# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:29:56 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(hexylsulfanyl)methyl]pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCSC[C@H]1CN(C[C@@H]1O)Cc2c[nH]c3c(N)ncnc23
#
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
 HT6  HT6  (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(hexylsulfanyl)methyl]pyrrolidin-3-ol  ligand  54  25  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HT6
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
 HT6  O3A  O  OH1   0  -0.675    0.9071   2.4766   1.8074
 HT6  C3A  C  CH1   0   0.054    0.2960   2.1341   0.5827
 HT6  C4A  C  CH1   0  -0.285   -0.6872   0.9686   0.8363
 HT6  C5A  C  CH2   0  -0.554   -2.1227   1.3356   0.5012
 HT6  S5A  S  S2    0  -0.041   -3.2154  -0.0737   0.8409
 HT6  C20  C  CH2   0  -0.541   -4.7867   0.5710   0.2002
 HT6  C21  C  CH2   0  -0.420   -5.8649  -0.4986   0.2891
 HT6  C22  C  CH2   0  -0.409   -7.2085  -0.0043  -0.2350
 HT6  C23  C  CH2   0  -0.407   -8.2928  -1.0733  -0.1789
 HT6  C24  C  CH2   0  -0.420   -9.6384  -0.5944  -0.7097
 HT6  C25  C  CH3   0  -0.662  -10.7117  -1.6729  -0.6587
 HT6  C2A  C  CH2   0  -0.295    1.2722   1.5620  -0.4443
 HT6  N1A  N  NT    0  -0.413    1.2618   0.1408  -0.1741
 HT6  C1A  C  CH2   0  -0.260   -0.1403  -0.1815  -0.0180
 HT6  C10  C  CH2   0  -0.361    1.9372  -0.6729  -1.1603
 HT6  C9   C  CR5   0  -0.043    3.4002  -0.3931  -1.2145
 HT6  C4   C  CR56  0   0.162    4.3659  -0.6792  -0.2080
 HT6  N3   N  N     0  -0.444    4.2226  -1.2776   0.9917
 HT6  C2   C  CR16  0   0.005    5.3408  -1.3884   1.6682
 HT6  N1   N  N     0  -0.471    6.5675  -0.9875   1.3165
 HT6  C6   C  CR6   0   0.455    6.7359  -0.3980   0.1365
 HT6  N6   N  NH2   0  -0.826    7.9649   0.0404  -0.1993
 HT6  C5   C  CR56  0   0.205    5.6051  -0.2288  -0.6780
 HT6  N7   N  NR15  0  -0.676    5.4124   0.3123  -1.9170
 HT6  C8   C  CR15  0  -0.054    4.0939   0.2109  -2.2325
 HT6  H1   H  HOH1  0   0.448    1.4960   3.2210   1.6498
 HT6  H2   H  HCH1  0   0.215   -0.2235   3.0037   0.1598
 HT6  H3   H  HCH1  0   0.260   -0.6262   0.7034   1.8957
 HT6  H4   H  HCH2  0   0.272   -2.4483   2.1955   1.0908
 HT6  H5   H  HCH2  0   0.258   -2.2106   1.6015  -0.5558
 HT6  H6   H  HCH2  0   0.255   -5.0753   1.4551   0.7735
 HT6  H7   H  HCH2  0   0.256   -4.6422   0.8795  -0.8377
 HT6  H8   H  HCH2  0   0.226   -5.5520  -1.3785  -0.2809
 HT6  H9   H  HCH2  0   0.226   -5.9754  -0.8227   1.3282
 HT6  H10  H  HCH2  0   0.214   -7.5268   0.8701   0.3426
 HT6  H11  H  HCH2  0   0.213   -7.0911   0.3386  -1.2684
 HT6  H12  H  HCH2  0   0.208   -7.9683  -1.9488  -0.7523
 HT6  H13  H  HCH2  0   0.208   -8.4122  -1.4158   0.8548
 HT6  H14  H  HCH2  0   0.211   -9.9649   0.2778  -0.1349
 HT6  H15  H  HCH2  0   0.211   -9.5180  -0.2487  -1.7411
 HT6  H16  H  HCH3  0   0.226  -11.6591  -1.3165  -1.0644
 HT6  H17  H  HCH3  0   0.216  -10.4149  -2.5504  -1.2366
 HT6  H18  H  HCH3  0   0.216  -10.8947  -2.0019   0.3659
 HT6  H19  H  HCH2  0   0.188    0.9017   1.7863  -1.4613
 HT6  H20  H  HCH2  0   0.241    2.2746   1.9882  -0.3629
 HT6  H22  H  HCH2  0   0.239   -0.2703  -1.1625   0.4440
