# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 14:15:24 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(prop-2-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](CSCC#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
 OS2  OS2  (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(prop-2-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol  ligand  41  22  .  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_OS2
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
 OS2  O3'  O  OH1   0  -0.674  -0.8253   1.6656   2.2562
 OS2  C3'  C  CH1   0   0.056  -1.2698   1.7041   0.9179
 OS2  C2'  C  CH2   0  -0.297  -0.1444   1.5528  -0.1065
 OS2  N1'  N  NT    0  -0.413  -0.0784   0.1269  -0.3428
 OS2  C1'  C  CH2   0  -0.262  -1.4626  -0.2699  -0.4841
 OS2  C4'  C  CH1   0  -0.289  -2.1617   0.4678   0.6621
 OS2  C5'  C  CH2   0  -0.562  -3.6016   0.8443   0.3600
 OS2  S5'  S  S2    0  -0.010  -4.5782  -0.6603   0.0753
 OS2  C20  C  CH2   0  -0.693  -6.1977   0.1102  -0.2528
 OS2  C21  C  CSP   0   0.296  -7.1651  -0.9175  -0.5883
 OS2  C22  C  CSP1  0  -0.513  -7.9576  -1.7789  -0.8604
 OS2  C10  C  CH2   0  -0.361   0.7604  -0.2688  -1.4526
 OS2  C9   C  CR5   0  -0.045   2.1917   0.0765  -1.2202
 OS2  C4   C  CR56  0   0.164   3.0502  -0.4404  -0.2081
 OS2  N3   N  N     0  -0.445   2.8177  -1.3632   0.7475
 OS2  C8   C  CR15  0  -0.053   2.9458   0.9853  -1.9181
 OS2  N7   N  NR15  0  -0.676   4.2027   1.0562  -1.4055
 OS2  C5   C  CR56  0   0.204   4.2913   0.1904  -0.3533
 OS2  C6   C  CR6   0   0.455   5.3255  -0.1438   0.5351
 OS2  N6   N  NH2   0  -0.827   6.5417   0.4359   0.5072
 OS2  N1   N  N     0  -0.471   5.0690  -1.0516   1.4720
 OS2  C2   C  CR16  0   0.004   3.8500  -1.6007   1.5208
 OS2  H1   H  HOH1  0   0.448  -0.2740   2.4392   2.4082
 OS2  H2   H  HCH1  0   0.216  -1.8216   2.6336   0.7271
 OS2  H3   H  HCH2  0   0.189  -0.4177   2.1023  -1.0254
 OS2  H4   H  HCH2  0   0.243   0.8076   1.9570   0.2443
 OS2  H6   H  HCH2  0   0.192  -1.8895   0.0524  -1.4527
 OS2  H7   H  HCH2  0   0.242  -1.5718  -1.3551  -0.4261
 OS2  H8   H  HCH1  0   0.264  -2.1367  -0.1523   1.5627
 OS2  H9   H  HCH2  0   0.280  -4.0359   1.3979   1.1953
 OS2  H10  H  HCH2  0   0.267  -3.6525   1.4760  -0.5306
 OS2  H11  H  HCH2  0   0.303  -6.5265   0.6624   0.6296
 OS2  H12  H  HCH2  0   0.303  -6.1024   0.8205  -1.0768
 OS2  H13  H  H     0   0.281  -8.6643  -2.5393  -1.1025
 OS2  H14  H  HCH2  0   0.239   0.6539  -1.3501  -1.5835
 OS2  H15  H  HCH2  0   0.204   0.4274   0.1943  -2.3984
 OS2  H16  H  HCR5  0   0.289   2.6643   1.5978  -2.7606
 OS2  H17  H  HNR5  0   0.415   4.9261   1.6612  -1.7552
 OS2  H18  H  HNH2  0   0.401   6.8539   0.9318  -0.3094
 OS2  H19  H  HNH2  0   0.397   7.2664   0.0351   1.0789
 OS2  H20  H  HCR6  0   0.237   3.7102  -2.3371   2.3064

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
 OS2  C22  C21  triple    1.202  0.020  1.202
 OS2  C21  C20  single    1.451  0.020  1.451
 OS2  C20  S5'  single    1.823  0.020  1.823
 OS2  C1'  C4'  single    1.532  0.020  1.532
 OS2  C1'  N1'  single    1.447  0.020  1.447
 OS2  S5'  C5'  single    1.816  0.020  1.816
 OS2  C5'  C4'  single    1.519  0.020  1.519
 OS2  C4'  C3'  single    1.546  0.020  1.546
 OS2  C8   N7   aromatic  1.359  0.020  1.359
