# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 02:58:31 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: 6-chloro-N-[(2-chlorophenyl)methyl]-1-[5-O-(phosphonomethyl)-beta-D-ribofuranosyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   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)n2ncc3c(NCc4ccccc4Cl)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
 VPG  VPG  6-chloro-N-[(2-chlorophenyl)methyl]-1-[5-O-(phosphonomethyl)-beta-D-ribofuranosyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  51  33  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VPG
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
 VPG  C2    C   CR6    0  -0.092  30.6809  -20.8473   2.5273
 VPG  C3    C   CR16   0  -0.196  30.0624  -19.7108   3.0223
 VPG  C4    C   CR16   0  -0.269  30.2819  -19.3368   4.3405
 VPG  C5    C   CR16   0  -0.229  31.1112  -20.0975   5.1506
 VPG  C6    C   CR16   0  -0.307  31.7231  -21.2319   4.6369
 VPG  C7    C   CR6    0   0.171  31.5190  -21.6296   3.3201
 VPG  C8    C   CH2    0  -0.364  32.1955  -22.8585   2.7820
 VPG  C12   C   CR6    0   0.295  34.9182  -23.2365  -1.0991
 VPG  C15   C   CR56   0   0.614  33.6832  -25.0010  -0.7508
 VPG  C16   C   CR56   0  -0.263  33.1749  -24.4837   0.4450
 VPG  C17   C   CR15   0  -0.064  32.3355  -25.5175   0.9372
 VPG  C23   C   CH2    0  -0.116  29.9694  -28.1421  -2.1096
 VPG  O28   O   O      0  -0.902  27.0605  -27.1556  -5.3300
 VPG  O29   O   OP    -1  -0.902  25.5388  -26.2539  -3.4544
 VPG  C30   C   CH1    0  -0.056  32.1996  -29.1668  -1.5229
 VPG  C32   C   CH1    0  -0.024  33.5992  -28.5460  -1.6459
 VPG  CL1   CL  CL     0  -0.119  30.3822  -21.3035   0.8812
 VPG  N9    N   NH1    0  -0.625  33.2342  -22.4881   1.8445
 VPG  C10   C   CR6    0   0.530  33.6299  -23.1870   0.7859
 VPG  N11   N   N      0  -0.463  34.5340  -22.6000  -0.0140
 VPG  N14   N   N      0  -0.439  34.5581  -24.4032  -1.5654
 VPG  N18   N   N      0  -0.248  32.3307  -26.5330   0.1187
 VPG  N19   N   NR5    0  -0.406  33.1458  -26.2251  -0.9065
 VPG  C20   C   CH1    0   0.154  33.2760  -27.1081  -2.0447
 VPG  O21   O   O2     0  -0.482  32.0823  -27.1559  -2.7685
 VPG  C22   C   CH1    0   0.007  31.3914  -28.3846  -2.5627
 VPG  C25   C   CH2    0  -0.466  27.8904  -27.2714  -2.7462
 VPG  P26   P   P      0   1.143  26.9502  -26.3120  -4.0542
 VPG  O27   O   OP    -1  -0.902  27.6545  -24.9519  -4.1405
 VPG  O31   O   OH1    0  -0.658  32.1778  -30.5365  -1.8312
 VPG  O33   O   OH1    0  -0.664  34.3013  -29.1268  -2.7112
 VPG  H1    H   HCR6   0   0.282  29.4139  -19.1241   2.3859
 VPG  H2    H   HCR6   0   0.270  29.7995  -18.4496   4.7286
 VPG  H3    H   HCR6   0   0.265  31.2837  -19.8095   6.1788
