# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 13:58:01 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: 6-chloro-N-cyclopentyl-1-{5-O-[(2R)-1-hydroxy-3-methoxy-2-phosphonopropan-2-yl]-beta-D-ribofuranosyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC[C@](CO)(OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2ncc3c(NC4CCCC4)nc(Cl)nc23)[P](O)(O)=O
#
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
 VPD  VPD  6-chloro-N-cyclopentyl-1-{5-O-[(2R)-1-hydroxy-3-methoxy-2-phosphonopropan-2-yl]-beta-D-ribofuranosyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  64  35  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VPD
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
 VPD  C5    C   CT    0  -0.087  44.8856  -28.7952  -39.0014
 VPD  C6    C   CH2   0  -0.159  45.5943  -27.4465  -38.8687
 VPD  C8    C   CH2   0  -0.186  45.7618  -29.7715  -39.7825
 VPD  O9    O   O2    0  -0.481  46.9495  -29.9784  -39.0719
 VPD  C16   C   CH1   0   0.146  42.0568  -30.6697  -34.7134
 VPD  C21   C   CR56  0  -0.261  38.7429  -30.9548  -36.1420
 VPD  C24   C   CR15  0  -0.142  36.5563  -31.7586  -38.0246
 VPD  C27   C   CH2   0  -0.446  35.8210  -30.0512  -39.5601
 VPD  C30   C   CR6   0   0.296  37.9612  -29.5220  -34.0650
 VPD  C33   C   CR56  0   0.609  39.5976  -30.4826  -35.1414
 VPD  C34   C   CH1   0  -0.048  42.7967  -31.9645  -34.3488
 VPD  C37   C   CH1   0  -0.010  43.7183  -32.1361  -35.5610
 VPD  P2    P   P     0   1.356  43.3269  -28.4710  -39.9753
 VPD  O3    O   OH1   0  -0.740  42.6016  -29.8823  -40.2299
 VPD  O4    O   OH1   0  -0.742  42.2852  -27.8728  -38.9229
 VPD  O7    O   OH1   0  -0.682  44.6754  -26.5108  -38.3376
 VPD  C10   C   CH3   0  -0.400  47.8141  -30.8720  -39.7304
 VPD  O11   O   O2    0  -0.491  44.5992  -29.1989  -37.6872
 VPD  C13   C   CH1   0   0.006  44.0342  -30.6878  -35.9443
 VPD  O15   O   O2    0  -0.483  42.9518  -29.9012  -35.4596
 VPD  N18   N   NR5   0  -0.405  40.8358  -30.9067  -35.4533
 VPD  N19   N   N     0  -0.246  40.8345  -31.6184  -36.5950
 VPD  C20   C   CR15  0  -0.060  39.6032  -31.6591  -37.0240
 VPD  C22   C   CR6   0   0.525  37.3741  -30.6301  -35.9749
 VPD  N23   N   NH1   0  -0.629  36.3968  -31.0117  -36.7871
 VPD  C25   C   CH2   0  -0.468  35.1850  -32.1951  -38.5338
 VPD  C26   C   CH2   0  -0.459  34.6092  -30.9600  -39.2512
 VPD  C28   C   CH2   0  -0.449  37.0570  -30.8656  -39.1630
 VPD  N29   N   N     0  -0.469  37.0224  -29.8959  -34.9058
 VPD  N32   N   N     0  -0.445  39.2477  -29.7526  -34.0770
 VPD  O36   O   OH1   0  -0.659  43.5956  -31.7699  -33.2155
 VPD  O39   O   OH1   0  -0.661  44.9041  -32.8343  -35.3244
 VPD  H1    H   HCH2  0   0.241  46.4611  -27.5631  -38.2101
 VPD  H2    H   HCH2  0   0.232  45.9594  -27.1332  -39.8499
 VPD  H3    H   HCH2  0   0.234  45.2401  -30.7240  -39.9551
 VPD  H4    H   HCH2  0   0.240  45.9589  -29.3449  -40.7772
 VPD  H7    H   HCH1  0   0.274  41.7473  -30.1200  -33.8210
 VPD  H8    H   HCR5  0   0.272  37.2036  -32.6180  -37.8390
