# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:13:45 2022
#   Inital geometry file: a 147 line input string
#   Ligand name: 7-[5-S-(4-{[(4-ethylpyridin-3-yl)methyl]amino}butyl)-5-thio-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccncc1CNCCCCSC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3ccc4c(N)ncnc34
#
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
 44T  44T  7-[5-S-(4-{[(4-ethylpyridin-3-yl)methyl]amino}butyl)-5-thio-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  65  33  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_44T
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
 44T  N1   N  NH1   0  -0.586  29.5105  16.1210  25.7398
 44T  C7   C  CH2   0  -0.358  28.8504  17.3497  25.3359
 44T  C8   C  CH2   0  -0.247  30.4776  15.6558  24.7633
 44T  N2   N  NR5   0  -0.559  37.0243  10.0061  26.6729
 44T  C9   C  CH2   0  -0.434  31.1670  14.3854  25.2333
 44T  O1   O  OH1   0  -0.649  37.0959  10.6151  23.5674
 44T  C1   C  CH2   0  -0.522  29.7544  18.6017  27.9308
 44T  C5   C  CR16  0  -0.102  26.5195  17.6748  26.1800
 44T  C6   C  CR6   0  -0.036  27.8862  17.8149  26.3914
 44T  N3   N  N     0  -0.463  39.3061   9.2841  26.9128
 44T  C4   C  CR16  0  -0.064  25.9844  18.5450  28.1992
 44T  C3   C  CR16  0  -0.376  27.3202  18.7280  28.5182
 44T  C2   C  CR6   0   0.204  28.3067  18.3591  27.6102
 44T  N4   N  N     0  -0.476  39.5512   7.2352  28.1058
 44T  O2   O  OH1   0  -0.664  37.7685  13.1650  23.8515
 44T  C16  C  CH1   0  -0.050  36.5167  12.8235  24.3927
 44T  C15  C  CH1   0  -0.009  36.5039  11.3188  24.6137
 44T  C14  C  CH1   0   0.186  37.2565  11.2196  25.9456
 44T  C20  C  CR56  0   0.510  37.9924   9.1485  27.1040
 44T  C21  C  CR16  0   0.042  40.0012   8.2963  27.4403
 44T  C22  C  CR6   0   0.442  38.2338   7.1094  28.2903
 44T  N5   N  NH2   0  -0.824  37.7850   6.0330  28.9480
 44T  C19  C  CR56  0  -0.085  37.3694   8.0975  27.7793
 44T  C18  C  CR15  0  -0.438  35.9643   8.3487  27.7526
 44T  C17  C  CR15  0  -0.008  35.7963   9.5154  27.0743
 44T  O    O  O2    0  -0.490  36.8030  12.3171  26.6974
 44T  C13  C  CH1   0   0.049  36.3514  13.3526  25.8288
 44T  C12  C  CH2   0  -0.601  34.9582  13.8068  26.2349
 44T  S    S  S2    0  -0.028  33.6590  12.5420  26.2887
 44T  C11  C  CH2   0  -0.573  32.9014  12.6059  24.6348
 44T  C10  C  CH2   0  -0.425  32.2444  13.9262  24.2634
 44T  C    C  CH3   0  -0.657  30.2171  19.9778  27.4521
 44T  N    N  N     0  -0.409  25.5779  18.0256  27.0479
 44T  H1   H  HNH1  0   0.342  28.8077  15.4038  25.8810
 44T  H3   H  HCH2  0   0.240  29.6199  18.1092  25.1717
 44T  H4   H  HCH2  0   0.222  28.3140  17.2516  24.3798
 44T  H5   H  HCH2  0   0.215  31.2275  16.4424  24.6292
 44T  H6   H  HCH2  0   0.189  30.0286  15.4875  23.7711
 44T  H7   H  HCH2  0   0.216  30.4242  13.5894  25.3580
 44T  H8   H  HCH2  0   0.223  31.6012  14.5634  26.2197
 44T  H9   H  HOH1  0   0.458  36.8683   9.6850  23.6620
 44T  H10  H  HCH2  0   0.248  29.8955  18.5318  29.0112
 44T  H11  H  HCH2  0   0.251  30.3704  17.8233  27.4810
