# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 18:34:10 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (2R,3S,4R,5R)-2-(hydroxymethyl)-5-[6-(4-phenylpiperazin-1-yl)-9H-purin-9-yl]tetrahydrofuran-3,4-diol (non-preferred name)
#   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)N4CCN(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
 ERS  ERS  '(2R,3S,4R,5R)-2-(hydroxymethyl)-5-[6-(4-phenylpiperazin-1-yl)-9H-purin-9-yl]tetrahydrofuran-3,4-diol (non-preferred name)'  ligand  54  30  .  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_ERS
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
 ERS  N1   N  N     0  -0.497  -0.7247   2.3332  -1.3962
 ERS  N3   N  N     0  -0.457   1.6150   2.1112  -1.7736
 ERS  C4   C  CR56  0   0.484   1.5798   1.2207  -0.7870
 ERS  C5   C  CR56  0  -0.017   0.4666   0.8179  -0.0538
 ERS  C6   C  CR6   0   0.537  -0.7614   1.4369  -0.3989
 ERS  C8   C  CR15  0   0.121   2.1129  -0.2940   0.6945
 ERS  C20  C  CH2   0  -0.336  -2.1622   0.2559   1.2692
 ERS  C21  C  CH2   0  -0.302  -3.1423  -0.8241   0.8383
 ERS  C24  C  CH2   0  -0.323  -3.1785   1.8130  -0.2511
 ERS  C26  C  CR16  0  -0.327  -6.7579  -0.4972  -0.0119
 ERS  C28  C  CR16  0  -0.288  -7.8136  -2.6645   0.1002
 ERS  C1'  C  CH1   0   0.203   4.0039   0.5753  -0.7209
 ERS  C2   C  CR16  0   0.049   0.4158   2.6122  -2.0109
 ERS  C2'  C  CH1   0  -0.017   4.9281   1.2309   0.3104
 ERS  C23  C  CH2   0  -0.302  -4.1593   0.7405  -0.6902
 ERS  C25  C  CR6   0   0.365  -5.4998  -1.0569   0.2599
 ERS  C27  C  CR16  0  -0.244  -7.8893  -1.2894  -0.0946
 ERS  C29  C  CR16  0  -0.243  -6.5778  -3.2277   0.3743
 ERS  C3'  C  CH1   0  -0.031   6.2544   0.5278   0.0207
 ERS  C30  C  CR16  0  -0.357  -5.4333  -2.4426   0.4459
 ERS  C4'  C  CH1   0  -0.057   5.7600  -0.8874  -0.2780
 ERS  C5'  C  CH2   0  -0.159   5.6313  -1.7353   0.9732
 ERS  N19  N  NT    0  -0.483  -1.9415   1.2054   0.1976
 ERS  N22  N  NT    0  -0.521  -4.3791  -0.2315   0.3723
 ERS  N7   N  N     0  -0.466   0.8358  -0.1364   0.8652
 ERS  N9   N  NR5   0  -0.538   2.6263   0.5009  -0.2897
 ERS  O2'  O  OH1   0  -0.653   4.9018   2.6123   0.1506
 ERS  O3'  O  OH1   0  -0.667   6.8293   1.1439  -1.1003
 ERS  O4'  O  O2    0  -0.489   4.4946  -0.7173  -0.9234
 ERS  O5'  O  OH1   0  -0.667   5.0621  -2.9700   0.6210
 ERS  H1   H  HCR5  0   0.299   2.7268  -0.9888   1.2474
 ERS  H2   H  HCH2  0   0.247  -2.5760   0.7938   2.1280
 ERS  H3   H  HCH2  0   0.295  -1.2298  -0.2028   1.5808
 ERS  H4   H  HCH2  0   0.220  -2.6698  -1.4611   0.0746
 ERS  H5   H  HCH2  0   0.259  -3.3436  -1.4503   1.7084
 ERS  H6   H  HCH2  0   0.280  -2.9827   2.4951  -1.0723