 VPD  H9    H   HCH2  0   0.233  35.7719  -29.1363  -38.9675
 VPD  H10   H   HCH2  0   0.240  35.8572  -29.7450  -40.6053
 VPD  H11   H   HCH1  0   0.256  42.1009  -32.8022  -34.2240
 VPD  H12   H   HCH1  0   0.244  43.1320  -32.6029  -36.3608
 VPD  H13   H   HOH1  0   0.494  42.7658  -30.2395  -41.1124
 VPD  H14   H   HOH1  0   0.488  42.7051  -27.1725  -38.3965
 VPD  H15   H   HOH1  0   0.472  44.9450  -25.6252  -38.5971
 VPD  H16   H   HCH3  0   0.239  48.6984  -31.0028  -39.1088
 VPD  H17   H   HCH3  0   0.209  47.3473  -31.8518  -39.8835
 VPD  H18   H   HCH3  0   0.210  48.1272  -30.4903  -40.7087
 VPD  H19   H   HCH1  0   0.238  44.9560  -30.3692  -35.4418
 VPD  H20   H   HCR5  0   0.280  39.3708  -32.1806  -37.9387
 VPD  H21   H   HNH1  0   0.405  35.4706  -30.7118  -36.5183
 VPD  H22   H   HCH2  0   0.254  34.5449  -32.5809  -37.7384
 VPD  H23   H   HCH2  0   0.257  35.3371  -33.0101  -39.2425
 VPD  H24   H   HCH2  0   0.237  33.8836  -30.4409  -38.6239
 VPD  H25   H   HCH2  0   0.241  34.0801  -31.2528  -40.1580
 VPD  H26   H   HCH2  0   0.241  37.3826  -31.5061  -39.9865
 VPD  H27   H   HCH2  0   0.248  37.9089  -30.2424  -38.8856
 VPD  H28   H   HOH1  0   0.460  43.0237  -31.7289  -32.4424
 VPD  H29   H   HOH1  0   0.459  44.7076  -33.7758  -35.3125
 VPD  C12   C   CH2   0  -0.162  44.1917  -30.5255  -37.4367
 VPD  O1    O   O     0  -0.707  43.5955  -27.6934  -41.2113
 VPD  CL31  CL  CL    0  -0.107  37.3949  -28.5723  -32.7268
 VPD  H5    H   HCH2  0   0.228  43.2448  -30.7720  -37.9258
 VPD  H6    H   HCH2  0   0.221  44.9446  -31.2483  -37.7721

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
 VPD  O1   P2    double    1.485  0.020  1.485
 VPD  O3   P2    single    1.607  0.020  1.607
 VPD  P2   O4    single    1.597  0.020  1.597
 VPD  P2   C5    single    1.866  0.020  1.866
 VPD  C8   C5    single    1.527  0.020  1.527
 VPD  C8   O9    single    1.399  0.020  1.399
 VPD  C5   C6    single    1.529  0.020  1.529
 VPD  C5   O11   single    1.404  0.020  1.404
 VPD  C10  O9    single    1.407  0.020  1.407
 VPD  C28  C27   single    1.532  0.020  1.532
 VPD  C28  C24   single    1.531  0.020  1.531
 VPD  C27  C26   single    1.546  0.020  1.546
 VPD  C6   O7    single    1.415  0.020  1.415
 VPD  C26  C25   single    1.540  0.020  1.540
 VPD  C25  C24   single    1.527  0.020  1.527
 VPD  O11  C12   single    1.410  0.020  1.410
 VPD  C24  N23   single    1.454  0.020  1.454
 VPD  C12  C13   single    1.509  0.020  1.509
 VPD  C20  N19   aromatic  1.304  0.020  1.304
 VPD  C20  C21   aromatic  1.419  0.020  1.419
 VPD  N19  N18   aromatic  1.345  0.020  1.345
 VPD  O15  C13   single    1.423  0.020  1.423
 VPD  O15  C16   single    1.396  0.020  1.396
 VPD  N23  C22   single    1.327  0.020  1.327
 VPD  C13  C37   single    1.531  0.020  1.531
 VPD  C21  C22   aromatic  1.417  0.020  1.417
 VPD  C21  C33   aromatic  1.398  0.020  1.398
 VPD  C37  O39   single    1.396  0.020  1.396
 VPD  C37  C34   single    1.532  0.020  1.532