 44T  H12  H  HCR6  0   0.251  26.1729  17.2504  25.2415
 44T  H13  H  HCR6  0   0.256  25.2120  18.8290  28.9060
 44T  H14  H  HCR6  0   0.258  27.5911  19.1572  29.4752
 44T  H15  H  HOH1  0   0.454  37.8005  14.1205  23.7399
 44T  H16  H  HCH1  0   0.248  35.6998  13.1612  23.7434
 44T  H17  H  HCH1  0   0.244  35.4621  11.0115  24.7756
 44T  H18  H  HCH1  0   0.249  38.3362  11.2691  25.7669
 44T  H19  H  HCR6  0   0.243  41.0786   8.3496  27.3199
 44T  H20  H  HNH2  0   0.397  38.4392   5.3887  29.3574
 44T  H21  H  HNH2  0   0.409  36.8150   5.9310  29.1877
 44T  H22  H  HCR5  0   0.255  35.1763   7.7491  28.1798
 44T  H23  H  HCR5  0   0.294  34.8910  10.0569  26.8497
 44T  H24  H  HCH1  0   0.250  37.0010  14.2291  25.9523
 44T  H25  H  HCH2  0   0.292  35.0068  14.2097  27.2480
 44T  H26  H  HCH2  0   0.282  34.6431  14.6327  25.5948
 44T  H27  H  HCH2  0   0.278  32.1539  11.8100  24.6674
 44T  H28  H  HCH2  0   0.273  33.6327  12.3162  23.8796
 44T  H29  H  HCH2  0   0.231  33.0050  14.7056  24.1553
 44T  H30  H  HCH2  0   0.240  31.8126  13.7973  23.2656
 44T  H31  H  HCH3  0   0.235  31.2687  20.1332  27.6930
 44T  H32  H  HCH3  0   0.229  30.1036  20.0849  26.3728
 44T  H33  H  HCH3  0   0.229  29.6432  20.7737  27.9278

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
 44T  O2   C16  single    1.406  0.020  1.406
 44T  O1   C15  single    1.393  0.020  1.393
 44T  C16  C15  single    1.521  0.020  1.521
 44T  C16  C13  single    1.539  0.020  1.539
 44T  C15  C14  single    1.533  0.020  1.533
 44T  C10  C11  single    1.521  0.020  1.521
 44T  C10  C9   single    1.521  0.020  1.521
 44T  C11  S    single    1.820  0.020  1.820
 44T  C8   C9   single    1.520  0.020  1.520
 44T  C8   N1   single    1.451  0.020  1.451
 44T  C13  C12  single    1.521  0.020  1.521
 44T  C13  O    single    1.425  0.020  1.425
 44T  C14  O    single    1.405  0.020  1.405
 44T  C14  N2   single    1.434  0.020  1.434
 44T  C7   N1   single    1.452  0.020  1.452
 44T  C7   C6   single    1.503  0.020  1.503
 44T  C5   N    aromatic  1.328  0.020  1.328
 44T  C5   C6   aromatic  1.390  0.020  1.390
 44T  C12  S    single    1.814  0.020  1.814
 44T  N    C4   aromatic  1.327  0.020  1.327
 44T  C6   C2   aromatic  1.399  0.020  1.399
 44T  N2   C17  aromatic  1.382  0.020  1.382
 44T  N2   C20  aromatic  1.363  0.020  1.363
 44T  C17  C18  aromatic  1.360  0.020  1.360
 44T  N3   C20  aromatic  1.335  0.020  1.335
 44T  N3   C21  aromatic  1.318  0.020  1.318
 44T  C20  C19  aromatic  1.396  0.020  1.396
 44T  C4   C3   aromatic  1.386  0.020  1.386
 44T  C2   C3   aromatic  1.391  0.020  1.391
 44T  C2   C1   single    1.502  0.020  1.502
 44T  C21  N4   aromatic  1.331  0.020  1.331
 44T  C18  C19  aromatic  1.428  0.020  1.428
 44T  C19  C22  aromatic  1.409  0.020  1.409
 44T  C1   C    single    1.529  0.020  1.529
 44T  N4   C22  aromatic  1.336  0.020  1.336
 44T  C22  N5   single    1.339  0.020  1.339
 44T  N1   H1   single    0.890  0.020  1.040
 44T  C7   H3   single    0.970  0.020  1.090
 44T  C7   H4   single    0.970  0.020  1.090
 44T  C8   H5   single    0.970  0.020  1.090
