# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 14:53:32 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(pyrazin-2-ylsulfanyl)methyl]pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSc4cnccn4)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
 4EH  4EH  (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(pyrazin-2-ylsulfanyl)methyl]pyrrolidin-3-ol  ligand  44  25  .  2022-07-23  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_4EH
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
 4EH  O3'  O  OH1   0  -0.673   0.1159  -1.4082   2.3226
 4EH  C3'  C  CR15  0   0.053   0.4874  -1.5029   0.9658
 4EH  C4'  C  CR15  0  -0.295   1.2928  -0.2393   0.5904
 4EH  C5'  C  CH2   0  -0.561   2.7628  -0.5461   0.3646
 4EH  S    S  S2    0   0.054   3.6267   1.0021  -0.0259
 4EH  C2'  C  CH2   0  -0.294  -0.6954  -1.4862  -0.0091
 4EH  N1'  N  NR5   0  -0.415  -0.8021  -0.1013  -0.4158
 4EH  C1'  C  CH2   0  -0.259   0.5647   0.3173  -0.6334
 4EH  C10  C  CH2   0  -0.361  -1.6766   0.1429  -1.5413
 4EH  C9   C  CR5   0  -0.046  -3.0910  -0.2175  -1.2405
 4EH  C4   C  CR56  0   0.163  -3.9511   0.3942  -0.2841
 4EH  N3   N  N     0  -0.445  -3.7350   1.4374   0.5430
 4EH  C2   C  CR16  0   0.005  -4.7627   1.7377   1.3004
 4EH  C8   C  CR15  0  -0.053  -3.8252  -1.2287  -1.8068
 4EH  N7   N  NR15  0  -0.677  -5.0708  -1.2752  -1.2646
 4EH  C5   C  CR56  0   0.204  -5.1722  -0.2887  -0.3256
 4EH  C6   C  CR6   0   0.456  -6.2016   0.1191   0.5379
 4EH  N1   N  N     0  -0.471  -5.9618   1.1467   1.3472
 4EH  N6   N  NH2   0  -0.827  -7.3952  -0.5007   0.6126
 4EH  C6'  C  CR6   0   0.058   5.2864   0.4661  -0.1975
 4EH  C9'  C  CR16  0  -0.083   6.2692   1.4271  -0.4776
 4EH  N3'  N  N     0  -0.343   7.5343   1.0918  -0.6170
 4EH  C8'  C  CR16  0  -0.118   7.8471  -0.1960  -0.4814
 4EH  C7'  C  CR16  0  -0.103   6.8765  -1.1403  -0.2052
 4EH  N2'  N  N     0  -0.368   5.5963  -0.8097  -0.0634
 4EH  H1   H  HOH1  0   0.450  -0.2956  -2.2389   2.5798
 4EH  H2   H  HCR5  0   0.219   1.0861  -2.4075   0.7991
 4EH  H3   H  HCR5  0   0.267   1.1937   0.4703   1.4169
 4EH  H4   H  HCH2  0   0.291   3.2105  -0.9807   1.2583
 4EH  H5   H  HCH2  0   0.279   2.8940  -1.2476  -0.4604
 4EH  H6   H  HCH2  0   0.191  -0.4687  -2.1468  -0.8650
 4EH  H7   H  HCH2  0   0.242  -1.6186  -1.8523   0.4450
 4EH  H9   H  HCH2  0   0.244   0.6354   1.4042  -0.7169
 4EH  H10  H  HCH2  0   0.193   0.9926  -0.1117  -1.5593
 4EH  H11  H  HCH2  0   0.239  -1.6091   1.2061  -1.7907
 4EH  H12  H  HCH2  0   0.205  -1.3463  -0.4090  -2.4392
 4EH  H13  H  HCR6  0   0.237  -4.6370   2.5736   1.9821
 4EH  H14  H  HCR5  0   0.289  -3.5367  -1.9312  -2.5732
 4EH  H15  H  HNR5  0   0.416  -5.7831  -1.9334  -1.5320
 4EH  H16  H  HNH2  0   0.401  -7.7025  -1.1162  -0.1199
 4EH  H17  H  HNH2  0   0.397  -8.1224  -0.0604   1.1511
