# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 11:30:52 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (3~{S})-3-oxidanylbutanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)CC(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 8LQ  8LQ  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (3~{S})-3-oxidanylbutanoate'  ligand  49  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8LQ
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
 8LQ  N9   N  NR5   0  -0.538  -2.7942   0.3267   0.2832
 8LQ  C8   C  CR15  0   0.104  -2.1905   1.0205  -0.7301
 8LQ  N7   N  N     0  -0.449  -2.9813   1.8741  -1.3128
 8LQ  C5   C  CR56  0  -0.002  -4.1707   1.7473  -0.6465
 8LQ  C6   C  CR6   0   0.459  -5.4182   2.3864  -0.7775
 8LQ  N6   N  NH2   0  -0.816  -5.6585   3.3142  -1.7045
 8LQ  N1   N  N     0  -0.474  -6.3947   2.0311   0.0648
 8LQ  C2   C  CR16  0   0.039  -6.1542   1.0980   0.9824
 8LQ  N3   N  N     0  -0.458  -5.0356   0.4289   1.2007
 8LQ  C4   C  CR56  0   0.488  -4.0736   0.7943   0.3547
 8LQ  CAA  C  CH3   0  -0.688   7.3692   2.4674   1.9535
 8LQ  CAZ  C  CH1   0   0.027   6.7492   1.9716   0.6568
 8LQ  OAE  O  OH1   0  -0.662   6.3631   3.0328  -0.1903
 8LQ  CAL  C  CH2   0  -0.606   5.5717   1.0472   0.9472
 8LQ  CAS  C  C     0   0.622   4.9908   0.4283  -0.2864
 8LQ  OAC  O  O     0  -0.401   5.5256   0.3014  -1.3479
 8LQ  OAQ  O  O2    0  -0.581   3.7356  -0.0454  -0.0551
 8LQ  PBC  P  P     0   1.473   2.8806  -0.8140  -1.2160
 8LQ  OAH  O  OH1   0  -0.728   3.6571  -2.1563  -1.5504
 8LQ  OAD  O  O     0  -0.679   2.5780  -0.0445  -2.4293
 8LQ  O5'  O  O2    0  -0.579   1.6615  -1.1827  -0.2626
 8LQ  C5'  C  CH2   0  -0.175   0.4656  -1.7482  -0.8132
 8LQ  C4'  C  CH1   0  -0.001  -0.5024  -1.9868   0.3156
 8LQ  O4'  O  O2    0  -0.493  -0.8459  -0.7587   0.9494
 8LQ  C3'  C  CH1   0  -0.040  -1.8271  -2.5747  -0.1687
 8LQ  O3'  O  OH1   0  -0.654  -1.7398  -3.9676  -0.2417
 8LQ  C2'  C  CH1   0  -0.045  -2.7960  -2.0633   0.9030
 8LQ  O2'  O  OH1   0  -0.663  -2.6744  -2.8051   2.0842
 8LQ  C1'  C  CH1   0   0.175  -2.2206  -0.6756   1.1759
 8LQ  H1   H  HCR5  0   0.291  -1.1553   0.8699  -0.9915
 8LQ  H2   H  HNH2  0   0.412  -4.9286   3.6366  -2.3149
 8LQ  H3   H  HNH2  0   0.404  -6.5461   3.7856  -1.7334
 8LQ  H4   H  HCR6  0   0.253  -6.9886   0.8595   1.6333
 8LQ  H6   H  HCH3  0   0.245   8.2070   3.1337   1.7486
 8LQ  H7   H  HCH3  0   0.226   6.6405   3.0105   2.5602
 8LQ  H8   H  HCH1  0   0.237   7.5045   1.4127   0.0998
 8LQ  H9   H  HOH1  0   0.444   5.7838   3.6224   0.3050
 8LQ  H10  H  HCH2  0   0.301   5.8900   0.2221   1.5943
 8LQ  H11  H  HCH2  0   0.283   4.7905   1.5749   1.5011
 8LQ  H12  H  HOH1  0   0.505   3.8369  -2.7551  -0.8119
 8LQ  H13  H  HCH2  0   0.243   0.0385  -1.0752  -1.5606
 8LQ  H14  H  HCH2  0   0.268   0.6790  -2.7046  -1.2977
