# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 12:49:02 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 9-beta-D-ribofuranosyl-6-(thiophen-3-yl)-9H-purine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c2ncnc3c4cscc4
#
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
 ERJ  ERJ  9-beta-D-ribofuranosyl-6-(thiophen-3-yl)-9H-purine  ligand  37  23  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ERJ
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
 ERJ  N1   N  N     0  -0.448  -2.4649   1.9492  -0.2616
 ERJ  N3   N  N     0  -0.415  -0.1156   2.2609  -0.4810
 ERJ  C4   C  CR56  0   0.505  -0.0218   0.9501  -0.3520
 ERJ  C5   C  CR56  0   0.059  -1.0890   0.0593  -0.1806
 ERJ  C6   C  CR6   0   0.227  -2.3650   0.6243  -0.1354
 ERJ  C8   C  CR15  0   0.126   0.6719  -1.1126  -0.2121
 ERJ  C20  C  CR15  0  -0.569  -3.6698  -1.4963   0.1807
 ERJ  C22  C  CR15  0  -0.472  -5.8887  -0.4294   0.2561
 ERJ  C1'  C  CR15  0   0.214   2.4712   0.6410  -0.4769
 ERJ  C19  C  CR5   0   0.139  -3.5986  -0.1340   0.0402
 ERJ  C2   C  CR16  0   0.031  -1.3695   2.6831  -0.4275
 ERJ  C2'  C  CR15  0  -0.015   3.1246   0.9204   0.8828
 ERJ  C23  C  CR15  0  -0.179  -4.8918   0.4748   0.0856
 ERJ  C3'  C  CR15  0  -0.028   4.5827   0.5407   0.6076
 ERJ  C4'  C  CR15  0  -0.060   4.3870  -0.6663  -0.3069
 ERJ  C5'  C  CH2   0  -0.168   4.2051  -1.9563   0.4731
 ERJ  N7   N  N     0  -0.465  -0.6198  -1.2251  -0.0989
 ERJ  N9   N  NR5   0  -0.544   1.0989   0.1753  -0.3667
 ERJ  O2'  O  OH1   0  -0.650   2.8848   2.2373   1.2586
 ERJ  O3'  O  OH1   0  -0.666   5.1905   1.6200  -0.0487
 ERJ  O4'  O  O     0  -0.490   3.2295  -0.3531  -1.0887
 ERJ  O5'  O  OH1   0  -0.665   3.8169  -2.9692  -0.4209
 ERJ  S21  S  S2    0   0.253  -5.2770  -2.0298   0.3638
 ERJ  H1   H  HCR5  0   0.304   1.3621  -1.9434  -0.2155
 ERJ  H3   H  HCR5  0   0.300  -6.9492  -0.2437   0.3238
 ERJ  H4   H  HCR5  0   0.269   2.4430   1.5533  -1.0823
 ERJ  H5   H  HCR6  0   0.260  -1.5232   3.7512  -0.5289
 ERJ  H6   H  HCR5  0   0.245   2.7213   0.2144   1.6212
 ERJ  H7   H  HCR5  0   0.268  -5.0548   1.5381  -0.0047
 ERJ  H8   H  HCR5  0   0.254   5.1149   0.2673   1.5280
 ERJ  H9   H  HCR5  0   0.266   5.2226  -0.7884  -1.0028
 ERJ  H10  H  HCH2  0   0.230   5.1604  -2.1832   0.9638
 ERJ  H11  H  HCH2  0   0.200   3.4644  -1.8218   1.2731
 ERJ  H12  H  HOH1  0   0.463   3.1376   2.3464   2.1807