 VPD  N18  C16   single    1.447  0.020  1.447
 VPD  N18  C33   aromatic  1.345  0.020  1.345
 VPD  C22  N29   aromatic  1.344  0.020  1.344
 VPD  C16  C34   single    1.535  0.020  1.535
 VPD  C33  N32   aromatic  1.337  0.020  1.337
 VPD  C34  O36   single    1.400  0.020  1.400
 VPD  N29  C30   aromatic  1.315  0.020  1.315
 VPD  N32  C30   aromatic  1.307  0.020  1.307
 VPD  C30  CL31  single    1.736  0.020  1.736
 VPD  C6   H1    single    0.970  0.020  1.090
 VPD  C6   H2    single    0.970  0.020  1.090
 VPD  C8   H3    single    0.970  0.020  1.090
 VPD  C8   H4    single    0.970  0.020  1.090
 VPD  C12  H5    single    0.970  0.020  1.090
 VPD  C12  H6    single    0.970  0.020  1.090
 VPD  C16  H7    single    0.970  0.020  1.090
 VPD  C24  H8    single    0.970  0.020  1.090
 VPD  C27  H9    single    0.970  0.020  1.090
 VPD  C27  H10   single    0.970  0.020  1.090
 VPD  C34  H11   single    0.970  0.020  1.090
 VPD  C37  H12   single    0.970  0.020  1.090
 VPD  O3   H13   single    0.850  0.020  0.980
 VPD  O4   H14   single    0.850  0.020  0.980
 VPD  O7   H15   single    0.850  0.020  0.980
 VPD  C10  H16   single    0.970  0.020  1.090
 VPD  C10  H17   single    0.970  0.020  1.090
 VPD  C10  H18   single    0.970  0.020  1.090
 VPD  C13  H19   single    0.970  0.020  1.090
 VPD  C20  H20   single    0.930  0.020  1.080
 VPD  N23  H21   single    0.860  0.020  1.020
 VPD  C25  H22   single    0.970  0.020  1.090
 VPD  C25  H23   single    0.970  0.020  1.090
 VPD  C26  H24   single    0.970  0.020  1.090
 VPD  C26  H25   single    0.970  0.020  1.090
 VPD  C28  H26   single    0.970  0.020  1.090
 VPD  C28  H27   single    0.970  0.020  1.090
 VPD  O36  H28   single    0.850  0.020  0.980
 VPD  O39  H29   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
 VPD  O11   C5   P2    111.59  3.000
 VPD  O11   C5   C8    114.33  3.000
 VPD  P2    C5   C8    108.87  3.000
 VPD  O11   C5   C6    105.47  3.000
 VPD  C8    C5   C6    110.02  3.000
 VPD  P2    C5   C6    106.21  3.000
 VPD  H2    C6   H1    107.83  3.000
 VPD  H2    C6   O7    111.37  3.000
 VPD  H1    C6   O7    111.03  3.000
 VPD  H2    C6   C5    109.25  3.000
 VPD  H1    C6   C5    108.98  3.000
 VPD  O7    C6   C5    108.35  3.000
 VPD  H4    C8   H3    106.20  3.000
 VPD  H4    C8   O9    111.37  3.000
 VPD  H3    C8   O9    110.75  3.000
 VPD  H4    C8   C5    108.50  3.000
 VPD  H3    C8   C5    111.22  3.000
 VPD  O9    C8   C5    108.78  3.000
 VPD  C10   O9   C8    112.20  3.000
 VPD  H7    C16  N18   105.12  3.000
 VPD  H7    C16  O15   109.95  3.000
 VPD  N18   C16  O15   110.96  3.000
 VPD  H7    C16  C34   111.52  3.000
 VPD  N18   C16  C34   112.95  3.000
 VPD  O15   C16  C34   106.40  3.000
 VPD  C22   C21  C20   140.60  3.000
 VPD  C22   C21  C33   115.40  3.000
 VPD  C20   C21  C33   104.00  3.000
 VPD  H8    C24  C28   113.06  3.000
 VPD  H8    C24  C25   111.36  3.000
 VPD  C28   C24  C25   102.27  3.000
 VPD  H8    C24  N23   108.95  3.000
 VPD  C25   C24  N23   109.40  3.000
