# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  2 20:06:55 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 9-[(5E)-5,6,7-trideoxy-7-{[(2,3-dihydroxy-5-nitrophenyl)carbonyl]amino}-beta-D-ribo-hept-5-enofuranosyl]-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](/C=C/CNC(=O)c4cc(cc(O)c4O)[N+]([O-])=O)[C@@H](O)[C@H]3O
#
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
 CL4  CL4  9-[(5E)-5,6,7-trideoxy-7-{[(2,3-dihydroxy-5-nitrophenyl)carbonyl]amino}-beta-D-ribo-hept-5-enofuranosyl]-9H-purin-6-amine  ligand  53  34  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CL4
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
 CL4  C1    C  C1     0  -0.274   0.6634  -2.5206  -0.9389
 CL4  C2    C  CH2    0  -0.310  -0.7681  -2.3778  -1.3465
 CL4  N3    N  NH1    0  -0.669  -1.2904  -1.0836  -0.9219
 CL4  C4    C  C1     0  -0.237   1.0615  -3.4086  -0.0367
 CL4  C5    C  CH1    0  -0.007   2.4561  -3.6132   0.4681
 CL4  O6    O  O2     0  -0.470   3.3918  -2.7297  -0.1245
 CL4  C7    C  CH1    0  -0.059   2.5269  -3.3820   1.9978
 CL4  O8    O  OH1    0  -0.658   2.7842  -4.5894   2.6624
 CL4  C9    C  CH1    0  -0.005   3.6799  -2.3642   2.1572
 CL4  O10   O  OH1    0  -0.667   4.8929  -3.0263   2.3679
 CL4  C11   C  CH1    0   0.118   3.7471  -1.7217   0.7755
 CL4  N12   N  NR5    0  -0.529   2.8782  -0.5660   0.6289
 CL4  C13   C  CR15   0   0.127   1.6872  -0.2872   1.2404
 CL4  N14   N  N      0  -0.473   1.0534   0.7177   0.7113
 CL4  C15   C  CR56   0   0.011   1.8642   1.1320  -0.3172
 CL4  C16   C  CR6    0   0.458   1.7677   2.1742  -1.2577
 CL4  N17   N  NH2    0  -0.821   0.7372   3.0261  -1.2918
 CL4  N18   N  N      0  -0.469   2.7461   2.2899  -2.1606
 CL4  C19   C  CR16   0   0.044   3.7687   1.4399  -2.1248
 CL4  N20   N  N      0  -0.455   3.9795   0.4456  -1.2794
 CL4  C21   C  CR56   0   0.496   2.9956   0.3388  -0.3924
 CL4  C22   C  CR6    0   0.286  -4.3235   0.9826  -1.2067
 CL4  C23   C  CR6    0   0.327  -4.9102   2.1802  -0.7408
 CL4  C24   C  CR16   0  -0.376  -4.2171   2.9920   0.1223
 CL4  C25   C  CR6    0   0.261  -2.9295   2.6223   0.5121
 CL4  C26   C  CR16   0  -0.372  -2.3317   1.4586   0.0767
 CL4  C27   C  CR6    0  -0.163  -3.0318   0.6196  -0.7884
 CL4  O29   O  OH1    0  -0.622  -5.0573   0.2567  -2.0307
 CL4  C30   C  C      0   0.653  -2.4953  -0.6699  -1.2995
 CL4  O31   O  O      0  -0.547  -3.1869  -1.3541  -2.0735
 CL4  N32   N  N      1   0.330  -2.2051   3.4932   1.4081
 CL4  O33   O  O      0  -0.391  -1.0088   3.3269   1.5288
 CL4  O34   O  O     -1  -0.373  -2.8218   4.3492   1.9969
 CL4  HC1   H  H      0   0.268   1.3737  -1.8645  -1.4323
 CL4  HC21  H  HCH2   0   0.264  -0.8566  -2.4545  -2.4322
 CL4  HC22  H  HCH2   0   0.260  -1.3684  -3.1814  -0.9129
 CL4  HN3   H  HNH1   0   0.420  -0.7431  -0.5529  -0.2600
