# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:46:15 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-[2-chloranyl-6-(cyclopentylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxymethylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COC[P](O)(O)=O)n2cnc3c(NC4CCCC4)nc(Cl)nc23
#
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
 OO2  OO2  '[(2~{R},3~{S},4~{R},5~{R})-5-[2-chloranyl-6-(cyclopentylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxymethylphosphonic acid'  ligand  53  30  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OO2
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
 OO2  C1   C   CR6   0   0.267  24.6003  31.7984   0.2026
 OO2  C2   C   CR56  0   0.501  23.7343  30.1039   1.2599
 OO2  N1   N   N     0  -0.464  25.3758  31.0724  -0.5769
 OO2  N2   N   N     0  -0.436  23.7584  31.4349   1.1361
 OO2  C3   C   CR6   0   0.525  25.3508  29.7390  -0.4401
 OO2  O1   O   OH1   0  -0.654  18.5985  29.7642   2.0661
 OO2  C4   C   CH1   0   0.002  19.9237  29.3765   2.2581
 OO2  C5   C   CH1   0  -0.059  20.8477  30.5724   2.4468
 OO2  O2   O   OH1   0  -0.658  20.2391  31.4631   3.3373
 OO2  C6   C   CH1   0  -0.026  20.1792  28.5829   3.5457
 OO2  C7   C   CH2   0  -0.150  19.9503  27.1047   3.3707
 OO2  O3   O   O2    0  -0.484  20.2030  26.4528   4.5941
 OO2  C8   C   CH2   0  -0.454  20.1549  25.0528   4.5184
 OO2  P1   P   P     0   1.351  21.7869  24.3630   4.0923
 OO2  O4   O   O     0  -0.701  22.4139  24.8970   2.8553
 OO2  O5   O   OH1   0  -0.742  21.5697  22.7686   4.1104
 OO2  O6   O   OH1   0  -0.742  22.6009  24.6000   5.4497
 OO2  O7   O   O2    0  -0.490  21.5472  28.8420   3.8724
 OO2  C9   C   CH1   0   0.164  22.0528  29.8893   3.1086
 OO2  N3   N   NR5   0  -0.542  22.9816  29.3544   2.1107
 OO2  C10  C   CR15  0   0.084  23.3219  28.0492   1.8714
 OO2  N4   N   N     0  -0.452  24.2146  27.9181   0.9313
 OO2  C11  C   CR56  0   0.004  24.4860  29.1974   0.5343
 OO2  CL1  CL  CL    0  -0.115  24.7204  33.5137  -0.0538
 OO2  N5   N   NH1   0  -0.650  26.1149  28.9785  -1.2177
 OO2  C12  C   CH1   0  -0.111  27.0160  29.4820  -2.2441
 OO2  C13  C   CH2   0  -0.440  28.3066  30.0431  -1.6465
 OO2  C14  C   CH2   0  -0.451  29.1020  28.7958  -1.2516
 OO2  C15  C   CH2   0  -0.455  28.6930  27.7094  -2.2718
 OO2  C16  C   CH2   0  -0.478  27.5261  28.3102  -3.0810
 OO2  H1   H   HOH1  0   0.462  18.1244  29.0425   1.6429
 OO2  H2   H   HCH1  0   0.242  20.2998  28.7981   1.4023
 OO2  H3   H   HCH1  0   0.272  21.1125  31.0517   1.4991
 OO2  H4   H   HOH1  0   0.463  20.7705  32.2641   3.3849
 OO2  H5   H   HCH1  0   0.251  19.5408  28.9642   4.3512
 OO2  H6   H   HCH2  0   0.226  18.9081  26.9485   3.0576
 OO2  H7   H   HCH2  0   0.217  20.5880  26.7211   2.5662
 OO2  H8   H   HCH2  0   0.261  19.4219  24.6941   3.7849
 OO2  H9   H   HCH2  0   0.289  19.8471  24.6598   5.4906
 OO2  H10  H   HOH1  0   0.497  21.3082  22.3976   3.2574
 OO2  H11  H   HOH1  0   0.497  23.5602  24.5212   5.3521
 OO2  H12  H   HCH1  0   0.289  22.6181  30.5788   3.7420
 OO2  H13  H   HCR5  0   0.307  22.8897  27.2273   2.4221
