# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 20:31:45 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 6-[([1,1'-biphenyl]-4-yl)ethynyl]-9-beta-D-ribofuranosyl-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)n2cnc3c(ncnc23)C#Cc4ccc(cc4)c5ccccc5
#
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
 ERP  ERP  6-[([1,1'-biphenyl]-4-yl)ethynyl]-9-beta-D-ribofuranosyl-9H-purine  ligand  52  32  .  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_ERP
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
 ERP  N1   N  N     0  -0.427    0.8234   3.0849  -0.1940
 ERP  N3   N  N     0  -0.412    3.1706   2.6807  -0.2754
 ERP  C4   C  CR56  0   0.494    2.8707   1.3970  -0.2644
 ERP  C5   C  CR56  0   0.056    1.5777   0.8574  -0.2238
 ERP  C6   C  CR6   0   0.058    0.5360   1.7797  -0.1859
 ERP  C8   C  CR15  0   0.117    2.8992  -0.7829  -0.2878
 ERP  C20  C  CSP   0   0.128   -1.9766   1.0198  -0.1041
 ERP  C21  C  CR6   0  -0.146   -3.3306   0.5984  -0.0601
 ERP  C22  C  CR16  0  -0.266   -4.3670   1.5370  -0.0559
 ERP  C24  C  CR6   0   0.093   -6.0100  -0.2386   0.0221
 ERP  C26  C  CR16  0  -0.277   -3.6478  -0.7629  -0.0218
 ERP  C28  C  CR16  0  -0.309   -7.7908  -1.8121   0.7875
 ERP  C1'  C  CH1   0   0.212    5.1564   0.3537  -0.3157
 ERP  C19  C  CSP   0   0.163   -0.8242   1.3776  -0.1410
 ERP  C2   C  CR16  0   0.030    2.0973   3.4597  -0.2410
 ERP  C2'  C  CH1   0  -0.014    5.7768   0.2173   1.0791
 ERP  C23  C  CR16  0  -0.304   -5.6836   1.1197  -0.0153
 ERP  C25  C  CR16  0  -0.301   -4.9679  -1.1697   0.0184
 ERP  C27  C  CR6   0   0.091   -7.4173  -0.6784   0.0628
 ERP  C29  C  CR16  0  -0.239   -9.1136  -2.2271   0.8235
 ERP  C3'  C  CH1   0  -0.034    7.0875  -0.5049   0.7589
 ERP  C30  C  CR16  0  -0.264  -10.0883  -1.5169   0.1348
 ERP  C31  C  CR16  0  -0.239   -9.7293  -0.3874  -0.5888
 ERP  C32  C  CR16  0  -0.310   -8.4069   0.0289  -0.6235
 ERP  C4'  C  CH1   0  -0.056    6.6208  -1.4522  -0.3457
 ERP  C5'  C  CH2   0  -0.166    6.0705  -2.7555   0.2030
 ERP  N7   N  N     0  -0.444    1.6275  -0.5076  -0.2420
 ERP  N9   N  NR5   0  -0.539    3.7049   0.3216  -0.3020
 ERP  O2'  O  OH1   0  -0.650    5.8807   1.4714   1.6694
 ERP  O3'  O  OH1   0  -0.666    8.0030   0.4510   0.2972
 ERP  O4'  O  O2    0  -0.490    5.6206  -0.7231  -1.0657
 ERP  O5'  O  OH1   0  -0.667    5.4855  -3.4742  -0.8534
 ERP  H1   H  HCR5  0   0.306    3.3059  -1.7821  -0.3407
 ERP  H2   H  HCR6  0   0.268   -4.1368   2.5937  -0.0775
 ERP  H3   H  HCR6  0   0.267   -2.8560  -1.4998  -0.0314
 ERP  H5   H  HCH1  0   0.269    5.4392   1.3119  -0.7649
 ERP  H6   H  HCR6  0   0.267    2.2787   4.5278  -0.2515
