# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 18:24:04 2022
#   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  62  35  .  2022-03-29  2022-03-29
;
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  -0.067  45.3843  -28.6443  -39.0178
 VPD  C6    C   CH2    0  -0.151  46.2548  -27.4230  -38.7425
 VPD  C8    C   CH2    0  -0.191  46.2802  -29.7178  -39.6263
 VPD  O9    O   O2     0  -0.489  47.3399  -30.0690  -38.7585
 VPD  C16   C   CH1    0   0.163  41.8503  -30.4080  -35.0176
 VPD  C21   C   CR56   0  -0.249  38.4684  -30.9531  -36.1800
 VPD  C24   C   CH1    0  -0.140  36.1881  -31.9395  -37.8798
 VPD  C27   C   CH2    0  -0.447  34.9837  -30.2555  -39.1080
 VPD  C30   C   CR6    0   0.294  37.7494  -29.9430  -33.8463
 VPD  C33   C   CR56   0   0.603  39.3610  -30.4696  -35.2180
 VPD  C34   C   CH1    0  -0.060  42.5487  -31.7243  -34.6386
 VPD  C37   C   CH1    0  -0.007  43.4800  -31.9159  -35.8377
 VPD  P2    P   P      0   1.169  43.9829  -28.2782  -40.2763
 VPD  O3    O   OP    -1  -0.892  43.5148  -29.6654  -40.7500
 VPD  O4    O   OP    -1  -0.888  42.9080  -27.5035  -39.5145
 VPD  O7    O   OH1    0  -0.672  45.5075  -26.3516  -38.2047
 VPD  C10   C   CH3    0  -0.387  48.1552  -31.0701  -39.2988
 VPD  O11   O   O2     0  -0.519  44.9020  -29.0403  -37.7272
 VPD  C13   C   CH1    0   0.017  43.8775  -30.4784  -36.1605
 VPD  O15   O   O2     0  -0.492  42.7365  -29.6903  -35.8196
 VPD  N18   N   NR5    0  -0.407  40.5996  -30.6289  -35.7174
 VPD  N19   N   N      0  -0.248  40.5656  -31.1922  -36.9386
 VPD  C20   C   CR15   0  -0.074  39.3094  -31.3860  -37.2382
 VPD  C22   C   CR6    0   0.522  37.0987  -30.8938  -35.8203
 VPD  N23   N   NH1    0  -0.628  36.0915  -31.3441  -36.5574
 VPD  C25   C   CH2    0  -0.468  34.8433  -32.5600  -38.2560
 VPD  C26   C   CH2    0  -0.453  33.9890  -31.3940  -38.7922
 VPD  C28   C   CH2    0  -0.447  36.3738  -30.8820  -38.9697
 VPD  N29   N   N      0  -0.466  36.7797  -30.3641  -34.6267
 VPD  N32   N   N      0  -0.443  39.0436  -29.9510  -34.0265
 VPD  O39   O   OH1    0  -0.657  44.6202  -32.6875  -35.6031
 VPD  H1    H   HCH2   0   0.178  47.0602  -27.7000  -38.0485
 VPD  H2    H   HCH2   0   0.170  46.7316  -27.1362  -39.6873
 VPD  H3    H   HCH2   0   0.207  45.6900  -30.6073  -39.8796
 VPD  H4    H   HCH2   0   0.198  46.6724  -29.3338  -40.5796
 VPD  H7    H   HCH1   0   0.267  41.5800  -29.8349  -34.1258
 VPD  H8    H   HCH1   0   0.271  36.9800  -32.6915  -37.8730
 VPD  H9    H   HCH2   0   0.232  34.8708  -29.4421  -38.3894
 VPD  H10   H   HCH2   0   0.239  34.8270  -29.8253  -40.0968
 VPD  H11   H   HCH1   0   0.254  41.8236  -32.5394  -34.5236
 VPD  H12   H   HCH1   0   0.236  42.8855  -32.3169  -36.6686
 VPD  H15   H   HOH1   0   0.438  46.1345  -25.6663  -37.9590
 VPD  H16   H   HCH3   0   0.225  48.9432  -31.2973  -38.5801
 VPD  H17   H   HCH3   0   0.193  47.5987  -31.9948  -39.5008
 VPD  H18   H   HCH3   0   0.194  48.6282  -30.7591  -40.2394
 VPD  H19   H   HCH1   0   0.221  44.7223  -30.1881  -35.5213
 VPD  H20   H   HCR5   0   0.281  39.0478  -31.8182  -38.1910
 VPD  H21   H   HNH1   0   0.406  35.1762  -31.2374  -36.1428
 VPD  H22   H   HCH2   0   0.252  34.3819  -33.0931  -37.4228
 VPD  H23   H   HCH2   0   0.256  35.0227  -33.2951  -39.0414
 VPD  H24   H   HCH2   0   0.236  33.2485  -31.0744  -38.0579
 VPD  H25   H   HCH2   0   0.238  33.4342  -31.7020  -39.6781
 VPD  H26   H   HCH2   0   0.239  36.6640  -31.3900  -39.8931
 VPD  H27   H   HCH2   0   0.249  37.1527  -30.1513  -38.7449
