# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 13:31:56 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl]sulfanyl}methyl)pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCn1cc(CCCSC[C@H]2CN(C[C@@H]2O)Cc3c[nH]c4c(N)ncnc34)nn1
#
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
 OS6  OS6  (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl]sulfanyl}methyl)pyrrolidin-3-ol  ligand  63  31  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OS6
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
 OS6  O    O  OH1   0  -0.675    3.3709   2.6975   1.7011
 OS6  C15  C  CH1   0   0.056    2.7124   2.3873   0.4922
 OS6  C14  C  CH2   0  -0.299    3.5974   1.6263  -0.4889
 OS6  N    N  NT    0  -0.412    3.4665   0.2513  -0.0602
 OS6  C7   C  CH2   0  -0.364    4.0381  -0.7262  -0.9610
 OS6  C8   C  CR5   0  -0.043    5.5176  -0.5938  -1.0810
 OS6  C13  C  CR56  0   0.161    6.4928  -0.9448  -0.1048
 OS6  N4   N  N     0  -0.446    6.3432  -1.4948   1.1173
 OS6  C12  C  CR16  0   0.006    7.4741  -1.7087   1.7466
 OS6  N3   N  N     0  -0.471    8.7184  -1.4473   1.3310
 OS6  C11  C  CR6   0   0.456    8.8924  -0.9085   0.1276
 OS6  N2   N  NH2   0  -0.827   10.1478  -0.6864  -0.3090
 OS6  C10  C  CR56  0   0.204    7.7490  -0.6386  -0.6407
 OS6  N1   N  NR15  0  -0.676    7.5574  -0.1188  -1.8889
 OS6  C9   C  CR15  0  -0.052    6.2232  -0.0953  -2.1472
 OS6  C6   C  CH2   0  -0.262    2.0437   0.0704   0.1490
 OS6  C5   C  CH1   0  -0.289    1.5803   1.3836   0.7999
 OS6  C4   C  CH2   0  -0.554    0.2354   1.8604   0.2763
 OS6  S    S  S2    0  -0.036   -1.0518   0.6555   0.7071
 OS6  C3   C  CH2   0  -0.548   -2.4767   1.3792  -0.1519
 OS6  C2   C  CH2   0  -0.422   -3.7234   0.5579   0.1376
 OS6  C1   C  CH2   0  -0.498   -4.9432   1.1091  -0.6027
 OS6  C    C  CR5   0   0.172   -6.1785   0.3257  -0.3200
 OS6  N5   N  N     0  -0.325   -6.2908  -0.9929  -0.5939
 OS6  N7   N  N     0  -0.111   -7.4544  -1.4102  -0.2221
 OS6  N6   N  NR5   0  -0.254   -8.1095  -0.3880   0.2902
 OS6  C16  C  CR15  0  -0.106   -7.3583   0.7262   0.2554
 OS6  C17  C  CH2   0  -0.274   -9.4637  -0.5522   0.7890
 OS6  C18  C  CH2   0  -0.430  -10.4462  -0.9358  -0.3067
 OS6  C20  C  CH3   0  -0.662  -12.8588  -1.4990  -0.8273
 OS6  C19  C  CH2   0  -0.429  -11.8602  -1.0809   0.2422
 OS6  H1   H  HOH1  0   0.447    4.1178   3.2687   1.4965
 OS6  H2   H  HCH1  0   0.216    2.3206   3.2991   0.0226
 OS6  H3   H  HCH2  0   0.189    3.2177   1.7799  -1.5162
 OS6  H4   H  HCH2  0   0.243    4.6362   1.9644  -0.4767
 OS6  H6   H  HCH2  0   0.239    3.7912  -1.7199  -0.5758
 OS6  H7   H  HCH2  0   0.203    3.5841  -0.6610  -1.9653
 OS6  H8   H  HCR6  0   0.237    7.4040  -2.1540   2.7345
 OS6  H9   H  HNH2  0   0.397   10.8975  -0.7616   0.3581
 OS6  H10  H  HNH2  0   0.401   10.3181  -0.0782  -1.0908
 OS6  H11  H  HNR5  0   0.416    8.2674   0.1800  -2.5363
 OS6  H12  H  HCR5  0   0.290    5.8567   0.2809  -3.0895
 OS6  H13  H  HCH2  0   0.192    1.5075  -0.0806  -0.8059