 8LQ  H15  H  HCH1  0   0.263  -0.0428  -2.6583   1.0502
 8LQ  H16  H  HCH1  0   0.252  -2.0991  -2.1356  -1.1376
 8LQ  H17  H  HOH1  0   0.471  -2.4345  -4.2927  -0.8234
 8LQ  H18  H  HCH1  0   0.267  -3.8322  -2.0201   0.5488
 8LQ  H19  H  HOH1  0   0.454  -2.6011  -3.7368   1.8431
 8LQ  H20  H  HCH1  0   0.290  -2.4172  -0.3513   2.2013
 8LQ  H5   H  HCH3  0   0.234   7.7422   1.6352   2.5512

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
 8LQ  OAD  PBC  double    1.468  0.020  1.468
 8LQ  OAH  PBC  single    1.586  0.020  1.586
 8LQ  PBC  OAQ  single    1.634  0.020  1.634
 8LQ  PBC  O5'  single    1.591  0.020  1.591
 8LQ  OAQ  CAS  single    1.361  0.020  1.361
 8LQ  O5'  C5'  single    1.433  0.020  1.433
 8LQ  CAA  CAZ  single    1.520  0.020  1.520
 8LQ  C5'  C4'  single    1.506  0.020  1.506
 8LQ  CAS  OAC  double    1.195  0.020  1.195
 8LQ  CAS  CAL  single    1.497  0.020  1.497
 8LQ  C4'  C3'  single    1.528  0.020  1.528
 8LQ  C4'  O4'  single    1.424  0.020  1.424
 8LQ  O3'  C3'  single    1.398  0.020  1.398
 8LQ  CAZ  CAL  single    1.525  0.020  1.525
 8LQ  CAZ  OAE  single    1.412  0.020  1.412
 8LQ  C3'  C2'  single    1.533  0.020  1.533
 8LQ  O4'  C1'  single    1.396  0.020  1.396
 8LQ  O2'  C2'  single    1.400  0.020  1.400
 8LQ  C2'  C1'  single    1.527  0.020  1.527
 8LQ  C1'  N9   single    1.460  0.020  1.460
 8LQ  C8   N9   aromatic  1.368  0.020  1.368
 8LQ  C8   N7   aromatic  1.301  0.020  1.301
 8LQ  N9   C4   aromatic  1.364  0.020  1.364
 8LQ  N7   C5   aromatic  1.369  0.020  1.369
 8LQ  C4   C5   aromatic  1.386  0.020  1.386
 8LQ  C4   N3   aromatic  1.332  0.020  1.332
 8LQ  C5   C6   aromatic  1.408  0.020  1.408
 8LQ  N3   C2   aromatic  1.322  0.020  1.322
 8LQ  C6   N6   single    1.333  0.020  1.333
 8LQ  C6   N1   aromatic  1.338  0.020  1.338
 8LQ  C2   N1   aromatic  1.331  0.020  1.331
 8LQ  C8   H1   single    0.930  0.020  1.080
 8LQ  N6   H2   single    0.860  0.020  1.020
 8LQ  N6   H3   single    0.860  0.020  1.020
 8LQ  C2   H4   single    0.930  0.020  1.080
 8LQ  CAA  H5   single    0.970  0.020  1.090
 8LQ  CAA  H6   single    0.970  0.020  1.090
 8LQ  CAA  H7   single    0.970  0.020  1.090
 8LQ  CAZ  H8   single    0.970  0.020  1.090
 8LQ  OAE  H9   single    0.850  0.020  0.980
 8LQ  CAL  H10  single    0.970  0.020  1.090
 8LQ  CAL  H11  single    0.970  0.020  1.090
 8LQ  OAH  H12  single    0.850  0.020  0.980
 8LQ  C5'  H13  single    0.970  0.020  1.090
 8LQ  C5'  H14  single    0.970  0.020  1.090
 8LQ  C4'  H15  single    0.970  0.020  1.090
 8LQ  C3'  H16  single    0.970  0.020  1.090
 8LQ  O3'  H17  single    0.850  0.020  0.980
 8LQ  C2'  H18  single    0.970  0.020  1.090
 8LQ  O2'  H19  single    0.850  0.020  0.980
 8LQ  C1'  H20  single    0.970  0.020  1.090