 ERJ  H13  H  HOH1  0   0.458   6.0925   1.3715  -0.2744
 ERJ  H14  H  HOH1  0   0.461   3.7270  -3.7876   0.0758
 ERJ  H2   H  HCR5  0   0.302  -2.8542  -2.2019   0.1835

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
 ERJ  O5'  C5'  single    1.406  0.020  1.406
 ERJ  C5'  C4'  single    1.518  0.020  1.518
 ERJ  C4'  C3'  single    1.527  0.020  1.527
 ERJ  C4'  O4'  single    1.431  0.020  1.431
 ERJ  O3'  C3'  single    1.402  0.020  1.402
 ERJ  C3'  C2'  single    1.532  0.020  1.532
 ERJ  O4'  C1'  single    1.392  0.020  1.392
 ERJ  C2'  C1'  single    1.534  0.020  1.534
 ERJ  C2'  O2'  single    1.390  0.020  1.390
 ERJ  C1'  N9   single    1.453  0.020  1.453
 ERJ  N9   C8   aromatic  1.366  0.020  1.366
 ERJ  N9   C4   aromatic  1.363  0.020  1.363
 ERJ  C8   N7   aromatic  1.302  0.020  1.302
 ERJ  C4   N3   aromatic  1.320  0.020  1.320
 ERJ  C4   C5   aromatic  1.401  0.020  1.401
 ERJ  N3   C2   aromatic  1.324  0.020  1.324
 ERJ  N7   C5   aromatic  1.370  0.020  1.370
 ERJ  C5   C6   aromatic  1.396  0.020  1.396
 ERJ  C2   N1   aromatic  1.329  0.020  1.329
 ERJ  C6   N1   aromatic  1.335  0.020  1.335
 ERJ  C6   C19  single    1.459  0.020  1.459
 ERJ  C19  C23  aromatic  1.430  0.020  1.430
 ERJ  C19  C20  aromatic  1.371  0.020  1.371
 ERJ  C23  C22  aromatic  1.357  0.020  1.357
 ERJ  C20  S21  aromatic  1.703  0.020  1.703
 ERJ  C22  S21  aromatic  1.717  0.020  1.717
 ERJ  C8   H1   single    0.930  0.020  1.080
 ERJ  C20  H2   single    0.930  0.020  1.080
 ERJ  C22  H3   single    0.930  0.020  1.080
 ERJ  C1'  H4   single    0.970  0.020  1.090
 ERJ  C2   H5   single    0.930  0.020  1.080
 ERJ  C2'  H6   single    0.970  0.020  1.090
 ERJ  C23  H7   single    0.930  0.020  1.080
 ERJ  C3'  H8   single    0.970  0.020  1.090
 ERJ  C4'  H9   single    0.970  0.020  1.090
 ERJ  C5'  H10  single    0.970  0.020  1.090
 ERJ  C5'  H11  single    0.970  0.020  1.090
 ERJ  O2'  H12  single    0.850  0.020  0.980
 ERJ  O3'  H13  single    0.850  0.020  0.980
 ERJ  O5'  H14  single    0.850  0.020  0.980

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
 ERJ  C2   N1   C6   119.89  3.000
 ERJ  C2   N3   C4   112.32  3.000
 ERJ  N9   C4   C5   105.45  3.000
 ERJ  C5   C4   N3   126.10  3.000
 ERJ  N9   C4   N3   128.45  3.000
 ERJ  N7   C5   C6   133.67  3.000
 ERJ  C6   C5   C4   116.29  3.000
 ERJ  N7   C5   C4   110.04  3.000
 ERJ  C19  C6   C5   124.50  3.000
 ERJ  C19  C6   N1   117.66  3.000