 44T  C8   H6   single    0.970  0.020  1.090
 44T  C9   H7   single    0.970  0.020  1.090
 44T  C9   H8   single    0.970  0.020  1.090
 44T  O1   H9   single    0.850  0.020  0.980
 44T  C1   H10  single    0.970  0.020  1.090
 44T  C1   H11  single    0.970  0.020  1.090
 44T  C5   H12  single    0.930  0.020  1.080
 44T  C4   H13  single    0.930  0.020  1.080
 44T  C3   H14  single    0.930  0.020  1.080
 44T  O2   H15  single    0.850  0.020  0.980
 44T  C16  H16  single    0.970  0.020  1.090
 44T  C15  H17  single    0.970  0.020  1.090
 44T  C14  H18  single    0.970  0.020  1.090
 44T  C21  H19  single    0.930  0.020  1.080
 44T  N5   H20  single    0.860  0.020  1.020
 44T  N5   H21  single    0.860  0.020  1.020
 44T  C18  H22  single    0.930  0.020  1.080
 44T  C17  H23  single    0.930  0.020  1.080
 44T  C13  H24  single    0.970  0.020  1.090
 44T  C12  H25  single    0.970  0.020  1.090
 44T  C12  H26  single    0.970  0.020  1.090
 44T  C11  H27  single    0.970  0.020  1.090
 44T  C11  H28  single    0.970  0.020  1.090
 44T  C10  H29  single    0.970  0.020  1.090
 44T  C10  H30  single    0.970  0.020  1.090
 44T  C    H31  single    0.970  0.020  1.090
 44T  C    H32  single    0.970  0.020  1.090
 44T  C    H33  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
 44T  H1   N1   C8   109.21  3.000
 44T  H1   N1   C7   108.79  3.000
 44T  C8   N1   C7   112.78  3.000
 44T  H4   C7   H3   105.92  3.000
 44T  H4   C7   C6   108.96  3.000
 44T  H3   C7   C6   109.98  3.000
 44T  H4   C7   N1   112.81  3.000
 44T  H3   C7   N1   108.04  3.000
 44T  C6   C7   N1   110.99  3.000
 44T  H6   C8   H5   106.17  3.000
 44T  H6   C8   C9   109.60  3.000
 44T  H5   C8   C9   109.13  3.000
 44T  H6   C8   N1   112.54  3.000
 44T  H5   C8   N1   107.97  3.000
 44T  C9   C8   N1   111.24  3.000
 44T  C17  N2   C20  108.41  3.000
 44T  C20  N2   C14  125.31  3.000
 44T  C17  N2   C14  126.28  3.000
 44T  H8   C9   H7   106.56  3.000
 44T  H8   C9   C10  110.09  3.000
 44T  H7   C9   C10  109.48  3.000
 44T  H8   C9   C8   108.86  3.000
 44T  H7   C9   C8   109.56  3.000
 44T  C10  C9   C8   112.12  3.000
 44T  H9   O1   C15  108.30  3.000
 44T  H11  C1   H10  106.84  3.000
 44T  H11  C1   C    110.04  3.000
 44T  H10  C1   C    109.17  3.000
 44T  H11  C1   C2   109.95  3.000
 44T  H10  C1   C2   108.98  3.000
 44T  C    C1   C2   111.72  3.000
 44T  H12  C5   N    116.20  3.000
 44T  H12  C5   C6   118.97  3.000
 44T  N    C5   C6   124.83  3.000
 44T  C2   C6   C5   117.85  3.000
 44T  C2   C6   C7   122.62  3.000
 44T  C5   C6   C7   119.51  3.000
 44T  C21  N3   C20  112.69  3.000
 44T  H13  C4   N    116.72  3.000
 44T  H13  C4   C3   120.12  3.000
 44T  N    C4   C3   123.15  3.000
 44T  H14  C3   C2   120.30  3.000
 44T  H14  C3   C4   119.79  3.000
 44T  C2   C3   C4   119.90  3.000
 44T  C3   C2   C6   117.30  3.000
 44T  C3   C2   C1   120.09  3.000
 44T  C6   C2   C1   122.56  3.000
 44T  C22  N4   C21  118.52  3.000
 44T  H15  O2   C16  108.38  3.000
 44T  H16  C16  C13  111.50  3.000
 44T  H16  C16  C15  112.61  3.000
