# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 21:21:34 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: 6-[1-[3-(dimethylamino)propyl]indol-5-yl]-2-methylsulfonyl-~{N}-propyl-pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCNc1cc(nc(n1)[S](C)(=O)=O)c2ccc3n(CCCN(C)C)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
 EUU  EUU  6-[1-[3-(dimethylamino)propyl]indol-5-yl]-2-methylsulfonyl-~{N}-propyl-pyrimidin-4-amine  ligand  58  29  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EUU
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
 EUU  C13  C  CH3   0  -0.796   7.1043  -2.0133  26.8195
 EUU  C15  C  CR16  0  -0.384   8.9107  -1.3491  31.2710
 EUU  C17  C  CR56  0   0.369   9.9708  -1.7708  33.4101
 EUU  C20  C  CR15  0  -0.423  11.4635  -1.3408  31.7421
 EUU  C21  C  CR15  0  -0.027  12.1238  -1.5799  32.9098
 EUU  C24  C  CH2   0  -0.477  11.3117  -3.7309  35.5192
 EUU  C28  C  CH3   0  -0.519  12.1463  -6.6375  35.9638
 EUU  C01  C  CR6   0   0.161   5.5418  -1.1721  29.0109
 EUU  C03  C  CR6   0   0.557   4.0806  -1.4541  30.6815
 EUU  C04  C  CR16  0  -0.452   5.1751  -1.5509  31.5640
 EUU  C05  C  CR6   0   0.314   6.4518  -1.4367  31.0472
 EUU  C09  C  CH2   0  -0.436   2.4214  -3.2743  32.8036
 EUU  C14  C  CR6   0   0.029   7.6701  -1.5367  31.8690
 EUU  C16  C  CR56  0   0.097  10.0704  -1.4622  32.0345
 EUU  C18  C  CR16  0  -0.279   8.7320  -1.9480  34.0277
 EUU  C19  C  CR16  0  -0.355   7.6024  -1.8293  33.2500
 EUU  C25  C  CH2   0  -0.288  12.1027  -4.6458  34.5809
 EUU  C27  C  CH3   0  -0.519  10.5022  -6.4310  34.2317
 EUU  C29  C  CH3   0  -0.666   1.9621  -3.5059  34.2354
 EUU  N02  N  N     0  -0.449   4.2900  -1.2721  29.3625
 EUU  N06  N  N     0  -0.457   6.6313  -1.2286  29.7262
 EUU  N07  N  NH1   0  -0.646   2.8084  -1.5243  31.0786
 EUU  N22  N  NR5   0  -0.516  11.2321  -1.8335  33.9210
 EUU  N26  N  NT    0  -0.398  11.8274  -6.0657  34.6762
 EUU  S10  S  S     0   1.197   5.8424  -0.8390  27.2545
 EUU  H1   H  HCH3  0   0.298   7.9923  -1.8378  27.4198
 EUU  H2   H  HCH3  0   0.295   6.7285  -3.0220  26.9758
 EUU  H3   H  HCH3  0   0.310   7.3264  -1.8575  25.7640
 EUU  H4   H  HCR6  0   0.255   8.9752  -1.1196  30.2158
 EUU  H5   H  HCR5  0   0.247  11.9142  -1.1057  30.7914
 EUU  H6   H  HCR5  0   0.286  13.1838  -1.5881  33.1128
 EUU  H7   H  HCH2  0   0.239  10.2403  -3.9276  35.4321
 EUU  H8   H  HCH2  0   0.244  11.5764  -3.9311  36.5604
 EUU  H9   H  HCH3  0   0.228  13.1662  -6.3723  36.2484
 EUU  H10  H  HCH3  0   0.193  11.4787  -6.3204  36.7788
 EUU  H11  H  HCH3  0   0.230  12.0912  -7.7265  35.9074
 EUU  H12  H  HCR6  0   0.287   5.0114  -1.7120  32.6176
 EUU  H13  H  HCH2  0   0.244   2.9486  -1.2017  33.1328
 EUU  H14  H  HCH2  0   0.267   1.3377  -1.4358  32.5041
 EUU  H15  H  HCH2  0   0.229   1.7954  -3.8417  32.1107