 4EH  H18  H  HCR6  0   0.281   6.0087   2.4744  -0.5849
 4EH  H19  H  HCR6  0   0.278   8.8862  -0.4775  -0.5941
 4EH  H20  H  HCR6  0   0.280   7.1315  -2.1872  -0.0951

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
 4EH  C7'  N2'  aromatic  1.330  0.020  1.330
 4EH  C7'  C8'  aromatic  1.382  0.020  1.382
 4EH  N2'  C6'  aromatic  1.320  0.020  1.320
 4EH  C8'  N3'  aromatic  1.332  0.020  1.332
 4EH  C6'  S    single    1.753  0.020  1.753
 4EH  C6'  C9'  aromatic  1.403  0.020  1.403
 4EH  S    C5'  single    1.815  0.020  1.815
 4EH  N3'  C9'  aromatic  1.316  0.020  1.316
 4EH  N1   C2   aromatic  1.338  0.020  1.338
 4EH  N1   C6   aromatic  1.330  0.020  1.330
 4EH  N6   C6   single    1.347  0.020  1.347
 4EH  C2   N3   aromatic  1.312  0.020  1.312
 4EH  C6   C5   aromatic  1.404  0.020  1.404
 4EH  C5'  C4'  single    1.519  0.020  1.519
 4EH  N3   C4   aromatic  1.349  0.020  1.349
 4EH  C5   C4   aromatic  1.400  0.020  1.400
 4EH  C5   N7   aromatic  1.366  0.020  1.366
 4EH  C4   C9   aromatic  1.424  0.020  1.424
 4EH  C4'  C3'  single    1.545  0.020  1.545
 4EH  C4'  C1'  single    1.529  0.020  1.529
 4EH  C3'  C2'  single    1.533  0.020  1.533
 4EH  C3'  O3'  single    1.410  0.020  1.410
 4EH  N7   C8   aromatic  1.359  0.020  1.359
 4EH  C2'  N1'  single    1.447  0.020  1.447
 4EH  C1'  N1'  single    1.446  0.020  1.446
 4EH  C9   C8   aromatic  1.372  0.020  1.372
 4EH  C9   C10  single    1.490  0.020  1.490
 4EH  N1'  C10  single    1.446  0.020  1.446
 4EH  O3'  H1   single    0.850  0.020  0.980
 4EH  C3'  H2   single    0.970  0.020  1.090
 4EH  C4'  H3   single    0.970  0.020  1.090
 4EH  C5'  H4   single    0.970  0.020  1.090
 4EH  C5'  H5   single    0.970  0.020  1.090
 4EH  C2'  H6   single    0.970  0.020  1.090
 4EH  C2'  H7   single    0.970  0.020  1.090
 4EH  C1'  H9   single    0.970  0.020  1.090
 4EH  C1'  H10  single    0.970  0.020  1.090
 4EH  C10  H11  single    0.970  0.020  1.090
 4EH  C10  H12  single    0.970  0.020  1.090
 4EH  C2   H13  single    0.930  0.020  1.080
 4EH  C8   H14  single    0.930  0.020  1.080
 4EH  N7   H15  single    0.860  0.020  1.020
 4EH  N6   H16  single    0.890  0.020  1.040
 4EH  N6   H17  single    0.890  0.020  1.040
 4EH  C9'  H18  single    0.930  0.020  1.080
 4EH  C8'  H19  single    0.930  0.020  1.080
 4EH  C7'  H20  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
 4EH  H1   O3'  C3'  108.18  3.000
 4EH  H2   C3'  C2'  109.47  3.000
 4EH  H2   C3'  C4'  110.67  3.000
 4EH  C2'  C3'  C4'  103.82  3.000
 4EH  H2   C3'  O3'  110.20  3.000
 4EH  C2'  C3'  O3'  114.08  3.000
 4EH  C4'  C3'  O3'  108.43  3.000
 4EH  H3   C4'  C1'  109.00  3.000
 4EH  H3   C4'  C5'  109.34  3.000
 4EH  C1'  C4'  C5'  114.55  3.000
 4EH  H3   C4'  C3'  107.45  3.000
