# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:04:06 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSCCCC#C)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
 OS3  OS3  (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol  ligand  47  24  .  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_OS3
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
 OS3  N6   N  NH2   0  -0.826    7.4644  -0.0082  -0.0542
 OS3  C6   C  CR6   0   0.455    6.2140   0.4293  -0.3041
 OS3  N1   N  N     0  -0.471    6.0054   1.1981  -1.3688
 OS3  C2   C  CR16  0   0.005    4.7733   1.6681  -1.5933
 OS3  N3   N  N     0  -0.445    3.6843   1.4676  -0.8902
 OS3  C5   C  CR56  0   0.205    5.1181   0.1506   0.5272
 OS3  C4   C  CR56  0   0.161    3.8691   0.6874   0.1942
 OS3  N7   N  NR15  0  -0.676    4.9736  -0.5667   1.6803
 OS3  C8   C  CR15  0  -0.051    3.6753  -0.4924   2.0750
 OS3  C9   C  CR5   0  -0.045    2.9473   0.2691   1.1956
 OS3  C10  C  CH2   0  -0.362    1.4905   0.5753   1.2673
 OS3  N1A  N  NT    0  -0.412    0.7261  -0.1303   0.2604
 OS3  C2A  C  CH2   0  -0.298    0.7546  -1.5733   0.3871
 OS3  C3A  C  CH1   0   0.054   -0.3537  -2.0552  -0.5524
 OS3  O3A  O  OH1   0  -0.675    0.0977  -2.3658  -1.8528
 OS3  C1A  C  CH2   0  -0.259   -0.6844   0.1987   0.2827
 OS3  C4A  C  CH1   0  -0.285   -1.3098  -0.8458  -0.6441
 OS3  C5A  C  CH2   0  -0.553   -2.7426  -1.2021  -0.2892
 OS3  S5A  S  S2    0  -0.033   -3.8080   0.2518  -0.5035
 OS3  C20  C  CH2   0  -0.549   -5.3866  -0.4181   0.0871
 OS3  C21  C  CH2   0  -0.428   -6.4675   0.6462  -0.0227
 OS3  C22  C  CH2   0  -0.569   -7.8115   0.1180   0.4877
 OS3  C23  C  CSP   0   0.284   -8.8755   1.1064   0.3715
 OS3  C24  C  CSP1  0  -0.562   -9.7417   1.9336   0.2630
 OS3  H1   H  HNH2  0   0.400    7.6189  -0.7799   0.5712
 OS3  H2   H  HNH2  0   0.397    8.1519   0.1080  -0.7801
 OS3  H3   H  HCR6  0   0.237    4.6741   2.2920  -2.4763
 OS3  H4   H  HNR5  0   0.416    5.6922  -1.0632   2.1798
 OS3  H5   H  HCR5  0   0.290    3.3480  -0.9932   2.9729
 OS3  H6   H  HCH2  0   0.203    1.1221   0.3428   2.2821
 OS3  H7   H  HCH2  0   0.238    1.3329   1.6475   1.1181
 OS3  H9   H  HCH2  0   0.241    1.7327  -1.9880   0.1340
 OS3  H10  H  HCH2  0   0.189    0.5209  -1.8943   1.4184
 OS3  H11  H  HCH1  0   0.216   -0.8596  -2.9226  -0.1100
 OS3  H12  H  HOH1  0   0.448    0.6391  -3.1595  -1.8012
 OS3  H13  H  HCH2  0   0.189   -1.1105   0.1041   1.2992
 OS3  H14  H  HCH2  0   0.241   -0.8556   1.2260  -0.0457
 OS3  H15  H  HCH1  0   0.261   -1.2794  -0.4801  -1.6749
 OS3  H16  H  HCH2  0   0.273   -3.1065  -2.0101  -0.9277
 OS3  H17  H  HCH2  0   0.260   -2.8064  -1.5396   0.7485
 OS3  H18  H  HCH2  0   0.262   -5.6528  -1.2939  -0.5090