 ERS  H7   H  HCH2  0   0.247  -3.6097   2.3869   0.5752
 ERS  H9   H  HCR6  0   0.248  -8.7007  -3.2809   0.0410
 ERS  H10  H  HCH1  0   0.265   3.9993   1.1552  -1.6500
 ERS  H11  H  HCR6  0   0.251   0.3506   3.3456  -2.8075
 ERS  H12  H  HCH1  0   0.244   4.6046   0.9403   1.3196
 ERS  H13  H  HCH2  0   0.262  -5.0951   1.2283  -0.9555
 ERS  H14  H  HCH2  0   0.225  -3.7799   0.2487  -1.5981
 ERS  H15  H  HCR6  0   0.252  -8.8438  -0.8225  -0.3021
 ERS  H16  H  HCR6  0   0.252  -6.4894  -4.2965   0.5230
 ERS  H17  H  HCH1  0   0.253   6.9286   0.5448   0.8868
 ERS  H18  H  HCR6  0   0.266  -4.4882  -2.9306   0.6401
 ERS  H19  H  HCH1  0   0.262   6.4252  -1.3998  -0.9806
 ERS  H20  H  HCH2  0   0.220   6.6359  -1.8497   1.4015
 ERS  H21  H  HCH2  0   0.195   5.0260  -1.2134   1.7271
 ERS  H22  H  HOH1  0   0.464   5.3251   3.0198   0.9127
 ERS  H23  H  HOH1  0   0.457   7.6333   0.6683  -1.3322
 ERS  H24  H  HOH1  0   0.459   4.9388  -3.4826   1.4248
 ERS  H8   H  HCR6  0   0.260  -6.8613   0.5729  -0.1363

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
 ERS  O5'  C5'  single    1.404  0.020  1.404
 ERS  C5'  C4'  single    1.517  0.020  1.517
 ERS  C4'  C3'  single    1.529  0.020  1.529
 ERS  C4'  O4'  single    1.431  0.020  1.431
 ERS  O3'  C3'  single    1.402  0.020  1.402
 ERS  C3'  C2'  single    1.529  0.020  1.529
 ERS  O4'  C1'  single    1.397  0.020  1.397
 ERS  C1'  C2'  single    1.532  0.020  1.532
 ERS  C1'  N9   single    1.445  0.020  1.445
 ERS  C2'  O2'  single    1.391  0.020  1.391
 ERS  N9   C4   aromatic  1.364  0.020  1.364
 ERS  N9   C8   aromatic  1.365  0.020  1.365
 ERS  N3   C4   aromatic  1.330  0.020  1.330
 ERS  N3   C2   aromatic  1.321  0.020  1.321
 ERS  C4   C5   aromatic  1.392  0.020  1.392
 ERS  C8   N7   aromatic  1.298  0.020  1.298
 ERS  C2   N1   aromatic  1.325  0.020  1.325
 ERS  C5   N7   aromatic  1.375  0.020  1.375
 ERS  C5   C6   aromatic  1.418  0.020  1.418
 ERS  N1   C6   aromatic  1.341  0.020  1.341
 ERS  C6   N19  single    1.342  0.020  1.342
 ERS  N19  C24  single    1.449  0.020  1.449
 ERS  N19  C20  single    1.449  0.020  1.449
 ERS  C24  C23  single    1.518  0.020  1.518
 ERS  C20  C21  single    1.521  0.020  1.521
 ERS  C27  C26  aromatic  1.384  0.020  1.384
 ERS  C27  C28  aromatic  1.391  0.020  1.391
 ERS  C26  C25  aromatic  1.404  0.020  1.404
 ERS  C23  N22  single    1.457  0.020  1.457
 ERS  C28  C29  aromatic  1.385  0.020  1.385
 ERS  C21  N22  single    1.449  0.020  1.449
 ERS  C25  N22  single    1.396  0.020  1.396
 ERS  C25  C30  aromatic  1.400  0.020  1.400
 ERS  C29  C30  aromatic  1.390  0.020  1.390
 ERS  C8   H1   single    0.930  0.020  1.080