 OS6  H14  H  HCH2  0   0.239    1.8470  -0.8075   0.7684
 OS6  H15  H  HCH1  0   0.262    1.5132   1.2670   1.8851
 OS6  H16  H  HCH2  0   0.273   -0.0233   2.8296   0.7079
 OS6  H17  H  HCH2  0   0.259    0.2693   1.9732  -0.8108
 OS6  H18  H  HCH2  0   0.259   -2.6126   2.4096   0.1849
 OS6  H19  H  HCH2  0   0.259   -2.2743   1.4023  -1.2252
 OS6  H20  H  HCH2  0   0.239   -3.5603  -0.4811  -0.1585
 OS6  H21  H  HCH2  0   0.239   -3.9202   0.5541   1.2126
 OS6  H22  H  HCH2  0   0.249   -5.1088   2.1508  -0.3205
 OS6  H23  H  HCH2  0   0.249   -4.7442   1.1069  -1.6784
 OS6  H24  H  HCR5  0   0.304   -7.7023   1.6771   0.6253
 OS6  H25  H  HCH2  0   0.268   -9.4469  -1.3060   1.5774
 OS6  H26  H  HCH2  0   0.263   -9.7473   0.3943   1.2475
 OS6  H27  H  HCH2  0   0.232  -10.4288  -0.1770  -1.0944
 OS6  H28  H  HCH2  0   0.234  -10.1301  -1.8768  -0.7636
 OS6  H29  H  HCH3  0   0.230  -13.8632  -1.5944  -0.4142
 OS6  H30  H  HCH3  0   0.220  -12.9023  -0.7681  -1.6367
 OS6  H31  H  HCH3  0   0.220  -12.5888  -2.4613  -1.2659
 OS6  H32  H  HCH2  0   0.221  -11.8625  -1.8159   1.0525
 OS6  H33  H  HCH2  0   0.221  -12.1767  -0.1334   0.6880

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
 OS6  C9   N1   aromatic  1.359  0.020  1.359
 OS6  C9   C8   aromatic  1.372  0.020  1.372
 OS6  N1   C10  aromatic  1.366  0.020  1.366
 OS6  N2   C11  single    1.348  0.020  1.348
 OS6  C10  C11  aromatic  1.404  0.020  1.404
 OS6  C10  C13  aromatic  1.400  0.020  1.400
 OS6  C8   C7   single    1.490  0.020  1.490
 OS6  C8   C13  aromatic  1.424  0.020  1.424
 OS6  C7   N    single    1.447  0.020  1.447
 OS6  C11  N3   aromatic  1.330  0.020  1.330
 OS6  C13  N4   aromatic  1.348  0.020  1.348
 OS6  N3   C12  aromatic  1.338  0.020  1.338
 OS6  N4   C12  aromatic  1.312  0.020  1.312
 OS6  N    C14  single    1.446  0.020  1.446
 OS6  N    C6   single    1.450  0.020  1.450
 OS6  C14  C15  single    1.525  0.020  1.525
 OS6  C6   C5   single    1.537  0.020  1.537
 OS6  O    C15  single    1.411  0.020  1.411
 OS6  C15  C5   single    1.544  0.020  1.544
 OS6  C5   C4   single    1.520  0.020  1.520
 OS6  C4   S    single    1.815  0.020  1.815
 OS6  S    C3   single    1.814  0.020  1.814
 OS6  C3   C2   single    1.521  0.020  1.521
 OS6  C2   C1   single    1.530  0.020  1.530
 OS6  C1   C    single    1.490  0.020  1.490
 OS6  C    C16  aromatic  1.372  0.020  1.372
 OS6  C    N5   aromatic  1.351  0.020  1.351
 OS6  C16  N6   aromatic  1.344  0.020  1.344
 OS6  N5   N7   aromatic  1.291  0.020  1.291
 OS6  C20  C19  single    1.522  0.020  1.522
 OS6  N6   N7   aromatic  1.318  0.020  1.318
 OS6  N6   C17  single    1.452  0.020  1.452
 OS6  C19  C18  single    1.524  0.020  1.524
 OS6  C17  C18  single    1.521  0.020  1.521
 OS6  O    H1   single    0.850  0.020  0.980
 OS6  C15  H2   single    0.970  0.020  1.090
 OS6  C14  H3   single    0.970  0.020  1.090
 OS6  C14  H4   single    0.970  0.020  1.090