 VPG  H4    H   HCR6   0   0.268  32.3729  -21.8269   5.2668
 VPG  H5    H   HCH2   0   0.274  31.4583  -23.4798   2.2741
 VPG  H6    H   HCH2   0   0.281  32.6051  -23.4455   3.6077
 VPG  H7    H   HCR5   0   0.281  31.7570  -25.5619   1.8461
 VPG  H8    H   HCH2   0   0.185  29.9812  -27.5607  -1.1742
 VPG  H9    H   HCH2   0   0.188  29.5238  -29.1207  -1.8659
 VPG  H11   H   HCH1   0   0.254  31.8077  -28.9787  -0.5185
 VPG  H12   H   HCH1   0   0.246  34.1695  -28.5929  -0.7101
 VPG  H13   H   HNH1   0   0.409  33.6890  -21.5962   1.9767
 VPG  H14   H   HCH1   0   0.275  34.0692  -26.6773  -2.6593
 VPG  H15   H   HCH1   0   0.234  31.3829  -28.9397  -3.5091
 VPG  H16   H   HCH2   0   0.160  27.8466  -26.7305  -1.7862
 VPG  H17   H   HCH2   0   0.160  27.4001  -28.2422  -2.5633
 VPG  H19   H   HOH1   0   0.465  32.3679  -31.0381  -1.0316
 VPG  H20   H   HOH1   0   0.447  34.0245  -30.0509  -2.7650
 VPG  O24   O   O2     0  -0.494  29.2468  -27.4885  -3.1074
 VPG  CL13  CL  CL     0  -0.104  36.0827  -22.3841  -2.0624

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
 VPG  O28   P26  deloc     1.533  0.020  1.533
 VPG  O27   P26  deloc     1.534  0.020  1.534
 VPG  P26   O29  deloc     1.535  0.020  1.535
 VPG  P26   C25  single    1.875  0.020  1.875
 VPG  O24   C25  single    1.420  0.020  1.420
 VPG  O24   C23  single    1.395  0.020  1.395
 VPG  O21   C22  single    1.425  0.020  1.425
 VPG  O21   C20  single    1.397  0.020  1.397
 VPG  C22   C23  single    1.512  0.020  1.512
 VPG  C22   C30  single    1.532  0.020  1.532
 VPG  O33   C32  single    1.402  0.020  1.402
 VPG  C20   C32  single    1.527  0.020  1.527
 VPG  C20   N19  single    1.446  0.020  1.446
 VPG  O31   C30  single    1.404  0.020  1.404
 VPG  C32   C30  single    1.536  0.020  1.536
 VPG  N19   C15  aromatic  1.346  0.020  1.346
 VPG  N19   N18  aromatic  1.345  0.020  1.345
 VPG  N14   C15  aromatic  1.336  0.020  1.336
 VPG  N14   C12  aromatic  1.307  0.020  1.307
 VPG  CL13  C12  single    1.735  0.020  1.735
 VPG  C15   C16  aromatic  1.399  0.020  1.399
 VPG  C12   N11  aromatic  1.315  0.020  1.315
 VPG  N18   C17  aromatic  1.304  0.020  1.304
 VPG  C16   C17  aromatic  1.420  0.020  1.420
 VPG  C16   C10  aromatic  1.416  0.020  1.416
 VPG  N11   C10  aromatic  1.342  0.020  1.342
 VPG  C10   N9   single    1.329  0.020  1.329
 VPG  CL1   C2   single    1.734  0.020  1.734
 VPG  N9    C8   single    1.447  0.020  1.447
 VPG  C8    C7   single    1.503  0.020  1.503
 VPG  C2    C7   aromatic  1.394  0.020  1.394
 VPG  C2    C3   aromatic  1.385  0.020  1.385
 VPG  C7    C6   aromatic  1.391  0.020  1.391
 VPG  C3    C4   aromatic  1.388  0.020  1.388