 EUU  H16  H  HCH2  0   0.230   3.4417  -3.6458  32.6768
 EUU  H17  H  HCR6  0   0.268   8.6453  -2.1714  35.0830
 EUU  H18  H  HCR6  0   0.251   6.6461  -1.9767  33.7324
 EUU  H19  H  HCH2  0   0.265  12.6371  -2.0258  35.4086
 EUU  H20  H  HCH2  0   0.267  11.0245  -1.6411  35.9799
 EUU  H21  H  HCH2  0   0.228  13.1727  -4.4931  34.7591
 EUU  H22  H  HCH2  0   0.231  11.9186  -4.3485  33.5440
 EUU  H23  H  HCH3  0   0.230  10.4280  -7.5172  34.1496
 EUU  H24  H  HCH3  0   0.192   9.6906  -6.1004  34.8968
 EUU  H25  H  HCH3  0   0.228  10.3109  -6.0104  33.2430
 EUU  H26  H  HCH3  0   0.235   1.9901  -4.5648  34.4908
 EUU  H27  H  HCH3  0   0.223   2.5997  -2.9773  34.9460
 EUU  H28  H  HCH3  0   0.222   0.9391  -3.1566  34.3858
 EUU  H29  H  HNH1  0   0.399   2.1142  -1.4911  30.3482
 EUU  C23  C  CH2   0  -0.324  11.5799  -2.2515  35.2652
 EUU  O11  O  OS    0  -0.669   6.4029   0.5075  27.1738
 EUU  C08  C  CH2   0  -0.302   2.3635  -1.7971  32.4271
 EUU  O12  O  OS    0  -0.662   4.6308  -1.1419  26.5028

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
 EUU  O12  S10  double    1.458  0.020  1.458
 EUU  C13  S10  single    1.778  0.020  1.778
 EUU  O11  S10  double    1.461  0.020  1.461
 EUU  S10  C01  single    1.813  0.020  1.813
 EUU  C01  N02  aromatic  1.304  0.020  1.304
 EUU  C01  N06  aromatic  1.304  0.020  1.304
 EUU  N02  C03  aromatic  1.348  0.020  1.348
 EUU  N06  C05  aromatic  1.349  0.020  1.349
 EUU  C03  N07  single    1.335  0.020  1.335
 EUU  C03  C04  aromatic  1.409  0.020  1.409
 EUU  C05  C04  aromatic  1.382  0.020  1.382
 EUU  C05  C14  single    1.473  0.020  1.473
 EUU  N07  C08  single    1.446  0.020  1.446
 EUU  C15  C14  aromatic  1.390  0.020  1.390
 EUU  C15  C16  aromatic  1.393  0.020  1.393
 EUU  C20  C16  aromatic  1.429  0.020  1.429
 EUU  C20  C21  aromatic  1.363  0.020  1.363
 EUU  C14  C19  aromatic  1.413  0.020  1.413
 EUU  C16  C17  aromatic  1.413  0.020  1.413
 EUU  C08  C09  single    1.526  0.020  1.526
 EUU  C09  C29  single    1.521  0.020  1.521
 EUU  C21  N22  aromatic  1.372  0.020  1.372
 EUU  C19  C18  aromatic  1.377  0.020  1.377
 EUU  C17  N22  aromatic  1.362  0.020  1.362
 EUU  C17  C18  aromatic  1.395  0.020  1.395
 EUU  N22  C23  single    1.450  0.020  1.450
 EUU  C27  N26  single    1.445  0.020  1.445
 EUU  C25  N26  single    1.450  0.020  1.450
 EUU  C25  C24  single    1.531  0.020  1.531
 EUU  N26  C28  single    1.445  0.020  1.445
 EUU  C23  C24  single    1.525  0.020  1.525
 EUU  C13  H1   single    0.970  0.020  1.090
 EUU  C13  H2   single    0.970  0.020  1.090
 EUU  C13  H3   single    0.970  0.020  1.090
 EUU  C15  H4   single    0.930  0.020  1.080
 EUU  C20  H5   single    0.930  0.020  1.080
 EUU  C21  H6   single    0.930  0.020  1.080
 EUU  C24  H7   single    0.970  0.020  1.090
 EUU  C24  H8   single    0.970  0.020  1.090
 EUU  C28  H9   single    0.970  0.020  1.090