 OS2  C8   C9   aromatic  1.372  0.020  1.372
 OS2  N7   C5   aromatic  1.365  0.020  1.365
 OS2  N1'  C10  single    1.446  0.020  1.446
 OS2  N1'  C2'  single    1.447  0.020  1.447
 OS2  C9   C10  single    1.491  0.020  1.491
 OS2  C9   C4   aromatic  1.424  0.020  1.424
 OS2  O3'  C3'  single    1.411  0.020  1.411
 OS2  C3'  C2'  single    1.529  0.020  1.529
 OS2  C5   C4   aromatic  1.400  0.020  1.400
 OS2  C5   C6   aromatic  1.404  0.020  1.404
 OS2  N6   C6   single    1.348  0.020  1.348
 OS2  C4   N3   aromatic  1.349  0.020  1.349
 OS2  C6   N1   aromatic  1.330  0.020  1.330
 OS2  N3   C2   aromatic  1.311  0.020  1.311
 OS2  N1   C2   aromatic  1.338  0.020  1.338
 OS2  O3'  H1   single    0.832  0.020  0.971
 OS2  C3'  H2   single    0.939  0.020  1.096
 OS2  C2'  H3   single    0.939  0.020  1.096
 OS2  C2'  H4   single    0.939  0.020  1.096
 OS2  C1'  H6   single    0.939  0.020  1.096
 OS2  C1'  H7   single    0.939  0.020  1.096
 OS2  C4'  H8   single    0.939  0.020  1.096
 OS2  C5'  H9   single    0.939  0.020  1.096
 OS2  C5'  H10  single    0.939  0.020  1.096
 OS2  C20  H11  single    0.939  0.020  1.096
 OS2  C20  H12  single    0.939  0.020  1.096
 OS2  C22  H13  single    0.913  0.020  1.066
 OS2  C10  H14  single    0.939  0.020  1.096
 OS2  C10  H15  single    0.939  0.020  1.096
 OS2  C8   H16  single    0.929  0.020  1.085
 OS2  N7   H17  single    0.868  0.020  1.014
 OS2  N6   H18  single    0.868  0.020  1.013
 OS2  N6   H19  single    0.868  0.020  1.013
 OS2  C2   H20  single    0.929  0.020  1.085

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
 OS2  H1   O3'  C3'  107.97  3.000
 OS2  H2   C3'  C4'  111.01  3.000
 OS2  H2   C3'  C2'  109.71  3.000
 OS2  C4'  C3'  C2'  103.57  3.000
 OS2  H2   C3'  O3'  110.27  3.000
 OS2  C2'  C3'  O3'  113.63  3.000
 OS2  C4'  C3'  O3'  108.48  3.000
 OS2  H4   C2'  H3   107.38  3.000
 OS2  H4   C2'  N1'  112.17  3.000
 OS2  H3   C2'  N1'  111.44  3.000
 OS2  H4   C2'  C3'  112.93  3.000
 OS2  H3   C2'  C3'  109.02  3.000
 OS2  N1'  C2'  C3'  103.92  3.000
 OS2  C10  N1'  C1'  113.88  3.000
 OS2  C10  N1'  C2'  114.92  3.000
 OS2  C1'  N1'  C2'  104.04  3.000
 OS2  H7   C1'  H6   107.30  3.000
 OS2  H7   C1'  C4'  113.15  3.000
 OS2  H6   C1'  C4'  109.80  3.000
 OS2  H7   C1'  N1'  111.28  3.000
 OS2  H6   C1'  N1'  112.00  3.000
 OS2  C4'  C1'  N1'  103.38  3.000
 OS2  H8   C4'  C5'  109.03  3.000
 OS2  H8   C4'  C1'  109.43  3.000
 OS2  C5'  C4'  C1'  113.78  3.000
 OS2  H8   C4'  C3'  107.69  3.000
 OS2  C5'  C4'  C3'  112.44  3.000
 OS2  C1'  C4'  C3'  104.22  3.000
 OS2  H10  C5'  H9   108.17  3.000
 OS2  H10  C5'  S5'  109.02  3.000
 OS2  H9   C5'  S5'  109.02  3.000
 OS2  H10  C5'  C4'  110.46  3.000
 OS2  H9   C5'  C4'  110.53  3.000
 OS2  S5'  C5'  C4'  109.61  3.000
 OS2  C20  S5'  C5'   98.96  3.000
 OS2  H12  C20  H11  107.89  3.000
 OS2  H12  C20  C21  110.15  3.000
 OS2  H11  C20  C21  110.15  3.000
 OS2  H12  C20  S5'  109.46  3.000
 OS2  H11  C20  S5'  109.63  3.000
 OS2  C21  C20  S5'  109.55  3.000
 OS2  C22  C21  C20  180.00  3.000
 OS2  H13  C22  C21  180.00  3.000
 OS2  H15  C10  H14  106.41  3.000
 OS2  H15  C10  C9   109.02  3.000
 OS2  H14  C10  C9   109.94  3.000
 OS2  H15  C10  N1'  111.56  3.000
 OS2  H14  C10  N1'  107.79  3.000
 OS2  C9   C10  N1'  111.95  3.000