 VPG  C6    C5   aromatic  1.387  0.020  1.387
 VPG  C4    C5   aromatic  1.387  0.020  1.387
 VPG  C3    H1   single    0.930  0.020  1.080
 VPG  C4    H2   single    0.930  0.020  1.080
 VPG  C5    H3   single    0.930  0.020  1.080
 VPG  C6    H4   single    0.930  0.020  1.080
 VPG  C8    H5   single    0.970  0.020  1.090
 VPG  C8    H6   single    0.970  0.020  1.090
 VPG  C17   H7   single    0.930  0.020  1.080
 VPG  C23   H8   single    0.970  0.020  1.090
 VPG  C23   H9   single    0.970  0.020  1.090
 VPG  C30   H11  single    0.970  0.020  1.090
 VPG  C32   H12  single    0.970  0.020  1.090
 VPG  N9    H13  single    0.860  0.020  1.020
 VPG  C20   H14  single    0.970  0.020  1.090
 VPG  C22   H15  single    0.970  0.020  1.090
 VPG  C25   H16  single    0.970  0.020  1.090
 VPG  C25   H17  single    0.970  0.020  1.090
 VPG  O31   H19  single    0.850  0.020  0.980
 VPG  O33   H20  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
 VPG  CL1   C2   C7    119.72  3.000
 VPG  C7    C2   C3    121.71  3.000
 VPG  CL1   C2   C3    118.56  3.000
 VPG  H1    C3   C4    120.50  3.000
 VPG  H1    C3   C2    120.16  3.000
 VPG  C4    C3   C2    119.33  3.000
 VPG  H2    C4   C5    120.46  3.000
 VPG  H2    C4   C3    119.42  3.000
 VPG  C5    C4   C3    120.11  3.000
 VPG  H3    C5   C6    119.96  3.000
 VPG  H3    C5   C4    120.31  3.000
 VPG  C6    C5   C4    119.74  3.000
 VPG  H4    C6   C7    118.80  3.000
 VPG  H4    C6   C5    119.89  3.000
 VPG  C7    C6   C5    121.31  3.000
 VPG  C8    C7   C6    120.46  3.000
 VPG  C6    C7   C2    117.80  3.000
 VPG  C8    C7   C2    121.74  3.000
 VPG  H6    C8   H5    107.42  3.000
 VPG  H6    C8   N9    110.97  3.000
 VPG  H5    C8   N9    109.24  3.000
 VPG  H6    C8   C7    109.73  3.000
 VPG  H5    C8   C7    109.19  3.000
 VPG  N9    C8   C7    110.23  3.000
 VPG  N14   C12  CL13  115.18  3.000
 VPG  CL13  C12  N11   114.60  3.000
 VPG  N14   C12  N11   130.22  3.000
 VPG  N19   C15  N14   126.71  3.000
 VPG  N14   C15  C16   126.41  3.000
 VPG  N19   C15  C16   106.86  3.000
 VPG  C10   C16  C17   140.66  3.000
 VPG  C10   C16  C15   115.33  3.000
 VPG  C17   C16  C15   104.00  3.000
 VPG  H7    C17  N18   119.66  3.000
 VPG  H7    C17  C16   129.75  3.000
 VPG  N18   C17  C16   110.58  3.000
 VPG  H9    C23  H8    106.57  3.000
 VPG  H9    C23  O24   111.39  3.000
 VPG  H8    C23  O24   111.46  3.000
 VPG  H9    C23  C22   107.69  3.000
 VPG  H8    C23  C22   109.22  3.000
 VPG  O24   C23  C22   110.37  3.000
 VPG  H11   C30  O31   111.32  3.000
 VPG  H11   C30  C22   110.27  3.000
 VPG  O31   C30  C22   109.93  3.000
 VPG  H11   C30  C32   109.29  3.000
 VPG  O31   C30  C32   113.00  3.000