 CL4  HC4   H  H      0   0.273   0.3275  -4.0671   0.4218
 CL4  HC5   H  HCH1   0   0.280   2.7730  -4.6380   0.2450
 CL4  HC7   H  HCH1   0   0.263   1.5907  -2.9474   2.3586
 CL4  HO8   H  HOH1   0   0.473   2.4617  -4.5223   3.5676
 CL4  HC9   H  HCH1   0   0.256   3.4841  -1.6312   2.9493
 CL4  H10   H  HOH1   0   0.452   4.6811  -3.8918   2.7448
 CL4  H11   H  HCH1   0   0.293   4.7548  -1.3835   0.5347
 CL4  H13   H  HCR5   0   0.303   1.3251  -0.8482   2.0878
 CL4  H171  H  HNH2   0   0.403   0.7918   3.8293  -1.8959
 CL4  H172  H  HNH2   0   0.402   0.1250   3.0980  -0.4963
 CL4  H19   H  HCR6   0   0.256   4.5270   1.5896  -2.8855
 CL4  H24   H  HCR6   0   0.310  -4.6733   3.9076   0.4725
 CL4  H26   H  HCR6   0   0.311  -1.3409   1.2091   0.4346
 CL4  H28   H  HOH1   0   0.482  -6.5022   1.8876  -1.7540
 CL4  H29   H  HOH1   0   0.493  -4.5030  -0.5502  -2.2575
 CL4  O28   O  OH1    0  -0.622  -6.1426   2.5334  -1.1325

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
 CL4  C1   C2    single    1.495  0.020  1.495
 CL4  C1   C4    double    1.327  0.020  1.327
 CL4  C1   HC1   single    0.930  0.020  1.080
 CL4  C2   N3    single    1.459  0.020  1.459
 CL4  C2   HC21  single    0.970  0.020  1.090
 CL4  C2   HC22  single    0.970  0.020  1.090
 CL4  N3   C30   single    1.329  0.020  1.329
 CL4  N3   HN3   single    0.860  0.020  1.020
 CL4  C4   C5    single    1.497  0.020  1.497
 CL4  C4   HC4   single    0.930  0.020  1.080
 CL4  C5   O6    single    1.417  0.020  1.417
 CL4  C5   C7    single    1.549  0.020  1.549
 CL4  C5   HC5   single    0.970  0.020  1.090
 CL4  O6   C11   single    1.397  0.020  1.397
 CL4  C7   O8    single    1.402  0.020  1.402
 CL4  C7   C9    single    1.546  0.020  1.546
 CL4  C7   HC7   single    0.970  0.020  1.090
 CL4  O8   HO8   single    0.850  0.020  0.980
 CL4  C9   O10   single    1.398  0.020  1.398
 CL4  C9   C11   single    1.525  0.020  1.525
 CL4  C9   HC9   single    0.970  0.020  1.090
 CL4  O10  H10   single    0.850  0.020  0.980
 CL4  C11  N12   single    1.453  0.020  1.453
 CL4  C11  H11   single    0.970  0.020  1.090
 CL4  N12  C13   aromatic  1.367  0.020  1.367
 CL4  N12  C21   aromatic  1.369  0.020  1.369
 CL4  C13  N14   aromatic  1.301  0.020  1.301
 CL4  C13  H13   single    0.930  0.020  1.080
 CL4  N14  C15   aromatic  1.374  0.020  1.374
 CL4  C15  C16   aromatic  1.407  0.020  1.407
 CL4  C15  C21   aromatic  1.384  0.020  1.384
 CL4  C16  N17   single    1.337  0.020  1.337
 CL4  C16  N18   aromatic  1.336  0.020  1.336
 CL4  N17  H171  single    0.890  0.020  1.040
 CL4  N17  H172  single    0.890  0.020  1.040
 CL4  N18  C19   aromatic  1.330  0.020  1.330
 CL4  C19  N20   aromatic  1.322  0.020  1.322
 CL4  C19  H19   single    0.930  0.020  1.080
 CL4  N20  C21   aromatic  1.329  0.020  1.329
