-[[4-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)phenyl]methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1ccc(cc1)C(=O)NCc2ccc(cc2)c3ncnc4[nH]ccc34
#
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
 S5M  S5M  4-~{tert}-butyl-~{N}-[[4-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)phenyl]methyl]benzamide  ligand  53  29  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S5M
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
 S5M  N1   N  N     0  -0.422   0.3828  18.0354   5.2842
 S5M  N3   N  NH1   0  -0.656   6.7998  23.7232   8.8225
 S5M  C4   C  CR56  0  -0.002   0.6584  20.3106   6.1078
 S5M  C5   C  CR6   0   0.210   2.0405  20.1023   6.1406
 S5M  C6   C  CR6   0   0.046   3.0060  21.1281   6.5701
 S5M  C7   C  CR16  0  -0.267   4.1777  20.7528   7.2252
 S5M  C8   C  CR16  0  -0.285   5.0936  21.7044   7.6451
 S5M  C13  C  CR16  0  -0.246  10.2355  22.7910   9.5988
 S5M  C15  C  CR6   0   0.197  10.4979  22.0340  11.8876
 S5M  C17  C  CH3   0  -0.636  10.8519  20.2495  13.6019
 S5M  C20  C  CR16  0  -0.293   9.1076  22.0886  12.0130
 S5M  C21  C  CR16  0  -0.286   8.2985  22.4867  10.9640
 S5M  C22  C  CR16  0  -0.277   3.7142  23.4305   6.7336
 S5M  C24  C  CR16  0   0.025   1.6978  17.9614   5.3822
 S5M  C1   C  CR56  0   0.496  -0.1058  19.2086   5.6579
 S5M  C11  C  C     0   0.532   8.0379  23.2651   8.5574
 S5M  C12  C  CR6   0  -0.053   8.8539  22.8512   9.7378
 S5M  C14  C  CR16  0  -0.325  11.0414  22.3965  10.6568
 S5M  C18  C  CH3   0  -0.628  11.2255  22.6623  14.1800
 S5M  C19  C  CH3   0  -0.666  12.8255  21.4559  12.7082
 S5M  C2   C  CR15  0   0.009  -1.5108  20.8431   6.1787
 S5M  C23  C  CR16  0  -0.300   2.7886  22.4845   6.3266
 S5M  C3   C  CR15  0  -0.471  -0.2711  21.3435   6.4427
 S5M  C9   C  CR6   0   0.087   4.8770  23.0563   7.4018
 S5M  N2   N  NR15  0  -0.659  -1.4099  19.5605   5.7054
 S5M  N4   N  N     0  -0.443   2.5317  18.9162   5.7862
 S5M  O1   O  O     0  -0.482   8.4851  23.1921   7.4208
 S5M  H1   H  HNH1  0   0.411   6.5050  23.8295   9.7783
 S5M  H2   H  HCR6  0   0.255   4.3697  19.7061   7.4203
 S5M  H3   H  HCR6  0   0.248   5.9799  21.3770   8.1727
 S5M  H4   H  HCH2  0   0.273   6.4221  24.4524   6.9245
 S5M  H5   H  HCH2  0   0.273   5.3238  24.9994   8.1676
 S5M  H6   H  HCR6  0   0.256  10.6930  23.0610   8.6562
 S5M  H7   H  HCH3  0   0.231  11.4600  19.9318  14.4509
 S5M  H8   H  HCH3  0   0.230   9.8165  20.2891  13.9414
 S5M  H9   H  HCH3  0   0.231  10.9220  19.4797  12.8318
 S5M  H10  H  HCR6  0   0.254   8.6348  21.8081  12.9457
 S5M  H11  H  HCR6  0   0.252   7.2261  22.4786  11.1163
 S5M  H12  H  HCR6  0   0.256   3.5252  24.4775   6.5272
 S5M  H13  H  HCR6  0   0.253   2.1521  17.0184   5.0995
 S5M  H14  H  HCR6  0   0.256  12.1112  22.3744  10.5012
