# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 05:34:04 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(benzylsulfanyl)methyl]pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSCc4ccccc4)C3)c[nH]c12
#
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
 DF9  DF9  (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(benzylsulfanyl)methyl]pyrrolidin-3-ol  ligand  49  26  .  2022-07-24  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_DF9
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
 DF9  N6    N  NH2   0  -0.827   7.8160   0.0349  -0.5221
 DF9  C6    C  CR6   0   0.454   6.5535   0.5001  -0.6063
 DF9  N1    N  N     0  -0.471   6.2337   1.3079  -1.6126
 DF9  C2    C  CR16  0   0.004   4.9718   1.7400  -1.7160
 DF9  N3    N  N     0  -0.444   3.9515   1.4704  -0.9372
 DF9  C5    C  CR56  0   0.204   5.5379   0.1416   0.2939
 DF9  C4    C  CR56  0   0.163   4.2483   0.6455   0.0877
 DF9  N7    N  NR15  0  -0.676   5.5083  -0.6470   1.4083
 DF9  C8    C  CR15  0  -0.052   4.2409  -0.6527   1.8992
 DF9  C9    C  CR5   0  -0.046   3.4213   0.1302   1.1262
 DF9  C10   C  CH2   0  -0.361   1.9593   0.3544   1.3118
 DF9  N1'   N  NT    0  -0.411   1.1767  -0.2740   0.2694
 DF9  C2'   C  CH2   0  -0.297   1.2708  -1.7183   0.2329
 DF9  C3'   C  CH1   0   0.053   0.1655  -2.1353  -0.7382
 DF9  O3'   O  OH1   0  -0.675   0.5971  -2.2339  -2.0779
 DF9  C1'   C  CH2   0  -0.262  -0.2440  -0.0175   0.3778
 DF9  C4'   C  CH1   0  -0.286  -0.8603  -0.9837  -0.6383
 DF9  C5'   C  CH2   0  -0.559  -2.2455  -1.4743  -0.2571
 DF9  S6'   S  S2    0  -0.021  -3.4097  -0.0817  -0.2113
 DF9  C7'   C  CH2   0  -0.616  -4.9414  -0.9690   0.2186
 DF9  C21   C  CR6   0   0.111  -6.0641   0.0217   0.2799
 DF9  C26   C  CR16  0  -0.289  -6.8256   0.3009  -0.8521
 DF9  C25   C  CR16  0  -0.242  -7.8506   1.2359  -0.8010
 DF9  C24   C  CR16  0  -0.267  -8.1214   1.9087   0.3836
 DF9  C23   C  CR16  0  -0.242  -7.3618   1.6418   1.5157
 DF9  C22   C  CR16  0  -0.287  -6.3380   0.7060   1.4617
 DF9  HN6   H  HNH2  0   0.397   8.5107   0.4588  -1.1144
 DF9  HN6A  H  HNH2  0   0.400   8.1591  -0.3549   0.3384
 DF9  H2    H  HCR6  0   0.237   4.7807   2.3998  -2.5569
 DF9  HN7   H  HNR5  0   0.416   6.2731  -1.1681   1.8026
 DF9  H8    H  HCR5  0   0.289   3.9996  -1.2254   2.7813
 DF9  H10   H  HCH2  0   0.203   1.6618  -0.0098   2.3112
 DF9  H10A  H  HCH2  0   0.239   1.7426   1.4267   1.2955
 DF9  H2'   H  HCH2  0   0.242   2.2607  -2.0580  -0.0784
 DF9  H2'A  H  HCH2  0   0.188   1.0676  -2.1607   1.2255
 DF9  H3'   H  HCH1  0   0.217  -0.2767  -3.0851  -0.4107
 DF9  HO3'  H  HOH1  0   0.449   1.1755  -2.9994  -2.1502
 DF9  H1'   H  HCH2  0   0.190  -0.6262  -0.2440   1.3913
 DF9  H1'A  H  HCH2  0   0.241  -0.4738   1.0297   0.1702
 DF9  H4'   H  HCH1  0   0.261  -0.9112  -0.4988  -1.6174
 DF9  H5'   H  HCH2  0   0.274  -2.6028  -2.2099  -0.9813
 DF9  H5'A  H  HCH2  0   0.261  -2.2220  -1.9553   0.7246
 DF9  H7'   H  HCH2  0   0.281  -5.1309  -1.7314  -0.5385
 DF9  H7'A  H  HCH2  0   0.281  -4.8071  -1.4686   1.1794
 DF9  H26   H  HCR6  0   0.253  -6.6188  -0.2224  -1.7784
 DF9  H25   H  HCR6  0   0.256  -8.4393   1.4379  -1.6867