 EUU  C28  H10  single    0.970  0.020  1.090
 EUU  C28  H11  single    0.970  0.020  1.090
 EUU  C04  H12  single    0.930  0.020  1.080
 EUU  C08  H13  single    0.970  0.020  1.090
 EUU  C08  H14  single    0.970  0.020  1.090
 EUU  C09  H15  single    0.970  0.020  1.090
 EUU  C09  H16  single    0.970  0.020  1.090
 EUU  C18  H17  single    0.930  0.020  1.080
 EUU  C19  H18  single    0.930  0.020  1.080
 EUU  C23  H19  single    0.970  0.020  1.090
 EUU  C23  H20  single    0.970  0.020  1.090
 EUU  C25  H21  single    0.970  0.020  1.090
 EUU  C25  H22  single    0.970  0.020  1.090
 EUU  C27  H23  single    0.970  0.020  1.090
 EUU  C27  H24  single    0.970  0.020  1.090
 EUU  C27  H25  single    0.970  0.020  1.090
 EUU  C29  H26  single    0.970  0.020  1.090
 EUU  C29  H27  single    0.970  0.020  1.090
 EUU  C29  H28  single    0.970  0.020  1.090
 EUU  N07  H29  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
 EUU  H3   C13  H2   110.01  3.000
 EUU  H3   C13  H1   110.22  3.000
 EUU  H2   C13  H1   110.67  3.000
 EUU  H3   C13  S10  106.69  3.000
 EUU  H2   C13  S10  109.40  3.000
 EUU  H1   C13  S10  109.78  3.000
 EUU  H4   C15  C16  120.14  3.000
 EUU  H4   C15  C14  120.10  3.000
 EUU  C16  C15  C14  119.75  3.000
 EUU  N22  C17  C18  130.55  3.000
 EUU  C18  C17  C16  121.40  3.000
 EUU  N22  C17  C16  108.05  3.000
 EUU  H5   C20  C16  127.34  3.000
 EUU  H5   C20  C21  126.26  3.000
 EUU  C16  C20  C21  106.40  3.000
 EUU  H6   C21  N22  119.89  3.000
 EUU  H6   C21  C20  129.68  3.000
 EUU  N22  C21  C20  110.43  3.000
 EUU  H8   C24  H7   106.29  3.000
 EUU  H8   C24  C25  110.45  3.000
 EUU  H7   C24  C25  110.50  3.000
 EUU  H8   C24  C23  107.09  3.000
 EUU  H7   C24  C23  109.50  3.000
 EUU  C25  C24  C23  112.76  3.000
 EUU  H11  C28  H10  107.17  3.000
 EUU  H11  C28  H9   107.64  3.000
 EUU  H10  C28  H9   107.68  3.000
 EUU  H11  C28  N26  109.73  3.000
 EUU  H10  C28  N26  114.35  3.000
 EUU  H9   C28  N26  110.03  3.000
 EUU  S10  C01  N06  113.62  3.000
 EUU  N06  C01  N02  130.58  3.000
 EUU  S10  C01  N02  115.75  3.000
 EUU  N07  C03  N02  116.51  3.000
 EUU  N07  C03  C04  123.40  3.000
 EUU  N02  C03  C04  120.09  3.000
 EUU  H12  C04  C05  121.19  3.000
 EUU  H12  C04  C03  120.27  3.000
 EUU  C05  C04  C03  118.53  3.000
 EUU  N06  C05  C14  116.53  3.000
 EUU  C14  C05  C04  123.36  3.000
 EUU  N06  C05  C04  120.11  3.000
 EUU  H16  C09  H15  106.54  3.000
 EUU  H16  C09  C29  109.83  3.000
 EUU  H15  C09  C29  110.17  3.000
 EUU  H16  C09  C08  109.63  3.000
 EUU  H15  C09  C08  108.94  3.000
 EUU  C29  C09  C08  111.60  3.000
 EUU  C19  C14  C05  121.30  3.000
 EUU  C19  C14  C15  119.42  3.000
 EUU  C05  C14  C15  119.28  3.000
 EUU  C20  C16  C17  106.64  3.000
 EUU  C17  C16  C15  119.51  3.000
 EUU  C20  C16  C15  133.85  3.000
 EUU  H17  C18  C19  120.20  3.000