 4EH  C1'  C4'  C3'  104.12  3.000
 4EH  C5'  C4'  C3'  112.06  3.000
 4EH  H5   C5'  H4   108.31  3.000
 4EH  H5   C5'  S    109.18  3.000
 4EH  H4   C5'  S    108.72  3.000
 4EH  H5   C5'  C4'  111.03  3.000
 4EH  H4   C5'  C4'  110.87  3.000
 4EH  S    C5'  C4'  108.68  3.000
 4EH  C6'  S    C5'  102.18  3.000
 4EH  H7   C2'  H6   107.17  3.000
 4EH  H7   C2'  N1'  112.04  3.000
 4EH  H6   C2'  N1'  111.69  3.000
 4EH  H7   C2'  C3'  112.59  3.000
 4EH  H6   C2'  C3'  109.14  3.000
 4EH  N1'  C2'  C3'  104.24  3.000
 4EH  C10  N1'  C1'  113.93  3.000
 4EH  C10  N1'  C2'  115.14  3.000
 4EH  C1'  N1'  C2'  104.45  3.000
 4EH  H10  C1'  H9   107.26  3.000
 4EH  H10  C1'  N1'  112.28  3.000
 4EH  H9   C1'  N1'  111.14  3.000
 4EH  H10  C1'  C4'  110.16  3.000
 4EH  H9   C1'  C4'  113.11  3.000
 4EH  N1'  C1'  C4'  102.96  3.000
 4EH  H12  C10  H11  106.37  3.000
 4EH  H12  C10  C9   109.09  3.000
 4EH  H11  C10  C9   109.85  3.000
 4EH  H12  C10  N1'  111.57  3.000
 4EH  H11  C10  N1'  107.71  3.000
 4EH  C9   C10  N1'  112.08  3.000
 4EH  C8   C9   C4   105.70  3.000
 4EH  C8   C9   C10  127.07  3.000
 4EH  C4   C9   C10  127.21  3.000
 4EH  C5   C4   N3   122.36  3.000
 4EH  C5   C4   C9   107.30  3.000
 4EH  N3   C4   C9   130.33  3.000
 4EH  C2   N3   C4   113.94  3.000
 4EH  H13  C2   N1   114.96  3.000
 4EH  H13  C2   N3   116.62  3.000
 4EH  N1   C2   N3   128.42  3.000
 4EH  H14  C8   N7   120.41  3.000
 4EH  H14  C8   C9   129.05  3.000
 4EH  N7   C8   C9   110.54  3.000
 4EH  H15  N7   C5   127.07  3.000
 4EH  H15  N7   C8   124.41  3.000
 4EH  C5   N7   C8   108.52  3.000
 4EH  C6   C5   N7   133.40  3.000
 4EH  N7   C5   C4   107.93  3.000
 4EH  C6   C5   C4   118.67  3.000
 4EH  N6   C6   N1   118.79  3.000
 4EH  N6   C6   C5   123.37  3.000
 4EH  N1   C6   C5   117.80  3.000
 4EH  C6   N1   C2   118.80  3.000
 4EH  H17  N6   H16  115.91  3.000
 4EH  H17  N6   C6   117.95  3.000
 4EH  H16  N6   C6   120.82  3.000
 4EH  N2'  C6'  C9'  121.20  3.000
 4EH  C9'  C6'  S    118.26  3.000
 4EH  N2'  C6'  S    120.54  3.000
 4EH  H18  C9'  N3'  117.80  3.000
 4EH  H18  C9'  C6'  120.87  3.000
 4EH  N3'  C9'  C6'  121.33  3.000
 4EH  C8'  N3'  C9'  117.47  3.000
 4EH  H19  C8'  C7'  121.15  3.000
 4EH  H19  C8'  N3'  117.79  3.000
 4EH  C7'  C8'  N3'  121.06  3.000
 4EH  H20  C7'  N2'  117.14  3.000
 4EH  H20  C7'  C8'  121.02  3.000
 4EH  N2'  C7'  C8'  121.84  3.000
 4EH  C7'  N2'  C6'  117.10  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
 4EH  CONST_01  C2   N3   C4   C9   180.00   0.0  0
 4EH  CONST_02  C6   C5   C4   C9   180.00   0.0  0
 4EH  CONST_03  N7   C5   C4   C9     0.00   0.0  0
 4EH  CONST_04  C5   N7   C8   C9     0.00   0.0  0
 4EH  CONST_05  N1   C2   N3   C4     0.00   0.0  0
 4EH  CONST_06  N1   C6   C5   C4     0.00   0.0  0