 DF9  H24   H  HCR6  0   0.257  -8.9216   2.6359   0.4246
 DF9  H23   H  HCR6  0   0.256  -7.5669   2.1624   2.4424
 DF9  H22   H  HCR6  0   0.253  -5.7482   0.5001   2.3475

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
 DF9  N6   C6    single    1.348  0.020  1.348
 DF9  C6   N1    aromatic  1.329  0.020  1.329
 DF9  C6   C5    aromatic  1.404  0.020  1.404
 DF9  N1   C2    aromatic  1.338  0.020  1.338
 DF9  C2   N3    aromatic  1.312  0.020  1.312
 DF9  N3   C4    aromatic  1.349  0.020  1.349
 DF9  C5   C4    aromatic  1.400  0.020  1.400
 DF9  C5   N7    aromatic  1.366  0.020  1.366
 DF9  C4   C9    aromatic  1.424  0.020  1.424
 DF9  N7   C8    aromatic  1.359  0.020  1.359
 DF9  C8   C9    aromatic  1.372  0.020  1.372
 DF9  C9   C10   single    1.491  0.020  1.491
 DF9  C10  N1'   single    1.447  0.020  1.447
 DF9  N1'  C2'   single    1.448  0.020  1.448
 DF9  N1'  C1'   single    1.448  0.020  1.448
 DF9  C2'  C3'   single    1.529  0.020  1.529
 DF9  C3'  O3'   single    1.411  0.020  1.411
 DF9  C3'  C4'   single    1.545  0.020  1.545
 DF9  C1'  C4'   single    1.532  0.020  1.532
 DF9  C4'  C5'   single    1.518  0.020  1.518
 DF9  C5'  S6'   single    1.816  0.020  1.816
 DF9  S6'  C7'   single    1.822  0.020  1.822
 DF9  C7'  C21   single    1.499  0.020  1.499
 DF9  C21  C26   aromatic  1.393  0.020  1.393
 DF9  C21  C22   aromatic  1.393  0.020  1.393
 DF9  C26  C25   aromatic  1.388  0.020  1.388
 DF9  C25  C24   aromatic  1.389  0.020  1.389
 DF9  C24  C23   aromatic  1.389  0.020  1.389
 DF9  C23  C22   aromatic  1.388  0.020  1.388
 DF9  N6   HN6   single    0.890  0.020  1.040
 DF9  N6   HN6A  single    0.890  0.020  1.040
 DF9  C2   H2    single    0.930  0.020  1.080
 DF9  N7   HN7   single    0.860  0.020  1.020
 DF9  C8   H8    single    0.930  0.020  1.080
 DF9  C10  H10   single    0.970  0.020  1.090
 DF9  C10  H10A  single    0.970  0.020  1.090
 DF9  C2'  H2'   single    0.970  0.020  1.090
 DF9  C2'  H2'A  single    0.970  0.020  1.090
 DF9  C3'  H3'   single    0.970  0.020  1.090
 DF9  O3'  HO3'  single    0.850  0.020  0.980
 DF9  C1'  H1'   single    0.970  0.020  1.090
 DF9  C1'  H1'A  single    0.970  0.020  1.090
 DF9  C4'  H4'   single    0.970  0.020  1.090
 DF9  C5'  H5'   single    0.970  0.020  1.090
 DF9  C5'  H5'A  single    0.970  0.020  1.090
 DF9  C7'  H7'   single    0.970  0.020  1.090
 DF9  C7'  H7'A  single    0.970  0.020  1.090
 DF9  C26  H26   single    0.930  0.020  1.080
 DF9  C25  H25   single    0.930  0.020  1.080
 DF9  C24  H24   single    0.930  0.020  1.080
 DF9  C23  H23   single    0.930  0.020  1.080
 DF9  C22  H22   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
 DF9  HN6A  N6   HN6  115.57  3.000
 DF9  HN6A  N6   C6   120.46  3.000
 DF9  HN6   N6   C6   117.66  3.000
 DF9  C5    C6   N1   117.81  3.000
 DF9  C5    C6   N6   123.33  3.000
 DF9  N1    C6   N6   118.83  3.000
 DF9  C2    N1   C6   118.79  3.000
 DF9  H2    C2   N3   116.61  3.000
 DF9  H2    C2   N1   114.97  3.000
 DF9  N3    C2   N1   128.43  3.000
 DF9  C4    N3   C2   113.94  3.000
 DF9  N7    C5   C4   107.94  3.000