 CL4  C22  C23   aromatic  1.413  0.020  1.413
 CL4  C22  C27   aromatic  1.405  0.020  1.405
 CL4  C22  O29   single    1.321  0.020  1.321
 CL4  C23  C24   aromatic  1.373  0.020  1.373
 CL4  C23  O28   single    1.341  0.020  1.341
 CL4  C24  C25   aromatic  1.395  0.020  1.395
 CL4  C24  H24   single    0.930  0.020  1.080
 CL4  C25  C26   aromatic  1.379  0.020  1.379
 CL4  C25  N32   single    1.444  0.020  1.444
 CL4  C26  C27   aromatic  1.394  0.020  1.394
 CL4  C26  H26   single    0.930  0.020  1.080
 CL4  C27  C30   single    1.487  0.020  1.487
 CL4  O28  H28   single    0.850  0.020  0.980
 CL4  O29  H29   single    0.850  0.020  0.980
 CL4  C30  O31   double    1.243  0.020  1.243
 CL4  N32  O33   double    1.214  0.020  1.214
 CL4  N32  O34   single    1.208  0.020  1.208

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
 CL4  HC1   C1   C4    121.14  3.000
 CL4  HC1   C1   C2    116.41  3.000
 CL4  C4    C1   C2    122.44  3.000
 CL4  HC22  C2   HC21  107.35  3.000
 CL4  HC22  C2   N3    109.89  3.000
 CL4  HC21  C2   N3    108.83  3.000
 CL4  HC22  C2   C1    110.33  3.000
 CL4  HC21  C2   C1    109.99  3.000
 CL4  N3    C2   C1    110.37  3.000
 CL4  HN3   N3   C30   120.95  3.000
 CL4  HN3   N3   C2    117.59  3.000
 CL4  C30   N3   C2    121.20  3.000
 CL4  HC4   C4   C5    113.82  3.000
 CL4  HC4   C4   C1    119.30  3.000
 CL4  C5    C4   C1    126.88  3.000
 CL4  HC5   C5   C7    109.12  3.000
 CL4  HC5   C5   O6    107.88  3.000
 CL4  C7    C5   O6    106.85  3.000
 CL4  HC5   C5   C4    109.19  3.000
 CL4  C7    C5   C4    110.81  3.000
 CL4  O6    C5   C4    112.89  3.000
 CL4  C11   O6   C5    110.39  3.000
 CL4  HC7   C7   C9    110.05  3.000
 CL4  HC7   C7   O8    110.06  3.000
 CL4  C9    C7   O8    112.41  3.000
 CL4  HC7   C7   C5    110.25  3.000
 CL4  C9    C7   C5    103.54  3.000
 CL4  O8    C7   C5    110.36  3.000
 CL4  HO8   O8   C7    108.90  3.000
 CL4  HC9   C9   C11   112.37  3.000
 CL4  HC9   C9   O10   111.26  3.000
 CL4  C11   C9   O10   107.33  3.000
 CL4  HC9   C9   C7    112.41  3.000
 CL4  C11   C9   C7    102.52  3.000
 CL4  O10   C9   C7    110.54  3.000
 CL4  H10   O10  C9    107.00  3.000
 CL4  H11   C11  N12   106.48  3.000
 CL4  H11   C11  C9    111.81  3.000
 CL4  N12   C11  C9    113.58  3.000
 CL4  H11   C11  O6    108.46  3.000
 CL4  N12   C11  O6    110.90  3.000
 CL4  C9    C11  O6    105.57  3.000
 CL4  C21   N12  C13   105.87  3.000
 CL4  C21   N12  C11   123.32  3.000
 CL4  C13   N12  C11   129.62  3.000
 CL4  H13   C13  N14   123.90  3.000
 CL4  H13   C13  N12   122.52  3.000
 CL4  N14   C13  N12   113.58  3.000
 CL4  C15   N14  C13   104.48  3.000
 CL4  C21   C15  C16   116.38  3.000
 CL4  C21   C15  N14   110.51  3.000
 CL4  C16   C15  N14   133.11  3.000
 CL4  N18   C16  N17   119.45  3.000