 OS3  H19  H  HCH2  0   0.262   -5.2713  -0.7415   1.1241
 OS3  H20  H  HCH2  0   0.247   -6.1823   1.5292   0.5531
 OS3  H21  H  HCH2  0   0.247   -6.5739   0.9610  -1.0629
 OS3  H22  H  HCH2  0   0.271   -8.0953  -0.7778  -0.0716
 OS3  H23  H  HCH2  0   0.272   -7.7191  -0.1884   1.5330
 OS3  H24  H  H     0   0.278  -10.5132   2.6625   0.1651

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
 OS3  C24  C23  triple    1.203  0.020  1.203
 OS3  C23  C22  single    1.457  0.020  1.457
 OS3  C22  C21  single    1.532  0.020  1.532
 OS3  C21  C20  single    1.521  0.020  1.521
 OS3  C20  S5A  single    1.814  0.020  1.814
 OS3  S5A  C5A  single    1.815  0.020  1.815
 OS3  C5A  C4A  single    1.518  0.020  1.518
 OS3  C4A  C3A  single    1.544  0.020  1.544
 OS3  C4A  C1A  single    1.530  0.020  1.530
 OS3  O3A  C3A  single    1.411  0.020  1.411
 OS3  C3A  C2A  single    1.531  0.020  1.531
 OS3  C1A  N1A  single    1.448  0.020  1.448
 OS3  C2A  N1A  single    1.449  0.020  1.449
 OS3  N1A  C10  single    1.448  0.020  1.448
 OS3  C2   N3   aromatic  1.312  0.020  1.312
 OS3  C2   N1   aromatic  1.338  0.020  1.338
 OS3  N3   C4   aromatic  1.349  0.020  1.349
 OS3  N1   C6   aromatic  1.330  0.020  1.330
 OS3  C4   C9   aromatic  1.424  0.020  1.424
 OS3  C4   C5   aromatic  1.400  0.020  1.400
 OS3  C6   C5   aromatic  1.403  0.020  1.403
 OS3  C6   N6   single    1.348  0.020  1.348
 OS3  C10  C9   single    1.490  0.020  1.490
 OS3  C9   C8   aromatic  1.372  0.020  1.372
 OS3  C5   N7   aromatic  1.366  0.020  1.366
 OS3  N7   C8   aromatic  1.359  0.020  1.359
 OS3  N6   H1   single    0.868  0.020  1.013
 OS3  N6   H2   single    0.868  0.020  1.013
 OS3  C2   H3   single    0.929  0.020  1.085
 OS3  N7   H4   single    0.868  0.020  1.014
 OS3  C8   H5   single    0.929  0.020  1.085
 OS3  C10  H6   single    0.939  0.020  1.096
 OS3  C10  H7   single    0.939  0.020  1.096
 OS3  C2A  H9   single    0.939  0.020  1.096
 OS3  C2A  H10  single    0.939  0.020  1.096
 OS3  C3A  H11  single    0.939  0.020  1.096
 OS3  O3A  H12  single    0.832  0.020  0.971
 OS3  C1A  H13  single    0.939  0.020  1.096
 OS3  C1A  H14  single    0.939  0.020  1.096
 OS3  C4A  H15  single    0.939  0.020  1.096
 OS3  C5A  H16  single    0.939  0.020  1.096
 OS3  C5A  H17  single    0.939  0.020  1.096
 OS3  C20  H18  single    0.939  0.020  1.096
 OS3  C20  H19  single    0.939  0.020  1.096
 OS3  C21  H20  single    0.939  0.020  1.096
 OS3  C21  H21  single    0.939  0.020  1.096
 OS3  C22  H22  single    0.939  0.020  1.096
 OS3  C22  H23  single    0.939  0.020  1.096
 OS3  C24  H24  single    0.913  0.020  1.066

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
 OS3  H2   N6   H1   115.61  3.000