 DF9  N7    C5   C6   133.36  3.000
 DF9  C4    C5   C6   118.69  3.000
 DF9  C9    C4   C5   107.30  3.000
 DF9  C9    C4   N3   130.37  3.000
 DF9  C5    C4   N3   122.33  3.000
 DF9  HN7   N7   C8   124.42  3.000
 DF9  HN7   N7   C5   127.05  3.000
 DF9  C8    N7   C5   108.51  3.000
 DF9  H8    C8   C9   129.04  3.000
 DF9  H8    C8   N7   120.40  3.000
 DF9  C9    C8   N7   110.56  3.000
 DF9  C10   C9   C8   126.98  3.000
 DF9  C10   C9   C4   127.30  3.000
 DF9  C8    C9   C4   105.69  3.000
 DF9  H10A  C10  H10  106.46  3.000
 DF9  H10A  C10  N1'  107.92  3.000
 DF9  H10   C10  N1'  111.28  3.000
 DF9  H10A  C10  C9   109.87  3.000
 DF9  H10   C10  C9   109.10  3.000
 DF9  N1'   C10  C9   112.05  3.000
 DF9  C1'   N1'  C2'  104.03  3.000
 DF9  C1'   N1'  C10  113.56  3.000
 DF9  C2'   N1'  C10  114.60  3.000
 DF9  H2'A  C2'  H2'  107.34  3.000
 DF9  H2'A  C2'  C3'  109.15  3.000
 DF9  H2'   C2'  C3'  112.92  3.000
 DF9  H2'A  C2'  N1'  111.39  3.000
 DF9  H2'   C2'  N1'  112.11  3.000
 DF9  C3'   C2'  N1'  103.95  3.000
 DF9  H3'   C3'  C4'  110.99  3.000
 DF9  H3'   C3'  O3'  110.25  3.000
 DF9  C4'   C3'  O3'  108.45  3.000
 DF9  H3'   C3'  C2'  109.74  3.000
 DF9  C4'   C3'  C2'  103.62  3.000
 DF9  O3'   C3'  C2'  113.63  3.000
 DF9  HO3'  O3'  C3'  108.11  3.000
 DF9  H1'A  C1'  H1'  107.32  3.000
 DF9  H1'A  C1'  C4'  113.21  3.000
 DF9  H1'   C1'  C4'  109.84  3.000
 DF9  H1'A  C1'  N1'  111.23  3.000
 DF9  H1'   C1'  N1'  111.80  3.000
 DF9  C4'   C1'  N1'  103.50  3.000
 DF9  H4'   C4'  C5'  109.00  3.000
 DF9  H4'   C4'  C1'  109.44  3.000
 DF9  C5'   C4'  C1'  113.85  3.000
 DF9  H4'   C4'  C3'  107.66  3.000
 DF9  C5'   C4'  C3'  112.40  3.000
 DF9  C1'   C4'  C3'  104.23  3.000
 DF9  H5'A  C5'  H5'  107.82  3.000
 DF9  H5'A  C5'  S6'  109.18  3.000
 DF9  H5'   C5'  S6'  108.87  3.000
 DF9  H5'A  C5'  C4'  110.36  3.000
 DF9  H5'   C5'  C4'  110.46  3.000
 DF9  S6'   C5'  C4'  110.09  3.000
 DF9  C7'   S6'  C5'   99.87  3.000
 DF9  H7'A  C7'  H7'  108.21  3.000
 DF9  H7'A  C7'  C21  111.03  3.000
 DF9  H7'   C7'  C21  111.11  3.000
 DF9  H7'A  C7'  S6'  109.11  3.000
 DF9  H7'   C7'  S6'  108.82  3.000
 DF9  C21   C7'  S6'  108.52  3.000
 DF9  C22   C21  C26  118.93  3.000
 DF9  C22   C21  C7'  120.45  3.000
 DF9  C26   C21  C7'  120.60  3.000
 DF9  H26   C26  C25  119.83  3.000
 DF9  H26   C26  C21  119.58  3.000
 DF9  C25   C26  C21  120.59  3.000
 DF9  H25   C25  C24  120.09  3.000
 DF9  H25   C25  C26  119.81  3.000
 DF9  C24   C25  C26  120.10  3.000
 DF9  H24   C24  C23  120.17  3.000
 DF9  H24   C24  C25  120.13  3.000
 DF9  C23   C24  C25  119.69  3.000
 DF9  H23   C23  C22  119.82  3.000
 DF9  H23   C23  C24  120.11  3.000
 DF9  C22   C23  C24  120.08  3.000
 DF9  H22   C22  C23  119.84  3.000
 DF9  H22   C22  C21  119.55  3.000
 DF9  C23   C22  C21  120.61  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
 DF9  CONST_01  N3   C2   N1   C6      0.00   0.0  0
 DF9  CONST_02  N3   C4   C5   C6      0.00   0.0  0
 DF9  CONST_03  C9   C4   C5   C6    180.00   0.0  0
 DF9  CONST_04  C8   N7   C5   C6    180.00   0.0  0
 DF9  CONST_05  C4   C5   C6   N1      0.00   0.0  0