 ERJ  C5   C6   N1   117.84  3.000
 ERJ  H1   C8   N9   121.69  3.000
 ERJ  H1   C8   N7   124.61  3.000
 ERJ  N9   C8   N7   113.68  3.000
 ERJ  H2   C20  S21  120.56  3.000
 ERJ  H2   C20  C19  127.66  3.000
 ERJ  S21  C20  C19  111.79  3.000
 ERJ  H3   C22  S21  120.46  3.000
 ERJ  H3   C22  C23  127.99  3.000
 ERJ  S21  C22  C23  111.55  3.000
 ERJ  H4   C1'  O4'  111.46  3.000
 ERJ  H4   C1'  N9   106.53  3.000
 ERJ  O4'  C1'  N9   108.60  3.000
 ERJ  H4   C1'  C2'  110.43  3.000
 ERJ  N9   C1'  C2'  113.16  3.000
 ERJ  O4'  C1'  C2'  106.71  3.000
 ERJ  C23  C19  C20  111.88  3.000
 ERJ  C20  C19  C6   124.94  3.000
 ERJ  C23  C19  C6   123.18  3.000
 ERJ  H5   C2   N3   116.40  3.000
 ERJ  H5   C2   N1   116.04  3.000
 ERJ  N3   C2   N1   127.55  3.000
 ERJ  H6   C2'  O2'  111.33  3.000
 ERJ  H6   C2'  C3'  108.12  3.000
 ERJ  O2'  C2'  C3'  116.59  3.000
 ERJ  H6   C2'  C1'  108.80  3.000
 ERJ  O2'  C2'  C1'  109.79  3.000
 ERJ  C3'  C2'  C1'  101.60  3.000
 ERJ  H7   C23  C19  123.59  3.000
 ERJ  H7   C23  C22  123.78  3.000
 ERJ  C19  C23  C22  112.63  3.000
 ERJ  H8   C3'  O3'  111.97  3.000
 ERJ  H8   C3'  C4'  111.55  3.000
 ERJ  O3'  C3'  C4'  112.57  3.000
 ERJ  H8   C3'  C2'  111.88  3.000
 ERJ  O3'  C3'  C2'  107.82  3.000
 ERJ  C4'  C3'  C2'  100.46  3.000
 ERJ  H9   C4'  O4'  107.14  3.000
 ERJ  H9   C4'  C5'  108.86  3.000
 ERJ  O4'  C4'  C5'  111.69  3.000
 ERJ  H9   C4'  C3'  111.79  3.000
 ERJ  O4'  C4'  C3'  104.94  3.000
 ERJ  C5'  C4'  C3'  112.29  3.000
 ERJ  H11  C5'  H10  106.65  3.000
 ERJ  H11  C5'  O5'  111.42  3.000
 ERJ  H10  C5'  O5'  112.07  3.000
 ERJ  H11  C5'  C4'  110.54  3.000
 ERJ  H10  C5'  C4'  107.52  3.000
 ERJ  O5'  C5'  C4'  108.58  3.000
 ERJ  C8   N7   C5   104.70  3.000
 ERJ  C1'  N9   C8   127.30  3.000
 ERJ  C8   N9   C4   106.14  3.000
 ERJ  C1'  N9   C4   126.53  3.000
 ERJ  H12  O2'  C2'  108.72  3.000
 ERJ  H13  O3'  C3'  108.50  3.000
 ERJ  C4'  O4'  C1'  110.90  3.000
 ERJ  H14  O5'  C5'  108.10  3.000
 ERJ  C22  S21  C20   92.15  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
 ERJ  CONST_01  C4   N3   C2   N1     0.00  0.0  0
 ERJ  CONST_02  C4   C5   C6   N1     0.00  0.0  0
 ERJ  CONST_03  N7   C5   C6   N1   180.00  0.0  0
 ERJ  CONST_04  C23  C19  C6   N1     0.00  0.0  0
 ERJ  CONST_05  C20  C19  C6   N1   180.00  0.0  0
 ERJ  CONST_06  C8   N9   C4   N3   180.00  0.0  0
 ERJ  CONST_07  N7   C5   C4   N3   180.00  0.0  0