 S5M  H15  H  HCH3  0   0.229  11.8000  22.3603  15.0582
 S5M  H16  H  HCH3  0   0.230  11.6093  23.6268  13.8433
 S5M  H17  H  HCH3  0   0.230  10.1912  22.8067  14.4957
 S5M  H18  H  HCH3  0   0.239  13.3871  21.1187  13.5810
 S5M  H19  H  HCH3  0   0.232  12.9777  20.7198  11.9165
 S5M  H20  H  HCH3  0   0.232  13.2673  22.3994  12.3838
 S5M  H21  H  HCR5  0   0.296  -2.4775  21.3031   6.3023
 S5M  H22  H  HCR6  0   0.259   1.9063  22.8123   5.7933
 S5M  H23  H  HCR5  0   0.263  -0.0633  22.3215   6.8426
 S5M  H24  H  HNR5  0   0.419  -2.1834  18.9770   5.4283
 S5M  C10  C  CH2   0  -0.337   5.8661  24.1256   7.8045
 S5M  C16  C  CT    0  -0.175  11.3489  21.6029  13.0757

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
 S5M  N1   C24  aromatic  1.321  0.020  1.321
 S5M  N1   C1   aromatic  1.325  0.020  1.325
 S5M  C24  N4   aromatic  1.330  0.020  1.330
 S5M  N2   C1   aromatic  1.352  0.020  1.352
 S5M  N2   C2   aromatic  1.371  0.020  1.371
 S5M  C1   C4   aromatic  1.414  0.020  1.414
 S5M  N4   C5   aromatic  1.332  0.020  1.332
 S5M  C2   C3   aromatic  1.363  0.020  1.363
 S5M  C4   C5   aromatic  1.398  0.020  1.398
 S5M  C4   C3   aromatic  1.429  0.020  1.429
 S5M  C5   C6   single    1.473  0.020  1.473
 S5M  C23  C6   aromatic  1.395  0.020  1.395
 S5M  C23  C22  aromatic  1.385  0.020  1.385
 S5M  C6   C7   aromatic  1.394  0.020  1.394
 S5M  C22  C9   aromatic  1.392  0.020  1.392
 S5M  C7   C8   aromatic  1.386  0.020  1.386
 S5M  O1   C11  double    1.224  0.020  1.224
 S5M  C9   C8   aromatic  1.391  0.020  1.391
 S5M  C9   C10  single    1.511  0.020  1.511
 S5M  C10  N3   single    1.439  0.020  1.439
 S5M  C11  N3   single    1.346  0.020  1.346
 S5M  C11  C12  single    1.494  0.020  1.494
 S5M  C13  C12  aromatic  1.390  0.020  1.390
 S5M  C13  C14  aromatic  1.387  0.020  1.387
 S5M  C12  C21  aromatic  1.395  0.020  1.395
 S5M  C14  C15  aromatic  1.393  0.020  1.393
 S5M  C21  C20  aromatic  1.383  0.020  1.383
 S5M  C15  C20  aromatic  1.397  0.020  1.397
 S5M  C15  C16  single    1.524  0.020  1.524
 S5M  C19  C16  single    1.529  0.020  1.529
 S5M  C16  C18  single    1.535  0.020  1.535
 S5M  C16  C17  single    1.535  0.020  1.535
 S5M  N3   H1   single    0.860  0.020  1.020
 S5M  C7   H2   single    0.930  0.020  1.080
 S5M  C8   H3   single    0.930  0.020  1.080
 S5M  C10  H4   single    0.970  0.020  1.090
 S5M  C10  H5   single    0.970  0.020  1.090
 S5M  C13  H6   single    0.930  0.020  1.080
 S5M  C17  H7   single    0.970  0.020  1.090
 S5M  C17  H8   single    0.970  0.020  1.090
 S5M  C17  H9   single    0.970  0.020  1.090
 S5M  C20  H10  single    0.930  0.020  1.080
 S5M  C21  H11  single    0.930  0.020  1.080
 S5M  C22  H12  single    0.930  0.020  1.080