 DF9  CONST_06  N7   C5   C6   N1    180.00   0.0  0
 DF9  CONST_07  C4   N3   C2   N1      0.00   0.0  0
 DF9  CONST_08  C5   C6   N1   C2      0.00   0.0  0
 DF9  CONST_09  C5   C4   N3   C2      0.00   0.0  0
 DF9  CONST_10  C9   C4   N3   C2    180.00   0.0  0
 DF9  CONST_11  N7   C5   C4   N3    180.00   0.0  0
 DF9  CONST_12  C8   C9   C4   N3    180.00   0.0  0
 DF9  CONST_13  C8   C9   C4   C5      0.00   0.0  0
 DF9  CONST_14  C9   C8   N7   C5      0.00   0.0  0
 DF9  CONST_15  C8   N7   C5   C4      0.00   0.0  0
 DF9  CONST_16  N7   C8   C9   C4      0.00   0.0  0
 DF9  CONST_17  C9   C4   C5   N7      0.00   0.0  0
 DF9  CONST_18  C24  C25  C26  C21     0.00   0.0  0
 DF9  CONST_19  C24  C23  C22  C21     0.00   0.0  0
 DF9  CONST_20  C23  C22  C21  C26     0.00   0.0  0
 DF9  CONST_21  C23  C24  C25  C26     0.00   0.0  0
 DF9  CONST_22  C22  C21  C26  C25     0.00   0.0  0
 DF9  CONST_23  C22  C23  C24  C25     0.00   0.0  0
 DF9  CONST_24  C2   N1   C6   N6    180.00   0.0  0
 DF9  CONST_25  C4   C5   C6   N6    180.00   0.0  0
 DF9  CONST_26  N7   C5   C6   N6      0.00   0.0  0
 DF9  CONST_27  C10  C9   C4   N3      0.00   0.0  0
 DF9  CONST_28  C10  C9   C4   C5    180.00   0.0  0
 DF9  CONST_29  C10  C9   C8   N7    180.00   0.0  0
 DF9  CONST_30  C25  C26  C21  C7'   180.00   0.0  0
 DF9  CONST_31  C23  C22  C21  C7'   180.00   0.0  0
 DF9  CONST_32  H2   C2   N1   C6    180.00   0.0  0
 DF9  CONST_33  HN7  N7   C5   C6      0.00   0.0  0
 DF9  CONST_34  H8   C8   N7   C5    180.00   0.0  0
 DF9  CONST_35  H25  C25  C26  C21   180.00   0.0  0
 DF9  CONST_36  H23  C23  C22  C21   180.00   0.0  0
 DF9  CONST_37  H22  C22  C21  C26   180.00   0.0  0
 DF9  CONST_38  H24  C24  C25  C26   180.00   0.0  0
 DF9  CONST_39  H26  C26  C25  C24   180.00   0.0  0
 DF9  CONST_40  HN6  N6   C6   N1      0.00   0.0  0
 DF9  Var_01    C4'  C1'  N1'  C2'   -44.19  30.0  1
 DF9  Var_02    C1'  N1'  C2'  C3'    44.48  30.0  1
 DF9  Var_03    N1'  C10  C9   C4     67.54  30.0  2
 DF9  Var_04    C2'  N1'  C10  C9     63.72  30.0  3
 DF9  Var_05    C26  C21  C7'  S6'    90.61  30.0  2
 DF9  Var_06    C21  C7'  S6'  C5'  -178.80  30.0  3
 DF9  Var_07    H5'  C5'  S6'  C7'    57.42  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
 DF9  chir_01  C3'  C2'  O3'  C4'  positiv
 DF9  chir_02  C4'  C3'  C1'  C5'  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
 DF9  plan-1  C7'   0.020
 DF9  plan-1  C21   0.020
 DF9  plan-1  C26   0.020
 DF9  plan-1  C25   0.020
 DF9  plan-1  C24   0.020
 DF9  plan-1  C23   0.020
 DF9  plan-1  C22   0.020
 DF9  plan-1  H26   0.020
 DF9  plan-1  H25   0.020
 DF9  plan-1  H24   0.020
 DF9  plan-1  H23   0.020
 DF9  plan-1  H22   0.020
 DF9  plan-2  N6    0.020
 DF9  plan-2  C6    0.020
 DF9  plan-2  N1    0.020
 DF9  plan-2  C2    0.020
 DF9  plan-2  N3    0.020
 DF9  plan-2  C5    0.020
 DF9  plan-2  C4    0.020
 DF9  plan-2  N7    0.020
 DF9  plan-2  C8    0.020
 DF9  plan-2  C9    0.020
 DF9  plan-2  C10   0.020
 DF9  plan-2  H2    0.020
 DF9  plan-2  HN7   0.020
 DF9  plan-2  H8    0.020
 DF9  plan-3  N6    0.020
 DF9  plan-3  C6    0.020
 DF9  plan-3  HN6   0.020
 DF9  plan-3  HN6A  0.020