 OS6  C7   H6   single    0.970  0.020  1.090
 OS6  C7   H7   single    0.970  0.020  1.090
 OS6  C12  H8   single    0.930  0.020  1.080
 OS6  N2   H9   single    0.890  0.020  1.040
 OS6  N2   H10  single    0.890  0.020  1.040
 OS6  N1   H11  single    0.860  0.020  1.020
 OS6  C9   H12  single    0.930  0.020  1.080
 OS6  C6   H13  single    0.970  0.020  1.090
 OS6  C6   H14  single    0.970  0.020  1.090
 OS6  C5   H15  single    0.970  0.020  1.090
 OS6  C4   H16  single    0.970  0.020  1.090
 OS6  C4   H17  single    0.970  0.020  1.090
 OS6  C3   H18  single    0.970  0.020  1.090
 OS6  C3   H19  single    0.970  0.020  1.090
 OS6  C2   H20  single    0.970  0.020  1.090
 OS6  C2   H21  single    0.970  0.020  1.090
 OS6  C1   H22  single    0.970  0.020  1.090
 OS6  C1   H23  single    0.970  0.020  1.090
 OS6  C16  H24  single    0.930  0.020  1.080
 OS6  C17  H25  single    0.970  0.020  1.090
 OS6  C17  H26  single    0.970  0.020  1.090
 OS6  C18  H27  single    0.970  0.020  1.090
 OS6  C18  H28  single    0.970  0.020  1.090
 OS6  C20  H29  single    0.970  0.020  1.090
 OS6  C20  H30  single    0.970  0.020  1.090
 OS6  C20  H31  single    0.970  0.020  1.090
 OS6  C19  H32  single    0.970  0.020  1.090
 OS6  C19  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
 OS6  H1   O    C15  108.09  3.000
 OS6  H2   C15  C5   111.31  3.000
 OS6  H2   C15  C14  110.27  3.000
 OS6  C5   C15  C14  103.26  3.000
 OS6  H2   C15  O    110.52  3.000
 OS6  C5   C15  O    108.32  3.000
 OS6  C14  C15  O    112.96  3.000
 OS6  H4   C14  H3   107.09  3.000
 OS6  H4   C14  N    112.15  3.000
 OS6  H3   C14  N    112.11  3.000
 OS6  H4   C14  C15  112.97  3.000
 OS6  H3   C14  C15  109.21  3.000
 OS6  N    C14  C15  103.37  3.000
 OS6  C6   N    C7   113.16  3.000
 OS6  C6   N    C14  104.49  3.000
 OS6  C7   N    C14  114.96  3.000
 OS6  H7   C7   H6   106.33  3.000
 OS6  H7   C7   C8   109.25  3.000
 OS6  H6   C7   C8   109.46  3.000
 OS6  H7   C7   N    111.34  3.000
 OS6  H6   C7   N    107.77  3.000
 OS6  C8   C7   N    112.47  3.000
 OS6  C9   C8   C13  105.67  3.000
 OS6  C13  C8   C7   127.08  3.000
 OS6  C9   C8   C7   127.25  3.000
 OS6  C10  C13  N4   122.40  3.000
 OS6  N4   C13  C8   130.24  3.000
 OS6  C10  C13  C8   107.35  3.000
 OS6  C12  N4   C13  113.93  3.000
 OS6  H8   C12  N3   115.02  3.000
 OS6  H8   C12  N4   116.59  3.000
 OS6  N3   C12  N4   128.39  3.000
 OS6  C11  N3   C12  118.82  3.000
 OS6  C10  C11  N2   123.35  3.000
 OS6  C10  C11  N3   117.81  3.000
 OS6  N2   C11  N3   118.81  3.000
 OS6  H10  N2   H9   115.76  3.000
 OS6  H10  N2   C11  120.64  3.000
 OS6  H9   N2   C11  117.84  3.000
 OS6  N1   C10  C11  133.45  3.000
 OS6  C11  C10  C13  118.65  3.000
 OS6  N1   C10  C13  107.90  3.000
 OS6  H11  N1   C9   124.42  3.000
 OS6  H11  N1   C10  127.02  3.000
 OS6  C9   N1   C10  108.54  3.000
 OS6  H12  C9   N1   120.36  3.000
 OS6  H12  C9   C8   129.10  3.000
 OS6  N1   C9   C8   110.54  3.000
 OS6  H14  C6   H13  107.02  3.000