 S5M  C24  H13  single    0.930  0.020  1.080
 S5M  C14  H14  single    0.930  0.020  1.080
 S5M  C18  H15  single    0.970  0.020  1.090
 S5M  C18  H16  single    0.970  0.020  1.090
 S5M  C18  H17  single    0.970  0.020  1.090
 S5M  C19  H18  single    0.970  0.020  1.090
 S5M  C19  H19  single    0.970  0.020  1.090
 S5M  C19  H20  single    0.970  0.020  1.090
 S5M  C2   H21  single    0.930  0.020  1.080
 S5M  C23  H22  single    0.930  0.020  1.080
 S5M  C3   H23  single    0.930  0.020  1.080
 S5M  N2   H24  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
 S5M  C1   N1   C24  113.32  3.000
 S5M  H1   N3   C11  119.51  3.000
 S5M  H1   N3   C10  116.91  3.000
 S5M  C11  N3   C10  123.54  3.000
 S5M  C3   C4   C1   106.63  3.000
 S5M  C3   C4   C5   138.16  3.000
 S5M  C1   C4   C5   115.18  3.000
 S5M  N4   C5   C6   117.14  3.000
 S5M  C6   C5   C4   123.44  3.000
 S5M  N4   C5   C4   119.41  3.000
 S5M  C23  C6   C7   118.34  3.000
 S5M  C7   C6   C5   120.04  3.000
 S5M  C23  C6   C5   121.61  3.000
 S5M  H2   C7   C8   119.50  3.000
 S5M  H2   C7   C6   119.63  3.000
 S5M  C8   C7   C6   120.87  3.000
 S5M  H3   C8   C9   120.46  3.000
 S5M  H3   C8   C7   118.77  3.000
 S5M  C9   C8   C7   120.77  3.000
 S5M  H6   C13  C14  119.32  3.000
 S5M  H6   C13  C12  119.78  3.000
 S5M  C14  C13  C12  120.90  3.000
 S5M  C16  C15  C14  122.99  3.000
 S5M  C16  C15  C20  119.79  3.000
 S5M  C14  C15  C20  117.21  3.000
 S5M  H9   C17  H8   107.84  3.000
 S5M  H9   C17  H7   107.93  3.000
 S5M  H8   C17  H7   107.30  3.000
 S5M  H9   C17  C16  111.06  3.000
 S5M  H8   C17  C16  112.47  3.000
 S5M  H7   C17  C16  110.05  3.000
 S5M  H10  C20  C21  118.19  3.000
 S5M  H10  C20  C15  120.12  3.000
 S5M  C21  C20  C15  121.68  3.000
 S5M  H11  C21  C12  121.33  3.000
 S5M  H11  C21  C20  118.05  3.000
 S5M  C12  C21  C20  120.60  3.000
 S5M  H12  C22  C9   119.78  3.000
 S5M  H12  C22  C23  119.17  3.000
 S5M  C9   C22  C23  121.05  3.000
 S5M  H13  C24  N4   116.15  3.000
 S5M  H13  C24  N1   116.52  3.000
 S5M  N4   C24  N1   127.33  3.000
 S5M  N2   C1   C4   107.89  3.000
 S5M  C4   C1   N1   125.49  3.000
 S5M  N2   C1   N1   126.61  3.000
 S5M  O1   C11  C12  121.19  3.000
 S5M  C12  C11  N3   116.17  3.000
 S5M  O1   C11  N3   122.64  3.000
 S5M  C11  C12  C21  123.35  3.000
 S5M  C21  C12  C13  118.20  3.000
 S5M  C11  C12  C13  118.43  3.000
 S5M  H14  C14  C15  120.51  3.000
 S5M  H14  C14  C13  118.09  3.000
 S5M  C15  C14  C13  121.40  3.000
 S5M  H17  C18  H16  107.81  3.000
 S5M  H17  C18  H15  107.61  3.000
 S5M  H16  C18  H15  107.91  3.000
 S5M  H17  C18  C16  112.06  3.000
 S5M  H16  C18  C16  111.08  3.000
 S5M  H15  C18  C16  110.20  3.000
 S5M  H20  C19  H19  108.11  3.000
 S5M  H20  C19  H18  107.26  3.000
 S5M  H19  C19  H18  107.45  3.000