 VPD  H29   H   HOH1   0   0.456  44.3748  -33.6169  -35.6358
 VPD  C12   C   CH2    0  -0.141  44.2687  -30.2795  -37.6059
 VPD  O1    O   O      0  -0.893  44.7025  -27.4779  -41.3717
 VPD  CL31  CL  CL     0  -0.108  37.2206  -29.2786  -32.3317
 VPD  H5    H   HCH2   0   0.191  43.3844  -30.3678  -38.2466
 VPD  H6    H   HCH2   0   0.190  44.9380  -31.1098  -37.8730
 VPD  O36   O   OH1    0  -0.656  43.3347  -31.5578  -33.4911
 VPD  H28   H   HOH1   0   0.457  42.7512  -31.4554  -32.7322

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    deloc     1.536  0.020  1.536
 VPD  O3   P2    deloc     1.539  0.020  1.539
 VPD  P2   O4    deloc     1.528  0.020  1.528
 VPD  P2   C5    single    1.919  0.020  1.919
 VPD  C8   C5    single    1.525  0.020  1.525
 VPD  C8   O9    single    1.414  0.020  1.414
 VPD  C5   C6    single    1.525  0.020  1.525
 VPD  C5   O11   single    1.433  0.020  1.433
 VPD  C10  O9    single    1.400  0.020  1.400
 VPD  C28  C27   single    1.531  0.020  1.531
 VPD  C28  C24   single    1.530  0.020  1.530
 VPD  C27  C26   single    1.544  0.020  1.544
 VPD  C6   O7    single    1.413  0.020  1.413
 VPD  C26  C25   single    1.542  0.020  1.542
 VPD  C25  C24   single    1.528  0.020  1.528
 VPD  O11  C12   single    1.397  0.020  1.397
 VPD  C24  N23   single    1.454  0.020  1.454
 VPD  C12  C13   single    1.511  0.020  1.511
 VPD  C20  N19   aromatic  1.306  0.020  1.306
 VPD  C20  C21   aromatic  1.419  0.020  1.419
 VPD  N19  N18   aromatic  1.345  0.020  1.345
 VPD  O15  C13   single    1.428  0.020  1.428
 VPD  O15  C16   single    1.394  0.020  1.394
 VPD  N23  C22   single    1.327  0.020  1.327
 VPD  C13  C37   single    1.526  0.020  1.526
 VPD  C21  C22   aromatic  1.417  0.020  1.417
 VPD  C21  C33   aromatic  1.399  0.020  1.399
 VPD  C37  O39   single    1.397  0.020  1.397
 VPD  C37  C34   single    1.530  0.020  1.530
 VPD  N18  C16   single    1.450  0.020  1.450
 VPD  N18  C33   aromatic  1.345  0.020  1.345
 VPD  C22  N29   aromatic  1.344  0.020  1.344
 VPD  C16  C34   single    1.538  0.020  1.538
 VPD  C33  N32   aromatic  1.338  0.020  1.338
 VPD  C34  O36   single    1.401  0.020  1.401
 VPD  N29  C30   aromatic  1.314  0.020  1.314
 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  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    113.42  3.000
 VPD  O11   C5   C8    111.25  3.000
 VPD  P2    C5   C8    107.56  3.000
 VPD  O11   C5   C6    104.53  3.000
 VPD  C8    C5   C6    107.49  3.000
 VPD  P2    C5   C6    112.49  3.000
 VPD  H2    C6   H1    106.94  3.000
 VPD  H2    C6   O7    111.08  3.000
 VPD  H1    C6   O7    109.79  3.000
 VPD  H2    C6   C5    107.59  3.000
 VPD  H1    C6   C5    109.31  3.000
 VPD  O7    C6   C5    111.97  3.000
 VPD  H4    C8   H3    105.95  3.000
 VPD  H4    C8   O9    110.56  3.000
 VPD  H3    C8   O9    110.09  3.000
 VPD  H4    C8   C5    108.04  3.000
 VPD  H3    C8   C5    110.30  3.000
 VPD  O9    C8   C5    111.73  3.000
 VPD  C10   O9   C8    112.17  3.000
 VPD  H7    C16  N18   105.07  3.000
 VPD  H7    C16  O15   110.88  3.000
 VPD  N18   C16  O15   110.43  3.000
 VPD  H7    C16  C34   111.09  3.000
 VPD  N18   C16  C34   112.35  3.000
 VPD  O15   C16  C34   107.09  3.000
 VPD  C22   C21  C20   140.77  3.000
 VPD  C22   C21  C33   115.32  3.000
 VPD  C20   C21  C33   103.89  3.000
 VPD  H8    C24  C28   113.10  3.000
 VPD  H8    C24  C25   111.11  3.000
 VPD  C28   C24  C25   102.25  3.000
 VPD  H8    C24  N23   108.94  3.000
 VPD  C25   C24  N23   109.37  3.000
 VPD  C28   C24  N23   111.90  3.000