 VPD  C28   C24  N23   111.65  3.000
 VPD  H10   C27  H9    106.66  3.000
 VPD  H10   C27  C28   111.78  3.000
 VPD  H9    C27  C28   109.95  3.000
 VPD  H10   C27  C26   112.51  3.000
 VPD  H9    C27  C26   110.43  3.000
 VPD  C28   C27  C26   105.55  3.000
 VPD  N32   C30  CL31  115.13  3.000
 VPD  CL31  C30  N29   114.56  3.000
 VPD  N32   C30  N29   130.30  3.000
 VPD  N32   C33  N18   126.68  3.000
 VPD  N32   C33  C21   126.45  3.000
 VPD  N18   C33  C21   106.87  3.000
 VPD  H11   C34  O36   112.10  3.000
 VPD  H11   C34  C37   112.73  3.000
 VPD  O36   C34  C37   108.22  3.000
 VPD  H11   C34  C16   111.45  3.000
 VPD  O36   C34  C16   110.48  3.000
 VPD  C37   C34  C16   101.33  3.000
 VPD  H12   C37  O39   111.41  3.000
 VPD  H12   C37  C13   109.30  3.000
 VPD  O39   C37  C13   109.89  3.000
 VPD  H12   C37  C34   107.65  3.000
 VPD  O39   C37  C34   115.64  3.000
 VPD  C13   C37  C34   102.49  3.000
 VPD  O4    P2   O3     97.98  3.000
 VPD  O4    P2   O1    118.06  3.000
 VPD  O3    P2   O1    114.18  3.000
 VPD  O4    P2   C5    105.43  3.000
 VPD  O3    P2   C5    107.88  3.000
 VPD  O1    P2   C5    111.98  3.000
 VPD  H13   O3   P2    113.12  3.000
 VPD  H14   O4   P2    110.19  3.000
 VPD  H15   O7   C6    109.00  3.000
 VPD  H18   C10  H17   107.96  3.000
 VPD  H18   C10  H16   108.63  3.000
 VPD  H17   C10  H16   108.56  3.000
 VPD  H18   C10  O9    111.85  3.000
 VPD  H17   C10  O9    111.81  3.000
 VPD  H16   C10  O9    107.95  3.000
 VPD  C12   O11  C5    119.70  3.000
 VPD  H19   C13  O15   108.81  3.000
 VPD  H19   C13  C37   109.48  3.000
 VPD  O15   C13  C37   106.30  3.000
 VPD  H19   C13  C12   109.51  3.000
 VPD  C37   C13  C12   111.77  3.000
 VPD  O15   C13  C12   110.89  3.000
 VPD  C13   O15  C16   111.43  3.000
 VPD  N19   N18  C33   111.26  3.000
 VPD  C33   N18  C16   127.32  3.000
 VPD  N19   N18  C16   121.42  3.000
 VPD  C20   N19  N18   107.25  3.000
 VPD  H20   C20  N19   119.84  3.000
 VPD  H20   C20  C21   129.53  3.000
 VPD  N19   C20  C21   110.62  3.000
 VPD  N29   C22  N23   116.83  3.000
 VPD  N29   C22  C21   118.16  3.000
 VPD  N23   C22  C21   125.00  3.000
 VPD  H21   N23  C22   115.29  3.000
 VPD  H21   N23  C24   118.66  3.000
 VPD  C22   N23  C24   126.00  3.000
 VPD  H23   C25  H22   106.93  3.000
 VPD  H23   C25  C26   110.41  3.000
 VPD  H22   C25  C26   113.81  3.000
 VPD  H23   C25  C24   107.77  3.000
 VPD  H22   C25  C24   112.63  3.000
 VPD  C26   C25  C24   105.18  3.000
 VPD  H25   C26  H24   106.47  3.000
 VPD  H25   C26  C25   110.71  3.000
 VPD  H24   C26  C25   111.25  3.000
 VPD  H25   C26  C27   111.85  3.000
 VPD  H24   C26  C27   110.90  3.000
 VPD  C25   C26  C27   105.75  3.000
 VPD  H27   C28  H26   107.07  3.000
 VPD  H27   C28  C27   113.08  3.000
 VPD  H26   C28  C27   110.89  3.000
 VPD  H27   C28  C24   113.54  3.000
 VPD  H26   C28  C24   108.41  3.000
 VPD  C27   C28  C24   103.82  3.000
 VPD  C22   N29  C30   118.51  3.000
 VPD  C33   N32  C30   111.17  3.000