 ERJ  CONST_08  C6   C5   C4   N3     0.00  0.0  0
 ERJ  CONST_09  C6   N1   C2   N3     0.00  0.0  0
 ERJ  CONST_10  N7   C8   N9   C4     0.00  0.0  0
 ERJ  CONST_11  C8   N7   C5   C4     0.00  0.0  0
 ERJ  CONST_12  C19  C6   C5   C4   180.00  0.0  0
 ERJ  CONST_13  C8   N9   C4   C5     0.00  0.0  0
 ERJ  CONST_14  C2   N3   C4   C5     0.00  0.0  0
 ERJ  CONST_15  N9   C8   N7   C5     0.00  0.0  0
 ERJ  CONST_16  C2   N1   C6   C5     0.00  0.0  0
 ERJ  CONST_17  C23  C19  C6   C5   180.00  0.0  0
 ERJ  CONST_18  C20  C19  C6   C5     0.00  0.0  0
 ERJ  CONST_19  N9   C4   C5   C6   180.00  0.0  0
 ERJ  CONST_20  C8   N7   C5   C6   180.00  0.0  0
 ERJ  CONST_21  C22  C23  C19  C6   180.00  0.0  0
 ERJ  CONST_22  S21  C20  C19  C6   180.00  0.0  0
 ERJ  CONST_23  C22  C23  C19  C20    0.00  0.0  0
 ERJ  CONST_24  C23  C22  S21  C20    0.00  0.0  0
 ERJ  CONST_25  C19  C20  S21  C22    0.00  0.0  0
 ERJ  CONST_26  N7   C5   C6   C19    0.00  0.0  0
 ERJ  CONST_27  C2   N1   C6   C19  180.00  0.0  0
 ERJ  CONST_28  S21  C22  C23  C19    0.00  0.0  0
 ERJ  CONST_29  N9   C4   N3   C2   180.00  0.0  0
 ERJ  CONST_30  S21  C20  C19  C23    0.00  0.0  0
 ERJ  CONST_31  N9   C4   C5   N7     0.00  0.0  0
 ERJ  CONST_32  C1'  N9   C4   N3     0.00  0.0  0
 ERJ  CONST_33  C1'  N9   C4   C5   180.00  0.0  0
 ERJ  CONST_34  N7   C8   N9   C1'  180.00  0.0  0
 ERJ  CONST_35  H1   C8   N9   C4   180.00  0.0  0
 ERJ  CONST_36  H5   C2   N3   C4   180.00  0.0  0
 ERJ  CONST_37  H7   C23  C19  C6     0.00  0.0  0
 ERJ  CONST_38  H2   C20  C19  C6     0.00  0.0  0
 ERJ  CONST_39  H3   C22  S21  C20  180.00  0.0  0

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
 ERJ  chir_01  C1'  O4'  C2'  N9   positiv
 ERJ  chir_02  C2'  O2'  C1'  C3'  negativ
 ERJ  chir_03  C3'  O3'  C4'  C2'  positiv
 ERJ  chir_04  C4'  O4'  C3'  C5'  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
 ERJ  plan-1  C6   0.020
 ERJ  plan-1  C20  0.020
 ERJ  plan-1  C22  0.020
 ERJ  plan-1  C19  0.020
 ERJ  plan-1  C23  0.020
 ERJ  plan-1  S21  0.020
 ERJ  plan-1  H3   0.020
 ERJ  plan-1  H7   0.020
 ERJ  plan-1  H2   0.020
 ERJ  plan-2  N1   0.020
 ERJ  plan-2  N3   0.020
 ERJ  plan-2  C4   0.020
 ERJ  plan-2  C5   0.020
 ERJ  plan-2  C6   0.020
 ERJ  plan-2  C8   0.020
 ERJ  plan-2  C1'  0.020
 ERJ  plan-2  C19  0.020
 ERJ  plan-2  C2   0.020
 ERJ  plan-2  N7   0.020
 ERJ  plan-2  N9   0.020
 ERJ  plan-2  H1   0.020
 ERJ  plan-2  H5   0.020