 ERS  C20  H2   single    0.970  0.020  1.090
 ERS  C20  H3   single    0.970  0.020  1.090
 ERS  C21  H4   single    0.970  0.020  1.090
 ERS  C21  H5   single    0.970  0.020  1.090
 ERS  C24  H6   single    0.970  0.020  1.090
 ERS  C24  H7   single    0.970  0.020  1.090
 ERS  C26  H8   single    0.930  0.020  1.080
 ERS  C28  H9   single    0.930  0.020  1.080
 ERS  C1'  H10  single    0.970  0.020  1.090
 ERS  C2   H11  single    0.930  0.020  1.080
 ERS  C2'  H12  single    0.970  0.020  1.090
 ERS  C23  H13  single    0.970  0.020  1.090
 ERS  C23  H14  single    0.970  0.020  1.090
 ERS  C27  H15  single    0.930  0.020  1.080
 ERS  C29  H16  single    0.930  0.020  1.080
 ERS  C3'  H17  single    0.970  0.020  1.090
 ERS  C30  H18  single    0.930  0.020  1.080
 ERS  C4'  H19  single    0.970  0.020  1.090
 ERS  C5'  H20  single    0.970  0.020  1.090
 ERS  C5'  H21  single    0.970  0.020  1.090
 ERS  O2'  H22  single    0.850  0.020  0.980
 ERS  O3'  H23  single    0.850  0.020  0.980
 ERS  O5'  H24  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
 ERS  C2   N1   C6   120.60  3.000
 ERS  C2   N3   C4   111.30  3.000
 ERS  N9   C4   C5   105.59  3.000
 ERS  C5   C4   N3   127.27  3.000
 ERS  N9   C4   N3   127.14  3.000
 ERS  N7   C5   C6   134.27  3.000
 ERS  C6   C5   C4   115.98  3.000
 ERS  N7   C5   C4   109.75  3.000
 ERS  N19  C6   C5   125.31  3.000
 ERS  N19  C6   N1   118.01  3.000
 ERS  C5   C6   N1   116.68  3.000
 ERS  H1   C8   N9   122.01  3.000
 ERS  H1   C8   N7   124.77  3.000
 ERS  N9   C8   N7   113.21  3.000
 ERS  H3   C20  H2   107.90  3.000
 ERS  H3   C20  N19  111.02  3.000
 ERS  H2   C20  N19  108.42  3.000
 ERS  H3   C20  C21  109.57  3.000
 ERS  H2   C20  C21  109.13  3.000
 ERS  N19  C20  C21  110.74  3.000
 ERS  H5   C21  H4   107.48  3.000
 ERS  H5   C21  N22  109.50  3.000
 ERS  H4   C21  N22  112.34  3.000
 ERS  H5   C21  C20  107.50  3.000
 ERS  H4   C21  C20  109.32  3.000
 ERS  N22  C21  C20  110.54  3.000
 ERS  H7   C24  H6   108.23  3.000
 ERS  H7   C24  N19  108.80  3.000
 ERS  H6   C24  N19  110.10  3.000
 ERS  H7   C24  C23  109.53  3.000
 ERS  H6   C24  C23  109.98  3.000
 ERS  N19  C24  C23  110.16  3.000
 ERS  H8   C26  C27  118.76  3.000
 ERS  H8   C26  C25  120.15  3.000
 ERS  C27  C26  C25  121.07  3.000
 ERS  H9   C28  C29  120.70  3.000
 ERS  H9   C28  C27  120.74  3.000
 ERS  C29  C28  C27  118.56  3.000
 ERS  H10  C1'  O4'  111.62  3.000
 ERS  H10  C1'  N9   106.04  3.000
 ERS  O4'  C1'  N9   109.29  3.000
 ERS  H10  C1'  C2'  110.30  3.000
 ERS  N9   C1'  C2'  113.33  3.000
 ERS  O4'  C1'  C2'  106.35  3.000
 ERS  H11  C2   N3   116.28  3.000
 ERS  H11  C2   N1   115.54  3.000