 OS3  H2   N6   C6   117.54  3.000
 OS3  H1   N6   C6   120.46  3.000
 OS3  C5   C6   N1   117.82  3.000
 OS3  C5   C6   N6   123.37  3.000
 OS3  N1   C6   N6   118.78  3.000
 OS3  C2   N1   C6   118.81  3.000
 OS3  H3   C2   N3   116.61  3.000
 OS3  H3   C2   N1   115.00  3.000
 OS3  N3   C2   N1   128.39  3.000
 OS3  C4   N3   C2   113.94  3.000
 OS3  N7   C5   C4   107.93  3.000
 OS3  N7   C5   C6   133.40  3.000
 OS3  C4   C5   C6   118.67  3.000
 OS3  C9   C4   C5   107.32  3.000
 OS3  C5   C4   N3   122.37  3.000
 OS3  C9   C4   N3   130.29  3.000
 OS3  H4   N7   C8   124.42  3.000
 OS3  H4   N7   C5   127.06  3.000
 OS3  C8   N7   C5   108.52  3.000
 OS3  H5   C8   C9   129.04  3.000
 OS3  H5   C8   N7   120.40  3.000
 OS3  C9   C8   N7   110.55  3.000
 OS3  C10  C9   C8   127.00  3.000
 OS3  C8   C9   C4   105.68  3.000
 OS3  C10  C9   C4   127.32  3.000
 OS3  H7   C10  H6   106.48  3.000
 OS3  H7   C10  N1A  107.87  3.000
 OS3  H6   C10  N1A  111.12  3.000
 OS3  H7   C10  C9   109.61  3.000
 OS3  H6   C10  C9   109.09  3.000
 OS3  N1A  C10  C9   112.49  3.000
 OS3  C1A  N1A  C2A  104.13  3.000
 OS3  C2A  N1A  C10  114.47  3.000
 OS3  C1A  N1A  C10  113.13  3.000
 OS3  H10  C2A  H9   107.18  3.000
 OS3  H10  C2A  C3A  109.16  3.000
 OS3  H9   C2A  C3A  112.75  3.000
 OS3  H10  C2A  N1A  111.51  3.000
 OS3  H9   C2A  N1A  112.06  3.000
 OS3  C3A  C2A  N1A  104.22  3.000
 OS3  H11  C3A  C4A  110.95  3.000
 OS3  H11  C3A  O3A  110.19  3.000
 OS3  C4A  C3A  O3A  108.40  3.000
 OS3  H11  C3A  C2A  109.58  3.000
 OS3  O3A  C3A  C2A  113.78  3.000
 OS3  C4A  C3A  C2A  103.78  3.000
 OS3  H12  O3A  C3A  108.19  3.000
 OS3  H14  C1A  H13  107.24  3.000
 OS3  H14  C1A  C4A  113.32  3.000
 OS3  H13  C1A  C4A  109.92  3.000
 OS3  H14  C1A  N1A  111.21  3.000
 OS3  H13  C1A  N1A  111.70  3.000
 OS3  C4A  C1A  N1A  103.51  3.000
 OS3  H15  C4A  C5A  108.95  3.000
 OS3  H15  C4A  C1A  109.34  3.000
 OS3  C5A  C4A  C1A  113.84  3.000
 OS3  H15  C4A  C3A  107.49  3.000
 OS3  C1A  C4A  C3A  104.22  3.000
 OS3  C5A  C4A  C3A  112.74  3.000
 OS3  H17  C5A  H16  107.88  3.000
 OS3  H17  C5A  S5A  108.98  3.000
 OS3  H16  C5A  S5A  109.14  3.000
 OS3  H17  C5A  C4A  110.45  3.000
 OS3  H16  C5A  C4A  110.57  3.000
 OS3  S5A  C5A  C4A  109.77  3.000
 OS3  C20  S5A  C5A  100.17  3.000
 OS3  H19  C20  H18  107.84  3.000
 OS3  H19  C20  C21  110.54  3.000
 OS3  H18  C20  C21  110.39  3.000
 OS3  H19  C20  S5A  109.06  3.000
 OS3  H18  C20  S5A  109.30  3.000
 OS3  C21  C20  S5A  109.67  3.000
 OS3  H21  C21  H20  107.14  3.000
 OS3  H21  C21  C22  109.35  3.000
 OS3  H20  C21  C22  109.41  3.000
 OS3  H21  C21  C20  109.86  3.000
 OS3  H20  C21  C20  110.00  3.000
 OS3  C22  C21  C20  110.99  3.000