 S5M  H20  C19  C16  112.30  3.000
 S5M  H19  C19  C16  111.95  3.000
 S5M  H18  C19  C16  109.55  3.000
 S5M  H21  C2   N2   120.33  3.000
 S5M  H21  C2   C3   129.57  3.000
 S5M  N2   C2   C3   110.09  3.000
 S5M  H22  C23  C22  118.89  3.000
 S5M  H22  C23  C6   120.51  3.000
 S5M  C22  C23  C6   120.58  3.000
 S5M  H23  C3   C2   125.52  3.000
 S5M  H23  C3   C4   128.16  3.000
 S5M  C2   C3   C4   106.31  3.000
 S5M  C22  C9   C10  118.97  3.000
 S5M  C10  C9   C8   122.64  3.000
 S5M  C22  C9   C8   118.38  3.000
 S5M  H24  N2   C2   125.47  3.000
 S5M  H24  N2   C1   125.46  3.000
 S5M  C2   N2   C1   109.07  3.000
 S5M  C24  N4   C5   119.25  3.000
 S5M  H5   C10  H4   106.38  3.000
 S5M  H5   C10  C9   109.28  3.000
 S5M  H4   C10  C9   109.30  3.000
 S5M  H5   C10  N3   108.13  3.000
 S5M  H4   C10  N3   108.89  3.000
 S5M  C9   C10  N3   114.54  3.000
 S5M  C19  C16  C18  108.48  3.000
 S5M  C18  C16  C17  109.63  3.000
 S5M  C19  C16  C17  108.08  3.000
 S5M  C17  C16  C15  109.63  3.000
 S5M  C18  C16  C15  108.71  3.000
 S5M  C19  C16  C15  112.28  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
 S5M  CONST_01  C5   N4   C24  N1      0.00   0.0  0
 S5M  CONST_02  C2   N2   C1   N1    180.00   0.0  0
 S5M  CONST_03  C5   C4   C1   N1      0.00   0.0  0
 S5M  CONST_04  C3   C4   C1   N1    180.00   0.0  0
 S5M  CONST_05  C24  N1   C1   C4      0.00   0.0  0
 S5M  CONST_06  C2   N2   C1   C4      0.00   0.0  0
 S5M  CONST_07  C24  N4   C5   C4      0.00   0.0  0
 S5M  CONST_10  N2   C2   C3   C4      0.00   0.0  0
 S5M  CONST_11  N2   C1   C4   C5    180.00   0.0  0
 S5M  CONST_12  C2   C3   C4   C5    180.00   0.0  0
 S5M  CONST_13  C22  C23  C6   C5    180.00   0.0  0
 S5M  CONST_14  C8   C7   C6   C5    180.00   0.0  0
 S5M  CONST_15  C24  N4   C5   C6    180.00   0.0  0
 S5M  CONST_16  C1   C4   C5   C6    180.00   0.0  0
 S5M  CONST_17  C3   C4   C5   C6      0.00   0.0  0
 S5M  CONST_18  C9   C22  C23  C6      0.00   0.0  0
 S5M  CONST_19  C9   C8   C7   C6      0.00   0.0  0
 S5M  CONST_21  C22  C23  C6   C7      0.00   0.0  0
 S5M  CONST_22  C22  C9   C8   C7      0.00   0.0  0
 S5M  CONST_23  C23  C6   C7   C8      0.00   0.0  0
 S5M  CONST_24  C23  C22  C9   C8      0.00   0.0  0
 S5M  CONST_25  C20  C21  C12  C13     0.00   0.0  0
 S5M  CONST_26  C20  C15  C14  C13     0.00   0.0  0
 S5M  CONST_27  C12  C13  C14  C15     0.00   0.0  0
 S5M  CONST_28  C12  C21  C20  C15     0.00   0.0  0
 S5M  CONST_29  C14  C13  C12  C21     0.00   0.0  0
 S5M  CONST_30  C14  C15  C20  C21     0.00   0.0  0
 S5M  CONST_31  N2   C1   N1   C24   180.00   0.0  0
 S5M  CONST_32  N4   C24  N1   C1      0.00   0.0  0
 S5M  CONST_33  C3   C2   N2   C1      0.00   0.0  0
 S5M  CONST_34  N4   C5   C4   C1      0.00   0.0  0