 44T  C13  C16  C15  101.75  3.000
 44T  H16  C16  O2   111.13  3.000
 44T  C13  C16  O2   111.79  3.000
 44T  C15  C16  O2   107.68  3.000
 44T  H17  C15  C14  108.63  3.000
 44T  H17  C15  C16  107.83  3.000
 44T  C14  C15  C16  100.73  3.000
 44T  H17  C15  O1   111.87  3.000
 44T  C14  C15  O1   114.28  3.000
 44T  C16  C15  O1   112.77  3.000
 44T  H18  C14  O    111.72  3.000
 44T  H18  C14  C15  109.83  3.000
 44T  O    C14  C15  104.82  3.000
 44T  H18  C14  N2   106.29  3.000
 44T  O    C14  N2   109.72  3.000
 44T  C15  C14  N2   114.58  3.000
 44T  C19  C20  N3   125.81  3.000
 44T  C19  C20  N2   108.04  3.000
 44T  N3   C20  N2   126.15  3.000
 44T  H19  C21  N4   115.48  3.000
 44T  H19  C21  N3   116.25  3.000
 44T  N4   C21  N3   128.27  3.000
 44T  C19  C22  N5   122.44  3.000
 44T  N5   C22  N4   118.29  3.000
 44T  C19  C22  N4   119.26  3.000
 44T  H21  N5   H20  117.79  3.000
 44T  H21  N5   C22  121.51  3.000
 44T  H20  N5   C22  119.82  3.000
 44T  C18  C19  C22  137.23  3.000
 44T  C22  C19  C20  115.45  3.000
 44T  C18  C19  C20  107.32  3.000
 44T  H22  C18  C17  125.75  3.000
 44T  H22  C18  C19  127.88  3.000
 44T  C17  C18  C19  106.37  3.000
 44T  H23  C17  C18  129.66  3.000
 44T  H23  C17  N2   120.47  3.000
 44T  C18  C17  N2   109.86  3.000
 44T  C13  O    C14  110.10  3.000
 44T  H24  C13  C12  105.88  3.000
 44T  H24  C13  O    108.90  3.000
 44T  C12  C13  O    110.16  3.000
 44T  H24  C13  C16  108.40  3.000
 44T  O    C13  C16  106.55  3.000
 44T  C12  C13  C16  116.76  3.000
 44T  H26  C12  H25  106.14  3.000
 44T  H26  C12  S    109.77  3.000
 44T  H25  C12  S    105.17  3.000
 44T  H26  C12  C13  109.51  3.000
 44T  H25  C12  C13  108.51  3.000
 44T  S    C12  C13  117.12  3.000
 44T  C11  S    C12  104.28  3.000
 44T  H28  C11  H27  106.62  3.000
 44T  H28  C11  C10  110.57  3.000
 44T  H27  C11  C10  110.13  3.000
 44T  H28  C11  S    109.93  3.000
 44T  H27  C11  S    103.42  3.000
 44T  C10  C11  S    115.60  3.000
 44T  H30  C10  H29  105.54  3.000
 44T  H30  C10  C11  106.91  3.000
 44T  H29  C10  C11  110.01  3.000
 44T  H30  C10  C9   109.72  3.000
 44T  H29  C10  C9   109.89  3.000
 44T  C11  C10  C9   114.36  3.000
 44T  H33  C    H32  107.78  3.000
 44T  H33  C    H31  107.90  3.000
 44T  H32  C    H31  107.76  3.000
 44T  H33  C    C1   111.17  3.000
 44T  H32  C    C1   111.52  3.000
 44T  H31  C    C1   110.56  3.000
 44T  C4   N    C5   116.96  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
 44T  CONST_01  C19  C18  C17  N2      0.00   0.0  0
 44T  CONST_02  C21  N3   C20  N2    180.00   0.0  0
 44T  CONST_03  C18  C19  C20  N2      0.00   0.0  0
 44T  CONST_04  C22  C19  C20  N2    180.00   0.0  0
 44T  CONST_05  C3   C4   N    C5      0.00   0.0  0
 44T  CONST_06  C3   C2   C6   C5      0.00   0.0  0
 44T  CONST_07  C4   N    C5   C6      0.00   0.0  0
 44T  CONST_08  C4   C3   C2   C6      0.00   0.0  0
 44T  CONST_09  C17  N2   C20  N3    180.00   0.0  0
 44T  CONST_10  C18  C19  C20  N3    180.00   0.0  0
 44T  CONST_11  C22  C19  C20  N3      0.00   0.0  0