 OO2  H14  H   HNH1  0   0.408  26.0542  27.9819  -1.0758
 OO2  H15  H   HCH1  0   0.260  26.4812  30.2185  -2.8462
 OO2  H16  H   HCH2  0   0.232  28.8319  30.6007  -2.4267
 OO2  H17  H   HCH2  0   0.245  28.1329  30.7313  -0.8194
 OO2  H18  H   HCH2  0   0.229  28.8339  28.4860  -0.2399
 OO2  H19  H   HCH2  0   0.236  30.1762  28.9813  -1.2489
 OO2  H20  H   HCH2  0   0.234  28.3893  26.7933  -1.7630
 OO2  H21  H   HCH2  0   0.237  29.5195  27.4385  -2.9289
 OO2  H22  H   HCH2  0   0.252  27.8834  28.7048  -4.0330
 OO2  H23  H   HCH2  0   0.248  26.7420  27.5867  -3.3125

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
 OO2  C16  C15  single    1.542  0.020  1.542
 OO2  C16  C12  single    1.528  0.020  1.528
 OO2  C15  C14  single    1.545  0.020  1.545
 OO2  C12  C13  single    1.529  0.020  1.529
 OO2  C12  N5   single    1.456  0.020  1.456
 OO2  C14  C13  single    1.531  0.020  1.531
 OO2  N5   C3   single    1.329  0.020  1.329
 OO2  C3   N1   aromatic  1.341  0.020  1.341
 OO2  C3   C11  aromatic  1.411  0.020  1.411
 OO2  N1   C1   aromatic  1.318  0.020  1.318
 OO2  C11  N4   aromatic  1.367  0.020  1.367
 OO2  C11  C2   aromatic  1.383  0.020  1.383
 OO2  N4   C10  aromatic  1.303  0.020  1.303
 OO2  C1   CL1  single    1.739  0.020  1.739
 OO2  C1   N2   aromatic  1.309  0.020  1.309
 OO2  C2   N2   aromatic  1.337  0.020  1.337
 OO2  C2   N3   aromatic  1.361  0.020  1.361
 OO2  C10  N3   aromatic  1.370  0.020  1.370
 OO2  N3   C9   single    1.464  0.020  1.464
 OO2  O1   C4   single    1.394  0.020  1.394
 OO2  C4   C5   single    1.523  0.020  1.523
 OO2  C4   C6   single    1.534  0.020  1.534
 OO2  C5   O2   single    1.399  0.020  1.399
 OO2  C5   C9   single    1.535  0.020  1.535
 OO2  C9   O7   single    1.391  0.020  1.391
 OO2  O4   P1   double    1.486  0.020  1.486
 OO2  C7   C6   single    1.506  0.020  1.506
 OO2  C7   O3   single    1.409  0.020  1.409
 OO2  C6   O7   single    1.430  0.020  1.430
 OO2  P1   O6   single    1.600  0.020  1.600
 OO2  P1   C8   single    1.822  0.020  1.822
 OO2  P1   O5   single    1.609  0.020  1.609
 OO2  C8   O3   single    1.403  0.020  1.403
 OO2  O1   H1   single    0.850  0.020  0.980
 OO2  C4   H2   single    0.970  0.020  1.090
 OO2  C5   H3   single    0.970  0.020  1.090
 OO2  O2   H4   single    0.850  0.020  0.980
 OO2  C6   H5   single    0.970  0.020  1.090
 OO2  C7   H6   single    0.970  0.020  1.090
 OO2  C7   H7   single    0.970  0.020  1.090
 OO2  C8   H8   single    0.970  0.020  1.090
 OO2  C8   H9   single    0.970  0.020  1.090
 OO2  O5   H10  single    0.850  0.020  0.980
 OO2  O6   H11  single    0.850  0.020  0.980
 OO2  C9   H12  single    0.970  0.020  1.090
 OO2  C10  H13  single    0.930  0.020  1.080
 OO2  N5   H14  single    0.860  0.020  1.020
 OO2  C12  H15  single    0.970  0.020  1.090
 OO2  C13  H16  single    0.970  0.020  1.090
 OO2  C13  H17  single    0.970  0.020  1.090
 OO2  C14  H18  single    0.970  0.020  1.090
 OO2  C14  H19  single    0.970  0.020  1.090
 OO2  C15  H20  single    0.970  0.020  1.090
 OO2  C15  H21  single    0.970  0.020  1.090
 OO2  C16  H22  single    0.970  0.020  1.090