 ERP  H7   H  HCH1  0   0.246    5.1544  -0.4582   1.6807
 ERP  H8   H  HCR6  0   0.265   -6.4671   1.8655   0.0075
 ERP  H9   H  HCR6  0   0.264   -5.1871  -2.2296   0.0272
 ERP  H10  H  HCR6  0   0.260   -9.3835  -3.1048   1.3962
 ERP  H11  H  HCH1  0   0.255    7.4746  -1.0565   1.6253
 ERP  H12  H  HCR6  0   0.260  -11.1203  -1.8414   0.1619
 ERP  H13  H  HCR6  0   0.260  -10.4793   0.1691  -1.1357
 ERP  H14  H  HCR6  0   0.258   -8.1425   0.9016  -1.2076
 ERP  H15  H  HCH1  0   0.265    7.4285  -1.6766  -1.0491
 ERP  H16  H  HCH2  0   0.228    6.9068  -3.2993   0.6608
 ERP  H17  H  HCH2  0   0.199    5.3452  -2.5626   1.0050
 ERP  H18  H  HOH1  0   0.464    6.1096   1.3583   2.5970
 ERP  H19  H  HOH1  0   0.458    8.8200   0.0007   0.0606
 ERP  H20  H  HOH1  0   0.460    5.1418  -4.2997  -0.5000
 ERP  H4   H  HCR6  0   0.258   -7.0476  -2.3649   1.3486

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
 ERP  O5'  C5'  single    1.405  0.020  1.405
 ERP  C5'  C4'  single    1.517  0.020  1.517
 ERP  C4'  C3'  single    1.528  0.020  1.528
 ERP  C4'  O4'  single    1.432  0.020  1.432
 ERP  O3'  C3'  single    1.402  0.020  1.402
 ERP  C3'  C2'  single    1.530  0.020  1.530
 ERP  O4'  C1'  single    1.392  0.020  1.392
 ERP  C1'  C2'  single    1.533  0.020  1.533
 ERP  C1'  N9   single    1.452  0.020  1.452
 ERP  C2'  O2'  single    1.390  0.020  1.390
 ERP  N9   C4   aromatic  1.362  0.020  1.362
 ERP  N9   C8   aromatic  1.367  0.020  1.367
 ERP  N3   C4   aromatic  1.318  0.020  1.318
 ERP  N3   C2   aromatic  1.327  0.020  1.327
 ERP  C4   C5   aromatic  1.402  0.020  1.402
 ERP  C8   N7   aromatic  1.302  0.020  1.302
 ERP  C2   N1   aromatic  1.329  0.020  1.329
 ERP  C5   N7   aromatic  1.366  0.020  1.366
 ERP  C5   C6   aromatic  1.392  0.020  1.392
 ERP  N1   C6   aromatic  1.336  0.020  1.336
 ERP  C6   C19  single    1.419  0.020  1.419
 ERP  C19  C20  triple    1.207  0.020  1.207
 ERP  C20  C21  single    1.419  0.020  1.419
 ERP  C21  C26  aromatic  1.398  0.020  1.398
 ERP  C21  C22  aromatic  1.398  0.020  1.398
 ERP  C26  C25  aromatic  1.382  0.020  1.382
 ERP  C22  C23  aromatic  1.382  0.020  1.382
 ERP  C25  C24  aromatic  1.397  0.020  1.397
 ERP  C23  C24  aromatic  1.397  0.020  1.397
 ERP  C24  C27  single    1.475  0.020  1.475
 ERP  C32  C27  aromatic  1.397  0.020  1.397
 ERP  C32  C31  aromatic  1.387  0.020  1.387
 ERP  C27  C28  aromatic  1.396  0.020  1.396
 ERP  C31  C30  aromatic  1.389  0.020  1.389
 ERP  C28  C29  aromatic  1.387  0.020  1.387
 ERP  C30  C29  aromatic  1.389  0.020  1.389
 ERP  C8   H1   single    0.930  0.020  1.080
 ERP  C22  H2   single    0.930  0.020  1.080