 OS3  H23  C22  H22  106.35  3.000
 OS3  H23  C22  C23  109.16  3.000
 OS3  H22  C22  C23  108.99  3.000
 OS3  H23  C22  C21  109.94  3.000
 OS3  H22  C22  C21  109.86  3.000
 OS3  C23  C22  C21  112.35  3.000
 OS3  C24  C23  C22  180.00  3.000
 OS3  H24  C24  C23  180.00  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
 OS3  CONST_01  N3   C2   N1   C6      0.00   0.0  0
 OS3  CONST_02  N3   C4   C5   C6      0.00   0.0  0
 OS3  CONST_03  C9   C4   C5   C6    180.00   0.0  0
 OS3  CONST_04  C8   N7   C5   C6    180.00   0.0  0
 OS3  CONST_05  C4   N3   C2   N1      0.00   0.0  0
 OS3  CONST_06  C4   C5   C6   N1      0.00   0.0  0
 OS3  CONST_07  N7   C5   C6   N1    180.00   0.0  0
 OS3  CONST_08  C9   C4   N3   C2    180.00   0.0  0
 OS3  CONST_09  C5   C4   N3   C2      0.00   0.0  0
 OS3  CONST_10  C5   C6   N1   C2      0.00   0.0  0
 OS3  CONST_11  C8   C9   C4   N3    180.00   0.0  0
 OS3  CONST_12  N7   C5   C4   N3    180.00   0.0  0
 OS3  CONST_13  C8   C9   C4   C5      0.00   0.0  0
 OS3  CONST_14  C9   C8   N7   C5      0.00   0.0  0
 OS3  CONST_15  N7   C8   C9   C4      0.00   0.0  0
 OS3  CONST_16  C8   N7   C5   C4      0.00   0.0  0
 OS3  CONST_17  C9   C4   C5   N7      0.00   0.0  0
 OS3  CONST_18  C2   N1   C6   N6    180.00   0.0  0
 OS3  CONST_19  C4   C5   C6   N6    180.00   0.0  0
 OS3  CONST_20  N7   C5   C6   N6      0.00   0.0  0
 OS3  CONST_21  C10  C9   C4   N3      0.00   0.0  0
 OS3  CONST_22  C10  C9   C4   C5    180.00   0.0  0
 OS3  CONST_23  C10  C9   C8   N7    180.00   0.0  0
 OS3  CONST_24  H3   C2   N1   C6    180.00   0.0  0
 OS3  CONST_25  H4   N7   C5   C6      0.00   0.0  0
 OS3  CONST_26  H5   C8   N7   C5    180.00   0.0  0
 OS3  CONST_28  H2   N6   C6   N1      0.00   0.0  0
 OS3  Var_01    C4A  C1A  N1A  C2A   -44.20  30.0  1
 OS3  Var_02    C1A  N1A  C2A  C3A    43.31  30.0  1
 OS3  Var_03    N1A  C10  C9   C4     71.26  30.0  2
 OS3  Var_04    C21  C20  S5A  C5A  -179.09  30.0  1
 OS3  Var_05    C22  C21  C20  S5A  -179.19  30.0  1
 OS3  Var_06    C23  C22  C21  C20  -178.87  30.0  1
 OS3  Var_07    H16  C5A  S5A  C20    62.40  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
 OS3  chir_01  C3A  C4A  O3A  C2A  negativ
 OS3  chir_02  C4A  C5A  C3A  C1A  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
 OS3  plan-1  N6   0.020
 OS3  plan-1  C6   0.020
 OS3  plan-1  N1   0.020
 OS3  plan-1  C2   0.020
 OS3  plan-1  N3   0.020
 OS3  plan-1  C5   0.020
 OS3  plan-1  C4   0.020
 OS3  plan-1  N7   0.020
 OS3  plan-1  C8   0.020
 OS3  plan-1  C9   0.020
 OS3  plan-1  C10  0.020
 OS3  plan-1  H3   0.020
 OS3  plan-1  H4   0.020
 OS3  plan-1  H5   0.020
 OS3  plan-2  N6   0.020
 OS3  plan-2  C6   0.020
 OS3  plan-2  H1   0.020
 OS3  plan-2  H2   0.020