 OO2  C16  H23  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
 OO2  CL1  C1   N2   115.07  3.000
 OO2  N2   C1   N1   130.36  3.000
 OO2  CL1  C1   N1   114.56  3.000
 OO2  C11  C2   N3   105.52  3.000
 OO2  N3   C2   N2   128.03  3.000
 OO2  C11  C2   N2   126.45  3.000
 OO2  C3   N1   C1   118.47  3.000
 OO2  C2   N2   C1   110.75  3.000
 OO2  N5   C3   C11  122.46  3.000
 OO2  C11  C3   N1   117.62  3.000
 OO2  N5   C3   N1   119.92  3.000
 OO2  H1   O1   C4   108.70  3.000
 OO2  H2   C4   C6   108.92  3.000
 OO2  H2   C4   C5   107.58  3.000
 OO2  C6   C4   C5   101.61  3.000
 OO2  H2   C4   O1   111.36  3.000
 OO2  C6   C4   O1   114.70  3.000
 OO2  C5   C4   O1   112.05  3.000
 OO2  H3   C5   C9   112.22  3.000
 OO2  H3   C5   O2   112.19  3.000
 OO2  C9   C5   O2   110.51  3.000
 OO2  H3   C5   C4   112.54  3.000
 OO2  C9   C5   C4   100.39  3.000
 OO2  O2   C5   C4   108.36  3.000
 OO2  H4   O2   C5   108.74  3.000
 OO2  H5   C6   O7   109.03  3.000
 OO2  H5   C6   C7   109.77  3.000
 OO2  O7   C6   C7   110.47  3.000
 OO2  H5   C6   C4   109.87  3.000
 OO2  O7   C6   C4   104.91  3.000
 OO2  C7   C6   C4   112.64  3.000
 OO2  H7   C7   H6   107.03  3.000
 OO2  H7   C7   O3   111.79  3.000
 OO2  H6   C7   O3   110.59  3.000
 OO2  H7   C7   C6   109.90  3.000
 OO2  H6   C7   C6   108.46  3.000
 OO2  O3   C7   C6   109.02  3.000
 OO2  C8   O3   C7   114.12  3.000
 OO2  H9   C8   H8   106.79  3.000
 OO2  H9   C8   P1   108.91  3.000
 OO2  H8   C8   P1   108.55  3.000
 OO2  H9   C8   O3   108.70  3.000
 OO2  H8   C8   O3   112.66  3.000
 OO2  P1   C8   O3   111.08  3.000
 OO2  O6   P1   O5   101.88  3.000
 OO2  O5   P1   O4   114.98  3.000
 OO2  O6   P1   O4   115.99  3.000
 OO2  O5   P1   C8   104.57  3.000
 OO2  O6   P1   C8   101.60  3.000
 OO2  O4   P1   C8   115.88  3.000
 OO2  H10  O5   P1   114.02  3.000
 OO2  H11  O6   P1   114.00  3.000
 OO2  C9   O7   C6   111.01  3.000
 OO2  H12  C9   N3   107.28  3.000
 OO2  H12  C9   O7   110.15  3.000
 OO2  N3   C9   O7   109.25  3.000
 OO2  H12  C9   C5   112.01  3.000
 OO2  O7   C9   C5   106.64  3.000
 OO2  N3   C9   C5   111.51  3.000
 OO2  C10  N3   C9   128.65  3.000
 OO2  C9   N3   C2   125.15  3.000
 OO2  C10  N3   C2   106.15  3.000
 OO2  H13  C10  N4   124.45  3.000
 OO2  H13  C10  N3   122.46  3.000
 OO2  N4   C10  N3   113.09  3.000
 OO2  C11  N4   C10  104.56  3.000
 OO2  N4   C11  C3   132.97  3.000
 OO2  N4   C11  C2   110.68  3.000
 OO2  C3   C11  C2   116.34  3.000
 OO2  H14  N5   C12  118.57  3.000
 OO2  H14  N5   C3   116.65  3.000
 OO2  C12  N5   C3   124.78  3.000
 OO2  H15  C12  C16  112.28  3.000
 OO2  H15  C12  C13  112.44  3.000
 OO2  C16  C12  C13  102.34  3.000
 OO2  H15  C12  N5   108.61  3.000
 OO2  C13  C12  N5   111.95  3.000
 OO2  C16  C12  N5   109.12  3.000
 OO2  H17  C13  H16  107.22  3.000
 OO2  H17  C13  C14  113.67  3.000
 OO2  H16  C13  C14  110.48  3.000
 OO2  H17  C13  C12  113.19  3.000
 OO2  H16  C13  C12  108.28  3.000
 OO2  C14  C13  C12  103.91  3.000
 OO2  H19  C14  H18  106.74  3.000
 OO2  H19  C14  C15  112.46  3.000
 OO2  H18  C14  C15  110.33  3.000