 ERS  N3   C2   N1   128.17  3.000
 ERS  H12  C2'  O2'  111.26  3.000
 ERS  H12  C2'  C3'  107.92  3.000
 ERS  O2'  C2'  C3'  116.83  3.000
 ERS  H12  C2'  C1'  109.12  3.000
 ERS  O2'  C2'  C1'  109.65  3.000
 ERS  C3'  C2'  C1'  101.48  3.000
 ERS  H14  C23  H13  107.20  3.000
 ERS  H14  C23  N22  110.84  3.000
 ERS  H13  C23  N22  110.31  3.000
 ERS  H14  C23  C24  109.38  3.000
 ERS  H13  C23  C24  108.02  3.000
 ERS  N22  C23  C24  110.97  3.000
 ERS  N22  C25  C30  122.43  3.000
 ERS  C30  C25  C26  117.59  3.000
 ERS  N22  C25  C26  119.95  3.000
 ERS  H15  C27  C28  120.08  3.000
 ERS  H15  C27  C26  119.04  3.000
 ERS  C28  C27  C26  120.88  3.000
 ERS  H16  C29  C30  118.90  3.000
 ERS  H16  C29  C28  120.08  3.000
 ERS  C30  C29  C28  121.01  3.000
 ERS  H17  C3'  O3'  111.85  3.000
 ERS  H17  C3'  C4'  111.54  3.000
 ERS  O3'  C3'  C4'  112.52  3.000
 ERS  H17  C3'  C2'  112.10  3.000
 ERS  O3'  C3'  C2'  107.76  3.000
 ERS  C4'  C3'  C2'  100.50  3.000
 ERS  H18  C30  C29  118.31  3.000
 ERS  H18  C30  C25  120.81  3.000
 ERS  C29  C30  C25  120.88  3.000
 ERS  H19  C4'  O4'  107.67  3.000
 ERS  H19  C4'  C5'  108.62  3.000
 ERS  O4'  C4'  C5'  111.32  3.000
 ERS  H19  C4'  C3'  111.23  3.000
 ERS  O4'  C4'  C3'  105.32  3.000
 ERS  C5'  C4'  C3'  112.57  3.000
 ERS  H21  C5'  H20  106.61  3.000
 ERS  H21  C5'  O5'  111.49  3.000
 ERS  H20  C5'  O5'  112.15  3.000
 ERS  H21  C5'  C4'  110.31  3.000
 ERS  H20  C5'  C4'  107.60  3.000
 ERS  O5'  C5'  C4'  108.60  3.000
 ERS  C24  N19  C20  111.95  3.000
 ERS  C20  N19  C6   125.15  3.000
 ERS  C24  N19  C6   122.71  3.000
 ERS  C25  N22  C23  117.18  3.000
 ERS  C25  N22  C21  117.99  3.000
 ERS  C23  N22  C21  112.25  3.000
 ERS  C8   N7   C5   105.10  3.000
 ERS  C1'  N9   C8   127.12  3.000
 ERS  C8   N9   C4   106.35  3.000
 ERS  C1'  N9   C4   126.53  3.000
 ERS  H22  O2'  C2'  108.75  3.000
 ERS  H23  O3'  C3'  108.54  3.000
 ERS  C4'  O4'  C1'  110.80  3.000
 ERS  H24  O5'  C5'  108.13  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
 ERS  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 ERS  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 ERS  CONST_03  N7   C5   C6   N1    180.00   0.0  0
 ERS  CONST_04  C8   N9   C4   N3    180.00   0.0  0
 ERS  CONST_05  N7   C5   C4   N3    180.00   0.0  0
 ERS  CONST_06  C6   C5   C4   N3      0.00   0.0  0
 ERS  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 ERS  CONST_08  N7   C8   N9   C4      0.00   0.0  0
 ERS  CONST_09  C8   N7   C5   C4      0.00   0.0  0
 ERS  CONST_10  C8   N9   C4   C5      0.00   0.0  0
 ERS  CONST_11  C2   N3   C4   C5      0.00   0.0  0
 ERS  CONST_12  N9   C8   N7   C5      0.00   0.0  0