 ERP  C26  H3   single    0.930  0.020  1.080
 ERP  C28  H4   single    0.930  0.020  1.080
 ERP  C1'  H5   single    0.970  0.020  1.090
 ERP  C2   H6   single    0.930  0.020  1.080
 ERP  C2'  H7   single    0.970  0.020  1.090
 ERP  C23  H8   single    0.930  0.020  1.080
 ERP  C25  H9   single    0.930  0.020  1.080
 ERP  C29  H10  single    0.930  0.020  1.080
 ERP  C3'  H11  single    0.970  0.020  1.090
 ERP  C30  H12  single    0.930  0.020  1.080
 ERP  C31  H13  single    0.930  0.020  1.080
 ERP  C32  H14  single    0.930  0.020  1.080
 ERP  C4'  H15  single    0.970  0.020  1.090
 ERP  C5'  H16  single    0.970  0.020  1.090
 ERP  C5'  H17  single    0.970  0.020  1.090
 ERP  O2'  H18  single    0.850  0.020  0.980
 ERP  O3'  H19  single    0.850  0.020  0.980
 ERP  O5'  H20  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
 ERP  C2   N1   C6   118.81  3.000
 ERP  C2   N3   C4   112.80  3.000
 ERP  N9   C4   C5   105.18  3.000
 ERP  C5   C4   N3   125.80  3.000
 ERP  N9   C4   N3   129.01  3.000
 ERP  N7   C5   C6   133.62  3.000
 ERP  C6   C5   C4   115.85  3.000
 ERP  N7   C5   C4   110.53  3.000
 ERP  C19  C6   C5   122.04  3.000
 ERP  C19  C6   N1   118.88  3.000
 ERP  C5   C6   N1   119.08  3.000
 ERP  H1   C8   N9   121.66  3.000
 ERP  H1   C8   N7   124.41  3.000
 ERP  N9   C8   N7   113.90  3.000
 ERP  C19  C20  C21  180.00  3.000
 ERP  C26  C21  C22  119.03  3.000
 ERP  C22  C21  C20  120.54  3.000
 ERP  C26  C21  C20  120.43  3.000
 ERP  H2   C22  C23  119.89  3.000
 ERP  H2   C22  C21  119.86  3.000
 ERP  C23  C22  C21  120.24  3.000
 ERP  C27  C24  C25  120.86  3.000
 ERP  C27  C24  C23  120.89  3.000
 ERP  C25  C24  C23  118.25  3.000
 ERP  H3   C26  C25  119.93  3.000
 ERP  H3   C26  C21  119.80  3.000
 ERP  C25  C26  C21  120.27  3.000
 ERP  H4   C28  C29  119.23  3.000
 ERP  H4   C28  C27  119.98  3.000
 ERP  C29  C28  C27  120.77  3.000
 ERP  H5   C1'  O4'  111.69  3.000
 ERP  H5   C1'  N9   106.34  3.000
 ERP  O4'  C1'  N9   108.74  3.000
 ERP  H5   C1'  C2'  110.28  3.000
 ERP  N9   C1'  C2'  113.21  3.000
 ERP  O4'  C1'  C2'  106.65  3.000
 ERP  C20  C19  C6   180.00  3.000
 ERP  H6   C2   N3   116.31  3.000
 ERP  H6   C2   N1   116.04  3.000
 ERP  N3   C2   N1   127.66  3.000
 ERP  H7   C2'  O2'  111.39  3.000
 ERP  H7   C2'  C3'  108.05  3.000
 ERP  O2'  C2'  C3'  116.79  3.000
 ERP  H7   C2'  C1'  108.90  3.000
 ERP  O2'  C2'  C1'  109.66  3.000
 ERP  C3'  C2'  C1'  101.44  3.000
 ERP  H8   C23  C24  120.02  3.000
 ERP  H8   C23  C22  118.84  3.000
 ERP  C24  C23  C22  121.12  3.000
 ERP  H9   C25  C26  118.82  3.000
 ERP  H9   C25  C24  120.09  3.000
 ERP  C26  C25  C24  121.09  3.000