 OO2  H19  C14  C13  111.95  3.000
 OO2  H18  C14  C13  110.04  3.000
 OO2  C15  C14  C13  105.36  3.000
 OO2  H21  C15  H20  106.46  3.000
 OO2  H21  C15  C16  110.76  3.000
 OO2  H20  C15  C16  111.18  3.000
 OO2  H21  C15  C14  111.84  3.000
 OO2  H20  C15  C14  110.86  3.000
 OO2  C16  C15  C14  105.83  3.000
 OO2  H23  C16  H22  106.85  3.000
 OO2  H23  C16  C15  113.37  3.000
 OO2  H22  C16  C15  110.56  3.000
 OO2  H23  C16  C12  112.62  3.000
 OO2  H22  C16  C12  108.06  3.000
 OO2  C15  C16  C12  105.31  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
 OO2  CONST_01  C11  C3   N1   C1     0.00   0.0  0
 OO2  CONST_02  C11  C2   N2   C1     0.00   0.0  0
 OO2  CONST_03  N3   C2   N2   C1   180.00   0.0  0
 OO2  CONST_04  N1   C3   C11  C2     0.00   0.0  0
 OO2  CONST_05  C10  N4   C11  C2     0.00   0.0  0
 OO2  CONST_06  N1   C1   N2   C2     0.00   0.0  0
 OO2  CONST_07  N4   C10  N3   C2     0.00   0.0  0
 OO2  CONST_08  N4   C11  C3   N1   180.00   0.0  0
 OO2  CONST_09  C3   N1   C1   N2     0.00   0.0  0
 OO2  CONST_10  C3   C11  C2   N2     0.00   0.0  0
 OO2  CONST_11  N4   C11  C2   N2   180.00   0.0  0
 OO2  CONST_12  C10  N3   C2   N2   180.00   0.0  0
 OO2  CONST_13  C10  N4   C11  C3   180.00   0.0  0
 OO2  CONST_14  N3   C2   C11  C3   180.00   0.0  0
 OO2  CONST_15  N4   C11  C2   N3     0.00   0.0  0
 OO2  CONST_16  C11  N4   C10  N3     0.00   0.0  0
 OO2  CONST_17  C11  C2   N3   C10    0.00   0.0  0
 OO2  CONST_18  C9   N3   C2   N2     0.00   0.0  0
 OO2  CONST_19  C11  C2   N3   C9   180.00   0.0  0
 OO2  CONST_20  N4   C10  N3   C9   180.00   0.0  0
 OO2  CONST_21  N5   C3   N1   C1   180.00   0.0  0
 OO2  CONST_22  N5   C3   C11  C2   180.00   0.0  0
 OO2  CONST_23  CL1  C1   N2   C2   180.00   0.0  0
 OO2  CONST_24  CL1  C1   N1   C3   180.00   0.0  0
 OO2  CONST_25  N5   C3   C11  N4     0.00   0.0  0
 OO2  CONST_26  C12  N5   C3   N1     0.00   0.0  0
 OO2  CONST_27  C12  N5   C3   C11  180.00   0.0  0
 OO2  CONST_28  H13  C10  N3   C2   180.00   0.0  0
 OO2  CONST_29  H14  N5   C3   N1   180.00   0.0  0
 OO2  Var_01    C14  C15  C16  C12  -17.58  30.0  1
 OO2  Var_02    C15  C14  C13  C12   30.91  30.0  1
 OO2  Var_03    C16  C15  C14  C13   -8.21  30.0  1
 OO2  Var_04    P1   C8   O3   C7    89.04  30.0  2
 OO2  Var_05    O4   P1   C8   O3   -54.70  30.0  2
 OO2  Var_06    H6   C7   O3   C8    67.04  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
 OO2  chir_01  C4   O1   C5   C6  negativ
 OO2  chir_02  C5   O2   C9   C4  negativ
 OO2  chir_03  C6   O7   C7   C4  positiv
 OO2  chir_04  C9   O7   N3   C5  negativ
 OO2  chir_05  C12  C16  C13  N5  positiv

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
 OO2  plan-1  C3   0.020
 OO2  plan-1  N5   0.020
 OO2  plan-1  C12  0.020
 OO2  plan-1  H14  0.020
 OO2  plan-2  C1   0.020
 OO2  plan-2  C2   0.020
 OO2  plan-2  N1   0.020
 OO2  plan-2  N2   0.020
 OO2  plan-2  C3   0.020
 OO2  plan-2  C9   0.020
 OO2  plan-2  N3   0.020
 OO2  plan-2  C10  0.020
 OO2  plan-2  N4   0.020
 OO2  plan-2  C11  0.020
 OO2  plan-2  CL1  0.020
 OO2  plan-2  N5   0.020
 OO2  plan-2  H13  0.020