 HT6  H23  H  HCH2  0   0.189   -0.6706  -0.2059  -0.9887
 HT6  H24  H  HCH2  0   0.238    1.7741  -1.7220  -0.8957
 HT6  H25  H  HCH2  0   0.203    1.5038  -0.5342  -2.1662
 HT6  H26  H  HCR6  0   0.237    5.2752  -1.8676   2.6404
 HT6  H27  H  HNH2  0   0.397    8.7396  -0.2708   0.3631
 HT6  H28  H  HNH2  0   0.400    8.1849   0.2593  -1.1553
 HT6  H29  H  HNR5  0   0.415    6.1122   0.7103  -2.5202
 HT6  H30  H  HCR5  0   0.290    3.7294   0.5833  -3.1771

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
 HT6  O3A  C3A  single    1.411  0.020  1.411
 HT6  C3A  C4A  single    1.546  0.020  1.546
 HT6  C3A  C2A  single    1.528  0.020  1.528
 HT6  N1A  C1A  single    1.447  0.020  1.447
 HT6  N1A  C2A  single    1.447  0.020  1.447
 HT6  N1A  C10  single    1.446  0.020  1.446
 HT6  C1A  C4A  single    1.534  0.020  1.534
 HT6  C4A  C5A  single    1.519  0.020  1.519
 HT6  C23  C22  single    1.524  0.020  1.524
 HT6  C23  C24  single    1.524  0.020  1.524
 HT6  C22  C21  single    1.525  0.020  1.525
 HT6  C10  C9   single    1.491  0.020  1.491
 HT6  C20  C21  single    1.521  0.020  1.521
 HT6  C20  S5A  single    1.815  0.020  1.815
 HT6  C25  C24  single    1.522  0.020  1.522
 HT6  S5A  C5A  single    1.815  0.020  1.815
 HT6  C9   C8   aromatic  1.372  0.020  1.372
 HT6  C9   C4   aromatic  1.424  0.020  1.424
 HT6  C8   N7   aromatic  1.360  0.020  1.360
 HT6  C4   N3   aromatic  1.348  0.020  1.348
 HT6  C4   C5   aromatic  1.400  0.020  1.400
 HT6  N3   C2   aromatic  1.312  0.020  1.312
 HT6  N7   C5   aromatic  1.366  0.020  1.366
 HT6  C5   C6   aromatic  1.404  0.020  1.404
 HT6  C2   N1   aromatic  1.338  0.020  1.338
 HT6  N1   C6   aromatic  1.330  0.020  1.330
 HT6  C6   N6   single    1.347  0.020  1.347
 HT6  O3A  H1   single    0.850  0.020  0.980
 HT6  C3A  H2   single    0.970  0.020  1.090
 HT6  C4A  H3   single    0.970  0.020  1.090
 HT6  C5A  H4   single    0.970  0.020  1.090
 HT6  C5A  H5   single    0.970  0.020  1.090
 HT6  C20  H6   single    0.970  0.020  1.090
 HT6  C20  H7   single    0.970  0.020  1.090
 HT6  C21  H8   single    0.970  0.020  1.090
 HT6  C21  H9   single    0.970  0.020  1.090
 HT6  C22  H10  single    0.970  0.020  1.090
 HT6  C22  H11  single    0.970  0.020  1.090
 HT6  C23  H12  single    0.970  0.020  1.090
 HT6  C23  H13  single    0.970  0.020  1.090
 HT6  C24  H14  single    0.970  0.020  1.090
 HT6  C24  H15  single    0.970  0.020  1.090
 HT6  C25  H16  single    0.970  0.020  1.090
 HT6  C25  H17  single    0.970  0.020  1.090
 HT6  C25  H18  single    0.970  0.020  1.090
 HT6  C2A  H19  single    0.970  0.020  1.090
 HT6  C2A  H20  single    0.970  0.020  1.090
 HT6  C1A  H22  single    0.970  0.020  1.090
 HT6  C1A  H23  single    0.970  0.020  1.090
 HT6  C10  H24  single    0.970  0.020  1.090
 HT6  C10  H25  single    0.970  0.020  1.090
 HT6  C2   H26  single    0.930  0.020  1.080
 HT6  N6   H27  single    0.890  0.020  1.040
 HT6  N6   H28  single    0.890  0.020  1.040
 HT6  N7   H29  single    0.860  0.020  1.020
 HT6  C8   H30  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