 ERS  CONST_13  C2   N1   C6   C5      0.00   0.0  0
 ERS  CONST_14  N9   C4   C5   C6    180.00   0.0  0
 ERS  CONST_15  C8   N7   C5   C6    180.00   0.0  0
 ERS  CONST_16  C29  C28  C27  C26     0.00   0.0  0
 ERS  CONST_17  C29  C30  C25  C26     0.00   0.0  0
 ERS  CONST_18  C25  C26  C27  C28     0.00   0.0  0
 ERS  CONST_19  C25  C30  C29  C28     0.00   0.0  0
 ERS  CONST_20  N9   C4   N3   C2    180.00   0.0  0
 ERS  CONST_21  C30  C25  C26  C27     0.00   0.0  0
 ERS  CONST_22  C30  C29  C28  C27     0.00   0.0  0
 ERS  CONST_23  N9   C4   C5   N7      0.00   0.0  0
 ERS  CONST_24  C1'  N9   C4   N3      0.00   0.0  0
 ERS  CONST_25  N19  C6   C5   C4    180.00   0.0  0
 ERS  CONST_26  C1'  N9   C4   C5    180.00   0.0  0
 ERS  CONST_27  N7   C8   N9   C1'   180.00   0.0  0
 ERS  CONST_28  N19  C6   N1   C2    180.00   0.0  0
 ERS  CONST_29  N22  C25  C26  C27   180.00   0.0  0
 ERS  CONST_30  N22  C25  C30  C29   180.00   0.0  0
 ERS  CONST_31  N7   C5   C6   N19     0.00   0.0  0
 ERS  CONST_32  H1   C8   N9   C4    180.00   0.0  0
 ERS  CONST_33  H11  C2   N3   C4    180.00   0.0  0
 ERS  CONST_34  H9   C28  C27  C26   180.00   0.0  0
 ERS  CONST_35  H18  C30  C25  C26   180.00   0.0  0
 ERS  CONST_36  H8   C26  C27  C28   180.00   0.0  0
 ERS  CONST_37  H15  C27  C26  C25   180.00   0.0  0
 ERS  CONST_38  H16  C29  C30  C25   180.00   0.0  0
 ERS  Var_01    C24  N19  C6   N1      4.28  30.0  2
 ERS  Var_02    C23  C24  N19  C6    118.34  30.0  1
 ERS  Var_03    C21  C20  N19  C6   -118.02  30.0  1
 ERS  Var_04    C23  N22  C21  C20    54.98  30.0  1
 ERS  Var_05    C24  C23  N22  C21   -55.37  30.0  1
 ERS  Var_06    C26  C25  N22  C21   171.42  30.0  2
 ERS  Var_07    N22  C23  C24  N19    55.21  30.0  1
 ERS  Var_08    N22  C21  C20  N19   -55.17  30.0  1

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
 ERS  chir_01  C1'  O4'  C2'  N9   positiv
 ERS  chir_02  C2'  O2'  C1'  C3'  negativ
 ERS  chir_03  C3'  O3'  C4'  C2'  positiv
 ERS  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
 ERS  plan-1  C26  0.020
 ERS  plan-1  C28  0.020
 ERS  plan-1  C25  0.020
 ERS  plan-1  C27  0.020
 ERS  plan-1  C29  0.020
 ERS  plan-1  C30  0.020
 ERS  plan-1  N22  0.020
 ERS  plan-1  H9   0.020
 ERS  plan-1  H15  0.020
 ERS  plan-1  H16  0.020
 ERS  plan-1  H18  0.020
 ERS  plan-1  H8   0.020
 ERS  plan-2  N1   0.020
 ERS  plan-2  N3   0.020
 ERS  plan-2  C4   0.020
 ERS  plan-2  C5   0.020
 ERS  plan-2  C6   0.020
 ERS  plan-2  C8   0.020
 ERS  plan-2  C1'  0.020
 ERS  plan-2  C2   0.020
 ERS  plan-2  N19  0.020
 ERS  plan-2  N7   0.020
 ERS  plan-2  N9   0.020
 ERS  plan-2  H1   0.020
 ERS  plan-2  H11  0.020