 S5M  CONST_35  C2   C3   C4   C1      0.00   0.0  0
 S5M  CONST_37  N2   C1   C4   C3      0.00   0.0  0
 S5M  CONST_38  N4   C5   C4   C3    180.00   0.0  0
 S5M  CONST_39  C10  C9   C8   C7    180.00   0.0  0
 S5M  CONST_40  C23  C22  C9   C10   180.00   0.0  0
 S5M  CONST_41  C16  C15  C14  C13   180.00   0.0  0
 S5M  CONST_42  C11  C12  C21  C20   180.00   0.0  0
 S5M  CONST_43  C16  C15  C20  C21   180.00   0.0  0
 S5M  CONST_44  C14  C13  C12  C11   180.00   0.0  0
 S5M  CONST_45  H24  N2   C1   N1      0.00   0.0  0
 S5M  CONST_46  H21  C2   C3   C4    180.00   0.0  0
 S5M  CONST_47  H13  C24  N4   C5    180.00   0.0  0
 S5M  CONST_48  H23  C3   C4   C5      0.00   0.0  0
 S5M  CONST_49  H22  C23  C6   C5      0.00   0.0  0
 S5M  CONST_50  H2   C7   C6   C5      0.00   0.0  0
 S5M  CONST_51  H12  C22  C23  C6    180.00   0.0  0
 S5M  CONST_52  H3   C8   C7   C6    180.00   0.0  0
 S5M  CONST_53  H11  C21  C12  C13   180.00   0.0  0
 S5M  CONST_54  H6   C13  C14  C15   180.00   0.0  0
 S5M  CONST_55  H14  C14  C15  C20   180.00   0.0  0
 S5M  CONST_56  H10  C20  C21  C12   180.00   0.0  0
 S5M  CONST_57  C12  C11  N3   C10   180.00   0.0  0
 S5M  CONST_58  H1   N3   C11  C12     0.00   0.0  0
 S5M  CONST_59  O1   C11  N3   C10     0.00   0.0  0
 S5M  Var_01    C22  C9   C10  N3    161.68  30.0  1
 S5M  Var_02    C13  C12  C11  N3   -159.34  30.0  2
 S5M  Var_03    C14  C15  C16  C17  -127.01  30.0  2
 S5M  Var_04    C9   C10  N3   C11    95.99  30.0  2
 S5M  Var_05    H18  C19  C16  C15  -178.36  30.0  3
 S5M  Var_06    H15  C18  C16  C15   178.07  30.0  3
 S5M  Var_07    H7   C17  C16  C15   179.74  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
 S5M  plan-1  C13  0.020
 S5M  plan-1  C15  0.020
 S5M  plan-1  C20  0.020
 S5M  plan-1  C21  0.020
 S5M  plan-1  C11  0.020
 S5M  plan-1  C12  0.020
 S5M  plan-1  C14  0.020
 S5M  plan-1  H6   0.020
 S5M  plan-1  H10  0.020
 S5M  plan-1  H11  0.020
 S5M  plan-1  H14  0.020
 S5M  plan-1  C16  0.020
 S5M  plan-2  C5   0.020
 S5M  plan-2  C6   0.020
 S5M  plan-2  C7   0.020
 S5M  plan-2  C8   0.020
 S5M  plan-2  C22  0.020
 S5M  plan-2  C23  0.020
 S5M  plan-2  C9   0.020
 S5M  plan-2  H2   0.020
 S5M  plan-2  H3   0.020
 S5M  plan-2  H12  0.020
 S5M  plan-2  H22  0.020
 S5M  plan-2  C10  0.020
 S5M  plan-3  N1   0.020
 S5M  plan-3  C4   0.020
 S5M  plan-3  C5   0.020
 S5M  plan-3  C6   0.020
 S5M  plan-3  C24  0.020
 S5M  plan-3  C1   0.020
 S5M  plan-3  C2   0.020
 S5M  plan-3  C3   0.020
 S5M  plan-3  N2   0.020
 S5M  plan-3  N4   0.020
 S5M  plan-3  H13  0.020
 S5M  plan-3  H21  0.020
 S5M  plan-3  H23  0.020
 S5M  plan-3  H24  0.020
 S5M  plan-4  N3   0.020
 S5M  plan-4  C11  0.020
 S5M  plan-4  C12  0.020
 S5M  plan-4  O1   0.020
 S5M  plan-4  H1   0.020
 S5M  plan-4  C10  0.020