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
 8LQ  C1'  N9   C4   124.89  3.000
 8LQ  C4   N9   C8   106.19  3.000
 8LQ  C1'  N9   C8   128.88  3.000
 8LQ  H1   C8   N7   124.50  3.000
 8LQ  H1   C8   N9   122.16  3.000
 8LQ  N7   C8   N9   113.33  3.000
 8LQ  C5   N7   C8   104.43  3.000
 8LQ  C4   C5   C6   116.20  3.000
 8LQ  C6   C5   N7   133.04  3.000
 8LQ  C4   C5   N7   110.76  3.000
 8LQ  N1   C6   N6   119.41  3.000
 8LQ  N1   C6   C5   117.89  3.000
 8LQ  N6   C6   C5   122.71  3.000
 8LQ  H3   N6   H2   118.26  3.000
 8LQ  H3   N6   C6   120.35  3.000
 8LQ  H2   N6   C6   120.98  3.000
 8LQ  C2   N1   C6   119.24  3.000
 8LQ  H4   C2   N3   116.15  3.000
 8LQ  H4   C2   N1   115.40  3.000
 8LQ  N3   C2   N1   128.46  3.000
 8LQ  C4   N3   C2   111.56  3.000
 8LQ  N3   C4   C5   126.65  3.000
 8LQ  N3   C4   N9   128.07  3.000
 8LQ  C5   C4   N9   105.28  3.000
 8LQ  H7   CAA  H6   108.25  3.000
 8LQ  H7   CAA  H5   107.64  3.000
 8LQ  H6   CAA  H5   107.86  3.000
 8LQ  H7   CAA  CAZ  111.33  3.000
 8LQ  H6   CAA  CAZ  110.64  3.000
 8LQ  H5   CAA  CAZ  110.99  3.000
 8LQ  H8   CAZ  CAL  108.71  3.000
 8LQ  H8   CAZ  OAE  105.54  3.000
 8LQ  CAL  CAZ  OAE  111.03  3.000
 8LQ  H8   CAZ  CAA  108.65  3.000
 8LQ  OAE  CAZ  CAA  112.22  3.000
 8LQ  CAL  CAZ  CAA  110.49  3.000
 8LQ  H9   OAE  CAZ  108.42  3.000
 8LQ  H11  CAL  H10  105.77  3.000
 8LQ  H11  CAL  CAS  109.86  3.000
 8LQ  H10  CAL  CAS  106.73  3.000
 8LQ  H11  CAL  CAZ  110.83  3.000
 8LQ  H10  CAL  CAZ  110.16  3.000
 8LQ  CAS  CAL  CAZ  113.15  3.000
 8LQ  OAQ  CAS  OAC  121.76  3.000
 8LQ  OAC  CAS  CAL  127.01  3.000
 8LQ  OAQ  CAS  CAL  111.19  3.000
 8LQ  PBC  OAQ  CAS  121.69  3.000
 8LQ  O5'  PBC  OAD  117.31  3.000
 8LQ  O5'  PBC  OAH  107.78  3.000
 8LQ  OAD  PBC  OAH  111.72  3.000
 8LQ  O5'  PBC  OAQ   94.83  3.000
 8LQ  OAH  PBC  OAQ  106.96  3.000
 8LQ  OAD  PBC  OAQ  116.65  3.000
 8LQ  H12  OAH  PBC  116.98  3.000
 8LQ  C5'  O5'  PBC  120.05  3.000
 8LQ  H14  C5'  H13  108.18  3.000
 8LQ  H14  C5'  C4'  108.60  3.000
 8LQ  H13  C5'  C4'  111.03  3.000
 8LQ  H14  C5'  O5'  110.65  3.000
 8LQ  H13  C5'  O5'  110.24  3.000
 8LQ  C4'  C5'  O5'  108.12  3.000
 8LQ  H15  C4'  C3'  109.89  3.000
 8LQ  H15  C4'  O4'  109.34  3.000
 8LQ  C3'  C4'  O4'  105.29  3.000
 8LQ  H15  C4'  C5'  109.25  3.000
 8LQ  O4'  C4'  C5'  110.61  3.000
 8LQ  C3'  C4'  C5'  112.37  3.000
 8LQ  C1'  O4'  C4'  111.17  3.000
 8LQ  H16  C3'  C2'  109.09  3.000
 8LQ  H16  C3'  O3'  111.60  3.000
 8LQ  C2'  C3'  O3'  114.11  3.000
 8LQ  H16  C3'  C4'  109.91  3.000
 8LQ  C2'  C3'  C4'  101.42  3.000
 8LQ  O3'  C3'  C4'  110.23  3.000
 8LQ  H17  O3'  C3'  108.84  3.000
 8LQ  H18  C2'  C1'  112.22  3.000
 8LQ  H18  C2'  O2'  112.06  3.000
 8LQ  C1'  C2'  O2'  107.34  3.000
 8LQ  H18  C2'  C3'  112.64  3.000
 8LQ  C1'  C2'  C3'  100.95  3.000