 EUU  H17  C18  C17  121.93  3.000
 EUU  C19  C18  C17  117.87  3.000
 EUU  H18  C19  C18  117.52  3.000
 EUU  H18  C19  C14  120.44  3.000
 EUU  C18  C19  C14  122.04  3.000
 EUU  H22  C25  H21  106.30  3.000
 EUU  H22  C25  N26  107.24  3.000
 EUU  H21  C25  N26  108.14  3.000
 EUU  H22  C25  C24  109.36  3.000
 EUU  H21  C25  C24  108.77  3.000
 EUU  N26  C25  C24  116.55  3.000
 EUU  H25  C27  H24  107.61  3.000
 EUU  H25  C27  H23  107.66  3.000
 EUU  H24  C27  H23  107.12  3.000
 EUU  H25  C27  N26  110.00  3.000
 EUU  H24  C27  N26  114.50  3.000
 EUU  H23  C27  N26  109.70  3.000
 EUU  H28  C29  H27  107.63  3.000
 EUU  H28  C29  H26  107.62  3.000
 EUU  H27  C29  H26  107.64  3.000
 EUU  H28  C29  C09  111.34  3.000
 EUU  H27  C29  C09  111.27  3.000
 EUU  H26  C29  C09  111.15  3.000
 EUU  C03  N02  C01  115.04  3.000
 EUU  C05  N06  C01  115.62  3.000
 EUU  H29  N07  C08  118.03  3.000
 EUU  H29  N07  C03  116.05  3.000
 EUU  C08  N07  C03  125.50  3.000
 EUU  C23  N22  C21  125.49  3.000
 EUU  C23  N22  C17  125.66  3.000
 EUU  C21  N22  C17  108.48  3.000
 EUU  C27  N26  C25  113.68  3.000
 EUU  C25  N26  C28  113.86  3.000
 EUU  C27  N26  C28  112.13  3.000
 EUU  O12  S10  O11  118.82  3.000
 EUU  O11  S10  C01  106.65  3.000
 EUU  O12  S10  C01  108.89  3.000
 EUU  C01  S10  C13  103.49  3.000
 EUU  O11  S10  C13  108.84  3.000
 EUU  O12  S10  C13  109.06  3.000
 EUU  H20  C23  H19  106.94  3.000
 EUU  H20  C23  N22  108.89  3.000
 EUU  H19  C23  N22  107.15  3.000
 EUU  H20  C23  C24  110.12  3.000
 EUU  H19  C23  C24  110.45  3.000
 EUU  N22  C23  C24  113.07  3.000
 EUU  H14  C08  H13  106.11  3.000
 EUU  H14  C08  N07  107.03  3.000
 EUU  H13  C08  N07  109.55  3.000
 EUU  H14  C08  C09  109.83  3.000
 EUU  H13  C08  C09  110.35  3.000
 EUU  N07  C08  C09  113.65  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
 EUU  CONST_01  N06  C05  C14  C15     0.00   0.0  0
 EUU  CONST_02  C04  C05  C14  C15   180.00   0.0  0
 EUU  CONST_03  C18  C19  C14  C15     0.00   0.0  0
 EUU  CONST_04  C21  C20  C16  C15   180.00   0.0  0
 EUU  CONST_05  N22  C17  C16  C15   180.00   0.0  0
 EUU  CONST_06  C18  C17  C16  C15     0.00   0.0  0
 EUU  CONST_07  C14  C15  C16  C17     0.00   0.0  0
 EUU  CONST_08  C21  C20  C16  C17     0.00   0.0  0
 EUU  CONST_09  C20  C21  N22  C17     0.00   0.0  0
 EUU  CONST_10  C14  C19  C18  C17     0.00   0.0  0
 EUU  CONST_11  C14  C15  C16  C20   180.00   0.0  0
 EUU  CONST_12  N22  C17  C16  C20     0.00   0.0  0
 EUU  CONST_13  C18  C17  C16  C20   180.00   0.0  0
 EUU  CONST_14  C16  C17  N22  C21     0.00   0.0  0
 EUU  CONST_15  C18  C17  N22  C21   180.00   0.0  0
 EUU  CONST_16  C04  C03  N02  C01     0.00   0.0  0
 EUU  CONST_17  C04  C05  N06  C01     0.00   0.0  0
 EUU  CONST_18  C14  C05  N06  C01   180.00   0.0  0
 EUU  CONST_19  N06  C01  N02  C03     0.00   0.0  0