 VPD  H28   O36  C34   108.48  3.000
 VPD  H29   O39  C37   108.55  3.000
 VPD  H6    C12  H5    108.01  3.000
 VPD  H6    C12  C13   107.65  3.000
 VPD  H5    C12  C13   109.12  3.000
 VPD  H6    C12  O11   111.56  3.000
 VPD  H5    C12  O11   112.50  3.000
 VPD  C13   C12  O11   107.87  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
 VPD  CONST_01  N18   N19  C20  C21     0.00   0.0  0
 VPD  CONST_02  C30   N29  C22  C21     0.00   0.0  0
 VPD  CONST_03  N19   N18  C33  C21     0.00   0.0  0
 VPD  CONST_04  C30   N32  C33  C21     0.00   0.0  0
 VPD  CONST_05  N18   C33  N32  C30   180.00   0.0  0
 VPD  CONST_06  N19   C20  C21  C33     0.00   0.0  0
 VPD  CONST_07  N29   C22  C21  C33     0.00   0.0  0
 VPD  CONST_08  C20   N19  N18  C33     0.00   0.0  0
 VPD  CONST_09  N29   C30  N32  C33     0.00   0.0  0
 VPD  CONST_10  C20   C21  C33  N18     0.00   0.0  0
 VPD  CONST_11  C22   C21  C33  N18   180.00   0.0  0
 VPD  CONST_12  C22   C21  C20  N19   180.00   0.0  0
 VPD  CONST_13  N32   C33  N18  N19   180.00   0.0  0
 VPD  CONST_14  N29   C22  C21  C20   180.00   0.0  0
 VPD  CONST_15  N32   C33  C21  C20   180.00   0.0  0
 VPD  CONST_16  N32   C33  C21  C22     0.00   0.0  0
 VPD  CONST_17  N32   C30  N29  C22     0.00   0.0  0
 VPD  CONST_18  C20   N19  N18  C16   180.00   0.0  0
 VPD  CONST_19  C21   C33  N18  C16   180.00   0.0  0
 VPD  CONST_20  N32   C33  N18  C16     0.00   0.0  0
 VPD  CONST_21  N23   C22  N29  C30   180.00   0.0  0
 VPD  CONST_22  N23   C22  C21  C33   180.00   0.0  0
 VPD  CONST_23  CL31  C30  N32  C33   180.00   0.0  0
 VPD  CONST_24  N23   C22  C21  C20     0.00   0.0  0
 VPD  CONST_25  CL31  C30  N29  C22   180.00   0.0  0
 VPD  CONST_26  C24   N23  C22  C21     0.00   0.0  0
 VPD  CONST_27  N29   C22  N23  C24   180.00   0.0  0
 VPD  CONST_28  H20   C20  C21  C33   180.00   0.0  0
 VPD  CONST_29  H21   N23  C22  C21   180.00   0.0  0
 VPD  Var_01    C26   C27  C28  C24   -29.80  30.0  1
 VPD  Var_02    C27   C26  C25  C24    19.29  30.0  1
 VPD  Var_03    C28   C27  C26  C25     6.53  30.0  1
 VPD  Var_04    C13   C12  O11  C5    176.80  30.0  3
 VPD  Var_05    H16   C10  O9   C8   -178.51  30.0  3
 VPD  Var_06    H3    C8   O9   C10    57.44  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
 VPD  chir_01  C5   C8   C6   O11  positiv
 VPD  chir_02  C16  O15  N18  C34  negativ
 VPD  chir_03  C24  N23  C28  C25  positiv
 VPD  chir_04  C34  C37  C16  O36  positiv
 VPD  chir_05  C37  O39  C13  C34  positiv
 VPD  chir_06  C13  O15  C37  C12  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
 VPD  plan-1  C24   0.020
 VPD  plan-1  C22   0.020
 VPD  plan-1  N23   0.020
 VPD  plan-1  H21   0.020
 VPD  plan-2  C16   0.020
 VPD  plan-2  C21   0.020
 VPD  plan-2  C30   0.020
 VPD  plan-2  C33   0.020
 VPD  plan-2  N18   0.020
 VPD  plan-2  N19   0.020
 VPD  plan-2  C20   0.020
 VPD  plan-2  C22   0.020
 VPD  plan-2  N23   0.020
 VPD  plan-2  N29   0.020
 VPD  plan-2  N32   0.020
 VPD  plan-2  H20   0.020
 VPD  plan-2  CL31  0.020