 CL4  N18   C16  C15   117.75  3.000
 CL4  N17   C16  C15   122.79  3.000
 CL4  H172  N17  H171  116.77  3.000
 CL4  H172  N17  C16   119.61  3.000
 CL4  H171  N17  C16   118.80  3.000
 CL4  C19   N18  C16   119.29  3.000
 CL4  H19   C19  N20   116.16  3.000
 CL4  H19   C19  N18   115.49  3.000
 CL4  N20   C19  N18   128.34  3.000
 CL4  C21   N20  C19   111.66  3.000
 CL4  N20   C21  C15   126.55  3.000
 CL4  N20   C21  N12   127.90  3.000
 CL4  C15   C21  N12   105.55  3.000
 CL4  O29   C22  C27   123.67  3.000
 CL4  O29   C22  C23   116.17  3.000
 CL4  C27   C22  C23   120.16  3.000
 CL4  O28   C23  C24   119.48  3.000
 CL4  O28   C23  C22   120.58  3.000
 CL4  C24   C23  C22   119.94  3.000
 CL4  H24   C24  C25   121.55  3.000
 CL4  H24   C24  C23   119.43  3.000
 CL4  C25   C24  C23   119.01  3.000
 CL4  N32   C25  C26   119.17  3.000
 CL4  N32   C25  C24   118.45  3.000
 CL4  C26   C25  C24   122.38  3.000
 CL4  H26   C26  C27   121.75  3.000
 CL4  H26   C26  C25   119.14  3.000
 CL4  C27   C26  C25   119.09  3.000
 CL4  C30   C27  C26   123.64  3.000
 CL4  C30   C27  C22   116.95  3.000
 CL4  C26   C27  C22   119.41  3.000
 CL4  H29   O29  C22   106.00  3.000
 CL4  O31   C30  C27   119.37  3.000
 CL4  O31   C30  N3    120.67  3.000
 CL4  C27   C30  N3    119.96  3.000
 CL4  O34   N32  O33   123.49  3.000
 CL4  O34   N32  C25   118.26  3.000
 CL4  O33   N32  C25   118.25  3.000
 CL4  H28   O28  C23   110.75  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
 CL4  CONST_01  C15   N14  C13  N12     0.00   0.0  0
 CL4  CONST_02  N14   C15  C21  N12     0.00   0.0  0
 CL4  CONST_03  C16   C15  C21  N12   180.00   0.0  0
 CL4  CONST_04  C19   N20  C21  N12   180.00   0.0  0
 CL4  CONST_05  C15   C21  N12  C13     0.00   0.0  0
 CL4  CONST_06  N20   C21  N12  C13   180.00   0.0  0
 CL4  CONST_07  C16   C15  N14  C13   180.00   0.0  0
 CL4  CONST_08  C21   C15  N14  C13     0.00   0.0  0
 CL4  CONST_09  C21   N12  C13  N14     0.00   0.0  0
 CL4  CONST_10  N18   C16  C15  N14   180.00   0.0  0
 CL4  CONST_11  N20   C21  C15  N14   180.00   0.0  0
 CL4  CONST_12  C19   N18  C16  C15     0.00   0.0  0
 CL4  CONST_13  C19   N20  C21  C15     0.00   0.0  0
 CL4  CONST_14  N20   C21  C15  C16     0.00   0.0  0
 CL4  CONST_15  N20   C19  N18  C16     0.00   0.0  0
 CL4  CONST_16  C21   C15  C16  N18     0.00   0.0  0
 CL4  CONST_17  C21   N20  C19  N18     0.00   0.0  0
 CL4  CONST_18  C25   C24  C23  C22     0.00   0.0  0
 CL4  CONST_19  C25   C26  C27  C22     0.00   0.0  0
 CL4  CONST_20  C26   C27  C22  C23     0.00   0.0  0
 CL4  CONST_21  C26   C25  C24  C23     0.00   0.0  0
 CL4  CONST_22  C27   C22  C23  C24     0.00   0.0  0
 CL4  CONST_23  C27   C26  C25  C24     0.00   0.0  0
 CL4  CONST_24  N14   C13  N12  C11   180.00   0.0  0
 CL4  CONST_25  C15   C21  N12  C11   180.00   0.0  0