 OS6  H14  C6   C5   113.10  3.000
 OS6  H13  C6   C5   109.65  3.000
 OS6  H14  C6   N    111.03  3.000
 OS6  H13  C6   N    111.62  3.000
 OS6  C5   C6   N    104.50  3.000
 OS6  H15  C5   C4   108.73  3.000
 OS6  H15  C5   C6   110.34  3.000
 OS6  C4   C5   C6   112.88  3.000
 OS6  H15  C5   C15  108.18  3.000
 OS6  C4   C5   C15  112.10  3.000
 OS6  C6   C5   C15  104.48  3.000
 OS6  H17  C4   H16  107.98  3.000
 OS6  H17  C4   S    109.05  3.000
 OS6  H16  C4   S    109.11  3.000
 OS6  H17  C4   C5   110.33  3.000
 OS6  H16  C4   C5   110.60  3.000
 OS6  S    C4   C5   109.72  3.000
 OS6  C3   S    C4   100.35  3.000
 OS6  H19  C3   H18  107.82  3.000
 OS6  H19  C3   C2   110.51  3.000
 OS6  H18  C3   C2   110.41  3.000
 OS6  H19  C3   S    109.15  3.000
 OS6  H18  C3   S    109.14  3.000
 OS6  C2   C3   S    109.77  3.000
 OS6  H21  C2   H20  106.87  3.000
 OS6  H21  C2   C1   109.49  3.000
 OS6  H20  C2   C1   109.30  3.000
 OS6  H21  C2   C3   109.68  3.000
 OS6  H20  C2   C3   109.86  3.000
 OS6  C1   C2   C3   111.53  3.000
 OS6  H23  C1   H22  106.48  3.000
 OS6  H23  C1   C    109.66  3.000
 OS6  H22  C1   C    109.07  3.000
 OS6  H23  C1   C2   109.28  3.000
 OS6  H22  C1   C2   109.86  3.000
 OS6  C    C1   C2   112.33  3.000
 OS6  C16  C    N5   107.35  3.000
 OS6  N5   C    C1   122.92  3.000
 OS6  C16  C    C1   129.71  3.000
 OS6  N7   N5   C    109.39  3.000
 OS6  N6   N7   N5   108.02  3.000
 OS6  C17  N6   C16  128.58  3.000
 OS6  C17  N6   N7   120.62  3.000
 OS6  C16  N6   N7   110.79  3.000
 OS6  H24  C16  N6   122.99  3.000
 OS6  H24  C16  C    132.57  3.000
 OS6  N6   C16  C    104.44  3.000
 OS6  H26  C17  H25  107.47  3.000
 OS6  H26  C17  C18  110.75  3.000
 OS6  H25  C17  C18  110.88  3.000
 OS6  H26  C17  N6   106.81  3.000
 OS6  H25  C17  N6   108.17  3.000
 OS6  C18  C17  N6   112.55  3.000
 OS6  H28  C18  H27  106.96  3.000
 OS6  H28  C18  C19  109.69  3.000
 OS6  H27  C18  C19  109.89  3.000
 OS6  H28  C18  C17  109.37  3.000
 OS6  H27  C18  C17  109.49  3.000
 OS6  C19  C18  C17  111.34  3.000
 OS6  H31  C20  H30  107.60  3.000
 OS6  H31  C20  H29  107.64  3.000
 OS6  H30  C20  H29  107.62  3.000
 OS6  H31  C20  C19  111.25  3.000
 OS6  H30  C20  C19  111.31  3.000
 OS6  H29  C20  C19  111.24  3.000
 OS6  H33  C19  H32  106.23  3.000
 OS6  H33  C19  C20  109.55  3.000
 OS6  H32  C19  C20  109.55  3.000
 OS6  H33  C19  C18  109.44  3.000
 OS6  H32  C19  C18  109.43  3.000
 OS6  C20  C19  C18  112.45  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
 OS6  CONST_01  C10  N1   C9   C8      0.00   0.0  0
 OS6  CONST_02  N1   C10  C13  C8      0.00   0.0  0
 OS6  CONST_03  C11  C10  C13  C8    180.00   0.0  0
 OS6  CONST_04  C12  N4   C13  C8    180.00   0.0  0
 OS6  CONST_05  C9   N1   C10  C13     0.00   0.0  0
 OS6  CONST_06  N3   C11  C10  C13     0.00   0.0  0
 OS6  CONST_07  N1   C9   C8   C13     0.00   0.0  0
 OS6  CONST_08  N3   C12  N4   C13     0.00   0.0  0
 OS6  CONST_09  N1   C10  C13  N4    180.00   0.0  0