 HT6  H1   O3A  C3A  108.10  3.000
 HT6  H2   C3A  C2A  109.88  3.000
 HT6  H2   C3A  C4A  111.07  3.000
 HT6  C2A  C3A  C4A  103.55  3.000
 HT6  H2   C3A  O3A  110.31  3.000
 HT6  C2A  C3A  O3A  113.43  3.000
 HT6  C4A  C3A  O3A  108.43  3.000
 HT6  H3   C4A  C1A  109.74  3.000
 HT6  H3   C4A  C5A  108.97  3.000
 HT6  C1A  C4A  C5A  113.29  3.000
 HT6  H3   C4A  C3A  107.83  3.000
 HT6  C5A  C4A  C3A  112.50  3.000
 HT6  C1A  C4A  C3A  104.31  3.000
 HT6  H5   C5A  H4   107.84  3.000
 HT6  H5   C5A  S5A  108.74  3.000
 HT6  H4   C5A  S5A  109.31  3.000
 HT6  H5   C5A  C4A  110.36  3.000
 HT6  H4   C5A  C4A  110.66  3.000
 HT6  S5A  C5A  C4A  109.88  3.000
 HT6  C20  S5A  C5A  100.33  3.000
 HT6  H7   C20  H6   107.76  3.000
 HT6  H7   C20  C21  110.35  3.000
 HT6  H6   C20  C21  110.55  3.000
 HT6  H7   C20  S5A  108.73  3.000
 HT6  H6   C20  S5A  109.32  3.000
 HT6  C21  C20  S5A  110.07  3.000
 HT6  H9   C21  H8   106.58  3.000
 HT6  H9   C21  C22  109.48  3.000
 HT6  H8   C21  C22  109.49  3.000
 HT6  H9   C21  C20  109.59  3.000
 HT6  H8   C21  C20  109.41  3.000
 HT6  C22  C21  C20  112.12  3.000
 HT6  H11  C22  H10  106.19  3.000
 HT6  H11  C22  C23  109.31  3.000
 HT6  H10  C22  C23  109.51  3.000
 HT6  H11  C22  C21  109.36  3.000
 HT6  H10  C22  C21  109.49  3.000
 HT6  C23  C22  C21  112.77  3.000
 HT6  H13  C23  H12  106.03  3.000
 HT6  H13  C23  C24  109.31  3.000
 HT6  H12  C23  C24  109.29  3.000
 HT6  H13  C23  C22  109.37  3.000
 HT6  H12  C23  C22  109.30  3.000
 HT6  C24  C23  C22  113.27  3.000
 HT6  H15  C24  H14  106.02  3.000
 HT6  H15  C24  C25  109.45  3.000
 HT6  H14  C24  C25  109.67  3.000
 HT6  H15  C24  C23  109.30  3.000
 HT6  H14  C24  C23  109.33  3.000
 HT6  C25  C24  C23  112.85  3.000
 HT6  H18  C25  H17  107.47  3.000
 HT6  H18  C25  H16  107.58  3.000
 HT6  H17  C25  H16  107.58  3.000
 HT6  H18  C25  C24  111.30  3.000
 HT6  H17  C25  C24  111.09  3.000
 HT6  H16  C25  C24  111.62  3.000
 HT6  H20  C2A  H19  107.27  3.000
 HT6  H20  C2A  N1A  112.09  3.000
 HT6  H19  C2A  N1A  111.64  3.000
 HT6  H20  C2A  C3A  112.96  3.000
 HT6  H19  C2A  C3A  109.16  3.000
 HT6  N1A  C2A  C3A  103.75  3.000
 HT6  C10  N1A  C1A  113.63  3.000
 HT6  C10  N1A  C2A  114.96  3.000
 HT6  C1A  N1A  C2A  104.24  3.000
 HT6  H23  C1A  H22  107.11  3.000
 HT6  H23  C1A  N1A  112.01  3.000
 HT6  H22  C1A  N1A  111.17  3.000
 HT6  H23  C1A  C4A  109.53  3.000
 HT6  H22  C1A  C4A  113.30  3.000
 HT6  N1A  C1A  C4A  103.80  3.000
 HT6  H25  C10  H24  106.39  3.000
 HT6  H25  C10  C9   109.19  3.000
 HT6  H24  C10  C9   109.58  3.000
 HT6  H25  C10  N1A  111.55  3.000
 HT6  H24  C10  N1A  107.75  3.000
 HT6  C9   C10  N1A  112.19  3.000
 HT6  C8   C9   C4   105.67  3.000
 HT6  C4   C9   C10  127.04  3.000
 HT6  C8   C9   C10  127.29  3.000
 HT6  C5   C4   N3   122.39  3.000
 HT6  C5   C4   C9   107.36  3.000
 HT6  N3   C4   C9   130.24  3.000
 HT6  C2   N3   C4   113.94  3.000
 HT6  H26  C2   N1   115.02  3.000
 HT6  H26  C2   N3   116.59  3.000
 HT6  N1   C2   N3   128.38  3.000
 HT6  C6   N1   C2   118.83  3.000
 HT6  C5   C6   N6   123.43  3.000
 HT6  N6   C6   N1   118.74  3.000
 HT6  C5   C6   N1   117.80  3.000