 ERP  C32  C27  C28  118.47  3.000
 ERP  C28  C27  C24  120.77  3.000
 ERP  C32  C27  C24  120.76  3.000
 ERP  H10  C29  C30  120.14  3.000
 ERP  H10  C29  C28  119.62  3.000
 ERP  C30  C29  C28  120.23  3.000
 ERP  H11  C3'  O3'  111.86  3.000
 ERP  H11  C3'  C4'  111.52  3.000
 ERP  O3'  C3'  C4'  112.59  3.000
 ERP  H11  C3'  C2'  111.96  3.000
 ERP  O3'  C3'  C2'  107.85  3.000
 ERP  C4'  C3'  C2'  100.50  3.000
 ERP  H12  C30  C31  120.24  3.000
 ERP  H12  C30  C29  120.23  3.000
 ERP  C31  C30  C29  119.53  3.000
 ERP  H13  C31  C32  119.60  3.000
 ERP  H13  C31  C30  120.15  3.000
 ERP  C32  C31  C30  120.25  3.000
 ERP  H14  C32  C31  119.22  3.000
 ERP  H14  C32  C27  120.01  3.000
 ERP  C31  C32  C27  120.76  3.000
 ERP  H15  C4'  O4'  107.26  3.000
 ERP  H15  C4'  C5'  108.90  3.000
 ERP  O4'  C4'  C5'  111.46  3.000
 ERP  H15  C4'  C3'  111.49  3.000
 ERP  O4'  C4'  C3'  105.14  3.000
 ERP  C5'  C4'  C3'  112.44  3.000
 ERP  H17  C5'  H16  106.60  3.000
 ERP  H17  C5'  O5'  111.34  3.000
 ERP  H16  C5'  O5'  112.17  3.000
 ERP  H17  C5'  C4'  110.65  3.000
 ERP  H16  C5'  C4'  107.46  3.000
 ERP  O5'  C5'  C4'  108.56  3.000
 ERP  C8   N7   C5   104.32  3.000
 ERP  C1'  N9   C8   127.38  3.000
 ERP  C8   N9   C4   106.07  3.000
 ERP  C1'  N9   C4   126.53  3.000
 ERP  H18  O2'  C2'  108.74  3.000
 ERP  H19  O3'  C3'  108.44  3.000
 ERP  C4'  O4'  C1'  110.84  3.000
 ERP  H20  O5'  C5'  108.15  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
 ERP  CONST_01  C4   N3   C2   N1     0.00  0.0  0
 ERP  CONST_02  C4   C5   C6   N1     0.00  0.0  0
 ERP  CONST_03  N7   C5   C6   N1   180.00  0.0  0
 ERP  CONST_04  C8   N9   C4   N3   180.00  0.0  0
 ERP  CONST_05  N7   C5   C4   N3   180.00  0.0  0
 ERP  CONST_06  C6   C5   C4   N3     0.00  0.0  0
 ERP  CONST_07  C6   N1   C2   N3     0.00  0.0  0
 ERP  CONST_08  N7   C8   N9   C4     0.00  0.0  0
 ERP  CONST_09  C8   N7   C5   C4     0.00  0.0  0
 ERP  CONST_10  C8   N9   C4   C5     0.00  0.0  0
 ERP  CONST_11  C2   N3   C4   C5     0.00  0.0  0
 ERP  CONST_12  N9   C8   N7   C5     0.00  0.0  0
 ERP  CONST_13  C2   N1   C6   C5     0.00  0.0  0
 ERP  CONST_14  N9   C4   C5   C6   180.00  0.0  0
 ERP  CONST_15  C8   N7   C5   C6   180.00  0.0  0
 ERP  CONST_16  C24  C25  C26  C21    0.00  0.0  0
 ERP  CONST_17  C24  C23  C22  C21    0.00  0.0  0
 ERP  CONST_18  C25  C26  C21  C22    0.00  0.0  0
 ERP  CONST_19  C25  C24  C23  C22    0.00  0.0  0
 ERP  CONST_20  C27  C24  C23  C22  180.00  0.0  0
 ERP  CONST_21  C31  C32  C27  C24  180.00  0.0  0
 ERP  CONST_22  C29  C28  C27  C24  180.00  0.0  0
 ERP  CONST_23  C23  C22  C21  C26    0.00  0.0  0