 OS6  CONST_10  C11  C10  C13  N4      0.00   0.0  0
 OS6  CONST_11  C9   C8   C13  N4    180.00   0.0  0
 OS6  CONST_12  C11  N3   C12  N4      0.00   0.0  0
 OS6  CONST_13  C10  C11  N3   C12     0.00   0.0  0
 OS6  CONST_14  C10  C13  N4   C12     0.00   0.0  0
 OS6  CONST_15  N1   C10  C11  N3    180.00   0.0  0
 OS6  CONST_16  C9   N1   C10  C11   180.00   0.0  0
 OS6  CONST_17  C9   C8   C13  C10     0.00   0.0  0
 OS6  CONST_18  N7   N6   C16  C       0.00   0.0  0
 OS6  CONST_19  N6   N7   N5   C       0.00   0.0  0
 OS6  CONST_20  N6   C16  C    N5      0.00   0.0  0
 OS6  CONST_21  C16  N6   N7   N5      0.00   0.0  0
 OS6  CONST_22  C16  C    N5   N7      0.00   0.0  0
 OS6  CONST_23  N1   C9   C8   C7    180.00   0.0  0
 OS6  CONST_24  C10  C13  C8   C7    180.00   0.0  0
 OS6  CONST_25  N4   C13  C8   C7      0.00   0.0  0
 OS6  CONST_26  N2   C11  C10  C13   180.00   0.0  0
 OS6  CONST_27  N2   C11  N3   C12   180.00   0.0  0
 OS6  CONST_28  N1   C10  C11  N2      0.00   0.0  0
 OS6  CONST_29  N6   C16  C    C1    180.00   0.0  0
 OS6  CONST_30  N7   N5   C    C1    180.00   0.0  0
 OS6  CONST_31  C17  N6   C16  C     180.00   0.0  0
 OS6  CONST_32  C17  N6   N7   N5    180.00   0.0  0
 OS6  CONST_33  H11  N1   C9   C8    180.00   0.0  0
 OS6  CONST_34  H12  C9   C8   C13   180.00   0.0  0
 OS6  CONST_35  H8   C12  N4   C13   180.00   0.0  0
 OS6  CONST_36  H24  C16  C    N5    180.00   0.0  0
 OS6  CONST_37  H9   N2   C11  N3      0.00   0.0  0
 OS6  Var_01    C6   N    C14  C15    45.67  30.0  1
 OS6  Var_02    C5   C6   N    C14   -39.61  30.0  1
 OS6  Var_03    C8   C7   N    C14    64.59  30.0  1
 OS6  Var_04    C9   C8   C7   N    -106.59  30.0  3
 OS6  Var_05    C16  C    C1   C2    119.01  30.0  2
 OS6  Var_06    C18  C17  N6   N7    -63.88  30.0  2
 OS6  Var_07    C    C1   C2   C3   -179.39  30.0  3
 OS6  Var_08    C19  C18  C17  N6   -179.17  30.0  3
 OS6  Var_09    C2   C3   S    C4   -176.83  30.0  3
 OS6  Var_10    C1   C2   C3   S    -178.27  30.0  3
 OS6  Var_11    C20  C19  C18  C17  -178.55  30.0  1
 OS6  Var_12    H16  C4   S    C3     63.70  30.0  1
 OS6  Var_13    H29  C20  C19  C18  -179.85  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
 OS6  chir_01  C15  C14  O    C5  positiv
 OS6  chir_02  C5   C6   C15  C4  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
 OS6  plan-1  C1   0.020
 OS6  plan-1  C    0.020
 OS6  plan-1  N5   0.020
 OS6  plan-1  N7   0.020
 OS6  plan-1  N6   0.020
 OS6  plan-1  C16  0.020
 OS6  plan-1  C17  0.020
 OS6  plan-1  H24  0.020
 OS6  plan-2  C7   0.020
 OS6  plan-2  C8   0.020
 OS6  plan-2  C13  0.020
 OS6  plan-2  N4   0.020
 OS6  plan-2  C12  0.020
 OS6  plan-2  N3   0.020
 OS6  plan-2  C11  0.020
 OS6  plan-2  N2   0.020
 OS6  plan-2  C10  0.020
 OS6  plan-2  N1   0.020
 OS6  plan-2  C9   0.020
 OS6  plan-2  H8   0.020
 OS6  plan-2  H11  0.020
 OS6  plan-2  H12  0.020
 OS6  plan-3  C11  0.020
 OS6  plan-3  N2   0.020
 OS6  plan-3  H9   0.020
 OS6  plan-3  H10  0.020