 4EH  CONST_07  C8   N7   C5   C4     0.00   0.0  0
 4EH  CONST_08  N7   C8   C9   C4     0.00   0.0  0
 4EH  CONST_09  C6   N1   C2   N3     0.00   0.0  0
 4EH  CONST_10  C6   C5   C4   N3     0.00   0.0  0
 4EH  CONST_11  N7   C5   C4   N3   180.00   0.0  0
 4EH  CONST_12  C8   C9   C4   N3   180.00   0.0  0
 4EH  CONST_13  C5   C6   N1   C2     0.00   0.0  0
 4EH  CONST_14  C5   C4   N3   C2     0.00   0.0  0
 4EH  CONST_15  C6   C5   N7   C8   180.00   0.0  0
 4EH  CONST_16  C5   C4   C9   C8     0.00   0.0  0
 4EH  CONST_17  N1   C6   C5   N7   180.00   0.0  0
 4EH  CONST_18  C8'  C7'  N2'  C6'    0.00   0.0  0
 4EH  CONST_19  C8'  N3'  C9'  C6'    0.00   0.0  0
 4EH  CONST_20  C7'  N2'  C6'  C9'    0.00   0.0  0
 4EH  CONST_21  C7'  C8'  N3'  C9'    0.00   0.0  0
 4EH  CONST_22  N2'  C7'  C8'  N3'    0.00   0.0  0
 4EH  CONST_23  N2'  C6'  C9'  N3'    0.00   0.0  0
 4EH  CONST_24  C7'  N2'  C6'  S    180.00   0.0  0
 4EH  CONST_25  N3'  C9'  C6'  S    180.00   0.0  0
 4EH  CONST_26  N3   C4   C9   C10    0.00   0.0  0
 4EH  CONST_27  C5   C4   C9   C10  180.00   0.0  0
 4EH  CONST_28  N7   C8   C9   C10  180.00   0.0  0
 4EH  CONST_29  N6   C6   C5   C4   180.00   0.0  0
 4EH  CONST_30  N6   C6   N1   C2   180.00   0.0  0
 4EH  CONST_31  N6   C6   C5   N7     0.00   0.0  0
 4EH  CONST_32  H15  N7   C8   C9   180.00   0.0  0
 4EH  CONST_33  H13  C2   N3   C4   180.00   0.0  0
 4EH  CONST_34  H14  C8   C9   C4   180.00   0.0  0
 4EH  CONST_35  H20  C7'  N2'  C6'  180.00   0.0  0
 4EH  CONST_36  H19  C8'  N3'  C9'  180.00   0.0  0
 4EH  CONST_37  H18  C9'  N3'  C8'  180.00   0.0  0
 4EH  CONST_39  H17  N6   C6   C5   180.00   0.0  0
 4EH  Var_01    C1'  N1'  C2'  C3'   42.51  30.0  1
 4EH  Var_02    C2'  N1'  C1'  C4'  -45.26  30.0  1
 4EH  Var_03    C9   C10  N1'  C2'   63.23  30.0  3
 4EH  Var_04    C4   C9   C10  N1'   64.96  30.0  3
 4EH  Var_05    N2'  C6'  S    C5'    1.36  30.0  3
 4EH  Var_06    H4   C5'  S    C6'   57.43  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
 4EH  chir_01  C3'  C4'  C2'  O3'  positiv
 4EH  chir_02  C4'  C5'  C3'  C1'  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
 4EH  plan-1  S    0.020
 4EH  plan-1  C6'  0.020
 4EH  plan-1  C9'  0.020
 4EH  plan-1  N3'  0.020
 4EH  plan-1  C8'  0.020
 4EH  plan-1  C7'  0.020
 4EH  plan-1  N2'  0.020
 4EH  plan-1  H18  0.020
 4EH  plan-1  H19  0.020
 4EH  plan-1  H20  0.020
 4EH  plan-2  C10  0.020
 4EH  plan-2  C9   0.020
 4EH  plan-2  C4   0.020
 4EH  plan-2  N3   0.020
 4EH  plan-2  C2   0.020
 4EH  plan-2  C8   0.020
 4EH  plan-2  N7   0.020
 4EH  plan-2  C5   0.020
 4EH  plan-2  C6   0.020
 4EH  plan-2  N1   0.020
 4EH  plan-2  N6   0.020
 4EH  plan-2  H13  0.020
 4EH  plan-2  H14  0.020
 4EH  plan-2  H15  0.020
 4EH  plan-3  C6   0.020
 4EH  plan-3  N6   0.020
 4EH  plan-3  H16  0.020
 4EH  plan-3  H17  0.020