 44T  CONST_12  C22  N4   C21  N3      0.00   0.0  0
 44T  CONST_13  N    C5   C6   C2      0.00   0.0  0
 44T  CONST_14  N    C4   C3   C2      0.00   0.0  0
 44T  CONST_15  C20  N3   C21  N4      0.00   0.0  0
 44T  CONST_16  C20  C19  C22  N4      0.00   0.0  0
 44T  CONST_17  C18  C19  C22  N4    180.00   0.0  0
 44T  CONST_18  C18  C17  N2   C20     0.00   0.0  0
 44T  CONST_19  C17  C18  C19  C20     0.00   0.0  0
 44T  CONST_20  C19  C20  N3   C21     0.00   0.0  0
 44T  CONST_21  C19  C22  N4   C21     0.00   0.0  0
 44T  CONST_22  C17  C18  C19  C22   180.00   0.0  0
 44T  CONST_23  C17  N2   C20  C19     0.00   0.0  0
 44T  CONST_24  C14  N2   C20  N3      0.00   0.0  0
 44T  CONST_25  C18  C17  N2   C14   180.00   0.0  0
 44T  CONST_26  C19  C20  N2   C14   180.00   0.0  0
 44T  CONST_27  N    C5   C6   C7    180.00   0.0  0
 44T  CONST_28  C3   C2   C6   C7    180.00   0.0  0
 44T  CONST_29  C5   C6   C2   C1    180.00   0.0  0
 44T  CONST_30  C4   C3   C2   C1    180.00   0.0  0
 44T  CONST_31  N5   C22  C19  C20   180.00   0.0  0
 44T  CONST_32  N5   C22  N4   C21   180.00   0.0  0
 44T  CONST_33  C18  C19  C22  N5      0.00   0.0  0
 44T  CONST_34  H22  C18  C17  N2    180.00   0.0  0
 44T  CONST_35  H13  C4   N    C5    180.00   0.0  0
 44T  CONST_36  H14  C3   C2   C6    180.00   0.0  0
 44T  CONST_37  H12  C5   N    C4    180.00   0.0  0
 44T  CONST_38  H23  C17  N2   C14     0.00   0.0  0
 44T  CONST_39  H19  C21  N3   C20   180.00   0.0  0
 44T  CONST_40  H20  N5   C22  N4      0.00   0.0  0
 44T  CONST_41  H21  N5   C22  N4    180.00   0.0  0
 44T  Var_01    C5   C6   C7   N1   -106.26  30.0  2
 44T  Var_02    C    C1   C2   C6     87.74  30.0  2
 44T  Var_03    C6   C7   N1   C8   -178.45  30.0  1
 44T  Var_04    H31  C    C1   C2   -179.93  30.0  3
 44T  Var_05    C10  C9   C8   N1   -176.56  30.0  3
 44T  Var_06    C9   C8   N1   C7    178.84  30.0  1
 44T  Var_07    C11  C10  C9   C8   -175.95  30.0  1
 44T  Var_08    S    C11  C10  C9    -56.59  30.0  3
 44T  Var_09    C10  C11  S    C12   -62.04  30.0  2
 44T  Var_10    H25  C12  S    C11   147.01  30.0  1

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
 44T  chir_01  C16  O2  C15  C13  negativ
 44T  chir_02  C15  O1  C14  C16  negativ
 44T  chir_03  C14  O   N2   C15  negativ
 44T  chir_04  C13  O   C16  C12  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
 44T  plan-1  C7   0.020
 44T  plan-1  C1   0.020
 44T  plan-1  C5   0.020
 44T  plan-1  C6   0.020
 44T  plan-1  C4   0.020
 44T  plan-1  C3   0.020
 44T  plan-1  C2   0.020
 44T  plan-1  N    0.020
 44T  plan-1  H12  0.020
 44T  plan-1  H13  0.020
 44T  plan-1  H14  0.020
 44T  plan-2  N2   0.020
 44T  plan-2  N3   0.020
 44T  plan-2  N4   0.020
 44T  plan-2  C14  0.020
 44T  plan-2  C20  0.020
 44T  plan-2  C21  0.020
 44T  plan-2  C22  0.020
 44T  plan-2  N5   0.020
 44T  plan-2  C19  0.020
 44T  plan-2  C18  0.020
 44T  plan-2  C17  0.020
 44T  plan-2  H19  0.020
 44T  plan-2  H22  0.020
 44T  plan-2  H23  0.020
 44T  plan-3  C22  0.020
 44T  plan-3  N5   0.020
 44T  plan-3  H20  0.020
 44T  plan-3  H21  0.020