 HT6  H28  N6   H27  115.48  3.000
 HT6  H28  N6   C6   120.50  3.000
 HT6  H27  N6   C6   117.53  3.000
 HT6  N7   C5   C6   133.46  3.000
 HT6  C6   C5   C4   118.65  3.000
 HT6  N7   C5   C4   107.89  3.000
 HT6  H29  N7   C8   124.40  3.000
 HT6  H29  N7   C5   127.06  3.000
 HT6  C8   N7   C5   108.53  3.000
 HT6  H30  C8   N7   120.34  3.000
 HT6  H30  C8   C9   129.12  3.000
 HT6  N7   C8   C9   110.54  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
 HT6  CONST_01  C5   N7   C8   C9      0.00   0.0  0
 HT6  CONST_02  C2   N3   C4   C9    180.00   0.0  0
 HT6  CONST_03  N7   C5   C4   C9      0.00   0.0  0
 HT6  CONST_04  C6   C5   C4   C9    180.00   0.0  0
 HT6  CONST_05  N7   C8   C9   C4      0.00   0.0  0
 HT6  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 HT6  CONST_07  C8   N7   C5   C4      0.00   0.0  0
 HT6  CONST_08  N1   C6   C5   C4      0.00   0.0  0
 HT6  CONST_09  C8   C9   C4   N3    180.00   0.0  0
 HT6  CONST_10  N7   C5   C4   N3    180.00   0.0  0
 HT6  CONST_11  C6   C5   C4   N3      0.00   0.0  0
 HT6  CONST_12  C6   N1   C2   N3      0.00   0.0  0
 HT6  CONST_13  C5   C4   N3   C2      0.00   0.0  0
 HT6  CONST_14  C5   C6   N1   C2      0.00   0.0  0
 HT6  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 HT6  CONST_16  C8   N7   C5   C6    180.00   0.0  0
 HT6  CONST_17  C8   C9   C4   C5      0.00   0.0  0
 HT6  CONST_18  N7   C8   C9   C10   180.00   0.0  0
 HT6  CONST_19  N3   C4   C9   C10     0.00   0.0  0
 HT6  CONST_20  C5   C4   C9   C10   180.00   0.0  0
 HT6  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 HT6  CONST_22  N6   C6   N1   C2    180.00   0.0  0
 HT6  CONST_23  N7   C5   C6   N6      0.00   0.0  0
 HT6  CONST_24  H29  N7   C8   C9    180.00   0.0  0
 HT6  CONST_25  H30  C8   C9   C4    180.00   0.0  0
 HT6  CONST_26  H26  C2   N3   C4    180.00   0.0  0
 HT6  CONST_27  H27  N6   C6   N1      0.00   0.0  0
 HT6  Var_01    C1A  N1A  C2A  C3A    44.94  30.0  1
 HT6  Var_02    C2A  N1A  C1A  C4A   -42.97  30.0  1
 HT6  Var_03    C9   C10  N1A  C2A    64.79  30.0  3
 HT6  Var_04    C8   C9   C10  N1A  -111.15  30.0  2
 HT6  Var_05    C21  C20  S5A  C5A   176.00  30.0  1
 HT6  Var_06    C22  C21  C20  S5A   179.86  30.0  3
 HT6  Var_07    C23  C22  C21  C20   178.85  30.0  1
 HT6  Var_08    C24  C23  C22  C21  -179.58  30.0  1
 HT6  Var_09    C25  C24  C23  C22   179.58  30.0  3
 HT6  Var_10    H4   C5A  S5A  C20    64.04  30.0  3
 HT6  Var_11    H16  C25  C24  C23  -178.67  30.0  3

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
 HT6  chir_01  C3A  O3A  C4A  C2A  positiv
 HT6  chir_02  C4A  C3A  C1A  C5A  positiv

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
 HT6  plan-1  C10  0.020
 HT6  plan-1  C9   0.020
 HT6  plan-1  C4   0.020
 HT6  plan-1  N3   0.020
 HT6  plan-1  C2   0.020
 HT6  plan-1  N1   0.020
 HT6  plan-1  C6   0.020
 HT6  plan-1  N6   0.020
 HT6  plan-1  C5   0.020
 HT6  plan-1  N7   0.020
 HT6  plan-1  C8   0.020
 HT6  plan-1  H26  0.020
 HT6  plan-1  H29  0.020
 HT6  plan-1  H30  0.020
 HT6  plan-2  C6   0.020
 HT6  plan-2  N6   0.020
 HT6  plan-2  H27  0.020
 HT6  plan-2  H28  0.020