 VPG  C22   C30  C32   102.71  3.000
 VPG  H12   C32  O33   111.72  3.000
 VPG  H12   C32  C20   111.92  3.000
 VPG  O33   C32  C20   107.32  3.000
 VPG  H12   C32  C30   112.84  3.000
 VPG  C20   C32  C30   102.05  3.000
 VPG  O33   C32  C30   110.47  3.000
 VPG  H13   N9   C10   115.77  3.000
 VPG  H13   N9   C8    117.67  3.000
 VPG  C10   N9   C8    126.52  3.000
 VPG  N11   C10  N9    116.45  3.000
 VPG  N9    C10  C16   125.30  3.000
 VPG  N11   C10  C16   118.26  3.000
 VPG  C10   N11  C12   118.47  3.000
 VPG  C15   N14  C12   111.23  3.000
 VPG  N19   N18  C17   107.32  3.000
 VPG  C20   N19  N18   120.96  3.000
 VPG  N18   N19  C15   111.22  3.000
 VPG  C20   N19  C15   127.60  3.000
 VPG  H14   C20  O21   110.04  3.000
 VPG  H14   C20  N19   105.52  3.000
 VPG  O21   C20  N19   110.59  3.000
 VPG  H14   C20  C32   111.39  3.000
 VPG  N19   C20  C32   112.86  3.000
 VPG  O21   C20  C32   106.50  3.000
 VPG  C22   O21  C20   111.67  3.000
 VPG  H15   C22  O21   108.39  3.000
 VPG  H15   C22  C30   109.35  3.000
 VPG  O21   C22  C30   106.41  3.000
 VPG  H15   C22  C23   109.41  3.000
 VPG  C30   C22  C23   112.01  3.000
 VPG  O21   C22  C23   111.17  3.000
 VPG  H17   C25  H16   105.65  3.000
 VPG  H17   C25  P26   110.08  3.000
 VPG  H16   C25  P26   109.66  3.000
 VPG  H17   C25  O24   109.40  3.000
 VPG  H16   C25  O24   109.53  3.000
 VPG  P26   C25  O24   112.31  3.000
 VPG  O27   P26  C25   105.23  3.000
 VPG  C25   P26  O29   102.00  3.000
 VPG  O27   P26  O29   114.25  3.000
 VPG  C25   P26  O28   105.24  3.000
 VPG  O29   P26  O28   114.34  3.000
 VPG  O27   P26  O28   114.07  3.000
 VPG  H19   O31  C30   108.84  3.000
 VPG  H20   O33  C32   107.17  3.000
 VPG  C25   O24  C23   112.61  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
 VPG  CONST_01  C5    C6   C7   C2      0.00   0.0  0
 VPG  CONST_02  C5    C4   C3   C2      0.00   0.0  0
 VPG  CONST_03  C6    C7   C2   C3      0.00   0.0  0
 VPG  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 VPG  CONST_05  C7    C2   C3   C4      0.00   0.0  0
 VPG  CONST_06  C7    C6   C5   C4      0.00   0.0  0
 VPG  CONST_07  N19   C15  N14  C12   180.00   0.0  0
 VPG  CONST_08  C16   C15  N14  C12     0.00   0.0  0
 VPG  CONST_09  C16   C10  N11  C12     0.00   0.0  0
 VPG  CONST_10  C17   N18  N19  C15     0.00   0.0  0
 VPG  CONST_11  N11   C12  N14  C15     0.00   0.0  0
 VPG  CONST_12  N18   C17  C16  C15     0.00   0.0  0
 VPG  CONST_13  N11   C10  C16  C15     0.00   0.0  0
 VPG  CONST_14  N18   N19  C15  C16     0.00   0.0  0
 VPG  CONST_15  N19   N18  C17  C16     0.00   0.0  0
 VPG  CONST_16  N19   C15  C16  C17     0.00   0.0  0
 VPG  CONST_17  N14   C15  C16  C17   180.00   0.0  0