 EUU  CONST_20  N06  C05  C04  C03     0.00   0.0  0
 EUU  CONST_21  C14  C05  C04  C03   180.00   0.0  0
 EUU  CONST_22  C19  C14  C05  C04     0.00   0.0  0
 EUU  CONST_23  N02  C01  N06  C05     0.00   0.0  0
 EUU  CONST_24  N02  C03  C04  C05     0.00   0.0  0
 EUU  CONST_25  C16  C15  C14  C05   180.00   0.0  0
 EUU  CONST_26  C18  C19  C14  C05   180.00   0.0  0
 EUU  CONST_27  C19  C14  C15  C16     0.00   0.0  0
 EUU  CONST_28  N22  C21  C20  C16     0.00   0.0  0
 EUU  CONST_29  C19  C18  C17  C16     0.00   0.0  0
 EUU  CONST_30  N06  C05  C14  C19   180.00   0.0  0
 EUU  CONST_31  N22  C17  C18  C19   180.00   0.0  0
 EUU  CONST_32  C23  N22  C21  C20   180.00   0.0  0
 EUU  CONST_33  N07  C03  N02  C01   180.00   0.0  0
 EUU  CONST_34  S10  C01  N02  C03   180.00   0.0  0
 EUU  CONST_35  S10  C01  N06  C05   180.00   0.0  0
 EUU  CONST_36  N07  C03  C04  C05   180.00   0.0  0
 EUU  CONST_37  C23  N22  C17  C16   180.00   0.0  0
 EUU  CONST_38  C23  N22  C17  C18     0.00   0.0  0
 EUU  CONST_39  H18  C19  C14  C15   180.00   0.0  0
 EUU  CONST_40  H5   C20  C16  C15     0.00   0.0  0
 EUU  CONST_41  H4   C15  C16  C17   180.00   0.0  0
 EUU  CONST_42  H6   C21  N22  C17   180.00   0.0  0
 EUU  CONST_43  H12  C04  C05  C14     0.00   0.0  0
 EUU  CONST_44  H17  C18  C19  C14   180.00   0.0  0
 EUU  CONST_45  C08  N07  C03  C04     0.00   0.0  0
 EUU  CONST_46  N02  C03  N07  C08   180.00   0.0  0
 EUU  CONST_47  H29  N07  C03  C04   180.00   0.0  0
 EUU  Var_01    N02  C01  S10  C13  -132.82  30.0  2
 EUU  Var_02    C24  C23  N22  C17    67.65  30.0  2
 EUU  Var_03    C09  C08  N07  C03   -78.80  30.0  3
 EUU  Var_04    N22  C23  C24  C25    60.04  30.0  1
 EUU  Var_05    H1   C13  S10  C01   -60.60  30.0  3
 EUU  Var_06    C27  N26  C25  C24    67.47  30.0  3
 EUU  Var_07    N26  C25  C24  C23  -175.08  30.0  1
 EUU  Var_08    N07  C08  C09  C29   179.22  30.0  1
 EUU  Var_09    H23  C27  N26  C28   -59.80  30.0  3
 EUU  Var_10    H26  C29  C09  C08   179.02  30.0  3
 EUU  Var_11    H9   C28  N26  C25   -51.33  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
 EUU  plan-1  C01  0.020
 EUU  plan-1  C03  0.020
 EUU  plan-1  C04  0.020
 EUU  plan-1  C05  0.020
 EUU  plan-1  C14  0.020
 EUU  plan-1  N02  0.020
 EUU  plan-1  N06  0.020
 EUU  plan-1  N07  0.020
 EUU  plan-1  S10  0.020
 EUU  plan-1  H12  0.020
 EUU  plan-2  C15  0.020
 EUU  plan-2  C17  0.020
 EUU  plan-2  C20  0.020
 EUU  plan-2  C21  0.020
 EUU  plan-2  C05  0.020
 EUU  plan-2  C14  0.020
 EUU  plan-2  C16  0.020
 EUU  plan-2  C18  0.020
 EUU  plan-2  C19  0.020
 EUU  plan-2  N22  0.020
 EUU  plan-2  H4   0.020
 EUU  plan-2  H5   0.020
 EUU  plan-2  H6   0.020
 EUU  plan-2  H17  0.020
 EUU  plan-2  H18  0.020
 EUU  plan-2  C23  0.020
 EUU  plan-3  C03  0.020
 EUU  plan-3  N07  0.020
 EUU  plan-3  H29  0.020
 EUU  plan-3  C08  0.020