 8LQ  O2'  C2'  C3'  110.99  3.000
 8LQ  H19  O2'  C2'  107.89  3.000
 8LQ  H20  C1'  C2'  111.68  3.000
 8LQ  H20  C1'  O4'  110.30  3.000
 8LQ  C2'  C1'  O4'  106.74  3.000
 8LQ  H20  C1'  N9   107.41  3.000
 8LQ  C2'  C1'  N9   111.52  3.000
 8LQ  O4'  C1'  N9   109.19  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
 8LQ  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 8LQ  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 8LQ  CONST_03  C6   C5   C4   N9    180.00   0.0  0
 8LQ  CONST_04  C2   N3   C4   N9    180.00   0.0  0
 8LQ  CONST_05  C5   C4   N9   C8      0.00   0.0  0
 8LQ  CONST_06  N3   C4   N9   C8    180.00   0.0  0
 8LQ  CONST_07  C4   C5   N7   C8      0.00   0.0  0
 8LQ  CONST_08  C6   C5   N7   C8    180.00   0.0  0
 8LQ  CONST_09  C4   N9   C8   N7      0.00   0.0  0
 8LQ  CONST_10  N3   C4   C5   N7    180.00   0.0  0
 8LQ  CONST_11  N1   C6   C5   N7    180.00   0.0  0
 8LQ  CONST_12  C2   N3   C4   C5      0.00   0.0  0
 8LQ  CONST_13  C2   N1   C6   C5      0.00   0.0  0
 8LQ  CONST_14  N3   C4   C5   C6      0.00   0.0  0
 8LQ  CONST_15  N3   C2   N1   C6      0.00   0.0  0
 8LQ  CONST_16  C4   C5   C6   N1      0.00   0.0  0
 8LQ  CONST_17  C4   N3   C2   N1      0.00   0.0  0
 8LQ  CONST_18  C1'  N9   C8   N7    180.00   0.0  0
 8LQ  CONST_19  C1'  N9   C4   C5    180.00   0.0  0
 8LQ  CONST_20  C1'  N9   C4   N3      0.00   0.0  0
 8LQ  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 8LQ  CONST_22  C4   C5   C6   N6    180.00   0.0  0
 8LQ  CONST_23  C2   N1   C6   N6    180.00   0.0  0
 8LQ  CONST_24  H1   C8   N7   C5    180.00   0.0  0
 8LQ  CONST_25  H4   C2   N1   C6    180.00   0.0  0
 8LQ  CONST_26  H2   N6   C6   C5      0.00   0.0  0
 8LQ  CONST_27  H3   N6   C6   C5    180.00   0.0  0
 8LQ  Var_01    C4'  C5'  O5'  PBC  -179.88  30.0  3
 8LQ  Var_02    OAQ  CAS  CAL  CAZ  -161.52  30.0  2
 8LQ  Var_03    OAD  PBC  OAQ  CAS   -61.03  30.0  2

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
 8LQ  chir_01  CAZ  CAA  CAL  OAE  negativ
 8LQ  chir_03  C4'  C5'  C3'  O4'  positiv
 8LQ  chir_04  C3'  O3'  C2'  C4'  negativ
 8LQ  chir_05  C2'  O2'  C1'  C3'  negativ
 8LQ  chir_06  C1'  O4'  N9   C2'  negativ
 8LQ  chir_07  PBC  OAH  OAQ  O5'  both

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
 8LQ  plan-1  N9   0.020
 8LQ  plan-1  C8   0.020
 8LQ  plan-1  N7   0.020
 8LQ  plan-1  C5   0.020
 8LQ  plan-1  C6   0.020
 8LQ  plan-1  N6   0.020
 8LQ  plan-1  N1   0.020
 8LQ  plan-1  C2   0.020
 8LQ  plan-1  N3   0.020
 8LQ  plan-1  C4   0.020
 8LQ  plan-1  C1'  0.020
 8LQ  plan-1  H1   0.020
 8LQ  plan-1  H4   0.020
 8LQ  plan-2  C6   0.020
 8LQ  plan-2  N6   0.020
 8LQ  plan-2  H2   0.020
 8LQ  plan-2  H3   0.020
 8LQ  plan-3  CAL  0.020
 8LQ  plan-3  CAS  0.020
 8LQ  plan-3  OAC  0.020
 8LQ  plan-3  OAQ  0.020