 ERP  CONST_24  C23  C24  C25  C26    0.00  0.0  0
 ERP  CONST_25  C27  C24  C25  C26  180.00  0.0  0
 ERP  CONST_28  C31  C32  C27  C28    0.00  0.0  0
 ERP  CONST_29  C31  C30  C29  C28    0.00  0.0  0
 ERP  CONST_30  N9   C4   N3   C2   180.00  0.0  0
 ERP  CONST_33  C30  C31  C32  C27    0.00  0.0  0
 ERP  CONST_34  C30  C29  C28  C27    0.00  0.0  0
 ERP  CONST_35  C32  C27  C28  C29    0.00  0.0  0
 ERP  CONST_36  C32  C31  C30  C29    0.00  0.0  0
 ERP  CONST_37  N9   C4   C5   N7     0.00  0.0  0
 ERP  CONST_38  C1'  N9   C4   N3     0.00  0.0  0
 ERP  CONST_39  C1'  N9   C4   C5   180.00  0.0  0
 ERP  CONST_40  N7   C8   N9   C1'  180.00  0.0  0
 ERP  CONST_41  C19  C6   C5   C4   180.00  0.0  0
 ERP  CONST_42  C25  C26  C21  C20  180.00  0.0  0
 ERP  CONST_43  C23  C22  C21  C20  180.00  0.0  0
 ERP  CONST_44  N7   C5   C6   C19    0.00  0.0  0
 ERP  CONST_45  C2   N1   C6   C19  180.00  0.0  0
 ERP  CONST_46  H1   C8   N9   C4   180.00  0.0  0
 ERP  CONST_47  H6   C2   N3   C4   180.00  0.0  0
 ERP  CONST_48  H9   C25  C26  C21  180.00  0.0  0
 ERP  CONST_49  H8   C23  C22  C21  180.00  0.0  0
 ERP  CONST_50  H3   C26  C21  C22  180.00  0.0  0
 ERP  CONST_51  H2   C22  C23  C24  180.00  0.0  0
 ERP  CONST_52  H14  C32  C27  C24    0.00  0.0  0
 ERP  CONST_53  H4   C28  C27  C24    0.00  0.0  0
 ERP  CONST_54  H12  C30  C29  C28  180.00  0.0  0
 ERP  CONST_55  H13  C31  C32  C27  180.00  0.0  0
 ERP  CONST_56  H10  C29  C28  C27  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
 ERP  chir_01  C1'  O4'  C2'  N9   positiv
 ERP  chir_02  C2'  O2'  C1'  C3'  negativ
 ERP  chir_03  C3'  O3'  C4'  C2'  positiv
 ERP  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
 ERP  plan-1  C20  0.020
 ERP  plan-1  C21  0.020
 ERP  plan-1  C22  0.020
 ERP  plan-1  C24  0.020
 ERP  plan-1  C26  0.020
 ERP  plan-1  C19  0.020
 ERP  plan-1  C23  0.020
 ERP  plan-1  C25  0.020
 ERP  plan-1  C27  0.020
 ERP  plan-1  H2   0.020
 ERP  plan-1  H3   0.020
 ERP  plan-1  H8   0.020
 ERP  plan-1  H9   0.020
 ERP  plan-2  C24  0.020
 ERP  plan-2  C28  0.020
 ERP  plan-2  C27  0.020
 ERP  plan-2  C29  0.020
 ERP  plan-2  C30  0.020
 ERP  plan-2  C31  0.020
 ERP  plan-2  C32  0.020
 ERP  plan-2  H10  0.020
 ERP  plan-2  H12  0.020
 ERP  plan-2  H13  0.020
 ERP  plan-2  H14  0.020
 ERP  plan-2  H4   0.020
 ERP  plan-3  N1   0.020
 ERP  plan-3  N3   0.020
 ERP  plan-3  C4   0.020
 ERP  plan-3  C5   0.020
 ERP  plan-3  C6   0.020
 ERP  plan-3  C8   0.020
 ERP  plan-3  C20  0.020
 ERP  plan-3  C1'  0.020
 ERP  plan-3  C19  0.020
 ERP  plan-3  C2   0.020
 ERP  plan-3  N7   0.020
 ERP  plan-3  N9   0.020
 ERP  plan-3  H1   0.020
 ERP  plan-3  H6   0.020