 OS2  C8   C9   C4   105.70  3.000
 OS2  C4   C9   C10  127.27  3.000
 OS2  C8   C9   C10  127.01  3.000
 OS2  C5   C4   N3   122.33  3.000
 OS2  N3   C4   C9   130.38  3.000
 OS2  C5   C4   C9   107.29  3.000
 OS2  C2   N3   C4   113.95  3.000
 OS2  H16  C8   N7   120.40  3.000
 OS2  H16  C8   C9   129.05  3.000
 OS2  N7   C8   C9   110.55  3.000
 OS2  H17  N7   C5   127.06  3.000
 OS2  H17  N7   C8   124.43  3.000
 OS2  C5   N7   C8   108.51  3.000
 OS2  C6   C5   N7   133.35  3.000
 OS2  C6   C5   C4   118.70  3.000
 OS2  N7   C5   C4   107.95  3.000
 OS2  N1   C6   N6   118.85  3.000
 OS2  N1   C6   C5   117.80  3.000
 OS2  N6   C6   C5   123.32  3.000
 OS2  H19  N6   H18  115.74  3.000
 OS2  H19  N6   C6   117.83  3.000
 OS2  H18  N6   C6   120.63  3.000
 OS2  C2   N1   C6   118.80  3.000
 OS2  H20  C2   N1   114.96  3.000
 OS2  H20  C2   N3   116.62  3.000
 OS2  N1   C2   N3   128.42  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
 OS2  CONST_01  C5   N7   C8   C9      0.00   0.0  0
 OS2  CONST_02  N7   C5   C4   C9      0.00   0.0  0
 OS2  CONST_03  C6   C5   C4   C9    180.00   0.0  0
 OS2  CONST_04  C2   N3   C4   C9    180.00   0.0  0
 OS2  CONST_05  N7   C8   C9   C4      0.00   0.0  0
 OS2  CONST_06  C8   N7   C5   C4      0.00   0.0  0
 OS2  CONST_07  N1   C6   C5   C4      0.00   0.0  0
 OS2  CONST_08  N1   C2   N3   C4      0.00   0.0  0
 OS2  CONST_09  C8   C9   C4   N3    180.00   0.0  0
 OS2  CONST_10  N7   C5   C4   N3    180.00   0.0  0
 OS2  CONST_11  C6   C5   C4   N3      0.00   0.0  0
 OS2  CONST_12  C6   N1   C2   N3      0.00   0.0  0
 OS2  CONST_13  C6   C5   N7   C8    180.00   0.0  0
 OS2  CONST_14  C5   C4   C9   C8      0.00   0.0  0
 OS2  CONST_15  N1   C6   C5   N7    180.00   0.0  0
 OS2  CONST_16  C2   N3   C4   C5      0.00   0.0  0
 OS2  CONST_17  C2   N1   C6   C5      0.00   0.0  0
 OS2  CONST_18  N7   C8   C9   C10   180.00   0.0  0
 OS2  CONST_19  C5   C4   C9   C10   180.00   0.0  0
 OS2  CONST_20  N3   C4   C9   C10     0.00   0.0  0
 OS2  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 OS2  CONST_22  N6   C6   C5   N7      0.00   0.0  0
 OS2  CONST_23  C2   N1   C6   N6    180.00   0.0  0
 OS2  CONST_24  H17  N7   C8   C9    180.00   0.0  0
 OS2  CONST_25  H16  C8   C9   C4    180.00   0.0  0
 OS2  CONST_26  H20  C2   N3   C4    180.00   0.0  0
 OS2  CONST_28  H19  N6   C6   C5    180.00   0.0  0
 OS2  Var_01    C1'  N1'  C2'  C3'    44.66  30.0  1
 OS2  Var_02    C4'  C1'  N1'  C2'   -44.45  30.0  1
 OS2  Var_03    C9   C10  N1'  C2'    64.09  30.0  3
 OS2  Var_04    C8   C9   C10  N1'  -114.15  30.0  2
 OS2  Var_05    C21  C20  S5'  C5'   176.98  30.0  1
 OS2  Var_06    H9   C5'  S5'  C20    59.02  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
 OS2  chir_01  C3'  C4'  O3'  C2'  negativ
 OS2  chir_02  C4'  C1'  C5'  C3'  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
 OS2  plan-1  C10  0.020
 OS2  plan-1  C9   0.020
 OS2  plan-1  C4   0.020
 OS2  plan-1  N3   0.020
 OS2  plan-1  C8   0.020
 OS2  plan-1  N7   0.020
 OS2  plan-1  C5   0.020
 OS2  plan-1  C6   0.020
 OS2  plan-1  N6   0.020
 OS2  plan-1  N1   0.020
 OS2  plan-1  C2   0.020
 OS2  plan-1  H16  0.020
 OS2  plan-1  H17  0.020
 OS2  plan-1  H20  0.020
 OS2  plan-2  C6   0.020
 OS2  plan-2  N6   0.020
 OS2  plan-2  H18  0.020
 OS2  plan-2  H19  0.020