 VPG  CONST_18  N11   C10  C16  C17   180.00   0.0  0
 VPG  CONST_19  N19   C15  C16  C10   180.00   0.0  0
 VPG  CONST_20  N14   C15  C16  C10     0.00   0.0  0
 VPG  CONST_21  N18   C17  C16  C10   180.00   0.0  0
 VPG  CONST_22  N14   C12  N11  C10     0.00   0.0  0
 VPG  CONST_23  N18   N19  C15  N14   180.00   0.0  0
 VPG  CONST_24  C20   N19  C15  C16   180.00   0.0  0
 VPG  CONST_25  C20   N19  N18  C17   180.00   0.0  0
 VPG  CONST_26  C20   N19  C15  N14     0.00   0.0  0
 VPG  CONST_27  C8    C7   C2   C3    180.00   0.0  0
 VPG  CONST_28  CL1   C2   C3   C4    180.00   0.0  0
 VPG  CONST_29  C8    C7   C6   C5    180.00   0.0  0
 VPG  CONST_30  CL1   C2   C7   C6    180.00   0.0  0
 VPG  CONST_31  N9    C10  N11  C12   180.00   0.0  0
 VPG  CONST_32  CL13  C12  N14  C15   180.00   0.0  0
 VPG  CONST_33  N9    C10  C16  C15   180.00   0.0  0
 VPG  CONST_34  N9    C10  C16  C17     0.00   0.0  0
 VPG  CONST_35  CL13  C12  N11  C10   180.00   0.0  0
 VPG  CONST_36  H4    C6   C7   C2    180.00   0.0  0
 VPG  CONST_37  H2    C4   C3   C2    180.00   0.0  0
 VPG  CONST_38  H3    C5   C4   C3    180.00   0.0  0
 VPG  CONST_39  H1    C3   C4   C5    180.00   0.0  0
 VPG  CONST_40  H7    C17  C16  C15   180.00   0.0  0
 VPG  CONST_41  C16   C10  N9   C8      0.00   0.0  0
 VPG  CONST_42  N11   C10  N9   C8    180.00   0.0  0
 VPG  CONST_43  H13   N9   C10  C16   180.00   0.0  0
 VPG  Var_01    N9    C8   C7   C2     70.80  30.0  2
 VPG  Var_02    C10   N9   C8   C7   -148.63  30.0  1
 VPG  Var_03    P26   C25  O24  C23   176.94  30.0  3
 VPG  Var_04    O24   C25  P26  O28    58.67  30.0  3
 VPG  Var_05    H8    C23  O24  C25   -60.19  30.0  3

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
 VPG  chir_01  C30  C22  O31  C32  negativ
 VPG  chir_02  C32  O33  C30  C20  positiv
 VPG  chir_03  C20  O21  N19  C32  negativ
 VPG  chir_04  C22  O21  C23  C30  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
 VPG  plan-1  C2    0.020
 VPG  plan-1  C3    0.020
 VPG  plan-1  C4    0.020
 VPG  plan-1  C5    0.020
 VPG  plan-1  C6    0.020
 VPG  plan-1  C7    0.020
 VPG  plan-1  C8    0.020
 VPG  plan-1  CL1   0.020
 VPG  plan-1  H1    0.020
 VPG  plan-1  H2    0.020
 VPG  plan-1  H3    0.020
 VPG  plan-1  H4    0.020
 VPG  plan-2  C12   0.020
 VPG  plan-2  C15   0.020
 VPG  plan-2  C16   0.020
 VPG  plan-2  C17   0.020
 VPG  plan-2  N9    0.020
 VPG  plan-2  C10   0.020
 VPG  plan-2  N11   0.020
 VPG  plan-2  N14   0.020
 VPG  plan-2  N18   0.020
 VPG  plan-2  N19   0.020
 VPG  plan-2  C20   0.020
 VPG  plan-2  H7    0.020
 VPG  plan-2  CL13  0.020
 VPG  plan-3  C8    0.020
 VPG  plan-3  N9    0.020
 VPG  plan-3  C10   0.020
 VPG  plan-3  H13   0.020