 VPD  H10   C27  H9    106.76  3.000
 VPD  H10   C27  C28   111.97  3.000
 VPD  H9    C27  C28   109.84  3.000
 VPD  H10   C27  C26   112.58  3.000
 VPD  H9    C27  C26   110.38  3.000
 VPD  C28   C27  C26   105.35  3.000
 VPD  N32   C30  CL31  115.10  3.000
 VPD  CL31  C30  N29   114.58  3.000
 VPD  N32   C30  N29   130.31  3.000
 VPD  N32   C33  N18   126.52  3.000
 VPD  N32   C33  C21   126.54  3.000
 VPD  N18   C33  C21   106.94  3.000
 VPD  H11   C34  O36   111.92  3.000
 VPD  H11   C34  C37   113.04  3.000
 VPD  O36   C34  C37   108.38  3.000
 VPD  H11   C34  C16   111.21  3.000
 VPD  O36   C34  C16   110.79  3.000
 VPD  C37   C34  C16   100.98  3.000
 VPD  H12   C37  O39   111.57  3.000
 VPD  H12   C37  C13   108.98  3.000
 VPD  O39   C37  C13   110.08  3.000
 VPD  H12   C37  C34   108.01  3.000
 VPD  O39   C37  C34   115.74  3.000
 VPD  C13   C37  C34   101.91  3.000
 VPD  O4    P2   O3    113.36  3.000
 VPD  O4    P2   O1    114.89  3.000
 VPD  O3    P2   O1    113.13  3.000
 VPD  O4    P2   C5    106.47  3.000
 VPD  O3    P2   C5    104.60  3.000
 VPD  O1    P2   C5    103.00  3.000
 VPD  H15   O7   C6    107.04  3.000
 VPD  H18   C10  H17   107.41  3.000
 VPD  H18   C10  H16   108.20  3.000
 VPD  H17   C10  H16   108.18  3.000
 VPD  H18   C10  O9    112.28  3.000
 VPD  H17   C10  O9    112.23  3.000
 VPD  H16   C10  O9    108.40  3.000
 VPD  C12   O11  C5    118.41  3.000
 VPD  H19   C13  O15   109.25  3.000
 VPD  H19   C13  C37   109.04  3.000
 VPD  O15   C13  C37   105.14  3.000
 VPD  H19   C13  C12   108.84  3.000
 VPD  C37   C13  C12   113.20  3.000
 VPD  O15   C13  C12   111.26  3.000
 VPD  C13   O15  C16   111.17  3.000
 VPD  N19   N18  C33   111.31  3.000
 VPD  C33   N18  C16   126.66  3.000
 VPD  N19   N18  C16   121.58  3.000
 VPD  C20   N19  N18   107.14  3.000
 VPD  H20   C20  N19   119.70  3.000
 VPD  H20   C20  C21   129.58  3.000
 VPD  N19   C20  C21   110.71  3.000
 VPD  N29   C22  N23   116.54  3.000
 VPD  N29   C22  C21   118.11  3.000
 VPD  N23   C22  C21   125.34  3.000
 VPD  H21   N23  C22   115.08  3.000
 VPD  H21   N23  C24   118.47  3.000
 VPD  C22   N23  C24   126.44  3.000
 VPD  H23   C25  H22   106.86  3.000
 VPD  H23   C25  C26   110.51  3.000
 VPD  H22   C25  C26   113.62  3.000
 VPD  H23   C25  C24   107.83  3.000
 VPD  H22   C25  C24   112.49  3.000
 VPD  C26   C25  C24   105.44  3.000
 VPD  H25   C26  H24   106.53  3.000
 VPD  H25   C26  C25   110.55  3.000
 VPD  H24   C26  C25   111.33  3.000
 VPD  H25   C26  C27   111.72  3.000
 VPD  H24   C26  C27   111.03  3.000
 VPD  C25   C26  C27   105.77  3.000
 VPD  H27   C28  H26   107.20  3.000
 VPD  H27   C28  C27   113.12  3.000
 VPD  H26   C28  C27   110.79  3.000
 VPD  H27   C28  C24   113.75  3.000
 VPD  H26   C28  C24   108.22  3.000
 VPD  C27   C28  C24   103.71  3.000
 VPD  C22   N29  C30   118.59  3.000
 VPD  C33   N32  C30   111.11  3.000
 VPD  H29   O39  C37   108.65  3.000
 VPD  H6    C12  H5    106.76  3.000
 VPD  H6    C12  C13   106.90  3.000
 VPD  H5    C12  C13   109.87  3.000
 VPD  H6    C12  O11   111.89  3.000
 VPD  H5    C12  O11   112.74  3.000
 VPD  C13   C12  O11   108.50  3.000
 VPD  H28   O36  C34   108.56  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   -31.81  30.0  1
 VPD  Var_02    C27   C26  C25  C24    16.78  30.0  1
 VPD  Var_03    C28   C27  C26  C25     9.27  30.0  1
 VPD  Var_04    C13   C12  O11  C5    178.96  30.0  3
 VPD  Var_05    H16   C10  O9   C8   -179.60  30.0  3
 VPD  Var_06    H3    C8   O9   C10    56.08  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