 CL4  CONST_26  N20   C21  N12  C11     0.00   0.0  0
 CL4  CONST_27  N17   C16  C15  N14     0.00   0.0  0
 CL4  CONST_28  C21   C15  C16  N17   180.00   0.0  0
 CL4  CONST_29  C19   N18  C16  N17   180.00   0.0  0
 CL4  CONST_30  C30   C27  C22  C23   180.00   0.0  0
 CL4  CONST_31  N32   C25  C24  C23   180.00   0.0  0
 CL4  CONST_32  O29   C22  C23  C24   180.00   0.0  0
 CL4  CONST_33  O28   C23  C24  C25   180.00   0.0  0
 CL4  CONST_34  C30   C27  C26  C25   180.00   0.0  0
 CL4  CONST_35  O29   C22  C27  C26   180.00   0.0  0
 CL4  CONST_36  O28   C23  C22  C27   180.00   0.0  0
 CL4  CONST_37  N32   C25  C26  C27   180.00   0.0  0
 CL4  CONST_38  H13   C13  N12  C11     0.00   0.0  0
 CL4  CONST_39  H19   C19  N18  C16   180.00   0.0  0
 CL4  CONST_40  H24   C24  C23  C22   180.00   0.0  0
 CL4  CONST_41  H26   C26  C27  C22   180.00   0.0  0
 CL4  CONST_42  O33   N32  C25  C24   180.00   0.0  0
 CL4  CONST_43  O34   N32  C25  C24     0.00   0.0  0
 CL4  CONST_46  H171  N17  C16  C15   180.00   0.0  0
 CL4  CONST_48  C27   C30  N3   C2    180.00   0.0  0
 CL4  CONST_49  HN3   N3   C30  C27     0.00   0.0  0
 CL4  CONST_50  O31   C30  N3   C2      0.00   0.0  0
 CL4  Var_01    C22   C27  C30  N3   -178.72  30.0  2
 CL4  Var_02    C5    C4   C1   C2   -178.38   0.0  2
 CL4  Var_03    C30   N3   C2   C1    172.53  30.0  3
 CL4  Var_04    C4    C1   C2   N3    113.57  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
 CL4  chir_01  C5   C4   O6   C7   negativ
 CL4  chir_02  C7   O8   C5   C9   positiv
 CL4  chir_03  C9   O10  C7   C11  positiv
 CL4  chir_04  C11  O6   N12  C9   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
 CL4  plan-1  C22   0.020
 CL4  plan-1  C23   0.020
 CL4  plan-1  C24   0.020
 CL4  plan-1  C25   0.020
 CL4  plan-1  C26   0.020
 CL4  plan-1  C27   0.020
 CL4  plan-1  O29   0.020
 CL4  plan-1  C30   0.020
 CL4  plan-1  N32   0.020
 CL4  plan-1  H24   0.020
 CL4  plan-1  H26   0.020
 CL4  plan-1  O28   0.020
 CL4  plan-2  C11   0.020
 CL4  plan-2  N12   0.020
 CL4  plan-2  C13   0.020
 CL4  plan-2  N14   0.020
 CL4  plan-2  C15   0.020
 CL4  plan-2  C16   0.020
 CL4  plan-2  N17   0.020
 CL4  plan-2  N18   0.020
 CL4  plan-2  C19   0.020
 CL4  plan-2  N20   0.020
 CL4  plan-2  C21   0.020
 CL4  plan-2  H13   0.020
 CL4  plan-2  H19   0.020
 CL4  plan-3  C16   0.020
 CL4  plan-3  N17   0.020
 CL4  plan-3  H171  0.020
 CL4  plan-3  H172  0.020
 CL4  plan-4  C25   0.020
 CL4  plan-4  N32   0.020
 CL4  plan-4  O33   0.020
 CL4  plan-4  O34   0.020
 CL4  plan-5  C2    0.020
 CL4  plan-5  N3    0.020
 CL4  plan-5  C27   0.020
 CL4  plan-5  C30   0.020
 CL4  plan-5  O31   0.020
 CL4  plan-5  HN3   0.020
 CL4  plan-6  C1    0.020
 CL4  plan-6  C2    0.020
 CL4  plan-6  C4    0.020
 CL4  plan-6  C5    0.020
 CL4  plan-6  HC1   0.020
 CL4  plan-6  HC4   0.020

